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Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications.

Prediction of which peptides can bind major histocompatibility complex (MHC) molecules is commonly used to assist in the identification of T cell epitopes. However, because of the large numbers of different MHC molecules of interest, each associated with different predictive tools, tool generation and evaluation can be a very resource intensive task. A methodology commonly used to predict MHC binding affinity is the matrix or linear coefficients method. Herein, we described Average Relative Binding (ARB) matrix methods that directly predict IC(50) values allowing combination of searches involving different peptide sizes and alleles into a single global prediction. A computer program was developed to automate the generation and evaluation of ARB predictive tools. Using an in-house MHC binding database, we generated a total of 85 and 13 MHC class I and class II matrices, respectively. Results from the automated evaluation of tool efficiency are presented. We anticipate that this automation framework will be generally applicable to the generation and evaluation of large numbers of MHC predictive methods and tools, and will be of value to centralize and rationalize the process of evaluation of MHC predictions. MHC binding predictions based on ARB matrices were made available at http://epitope.liai.org:8080/matrix web server.

Animals↗

MHC expression in syngeneic and allogeneic retinal cell transplants in the rat.

BACKGROUND: The major histocompatibility complexes, MHC class I and II, are found only sparsely or not at all in the retina. Since the eye is immunoprivileged, we decided to investigate how the MHC class I and II antigens were influenced by a retinal transplant and whether this could be correlated to rejection of the transplant. METHODS: Fetal neural retinas of Sprague-Dawley (SD) rats were implanted in the subretinal space of adult Lewis and SD rats. After 5 weeks the retinas and the transplants were evaluated with antibodies against MHC class I and II antigens as well as microglia. RESULTS: In the syngeneic transplants no upregulation of MHC class I antigen was seen and no MHC class II-positive cells could be detected. In the allogeneic transplants, on the other hand, there was marked upregulation of MHC class I antigen. Numerous MHC class II antigen-positive cells were seen in the subretinal transplant but also in the host retina. CONCLUSION: Allogeneic retinal transplants seem to grow and thrive just as well as syngeneic transplants, but in the former there is considerable upregulation of MHC expression. Our interpretation of these results is that the allogeneic transplants are recognized as nonself, but that there is also something that modifies this reaction of the immune system at this level, preventing the rejection that would normally ensue.

Animals↗

Influence of donor MHC class I antigen expression on graft survival after rat parathyroid allotransplantation.

BACKGROUND AND AIMS: We investigated the influence of donor MHC antigen expression on graft survival after parathyroid transplantation in three different strain combinations. METHODS: MHC class I and II expression on parathyroid tissue of Lewis (LEW), Dark Agouti (DA), and Wistar-Furth (WF) rats was first analysed semiquantitatively by immunohistochemistry. Additionally, five groups were transplanted: (1) LEW to LEW, (2) DA to DA, (3) LEW to DA, (4) WF to LEW, and (5) DA to LEW. METHODS: MHC class I expression was strong in DA, moderate in WF, and weak in LEW rats; MHC class II expression was negative in all three strains. In the interstitium of all investigated tissue specimens, the proportion of MHC class II-expressing cells was low. RESULTS: After syngeneic transplantation, graft survival could be documented over the whole observation period. A mean graft survival of 20 (+/-2) days was observed following transplantation from LEW to DA, grafts in the group WF to LEW were rejected after 13 (+/-1) days, and graft function lasted 8 (+/-2) days in the group DA to LEW. The number of intragraft leukocytes expressing MHC class II molecules was equal in all groups, whereas increased levels of MHC class I on rat parathyroid tissue before transplantation resulted in a more rapid rejection. CONCLUSION: These results demonstrate that immunogenicity of rat parathyroid tissue seems to be determined by the amount of MHC class I expressed on donor parenchymal cells.

Animals↗

Comparative genomics of medaka: the major histocompatibility complex (MHC).

