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1.
Viruses ; 13(7)2021 06 27.
Artigo em Inglês | MEDLINE | ID: mdl-34199077

RESUMO

Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.


Assuntos
Vírus de DNA/genética , Vírus de DNA/imunologia , Antígenos de Histocompatibilidade Classe I/imunologia , Evasão da Resposta Imune , Vírus de RNA/genética , Antivirais/farmacologia , Códon de Terminação , Vírus de DNA/efeitos dos fármacos , Mudança da Fase de Leitura do Gene Ribossômico , Antígenos de Histocompatibilidade Classe I/genética , Conformação de Ácido Nucleico , Peptídeos/imunologia , Biossíntese de Proteínas , Vírus de RNA/efeitos dos fármacos , Vírus de RNA/imunologia
2.
Nat Commun ; 12(1): 4236, 2021 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-34244493

RESUMO

The repertoire of peptides presented by major histocompatibility complex class I (MHC-I) molecules on the cell surface is tailored by the ER-resident peptide loading complex (PLC), which contains the exchange catalyst tapasin. Tapasin stabilizes MHC-I molecules and promotes the formation of stable peptide-MHC-I (pMHC-I) complexes that serve as T cell antigens. Exchange of suboptimal by high-affinity ligands is catalyzed by tapasin, but the underlying mechanism is still elusive. Here we analyze the tapasin-induced changes in MHC-I dynamics, and find the catalyst to exploit two essential features of MHC-I. First, tapasin recognizes a conserved allosteric site underneath the α2-1-helix of MHC-I, 'loosening' the MHC-I F-pocket region that accomodates the C-terminus of the peptide. Second, the scoop loop11-20 of tapasin relies on residue L18 to target the MHC-I F-pocket, enabling peptide exchange. Meanwhile, tapasin residue K16 plays an accessory role in catalysis of MHC-I allotypes bearing an acidic F-pocket. Thus, our results provide an explanation for the observed allele-specificity of catalyzed peptide exchange.


Assuntos
Alelos , Apresentação do Antígeno/genética , Antígenos de Histocompatibilidade Classe I/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , Regulação Alostérica , Biocatálise , Cristalografia por Raios X , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/isolamento & purificação , Antígenos de Histocompatibilidade Classe I/ultraestrutura , Humanos , Imunoglobulinas/metabolismo , Imunoglobulinas/ultraestrutura , Proteínas de Membrana/metabolismo , Proteínas de Membrana/ultraestrutura , Proteínas de Membrana Transportadoras/genética , Proteínas de Membrana Transportadoras/isolamento & purificação , Proteínas de Membrana Transportadoras/ultraestrutura , Simulação de Dinâmica Molecular , Mutação , Ressonância Magnética Nuclear Biomolecular , Conformação Proteica em alfa-Hélice , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo
3.
Bioinformatics ; 37(Suppl_1): i254-i261, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34252932

RESUMO

MOTIVATION: The prediction of the binding between peptides and major histocompatibility complex (MHC) molecules plays an important role in neoantigen identification. Although a large number of computational methods have been developed to address this problem, they produce high false-positive rates in practical applications, since in most cases, a single residue mutation may largely alter the binding affinity of a peptide binding to MHC which cannot be identified by conventional deep learning methods. RESULTS: We developed a differential boundary tree-based model, named DBTpred, to address this problem. We demonstrated that DBTpred can accurately predict MHC class I binding affinity compared to the state-of-art deep learning methods. We also presented a parallel training algorithm to accelerate the training and inference process which enables DBTpred to be applied to large datasets. By investigating the statistical properties of differential boundary trees and the prediction paths to test samples, we revealed that DBTpred can provide an intuitive interpretation and possible hints in detecting important residue mutations that can largely influence binding affinity. AVAILABILITY AND IMPLEMENTATION: The DBTpred package is implemented in Python and freely available at: https://github.com/fpy94/DBT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Antígenos de Histocompatibilidade Classe I , Peptídeos , Algoritmos , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/metabolismo , Humanos , Complexo Principal de Histocompatibilidade , Peptídeos/metabolismo , Ligação Proteica
4.
Int J Mol Sci ; 22(12)2021 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-34204226

RESUMO

FcRn plays a major role in regulating immune homeostasis, but it is also able to transport biologics across cellular barriers. The question of whether FcRn could be an efficient transporter of biologics across the nasal epithelial barrier is of particular interest, as it would allow a less invasive strategy for the administration of biologics in comparison to subcutaneous, intramuscular or intravenous administrations, which are often used in clinical practice. A focused systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. It was registered on the international prospective register of systematic reviews PROSPERO, which helped in identifying articles that met the inclusion criteria. Clinical and preclinical studies involving FcRn and the nasal delivery of biologics were screened, and the risk of bias was assessed across studies using the Oral Health Assessment Tool (OHAT). Among the 12 studies finally included in this systematic review (out of the 758 studies screened), 11 demonstrated efficient transcytosis of biologics through the nasal epithelium. Only three studies evaluated the potential toxicity of biologics' intranasal delivery, and they all showed that it was safe. This systematic review confirmed that FcRn is expressed in the nasal airway and the olfactory epithelium, and that FcRn may play a role in IgG and/or IgG-derived molecule-transcytosis across the airway epithelium. However, additional research is needed to better characterize the pharmacokinetic and pharmacodynamic properties of biologics after their intranasal delivery.


