MHC Cluster Research Articles

Prediction of Antigenic Vaccine Peptide Candidates From BfmRS Associated With Biofilm Formation in Acinetobacter baumannii.

A. baumannii is categorized as a priority pathogen due to its propensity for multi-drug resistance, exhibiting resistance against the last resort of antibiotics. It is also considered a potent nosocomial pathogen, so targeting the microbe using novel strategies would be the need of the hour. In this context, the in-silico computational approach would serve the best to design the possible epitope peptides, which may be further considered for the experimental trials for their immunological response. Objective: To predict the immune-dominant epitope peptide candidates against the bfmRandbfmS proteins mediating the two-component system adaptation in the formation of biofilm in A. baumannii. 11 different FASTA sequences ofbfmRandbfmSfromA. baumannii strains retrieved based on the blast-p similarity search tool were subjected to linear epitope B-cell epitope predictions under the IEDB B-cell epitope prediction server. Further analysis on antigenicity, allergenicity, and toxigenicity was achieved using the AntigenPro, Vaxijen, and AlgPred tools, with the physical and chemical properties evaluated using the Expasy Protparam server. Selection of the immunodominant peptides for T-cells was done through the databases under IEDB. The final assessment of protein-TLR2 interactions was done by MHC cluster servers. Four peptide sequences (E1-E4) were predicted for B-cell dominance, with E1, E2, and E4 as probable antigens. All were soluble and non-toxigenic. E1 and E3 were considered non-allergens. GRAVY values were negative for all the peptides, indicating the protein to be hydrophilic in nature. Analysis of the T-cell epitopes was promising, with 100% conservancy for class-I HLA alleles, high interaction scores for similarity with TLR2, and more hydrogen bonds for E2, followed by other epitope peptides. The promising four epitopes, as predicted for bfmRandbfmS in the present study, suggest their potent role as possible candidates for the design of vaccines targeting the TCSofA. baumannii, recommending further in vitroand in vivoexperimental validation.

Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population

Characterizing natural selection signatures and relationships with phenotype spectra is important for understanding human evolution and both biological and pathological mechanisms. Here, we identified 24 genetic loci under recent selection by analyzing rare singletons in 3946 high-depth whole-genome sequencing data of Han Chinese. The loci include immune-related gene regions (MHC cluster, IGH cluster, STING1, and PSG), alcohol metabolism-related gene regions (ADH1B, ALDH2, and ALDH3B2), and the olfactory perception gene OR4C16, in which the MHC cluster, ADH1B, and ALDH2 were also identified by TOPMed and WestLake Biobank. Among the signals, the IGH cluster is particularly interesting, in which the favored allele of variant 14_105737776_C_T (rs117518546, IgG1-G396R) promotes immune response, but also increases the risk of an autoimmune disease systemic lupus erythematosus (SLE). It is also surprising that our newly discovered ALDH3B2 evolved in the opposite direction to ALDH2 for alcohol metabolism. Besides monogenic traits, we found that multiple complex traits experienced polygenic adaptation. Particularly, multi-methods consistently revealed that lower blood pressure was favored in natural selection. Finally, we built a database named RePoS (recent positive selection, http://bigdata.ibp.ac.cn/RePoS/) to integrate and display multi-population selection signals. Our study extended our understanding of natural evolution and phenotype adaptation in Han Chinese as well as other populations.

Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in Acinetobacter baumannii Using an In Silico Approach

Background and Objectives: The BaeR protein is involved in the adaptation system of A. baumannii and is associated with virulence factors responsible for systemic infections in hospitalized patients. This study was conducted to characterize putative epitope peptides for the design of vaccines against BaeR protein, using an immune-informatic approach. Materials and Methods: FASTA sequences of BaeR from five different strains of A. baumannii were retrieved from the UNIPROT database and evaluated for their antigenicity, allergenicity and vaccine properties using BepiPred, Vaxijen, AlgPred, AntigenPro and SolPro. Their physio-chemical properties were assessed using the Expasy Protparam server. Immuno-dominant B-cell and T-cell epitope peptides were predicted using the IEDB database and MHC cluster server with a final assessment of their interactions with TLR-2. Results: A final selection of two peptide sequences (36aa and 22aa) was made from the 38 antigenic peptides. E1 was considered a soluble, non-allergenic antigen, and possessed negative GRAVY values, substantiating the hydrophilic nature of the proteins. Further analysis on the T-cell epitopes, class I immunogenicity and HLA allele frequencies yielded T-cell immuno-dominant peptides. The protein-peptide interactions of the TLR-2 receptor showed good similarity scores in terms of the high number of hydrogen bonds compared to other protein-peptide interactions. Conclusions: The two epitopes predicted from BaeR in the present investigation are promising vaccine candidates for targeting the TCS of A. baumannii in systemic and nosocomial infections. This study also demonstrates an alternative strategy to tackling and mitigating MDR strains of A. baumannii and provides a useful reference for the design and construction of novel vaccine candidates against this bacteria.