The major histocompatibility complex (MHC) is one of the best characterized regions of the vertebrate genome. The human MHC has three subregions, classes I, II, and III. The MHC of chicken and Xenopus contain all three subregions. In contrast, in all teleost species so far analyzed, the class I and II genes are not linked to each other, suggesting that there was extensive genomic reorganization of the MHC region during an early stage of vertebrate evolution. To elucidate the details of this reorganization, we carried out genetic and physical analyses of the medaka MHC genes. We isolated the medaka counterparts of human MHC genes, class I A, class II B, LMP2, LMP7, TAP2, complement Bf and C4, and subjected them to linkage analysis. Except for the linkage of class IA, LMP2, LMP7, and TAP2 on linkage group (LG)11, all other genes were assigned to separate linkage groups. Thus, the class IA gene and the genes involved in class I antigen presentation seem to form the evolutionary stable core of the MHC. A physical analysis of medaka MHC class I region is in progress.

Journal Article↗

Hypothesis: the MHC-restricted T-cell receptor as a structure with two multistate allosteric combining sites.

This paper presents a dual-recognition model of the T-cell receptor that has been constructed to account for the phenomenon of MHC restriction as well as the paradoxical ability of T-cells to be both multispecific and precisely specific at the same time. In our model the combining sites for antigen and MHC are not independent as in classical dual-recognition models, but interact with each other by an allosteric mechanism. We envision a flexible receptor with combining sites for antigen and MHC that are capable of existing in a multitude of distinct complementarity states. MHC and antigen molecules act as allosteric effectors such that one ligand perturbs the conformation and therefore the specificity of the site for the other ligand. An essential feature of the model is that different MHC determinants induce different conformations at the anti-antigen site. In this way the receptor acquires multiple specificities. Within a particular complementarity state, precise recognition results from the requirement that antigen and MHC exhibit positive cooperativity in their binding to the T-cell receptor. Positive cooperativity is also the basis for MHC restriction. Reaction mechanisms are presented which describe the requirement that antigen and MHC both induce conformational changes in order to generate high-affinity binding to either ligand. As a precedent for the multistate allosteric receptor model, we discuss the properties of allosteric enzymes, especially ribonucleotide reductase, whose properties are analogous to those we have postulated for the T-cell receptor. Also discussed is the possibility that molecules such as Ly2, L3T4 and the Mls antigen, which have been found to play a role in antigen recognition, function as affinity-enhancing allosteric effectors that interact with the constant portion of the T-cell receptor.

Allosteric Site↗

Antigenic peptide binding to MHC class II molecules at increased peptide concentrations.

Affinity-purified major histocompatibility complex (MHC) class II molecules are known to bind antigenic peptides in vitro. The percentage of MHC class II molecules occupied with such peptides is usually very low and varies significantly depending upon the sequence and size of a given antigenic peptide. The present study describes a method by which complete saturation of affinity-purified MHC class II with antigenic peptide can be achieved by simply incubating purified MHC class II molecules at neutral pH in the presence of several 100-fold molar excess of antigenic peptide. Complexes of human HLA-DR2 and a peptide analog from human myelin basic protein MBP (83-102)Y83 were selected for this study. The on-rate kinetic results showed saturation of MHC class II occupancy at 300-500-fold molar excess peptide concentrations. The specificity of the MBP (83-102)Y83 peptide binding to HLA-DR2 at higher peptide concentration was demonstrated by incubating an equivalent amount of another epitope from myelin basic protein [MBP (1-14) peptide] as well as by competitive binding assays. The quantitation of bound peptide was carried out using biotinylated-MBP (83-102)Y83 peptide which showed 100-125% occupancy of HLA-DR2 with a recovery of 100%. The presence of a single peptide entity in purified complexes was confirmed by reverse-phase narrowbore HPLC analysis of the acid extracted supernatant and by mass spectrometry analysis. Two-dimensional gel electrophoresis (IEF/SDS) of purified HLA-DR2 and DR2.MBP (83-102)Y83 complexes showed the absence of various endogenous polypeptides in 100% loaded complexes. These results demonstrate that higher peptide concentrations can be useful in generating MHC class II-peptide complexes of defined composition. Such complexes of MHC class II occupied with a single peptide may have significant clinical relevance for antigen-specific therapy of various autoimmune diseases and may provide better understanding of MHC-peptide-TCR interactions.

Amino Acid Sequence↗

Changes in LAK susceptibility of tumor cells as their MHC class I antigen expression levels regenerate after treatment at pH 3.0.

