HLA Molecules Research Articles

Does Antigen Glycosylation Impact the HIV-Specific T Cell Immunity?

It is largely unknown how post-translational protein modifications, including glycosylation, impacts recognition of self and non-self T cell epitopes presented by HLA molecules. Data in the literature indicate that O- and N-linked glycosylation can survive epitope processing and influence antigen presentation and T cell recognition. In this perspective, we hypothesize that glycosylation of viral proteins and processed epitopes contribute to the T cell response to HIV. Although there is some evidence for T cell responses to glycosylated epitopes (glyco-epitopes) during viral infections in the literature, this aspect has been largely neglected for HIV. To explore the role of glyco-epitope specific T cell responses in HIV infection we conducted in silico and ex vivo immune studies in individuals with chronic HIV infection. We found that in silico viral protein segments with potentially glycosylable epitopes were less frequently targeted by T cells. Ex vivo synthetically added glycosylation moieties generally masked T cell recognition of HIV derived peptides. Nonetheless, in some cases, addition of simple glycosylation moieties produced neo-epitopes that were recognized by T cells from HIV infected individuals. Herein, we discuss the potential importance of these observations and compare limitations of the employed technology with new methodologies that may have the potential to provide a more accurate assessment of glyco-epitope specific T cell immunity. Overall, this perspective is aimed to support future research on T cells recognizing glycosylated epitopes in order to expand our understanding on how glycosylation of viral proteins could alter host T cell immunity against viral infections.

CD8+ T-Cell Repertoire in Human Leukocyte Antigen Class I-Mismatched Alloreactive Immune Response.

In transplantation, direct allorecognition is a complex interplay between T-cell receptors (TCR) and HLA molecules and their bound peptides expressed on antigen-presenting cells. In analogy to HLA mismatched hematopoietic stem cell transplantation (HSCT), the TCR CDR3β repertoires of alloreactive cytotoxic CD8+ responder T cells, defined by the cell surface expression of CD137 and triggered in vitro by HLA mismatched stimulating cells, were analyzed in different HLA class I mismatched combinations. The same HLA mismatched stimulatory cells induced very different repertoires in distinct but HLA identical responders. Likewise, stimulator cells derived from HLA identical donors activated CD8+ cells expressing very different repertoires in the same mismatched responder. To mimic in vivo inflammation, expression of HLA class l antigens was upregulated in vitro on stimulating cells by the inflammatory cytokines TNFα and IFNβ. The repertoires differed whether the same responder cells were stimulated with cells treated or not with both cytokines. In conclusion, the selection and expansion of alloreactive cytotoxic T-cell clonotypes expressing a very diverse repertoire is observed repeatedly despite controlling for HLA disparities and is significantly influenced by the inflammatory status. This makes prediction of alloreactive T-cell repertoires a major challenge in HLA mismatched HSCT.

Incidence and impact of allele-specific anti-HLA antibodies and high-resolution HLA genotyping on assessing immunologic compatibility

The ability to identify specific HLA molecules against which a patient has alloantibodies has revolutionized assessment of immunologic compatibility. Anti-HLA antibodies are typically evaluated as reactive against well-defined serologic antigen groups. Thus, donor HLA genotyping is aimed at defining HLA at the serologic split-antigen level to avoid incompatible antigen-antibody combinations. However, anti-HLA antibodies can have reactivities not accurately described by well-defined serologic antigens. While existence of these antibodies is acknowledged, their precise impact on clinical practice is not clear. We performed a single-center review of 2 years of pre-and post-transplant anti-HLA antibody testing data combined with high-resolution HLA genotyping data for living and deceased organ donors to evaluate the clinical impact of anti-HLA antibodies with reactivities outside of commonly defined serologic antigen groups. We find approximately 15% of patients awaiting transplantation have alloantibodies with differential reactivity for HLA proteins encoded by specific alleles within a serologic antigen group. Allele-specific antibodies are associated with positive cellular crossmatches not accurately predicted by standard donor HLA genotyping and can manifest as post-transplant donor-specific antibodies. Our data highlights the importance of evaluating anti-HLA antibodies at the allele-level and provides evidence supporting utility for high-resolution HLA genotyping in solid organ transplantation.

