Making sense of mass destruction: quantitating MHC class I antigen presentation

Cross-presentation by intercellular peptide transfer through gap junctions

Major histocompatibility complex (MHC) class I molecules present peptides that are derived from endogenous proteins. These antigens can also be transferred to professional antigen-presenting cells in a process called cross-presentation, which precedes initiation of a proper T-cell response; but exactly how they do this is unclear. We tested whether peptides can be transferred directly from the cytoplasm of one cell into the cytoplasm of its neighbour through gap junctions. Here we show that peptides with a relative molecular mass of up to approximately 1,800 diffuse intercellularly through gap junctions unless a three-dimensional structure is imposed. This intercellular peptide transfer causes cytotoxic T-cell recognition of adjacent, innocent bystander cells as well as activated monocytes. Gap-junction-mediated peptide transfer is restricted to a few coupling cells owing to the high cytosolic peptidase activity. We present a mechanism of antigen acquisition for cross-presentation that couples the antigen presentation system of two adjacent cells and is lost in most tumours: gap-junction-mediated intercellular peptide coupling for presentation by bystander MHC class I molecules and transfer to professional antigen presenting cells for cross-priming.

Viral immune evasion molecules attack the ER peptide-loading complex and exploit ER-associated degradation pathways

The CD8+ cytotoxic-T-cell response is a potent mechanism that controls intracellular pathogens, including many viruses. To facilitate transmission, viruses often counter this response by inhibiting the cell surface display of virus-derived peptides on MHC class I molecules. More specifically, recent studies have demonstrated that viruses have evolved remarkable mechanisms to inhibit MHC class I expression by interfering with the function of the MHC class I assembly machinery (the peptide-loading complex) in the endoplasmic reticulum and/or by exploiting endoplasmic-reticulum-associated degradation pathways. These viral molecules are proving invaluable as research tools to illuminate the novel features of physiological pathways that are central to normal cell biology. Furthermore, the detailed characterization of such pathways has yielded significant new insights into host-pathogen interplay.

A mathematical model of protein degradation by the proteasome

The proteasome is the major protease for intracellular protein degradation. The influx rate of protein substrates and the exit rate of the fragments/products are regulated by the size of the axial channels. Opening the channels is known to increase the overall degradation rate and to change the length distribution of fragments. We develop a mathematical model with a flux that depends on the gate size and a phenomenological cleavage mechanism. The model has Michaelis-Menten kinetics with a V(max) that is inversely related to the length of the substrate, as observed in the in vitro experiments. We study the distribution of fragment lengths assuming that proteasomal cleavage takes place at a preferred distance from the ends of a protein fragment, and find multipeaked fragment length distributions similar to those found experimentally. Opening the gates in the model increases the degradation rate, increases the average length of the fragments, and increases the peak in the distribution around a length of 8-10 amino acids. This behavior is also observed in immunoproteasomes equipped with PA28. Finally, we study the effect of re-entry of processed fragments in the degradation kinetics and conclude that re-entry is only expected to affect the cleavage dynamics when short fragments enter the proteasome much faster than the original substrate. In summary, the model proposed in this study captures the known characteristics of proteasomal degradation, and can therefore help to quantify MHC class I antigen processing and presentation.

Monitoring the Distribution and Dynamics of Proteasomes in Living Cells

The proteasome is a large protease complex present in the cytoplasm and the nucleus of eukaryotic cells. This chapter describes how proteasomes in living cells can be visualized using fluorescently tagged subunits. The use of noninvasive fluorescent tags like the green fluorescent protein enables visualization of various subunits of the ubiquitin-proteasome system and prevents possible artefacts like disruption by microinjection or altered fluorescence distribution caused by fixation. Once quantitative incorporation of tagged subunits into proteasomes is ensured, the distribution of proteasome complexes can be visualized in vivo. In addition, different bleaching techniques can be applied to study the dynamics of proteasomes within the cell. Finally, we describe how proteasomes can be recruited to particular sites of degradation during various cellular conditions like aggregate formation and virus infection.

Regulation of Antigen Presentation and Cross-Presentation in the Dendritic Cell Network: Facts, Hypothesis, and Immunological Implications

Dendritic cells (DCs) are central to the maintenance of immunological tolerance and the initiation and control of immunity. The antigen-presenting properties of DCs enable them to present a sample of self and foreign proteins, contained within an organism at any given time, to the T-cell repertoire. DCs achieve this communication with T cells by displaying antigenic peptides bound to MHC I and MHC II molecules. Here we review the studies carried out over the past 15 years to characterize these antigen presentation mechanisms, emphasizing their significance in relation to DC function in vivo. The life cycles of different DC populations found in vivo are described. Furthermore, we provide a critical assessment of the studies that examine the mechanisms controlling DC MHC class II antigen presentation, which have often reached contradictory conclusions. Finally, we review findings pertaining to the biological mechanisms that enable DCs to present exogenous antigens on their MHC class I molecules, a process known as cross-presentation. Throughout, we highlight what we consider to be major knowledge gaps in the field and speculate on possible directions for future research.

