Prediction of MHC class II binding peptides based on an iterative learning model

Coxsackieviruses are non-enveloped viruses with linear single-stranded RNA. Group B coxsackieviruses were noted to cause a spastic paralysis due to focal muscle injury and degeneration of neuronal tissue. Peptide fragments of Coxsackievirus-B coat protein can be used to select nonamers for use in rational vaccine design and to increase the understanding of roles of the immune system in infectious diseases. Analysis shows MHC class II binding peptides of coat protein from Coxsackievirus-B are important determinant for protection of host form viral infection. In this assay we predicted the binding affinity of coat protein having 281 amino acids, which shows 273 nonamers. These peptides are from a set of aligned peptides known to bind to a given MHC molecule as the predictor of MHC-peptide binding. MHCII molecules bind peptides in similar yet different modes and alignments of MHCII-ligands were obtained to be consistent with the binding mode of the peptides to their MHC class, this means the increase in affinity of MHC binding peptides may result in enhancement of immunogenicity of coat protein nonamers. Binding ability prediction of antigen peptides to major histocompatibility complex (MHC) class I & II molecules is important in vaccine development from Coxsackievirus.

Heat shock protein 90 (hsp90) and the proteasome activator PA28 stimulate major histocompatibility complex (MHC) class I antigen processing. It is unknown whether hsp90 influences the proteasome activity to produce T cell epitopes, although association of PA28 with the 20 S proteasome stimulates the enzyme activity. Here, we show that hsp90 is essential in assembly of the 26 S proteasome and as a result, is involved in epitope production. Addition of recombinant hsp90alpha to cell lysate enhanced chymotrypsin-like activity of the 26 S proteasome in an ATP-dependent manner as determined by an in-gel hydrolysis assay. We successfully pulled down histidine-tagged hsp90alpha- and PA28alpha-induced, newly assembled 26 S proteasomes from the cell extracts for in vitro epitope production assay, and we found these structures to be sensitive to geldanamycin, an hsp90 inhibitor. We found a cleaved epitope unique to the proteasome pulled down by both hsp90alpha and PA28alpha, whereas two different epitopes were identified in the hsp90alpha- and PA28alpha-pulldowns, respectively. Processing of these respective peptides in vivo was enhanced faithfully by the protein combinations used for the proteasome pulldowns. Inhibition of hsp90 in vivo by geldanamycin partly disrupted the 26 S proteasome structure, consistent with down-regulated MHC class I expression. Our results indicate that hsp90 facilitates MHC class I antigen processing through epitope production in a complex of the 26 S proteasome.

We have previously described the induction of murine CD8+ major histocompatibility complex (MHC) class I-restricted cytotoxic T cells (CTL) recognizing the 20-amino acid repeat region of the human mucin 1 (MUC1) variable number of tandem repeats region (VNTR), a mucin greatly increased in expression in breast cancer and proposed as a target for immunotherapy. In that study, CTL could detect MUC1 peptides associated with the MHC of all nine strains examined, and we now report the different epitopes presented by five different MHC class I molecules. The epitopes were defined in CTL assays using peptide-pulsed phytohemagglutinin blasts or MHC class I-transfected L cells as targets; in addition, peptide binding assays and T cell proliferation studies were performed. Within the 20-amino acid VNTR, nine potential epitopes could be defined. The epitopes for the four MHC class I molecules [Kb (three epitopes), Dd, Ld and Kk] were closely related, all containing the amino acids PDTRPAP. For Db, three epitopes were identified, all containing APGSTAP. Most of the epitopes did not contain a consensus motif for the particular MHC class I allele, and bound with low 'affinity', compared with known high-affinity peptides. CD8+ T cell proliferation also occurred to the same MHC class I-presented epitopes. Finally, when conventional anchor residues were introduced into the peptides, peptide binding increased, whereas CTL recognition was either retained (Kb) or lost (Db) depending on the epitope.