Matchmaker, matchmaker make me a match: Opportunities and challenges in optimizing compatibility of HLA eplets in transplantation.

The development of donor-specific antibodies (DSAs) is a major complication in transplantation, which is associated with inferior graft survival, impaired quality of life, and increased healthcare costs. DSA develop upon recognition of nonself HLA by the recipient's immune system. HLA molecules contain epitopes, which are the surface regions of HLA molecules recognized by antibodies. HLAMatchmaker is an algorithm for assessing donor:recipient HLA compatibility at the level of structurally defined HLA targets called eplets. The consideration of eplets, rather than the whole HLA molecule, could offer some advantages when classifying the immune risk associated with particular donor:recipient pairs. Assessing compatibility at the level of HLA eplets could decrease misclassification of post-transplant immune risk by improving specificity, when antibodies are confirmed to be directed against donor eplets missing from the recipient's repertoire of eplets. Consideration of eplets may also increase the sensitivity of immune risk assessment, when identifying mismatched eplets that could give rise to new, not previously detected, donor-specific antibodies post-transplant. Eplet matching can serve as a rational strategy for immune risk mitigation. Herein, we review the evolution of HLA (in) compatibility assessment for organ allocation. We outline challenges in the implementation of eplet-based donor:recipient matching, including unavailability of allele-level donor genotypes for 11 HLA loci at the time of organ allocation and difficulty in assessing the hierarchy of immune risk associated with particular HLA eplet mismatches. Opportunities to address some of the current shortcomings of donor genotyping and HLAMatchmaker are also discussed. While there is a demonstrated benefit in the application of HLAMatchmaker for donor: recipient HLA (in)compatibility assessment, evolving long-read genotyping methods, compilation of large data sets with allele-level genotypes, and standardization of methods to verify eplets as determinants of immune-mediated injuries are required before HLA eplet matching is implemented in organ allocation to improve upon transplant outcomes.

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer

BackgroundLong-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recognized as neoantigens. This study used a long-read sequencer (MinION) to construct a comprehensive catalog of aberrant splicing isoforms in non-small-cell lung cancers, by which novel isoforms and potential neoantigens are identified.ResultsFull-length cDNA sequencing is performed using 22 cell lines, and a total of 2021 novel splicing isoforms are identified. The protein expression of some of these isoforms is then validated by proteome analysis. Ablations of a nonsense-mediated mRNA decay (NMD) factor, UPF1, and a splicing factor, SF3B1, are found to increase the proportion of aberrant transcripts. NetMHC evaluation of the binding affinities to each type of HLA molecule reveals that some of the isoforms potentially generate neoantigen candidates. We also identify aberrant splicing isoforms in seven non-small-cell lung cancer specimens. An enzyme-linked immune absorbent spot assay indicates that approximately half the peptide candidates have the potential to activate T cell responses through their interaction with HLA molecules. Finally, we estimate the number of isoforms in The Cancer Genome Atlas (TCGA) datasets by referring to the constructed catalog and found that disruption of NMD factors is significantly correlated with the number of splicing isoforms found in the TCGA-Lung Adenocarcinoma data collection.ConclusionsOur results indicate that long-read sequencing of full-length cDNAs is essential for the precise identification of aberrant transcript structures in cancer cells.

Residue substitution enhances the immunogenicity of neoepitopes from gastric cancers.