MHC clustering mediates rapid scanning of MHC by CD8 and ensures efficient destruction of target cells by CTL

MHC proteins bearing peptide antigens form nano-scale clusters on the surface of antigen-presenting cells. MHC clustering controls antigen presentation and T-cell responsiveness. Peptide-MHC (pMHC) ligands are recognized by antigen-specific T-cell receptor (TCR) and binds to CD8 co-receptor. The latter plays a critical role in controlling cytolytic activity of cytotoxic T lymphocytes (CTL). Using nanolipoprotein discoidal membrane mimetics that display pMHC ligands, we have found that close proximity of pMHC ligands within model membrane clusters ensures rapid rebinding of CD8 to MHC accounting for a dual role of CD8, namely, facilitating the T cells’ hunt for a rare foreign pMHC ligand and the induction of rapid TCR-mediated Ca2+ signaling and target cell destruction of target cells by CTL 1 . Our findings provide a new understanding of how MHC clustering influences multivalent interactions of pMHC ligands with CD8 and TCR occurring at the CTL/target cell interface that regulate antigen recognition, kinetics of intracellular signaling, and efficiency of CTL responses.

Designing of a Multi-epitope Vaccine against the Structural Proteins of Marburg Virus Exploiting the Immunoinformatics Approach.

Marburg virus disease (MVD) caused by the Marburg virus (MARV) generally appears with flu-like symptoms and leads to severe hemorrhagic fever. It spreads via direct contact with infected individuals or animals. Despite being considered to be less threatening in terms of appearances and the number of infected patients, the high fatality rate of this pathogenic virus is a major concern. Until now, no vaccine has been developed to combat this deadly virus. Therefore, vaccination for this virus is necessary to reduce its mortality. Our current investigation focuses on the design and formulation of a multi-epitope vaccine based on the structural proteins of MARV employing immunoinformatics approaches. The screening of potential T-cell and B-cell epitopes from the seven structural proteins of MARV was carried out through specific selection parameters. Afterward, we compiled the shortlisted epitopes by attaching them to an appropriate adjuvant and linkers. Population coverage analysis, conservancy analysis, and MHC cluster analysis of the shortlisted epitopes were satisfactory. Importantly, physicochemical characteristics, human homology assessment, and structure validation of the vaccine construct delineated convenient outcomes. We implemented disulfide bond engineering to stabilize the tertiary or quaternary interactions. Furthermore, stability and physical movements of the vaccine protein were explored using normal-mode analysis. The immune simulation study of the vaccine complexes also exhibited significant results. Additionally, the protein–protein docking and molecular dynamics simulation of the final construct exhibited a higher affinity toward toll-like receptor-4 (TLR4). From simulation trajectories, multiple descriptors, namely, root mean square deviations (rmsd), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent-accessible surface area (SASA), and hydrogen bonds, have been taken into account to demonstrate the inflexible and rigid nature of receptor molecules and the constructed vaccine. Inclusively, our findings suggested the vaccine constructs’ ability to regulate promising immune responses against MARV pathogenesis.

Genetic variations in the Orf7a protein of SARS-CoV-2 and its possible role in vaccine development

Introduction: SARS-CoV-2 (Severe Acute Respiratory Syndrome) is the causative agent of the novel coronavirus disease (COVID-19) that has been creating an unprecedented situation globally. The recurrent mutations in SARS-CoV-2 genomes impact on the vaccine designing strategies. The Orf7a is a 121-amino acid-long type I transmembrane accessory protein encoded by the genome of SARSCoV- 2 and plays a crucial role in the virus–host interaction. The present study aimed to analyze the variations occurring in Orf7a due to multiple mutations and its immunological role in developing a promising therapeutic target to curb SARS-CoV-2 infections. Methods: 16,161 sequences of Orf7a reported from the onset of this disease until 13 June 2021 from five continents were compared to identify genetic variations in the protein. Results: A total of 470 point mutations were detected in the sequences submitted. Subsequently, the nature of mutations (deleterious or neutral) was determined. Furthermore, the physicochemical properties, antigenicity, allergenicity, toxicity, and stability of Orf7a protein were estimated to demonstrate the stability of the protein. Additionally, we identified three B-cell immune epitopes, and their MHC cluster analysis was also performed. Conclusion: The recurrent mutations in Orf7a of SARS-CoV-2 provide a deep understanding of its role in the virus–host interactions. Findings of our study revealed that the predicted epitopes could be promising candidates for a vaccine against COVID-19 infections.

