Mechanistic understanding and significance of small peptides interaction with MHC class II molecules for therapeutic applications

Major histocompatibility complex (MHC) class II molecules are expressed by antigen-presenting cells and stimulate CD4⁺ T cells, which initiate humoral immune responses. Over the past decade, interest has developed to therapeutically impact the peptides to be exposed to CD4⁺ T cells. Structurally diverse small molecules have been discovered that act on the endogenous peptide exchanger HLA-DM by different mechanisms. Exogenously delivered peptides are highly susceptible to proteolytic cleavage in vivo; however, it is only when successfully incorporated into stable MHC II–peptide complexes that these peptides can induce an immune response. Many of the small molecules so far discovered have highlighted the molecular interactions mediating the formation of MHC II–peptide complexes. As potential drugs, these small molecules open new therapeutic approaches to modulate MHC II antigen presentation pathways and influence the quality and specificity of immune responses. This review briefly introduces how CD4⁺ T cells recognize antigen when displayed by MHC class II molecules, as well as MHC class II–peptide-loading pathways, structural basis of peptide binding and stabilization of the peptide–MHC complexes. We discuss the concept of MHC-loading enhancers, how they could modulate immune responses and how these molecules have been identified. Finally, we suggest mechanisms whereby MHC-loading enhancers could act upon MHC class II molecules.     

Presentation of cytosolic antigens via MHC class II molecules

Major histocompatibility (MHC) class II molecules function to present antigenic peptides to CD4 T lymphocytes. The pathways by which these molecules present exogenous antigens have been extensively studied. However by contrast, far less is known about the processing and trafficking of cytosolic antigens, which can also serve as an alternative source of ligands for MHC class II molecules. Self-proteins, tumor antigens, as well as viral proteins found within the cytosol of cells, can be presented via MHC class II molecules, resulting in the activation of specific CD4 T cells. Studies have begun to reveal unique steps as well as some similarities in the pathways for cytosolic and exogenous antigen presentation. Recent developments in this area are summarized here.     

LAMP-2-deficient human B cells exhibit altered MHC class II presentation of exogenous antigens

Major histocompatibility complex (MHC) class II molecules present antigenic peptides derived from engulfed exogenous proteins to CD4⁺ T cells. Exogenous antigens are processed in mature endosomes and lysosomes where acidic proteases reside and peptide‐binding to class II alleles is favoured. Hence, maintenance of the microenvironment within these organelles is probably central to efficient MHC class II‐mediated antigen presentation. Lysosome‐associated membrane proteins such as LAMP‐2 reside in mature endosomes and lysosomes, yet their role in exogenous antigen presentation pathways remains untested. In this study, human B cells lacking LAMP‐2 were examined for changes in MHC class II‐restricted antigen presentation. MHC class II presentation of exogenous antigen and peptides to CD4⁺ T cells was impaired in the LAMP‐2‐deficient B cells. Peptide‐binding to MHC class II on LAMP‐2‐deficient B cells was reduced at physiological pH compared with wild‐type cells. However, peptide‐binding and class II‐restricted antigen presentation were restored by incubation of LAMP‐2‐negative B cells at acidic pH, suggesting that efficient loading of exogenous epitopes by MHC class II molecules is dependent upon LAMP‐2 expression in B cells. Interestingly, class II presentation of an epitope derived from an endogenous transmembrane protein was detected using LAMP‐2‐deficient B cells. Consequently, LAMP‐2 may control the repertoire of peptides displayed by MHC class II molecules on B cells and influence the balance between endogenous and exogenous antigen presentation.     

The co-receptor function of CD4.