Immunotherapy is a treatment option that has had limited success with prostate cancer patients. The major histocompatibility complex (MHC) Class I plays a pivotal role in the adaptive immune response by presenting neo-antigens on the surface of cancer cells to CD8+ T-cells. Prostate cancer cells have markedly lower expression of MHC Class I genes compared to immune-responsive cancers. Loss of MHC Class I is also associated with more aggressive disease and immune evasion in prostate cancer. However, the molecular mechanisms that control MHC Class I downregulation in prostate cancer are still unknown. We hypothesize that increasing MHC Class I expression in prostate cancer cells will increase antigen presentation and improve the efficacy of immunotherapy agents. To investigate the mechanism of MHC Class I regulation in prostate cancer cells, we conducted a whole-genome CRISPRi flow cytometry screen. In this screen, C42B cells containing a non-catalytic Cas9 (dCas9) were infected with a lentivirus that contained a sgRNA library of 100,000 guides targeting 20,000 genes. Infected cells were selected and stained with a pan-Class I MHC antibody, sorted, and the highest and lowest 25-30% of MHC Class I expressing cells were collected for analysis. As expected, knockdown of MHC Class I genes such as B2M, HLA-A, and TAP1 decreased MHC Class I expression. Surprisingly, knockdown of AR and AR co-factors GRHL2 and FOXA1 resulted in a dramatic increase of MHC Class I surface expression. Additional AR inhibition experiments using enzalutamide, an AR degrader, or charcoal-stripped serum also showed increased MHC Class I expression over time. These in vitro results were substantiated with RNA expression analyses of patient biopsy samples taken before or after neoadjuvant enzalutamide treatment, which showed significantly increased MHC Class I expression post-treatment. Results from a small library CRISPR screen, showed that elimination of androgen response elements upstream of MHC Class I genes increased MHC expression, providing a mechanism by which AR regulates MHC Class I. Importantly, AR knockdown was shown to increase antigen-specific T-cell response in co-culture and transgenic mouse models. These observations were further validated in a mCRPC phase II clinical trial. Bulk RNA expression analyses comparing responders and non-responders to anti-PD1 therapy in enzalutamide treated patients, showed decreased expression of AR and increased expression of MHC Class I in patients who responded to immunotherapy. Overall, our data show that AR suppresses MHC Class I expression in prostate cancer, and that androgen-targeted therapies can increase antigen presentation and improve T-cell response. By understanding how AR regulates MHC Class I expression, we can identify new combination treatments utilizing AR signaling inhibition and immunotherapy that lead to a improved anti-cancer response. Citation Format: Lisa Chesner, Julie Graff, Fanny Polesso, Alexis Smith, Arian Lundberg, Martin Sjoestroem, Zheng Xia, Simon Linder, Andries Bergman, Alan Ashworth, David Quigley, Wilbert Zwart, Luke Gilbert, Amy Moran, Felix Feng. AR suppresses MHC Class I expression and T-cell response in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B041.

The effect of bovine peripheral nerve myelin (BPM) used for induction of experimental allergic neuritis (EAN) in Lewis rats, on antidepressants' modulation of interferon-gamma (IFN-γ)-induced major histocompatibility complex (MHC) class I and II antigen expression on peritoneal macrophages in EAN rats was studied. Antidepressants with different profiles concerning inhibition of the neuronal reuptake of the monoamines serotonin (5-HT) and noradrenalin (NA), respectively, in concentrations of 10−4 to 10−8 M were used. At the concentration of 1.0 U/ml IFN-γ, most antidepressants significantly enhanced both MHC class I and class II expression, except maprotiline, a selective NA reuptake inhibiting antidepressant that suppressed MHC class I expression. Zimeldine, a selective 5-HT reuptake inhibitor did not affect MHC class II expression. BPM in general had an enhancing effect on modulation of both MHC class I and class II expression by antidepressants. By itself BPM enhanced MHC class I expression, but did not affect class II expression at IFN-γ 1.0 U/ml. The modulating effect of BPM on regulation of MHC expression by antidepressants could be the result of contaminating T cells and release of IFN-γ into cultures. The modulatory effect of antidepressants on MHC expression may to some extent be exerted by the action on 5-HT and/or NA regulation, but also by direct effects of antidepressants on macrophages. They probably play a role in zimeldine-induced Guillain-Barré syndrome in some patients and in the suppression of clinical signs of EAN in Lewis rats reported for some antidepressants.

