Origin and plasticity of MHC I-associated self peptides

Endogenous peptides presented by MHC I molecules represent the essence of self for CD8 T lymphocytes. These MHC I peptides (MIPs) regulate all key events that occur during the lifetime of CD8 T cells. CD8 T cells are selected on self-MIPs, sustained by self-MIPs, and activated in the presence of self-MIPs. Recently, large-scale mass spectrometry studies have revealed that the self-MIP repertoire is more complex and plastic than previously anticipated. The composition of the self-MIP repertoire varies from one cell type to another and can be perturbed by cell-intrinsic and -extrinsic factors including dysregulation of cellular metabolism and infection. The complexity and plasticity of the self-MIP repertoire represent a major challenge for the maintenance of self tolerance and can have pervasive effects on the global functioning of the immune system.     

MHC class I-associated peptides identified from normal platelets and from individuals with idiopathic thrombocytopenic purpura

Major histocompatibility complex (MHC) class I molecules bind and display peptide antigens on the cell surface. CD8(+) T lymphocytes recognize peptides in association with class I proteins to initiate a cytotoxic immune response. To understand the specificity of such immune responses and to facilitate the development of therapies for disease, it is important to identify MHC-presented peptides. In this study, platelets, easily obtainable and often associated with immune-mediated disease, were selected to identify MHC class I-associated peptides. MHC-associated peptides presented on platelets of normal individuals and individuals with idiopathic thrombocytopenic purpura (ITP) were characterized. ITP is characterized by the premature immune destruction of platelets. It is associated with the production of antiplatelet autoantibodies, most often targeting platelet membrane GPIIb/IIIa or GPIb/IX. In addition to characterizing five fully and several partially sequenced peptides from platelets, the peptide GPRGA(L/I)S(L/I)(L/I) was identified from four of the five ITP patients. The anchor motif of this peptide correlates with the presence of the HLA-B7 allele. A BLAST search identified this peptide as GPIb (4-12). In conclusion, platelets from normal and ITP individuals can present peptides from general cellular proteins and platelet specific proteins, such as GPIb, to the immune system via MHC class I.     

Modeling MHC class II molecules and their bound peptides as expressed at the cell surface

A detailed insight to the structure of a given major histocompatibility complex (MHC)-peptide complex can strongly support and also improve the analysis of the peptide binding capabilities of the MHC molecule and the characterization of the developing T cell response. The number of MHC class II-peptide crystal structures is limited, therefore constructing and analyzing computer models can serve as efficient complementary tools when someone deals with experimentally determined binding and/or functional data. Commercial programs are available for modeling protein and protein-protein complexes, in general. However, more accurate results can be obtained if the parameters are directly optimized to a given complex, especially in the case of special proteins as MHC class II, an integral membrane protein, whose functional parts behave like regular globular proteins. Here, we present the optimization of an approach used for modeling MHC class II molecules complexed with various peptides fitting into the binding groove and several ways to analyze them with the help of experimental data.     

Features of TAP-independent MHC class I ligands revealed by quantitative mass spectrometry

TAP is responsible for transferring cytosolic peptides into the ER, where they can be loaded onto MHC molecules. Deletion of TAP results in a drastic reduction of MHC class I surface expression and alters the presented peptide pattern. This key molecule in antigen processing is tackled by several viruses and lost in some tumors, rendering the altered cells less vulnerable to T cell-based immune surveillance. Using the TAP-deficient cell line LCL721.174 and its TAP-expressing progenitor cell line LCL721.45, we identified and quantified more than 160 HLA ligands, 50 of which were presented TAP-independently. Peptides which were predominantly presented on the TAP-deficient LCL721.174 cell line had a decreased MHC binding affinity according to their SYFPEITHI and BIMAS score. About half of the identified TAP-independently presented peptides were not derived from signal sequences and may partly be generated by the proteasome. Furthermore, we have excluded the possibility that differences in HLA ligand presentation between LCL721.45 and LCL721.174 were due to varying expression of the source proteins or due to changes in the antigen loading complex. Features of peptides presented independently of TAP as well as proteasomal contribution to their generation provide an insight into basic immunological mechanisms.     

alpha-Interferon treatment induces quantitative modifications of HLA class I-associated peptides eluted from cultured cancer cell lines