CD4 is a critical component of the T cell receptor complex that recognizes peptides bound to MHC class II molecules. This can be observed at all stages of T cell development, activation, and function. CD4 has been termed a co-receptor to indicate that its most important activity is to bind the same peptide: self class II MHC complex as the T cell receptor and to transduce positive activating signals in conjunction with the T cell receptor. This behavior has been shown by several independent experimental systems: direct cross-linking of the T cell receptor to CD4, the inhibition of T cell activation by anti-CD4, the transfection of CD4 into CD4- T cells, and by the phenomenon of epitope interference, as described in this review. All of these approaches suggest that the participation of CD4 as a co-receptor in antigen: self class II MHC recognition potentiates activation by 100-fold. Given the complex nature of the ligand recognized by the T cell receptor, the co-receptor function of CD4 virtually eliminates the possibility of CD4 T cells recognizing peptides presented by class I MHC molecules, in keeping with many in vivo observations.     

MHC II and the Endocytic Pathway: Regulation by Invariant Chain

The major histocompatibility complex (MHC) class I and II molecules perform vital functions in innate and adaptive immune responses towards invading pathogens. MHC class I molecules load peptides in the endoplasmatic reticulum (ER) and display them to the T cell receptors (TcR) on CD8⁺ T lymphocytes. MHC class II molecules (MHC II) acquire their peptides in endosomes and present these to the TcR on CD4+ T lymphocytes. They are vital for the generation of humoral immune responses. MHC II assembly in the ER and trafficking to endosomes is guided by a specialized MHC II chaperone termed the invariant chain (Ii). Ii self-associates into a trimer in the ER, this provides a scaffold for the assembly of three MHC II heterodimers and blocks their peptide binding grooves, thereby avoiding premature peptide binding. Ii then transports the nascent MHC II to more or less specialized compartment where they can load peptides derived from internalized pathogens.     

Small molecule modulators of MHC class II antigen presentation: mechanistic insights and implications for therapeutic application

Antigen presenting cells express MHC class II molecules bound to peptide fragments and are responsible for activating CD4(+) T cells that then broadly influence many branches of the immune response. A growing interest in developing strategies to therapeutically influence the peptides to which na?ve CD4(+) T cells are exposed has led to the hunt for small molecules that modulate peptide presentation through the MHC class II pathway. Over the past decade a number of small molecules have been discovered that show surprising diversity in both structure and putative mechanisms. This review discusses how these small molecules were identified and compares the mechanisms by which they may act with what is known about the endogenous peptide exchanger, HLA-DM.     

MHC presentation via autophagy and how viruses escape from it

T cells detect infected and transformed cells via antigen presentation by major histocompatibility complex (MHC) molecules on the cell surface. For T cell stimulation, these MHC molecules present fragments of proteins that are expressed or taken up by the cell. These fragments are generated by distinct proteolytic mechanisms for presentation on MHC class I molecules to cytotoxic CD8⁺ and on MHC class II molecules to helper CD4⁺ T cells. Proteasomes are primarily involved in MHC class I ligand and lysosomes, in MHC class II ligand generation. Autophagy delivers cytoplasmic material to lysosomes and, therefore, contributes to cytoplasmic antigen presentation by MHC class II molecules. In addition, it has been recently realized that this process also supports extracellular antigen processing for MHC class II presentation and cross-presentation on MHC class I molecules. Although the exact mechanisms for the regulation of these antigen processing pathways by autophagy are still unknown, recent studies, summarized in this review, suggest that they contribute to immune responses against infections and to maintain tolerance. Moreover, they are targeted by viruses for immune escape and could maybe be harnessed for immunotherapy.     

Small molecule modulators of MHC class II antigen presentation: Mechanistic insights and implications for therapeutic application

Antigen presenting cells express MHC class II molecules bound to peptide fragments and are responsible for activating CD4⁺ T cells that then broadly influence many branches of the immune response. A growing interest in developing strategies to therapeutically influence the peptides to which naïve CD4⁺ T cells are exposed has led to the hunt for small molecules that modulate peptide presentation through the MHC class II pathway. Over the past decade a number of small molecules have been discovered that show surprising diversity in both structure and putative mechanisms. This review discusses how these small molecules were identified and compares the mechanisms by which they may act with what is known about the endogenous peptide exchanger, HLA-DM.     