Objective:Neoantigens arising from gene mutations in tumors can induce specific immune responses, and neoantigen-based immunotherapies have been tested in clinical trials. Here, we characterized the efficacy of altered neoepitopes in improving immunogenicity against gastric cancer.Methods:Raw data of whole-exome sequencing derived from a patient with gastric cancer were analyzed using bioinformatics methods to identify neoepitopes. Neoepitopes were modified by P1Y (the first amino acid was replaced by tyrosine) and P2L (the second amino acid was replaced by leucine). T2 binding and stability assays were used to detect the affinities between the neoepitopes and the HLA molecules, as well as the stabilities of complexes. Dendritic cells (DCs) presented with neoepitopes stimulated naïve CD8+ T cells to induce specific cytotoxic T lymphocytes. ELISA and carboxyfluorescein succinimidyl ester were used to detect IFN-γ and TNF-α levels, and T cell proliferation. Perforin was detected by flow cytometry. The cytotoxicity of T cells was determined using the lactate dehydrogenase assay.Results:Bioinformatics analysis, T2 binding, and stability assays indicated that residue substitution increased the affinity between neoepitopes and HLA molecules, as well as the stabilities of complexes. DCs presented with altered neoepitopes stimulated CD8+T cells to release more IFN-γ and had a greater effect on promoting proliferation than wild-type neoepitopes. CD8+T cells stimulated with altered neoepitopes killed more wild-type neoepitope-pulsed T2 cells than those stimulated with wild-type neoepitopes, by secreting more IFN-γ, TNF-α, and perforin.Conclusions:Altered neoepitopes exhibited greater immunogenicity than wild-type neoepitopes. Residue substitution could be used as a new strategy for immunotherapy to target neoantigens.

Identification of CD4+ T cell epitopes from Staphylococcus aureus secretome using immunoinformatic prediction and molecular docking.

One major reason for the lack of clinical success of Staphylococcus aureus vaccine candidates is the inability of the antigens to develop a CD4+ T cell-mediated immune response. Hence, it is important to identify CD4+ T cell antigens from S. aureus. CD4+ T cells are activated following the presentation of epitopes derived from exogenous proteins on HLA class II molecules. Fifty-nine secretory proteins of S. aureus were analyzed computationally for the presence of HLA class II binding peptides. Fifteen-mer peptides were generated, and their binding to 26 HLA class II alleles was predicted. The structural feasibility of the peptides binding to HLA-II was studied using molecular docking. Of the 16,724 peptides generated, 6991 (41.8%) were predicted to bind to any one of the alleles with an IC50 value below 50 nM. Comparative sequence analysis revealed that only 545 of the strong binding peptides are non-self in the human system. Approximately 50% of the binding peptides were monoallele-specific. Moreover, approximately 95% of the predicted strong binding non-self peptides interacted with the binding groove of at least one HLA class II molecule with a glide score better than -10 kcal/mol. On the basis of the analysis of the strength of binding, non-self presentation in the human host, propensity to bind to a higher number of alleles, and energetically favorable interactions with HLA molecules, a set of 11 CD4+ T cell epitopes that can be used as vaccine candidates was identified.

Lack of anti-paternal cytotoxic antibody production in the presence of spermatozoa in recurrent spontaneous abortion couples in contrast to fertile couples: a pilot study

Background: Anti-paternal cytotoxic antibody (APCA) is a pregnancy alloantibody and is directed to paternal HLA molecules. A recent study showed that this antibody is produced in the presence of the husband’s spermatozoa. Several studies have shown the absence or reduction of this antibody in the serum of recurrent spontaneous abortion (RSA) women. Note that the production of APCA has not been determined in the presence of spermatozoa in RSA women. A reason for the reduction or absence of APCA in the serum of RSA women may be the inability of the husband’s spermatozoa to induce APCA production by lymphocytes. Therefore, this study aims to investigate APCA production by the wife’s peripheral blood mononuclear cells (PBMCs) in the presence of the husband’s spermatozoa in RSA couples. Methods: Ten RSA couples and ten fertile couples were included in this study. The wife’s PBMCs (peripheral blood mononuclear cells) were cocultured with her husband’s spermatozoa and the supernatant assessed for the presence of IgG by the ELISA method and APCA by complement-dependent cytotoxicity (CDC) assay. Results: Results showed that the production of IgG (median = 740 ng/mL in the fertile and 64 ng/mL in the RSA group) and APCA (median = 78% in the fertile and 48.5% in the RSA group) was significantly lower in the RSA group as compared to the fertile group. Conclusions: We concluded that a possible cause for APCA reduction in RSA women may be the inability of the husband’s spermatozoa in induction of antibody production by the wife’s PBMC. Nevertheless, large studies are needed to confirm the results of the present study.

