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1.
Immunohorizons ; 8(6): 415-430, 2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38885041

RESUMO

The individual HLA-related susceptibility to emerging viral diseases such as COVID-19 underscores the importance of understanding how HLA polymorphism influences peptide presentation and T cell recognition. Similar to HLA-A*0101, which is one of the earliest identified HLA alleles among the human population, HLA-A*2601 possesses a similar characteristic for the binding peptide and acts as a prevalent allomorph in HLA-I. In this study, we found that, compared with HLA-A*0101, HLA-A*2601 individuals exhibit distinctive features for the T cell responses to SARS-CoV-2 and influenza virus after infection and/or vaccination. The heterogeneous T cell responses can be attributed to the distinct preference of HLA-A*2601 and HLA-A*0101 to T cell epitope motifs with negative-charged residues at the P1 and P3 positions, respectively. Furthermore, we determined the crystal structures of the HLA-A*2601 complexed to four peptides derived from SARS-CoV-2 and human papillomavirus, with one structure of HLA-A*0101 for comparison. The shallow pocket C of HLA-A*2601 results in the promiscuous presentation of peptides with "switchable" bulged conformations because of the secondary anchor in the median portion. Notably, the hydrogen bond network formed between the negative-charged P1 anchors and the HLA-A*2601-specific residues lead to a "closed" conformation and solid placement for the P1 secondary anchor accommodation in pocket A. This insight sheds light on the intricate relationship between HLA I allelic allomorphs, peptide binding, and the immune response and provides valuable implications for understanding disease susceptibility and potential vaccine design.


Assuntos
COVID-19 , Epitopos de Linfócito T , SARS-CoV-2 , Humanos , Epitopos de Linfócito T/imunologia , Epitopos de Linfócito T/genética , SARS-CoV-2/imunologia , SARS-CoV-2/genética , COVID-19/imunologia , COVID-19/virologia , Antígenos HLA-A/imunologia , Antígenos HLA-A/genética , Antígenos HLA-A/metabolismo , Antígenos HLA-A/química , Peptídeos/imunologia , Peptídeos/química , Alelos , Antígeno HLA-A1
2.
Nature ; 623(7988): 820-827, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37938771

RESUMO

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.


Assuntos
Antígenos de Neoplasias , Neuroblastoma , Proteínas Oncogênicas , Peptídeos , Receptores de Antígenos Quiméricos , Animais , Humanos , Camundongos , África/etnologia , Alelos , Sequência de Aminoácidos , Carcinogênese , Reações Cruzadas , Antígenos HLA-A/química , Antígenos HLA-A/imunologia , Neuroblastoma/genética , Neuroblastoma/imunologia , Neuroblastoma/terapia , Proteínas Oncogênicas/antagonistas & inibidores , Proteínas Oncogênicas/imunologia , Peptídeos/antagonistas & inibidores , Peptídeos/química , Peptídeos/imunologia , Receptores de Antígenos Quiméricos/imunologia , Receptores de Antígenos Quiméricos/uso terapêutico
3.
Front Immunol ; 13: 887759, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35547730

RESUMO

There is long-standing interest in accurately modeling the structural features of peptides bound and presented by class I MHC proteins. This interest has grown with the advent of rapid genome sequencing and the prospect of personalized, peptide-based cancer vaccines, as well as the development of molecular and cellular therapeutics based on T cell receptor recognition of peptide-MHC. However, while the speed and accessibility of peptide-MHC modeling has improved substantially over the years, improvements in accuracy have been modest. Accuracy is crucial in peptide-MHC modeling, as T cell receptors are highly sensitive to peptide conformation and capturing fine details is therefore necessary for useful models. Studying nonameric peptides presented by the common class I MHC protein HLA-A*02:01, here we addressed a key question common to modern modeling efforts: from a set of models (or decoys) generated through conformational sampling, which is best? We found that the common strategy of decoy selection by lowest energy can lead to substantial errors in predicted structures. We therefore adopted a data-driven approach and trained functions capable of predicting near native decoys with exceptionally high accuracy. Although our implementation is limited to nonamer/HLA-A*02:01 complexes, our results serve as an important proof of concept from which improvements can be made and, given the significance of HLA-A*02:01 and its preference for nonameric peptides, should have immediate utility in select immunotherapeutic and other efforts for which structural information would be advantageous.