Changes in LAK susceptibility of tumor cells in which MHC class I antigen expression was undergoing regeneration following treatment at pH 3.0, were studied. P815 (murine mastocytoma) and RAJI (human B-cell leukemia) cell lines were briefly exposed to pH 3.0 buffer which brought down the MHC class I expression on these cells by 70-80% and resulted in a 3-fold increase in their susceptibility to murine and human LAK cells, respectively. During the MHC class I regeneration phase, LAK susceptibility fell and reached normal levels at a time point when MHC class I antigens had regenerated to a level which was 60-70% of the normal. Highly significant inverse correlations were obtained between LAK susceptibility and the log of MHC class I antigen expression, for both P815 and RAJI cell lines. These results indicate that during the MHC class I regeneration phase, there is an inverse correlation between MHC class I antigen levels and LAK susceptibility. Moreover, these results also suggest that the extent of change in LAK susceptibility may depend upon the levels of basal MHC class I expression on the tumor cells.

Animals↗

ICAM-1 inhibits the homocluster formation of MHC-I in colon carcinoma cells.

ICAM-1 and MHC-I proteins play fundamental roles in antigen presentation, activation of T lymphocytes, and immune responses against tumor cells. Both of them participate in the formation of lipid raft-associated membrane protein clusters. We found significant colocalization between ICAM-1 and MHC-I at the level of large-scale associations. We combined RNA interference and fluorescence resonance energy transfer studies to show that ICAM-1 promotes the partial disassembly of MHC-I homoclusters on LS-174T colon carcinoma cells. Interferon-gamma (IFN-gamma) treatment induced an increase in the expression of MHC-I and ICAM-1 resulting in decreased MHC-I homoassociation. Small interfering RNAs directed against ICAM-1 restored the homoassociation of MHC-I without influencing the expression level of MHC-I by eliminating ICAM-1 molecules interspersed in MHC-I clusters. We conclude that the composition of membrane protein clusters is dynamically altered in response to both physiological and experimentally elicited changes in antigen expression levels.

Cell Line, Tumor↗

MHC expression in a human adult stem cell line and its down-regulation by hCMV US gene transfection.

Due to their unique capacity to self-renew and for multiple differentiation, stem cells are considered promising candidates for cell replacement therapy in many devastating diseases. However, studies on immune rejection, which is a major problem facing successful stem cell therapy, are rare. In this study, we examined MHC expression in the M13SV1 cell line, which has previously been shown to have stem cell properties and to be non-tumorigenic, in order to determine whether human adult stem cells might be rejected after transplantation. Our results show low expression levels of MHC class I molecules on the surface of these cells. An induction of MHC class I expression was observed when the cells were treated with IFN-gamma. Maximal induction of MHC class protein expression was observed at 48 h after treatment with concentrations above 5 ng/ml of IFN-gamma. Elevated MHC class I levels were sustained for 72 h after withdrawing IFN-gamma. Therefore, we introduced human cytomegalovirus (hCMV) US genes, which are known to be able to reduce MHC class I expression on the cell surface after infection, into M13SV1 cells. Cells transfected with the hCMV US2, US3, US6 or US11 genes exhibited a reduction (40-60%) of MHC class I expression compared with mock-transfected cells. These results suggest that human adult stem cells are capable of expressing high levels of MHC class I proteins, and thus may be rejected on transplantation unless they are modified. In addition, viral stealth mechanisms can be exploited for stem cell transplantation.

Animals↗

Turning tumor cells in situ into T-helper cell-stimulating, MHC class II tumor epitope-presenters: immuno-curing and immuno-consolidation.

Immunological control or cure of tumors depends on initiating a robust T helper cell response to MHC class II epitopes of tumor-associated antigens. T helper cells regulate the potency of cytotoxic T lymphocyte and antibody responses. We have developed a novel approach to stimulate T helper cells by converting tumor cells into MHC class II molecule-positive, antigen presenting cells. Furthermore, using antisense methods, we suppress expression of the Ii protein, that normally blocks the antigenic peptide binding site of MHC class II molecules during synthesis in the endoplasmic reticulum. In such gene-engineered tumor cells, the MHC class II molecules pick up antigenic peptides, which have been transported into the endoplasmic reticulum for binding to MHC class I molecules. All nucleated cells create such "surveys of self" to detect viral or malignant transformation. Our method extends that survey of self to MHC class II endogenous tumor-associated antigens. Simultaneous presentation of tumor antigens by both MHC class I and II generates a robust and long-lasting antitumor immune response. Injecting murine tumors with genes, which induce MHC class II molecules and suppress Ii protein, cures a significant number of animals with renal and prostate tumors. We have developed analogous human gene vectors that are suitable for most patients and cancers, because they are monomorphic and active in all HLA-DR alleles. We review our findings, and analyze remaining issues for preclinical study and the design of clinical trials.