Epitope-based peptide vaccine against Bombali Ebolavirus viral protein 40: An immunoinformatics combined with molecular docking studies

Abstract Bombali Ebolavirus belongs to the RNA group of viruses which causes lethal hemorrhagic fever with a high mortality rate. Despite these facts, yet there is no approved vaccine have been developed for the eradication of Bombali Ebolavirus infections. Therefore, this study described a multi epitope-based peptide vaccine against Bombali Ebolavirus VP40, using several immunoinformatics tools combined with molecular docking studies. The VP40 sequences of the sixty-six Ebolavirus strains were retrieved from National Center for Biotechnology Information (NCBI) and Uniprot, and then submitted to VaxiJen for identification of the most antigenic protein. B-cell and T-cell prediction, population coverage and molecular docking analysis were achieved to determine the most promising Bombali VP40 epitopes. The VP40 (YP_009513276.1) of Bombali Ebola virus was found to be the most antigenic protein among all the analyzed ones, and thus selected for the further predictions. For T cell prediction, two epitopes showed high affinity to MHC class I with high population coverage against Africa and the world. Furthermore, in MHC class II, three promising epitopes were found associated with most common MHC class II alleles. The above results indicate that these peptides capable of provoking T-cell response and being interacted with a wide range of HLA molecules that suggested a strong potential for a vaccine candidate against Bombali Ebolavirus.

TACI Mutasyonu Bulunan Yaygın Değişken İmmün Yetmezlik Hastalarında T Hücre Vβ Repertuvarının Akan Hücre Sistemi ile Analizi

Objective: TCR (T Cell Receptor) which is expressed on T cells is responsible for recognizing antigens presented by HLA molecules of the APCs (Antigen Presenting Cells) and initiation of the immune response. It has been reported that TACI (Transmembrane activator and calcium modulating cyclophilin ligand interactor) mediates the interaction of B cells and dendritic cells which are both responsible for the processing of T cells. Materials and Methods: In this study, 24 TCRVβ clones were analyzed by using multiparametric flow cytometry in seven patients with TACI mutation [two homozygous (c.310T> C) five heterozygous (c.310T> C, c.226G> C, c.260T> A)], four CVID (Common Variable Immunodeficiency) patients who had not TACI defect (non-TACI) and five healthy controls. In this study group, serum Ig levels and infection history, CD4+ and CD8+ cell percentages, and HLA profiles were investigated. Results: Increased TCRVβ13.2 clone was observed in patients with TACI defects unlike control individuals and non-TACI-CVID patients (p=0.02). We found that there was a statistically significant decrease in TCRVβ8 clone (p=0.012) in TACI deficient CVID patients and non-TACI-CVID patients compared to control individuals. TCRVβ20 clones in non-TACI-CVID patients were decreased compared to TACI-CVID patients and control individuals (p=0.009). Decreased TCRVβ8 was also associated with TACI deficient CVID patients. Conclusion: Further studies and large cohorts are needed to understand the relationship between TCRVβ8, TCRVβ13.2, and CVID with TACI mutations.

Immunoinformatics aided design of peptide-based vaccines against ebolaviruses.

Ebolaviruses are at the forefront of emerging viruses and present a very perceptible threat to global peace and harmony. In the last decade, Ebola virus disease has claimed more than 90% of total lives since its inception in 1976. Owing to multiple host immune evasion methods employed by the virus and the limitations of traditional vaccine development approaches, finding a globally effective and reliable counter measure against Ebola virus remains a challenge. Highly conserved peptide fragments belonging to critical viral proteins and containing multiple epitopes which have the capacity to interact with a wide array of HLA molecules present a viable solution. Immunoinformatics or computational immunology enables rapid screening and shortlisting of plausible epitopes with a high immunogenic potential, thus, supporting expeditious elucidation of efficacious vaccine candidates. In light of above facts, we describe a computational methodology in this chapter for identification of potent peptide vaccine candidates against human infecting viruses. By applying this stringent methodology, we were able to identify multiple, immunogenic ebolavirus peptide fragments which, after verification in animal models, might be considered as part of future synthetic Ebola vaccine.