Assuntos
Heurística , Antígenos de Histocompatibilidade Classe I , Antígenos HLA-A/química , Antígenos de Histocompatibilidade Classe I/metabolismo , Modelos Estruturais , Peptídeos , Receptores de Antígenos de Linfócitos T
4.
J Phys Chem B ; 125(49): 13376-13384, 2021 12 16.
Artigo em Inglês | MEDLINE | ID: mdl-34856806

RESUMO

We have applied our advanced multicanonical molecular dynamics (McMD)-based dynamic docking methodology to investigate the binding mechanism of an HIV-1 Nef protein epitope to the Asian-dominant allele human leukocyte antigen (HLA)-A*2402. Even though pMHC complex formation [between a Major histocompatibility complex (MHC) class I molecule, which is encoded by an HLA allele, and an antigen peptide] is one of the fundamental processes of the adaptive human immune response, its binding mechanism has not yet been well studied, partially due to the high allelic variation of HLAs in the population. We have used our developed McMD-based dynamic docking method and have successfully reproduced the native complex structure, which is located near the free energy global minimum. Subsequent path sampling MD simulations elucidated the atomic details of the binding process and indicated that the peptide binding is initially driven by the highly positively charged N-terminus of the peptide that is attracted to the various negatively charged residues on the MHC molecule's surface. Upon nearing the pocket, the second tyrosine residue of the peptide anchors the peptide by strongly binding to the B-site of the MHC molecule via hydrophobic driven interactions, resulting in a very strong bound complex structure. Our methodology can be effectively used to predict the bound complex structures between MHC molecules and their antigens to study their binding mechanism in close detail, which would help with the development of new vaccines against cancers, as well as viral infections such as HIV and COVID-19.


Assuntos
Antígenos HLA-A/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Humanos , Peptídeos
5.
Proteins ; 89(7): 866-883, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33594723

RESUMO

Accurate prediction of peptide binding affinity to the major histocompatibility complex (MHC) proteins has the potential to design better therapeutic vaccines. Previous work has shown that pan-specific prediction algorithms can achieve better prediction performance than other approaches. However, most of the top algorithms are neural networks based black box models. Here, we propose DeepAttentionPan, an improved pan-specific model, based on convolutional neural networks and attention mechanisms for more flexible, stable and interpretable MHC-I binding prediction. With the attention mechanism, our ensemble model consisting of 20 trained networks achieves high and more stabilized prediction performance. Extensive tests on IEDB's weekly benchmark dataset show that our method achieves state-of-the-art prediction performance on 21 test allele datasets. Analysis of the peptide positional attention weights learned by our model demonstrates its capability to capture critical binding positions of the peptides, which leads to mechanistic understanding of MHC-peptide binding with high alignment with experimentally verified results. Furthermore, we show that with transfer learning, our pan model can be fine-tuned for alleles with few samples to achieve additional performance improvement. DeepAttentionPan is freely available as an open-source software at https://github.com/jjin49/DeepAttentionPan.


Assuntos
Aprendizado Profundo , Antígenos HLA-A/química , Peptídeos/química , Alelos , Área Sob a Curva , Benchmarking , Sítios de Ligação , Bases de Dados de Proteínas , Conjuntos de Dados como Assunto , Antígenos HLA-A/imunologia , Antígenos HLA-A/metabolismo , Humanos , Peptídeos/imunologia , Peptídeos/metabolismo , Ligação Proteica
6.
J Immunol ; 206(4): 849-860, 2021 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-33441440

RESUMO

HLA class I molecules that represent ligands for the inhibitory killer cell Ig-like receptor (KIR) 3DL1 found on NK cells are categorically defined as those HLA-A and HLA-B allotypes containing the Bw4 motif, yet KIR3DL1 demonstrates hierarchical recognition of these HLA-Bw4 ligands. To better understand the molecular basis underpinning differential KIR3DL1 recognition, the HLA-ABw4 family of allotypes were investigated. Transfected human 721.221 cells expressing HLA-A*32:01 strongly inhibited primary human KIR3DL1+ NK cells, whereas HLA-A*24:02 and HLA-A*23:01 displayed intermediate potency and HLA-A*25:01 failed to inhibit activation of KIR3DL1+ NK cells. Structural studies demonstrated that recognition of HLA-A*24:02 by KIR3DL1 used identical contacts as the potent HLA-B*57:01 ligand. Namely, the D1-D2 domains of KIR3DL1 were placed over the α1 helix and α2 helix of the HLA-A*24:02 binding cleft, respectively, whereas the D0 domain contacted the side of the HLA-A*24:02 molecule. Nevertheless, functional analyses showed KIR3DL1 recognition of HLA-A*24:02 was more sensitive to substitutions within the α2 helix of HLA-A*24:02, including residues Ile142 and Lys144 Furthermore, the presence of Thr149 in the α2 helix of HLA-A*25:01 abrogated KIR3DL1+ NK inhibition. Together, these data demonstrate a role for the HLA class I α2 helix in determining the hierarchy of KIR3DL1 ligands. Thus, recognition of HLA class I is dependent on a complex interplay between the peptide repertoire, polymorphisms within and proximal to the Bw4 motif, and the α2 helix. Collectively, the data furthers our understanding of KIR3DL1 ligands and will inform genetic association and immunogenetics studies examining the role of KIR3DL1 in disease settings.