Composition of the HLA‐DR‐associated human thymus peptidome

Major histocompatibility complex class II (MHC‐II) molecules bind to and display antigenic peptides on the surface of antigen‐presenting cells (APCs). In the absence of infection, MHC‐II molecules on APCs present self‐peptides and interact with CD4⁺ T cells to maintain tolerance and homeostasis. In the thymus, self‐peptides bind to MHC‐II molecules expressed by defined populations of APCs specialised for the different steps of T‐cell selection. Cortical epithelial cells present peptides for positive selection, whereas medullary epithelial cells and dendritic cells are responsible for peptide presentation for negative selection. However, few data are available on the peptides presented by MHC molecules in the thymus. Here, we apply mass spectrometry to analyse and identify MHC‐II‐associated peptides from five fresh human thymus samples. The data show a diverse self‐peptide repertoire, mostly consisting of predicted MHC‐II high binders. Despite technical limitations preventing single cell population analyses of peptides, these data constitute the first direct assessment of the HLA‐II‐bound peptidome and provide insight into how this peptidome is generated and how it drives T‐cell repertoire formation.     

Endogenous antigen presentation by MHC class II molecules

T cell recognition of antigen requires that a complex form between peptides derived from the protein antigen and cell surface glycoproteins encoded by genes within the major histocompatibility complex (MHC). MHC class II molecules present both extracellular (exogenous) and internally synthesized (endogenous) antigens to the CD4 T cell subset of lymphocytes. The mechanisms of endogenous antigen presentation are the subject of this review. Isolation and amino acid sequencing of peptides bound to the class II molecule indicate that a very high proportion (70–90%) of the total peptides presented by the class II molecule are in fact derived from the pool of proteins that are synthetized within the antigen-presenting cell (APC). This type of sequence information as well as the study of model antigens has indicated that proteins expressed in a diversity of intracellular sites, including the cell surface, endoplasmic reticulum and cytosol can gain access to the class II molecule, albeit with different efficiencies. The main questions that remain to be answered are the intracellular trafficking patterns that allow colocalization of internally synthesized antigens with the class II molecule, the site(s) within the cell where peptide: class II molecule complex formation can take place and whether presentation of ‘foreign’ as well as ‘self’ antigens takes place by mechanisms that vary from one cell type to another or that vary with the metabolic state of the APC. If such variability exists, is would imply that the array of peptides displayed by class II molecules at the cell surface has similar variability, a possibility that would impact on self tolerance and autoimmunity.     

CD4-Ia interactions can occur in the absence of T-cell receptor/antigen-Ia recognition

The T-cell differentiation antigen, CD4, is expressed by major histocompatibility (MHC) class II restricted T lymphocytes. CD4+CD8- T cells use their T-cell receptor to recognize foreign antigens in association with MHC class II products (Ia). The association between CD4 expression and restriction by MHC class II products has led to the hypothesis that CD4 may interact with monomorphic determinants of MHC class II molecules. A large body of experimental evidence suggests that CD4 interaction with MHC class II molecules leads to an increase in the binding avidity of T cell-stimulator cell interactions. A direct test for a functional CD4-MHC class II interaction in T-cell activation requires a separate evaluation of CD4-Ia interactions from T-cell receptor (TcR)-antigen (Ag)/Ia recognition. However, a separate evaluation proves difficult since the T-cell receptor and CD4 may interact with the same MHC class II molecule. In this report, we use a T-cell activation protocol where TcR-Ag/Ia recognition is replaced by TcR complex-anti-CD3 antibody interactions. Therefore, the affinity of the TcR complex for its ligand (the anti-CD3 mAb) is independent from MHC expression on target cells and allows a separate evaluation of the role of accessory molecules in T-cell activation. We have analysed the effects of monoclonal anti-MHC class II antibodies on the activation of a CD4+ T-cell hybridoma in the absence of its TcR restricting MHC class II molecule (I-Ek) but in the presence of unrelated MHC class II molecules (I-Ed, I-Ad). The data obtained indicate a functional interaction between the CD4 molecule and a non-polymorphic region of the MHC class II product in T-cell triggering.     