Interferons upregulate the expression of HLA class I antigens on cancer cells. Nevertheless, little is known about the panel of HLA class I antigen-associated peptides presented by recombinant alpha-interferon (r(alpha)-IFN)-treated cells. For this reason, peptides were eluted from five cancer cell lines (four melanoma and one non-small cell lung cancer) following treatment with r(alpha)-IFN. High-performance liquid chromatography (HPLC) profiles of the peptide fractions were compared with those obtained from untreated cells. No significant differences in peptide characteristics (detectable on the basis of retention times) were observed, but significant differences in terms of peptide quantities were observed. Mass spectrometry performed on HPLC peaks allowed not only the detection of three different peptides (two derived from the MAGE family of genes and one from the mart-1) both in untreated and in treated cells, but also gave an indication of the number of peptides within one HPLC peak. This data demonstrates that r(alpha)-IFN-treated cells express a similar peptide pattern as untreated cells, with significant quantitative differences. Interestingly, this finding also explains the higher susceptibility to lysis (mediated by specific cytolytic lymphocytes, which recognize cancer cells in an HLA-restricted fashion) of r(alpha)-IFN-treated cells.     

MHC class II restricted recognition of FMDV peptides by bovine T cells.

A putative synthetic vaccine for foot-and-mouth disease (FMDV15) has proved less successful in a host species, cattle, than predicted by results in a small-animal model. Possible reasons for this include non-recognition by T cells influenced by major histocompatibility complex (MHC)-linked immune response gene control. It is now possible to type for human leucocyte antigen (HLA) DR-like bovine MHC (BoLA) class II polymorphisms with a one-dimensional isoelectric focusing (IEF) technique. Using this method 14 unrelated cattle were selected with eight different BoLA class II IEF types. After immunization with FMDV15, 13 cattle generated a T-cell response to FMDV15. However, the fine specificity and magnitude of the response was related to BoLA class II type. The non-response by one animal and low response by two other animals were associated with two of the BoLA class II types. Response to the region 149-158 was immunodominant and animals which did not respond to this region had low responses to the whole peptide. Using FMDV-specific T-cell lines five BoLA class II types associated with responder animals were able to present FMDV15 in an MHC class II-restricted fashion, indicating that this peptide is capable of binding to different MHC class II molecules and may account for the broad response observed. The restriction patterns of the lines indicated that the IEF method does not distinguish all functional polymorphisms. At least two of the IEF-defined types could each be split into two distinct specificities and revealed that the three sets of animals with identical IEF types in fact expressed distinct restriction elements.     

Application of SELDI-TOF mass spectrometry for the identification of differentially expressed proteins in transformed follicular lymphoma.

Completion of the human genome project has focused scientific attention on the development of methods that permit rapid characterization of proteins that are encoded by the genome. Recent improvements in two-dimensional separation techniques in combination with protein identification software/databases and mass spectrometry (MS) now permit rapid comprehensive large-scale analysis of individual proteins within complex protein mixtures. We have performed pairwise comparisons of low-grade and transformed follicular lymphomas (FLs) in order to identify proteins that may be involved in FL progression using surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometer (ProteinChip, Ciphergen Biosystems). This system utilizes preactivated differential binding surfaces to achieve multidimensional chromatography. The protein-bound chips were then analyzed by a SELDI-TOF mass spectrometer to generate protein profiles. In preliminary experiments, we established that the MS data obtained from SELDI-TOF MS were reproducible, and that reduction in sample complexity improved the ability to detect lower abundance proteins. With specific regard to FL transformation, we rapidly identified a number of potential candidate proteins involved in this process. These included an upregulated 32 kDa protein and a down-regulated 11.8 kDa protein. Protein database searches revealed several candidates, among them cyclin D3 (32.5 kDa) and caspase 3 (11.8 kDa) whose differential expression were confirmed by immunoblotting and/or immunohistochemical analysis on the primary tissue specimens. Our studies demonstrate the utility of SELDI-TOF-MS for the rapid discovery of differentially expressed proteins using femtomolar quantities of crude protein derived from biopsy material. The versatility of this methodology supports its application to the rapid discovery of potential biomarkers in a variety of cellular systems.     