Assuntos
Produtos Biológicos/administração & dosagem , Antígenos de Histocompatibilidade Classe I/metabolismo , Mucosa Nasal/efeitos dos fármacos , Mucosa Nasal/metabolismo , Receptores Fc/metabolismo , Animais , Produtos Biológicos/metabolismo , Transporte Biológico , Biomarcadores , Sistemas de Liberação de Medicamentos , Expressão Gênica , Antígenos de Histocompatibilidade Classe I/química , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Ligação Proteica , Receptores Fc/química , Receptores Fc/genética , Transcitose
5.
Nat Commun ; 12(1): 3174, 2021 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-34039964

RESUMO

Chaperones Tapasin and TAP-binding protein related (TAPBPR) perform the important functions of stabilizing nascent MHC-I molecules (chaperoning) and selecting high-affinity peptides in the MHC-I groove (editing). While X-ray and cryo-EM snapshots of MHC-I in complex with TAPBPR and Tapasin, respectively, have provided important insights into the peptide-deficient MHC-I groove structure, the molecular mechanism through which these chaperones influence the selection of specific amino acid sequences remains incompletely characterized. Based on structural and functional data, a loop sequence of variable lengths has been proposed to stabilize empty MHC-I molecules through direct interactions with the floor of the groove. Using deep mutagenesis on two complementary expression systems, we find that important residues for the Tapasin/TAPBPR chaperoning activity are located on a large scaffolding surface, excluding the loop. Conversely, loop mutations influence TAPBPR interactions with properly conformed MHC-I molecules, relevant for peptide editing. Detailed biophysical characterization by solution NMR, ITC and FP-based assays shows that the loop hovers above the MHC-I groove to promote the capture of incoming peptides. Our results suggest that the longer loop of TAPBPR lowers the affinity requirements for peptide selection to facilitate peptide loading under conditions and subcellular compartments of reduced ligand concentration, and to prevent disassembly of high-affinity peptide-MHC-I complexes that are transiently interrogated by TAPBPR during editing.


Assuntos
Apresentação do Antígeno , Antígenos de Histocompatibilidade Classe I/metabolismo , Imunoglobulinas/metabolismo , Proteínas de Membrana/metabolismo , Chaperonas Moleculares/metabolismo , Antígenos/metabolismo , Microscopia Crioeletrônica , Cristalografia por Raios X , Técnicas de Inativação de Genes , Células HEK293 , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/isolamento & purificação , Antígenos de Histocompatibilidade Classe I/ultraestrutura , Humanos , Imunoglobulinas/genética , Imunoglobulinas/isolamento & purificação , Imunoglobulinas/ultraestrutura , Ligantes , Proteínas de Membrana/genética , Proteínas de Membrana/isolamento & purificação , Proteínas de Membrana/ultraestrutura , Proteínas de Membrana Transportadoras/genética , Proteínas de Membrana Transportadoras/metabolismo , Chaperonas Moleculares/genética , Chaperonas Moleculares/ultraestrutura , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Mutação , Biblioteca de Peptídeos , Ligação Proteica/genética , Ligação Proteica/imunologia , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/ultraestrutura
6.
Proc Natl Acad Sci U S A ; 118(23)2021 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-34021074

RESUMO

COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic and has claimed over 2 million lives worldwide. Although the genetic sequences of SARS-CoV and SARS-CoV-2 have high homology, the clinical and pathological characteristics of COVID-19 differ significantly from those of SARS. How and whether SARS-CoV-2 evades (cellular) immune surveillance requires further elucidation. In this study, we show that SARS-CoV-2 infection leads to major histocompability complex class Ι (MHC-Ι) down-regulation both in vitro and in vivo. The viral protein encoded by open reading frame 8 (ORF8) of SARS-CoV-2, which shares the least homology with SARS-CoV among all viral proteins, directly interacts with MHC-Ι molecules and mediates their down-regulation. In ORF8-expressing cells, MHC-Ι molecules are selectively targeted for lysosomal degradation via autophagy. Thus, SARS-CoV-2-infected cells are much less sensitive to lysis by cytotoxic T lymphocytes. Because ORF8 protein impairs the antigen presentation system, inhibition of ORF8 could be a strategy to improve immune surveillance.