Background: Immunotherapy, especially anti-programmed cell death protein 1 (PD-1) antibodies, has yielded significant and durable tumor response in melanoma, renal cell carcinoma, and other cancer types. In contrast, immunotherapy applied major breakthrough achievement only on patients with microsatellite instability high (MSI-H) metastatic colorectal cancer (mCRC). However, MSI-H mCRC comprised only 1.8-4% of total mCRC patients. It is crucial to investigate immune pathways to develop a new strategy for immunotherapy in treatment of microsatellite stable (MSS) mCRC. Recently, some evidences indicate that interferon (IFN)-γ pathway is critical for anti-PD-1 therapy. In this study, we emphasized on evaluating the response of MSS CRC cell lines to IFN-γ. Methods: We characterized two MSS CRC cell lines, namely SW480 (KRAS G12V mutation, BRAF wild type) and COLO320 (KRAS wild type, BRAF wild type) for our studies. The impacts of interferon-γ (IFN-γ) on cell surface expressions of different isotypes of major histocompatibility complex (MHC) class I and MHC class 1 related molecule A/B (MICA/B, the NK cell ligand) were explored. Different concentration of IFN-γ with different incubation time were also examined. Results: Both cell lines demonstrated low baseline human leukocyte antigen (HLA)-ABC and HLA-BC expression and the expression significantly increased in response to IFN-γ stimulation. We further focused on the SW480 cell line. The SW480 demonstrated low expression of all MHC class I isotypes, including HLA-ABC, HLA-BC, HLA-A, HLA-C, HLA-E, HLA-F, HLA-G and NK cell ligand MICA/B. The IFN-γ specifically stimulated the expression of HLA-A, but all other isotypes were not responsive to IFN-γ stimulation. In summary, IFN-γ significantly stimulates the expression of HLA-ABC, HLA-BC and HLA-A without stimulating HLA-C. The NK cell ligand MIC A/B was also not responsive to IFN-γ stimulation. The stimulatory effect of HLA-ABC and HLA-A in response to IFN-γ stimulation was positively correlated with IFN-γ dosage, which demonstrated highest expression level in response to 800U/ml IFN-γ stimulation. The stimulatory effect in response to IFN-γ stimulation was also positively correlated with increased incubation time with IFN-γ. Conclusion: These findings reveal that regardless of their KRAS mutation status, both MSS CRC cell lines possess a phenotype that may be not responsive to anti-PD-1 therapy due to low expression of MHC class I molecules. The IFN-γ specifically elicits the expression of stimulatory isotype, HLA-A and HLA-B, without eliciting all other inhibitory MHC class I isotypes. These results indicated that IFN-γ demonstrated pure adaptive immune stimulatory effect on CRC cell lines. Analysis of T- and NK cell-responsive immune markers along with IFN-γ signaling pathway may help us to survey possible combination therapy with anti-PD-1 treatment in CRC. Citation Format: Yi-Hsin Liang, Kuan-Yu Chan, Chang-Cheng Lee, Te-Jung Chen, Ann-Lii Cheng, Kun-Huei Yeh. IFN-γ elicits stimulatory MHC class I isotypes in human colorectal carcinoma cell lines with genetic features of microsatellite stable [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 608.

This forum deals with the interactions between major histocompatibility complex (MHC) class I heavy chains (CIH) and other proteins. Most familiar to immunologists are the noncovalent association of class I heavy chain with β 2-microglobulin (β 2m) and the binding of peptide antigens (Ags) to MHC class I molecules. The latter interaction, which results in MHC-restricted Ag presentation, is commonly referred to as MHC + X, signifying the expression of new antigenic determinants in the complex. Several other manuscripts in this volume deal with changes in antigenic determinants on class I heavy chains generated when a given CIH associates with β 2m of different species. These interactions are considered to represent special cases of MHC + X. MHC class I Ags also interact with cell surface proteins (MHC + Y). The notion that MHC + Y are biologically relevant complexes is not new (reviewed in Meruelo and Edidin 1980; Dausset and Contu 1980; Ivanyi 1978; Edidin 1983). It is derived from observations that particular MHC haplotypes are associated with specific diseases and with variations in physiological responses. It is also invoked as an explanation for the MHC-restricted recognition of “minor” transplantation antigens. In this manuscript we will specifically discuss the possibility that MHC class I Ags are subunits of a compound insulin receptor on cell membranes.