Identification of MHC class II restricted T-cell-mediated reactivity against MHC class I binding Mycobacterium tuberculosis peptides

Major histocompatibility complex (MHC) class I restricted cytotoxic T lymphocytes (CTL) are known to play an important role in the control of Mycobacterium tuberculosis infection so identification of CTL epitopes from M. tuberculosis is of importance for the development of effective peptide-based vaccines. In the present work, bioinformatics technology was employed to predict binding motifs of 9mer peptides derived from M. tuberculosis for the 12 HLA-I supertypes. Subsequently, the predicted peptides were synthesized and assayed for binding to HLA-I molecules in a biochemically based system. The antigenicity of a total of 157 peptides with measured affinity for HLA-I molecules of K(D) ≤ 500 nM were evaluated using peripheral blood T cells from strongly purified protein derivative reactive healthy donors. Of the 157 peptides, eight peptides (5%) were found to induce T-cell responses. As judged from blocking with HLA class I and II subtype antibodies in the ELISPOT assay culture, none of the eight antigenic peptides induced HLA class I restricted CD8(+) T-cell responses. Instead all responses were blocked by pan-HLA class II and anti-HLA-DR antibodies. In addition, CD4(+) T-cell depletion before the 10 days of expansion, resulted in total loss of reactivity in the ELISPOT culture for most peptide specificities. FACS analyses with intracellular interferon-γ staining of T cells expanded in the presence of M. tuberculosis peptides confirmed that the responsive cells were indeed CD4(+). In conclusion, T-cell immunity against HLA-I binding 9mer M. tuberculosis-derived peptides might in many cases turn out to be mediated by CD4(+) T cells and restricted by HLA-II molecules. The use of 9mer peptides recognized by both CD8(+) and CD4(+) T cells might be of importance for the development of future M. tuberculosis peptide-based vaccines.     

MHC class I-associated presentation of exogenous peptides is not only enhanced but also prolonged by linking with a C-terminal Lys-Asp-Glu-Leu endoplasmic reticulum retrieval signal

Vaccination with antigenic peptide-pulsed antigen-presenting cells (APC) represents an attractive approach for therapy for cancer and diseases caused by intracellular infections. It has been suggested that sufficient stable MHC/peptide complexes on the surface of APC might play an important role in the generation of antitumor and antiviral immunity in vivo. In this study, we observed that exogenous peptides that were artificially fused with an endoplasmic reticulum (ER) retrieval signal, a C-terminal Lys-Asp-Glu-Leu sequence, could be efficiently presented by intracellular MHC class I molecules in a TAP- and proteasome-independent, but brefeldin A-sensitive manner. The APC retained the capacity to display surface MHC/peptide complexes for a prolonged period. In addition, our results show that vaccination with DC bearing our fusion peptides induced greatly enhanced specific CTL response, and resulted in significant inhibition of tumor growth. Thus, the ER retrieval signal modification can be regarded as a novel method for targeting exogenous peptides into the intracellular MHC class I presentation pathway, and may improve the clinical utility of vaccines based on synthetic peptide pulsed DC.     

Reconstitution of class I MHC molecules expressed in E. coli and complexed with single antigenic peptides.

The HLA-Cw3 heavy chain has been expressed at high level as insoluble protein aggregates in E. coli. The protein aggregates dissolved in strong denaturant solution were efficiently reconstituted by removal of denaturant in the presence of an HLA-Cw3 binding peptide (FAM) and beta 2m. The reconstituted HLA-Cw3/FAM protein binds specifically to a p58 natural killer cell inhibitory receptor, a natural ligand. The HLA-A2 molecule has also been reconstituted in complex with either of a peptide from myelin associated glycoprotein (MAG) or a peptide from the GAG protein of human immunodeficiency virus. The HLA-A2/MAG protein crystallized under the identical conditions as HLA-A2 purified from human lymphoblastoid cells. The reconstitution method has yielded an abundant supply of HLA molecules complexed with single antigenic peptides, and may be of general utility in reconstituting any class I MHC molecules. However, the HLA molecules could not be reconstituted either without a peptide or with an irrelevant peptide. Using this property, the reconstitution method could be used to determine whether a peptide is restricted/bound to certain class I MHC molecule.     