Autophagy in MHC class II antigen processing

Durable adaptive immunity is dependent upon CD4 T-cell recognition of MHC class II molecules that display peptides from exogenous and endogenous antigens. Endogenously expressed cytosolic and nuclear antigens access MHC class II by way of several intracellular autophagic routes. These pathways include macroautophagy, microautophagy and chaperone-mediated autophagy. Macroautophagy can deliver antigens into autophagosomes for processing by acidic proteases before MHC class II presentation. However, other endogenous antigens are processed by cytoplasmic proteases, yielding fragments that translocate via chaperone-mediated autophagy into the endosomal network to intersect MHC class II. Cross-talk between autophagy pathways, particularly in response to stress, appears to balance the relative efficiency of each pathway. This might limit redundancy, giving MHC class II broader access to antigens within intracellular compartments distinct from the endosomal network.     

Mixed-haplotype MHC class II molecules select functional CD4+ T cells

MHC class II molecules are formed from polymorphic alpha and beta chains. While pairing of chains is most efficient within class II isotypes and haplotypes, limited pairing and surface expression of mixed-haplotype and -isotype class II molecules is common. The function of such molecules in antigen presentation has been established by the unique restriction of responses in F1 mice. However, it has not been established whether mixed class II molecules are able to mediate selection of functional T cells and how the reduced avidity of the TCR/MHC interaction influences the repertoire. In this report we have addressed these issues through the production of mice expressing solely mixed-haplotype class II molecules. The mixed class II molecules promote selection of a small CD4+ T cell repertoire with modified TCR use. The selected CD4+ T cells are functional in vivo and in vitro.     

Effective formation of major histocompatibility complex class II-peptide complexes from endogenous antigen by thyroid epithelial cells

In autoimmune thyroid disease, thyroid epithelial cells (TEC) express major histocompatibility complex (MHC) class II molecules, potentially enabling them to present thyroid self-antigens to CD4-positive T cells. However, despite this, TEC may fail to present endogenous antigen as a result of limited processing or MHC class II loading capacity, or inadequate MHC class II levels. We addressed these issues using the cloned rat TEC line, Fischer rat thyroid cell line (FRTL5), which was transfected using an adenoviral expression vector that expressed ovalbumin (OVA) as an integral membrane protein. OVA-expressing FRTL5 cells very efficiently activated a panel of OVA-specific, class II-restricted T-cell hybridomas. This response was dependent on induction of MHC class II molecules by interferon-gamma (IFN-gamma) and was blocked by anti-MHC class II antibodies. Poor responses were seen to exogenously added OVA or OVA peptides. These results provide the most direct evidence to date that TEC can form MHC class II-peptide complexes derived from self-antigen in sufficient quantities to activate T cells.     

CD4 and CD8 recognition of class II and class I molecules of the major histocompatibility complex

T cells recognize their specific antigen when associated to the class I or class II molecules of the major histocompatibility complex (MHC). The T cell receptors, the effector molecules of specific antigen recognition are selected to have low affinity for self MHC molecules. Other molecules have been shown to play a major role in stabilizing the interaction between the TCR, self MHC and antigen. This review will focus on two of these molecules, namely CD4 and CD8. In contrast to other accessory molecules, the ligands of CD4 and CD8 are the same MHC molecules which are recognized by the T cell receptor. The structural analysis of the interaction between CD8, CD4 and their respective ligands, namely class I and class II molecules of the MHC, will be treated in this review. We will also discuss the possible differences which exist in the interaction of CD4 and CD8 with their respective ligands.     