Assuntos
Apresentação do Antígeno , COVID-19/imunologia , Regulação para Baixo/imunologia , Antígenos de Histocompatibilidade Classe I/imunologia , Evasão da Resposta Imune , SARS-CoV-2/imunologia , Proteínas Virais/imunologia , Animais , Autofagia/genética , Autofagia/imunologia , COVID-19/genética , Chlorocebus aethiops , Células HEK293 , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Lisossomos/genética , Lisossomos/imunologia , Lisossomos/virologia , Camundongos , Camundongos Transgênicos , SARS-CoV-2/genética , Células Vero , Proteínas Virais/genética
7.
Nat Commun ; 12(1): 2593, 2021 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-33972535

RESUMO

The COVID-19 pandemic caused by SARS-CoV-2 is a continuous challenge worldwide, and there is an urgent need to map the landscape of immunogenic and immunodominant epitopes recognized by CD8+ T cells. Here, we analyze samples from 31 patients with COVID-19 for CD8+ T cell recognition of 500 peptide-HLA class I complexes, restricted by 10 common HLA alleles. We identify 18 CD8+ T cell recognized SARS-CoV-2 epitopes, including an epitope with immunodominant features derived from ORF1ab and restricted by HLA-A*01:01. In-depth characterization of SARS-CoV-2-specific CD8+ T cell responses of patients with acute critical and severe disease reveals high expression of NKG2A, lack of cytokine production and a gene expression profile inhibiting T cell re-activation and migration while sustaining survival. SARS-CoV-2-specific CD8+ T cell responses are detectable up to 5 months after recovery from critical and severe disease, and these responses convert from dysfunctional effector to functional memory CD8+ T cells during convalescence.


Assuntos
Linfócitos T CD8-Positivos/imunologia , COVID-19/imunologia , Epitopos Imunodominantes/imunologia , SARS-CoV-2/imunologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Alelos , Linfócitos T CD8-Positivos/patologia , COVID-19/patologia , Epitopos de Linfócito T/imunologia , Feminino , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Humanos , Epitopos Imunodominantes/química , Memória Imunológica , Ativação Linfocitária , Masculino , Pessoa de Meia-Idade , Poliproteínas/imunologia , Proteínas Virais/imunologia
8.
Nat Commun ; 12(1): 2637, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33976146

RESUMO

Checkpoint inhibitors and T-cell therapies have highlighted the critical role of T cells in anti-cancer immunity. However, limitations associated with these treatments drive the need for alternative approaches. Here, we engineer red blood cells into artificial antigen-presenting cells (aAPCs) presenting a peptide bound to the major histocompatibility complex I, the costimulatory ligand 4-1BBL, and interleukin (IL)-12. This leads to robust, antigen-specific T-cell expansion, memory formation, additional immune activation, tumor control, and antigen spreading in tumor models in vivo. The presence of 4-1BBL and IL-12 induces minimal toxicities due to restriction to the vasculature and spleen. The allogeneic aAPC, RTX-321, comprised of human leukocyte antigen-A*02:01 presenting the human papilloma virus (HPV) peptide HPV16 E711-19, 4-1BBL, and IL-12 on the surface, activates HPV-specific T cells and promotes effector function in vitro. Thus, RTX-321 is a potential 'off-the-shelf' in vivo cellular immunotherapy for treating HPV + cancers, including cervical and head/neck cancers.


Assuntos
Células Apresentadoras de Antígenos/transplante , Engenharia Celular/métodos , Eritrócitos/imunologia , Imunoterapia Adotiva/métodos , Neoplasias/terapia , Ligante 4-1BB/genética , Ligante 4-1BB/imunologia , Ligante 4-1BB/metabolismo , Animais , Células Apresentadoras de Antígenos/imunologia , Células Apresentadoras de Antígenos/metabolismo , Linhagem Celular Tumoral , Técnicas de Cocultura , Modelos Animais de Doenças , Eritrócitos/metabolismo , Feminino , Antígeno HLA-A2/genética , Antígeno HLA-A2/imunologia , Antígeno HLA-A2/metabolismo , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Antígenos de Histocompatibilidade Classe I/metabolismo , Humanos , Interleucina-12/genética , Interleucina-12/imunologia , Interleucina-12/metabolismo , Ativação Linfocitária , Neoplasias/imunologia , Proteínas E7 de Papillomavirus/genética , Proteínas E7 de Papillomavirus/imunologia , Proteínas E7 de Papillomavirus/metabolismo , Cultura Primária de Células , Linfócitos T/imunologia , Linfócitos T/transplante , Transplante Homólogo/métodos
9.
J Pak Med Assoc ; 71(2(B)): 608-613, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33941944

