Current Pharmaceutical Design - Volume 15, Issue 28, 2009

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T cell immune responses are driven by the recognition of peptide antigens (T cell epitopes) that are bound to major histocompatibility complex (MHC) molecules. T cell epitope immunogenicity is thus contingent on several events, including appropriate and effective processing of the peptide from its protein source, stable peptide binding to the MHC molecule, and recognition of the MHC-bound peptide by the T cell receptor. Of these three hallmarks, MHC-peptide binding is the most selective event that determines T cell epitopes. Therefore, prediction of MHC-peptide binding constitutes the principal basis for anticipating potential T cell epitopes. The tremendous relevance of epitope identification in vaccine design and in the monitoring of T cell responses has spurred the development of many computational methods for predicting MHC-peptide binding that improve the efficiency and economics of T cell epitope identification. In this report, we will systematically examine the available methods for predicting MHC-peptide binding and discuss their most relevant advantages and drawbacks.

Short peptides derived from cellular proteins may escape complete destruction during protein catabolism and finally serve as a showcase in the immune system. Exposed at the cell surface to scrutiny by T cells, MHC:peptide complexes mediate a highly specific and immediate information transfer from diseased cells to the cellular immune system. Numerous clinical vaccination trials have been carried out employing MHC-presented peptides for T-cell activation with encouraging results but so far without a final breakthrough. In this review, we briefly highlight the molecular basis of MHC-peptide interactions governed by specificity pockets and anchor residues, as summarized in allele-specific peptide motifs. State-of-the-art technology is comprehensively presented and gives an overview of modern mass spectrometric strategies used for qualitative and quantitative analysis of MHC ligands. We describe the details of the HLA-B*3801 peptide motif by comparing features of natural MHC ligands, resulting in a scoring matrix that enables epitope prediction from any viral or tumor antigen. The pronounced individuality in peptide presentation by MHC molecules, as reflected in the highly specific peptide motifs of different MHC allotypes or the tissue-specific MHC ligandomes, represents a current area of interest within this field. Finally, the identification of post-translational modifications - most important phosphorylations - and the promises this holds will be discussed in this chapter.

Vaccination techniques have developed rapidly over the last several decades from the immunization with live attenuated pathogens to the use of peptide and DNA subunit vaccines, from the use of classical adjuvants to cell-directed delivery. Vaccination techiques are also under investigation for the treatment of tumors and autoimmune diseases. However, profound knowledge of activation mechanisms of the immune cells on a molecular level is prerequisite for a better understanding of the immune response, and for the development of effective immunomodulatory tools. In this review we discuss the models of BCR and TCR activation, and using the example of some vacciantion technologies, we show, how the understanding of these models could help in the design of a new generation of vaccines.

Vaccines are one of the most cost effective methods to control infectious diseases and at the same time one of the most complex products of the pharmaceutical industry. In contrast to other drugs, vaccines are used mainly in healthy individuals, often in children. For this reason, very high standards are set for their production. Subunit vaccines, especially peptide vaccines, can provide a safe and cost-effective alternative to vaccines produced from attenuated or inactivated pathogen preparations. Biochemical and structural studies of class II MHC - peptide complexes are beginning to provide a conceptual foundation for the rational design of subunit and peptide vaccines. In this review, we show how analysis of peptide-class II MHC complexes together with developing understanding of antigen processing pathways has opened the door to understanding the major rules that govern selection of T cell epitopes. We review progress towards computational prediction of such epitopes, and efforts to evaluate algorithms that incorporate various structural and/or biochemical aspects of the MHC-peptide interaction. Finally, using malaria as a model, we describe the development of a minimal subunit vaccine for the human malaria parasite Plasmodium falciparum.

The Major Histocompatibility Complex Class II locus is the primary genetic linkage to autoimmune diseases. Susceptibility to each such disease is linked to different alleles, with a few alleles showing also dominant protection. The design of vaccines for autoimmune diseases is a long sought-after goal. As knowledge about the pathogenesis of these diseases has increased, the tools for such an approach have of necessity been refined. We review below the structural essence of MHC II-linked autoimmune diseases which centers on the binding of antigenic peptides to the disease-linked MHC II proteins, and the consequent activation of cognate TCRs from pathogenic CD4+ T cells. The state of affairs in two organ-specific autoimmune diseases, type 1 diabetes, celiac disease are covered, including attempts to treat these via antigen-specific MHC II-guided measures. We offer a couple of testable suggestions as to how this approach could be improved.

Central to the initiation of a T cell dependent immune response is the recognition of major histocompatibility complex (MHC) class I or class II molecules (in humans termed HLA and in mice termed H-2) bound to antigenic peptide. T cell receptors (TCR) have programmed specificity for particular peptide/MHC complexes, which ensures focused immune responses are generated against the antigen source. To design effective peptide based vaccines a comprehensive understanding of the specific interactions between MHC molecules and peptide, and of TCR recognition of MHC/peptide is valuable. We place particular emphasis on non-canonical bound peptides and their use in immunotherapy studies.

What makes a peptide an epitope? This is a central question in immunology. The clear identification of precise molecular characteristics of epitopes would help define the basic mechanisms of self/non-self distinction and lead to a greater understanding of phenomena such as tolerance, autoimmunity, allergy, and tumor escape of immune surveillance. Importantly, clarifying the properties an epitope is paramount to the development of diagnostic and therapeutic vaccines. This review analyzes recent reports on experimentally identified B cell epitopes associated with multiple infectious disease pathologies, cancer, autoimmunity, hypertension, obesity, and allergy. It illustrates data that further support the notion that only a low level of sequence similarity to the host proteome is needed to modulate the B cell epitope-specific peptidome. Amino acid sequences that are unique to the antigen and are not shared with the host proteome are specifically targeted by the humoral immune response. Therefore, low-similarity peptides may be significant to the rational development of peptide-based clinical treatments in cancer, autoimmunity, infection, and allergy. Biologically, the lowsimilarity hypothesis further supports sequence uniqueness as the molecular signature of “nonselfness” in the currently ongoing self/non-self debate.