Assuntos
Antígenos HLA-A , Células Matadoras Naturais , Receptores KIR3DL1 , Antígenos HLA-A/química , Antígenos HLA-A/imunologia , Humanos , Células Matadoras Naturais/química , Células Matadoras Naturais/imunologia , Conformação Proteica em alfa-Hélice , Domínios Proteicos , Receptores KIR3DL1/química , Receptores KIR3DL1/imunologia
7.
Mol Biol Evol ; 38(4): 1580-1594, 2021 04 13.
Artigo em Inglês | MEDLINE | ID: mdl-33320202

RESUMO

Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all human populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence analysis and linear modeling) on 2,909 common and rare HLA-A, HLA-B, and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defense. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intraprotein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.


Assuntos
Evolução Molecular , Antígenos HLA-A/genética , Antígenos HLA-B/genética , Seleção Genética , Alelos , Sequência de Aminoácidos , Antígenos HLA-A/química , Antígenos HLA-B/química , Humanos
8.
Med Hypotheses ; 145: 110342, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33069093

RESUMO

This study aimed at identifying human neural proteins that can be attacked by cross-reacting SARS-COV-2 antibodies causing Guillain-Barré syndrome. These markers can be used for the diagnosis of Guillain-Barré syndrome (GBS). To achieve this goal, proteins implicated in the development of GBS were retrieved from literature. These human proteins were compared to SARS-COV-2 surface proteins to identify homologous sequences using Blastp. Then, MHC-I and MHC-II epitopes were determined in the homologous sequences and used for further analysis. Similar human and SARS-COV-2 epitopes were docked to the corresponding MHC molecule to compare the binding pattern of human and SARS-COV-2 proteins to the MHC molecule. Neural cell adhesion molecule is the only neural protein that showed homologous sequence to SARS-COV-2 envelope protein. The homologous sequence was part of HLA-A68 and HLA-DQA/HLA-DQB epitopes had a similar binding pattern to SARS-COV-2 envelope protein. Based on these results, the study suggests that NCAM may play a significant role in the immunopathogenesis of GBS. NCAM antibodies can be used as a marker for Guillain-Barré syndrome. However, more experimental studies are needed to prove these results.


Assuntos
Antígeno CD56/química , Proteínas do Envelope de Coronavírus/química , Síndrome de Guillain-Barré/imunologia , SARS-CoV-2 , Proteínas Virais/química , Motivos de Aminoácidos , COVID-19/imunologia , Biologia Computacional , Simulação por Computador , Cristalografia por Raios X , Epitopos/química , Antígenos HLA-A/química , Cadeias alfa de HLA-DQ/química , Cadeias beta de HLA-DQ/química , Humanos , Complexo Principal de Histocompatibilidade , Modelos Teóricos , Peptídeos/química , Ligação Proteica
9.
Immunogenetics ; 72(3): 143-153, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31970435

RESUMO

Specificity analyses of peptide binding to human leukocyte antigen (HLA)-A molecules have been hampered due to a lack of proper monoclonal antibodies (mAbs) for certain allomorphs, such as the prevalent HLA-A1 for Caucasians and HLA-A11 for Asians. We developed a mAb that recognizes a conformational epitope common to most HLA-A allomorphs. The mAb, named A-1, does not discriminate peptides by amino acid sequences, making it suitable for measuring peptide binding. A stabilization assay using TAP-deficient cell lines and A-1 was developed to investigate the specificity of peptide binding to HLA-A molecules. Regarding the evolution of HLA-A genes, the A-1 epitope has been conserved among most HLA-A allomorphs but was lost when the HLA-A gene diversified into the HLA-A*32, HLA-A*31, and HLA-A*33 lineages together with HLA-A*29 after bifurcating from the HLA-A*25 and HLA-A*26 branchs. The establishment of A-1 is expected to help researchers investigate the peptide repertoire and develop computational tools to identify cognate peptides. Since no HLA-A locus-specific mAb has been available, A-1 will also be useful for analyzing the locus-specific regulation of the HLA gene expression.