RESUMO

Objective: The Aim of this study was to investigate the relationship of 3 common polymorphisms in the HFE gene (C282Y, H63D and S65C) with high body iron status in a population of Pakistani subjects with type 2 diabetes mellitus (DM) and to explore if there is any novel mutation in HFE gene in a sample of Pakistani subjects with type 2 DM. METHODS: In a case-control design, 200 healthy controls and 200 consecutive adult subjects with type 2 DM (both gender; age range of 30-70 years) were enrolled with informed consent. Their serum samples were analyzed for body iron status (ratio of concentration of soluble transferrin receptor to ferritin concentration). DNA from blood was screened for HFE gene polymorphisms via polymerase chain reaction, followed by restriction fragment length polymorphism or via Sanger sequencing to identify any novel mutation(s) in HFE gene. RESULTS: We found that there was lack of any association between HFE polymorphism and body iron status in Pakistani subjects with type 2 DM and healthy controls. H63D was the most common polymorphism found in this population. Single base substitution of G nucleotide instead of C at the codon position 187 in the HFE gene exon 2 was discovered in one subject with DM. There was also a lack of association between D allele (variant allele of H63D) and type 2 DM. A significant relationship was found between CG genotype and abnormal albuminuria in subjects with type 2 DM (p = 0.036). Conclusion: In conclusion, HFE gene polymorphism is not associated either with high body iron status or type 2 DM in a hospital based Pakistani population and variant allele of H63D polymorphism appears to be associated with diabetic nephropathy.


Assuntos
Diabetes Mellitus Tipo 2 , Adulto , Idoso , Diabetes Mellitus Tipo 2/epidemiologia , Diabetes Mellitus Tipo 2/genética , Frequência do Gene , Genótipo , Proteína da Hemocromatose/genética , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Ferro , Proteínas de Membrana/genética , Pessoa de Meia-Idade , Mutação , Paquistão/epidemiologia , Polimorfismo Genético
10.
Anticancer Res ; 41(5): 2307-2320, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33952456

RESUMO

BACKGROUND/AIM: The association between MHC class I polypeptide-related sequence A (MICA) and hepatocellular carcinoma (HCC) development was identified in our previous genome-wide association study. Decreasing soluble MICA (sMICA) through MICA sheddases suppression facilitates natural killer (NK) cell-mediated cytotoxicity. The expression of ADAM9 in HCC has been correlated with poor prognosis, and our recent study showed that its suppression contributes to cancer elimination by decreasing sMICA. MATERIALS AND METHODS: Human HCC cell line PLC/PRF/5 and HepG2 cells were used. sMICA levels were measured by ELISA. Expression of retinoid X receptors (RXRs) and retinoic acid receptors (RARs) was knocked down by siRNA. RESULTS: In our screening of FDA-approved drugs in vitro, retinoids were found to be efficient ADAM9 and ADAM10 inhibitors. Treatment with retinoids reduced sMICA levels in human HCC cells. Interestingly, the effects were abrogated by depletion of the retinoid receptor RXRα. CONCLUSION: Retinoids can be potential novel agents for HCC treatment.


Assuntos
Proteínas ADAM/metabolismo , Proteína ADAM10/metabolismo , Antígenos de Histocompatibilidade Classe I/metabolismo , Proteínas de Membrana/metabolismo , Retinoides/farmacologia , Proteínas ADAM/antagonistas & inibidores , Proteínas ADAM/genética , Proteína ADAM10/antagonistas & inibidores , Proteína ADAM10/genética , Biocatálise/efeitos dos fármacos , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Sinergismo Farmacológico , Células Hep G2 , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Proteínas de Membrana/antagonistas & inibidores , Proteínas de Membrana/genética , Estrutura Molecular , Compostos de Fenilureia/farmacologia , Piridinas/farmacologia , Interferência de RNA , Receptores X de Retinoides/genética , Receptores X de Retinoides/metabolismo , Retinoides/química , Solubilidade
11.
J Cancer Res Clin Oncol ; 147(7): 1973-1991, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33797607

RESUMO

PURPOSE: Downregulation of MHC class I (MHC-I) is a common immune evasion strategy of many cancers. Similarly, two allogeneic clonal transmissible cancers have killed thousands of wild Tasmanian devils (Sarcophilus harrisii) and also modulate MHC-I expression to evade anti-cancer and allograft responses. IFNG treatment restores MHC-I expression on devil facial tumor (DFT) cells but is insufficient to control tumor growth. Transcriptional co-activator NLRC5 is a master regulator of MHC-I in humans and mice but its role in transmissible cancers remains unknown. In this study, we explored the regulation and role of MHC-I in these unique genetically mis-matched tumors. METHODS: We used transcriptome and flow cytometric analyses to determine how MHC-I shapes allogeneic and anti-tumor responses. Cell lines that overexpress NLRC5 to drive antigen presentation, and B2M-knockout cell lines incapable of presenting antigen on MHC-I were used to probe the role of MHC-I in rare cases of tumor regressions. RESULTS: Transcriptomic results suggest that NLRC5 plays a major role in MHC-I regulation in devils. NLRC5 was shown to drive the expression of many components of the antigen presentation pathway but did not upregulate PDL1. Serum from devils with tumor regressions showed strong binding to IFNG-treated and NLRC5 cell lines; antibody binding to IFNG-treated and NRLC5 transgenic tumor cells was diminished or absent following B2M knockout. CONCLUSION: MHC-I could be identified as a target for anti-tumor and allogeneic immunity. Consequently, NLRC5 could be a promising target for immunotherapy and vaccines to protect devils from transmissible cancers and inform development of transplant and cancer therapies for humans.