Dendritic Cells Prime Anti-Tumor CD8 <sup>+</sup> T Cell Responses Through MHC-Dressing

Antigen cross-presentation, wherein dendritic cells (DC) present exogenous antigen on MHC-I molecules, is considered the primary mechanism by which DCs initiate tumor-specific CD8+ T cell responses. Here, we demonstrate that MHC-dressing, an antigen presentation pathway in which DCs acquire and display intact peptide:MHC-I molecules, is critical for anti-tumor immunity. Cancer cell MHC-I expression was required for optimal CD8+ T cell activation in wo subcutaneous tumor models. In vivo acquisition of tumor-derived peptide:MHC-I molecules by DCs was sufficient to induce antigen-specific CD8+ T cell priming, which was not ablated upon genetic inactivation of tumor antigen cross-presentation. Transfer of human tumor-derived HLA molecules to myeloid cells was detected in vitro and in human tumor xenografts. Inconclusion, MHC-I-dressing is crucial for anti-tumor CD8+ T cell priming by DCs. In addition to quantitatively enhancing tumor antigen presentation, MHC-dressing might also enable DCs to more faithfully and efficiently mirror the cancer cell peptidome.

Changes in the Tumor Immune Microenvironment during Disease Progression in Patients with Ovarian Cancer.

Simple SummaryImmunotherapy has been a successful treatment for many cancers. However, no immunotherapy treatment has been approved for ovarian cancer due to low efficacy in this patient group. This study investigated the cellular and molecular changes from primary ovarian tumors, at the time of diagnosis, to recurrence, where the disease returns after surgery and chemotherapies. Here we examined the immune contexture to better understand subdued responses to immunotherapy and identify additional, potentially complimentary, therapeutic targets. Indications of the development of adaptive immune resistance during disease progression were observed, with increases in immune and stromal cell infiltration accompanied by the expression of immune suppressive markers. We observed high gene expression of the immune checkpoint genes LAG3 and HAVCR2 (TIM3) in most tumors and increased expression of the immune checkpoint genes TIGIT and CTLA4 in recurrent tumors, compared to the primaries. These markers may be potential candidates for immunotherapy targeting in ovarian cancer.Anti-PD1/PDL1 therapy has proven efficacious against many cancers but only reached modest objective response rates against recurrent ovarian cancer. A deeper understanding of the tumor microenvironment (TME) may reveal other immunosuppressive mechanisms that warrant investigation as immunotherapeutic targets for this challenging disease. Matched primary and recurrent tumors from patients with high-grade serous ovarian carcinoma (HGSC) were analyzed by multicolor immunohistochemistry/immunofluorescence for the presence of T cells, B cells, macrophages, and for the expression of immunosuppressive and HLA molecules. Cancer- and immune-related gene expression was assessed by NanoString analysis. Recurrent tumors showed increased infiltration by immune cells, displayed higher expression of PDL1, IDO, and HLA molecules, and contained more stromal tissue. NanoString analysis demonstrated increased expression of gene signatures related to chemokines and T cell functions in recurrent tumors. The ovarian tumors showed high gene expression of LAG3 and HAVCR2 (TIM3) and enhanced levels of TIGIT and CTLA4 in recurrent tumors compared to primary tumors. The majority of HGSC developed into a more inflamed phenotype during progression from primary to recurrent disease, including indications of adaptive immune resistance. This suggests that recurrent tumors may be particularly sensitive to inhibition of adaptive immune resistance mechanisms.

RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles.