Assuntos
Anticorpos Monoclonais/metabolismo , Antígenos HLA-A/imunologia , Antígeno HLA-A1/imunologia , Sequência de Aminoácidos , Anticorpos Monoclonais/imunologia , Linhagem Celular Tumoral , Epitopos/imunologia , Antígenos HLA-A/química , Antígeno HLA-A1/química , Humanos , Modelos Moleculares , Peptídeos/imunologia , Ligação Proteica/imunologia , Conformação Proteica
10.
Nat Commun ; 10(1): 5579, 2019 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-31811120

RESUMO

Although influenza viruses lead to severe illness in high-risk populations, host genetic factors associated with severe disease are largely unknown. As the HLA-A*68:01 allele can be linked to severe pandemic 2009-H1N1 disease, we investigate a potential impairment of HLA-A*68:01-restricted CD8+ T cells to mount robust responses. We elucidate the HLA-A*68:01+CD8+ T cell response directed toward an extended influenza-derived nucleoprotein (NP) peptide and show that only ~35% individuals have immunodominant A68/NP145+CD8+ T cell responses. Dissecting A68/NP145+CD8+ T cells in low vs. medium/high responders reveals that high responding donors have A68/NP145+CD8+ memory T cells with clonally expanded TCRαßs, while low-responders display A68/NP145+CD8+ T cells with predominantly naïve phenotypes and non-expanded TCRαßs. Single-cell index sorting and TCRαß analyses link expansion of A68/NP145+CD8+ T cells to their memory potential. Our study demonstrates the immunodominance potential of influenza-specific CD8+ T cells presented by a risk HLA-A*68:01 molecule and advocates for priming CD8+ T cell compartments in HLA-A*68:01-expressing individuals for establishment of pre-existing protective memory T cell pools.


Assuntos
Linfócitos T CD8-Positivos/imunologia , Antígenos HLA-A/imunologia , Antígenos HLA-A/metabolismo , Vírus da Influenza A/imunologia , Influenza Humana/imunologia , Apresentação de Antígeno , Antígenos Virais/química , Linhagem Celular , Proteção Cruzada , Reações Cruzadas/imunologia , Epitopos de Linfócito T/imunologia , Antígenos HLA-A/química , Antígenos HLA-A/genética , Humanos , Memória Imunológica/imunologia , Vírus da Influenza A Subtipo H1N1/imunologia , Modelos Moleculares , Nucleoproteínas/química , Orthomyxoviridae/genética , Orthomyxoviridae/imunologia , Fragmentos de Peptídeos/química , Fenótipo , Conformação Proteica , Receptores de Antígenos de Linfócitos T alfa-beta/metabolismo , Proteínas do Core Viral/genética
11.
Front Immunol ; 10: 2572, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31803176

RESUMO

Targeting CD8+ T cells to recurrent tumor-specific mutations can profoundly contribute to cancer treatment. Some of these mutations are potential tumor antigens although they can be displayed by non-spliced epitopes only in a few patients, because of the low affinity of the mutated non-spliced peptides for the predominant HLA class I alleles. Here, we describe a pipeline that uses the large sequence variety of proteasome-generated spliced peptides and identifies spliced epitope candidates, which carry the mutations and bind the predominant HLA-I alleles with high affinity. They could be used in adoptive T cell therapy and other anti-cancer immunotherapies for large cohorts of cancer patients. As a proof of principle, the application of this pipeline led to the identification of a KRAS G12V mutation-carrying spliced epitope candidate, which is produced by proteasomes, transported by TAPs and efficiently presented by the most prevalent HLA class I molecules, HLA-A*02:01 complexes.


Assuntos
Processamento Alternativo , Biologia Computacional , Mapeamento de Epitopos , Epitopos/genética , Antígenos HLA-A/genética , Neoplasias/genética , Neoplasias/imunologia , Proteínas Proto-Oncogênicas p21(ras)/genética , Sequência de Aminoácidos , Antígenos de Neoplasias/genética , Antígenos de Neoplasias/imunologia , Sítios de Ligação , Biologia Computacional/métodos , Epitopos/química , Epitopos/imunologia , Regulação Neoplásica da Expressão Gênica , Antígenos HLA-A/química , Antígenos HLA-A/imunologia , Humanos , Modelos Moleculares , Conformação Molecular , Neoplasias/metabolismo , Peptídeos/química , Peptídeos/genética , Peptídeos/imunologia , Complexo de Endopeptidases do Proteassoma/metabolismo , Ligação Proteica , Proteínas Proto-Oncogênicas p21(ras)/química , Proteínas Proto-Oncogênicas p21(ras)/imunologia , Relação Estrutura-Atividade
12.
Sci Rep ; 9(1): 16660, 2019 11 13.
Artigo em Inglês | MEDLINE | ID: mdl-31723204