Because of the role major histocompatibility complex (MHC) class I b molecules may play during mouse embryonic development, we thought it would be interesting to search for additional MHC class I b molecules that might be expressed in preimplantation embryos, and in particular in the trophoblastic lineage. We therefore screened a mouse preimplantation blastocyst cDNA library for MHC class I sequences. This search led to the identification and characterization of a new MHC class I b gene, blastocyst MHC. Sequences identical to the exons and 3' untranslated region of this gene have been found in many laboratory mouse strains, as well as in the related mouse species Mus spreciligus. The presence of this gene in mouse strains of different MHC class I haplotypes argues that blastocyst MHC is a unique, newly-described gene rather than a new allele of a previously described mouse MHC class I gene. Blastocyst MHC has the structure of an MHC class I b gene, with the six exons characteristic of T-region genes. It is linked to H2-D. The amino acid sequence encoded by this gene maintains all the features of a functional antigen-presentation domain. The blastocyst MHC gene, like the human class I b gene HLA-G, is expressed at the blastocyst stage and in the placenta, and may be the mouse analog for HLA-G.

Immune responses depend on the identification and prediction of peptides that bind to MHC (major histocompatibility complex) class I molecules, especially when it comes to the creation of vaccines, cancer immunotherapy, and autoimmune disorders. The ability to predict and evaluate MHC class immunoproteomics have completely transformed I epitopes in conjunction with immunoinformatics technologies. However, precisely identifying epitopes across various populations and situations is extremely difficult due to the complexity and diversity of MHC class I binding peptides. The most recent developments in immunoinformatics technology that have improved MHC class I epitope prediction are examined in this article. The sensitivity and specificity of epitope prediction have been greatly enhanced by recent developments that have concentrated on bioinformatics algorithms, artificial intelligence, and machine learning models. Potential epitopes are predicted using large-scale peptide-MHC binding data, structural characteristics, and interaction dynamics using tools like NetMHC, IEDB, and MHCflurry. Additionally, the integration of proteomic, transcriptomic, and genomic data has improved prediction accuracy in real-world scenarios by enabling more accurate identification of naturally occurring peptides. Furthermore, newer techniques like deep learning and multi-omics data integration have the potential to overcome peptide binding prediction constraints. Utilizing these technologies is expected to speed up the identification of new epitopes, improve the accuracy of immunotherapy techniques, and enable customized vaccine development. These innovative techniques, their uses, and potential future developments for improving MHC class I epitope prediction in immunoproteomics are highlighted in this study.

The major histocompatibility complex (MHC) of the mouse, which is called the H2 complex, is located on chromosome 17. It contains genes critical to the functioning of the immune system, the products of which are intimately involved in the initiation of immune responses. The proteins made by these genes display a significant amount of polymorphism, or sequence variability. Few genes possess this degree of polymorphism, but it is critical to the immune response and to the survival of a species. The chief characteristic of MHC molecules is their ability to bind small peptides. These bound peptides along with specific areas of the MHC molecule are the structures that interact with the T‐cell receptor (TCR) leading to activation of a T‐cell immune response, which in turn can active other cells of immune system. Thus, they determine which TCRs are functional which in turn indicates which peptides a T cell will respond to. Key Concepts The historical background and the genetics of MHC development are described. The expression and function of MHC class I genes is described. MHC class I molecules are expressed on virtually all nucleated cells and function to present foreign and self‐antigens to the immune system. MHC class I expression is dependent on peptide binding in the peptide binding groove of the molecule. MHC class I polymorphism is important for species resistance to infectious disease. The expression and function of MHC class II genes is described. MHC class II expression is required for generation and function of CD4 T cells. Nonclassical class I molecules bind a variety of peptide and nonpeptide antigens that are commonly expressed by pathogenic organisms. . The function of other genes found within the H2 complex is described.