Assuntos
Apresentação do Antígeno/imunologia , Biomarcadores Tumorais/metabolismo , Neoplasias Faciais/imunologia , Regulação Neoplásica da Expressão Gênica , Antígenos de Histocompatibilidade Classe I/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Animais , Biomarcadores Tumorais/genética , Neoplasias Faciais/genética , Neoplasias Faciais/metabolismo , Neoplasias Faciais/patologia , Antígenos de Histocompatibilidade Classe I/genética , Peptídeos e Proteínas de Sinalização Intracelular/genética , Marsupiais , Transcriptoma , Células Tumorais Cultivadas
12.
Int J Mol Sci ; 22(5)2021 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-33807854

RESUMO

We observed substantial differences in predicted Major Histocompatibility Complex II (MHCII) epitope presentation of SARS-CoV-2 proteins for different populations but only minor differences in predicted MHCI epitope presentation. A comparison of this predicted epitope MHC-coverage revealed for the early phase of infection spread (till day 15 after reaching 128 observed infection cases) highly significant negative correlations with the case fatality rate. Specifically, this was observed in different populations for MHC class II presentation of the viral spike protein (p-value: 0.0733 for linear regression), the envelope protein (p-value: 0.023), and the membrane protein (p-value: 0.00053), indicating that the high case fatality rates of COVID-19 observed in some countries seem to be related with poor MHC class II presentation and hence weak adaptive immune response against these viral envelope proteins. Our results highlight the general importance of the SARS-CoV-2 structural proteins in immunological control in early infection spread looking at a global census in various countries and taking case fatality rate into account. Other factors such as health system and control measures become more important after the early spread. Our study should encourage further studies on MHCII alleles as potential risk factors in COVID-19 including assessment of local populations and specific allele distributions.


Assuntos
COVID-19/mortalidade , Antígenos de Histocompatibilidade Classe II/genética , Antígenos de Histocompatibilidade Classe II/imunologia , SARS-CoV-2/química , Proteínas Estruturais Virais/química , Imunidade Adaptativa , Alelos , COVID-19/imunologia , COVID-19/transmissão , Biologia Computacional/métodos , Correlação de Dados , Epitopos de Linfócito B/genética , Epitopos de Linfócito B/imunologia , Epitopos de Linfócito T/genética , Epitopos de Linfócito T/imunologia , Antígenos HLA/genética , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Humanos , Mortalidade , SARS-CoV-2/imunologia , Proteínas Estruturais Virais/imunologia
13.
HLA ; 97(6): 512-519, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33719220

RESUMO

The International human leukocyte antigen (HLA) and Immunogenetics Workshops (IHIWs) have fostered international collaborations of researchers and experts in the fields of HLA, histocompatibility and immunology. These IHIW collaborations have comprised many projects focused on achieving a variety of specific goals. The international and collaborative nature of these projects necessitates the collection and analysis of complex data generated in multiple laboratories, often using multiple methods of acquisition. Collection and storage of these data in a consistent way adds value to IHIW projects, which can be extended to future work. DNA-based genotyping data, especially HLA genotyping data, can be transmitted in the form of a Histoimmunogenetics Markup Language (HML) document. HML facilitates clear communication of a genotype and supporting metadata, such as, sequencing platform, laboratory assays, consensus sequence, and interpretation. Sequence information can be reported relative to known reference sequences, which add meaning and context to genotypes. Selecting the correct reference sequence for a given allele sequence is nuanced, and guidelines have emerged through collaborative community efforts such as Data Standards Hackathons. Here, we describe the guidelines established for the selection of reference sequences to be used in transmission of HLA (and MICA/MICB) genotyping data for the 18th IHIW.


Assuntos
Antígenos HLA , Imunogenética , Alelos , Genótipo , Antígenos HLA/genética , Antígenos de Histocompatibilidade Classe I/genética , Teste de Histocompatibilidade , Humanos
14.
Mol Med Rep ; 23(5)2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33760196