Animals↗

Oct-1 DNA binding activity unresponsive to retinoblastoma protein expression prevents MHC class II induction in a non-small cell lung carcinoma cell line.

Numerous human tumor lines fail to induce major histocompatibility (MHC) class II expression following interferon-gamma (IFN-gamma) treatment, a response that is considered to be a normal function for almost all human parenchymal and connective tissue cell-types. The effect of MHC class II non-inducibility on solid tumor growth is controversial, but an extensive body of literature indicates that tumor cell MHC class II expression can lead to an antitumor response or tumor tolerance, depending on a number of variables. Thus, understanding the molecular basis for MHC class II induction failures in solid tumor cells will likely lead to ideas for manipulating the antitumor immune response. To date, a handful of tumor associated molecular anomalies have accounted for all the known failures of MHC class II inducibility. In particular, lack of the retinoblastoma tumor suppressor protein (Rb) has been shown in both human and mouse cells to be strongly associated with failure to induce MHC class II. The basis for this relationship is traceable to, among other things, high level Oct-1 DNA binding activity in Rb-defective cells, which represses the prototypical human MHC class II gene, HLA-DRA. Ordinarily, re-establishment of Rb expression leads to elimination of, or substantially reduced Oct-1 DNA binding activity and to rescue of HLA-DRA inducibility. However, in the case of one non-small cell lung carcinoma line (NSCLC), Rb re-expression failed to rescue HLA-DRA inducibility despite successful re-establishment of Rb-function. We now report that this failure is traceable to the failure of Rb to rescue normal Oct-1 function. Furthermore, histone deacetylase inhibitor treatment allows a bypass of the Rb requirement and facilitates the MHC class II induction in this NSCLC line.

Carcinoma, Non-Small-Cell Lung↗

Time frame of pancreas allograft rejection: an immunogenetic analysis in MHC-disparate, presensitized inbred rat strains.

AIM: The pattern of rejection of vascularized pancreas allografts in presensitized recipients was studied among congeneic and recombinant rat strains in order to establish the time frame of rejection. Donors and recipients differed either in their entire MHC or in class I or class II MHC antigens. MATERIAL AND METHODS: Streptozotocin diabetic (55 mg/kg bone weight) recipients underwent an intra-abdominal heterotopic pancreas whole organ transplantation. The exocrine secretion of the pancreas was suppressed by ligation of the duct. Rejection was defined as recurrence of diabetic hyperglycemia exceeding 14 mmol/L, which was subsequently confirmed by histologic examination. The pancreas recipients were presensitized by repetitive donor-specific skin transplants performed 12, 8, and 4 weeks prior to pancreas grafting. RESULTS: The results shown accelerated rejection in all instances. Animals with incompatibility for the entire MHC showed a median rejection time in naive recipients of 12.5 days and in presensitized recipients of 8 days. Class I MHC incompatible native recipients rejected the allografts after 16.5 days (median) and presensitized recipients after 9 days (median). Concerning class II MHC incompatibility rejection appeared in naive recipients after 16 days (median) and in presensitized recipients after 7 days (median). Hyperacute rejection, however, was not observed. DISCUSSION: These results show an accelerated pattern of rejection in all instances caused by donor MHC antigens. Hyperacute rejection, however, was not observed. The effect is slightly pronounced in class II MHC incompatibility. Acceleration of rejection may be caused by stimulation of the humoral as well as the cellular pathway of the immune response. The underlying mechanisms concerning the different MHC incompatibilities, however, remain speculative.

Animals↗

New evidence that the MHC influences odor perception in humans: a study with 58 Southern Brazilian students.