The importance of immune complexes in the pathogenesis of malarial nephritis is well established. The expression was studied of major histocompatibility complex (MHC) class I and class II antigens and the infiltration of inflammatory cells, with their possible roles in cellular immune reactions in the pathogenesis of nephritis in a murine malaria model. Thirty-six kidney sections obtained on days 5, 8-10, 15, and 20 from C57BL/6J mice acutely infected with Plasmodium berghei and uninfected control mice were stained with specific antibodies for cellular immune markers by immunohistochemistry. From day 10 post-infection, markedly enhanced expression of both MHC class I and class II (Ia) antigens was observed in the kidneys. In the glomeruli, the expression was in the mesangium and along the capillaries. MHC class II was strongly expressed in the proximal tubules. Enhanced expression of MHC class I and class II was found in the endothelium of blood vessels, especially the peritubular capillaries. In addition, immune cells positive for CD4+ and CD8a+ markers, and class I and class II antigens were present around small arteries, or in focal areas of the interstitium. There were strong correlations between MHC class I expression in the glomeruli; MHC class II expression in the glomeruli/proximal tubules; and CD4+, CD8a+ infiltrates in the tubulointerstitium; with the severity of renal dysfunction (proteinuria). These findings indicate the importance of cellular immune reactions in the pathogenesis of acute murine malarial nephritis.