Efficient generation and expansion of antigen-specific CD4+ T cells by recombinant influenza viruses

Adoptive transfer of in vitro generated antigen-specific T cells has been successfully used to treat viral infections in immunodeficient patients. Therefore, methods for the rapid in vitro expansion of antigen-specific T cells are needed. Influenza virus efficiently infects dendritic cells, and peptides derived from viral proteins are processed and presented to CD8(+) cytotoxic T cells. However, both, CD4(+) and CD8(+) T cells are necessary for the efficient control of viral infections, and it is becoming increasingly clear that a T helper cell response is very important for the maintenance and strength of the immune response. Here we show that recombinant influenza virus efficiently infects a wide range of professional antigen-presenting cells and does not interfere with antigen presentation pathways. Using T cell clones for three different MHC class II-restricted antigens we demonstrate that peptides derived from these antigens are efficiently presented on MHC class II molecules. Importantly, it was possible to generate and expand antigen-specific CD4(+) T cells following in vitro infection of professional antigen-presenting cells with recombinant influenza virus. These findings support the notion that recombinant influenza virus is a valuable tool for the expansion of antigen-specific CD4(+) T cells in vitro.     

The exogenous pathway for antigen presentation on major histocompatibility complex class II and CD1 molecules

The endosomes and lysosomes of antigen-presenting cells host the processing and assembly reactions that result in the display of peptides on major histocompatibility complex (MHC) class II molecules and lipid-linked products on CD1 molecules. This environment is potentially hostile for T cell epitope and MHC class II survival, and the influence of regulators of protease activity and specialized chaperones that assist MHC class II assembly is crucial. At present, evidence indicates that individual proteases make both constructive and destructive contributions to antigen processing for MHC class II presentation to CD4 T cells. Some features of CD1 antigen capture within the endocytic pathway are also discussed.     

Association of distinct tetraspanins with MHC class II molecules at different subcellular locations in human immature dendritic cells

Dendritic cells have the capacity to trigger T cell responses in lymphoid organs against antigens captured in the periphery. T cell stimulation depends on the ability of MHC class II molecules to present peptides at the cell surface that are acquired in MHC class II compartments. The high capacity of dendritic cells to stimulate T lymphocytes is related to their ability to regulate the distribution of MHC class II molecules intracellularly. To analyze the molecular components involved in the generation of MHC class II-peptide complexes in human immature dendritic cells, mAb were raised against purified MHC class II compartments. One of the antigens turned out to be CD63, a member of the tetraspanin superfamily. CD63 localized exclusively intracellularly where it associated with peptide-loaded class II molecules. In contrast, the tetraspanins CD9, CD53 and CD81 associated with class II molecules at the plasma membrane. Selective association of distinct tetraspanins may be involved in the regulation of MHC class II distribution in human dendritic cells.     

Pathways of antigen processing and presentation

CD8+ and CD4+ T lymphocytes recognise peptides stably bound to class I or class II MHC molecules, respectively. These complexes are assembled intracellularly during the biosynthesis and trafficking of MHC molecules. It is now clear that a number of different molecules and macromolecular complexes are drafted in to assist this process. Some of these are chaperones which appear to be dedicated to assisting MHC molecules capture peptides, whilst others may have additional cellular functions. Peptides form an integral part of the final MHC glycoprotein structure and their availability can regulate the kinetics and level of expression of MHC molecules on the cell surface. In vivo, significant time may elapse between generation of peptide/MHC complexes and their recognition by T cells. This requires that the complexes generated are stable and long-lived on the cell surface. Several mechanisms appear to contribute to the generation and display of long-lived complexes. Some pathogens have evolved mechanisms to evade and interfere with presentation of their own antigens. The strategies used are many and varied and are particularly well exemplified by the interaction of viral gene products with the MHC class I assembly pathway. Here, we provide an overview of what is currently known about the cellular biochemistry of antigen processing and the assembly of class I and class II MHC molecules.