RESUMO

Peptides presented by Human leukocyte antigen (HLA) class-I molecules are generally 8-10 amino acids in length. However, the predominant pool of peptide fragments generated by proteasomes is less than 8 amino acids in length. Using the Epstein - Barr virus (EBV) Rta-epitope (ATIGTAMYK, residues 134-142) restricted by HLA-A*11:01 which generates a strong immunodominant response, we investigated the minimum length of a viral peptide that can constitute a viral epitope recognition by CD8 T cells. The results showed that Peripheral blood mononuclear cells (PBMCs) from healthy donors can be stimulated by a viral peptide fragment as short as 4-mer (AMYK), together with a 5-mer (ATIGT) to recapitulate the full length EBV Rta epitope. This was confirmed by generating crystals of the tetra-complex (2 peptides, HLA and ß2-microglobulin). The solved crystal structure of HLA-A*11:01 in complex with these two short peptides revealed that they can bind in the same orientation similar to parental peptide (9-mer) and the free ends of two short peptides acquires a bulged conformation that is directed towards the T cell receptor. Our data shows that suboptimal length of 4-mer and 5-mer peptides can complement each other to form a stable peptide-MHC (pMHC) complex.


Assuntos
Linfócitos T CD8-Positivos/imunologia , Infecções por Vírus Epstein-Barr/imunologia , Antígenos HLA-A/química , Herpesvirus Humano 4/imunologia , Proteínas Imediatamente Precoces/química , Leucócitos Mononucleares/imunologia , Fragmentos de Peptídeos/química , Transativadores/química , Epitopos de Linfócito T/química , Epitopos de Linfócito T/imunologia , Infecções por Vírus Epstein-Barr/virologia , Antígenos HLA-A/imunologia , Humanos , Proteínas Imediatamente Precoces/imunologia , Leucócitos Mononucleares/virologia , Fragmentos de Peptídeos/imunologia , Conformação Proteica , Linfócitos T Citotóxicos/imunologia , Transativadores/imunologia
13.
Cell Rep ; 29(6): 1621-1632.e3, 2019 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-31693900

RESUMO

Understanding how peptide selection is controlled on different major histocompatibility complex class I (MHC I) molecules is pivotal for determining how variations in these proteins influence our predisposition to infectious diseases, cancer, and autoinflammatory conditions. Although the intracellular chaperone TAPBPR edits MHC I peptides, it is unclear which allotypes are subjected to TAPBPR-mediated peptide editing. Here, we examine the ability of 97 different human leukocyte antigen (HLA) class I allotypes to interact with TAPBPR. We reveal a striking preference of TAPBPR for HLA-A, particularly for supertypes A2 and A24, over HLA-B and -C molecules. We demonstrate that the increased propensity of these HLA-A molecules to undergo TAPBPR-mediated peptide editing is determined by molecular features of the HLA-A F pocket, specifically residues H114 and Y116. This work reveals that specific polymorphisms in MHC I strongly influence their susceptibility to chaperone-mediated peptide editing, which may play a significant role in disease predisposition.


Assuntos
Antígenos HLA-A/química , Antígenos HLA-A/metabolismo , Antígenos de Histocompatibilidade Classe I/química , Antígenos de Histocompatibilidade Classe I/metabolismo , Imunoglobulinas/metabolismo , Proteínas de Membrana/metabolismo , Apresentação de Antígeno , Células HEK293 , Antígeno HLA-A2/química , Antígeno HLA-A2/metabolismo , Antígeno HLA-A24/química , Antígeno HLA-A24/metabolismo , Antígenos HLA-B/genética , Antígenos HLA-B/metabolismo , Antígenos HLA-C/metabolismo , Células HeLa , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Alótipos de Imunoglobulina , Imunoglobulinas/genética , Proteínas de Membrana/genética , Proteínas de Membrana Transportadoras/genética , Proteínas de Membrana Transportadoras/metabolismo , Chaperonas Moleculares/química , Chaperonas Moleculares/metabolismo , Peptídeos/química , Peptídeos/metabolismo , Polimorfismo Genético , Ligação Proteica , Domínios Proteicos/genética
14.
Front Immunol ; 10: 1709, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31396224