Παρά τις προόδους των κλασικών θεραπευτικών στρατηγικών για τον καρκίνο η μεγάλη πλειοψηφία των ασθενών υποτροπιάζει και καταλήγει. Η ανάγκη για την αντιμετώπιση της νόσου με εναλλακτικό τρόπο οδήγησε στην ανάπτυξη ανοσοθεραπευτικών μεθόδων. Η ταυτοποίηση ογκοειδικών αντιγόνων, έδωσε ιδιαίτερη ώθηση στην ανάπτυξη της κατευθυνόμενης από τα Τ κύτταρα ανοσολογικής απάντησης, και έθεσε τις βάσεις για τη χρησιμοποίηση πεπτιδικών εμβολίων στην ανοσοθεραπεία του καρκίνου. Από τα γνωστά καρκινικά αντίγονα η διαμεμβρανική ογκοπρωτεΐνη HER-2/neu παρουσιάζει το πλεονέκτημα της υπερέκφρασης σε ποικίλους τύπους καρκίνου, και επομένως καθίσταται στόχος για ανοσοθεραπευτικές προσεγγίσεις. Στην παρούσα μελέτη διερευνήθηκε ο τύπος της ανοσοαπόκρισης που λαμβάνεται in vivo μετά την χορήγηση πεπτιδίων της HER-2/neu συνδεμένων (προσροφημένο ή απλά αναμεμιγμένο) σε πολύ-γαλακτικού οξέος (PLA) και PLGA μικροσφαίρες. Τα αντιγόνα ήταν δύο: α) το πεπτίδιο GSPYVSRLLGICLTSTVQLVQL που αντιστοιχεί στην περιοχή 778-799 της HER-2/neu. Η πεπτιδική αυτή ακολουθία περιλαμβάνει τον κυτταροτοξικό (CTL) επίτοπο CLTSTVQLV (789-797) σε συνδυασμό με τον Τ βοηθητικό (Th) επίτοπο GSPYVSRLLGICL (778-790) και β) το πεπτίδιο CLTSTVQLV (789-797) δηλαδή μόνο ο CTL επίτοπος. Ως πειραματόζωα στην συγκεκριμένη περίπτωση χρησιμοποιήθηκαν HHD διαγονιδιακοί μύες, οι οποίοι εκφράζουν ανθρωπινά HLA-Α2.1 μόρια ιστοσυμβατότητας δεδομένου ότι η ακολουθία του πεπτιδίου που έχει επιλεγεί προέρχεται από την ανθρώπινη HER-2/neu. Η μετατροπή της ανοσοαπόκρισης Th2 τύπου, εναντίον διαλυτών αντιγόνων που εκφράζονται σε καρκινικούς όγκους σε Th1 τύπο ανοσοαπόκρισης είναι σημαντική στην ανοσοθεραπεία του καρκίνου. Η ταυτοποίηση του τύπου της ανοσοαπόκρισης έγινε με τον προσδιορισμό του τύπου της ανοσοαπόκρισης σε κυτταρικό επίπεδο με την ανάπτυξη τεχνικών μέτρησης της ικανότητας του πολλαπλασιασμού των λεμφοκυττάρων και με μέτρηση των κυτοκινών σε υπερκείμενα καλλιεργειών λεμφοκυττάρων. Η in vivo χορήγηση του πεπτιδικού αντιγόνου που απλά και μονό αναμίχθηκε με PLA μικροσφαίρες προκάλεσε μια ισχυρή ανοσολογική απόκριση που ήταν συγκρίσιμη με αυτήν που προκλήθηκε από το συνδυασμό του αντιγόνου με πλήρες ανοσοενισχυτικό του Freund (CFA). Επιπλέον, μετά από ανάλυση του προφίλ των κυτοκινών που εκκρίνονται από τα Τ λεμφοκύτταρα των ανοσοποιημένων μυών αποδείχθηκε ότι ο συνδυασμός του αντιγόνου πεπτιδίων με τις PLA μικροσφαίρες προκάλεσε μια ισχυρή ΤΜ ανοσολογική απόκριση στο αντιγόνο. Ο χρόνος της επώασης πεπτιδίων με τις μικροσφαίρες πριν από τη χορήγηση δεν είχε επιπτώσεις στην ανοσολογική απόκριση γεγονός που απλοποιεί περαιτέρω την παράγωγη σε ευρεία κλίμακα αυτού του τύπου εμβολίων. Τα αποτελέσματα που ελήφθησαν δικαιολογούν την περαιτέρω διερεύνηση σε in vivo πειραματικά μοντέλα καρκίνου της δυνατότητας επαγωγής ισχυρής κυτταρικής ανοσοαπόκρισης έναντι των καρκινικών κυττάρων που υπερεκφράζουν την HER-2/neu πρωτεΐνη με απλή ανάμιξη κατάλληλων πεπτιδικών αντιγόνων της HER-2/neu με PLA μικροσφαίρες.

Identification of B and T cell epitope based peptide vaccine from IGF-1 receptor in breast cancer

Enzyme immunoassay detection of induction of MHC class I expression by synthetic peptides from the E6 and E7 regions of human papillomavirus type 16

Increased major histocompatibility complex (MHC) class I gene expression in target tissues may be relevant to the pathogenesis of autoimmune diseases. In this study, we questioned whether high glucose levels might increase MHC class I levels and thereby contribute to autoimmune complications. We used thyrocytes in continuous culture, because there is an increased incidence of autoimmune thyroiditis in type 2 diabetics and because transcriptional regulation of MHC class I is well studied in these cells. Northern analysis and flow cytometry showed that 20 and 30 mM D-glucose up-regulated MHC class I expression and that the glucose effect was additive to and independent of interferon-gamma. The effect was specific, because L-glucose did not modify class I expression. The glucose acted transcriptionally, requiring both enhancer A and a cAMP-response element-like element located in the hormone-sensitive region of the MHC class I 5'flanking region. These elements are different from those activated by interferon-gamma. High glucose levels increase formation of the MOD-1 complex with enhancer A; MOD-1 is a heterodimer of fra-2 and the p50 subunit of NF-kappaB. Both TSH and insulin are required for full expression of the glucose activity in thyrocytes. The glucose effect is partially blocked by wortmannin, suggesting involvement of the PI3K signal system. The data support the possibility that high serum glucose levels in type 2 diabetic patients may increase MHC class I levels in target tissues and contribute to autoimmune complications of the disease.