SummaryThe recent increase of immunopeptidomics data, obtained by mass spectrometry or binding assays, opens up possibilities for investigating endogenous antigen presentation by the highly polymorphic human leukocyte antigen class I (HLA-I) protein. State-of-the-art methods predict with high accuracy presentation by HLA alleles that are well represented in databases at the time of release but have a poorer performance for rarer and less characterized alleles. Here, we introduce a method based on Restricted Boltzmann Machines (RBMs) for prediction of antigens presented on the Major Histocompatibility Complex (MHC) encoded by HLA genes—RBM-MHC. RBM-MHC can be trained on custom and newly available samples with no or a small amount of HLA annotations. RBM-MHC ensures improved predictions for rare alleles and matches state-of-the-art performance for well-characterized alleles while being less data demanding. RBM-MHC is shown to be a flexible and easily interpretable method that can be used as a predictor of cancer neoantigens and viral epitopes, as a tool for feature discovery, and to reconstruct peptide motifs presented on specific HLA molecules.

HLA-B8 and HLA-A3 Coexpressed With HLA-B8 Are Associated With a Reduced Risk of the Development of Chronic Myeloid Leukemia

AbstractChronic myeloid leukemia (CML) is characterized by the chromosomal translocation t(9;22) resulting in the chimeric bcr-abl oncogene that encodes the P210 fusion protein, which contains a unique amino acid sequence. If peptides derived from the leukemia-specific part of P210 are expressed in HLA molecules on the cell membrane of leukemic cells, an immunological response may occur. Recent studies using synthetic peptides identical to the bcr-abl fusion region showed that some peptides are capable of binding to HLA-A3, -A11, and -B8 molecules. Cytotoxic T-cell responses have been induced against bcr-abl–derived synthetic peptides bound to HLA-A3 and -B8. We hypothesized that if antigen processing of the P210 fusion protein leads to presentation of peptides from the fusion region by major histocompatibility complex (MHC) molecules in vivo, this may be reflected in a diminished incidence of CML in individuals expressing HLA-A3, -A11, or -B8. Consequently, lower frequencies of these antigens would be expected in patients with CML compared with unaffected individuals. A case-control study and a meta-analysis were performed to test this hypothesis. The multicenter case-control study compared patients with CML from the data base of the European Group for Blood and Marrow Transplantation (EBMT) with unaffected individuals from the registry of Bone Marrow Donors Worldwide. Patients and controls were matched per country. The meta-analysis consisted of five studies reported in the literature. The multicenter case-control study consisting of 1,899 patients and 512,363 bone marrow donors as controls yielded odds ratios (ORs) of 0.90 (95% confidence interval [CI], 0.80 to 1.00) for HLA-A3, 1.16 (95% CI, 1.02 to 1.33) for HLA-A11, and an OR of 0.73 (95% CI, 0.65 to 0.82) for HLA-B8. Coexpression of HLA-A3 and HLA-B8 gave an OR of 0.51 (95% CI, 0.40 to 0.67). This can be translated in a protective effect of 27% for HLA-B8, 10% for HLA-A3, and 49% protection for the combination of HLA-A3 and HLA-B8. The meta-analysis comprising 463 CML patients and 4,912 controls showed a 29% risk reduction for individuals expressing HLA-B8 (OR of 0.71; 95% CI, 0.52 to 0.97), but an OR of 1.19 (95% CI, 0.90 to 1.56) for HLA-A3 and an OR of 1.09 (95% CI, 0.80 to 1.50) for HLA-A11. In conclusion, these results indicate that HLA-B8 expression, in particular when HLA-A3 is coexpressed, is associated with a diminished incidence of CML. A biological mechanism may be that presentation of bcr-abl breakpoint peptides in these HLA molecules can induce a protective immune response.