The success of vaccination is directly or indirectly based on the specificity of antigen recognition by T lymphocytes, their efficient activation and expansion, and the generation of vaccine-specific effector and memory cells. These traits are largely dependent on the correct assembly and expression of sufficient number of functional TCR/CD3 complexes in the cell surface. In this review, some of the genetic and epigenetic factors that determine the correct assembly and structure of the TCR/CD3 complex are summarized. Those physiologic or pathologic factors leading to natural variations, or pathologic alterations of the standard that might lead to poor response to vaccination and that could give some possibilities to pharmacological intervention are emphasized.

MHC-specific Natural Killer inhibitory receptors display a conserved and fundamental function in the regulation of NK-mediated cytolysis. Their importance is substantiated by the fact that during speciation different molecular receptor structures have evolved to maintain inhibitory regulation of NK cells. The information gained during these last twenty years begins to be fruitfully used in the therapy of leukemias, but a lot has to be still done. In particular, we need to understand the role of activating KIR and their ligand(s), since their role in the course of different viral diseases is still intriguing.

CD1 molecules are a family of non-polymorphic, class I antigen-presenting glycoproteins, which bind and present amphiphilic lipid antigens for recognition to T cells. Two groups of CD1 molecules are involved in presentation of self and foreign lipid antigens: group 1 (CD1a, CD1b and CD1c) and group 2 (CD1d). Crystal structures of CD1a, CD1b and CD1d in complex with different ligands have revealed the key principles of lipid presentation and defined unique binding groove architectures for the individual CD1 isoforms, which enable binding and presentation of an enormous variety of lipids. Structural and biochemical insights into presentation of glycolipids by CD1d have led to the discovery of novel lipid antigens and to a broader understanding of the underlying structural and mechanistic principles of NKT cell stimulation. Some of these glycolipids show enhanced and more specific stimulatory properties and crystal structures have suggested further design strategies for elicitation of immuno-stimulatory compounds that may enable selective control of the secretion of regulatory T helper cytokines.

Human leukocyte antigen-G (HLA-G) is a non-classical HLA class I molecule, which was first discovered in 1987 by Geraghty and colleagues [1]. While classical HLA class I molecules are expressed on all nucleated cells, the expression of the HLA-G molecule is highly tissue-restricted, such as to placental trophoblast cells. HLA-G binds inhibitory receptors such as leukocyte immunoglobulin-like receptors B1 (LILRB1/ILT2/CD85j) and LILRB2 (ILT4/CD85d), which are widely expressed on immune cells, to suppress a broad range of immune responses [2-4]. Thus, the expression of HLA-G in placenta protects the fetus from the maternal immune system. On the other hand, emerging studies have shown the relevance of the HLA-G molecule in pathologic conditions, such as transplantation rejection, autoimmunity, and cancer. HLA-G has other unique characteristics, in contrast with classical HLA molecules, including the existence of various forms of HLA-G: several splice variants, subunit-deficient conformations, homodimers, and their combinations have been found [5]. In this review, we highlight the molecular basis for the tolerogenic ability of the HLA-G molecule, especially by LILR recognition of various forms of HLA-G. We also discuss the potential clinical applications of HLA-G molecules.

In addition to a variety of other techniques used in T-cell epitope identification, mass spectrometery coupled to liquid chromatography have now become an important and sensitive tool in separation, detection, and sequence analysis of highly complex natural major histocompatibility complex (MHC) ligand mixtures. In this article, we present current strategies for the identification of MHC eluted peptides using high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) with a particular recall to those presented in the context of the non classical human leukocytes antigen (HLA) class I molecule HLA-E. In addition we also discuss the advantages and disadvantages of the methods available in the literature to concentrate and fractionate the peptides prior to analysis by mass spectrometry. An application of our method for isolation and characterization of peptides presented in the context of HLA-E is finally reported.

In humans, major histocompatibility complex (MHC) class I molecules comprise the classical (class Ia) human leukocyte antigens (HLA)-A, -B, and -C, and the non-classical (class Ib) HLA-E, -F, -G and -H (HFE) molecules. The best-characterized MHC class Ib molecule is HLA-E. HLA-E was first described as a non-polymorphic ligand of the CD94/NKG2 receptors expressed mainly by natural killer (NK) cells and its role was thus confined to the regulation of NK cell function. Therefore, interaction of HLA-E with the CD94/NKG2 receptors can result in either inhibition or activation of NK cells, depending on the peptide presented and on the NKG2 receptor CD94 is associated with. Thus, CD94/NKG2A functions as an inhibitory receptor, whereas CD94/NKG2C functions as an activating receptor. However, recent evidences obtained by our group and others indicated that HLA-E represents a novel restriction element for ab Tcell receptor (TCR)-mediated recognition. Although HLA-E displays a selective preference for nonameric peptides derived from the leader sequences of various HLA class I alleles, several reports showed that it can also present “noncanonical” peptides derived from both stress-related and pathogen-associated proteins. Because HLA-E displays binding specificity for innate CD94/NKG2 receptors but also has the features of an antigen-presenting molecule - including the ability to be recognized by ab T cells - it does appear that this MHC class Ib molecule plays an important role in both natural and acquired immune responses.