Delineating the Immuno-Dominant Antigenic Vaccine Peptides Against gacS-Sensor Kinase in Acinetobacter baumannii: An in silico Investigational Approach

ObjectivesTo predict the novel vaccine peptide candidates against gacS protein involved with the citrate utilization in the two-component system of A. baumannii-associated virulence as an alternative strategy to combat the multi-drug resistant strains using an immuno-informatic approach.MethodsThe study is designed as an observational in silico study design with the application of BepiPred, AlgPred, VaxiJen, AntigenPro, SolPro, Expasy ProtParam server, IEDB database, and MHC cluster analytical tools and servers to predict the immuno-dominant B-cell and T-cell epitopes from gacS FASTA sequences retrieved from UNIPROT database. Further peptide interactions with TLR-4 was assessed based on the number of hydrogen bonds.ResultsNine peptides (20aa) with the highest score of 1 were selected from the 137 epitopes, and five were predicted as antigenic epitopes (E1–E5). E3 was selected as the potent antigen (score: 0.939537) and E1 as the best vaccine candidate (score: 0.9803) under AntigenPro and Vaxijen server, respectively. SolPro predicted all epitopes as soluble peptides. ProtParam predictions showed E3 and E5 as stable proteins with a shelf life of 3.5 and 1.9 h and possessed negative GRAVY values. PsortB server predicted a final localization score of 7.88 for the gacS protein sequence as a cytoplasmic membrane protein. IEDB conservancy analysis showed 100% conserved sequences within the gacS sequence, and class I conservancy yielded positive values for all epitopes. Cluster analysis showed strong interactions, and the protein-peptide interactions with TLR-2 finally detected E5 as the best interacting peptide (H bonds = 14) followed by E3 (H bonds = 12).ConclusionThe study suggests five antigenic peptides as promiscuous vaccine candidates to target the gacS of A. baumannii using immuno-informatic approach toward the peptide synthesis and in vitro analysis. However, the study recommends further experimental validation for immunological response and memory through in vivo studies.

MHC clustering regulates selectivity and effectiveness of T-cell responses

Abstract Although formation of nano-scale MHC clusters on the cell membrane of antigen-presenting cells has been well documented, the essence of MHC clustering and the role in controlling antigen presentation and T-cell responses have been not systematically studied. This is due to the absence of available approaches to evaluate how the clusters’ size, density and composition of MHC clusters influence TCR engagement and triggering of TCR signaling. We exploited nano-scale discoidal membrane mimetics (nanolipoprotein particles, or NLPs) to capture and present pMHC ligands at various densities and examined the binding of these model membrane clusters to the surface of live human CD8+ T cells and the subsequent triggering of intracellular Ca2+ signaling. The data demonstrate that the proximity of pMHC ligands, high association rate of CD8-MHC interactions, and relatively long lifetime of cognate TCR-pMHC complexes emerge as essential parameters explaining the significance of MHC clustering. Rapid rebinding of CD8 to clustered MHC suggests a dual role of CD8 in facilitating the T cells’ hunt for a rare foreign pMHC ligand and the induction of rapid T-cell response. Thus, our findings provide a new understanding of how MHC clustering influences multivalent interactions of pMHC ligands with CD8 and TCR on live T cells that regulate antigen recognition, kinetics of intracellular signaling, and the selectivity and efficiency of T-cell responses.

Extent of MHC Clustering Regulates Selectivity and Effectiveness of T Cell Responses.

MHC proteins that present peptide ligands for recognition by TCR form nanoscale clusters on the cell membrane of APCs. How the extent of MHC clustering controls productive TCR engagement and TCR-mediated signaling has not been systematically studied. To evaluate the role of MHC clustering, we exploited nanoscale discoidal membrane mimetics (nanolipoprotein particles) to capture and present peptide-MHC (pMHC) ligands at various densities. We examined the binding of these model membrane clusters to the surface of live human CD8+ T cells and the subsequent triggering of intracellular signaling. The data demonstrate that the proximity of pMHC ligands, high association rate of CD8-MHC interactions, and relatively long lifetime of cognate TCR-pMHC complexes emerge as essential parameters, explaining the significance of MHC clustering. Rapid rebinding of CD8 to MHC suggests a dual role of CD8 in facilitating the T cells' hunt for a rare foreign pMHC ligand and the induction of rapid T cell response. Thus, our findings provide a new understanding of how MHC clustering influences multivalent interactions of pMHC ligands with CD8 and TCR on live T cells that regulate Ag recognition, kinetics of intracellular signaling, and the selectivity and efficiency of T cell responses.