Genes Encoding Tumor-Specific Antigens Are Expressed in Human Myeloma Cells

AbstractGenes of the MAGE, BAGE, GAGE, and LAGE-1/NY-ESO-1families encode antigenic peptides that are presented by HLA class I molecules and that are recognized on human tumors by autologous cytolytic T lymphocytes. These genes are expressed in many solid tumor types but not in normal tissues, except male germline cells. Because the latter cells are devoid of HLA molecules, the derived antigens are strictly tumor-specific and should constitute safe immunogens for cancer immunotherapy. We detected a significant expression of these genes in a high proportion of bone marrow samples from patients with advanced multiple myeloma. This observation provides a basis for clinical trials aimed at inducing a cellular immune response directed at malignant plasma cells in advanced myeloma patients.

HDAC Inhibition Increases HLA Class I Expression in Uveal Melanoma.

Simple SummaryChemotherapy and immunotherapy are both used to treat malignancies. The immunotherapy of cancer often involves T cells, which recognise the antigens presented in HLA molecules. Uveal melanoma (UM) is an intraocular malignancy, which often gives rise to metastases. We determined whether high-risk tumours expressed the target of two drugs, histone deacetylase (HDAC) inhibitor Quisinostat and Tazemetostat, an inhibitor of Enhancer of zeste homologue 2 (EZH2). We observed that especially high-risk UM tumours (monosomy 3, gain of 8q, loss of BAP1) expressed several HDACs, and showed a high HLA Class I expression. We further tested whether these drugs influenced HLA Class I expression on three UM cell lines. The drug Quisinostat led to an upregulation of HLA protein and mRNA levels in three UM cell lines, while Tazemetostat had little effect. We concluded that the use of drugs that influence epigenetic regulators may impact immunotherapy approaches.The treatment of uveal melanoma (UM) metastases or adjuvant treatment may imply immunological approaches or chemotherapy. It is to date unknown how epigenetic modifiers affect the expression of immunologically relevant targets, such as the HLA Class I antigens, in UM. We investigated the expression of HDACs and the histone methyl transferase EZH2 in a set of 64 UMs, using an Illumina HT12V4 array, and determined whether a histone deacetylase (HDAC) inhibitor and EZH2 inhibitor modified the expression of HLA Class I on three UM cell lines. Several HDACs (HDAC1, HDAC3, HDAC4, and HDAC8) showed an increased expression in high-risk UM, and were correlated with an increased HLA expression. HDAC11 had the opposite expression pattern. While in vitro tests showed that Tazemetostat did not influence cell growth, Quisinostat decreased cell survival. In the three tested cell lines, Quisinostat increased HLA Class I expression at the protein and mRNA level, while Tazemetostat did not have an effect on the cell surface HLA Class I levels. Combination therapy mostly followed the Quisinostat results. Our findings indicate that epigenetic drugs (in this case an HDAC inhibitor) may influence the expression of immunologically relevant cell surface molecules in UM, demonstrating that these drugs potentially influence immunotherapy.

The role of HLA genes: from autoimmune diseases to COVID-19

Genes of HLA system (Human Leukocyte Antigen) play an essential role in the normal functioning of the immune system. There are three classes of genes: I, II, and III. The function of HLA molecules class I is to present antigens of peptides from the cytoplasm to T-lymphocytes on the cell surface, and class II - to present antigens of peptides from the extracellular space. In the classical view, the pathological activation of the immune system in patients with a genetic predisposition can result in the development of autoimmune diseases. However, the influence of this system on the development of non-autoimmune diseases, their severity and prognosis, has been recently considered. Besides, HLA molecules provide a presentation of various infectious agents. In this connection, the loci of the main histocompatibility complex can be considered candidates for determining the genetic predisposition to infectious diseases themselves and their course. This review hypothesizes that specific variants of HLA genes may cause the formation of a «cytokine storm» in patients with COVID-19. Identification of a group of patients with particular genetic variations that cause violation of immune tolerance and hyperresponse in the setting of viral infection will help to optimize the algorithm for disease prevention and treatment of such patients and, as a result, to reduce the severity of the epidemiological situation.

Monocytic Cytokines in Autoimmune Polyglandular Syndrome Type 2 Are Modulated by VitaminD and HLA-DQ.