RESUMO

Human leukocyte antigen (HLA) alleles have a high degree of polymorphism, which determines their peptide-binding motifs and subsequent T-cell receptor recognition. The simplest way to understand the cross-presentation of peptides by different alleles is to classify these alleles into supertypes. A1 and A3 HLA supertypes are widely distributed in humans. However, direct structural and functional evidence for peptide presentation features of key alleles (e.g., HLA-A*30:01 and -A*30:03) are lacking. Herein, the molecular basis of peptide presentation of HLA-A*30:01 and -A*30:03 was demonstrated by crystal structure determination and thermostability measurements of complexes with T-cell epitopes from influenza virus (NP44), human immunodeficiency virus (RT313), and Mycobacterium tuberculosis (MTB). When binding to the HIV peptide, RT313, the PΩ-Lys anchoring modes of HLA-A*30:01, and -A*30:03 were similar to those of HLA-A*11:01 in the A3 supertype. However, HLA-A*30:03, but not -A*30:01, also showed binding with the HLA*01:01-favored peptide, NP44, but with a specific structural conformation. Thus, different from our previous understanding, HLA-A*30:01 and -A*30:03 have specific peptide-binding characteristics that may lead to their distinct supertype-featured binding peptide motifs. Moreover, we also found that residue 77 in the F pocket was one of the key residues for the divergent peptide presentation characteristics of HLA-A*30:01 and -A*30:03. Interchanging residue 77 between HLA-A*30:01 and HLA-A*30:03 switched their presented peptide profiles. Our results provide important recommendations for screening virus and tumor-specific peptides among the population with prevalent HLA supertypes for vaccine development and immune interventions.


Assuntos
Apresentação de Antígeno/imunologia , Apresentação Cruzada/imunologia , Epitopos de Linfócito T/imunologia , Antígenos HLA-A/imunologia , Ativação Linfocitária/imunologia , HIV/imunologia , Antígenos HLA-A/química , Humanos , Mycobacterium tuberculosis/imunologia , Orthomyxoviridae/imunologia , Peptídeos/imunologia
15.
J Immunother ; 42(7): 244-250, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31398179

RESUMO

We previously found that heat-shock protein 70 (HSP70) is expressed on hepatocellular carcinoma cells and developed an HSP70 mRNA-transfected dendritic cell therapy for treating unresectable or recurrent hepatocellular carcinoma. The phase I trial was completed successfully. The purpose of this study is to identify a promiscuous epitope peptide derived from HSP70 for the purpose of developing a novel cancer peptide vaccine. Using a computational algorithm to analyze the specificity of previously reported major histocompatibility complex class I-binding peptides, we selected candidates that bound to >2 of the 3 HLA types. Twenty-nine HSP70-derived peptides (9-mers) that bound to HLA-class I was selected. The peptides were prioritized based on the results of peptide binding experiments. Using dendritic cells stimulated with the candidate peptide described previously as stimulators and CD8 T cells as effectors, an ELISPOT assay was performed. Cytotoxicity of CD8 lymphocytes stimulated with the candidate peptides toward HSP70-expressing cancer cells was analyzed using an xCELLigence System. Peptides were administered to HLA-A 24 transgenic mice as vaccines, and peptide-specific T-cell induction was measured in vivo. We identified a multi-HLA-class I-binding epitope peptide that bound to HLA-A*02:01, *02:06, and *24:02 in vitro using an interferon-γ ELISPOT immune response induction assay. Cytotoxicity was confirmed in vitro, and safety and immune response induction were confirmed in vivo using HLA-A 24 transgenic mice. Our study demonstrated that the promiscuous HSP70-derived peptide is applicable to cancer immunotherapy in patients with HLA-A*24:02-positive, *02:01-positive, and *02:06-positive HSP70-expressing cancers.


Assuntos
Epitopos/imunologia , Proteínas de Choque Térmico HSP70/imunologia , Peptídeos/imunologia , Sequência de Aminoácidos , Animais , Antígenos de Neoplasias/imunologia , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/metabolismo , Vacinas Anticâncer/imunologia , Células Dendríticas/imunologia , Células Dendríticas/metabolismo , Epitopos/química , Antígenos HLA-A/química , Antígenos HLA-A/imunologia , Antígenos HLA-A/metabolismo , Proteínas de Choque Térmico HSP70/química , Humanos , Interferon gama/metabolismo , Camundongos , Peptídeos/química , Linfócitos T Citotóxicos/imunologia , Linfócitos T Citotóxicos/metabolismo
16.
J Allergy Clin Immunol ; 144(1): 183-192, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30776417