Increasing evidence suggests a correlation between mate choice, odor preference, and genetic similarity at the Major Histocompatibility Complex (MHC) in a variety of animals, including our species. The MHC is a highly polymorphic group of genes that play an important role in the immunological self/nonself recognition. Its products have been reported to take part on the variety of compounds and reactions that together build an individual's body odor. It has been suggested, therefore, that animals use body odor as a guide to identify possible mates as MHC-similar or MHC-dissimilar from their own genotype. Preference for a MHC-dissimilar partner enhances MHC heterozygosity of an individual's offspring. The possible adaptive advantages are clear: it is a mechanism of avoiding inbreeding and MHC-heterozygous offspring may have enhanced immunocompetence. The aim of this study was to search, in our species, new evidence on the correlation between specificities at HLA-A and HLA-B and assessments of pleasantness regarding specific body odors. HLA is the name for the human MHC. Four olfactory sessions were performed with 58 young Southern Brazilian students, in order to investigate whether assessments of pleasantness of body odors from individuals correlate to a person's HLA phenotype. Body odors were collected via sweat and urine from all participants. Women smelled and scored all male odor samples and men did the same with all female samples. We found a significant correlation only when female smellers evaluated male sweat odors.

Adolescent↗

Collapse and restoration of MHC class-I-dependent immune privilege: exploiting the human hair follicle as a model.

The collapse of major histocompatibility complex (MHC) class-I-dependent immune privilege can lead to autoimmune disease or fetal rejection. Pragmatic and instructive models are needed to clarify the as yet obscure controls of MHC class I down-regulation in situ, to dissect the principles of immune privilege generation, maintenance, and collapse as well as to develop more effective strategies for immune privilege restoration. Here, we propose that human scalp hair follicles, which are abundantly available and easily studied, are ideally suited for this purpose: interferon-gamma induces ectopic MHC class I expression in the constitutively MHC class-I-negative hair matrix epithelium of organ-cultured anagen hair bulbs, likely via interferon regulatory factor-1, along with up-regulation of the MHC class I pathway molecules beta(2)microglobulin and transporter associated with antigen processing (TAP-2). In the first report to identify natural immunomodulators capable of down-regulating MHC class I expression in situ in a normal, neuroectoderm-derived human tissue, we show that ectopic MHC class I expression in human anagen hair bulbs can be normalized by treatment with alpha-MSH, IGF-1, or TGF-beta1, all of which are locally generated, as well as by FK506. These agents are promising candidates for immune privilege restoration and for suppressing MHC class I expression where this is clinically desired (eg, in alopecia areata, multiple sclerosis, autoimmune uveitis, mumps orchitis, and fetal or allograft rejection).

Down-Regulation↗

Cytokine induced modulation of MHC class I and class II molecules on human cervical epithelial cells.

Our purpose was to determine the expression of the major histocompatibility complex (MHC) class I and class II gene products as well as the costimulatory molecules B7-1 and B7-2 on cervical epithelial cells, and to determine to what extent inflammatory cytokines regulate their expression. Immunohistology and flow cytometry techniques were used to identify and quantify MHC class I and class II molecules, and the costimulatory molecules B7.1 and B7.2, on sections and primary epithelial cell cultures of human endo- and ectocervix. MHC class I but not class II molecules were constitutively expressed on tissue sections and primary epithelial cell cultures derived from endo- and ectocervix. Expression of MHC class I and class II was upregulated in vitro by IFN-gamma in a time and dose dependent fashion. The induction of class II expression was more pronounced on ectocervical cells than on endocervical cells. MHC class I but not class II expression was also enhanced by IFN-alpha as well as TNF-alpha. TNF-alpha and TGF-beta1 inhibited the IFN-gamma induced MHC class II expression. Expression of the costimulatory molecules B7-1 and B7-2 were not detected in tissue sections or on resting or cytokine-treated cervical epithelial cells in vitro. The present results support the concept that endo- and ectocervical epithelial cells, like their counterparts at other mucosal sites. constitutively express MHC class I molecules and can express MHC class II upon cytokine stimulation, indicating that they are capable of presenting antigens to T-cells.

3T3 Cells↗

Differential glycosylation of MHC class II molecules on gastric epithelial cells: implications in local immune responses.