RESUMO

In antibody­mediated rejection (ABMR), the graft endothelium is at the forefront of the kidney transplant against the assault from the recipient's humoral immune system, and is a target of the latter. The present study investigated the effect of antibodies against human leukocyte antigen (HLA) class I (anti­HLAI) on the immunological properties of human glomerular endothelial cells. Additionally, the effect of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1) inhibitor (everolimus), or the general control nonderepressible 2 kinase (GCN2K) activator (halofuginone) on anti­HLAI antibody­mediated alterations was assessed. Cell integrity was examined, an lactate dehydrogenase (LDH) release assay was performed and cleaved caspase­3 levels were determined. Furthermore, cell proliferation was analyzed by performing a bromodeoxyuridine assay and the cellular proteins involved in signal transduction or immune effector mechanisms were assessed via western blotting. IL­8, monocyte chemoattractive protein­1 (MCP­1), von Willebrand factor (vWF) and transforming growth factor­beta 1 (TGF­ß1) were assayed via ELISA. The results revealed that anti­HLAI triggered integrin signaling, activated mTOR and GCN2K, preserved cell integrity and promoted cell proliferation. Additionally, by increasing intercellular adhesion molecule 1 (ICAM­1), HLA­DR, IL­8 and MCP­1 levels, anti­HLAI enhanced the ability of immune cells to interact with endothelial cells thus facilitating graft rejection. Contrarily, by upregulating CD46 and CD59, anti­HLAI rendered the endothelium less vulnerable to complement­mediated injury. Finally, by enhancing vWF and TGF­ß1, anti­HLAI may render the endothelium prothrombotic and facilitate fibrosis and graft failure, respectively. According to our results, mTORC1 inhibition and GCN2K activation may prove useful pharmaceutical targets, as they prevent cell proliferation and downregulate ICAM­1, IL­8, MCP­1 and TGF­ß1. mTORC1 inhibition also decreases vWF.


Assuntos
Rejeição de Enxerto/imunologia , Antígenos de Histocompatibilidade Classe I/imunologia , Proteínas Serina-Treonina Quinases/genética , Serina-Treonina Quinases TOR/genética , Anticorpos Anti-Idiotípicos/imunologia , Antígenos CD59/genética , Antígenos CD59/imunologia , Proliferação de Células/efeitos dos fármacos , Células Endoteliais/imunologia , Everolimo/farmacologia , Rejeição de Enxerto/genética , Rejeição de Enxerto/patologia , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Imunidade Humoral/genética , Imunidade Humoral/imunologia , Transplante de Rim/efeitos adversos , Alvo Mecanístico do Complexo 1 de Rapamicina/imunologia , Proteína Cofatora de Membrana/genética , Proteína Cofatora de Membrana/imunologia , Cultura Primária de Células , Proteínas Serina-Treonina Quinases/imunologia , Transdução de Sinais , Serina-Treonina Quinases TOR/imunologia , Fator de von Willebrand/genética
15.
Front Immunol ; 12: 592447, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33717070

RESUMO

The micropolymorphism of major histocompatibility complex class I (MHC-I) can greatly alter the plasticity of peptide presentation, but elucidating the underlying mechanism remains a challenge. Here we investigated the impact of the micropolymorphism on peptide presentation of swine MHC-I (termed swine leukocyte antigen class I, SLA-I) molecules via immunopeptidomes that were determined by our newly developed random peptide library combined with the mass spectrometry (MS) de novo sequencing method (termed RPLD-MS) and the corresponding crystal structures. The immunopeptidomes of SLA-1*04:01, SLA-1*13:01, and their mutants showed that mutations of residues 156 and 99 could expand and narrow the ranges of peptides presented by SLA-I molecules, respectively. R156A mutation of SLA-1*04:01 altered the charge properties and enlarged the volume size of pocket D, which eliminated the harsh restriction to accommodate the third (P3) anchor residue of the peptide and expanded the peptide binding scope. Compared with 99Tyr of SLA-1*0401, 99Phe of SLA-1*13:01 could not form a conservative hydrogen bond with the backbone of the P3 residues, leading to fewer changes in the pocket properties but a significant decrease in quantitative of immunopeptidomes. This absent force could be compensated by the salt bridge formed by P1-E and 170Arg. These data illustrate two distinguishing manners that show how micropolymorphism alters the peptide-binding plasticity of SLA-I alleles, verifying the sensitivity and accuracy of the RPLD-MS method for determining the peptide binding characteristics of MHC-I in vitro and helping to more accurately predict and identify MHC-I restricted epitopes.


Assuntos
Epitopos de Linfócito T/química , Antígenos de Histocompatibilidade Classe I/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Peptídeos/química , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Sítios de Ligação , Cromatografia Líquida , Dicroísmo Circular , Epitopos de Linfócito T/genética , Epitopos de Linfócito T/imunologia , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Mutação , Biblioteca de Peptídeos , Peptídeos/genética , Peptídeos/imunologia , Matrizes de Pontuação de Posição Específica , Ligação Proteica , Conformação Proteica , Relação Estrutura-Atividade , Suínos , Espectrometria de Massas em Tandem , Difração de Raios X
16.
Nat Commun ; 12(1): 1639, 2021 03 12.
Artigo em Inglês | MEDLINE | ID: mdl-33712626