RESUMO

BACKGROUND: Vancomycin is a prevalent cause of the severe hypersensitivity syndrome drug reaction with eosinophilia and systemic symptoms (DRESS), which leads to significant morbidity and mortality and commonly occurs in the setting of combination antibiotic therapy, affecting future treatment choices. Variations in HLA class I in particular have been associated with serious T cell-mediated adverse drug reactions, which has led to preventive screening strategies for some drugs. OBJECTIVE: We sought to determine whether variation in the HLA region is associated with vancomycin-induced DRESS. METHODS: Probable vancomycin-induced DRESS cases were matched 1:2 with tolerant control subjects based on sex, race, and age by using BioVU, Vanderbilt's deidentified electronic health record database. Associations between DRESS and carriage of HLA class I and II alleles were assessed by means of conditional logistic regression. An extended sample set from BioVU was used to conduct a time-to-event analysis of those exposed to vancomycin with and without the identified HLA risk allele. RESULTS: Twenty-three subjects met the inclusion criteria for vancomycin-associated DRESS. Nineteen (82.6%) of 23 cases carried HLA-A*32:01 compared with 0 (0%) of 46 of the matched vancomycin-tolerant control subjects (P = 1 × 10-8) and 6.3% of the BioVU population (n = 54,249, P = 2 × 10-16). Time-to-event analysis of DRESS development during vancomycin treatment among the HLA-A*32:01-positive group indicated that 19.2% had DRESS and did so within 4 weeks. CONCLUSIONS: HLA-A*32:01 is strongly associated with vancomycin-induced DRESS in a population of predominantly European ancestry. HLA-A*32:01 testing could improve antibiotic safety, help implicate vancomycin as the causal drug, and preserve future treatment options with coadministered antibiotics.


Assuntos
Antibacterianos/efeitos adversos , Síndrome de Hipersensibilidade a Medicamentos/imunologia , Antígenos HLA-A/imunologia , Vancomicina/efeitos adversos , Adolescente , Adulto , Idoso , Antibacterianos/química , Síndrome de Hipersensibilidade a Medicamentos/etiologia , Feminino , Antígenos HLA-A/química , Humanos , Masculino , Pessoa de Meia-Idade , Simulação de Acoplamento Molecular , Vancomicina/química , Adulto Jovem
17.
Elife ; 72018 11 28.
Artigo em Inglês | MEDLINE | ID: mdl-30484775

RESUMO

Tapasin and TAPBPR are known to perform peptide editing on major histocompatibility complex class I (MHC I) molecules; however, the precise molecular mechanism(s) involved in this process remain largely enigmatic. Here, using immunopeptidomics in combination with novel cell-based assays that assess TAPBPR-mediated peptide exchange, we reveal a critical role for the K22-D35 loop of TAPBPR in mediating peptide exchange on MHC I. We identify a specific leucine within this loop that enables TAPBPR to facilitate peptide dissociation from MHC I. Moreover, we delineate the molecular features of the MHC I F pocket required for TAPBPR to promote peptide dissociation in a loop-dependent manner. These data reveal that chaperone-mediated peptide editing on MHC I can occur by different mechanisms dependent on the C-terminal residue that the MHC I accommodates in its F pocket and provide novel insights that may inform the therapeutic potential of TAPBPR manipulation to increase tumour immunogenicity.


Assuntos
Antígenos de Histocompatibilidade Classe I/imunologia , Imunoglobulinas/imunologia , Proteínas de Membrana/imunologia , Simulação de Acoplamento Molecular , Peptídeos/imunologia , Sequência de Aminoácidos , Apresentação de Antígeno/imunologia , Sítios de Ligação/genética , Antígenos HLA-A/química , Antígenos HLA-A/imunologia , Antígenos HLA-A/metabolismo , Células HeLa , Antígenos de Histocompatibilidade Classe I/química , Antígenos de Histocompatibilidade Classe I/metabolismo , Humanos , Imunoglobulinas/química , Imunoglobulinas/metabolismo , Leucina/química , Leucina/imunologia , Leucina/metabolismo , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Mutação , Peptídeos/metabolismo , Ligação Proteica , Domínios Proteicos
18.
J Hepatol ; 69(6): 1317-1325, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30138689