Effect of MHC clustering on antigen recognition and T cell responses

Abstract MHC proteins that present peptide ligands to T cells form nano-scale clusters on the cell membrane of antigen-presenting cells. While MHC clustering is thought to influence antigen presentation to T cells and may depend on cell type and pathophysiological conditions, how the extent of MHC clustering controls productive TCR engagement and T cell responses has not been systematically studied. To evaluate the effect of MHC clustering on T cell responses, we utilized nano-scale discoidal membrane mimetics to capture and present pMHC ligands at various densities. We examined the binding parameters of these model membrane clusters interacting with live CD8+ T cells and their impact on the triggering of TCR signaling. Our data show that not just the level of expression of pMHC ligands but the extent of their clustering controls antigen recognition and responses by T cells. Variations in the density of pMHC with MHC clusters regulate CD8-MHC and TCR-pMHC interactions, each contributing in a unique way to antigen recognition and the quality of TCR-mediated signaling. Along with well-documented co-clustering of TCR and CD8 on activated, but not naïve T cells, these findings provide new understanding of how the immune receptor clustering controls the specificity and effectiveness of antigen-specific responses by naïve and activated T cells during acute and chronic viral infection.

Sepsis induces specific changes in histone modification patterns in human monocytes.

BackgroundSepsis is a global burden and the primary cause of death in intensive care units worldwide. The pathophysiological changes induced by the host’s systemic inflammatory response to infection are not yet fully understood. During sepsis, the immune system is confronted with a variety of factors, which are integrated within the individual cells and result in changes of their basal state of responsiveness. Epigenetic mechanisms like histone modifications are known to participate in the control of immune reactions, but so far the situation during sepsis is unknown.Methods and FindingsIn a pilot approach, we performed combined chromatin immunoprecipitation followed by high-throughput sequencing to assess the genome-wide distribution of the chromatin modifications histone 3 lysine 4 and 27 trimethylation and lysine 9 acetylation in monocytes isolated from healthy donors (n = 4) and patients with sepsis (n = 2). Despite different underlying causes for sepsis, a comparison over promoter regions shows a high correlation between the patients for all chromatin marks. These findings hold true also when comparing patients to healthy controls. Despite the global similarity, differential analysis reveals a set of distinct promoters with significant enrichment or depletion of histone marks. Further analysis of overrepresented GO terms show an enrichment of genes involved in immune function. To the most prominent ones belong different members of the HLA family located within the MHC cluster together with the gene coding for the major regulator of this locus—CIITA.ConclusionsWe are able to show for the first time that sepsis in humans induces selective and precise changes of chromatin modifications in distinct promoter regions of immunologically relevant genes, shedding light on basal regulatory mechanisms that might be contributing to the functional changes occurring in monocytes.

Evidence that the Density of Self Peptide-MHC Ligands Regulates T-Cell Receptor Signaling

Noncognate or self peptide-MHC (pMHC) ligands productively interact with T-cell receptor (TCR) and are always in a large access over the cognate pMHC on the surface of antigen presenting cells. We assembled soluble cognate and noncognate pMHC class I (pMHC-I) ligands at designated ratios on various scaffolds into oligomers that mimic pMHC clustering and examined how multivalency and density of the pMHCs in model clusters influences the binding to live CD8 T cells and the kinetics of TCR signaling. Our data demonstrate that the density of self pMHC-I proteins promotes their interaction with CD8 co-receptor, which plays a critical role in recognition of a small number of cognate pMHC-I ligands. This suggests that MHC clustering on live target cells could be utilized as a sensitive mechanism to regulate T cell responsiveness.

Role of MHC-Linked Genes in Autoantigen Selection and Renal Disease in a Murine Model of Systemic Lupus Erythematosus

We previously described a renal protective effect of factor B deficiency in MRL/lpr mice. Factor B is in the MHC cluster; thus, the deficient mice were H2b, the haplotype on which the knockout was derived, whereas the wild-type littermates were H2k, the H2 of MRL/lpr mice. To determine which protective effects were due to H2 vs factor B deficiency, we derived H2b congenic MRL/lpr mice from the 129/Sv (H2b) strain. Autoantibody profiling using autoantigen microarrays revealed that serum anti-Smith and anti-small nuclear ribonucleoprotein complex autoantibodies, while present in the majority of H2k/k MRL/lpr mice, were absent in the H2b/b MRL/lpr mice. Surprisingly, 70% of MRL/lpr H2b/b mice were found to be serum IgG3 deficient (with few to no IgG3-producing B cells). In addition, H2b/b IgG3-deficient MRL/lpr mice had significantly less proteinuria, decreased glomerular immune complex deposition, and absence of glomerular subepithelial deposits compared with MRL/lpr mice of any H2 type with detectable serum IgG3. Despite these differences, total histopathologic renal scores and survival were similar among the groups. These results indicate that genes encoded within or closely linked to the MHC region regulate autoantigen selection and isotype switching to IgG3 but have minimal effect on end-organ damage or survival in MRL/lpr mice.