RESUMO

Conventional human leukocyte antigen (HLA) imputation methods drop their performance for infrequent alleles, which is one of the factors that reduce the reliability of trans-ethnic major histocompatibility complex (MHC) fine-mapping due to inter-ethnic heterogeneity in allele frequency spectra. We develop DEEP*HLA, a deep learning method for imputing HLA genotypes. Through validation using the Japanese and European HLA reference panels (n = 1,118 and 5,122), DEEP*HLA achieves the highest accuracies with significant superiority for low-frequency and rare alleles. DEEP*HLA is less dependent on distance-dependent linkage disequilibrium decay of the target alleles and might capture the complicated region-wide information. We apply DEEP*HLA to type 1 diabetes GWAS data from BioBank Japan (n = 62,387) and UK Biobank (n = 354,459), and successfully disentangle independently associated class I and II HLA variants with shared risk among diverse populations (the top signal at amino acid position 71 of HLA-DRß1; P = 7.5 × 10-120). Our study illustrates the value of deep learning in genotype imputation and trans-ethnic MHC fine-mapping.


Assuntos
Aprendizado Profundo , Diabetes Mellitus Tipo 1/genética , Predisposição Genética para Doença/genética , Antígenos HLA/genética , Complexo Principal de Histocompatibilidade/genética , Alelos , Grupos de Populações Continentais , Grupos Étnicos/genética , Estudo de Associação Genômica Ampla , Genótipo , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe II/genética , Humanos , Desequilíbrio de Ligação
17.
Science ; 372(6541)2021 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-33766941

RESUMO

Strain 68-1 rhesus cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) antigens elicit CD8+ T cells recognizing epitopes presented by major histocompatibility complex II (MHC-II) and MHC-E but not MHC-Ia. These immune responses mediate replication arrest of SIV in 50 to 60% of monkeys. We show that the peptide VMAPRTLLL (VL9) embedded within the RhCMV protein Rh67 promotes intracellular MHC-E transport and recognition of RhCMV-infected fibroblasts by MHC-E-restricted CD8+ T cells. Deletion or mutation of viral VL9 abrogated MHC-E-restricted CD8+ T cell priming, resulting in CD8+ T cell responses exclusively targeting MHC-II-restricted epitopes. These responses were comparable in magnitude and differentiation to responses elicited by 68-1 vectors but did not protect against SIV. Thus, Rh67-enabled direct priming of MHC-E-restricted T cells is crucial for RhCMV/SIV vaccine efficacy.


Assuntos
Linfócitos T CD8-Positivos/imunologia , Citomegalovirus/metabolismo , Vetores Genéticos/metabolismo , Antígenos de Histocompatibilidade Classe I/metabolismo , Fragmentos de Peptídeos/metabolismo , Vacinas contra a SAIDS/imunologia , Animais , Linhagem Celular , Citomegalovirus/genética , Epitopos de Linfócito T/imunologia , Fibroblastos/metabolismo , Vetores Genéticos/genética , Antígenos de Histocompatibilidade Classe I/genética , Ligantes , Macaca mulatta , Fragmentos de Peptídeos/genética , Transporte Proteico , Vírus da Imunodeficiência Símia
18.
J Clin Invest ; 131(10)2021 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-33705359

RESUMO

Multisystem inflammatory syndrome in children (MIS-C), a hyperinflammatory syndrome associated with SARS-CoV-2 infection, shares clinical features with toxic shock syndrome, which is triggered by bacterial superantigens. Superantigen specificity for different Vß chains results in Vß skewing, whereby T cells with specific Vß chains and diverse antigen specificity are overrepresented in the T cell receptor (TCR) repertoire. Here, we characterized the TCR repertoire of MIS-C patients and found a profound expansion of TCRß variable gene 11-2 (TRBV11-2), with up to 24% of clonal T cell space occupied by TRBV11-2 T cells, which correlated with MIS-C severity and serum cytokine levels. Analysis of TRBJ gene usage and complementarity-determining region 3 (CDR3) length distribution of MIS-C expanded TRBV11-2 clones revealed extensive junctional diversity. Patients with TRBV11-2 expansion shared HLA class I alleles A02, B35, and C04, indicating what we believe is a novel mechanism for CDR3-independent T cell expansion. In silico modeling indicated that polyacidic residues in the Vß chain encoded by TRBV11-2 (Vß21.3) strongly interact with the superantigen-like motif of SARS-CoV-2 spike glycoprotein, suggesting that unprocessed SARS-CoV-2 spike may directly mediate TRBV11-2 expansion. Overall, our data indicate that a CDR3-independent interaction between SARS-CoV-2 spike and TCR leads to T cell expansion and possibly activation, which may account for the clinical presentation of MIS-C.