Biochemical properties of MHC class II molecules endogenously synthesized and expressed by mouse Langerhans cells

The cell surface expression and biosynthesis of Langerhans cells (LC)-derived major histocompatibility complex (MHC) class II molecules from epidermal cells (EC) prepared freshly and cultured for up to 3 days was investigated. Based on the constitutive expression of MHC class II determinants by LC, a panning and magnetic bead selection procedure was employed, yielding 65% and 86% of I-A+ cells, respectively. Phenotypical and cytochemical examinations revealed that the two LC preparations were free of contaminating macrophages as well as B and T cells. Freshly prepared enriched LC were highly efficient in the stimulation of protein antigen-specific T cell clones, while LC purified from short-term cultured EC suspensions proved to be more efficient allogeneic stimulator cells than fresh LC. Comparative analysis of LC obtained from freshly prepared and from short-term-cultured EC preparations indicated an up-regulation of MHC class II determinants during short-term culture. Radioiodination analysis of LC selected by magnetic beads demonstrated prominent class II alpha and beta chain signals with only a minute fraction of invariant chains p35 and p45 being expressed at the cell surface. Unlike class II complexes derived from B cells, those from LC contained invariant chain fragment p20 in association with alpha/beta heterodimers at the plasma membrane. No qualitative differences between freshly isolated and 3-day cultured LC in cell surface expressed MHC class II components were detectable. Metabolic labeling with subsequent two-dimensional electrophoresis revealed distinct features of LC-derived MHC class II molecules with a high proportion of invariant chains in particular gamma and p40 and their extensive sialylation. While fresh and 1-day cultured LC exhibited appreciable levels of newly synthesized class II molecules, a dramatic down-regulation in class II and invariant chain synthesis was measured after 3 days of continuous in vitro culture.     

Natural killer cells infiltrating colorectal cancer and MHC class I expression

A majority of colorectal adenocarcinomas displays diminished MHC class I expression, making them particularly vulnerable for NK cell-mediated killing. Generally, these tumors also show a substantial inflammatory infiltrate. Most inflammatory cells, however, reside in the tumor stroma, where they do not have direct contact with tumor cells in the tumor epithelium. In this study, we investigated the correlation between colorectal tumor MHC class I aberrations and infiltration of NK cells. We studied 88 tumor specimens obtained from 88 colorectal cancer patients for locus-specific HLA aberrations and correlated these data to infiltration of CD4, CD8+ and CD56+ lymphocytes. The lymphocyte markers were individually combined with laminin as a second marker to facilitate quantification in the different tumor compartments, i.e. tumor epithelium and tumor stroma. Locus-specific partial or total HLA class I loss was detected in 72% of the tumors studied. Twenty-eight percent had no HLA loss at all. Mean overall intra-epithelial infiltration of CD56+ lymphocytes was 7 cells/mm(2) compared to 76 cells/mm(2) for CD8 and 19 cells/mm(2) for CD4+ lymphocytes. Locus-specific partial or total loss of tumor cell MHC class I expression was positively correlated with the intra-epithelial infiltration of CD8+ cells (P = 0.01), but not with CD4+ or CD56+ lymphocytes. Triple immunofluorescence staining showed that these cells were CD8 and granzyme-B positive T-lymphocytes. Our data showed that colorectal tumors are sparsely infiltrated by CD56+ cells compared to CD8+ T-cells and that loss of MHC is associated with T-cell infiltration instead of NK cell infiltration. Considering the fact that MHC loss is quite common in colorectal cancer and that, due to local absence of NK cells, it is unlikely that there has been selection for NK-escape variants, improvement of the intra-epithelial infiltration/migration of NK cells may be an important basis for the development of an effective adjuvant NK-based immunotherapy of colorectal cancer.     

Hierarchical immunogenicity of donor MHC class I peptides in allotransplantation

The recognition of major histocompatibility complex (MHC) allopeptides by recipient MHC class II-restricted CD4(+) T cells via indirect pathway is a prerequisite for the generation of an immune response to the allograft. We tested 13-mer to 24-mer peptides from the MHC class I molecule for their possible immunogenicity in a fully MHC-mismatched rat strain combination. Our results confirm the hierarchical distribution of the immunogenicity of donor MHC class I peptides in the T cell alloactivation via indirect pathway. In addition, we show that allopeptide-induced immune response is critical for acute rejection of heart allografts. Among the seven allopeptides tested, peptide P1 was identified as immunodominant; it induced the greatest T cell proliferation and cytokine production in vitro as well as a significant reduction in allograft survival time. The TCR repertoire of T cells involved in the in vitro and in vivo responses induced by the dominant allopeptide P1 was found to be limited to the Vbeta10 and Vbeta 19 gene families. The identification of dominant allopeptides should greatly facilitate characterization of the specific T cell population responsible for allograft rejection and may be used to modulate the alloimmune response through antigen-specific therapy.     