Class II major histocompatibility complex (MHC) expression is a hallmark of antigen presenting cells (APC). Human gastric epithelial cells (GEC) express class II MHC and this expression increases during infection with Helicobacter pylori as does the number of CD4 T cells found adjacent or in between epithelial cells. These observations suggested that human GEC act as APCs. To characterize and compare class II MHC complexes with those present in conventional APC, immunoprecipitated class II MHC from GEC and B cells, as prototypic APC, were separated by two-dimensional electrophoresis. Although the composition of class II MHC from both cell phenotypes was similar, their electrophoretic mobility differed. Methodical elimination of carbohydrates, either enzymatically with endoglycosidase-H or blocking with tunicamycin, revealed that the deviations were due to differences in glycosylation in both cell phenotypes. When deglycosylated class II MHC alpha chains, beta chains, and the invariant chain from both cell phenotypes were mixed and run in the same gel, the core proteins had identical migration patterns. Because differences in glycosylation of class II MHC proteins may affect peptide selection and/or recognition by T cells, the noted differences in glycosylation of class II MHC expressed by GEC could be important in considering their potential role as APC locally.

Antigen-Presenting Cells↗

Prediction of MHC class I binding peptides using profile motifs.

Peptides that bind to a given major histocompatibility complex (MHC) molecule share sequence similarity. Therefore, a position specific scoring matrix (PSSM) or profile derived from a set of peptides known to bind to a specific MHC molecule would be a suitable predictor of whether other peptides might bind, thus anticipating possible T-cell epitopes within a protein. In this approach, the binding potential of any peptide sequence (query) to a given MHC molecule is linked to its similarity to a group of aligned peptides known to bind to that MHC, and can be obtained by comparing the query to the PSSM. This article describes the derivation of alignments and profiles from a collection of peptides known to bind a specific MHC, compatible with the structural and molecular basis of the peptide-MHC class I (MHCI) interaction. Moreover, in order to apply these profiles to the prediction of peptide-MHCI binding, we have developed a new search algorithm (RANKPEP) that ranks all possible peptides from an input protein using the PSSM coefficients. The predictive power of the method was evaluated by running RANKPEP on proteins known to bear MHCI K(b)- and D(b)-restricted T-cell epitopes. Analysis of the results indicates that > 80% of these epitopes are among the top 2% of scoring peptides. Prediction of peptide-MHC binding using a variety of MHCI-specific PSSMs is available on line at our RANKPEP web server (www.mifoundation.org/Tools/rankpep.html). In addition, the RANKPEP server also allows the user to enter additional profiles, making the server a powerful and versatile computational biology benchmark for the prediction of peptide-MHC binding.

Algorithms↗

A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets.

Binding of peptides to MHC class I molecules is a prerequisite for their recognition by cytotoxic T cells. Consequently, identification of peptides that will bind to a given MHC molecule must constitute a central part of any algorithm for prediction of T-cell antigenic peptides based on the amino acid sequence of the protein. Binding motifs, defined by anchor positions only, have proven to be insufficient to ensure binding, suggesting that other positions along the peptide sequence also affect peptide-MHC interaction. The second phase of prediction schemes therefore take into account the effect of all positions along the peptide sequence, and are based on position-dependent-coefficients that are used in the calculation of a peptide score. These coefficients can be extracted from a large ensemble of binding sequences that were tested experimentally, or derived from structural considerations, as in the algorithm developed by us recently. This algorithm uses the coordinates of solved complexes to evaluate the interactions of peptide amino acids with MHC contact residues, and results in a peptide score that reflects its binding energy. Here we present our analysis for peptide binding to four MHC alleles (HLA-A2, HLA-A68, HLA-B27 and H-2Kb), and compare the predictions of the algorithm to experimental binding data. The algorithm performs successfully in predicting peptide binding to MHC molecules with hydrophobic binding pockets but not when MHC molecules with hydrophilic, charged pockets are considered. For MHC molecules with hydrophobic pockets it is demonstrated how the algorithm succeeds in distinguishing binding from non-binding peptides, and in high ranking of immunogenic peptides within all overlapping same-length peptides spanning their respective protein sequences. The latter property of the algorithm makes it a useful tool in the rational design of peptide vaccines aimed at T-cell immunity.

Algorithms↗