Assuntos
COVID-19/imunologia , Regiões Determinantes de Complementaridade/imunologia , Antígenos de Histocompatibilidade Classe I/imunologia , Receptores de Antígenos de Linfócitos T alfa-beta/imunologia , SARS-CoV-2/imunologia , Glicoproteína da Espícula de Coronavírus/imunologia , Síndrome de Resposta Inflamatória Sistêmica/imunologia , Linfócitos T/imunologia , COVID-19/genética , Criança , Regiões Determinantes de Complementaridade/genética , Feminino , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Masculino , Receptores de Antígenos de Linfócitos T alfa-beta/genética , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética , Síndrome de Resposta Inflamatória Sistêmica/genética
19.
HLA ; 97(5): 420-427, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33599111

RESUMO

Similarly to HLA class I molecules, certain non-classical HLA class I genes and MHC class I polypeptide-related sequences A and B (MICA and MICB) act as ligands for KIR and NKG2D natural killer receptors. Although these genes are less polymorphic than HLA class I, few studies have analyzed their association with diseases. Information on allele frequencies in healthy donors is needed to map their distribution worldwide. This study is the first to analyze high-resolution HLA-G, HLA-F, MICA, and MICB allele frequencies using a novel high-throughput next generation-sequencing method. We analyzed DNA samples from 96 unrelated blood donors resident in Catalonia, Spain, and registered in the Barcelona Blood and Tissue Bank. Using the first two fields of the HLA nomenclature, we detected six HLA-G and two HLA-F alleles. The most frequent alleles were HLA-G*01:01 (77.08%) and HLA-F*01:01(84.90%). When the four fields were analyzed, we detected 16 and 10 alleles, respectively. Nineteen alleles were detected for MICA and 10 for MICB. The most frequent alleles in these cases were MICA*008:01 (16.15%) and MICB*005:02 (46.84%). All frequencies were in Hardy Weinberg equilibrium except MICA. We also estimated maximum-likelihood haplotype frequencies and calculated corresponding linkage disequilibrium (LD) values and found that few allele pairs were in disequilibrium. Strong LD between MICA and HLA-B (using data from a previous study) was observed. Our findings will be useful for guiding further research evaluating the functional role of these genes in different diseases and populations.


Assuntos
Genes MHC Classe I , Antígenos HLA-G , Alelos , Doadores de Sangue , Frequência do Gene , Genótipo , Antígenos HLA-B/genética , Haplótipos , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Polimorfismo Genético , Espanha
20.
J Med Case Rep ; 15(1): 84, 2021 Feb 17.
Artigo em Inglês | MEDLINE | ID: mdl-33596964

RESUMO

BACKGROUND: Hereditary hemochromatosis is an autosomal recessive disorder where the clinical phenotype of skin pigmentation and organ damage occurs only in homozygotes. Simple heterozygotes, that is, just C282Y, typically do not develop iron overload. Here we present a case where a simple heterozygote in combination with alcoholism developed high ferritin and high transferrin saturation levels indicative of iron overload. Though alcoholism alone could explain her presentation, we hypothesize that an inflammatory cocktail of iron and alcohol probably caused our patient to succumb to acute liver failure at a very young age. CASE PRESENTATION: A 29-year-old Caucasian woman presented to the hospital with progressively worsening yellowish discoloration of her eyes and skin associated with anorexia, nausea, vomiting, diffuse abdominal discomfort, increasing abdominal girth, dark urine and pale stools for about 2 weeks. Family history was significant for hereditary hemochromatosis. Her father was a simple heterozygote and her grandmother was homozygous for C282Y. Physical examination showed scleral icterus, distended abdomen with hepatomegaly and mild generalized tenderness. Lab test results showed an elevated white blood cell count, ferritin 539 ng/dL, transferrin saturation 58.23%, elevated liver enzymes, elevated international normalized ratio (INR), low albumin, Alcoholic Liver Disease/Nonalcoholic Fatty Liver Disease (ALD/NAFLD) Index (ANI) of 2.6, suggesting a 93.2% probability of alcoholic liver disease, and phosphatidyl ethanol level of 537ng/ml. Genetic testing showed that the patient was heterozygous for human homeostatic iron regulator protein (HFE) C282Y mutation and the normal allele. Computed tomography (CT) of the abdomen revealed hepatomegaly, portal hypertension and generalized anasarca. Magnetic resonance cholangiopancreatography (MRCP) showed negative results for bile duct pathology. Workup for other causes of liver disease was negative. A diagnosis of acute alcoholic hepatitis was made, with Maddrey's discriminant function of > 32, so prednisolone was started. Her bilirubin and INR continued to increase despite steroids, and the patient unfortunately died. CONCLUSION: Our case highlights the importance of considering hemochromatosis in the differential diagnosis of young patients presenting with liver failure, including cases suggestive of alcoholism as the likely etiology. Larger studies are needed to investigate the role of non-iron factors like alcohol and viral hepatitis in the progression of liver disease in simple heterozygotes with hereditary hemochromatosis, given the high prevalence of this mutation in persons of Northern European descent.


Assuntos
Alcoolismo , Hemocromatose , Adulto , Alcoolismo/complicações , Gorduras na Dieta , Feminino , Hemocromatose/genética , Heterozigoto , Antígenos de Histocompatibilidade Classe I/genética , Homozigoto , Humanos , Proteínas de Membrana/genética , Mutação
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