Dendritic cells permit identification of genes encoding MHC class II-restricted epitopes of transplantation antigens

Minor or histocompatibility (H) antigens are recognized by CD4+ and CD8+ T lymphocytes as short polymorphic peptides associated with MHC molecules. They are the targets of graft versus host and graft versus leukemia responses following bone marrow transplantation between HLA-identical siblings. Several genes encoding class I-restricted minor H epitopes have been identified, but approaches used for these have proved difficult to adapt for cloning class II-restricted minor H genes. We have combined the unique antigen-presenting properties of dendritic cells and high levels of episomal expression following transfection of COS cells to identify a Y chromosome gene encoding two HY peptide epitopes, HYAb and HYEk.     

Electrospray ionization mass spectrometry of low-molecular-mass S-nitroso compounds and their thiols

Low-molecular-mass S-nitroso compounds (R-S-N=O) are potent vasodilators and inhibitors of platelet aggregation. This work describes the electrospray ionization mass spectrometric (ESI-MS) analysis of physiological and synthetic low-molecular-mass S-nitroso compounds and their thiols including S-nitrosoglutathione, S-nitrosocysteine, glutathione and cysteine. Mass spectra of the unlabeled and S-15N-labeled low-molecular-mass S-nitroso compounds investigated are characterized by abundant cations due to [M+H]+, [M+Na]+, [(M+H)-NO]+, [2 M+H]+, and [(2 M+H)-2NO]+. Mass spectra of low-molecular-mass thiols are characterized by abundant cations due to [M+H]+, [M+Na]+ and [2M+H]+. Using off-line electrospray ionization tandem mass spectrometry we unequivocally identified S-[15N]nitrosoglutathione in human red blood cells formed after their incubation with S-[15N]nitrosocysteine. These results suggest that ESI-MS in combination with an appropriate liquid chromatographic system should be a useful analytical approach for the on-line quantitative determination of low-molecular-mass S-nitroso compounds in biological fluids in the presence of their thiols and nitrite. Considerations were made about on-line ESI-MS and quantitative measurements.     

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.     

Short peptides sensitize target cells to CTL specific for the MHC class Ib molecule,H2-M3

The MHC class Ib molecule H2-M3 presents N-formylated peptides from the N terminus of proteins encoded by the mitochondrial genome to CTL. A panel of CTL specific for a peptide derived from a mitochondrial protein, either COI or ND1, was used to determine the optimal peptide length for sensitizing antigen-deficient target cells. All long-term CTL lines and most CTL clones lysed target cells sensitized with either a COI hexamer or an ND1 heptamer. Only 3 out of 12 anti-ND1 clones preferred an octamer or nonamer peptide and no CTL required to longer peptides. The CTL preference for short peptides matches a shortened groove in M3. The CTL all lysed lymphoblasts encoding the appropriate mitochondrial antigen, suggesting that these target cells express naturally processed, endogenous, formylated peptides, ranging from six to nine amino acids in length.     

MHC class II antigens on canine bronchoalveolar cells

To evaluate the expression of MHC (major histocompatibility complex) antigens on canine bronchoalveolar cells (BAC), bronchoalveolar lavages (BAL) were performed in mongrel and German shepherd dogs. MHC class II antigens on canine BAC and peripheral blood mononuclear cells (PBMC) were detected by monoclonal antibodies (mAbs) B1F6, 7.5.10.1 and Q5/13 recognising canine MHC class II antigens, using cytofluorometry. These mAbs reacted with more than 20% of BAC and PBMC in both breeds of dog. The percentage of MHC class II positive cells in BAC were lower than those in PBMC. There was no significant difference in the percentages of MHC class II positive BAC and PBMC in mongrel and German shepherd dogs. To further identify the expression of MHC class II antigens on BAC, the cells were separated into adherent and nonadherent cells by petri dish adherence. The percentages of MHC class II positive cells in adherent and non-adherent cell populations were similar. Nearly half the lymphocytes in normal BAC were T cells detected by mAbs F3-20-7 and 1A1; B cells were scarce and represented less than 10% of nonadherent cells. Immunoprecipitation by anti-MHC class II mAbs, and SDS-polyacrylamide gel electrophoresis (SDS-PAGE) revealed MHC class II-like molecules on canine BAC and PBMC. After stimulation with phytohaemagglutinin (PHA), the percentages of class II positive cells in BAC and PBMC were significantly increased. Thus, these anti-MHC class II mAbs may prove to be of advantage in experiments designed to evaluate the changes in class II antigen expression on canine BAC during the course of immune response in the lung, as in pulmonary allograft rejection.