ContextAutoimmune polyglandular syndrome (APS-2: autoimmune Addison’s disease or type 1 diabetes) is conferred by predisposing HLA molecules, vitamin D deficiency, and heritable susceptibility. Organ destruction is accompanied by cytokine alterations. We addressed the monocytic cytokines of two distinct APS-2 cohorts, effects of vitamin D and HLA DQ risk.MethodsAPS-2 patients (n = 30) and healthy controls (n = 30) were genotyped for HLA DQA1/DQB1 and their CD14+ monocytes stimulated with IL1β and/or 1,25(OH)2D3 for 24 h. Immune regulatory molecules (IL-6, IL-10, IL-23A, IL-15, CCL-2, PD-L1), vitamin D pathway gene transcripts (CYP24A1, CYP27B1, VDR), and CD14 were analyzed by enzyme-linked immunosorbent assay and RTqPCR.ResultsPro-inflammatory CCL-2 was higher in APS-2 patients than in controls (p = 0.001), whereas IL-6 showed a trend – (p = 0.1). In vitro treatment with 1,25(OH)2D3 reduced proinflammatory cytokines (IL-6, CCL-2, IL-23A, IL-15) whereas anti-inflammatory cytokines (IL-10 and PD-L1) rose both in APS-type 1 diabetes and APS-Addison´s disease. Patients with adrenal autoimmunity showed a stronger response to vitamin D. Expression of IL-23A and vitamin D pathway genes VDR and CYP27B1 varied by HLA genotype and was lower in healthy individuals with high-risk HLA (p = 0.0025; p = 0.04), while healthy controls with low-risk HLA showed a stronger IL-10 and CD14 expression (p = 0.01; p = 0.03).Conclusion1,25(OH)2D3 regulates the monocytic response in APS-2 disorders type 1 diabetes or Addison´s disease. The monocytic cytokine profile of individuals carrying HLA high-risk alleles is proinflammatory, enhances polyglandular autoimmunity and can be targeted by vitamin D.

In-silico design of an epitope-based vaccine against Human Norovirus

Background: Every year, noroviruses cause about 20% of endemic and 50% of food-borne acute gastroenteritis in all age groups worldwide, causing ∼700 million illnesses and >200,000 deaths mainly in young children and the elderly. Moreover has emerged as the mainly cause of severe childhood diarrhea in countries that include rotavirus in its vaccination national card like Mexico is. Nowadays, reverse vaccinology is use for the predicting epitopes and identify suitable peptide targets for eventual development of vaccines. In this study, a computational approach was carried out to identify an epitope-based vaccine candidate against norovirus protein that could be suitable to trigger a significant immune response. Methods and materials: 14 sequences of Human Norovirus were obtained from the NCBI. The aminoacidic consensus sequence was used to predict the T-cell and B-cell epitopes. The whole protein consensus sequence was submitted in the NetCTL server and all the super types T-cell were chosen, whit algorithm of MHC-1 binding, TAP proteins transport efficiency and proteosomal cleavage efficiency were involved to predict overall scores. Epitope conservancy for individual peptides was predicted using the epitope tool from IEDB analysis resource. The results from all these sites were cross-referenced, and common findings were taken as the B-cell epitopes. Results: We found in silico analysis that epitopes denominated LTVP1A, LTVP1E, LTVP2A, LTVP2C and LTTPPB, proved to be able to arise the humoral and cellular immune response. The chosen epitopes could generate an activation of T cells and B cells in the Zapoteca and Taraumara Mexican population. However, the genetic diversity that our country presents and the few records of allelic frequency, complicate the effectiveness of this theoretical vaccine. Nevertheless, does not imply that the selected epitopes can be linked to other alleles, which opens the possibility of being use in other countries besides Mexico. Conclusion: For the first time, epitopes obtained with norovirus aminoacidics sequences were tested for binding against the HLA molecules using in silico vaccinology techniques to verify the binding cleft epitope interaction. Nevertheless, further experiments in vitro and in vivo are required to validate this proposal, as well as to assess their potential design of new norovirus vaccines.