Signaling at the inhibitory natural killer cell immune synapse regulates lipid raft polarization but not class I MHC clustering.

Natural killer (NK) cell cytotoxicity is determined by a balance of positive and negative signals. Negative signals are transmitted by NK inhibitory receptors (killer immunoglobulin-like receptors, KIR) at the site of membrane apposition between an NK cell and a target cell, where inhibitory receptors become clustered with class I MHC ligands in an organized structure known as an inhibitory NK immune synapse. Immune synapse formation in NK cells is poorly understood. Because signaling by NK inhibitory receptors could be involved in this process, the human NK tumor line YTS was transfected with signal-competent and signal-incompetent KIR2DL1. The latter were generated by truncating the KIR2DL1 cytoplasmic tail or by introducing mutations in the immunoreceptor tyrosine-based inhibition motifs. The KIR2DL1 mutants retained their ability to cluster class I MHC ligands on NK cell interaction with appropriate target cells. Therefore, receptor-ligand clustering at the inhibitory NK immune synapse occurs independently of KIR2DL1 signal transduction. However, parallel examination of NK cell membrane lipid rafts revealed that KIR2DL1 signaling is critical for blocking lipid raft polarization and NK cell cytotoxicity. Moreover, raft polarization was inhibited by reagents that disrupt microtubules and actin filaments, whereas synapse formation was not. Thus, NK lipid raft polarization and inhibitory NK immune synapse formation occur by fundamentally distinct mechanisms.

Tel-2 Is a Novel Transcriptional Repressor Related to the Ets Factor Tel/ETV-6

We report here the isolation of Tel-2, a novel member of the Ets transcription factor family, with high homology to Tel/ETV-6. Tel-2 is the second mammalian member of the Tel Ets family subclass whose prototype Tel is involved in various chromosomal translocations in human cancers. Six differentially expressed alternative splice products of Tel-2 were characterized encoding different Tel-2 isoforms which either contain or lack the amino-terminal Pointed domain and also vary at the carboxyl terminus. In contrast to Tel, which is highly expressed in several different cell types and tissues, Tel-2 is only weakly expressed in a variety of tissues and cell types, including placenta, prostate, spleen, liver, and lung. Tel-2 binds to functionally relevant Ets-binding sites of several genes and only the Tel-2 isoform containing the Pointed domain and the DNA-binding domain acts as a strong repressor of transcription. The retinoic acid receptor alpha and bone morphogenetic protein-6B (BMP-6) genes are specifically repressed by Tel-2 indicating a function for Tel-2 as an inhibitor of differentiation. Due to the important involvement of Tel in human cancer and the location of Tel-2 within the MHC cluster region, Tel-2 might be involved in chromosomal translocations in human cancer as well.

Fourth component of Xenopus laevis complement: cDNA cloning and linkage analysis of the frog MHC.

Complement C4 shows extensive structural and functional similarity to complement C3, hence these components are believed to have originated by gene duplication from a common ancestor. Although to date C3 cDNA clones have been isolated from all major classes of extant vertebrates including Xenopus, C4 cDNA clones have been isolated from mammalian species only. We describe here the molecular cloning and structural analysis of Xenopus C4 cDNA. The cDNA sequence encoding the thioester region of Xenopus C4 was amplified by reverse transcriptase-polymerase chain reaction using Xenopus liver mRNA as a template, and then used to screen a liver cDNA library. The amino acid sequence of Xenopus C4 deduced from a clone containing the entire protein-coding sequence showed 39%, 30%, 25%, and 20% overall identity with those of human C4, C3, C5, and alpha2-macroglobulin, respectively. The predicted amino acid sequence consisted of a 22-residue putative signal peptide, a 634-residue beta chain, a 732-residue alpha chain, and a 287-residue gamma chain. Of 30 cysteine residues, 27 were found in exactly the same positions as in human C4. Genomic Southern blotting analysis indicated that C4 is a single copy gene in Xenopus and is part of the frog MHC cluster. These results clearly demonstrate that C3/C4 gene duplication and linkage between the C4 gene and the major histocompatibility complex predate mammalian/amphibian divergence.