RESUMO

BACKGROUND & AIMS: Terbinafine is an antifungal agent that has been associated with rare instances of hepatotoxicity. In this study we aimed to describe the presenting features and outcomes of patients with terbinafine hepatotoxicity and to investigate the role of human leukocyte antigen (HLA)-A*33:01. METHODS: Consecutive high causality cases of terbinafine hepatotoxicity enrolled into the Drug Induced Liver Injury Network were reviewed. DNA samples underwent high-resolution confirmatory HLA sequencing using the Ilumina MiSeq platform. RESULTS: All 15 patients with terbinafine hepatotoxicity were more than 40 years old (median = 57 years), 53% were female and the median latency to onset was 38 days (range 24 to 114 days). At the onset of drug-induced liver injury, 80% were jaundiced, median serum alanine aminotransferase was 448 U/L and alkaline phosphatase was 333 U/L. One individual required liver transplantation for acute liver failure during follow-up, and 7 of the 13 (54%) remaining individuals had ongoing liver injury at 6 months, with 4 demonstrating persistently abnormal liver biochemistries at month 24. High-resolution HLA genotyping confirmed that 10 of the 11 (91%) European ancestry participants were carriers of the HLA-A*33:01, B*14:02, C*08:02 haplotype, which has a carrier frequency of 1.6% in European Ancestry population controls. One African American patient was also an HLA-A*33:01 carrier while 2 East Asian patients were carriers of a similar HLA type: A*33:03. Molecular docking studies indicated that terbinafine may interact with HLA-A*33:01 and A*33:03. CONCLUSIONS: Patients with terbinafine hepatotoxicity most commonly present with a mixed or cholestatic liver injury profile and frequently have residual evidence of chronic cholestatic injury. A strong genetic association of HLA-A*33:01 with terbinafine drug-induced liver injury was confirmed amongst Caucasians. LAY SUMMARY: A locus in the human leukocyte antigen gene (HLA-A*33:01, B*14:02, C*08:02) was significantly overrepresented in Caucasian and African American patients with liver injury attributed to the antifungal medication, terbinafine. These data along with the molecular docking studies demonstrate that this genetic polymorphism is a plausible risk factor for developing terbinafine hepatotoxicity and could be used in the future to help doctors make a diagnosis more rapidly and confidently.


Assuntos
Antifúngicos/efeitos adversos , Doença Hepática Induzida por Substâncias e Drogas/etiologia , Doença Hepática Induzida por Substâncias e Drogas/genética , Colestase/induzido quimicamente , Antígenos HLA-A/genética , Terbinafina/efeitos adversos , Adulto , Idoso , Alanina Transaminase/sangue , Fosfatase Alcalina/sangue , Antifúngicos/administração & dosagem , Antifúngicos/química , Biomarcadores/química , Doença Hepática Induzida por Substâncias e Drogas/diagnóstico , Feminino , Seguimentos , Antígenos HLA-A/química , Antígeno HLA-B14/química , Antígeno HLA-B14/genética , Haplótipos , Humanos , Fígado/patologia , Masculino , Pessoa de Meia-Idade , Simulação de Acoplamento Molecular , Polimorfismo Genético , Estudos Prospectivos , Ligação Proteica , Terbinafina/administração & dosagem , Terbinafina/química
19.
Molecules ; 23(3)2018 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-29534537

RESUMO

A series of oxime ethers with C6-C4 fragment was designed and virtually bioactively screened by docking with a target, then provided by a Friedel-Crafts reaction, esterification (or amidation), and oximation from p-substituted phenyl derivatives (Methylbenzene, Methoxybenzene, Chlorobenzene). Anti-hepatitis B virus (HBV) activities of all synthesized compounds were evaluated with HepG2.2.15 cells in vitro. Results showed that most of compounds exhibited low cytotoxicity on HepG2.2.15 cells and significant inhibition on the secretion of HBsAg and HBeAg. Among them, compound 5c-1 showed the most potent activity on inhibiting HBsAg secretion (IC50 = 39.93 µM, SI = 28.51). Results of the bioactive screening showed that stronger the compounds bound to target human leukocyte antigen A protein in docking, the more active they were in anti-HBV activities in vitro.


Assuntos
Antivirais/farmacologia , Éteres/farmacologia , Vírus da Hepatite B/metabolismo , Oximas/farmacologia , Antivirais/química , Avaliação Pré-Clínica de Medicamentos , Éteres/química , Antígenos HLA-A/química , Antígenos HLA-A/metabolismo , Células Hep G2 , Antígenos de Superfície da Hepatite B/metabolismo , Antígenos E da Hepatite B/metabolismo , Vírus da Hepatite B/crescimento & desenvolvimento , Humanos , Modelos Moleculares , Simulação de Acoplamento Molecular , Oximas/química
20.
Int J Immunogenet ; 45(3): 140-142, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29516629

RESUMO

Three new HLA class I alleles were described in the Spanish population. HLA-A*68:169 and -B*39:129 show one amino acid replacement at the α1-domain, compared to A*68:02 (P47 > L47) and -B*39:06 (S11 > A11), respectively. HLA-B*07:298 presents one nucleotide mutation within exon 1, resulting in a new amino acid position -14, L>Q, which has not been previously described in any HLA protein. Prediction of the B*07:298 signal peptide cleavage did not show significant differences in comparison with that obtained for the rest of HLA-B genes.


Assuntos
Alelos , Sequência de Bases , Antígenos HLA-A/genética , Antígenos HLA-B/genética , Antígeno HLA-B7/genética , Análise de Sequência de DNA , Sequência de Aminoácidos , Antígenos HLA-A/química , Antígenos HLA-B/química , Antígeno HLA-B7/química , Haplótipos , Humanos , Peptídeos/química
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