Functional Role of C-Terminal Sequence Elements in the Transporter Associated with Antigen Processing

TAP delivers antigenic peptides into the endoplasmic reticulum (ER) that are subsequently bound by MHC class I molecules. TAP consists of two subunits (TAP1 and TAP2), each with a transmembrane (TMD) and a nucleotide-binding (NBD) domain. The two TAP-NBDs have distinct biochemical properties and control different steps during the peptide translocation process. We noted previously that the nonhomologous C-terminal tails of rat TAP1 and TAP2 determine the distinct functions of TAP-NBD1 and -NBD2. To identify the sequence elements responsible for the asymmetrical NBD function, we constructed chimeric rat TAP variants in which we systematically exchanged sequence regions of different length between the two TAP-NBDs. Our fine-mapping studies demonstrate that a nonhomologous region containing the alpha6/beta10-loop in conjunction with the downstream switch region is directly responsible for the functional separation of the TAP-NBDs. The alpha6/beta10-loop determines the nonsynonymous nucleotide binding of NBD1 and NBD2, whereas the switch region seems to play a critical role in regulating the functional cross-talk between the structural domains of TAP. Based on our findings, we postulate that these two sequence elements build a minimal functional unit that controls the asymmetry of the two TAP-NBDs.

MHC-bound antigens and proteomics for novel target discovery

The MHC molecules present normal as well as disease-related and pathogen-derived peptides to T cells as a way of alerting the immune system of the health status of a cell. Proteomic technologies involving immunoaffinity purification are now extensively used to separate MHC complexes from their peptide cargo, and then the petides are sequenced by tandem mass spectrometry. The identified peptides are tested as vaccine candidates for viral diseases, immunostimulants for treating cancer, and immune-tolerance-inducing agents for autoimmune disorders. One of the challenges in devising novel HLA-peptide-based immunotherapies is to decipher whether a therapeutic window exists between the induction of tumor immunity and the onset of autoimmunity, which can have dangerous sequelae. This review will cover these topics with an overview of the vast possibilities emerging in the field of proteomic analyses of MHC-bound antigens as novel targets for immunotherapy.

Endogenous presentation of CD8+ T cell epitopes from Epstein-Barr virus-encoded nuclear antigen 1

Epstein-Barr virus (EBV)–encoded nuclear antigen (EBNA)1 is thought to escape cytotoxic T lymphocyte (CTL) recognition through either self-inhibition of synthesis or by blockade of proteasomal degradation by the glycine-alanine repeat (GAr) domain. Here we show that EBNA1 has a remarkably varied cell type–dependent stability. However, these different degradation rates do not correspond to the level of major histocompatibility complex class I–restricted presentation of EBNA1 epitopes. In spite of the highly stable expression of EBNA1 in B cells, CTL epitopes derived from this protein are efficiently processed and presented to CD8⁺ T cells. Furthermore, we show that EBV-infected B cells can readily activate EBNA1-specific memory T cell responses from healthy virus carriers. Functional assays revealed that processing of these EBNA1 epitopes is proteasome and transporter associated with antigen processing dependent. We also show that the endogenous presentation of these epitopes is dependent on the newly synthesized protein rather than the long-lived stable EBNA1. Based on these observations, we propose that defective ribosomal products, not the full-length antigen, are the primary source of endogenously processed CD8⁺ T cell epitopes from EBNA1.

Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII

The proteasome is key in the cascade of proteolytic processing required for the generation of peptides presented at the cell surface to cytotoxic T lymphocytes by major histocompatibility complex class I molecules. Proteasome-dependent epitope processing is greatly improved through the interferon-gamma-induced formation of immunoproteasomes and the activator complex PA28. Tripeptidyl aminopeptidase II also has a strong effect on epitope generation. With its endoproteolytic and exoproteolytic activities, TPPII acts 'downstream' of the proteasome and relies on products released by the proteasome. The antigen-processing cascade involving different proteolytic systems raises anew the question of how antigenic peptides are generated. We therefore revisit the interferon-gamma-induced immune adaptation of the proteasome and attempt to redefine its function in connection with the emerging importance of TPPII.

Discriminating self from nonself with short peptides from large proteomes

We studied whether the peptides of nine amino acids (9-mers) that are typically used in MHC class I presentation are sufficiently unique for self:nonself discrimination. The human proteome contains 28,783 proteins, comprising 10(7) distinct 9-mers. Enumerating distinct 9-mers for a variety of microorganisms we found that the average overlap, i.e., the probability that a foreign peptide also occurs in the human self, is about 0.2%. This self:nonself overlap increased when shorter peptides were used, e.g., was 30% for 6-mers and 3% for 7-mers. Predicting all 9-mers that are expected to be cleaved by the immunoproteasome and to be translocated by TAP, we find that about 25% of the self and the nonself 9-mers are processed successfully. For the HLA-A*0201 and HLA-A*0204 alleles, we predicted which of the processed 9-mers from each proteome are expected to be presented on the MHC. Both alleles prefer to present processed 9-mers to nonprocessed 9-mers, and both have small preference to present foreign peptides. Because a number of amino acids from each 9-mer bind the MHC, and are therefore not exposed to the TCR, antigen presentation seems to involve a significant loss of information. Our results show that this is not the case because the HLA molecules are fairly specific. Removing the two anchor residues from each presented peptide, we find that the self:nonself overlap of these exposed 7-mers resembles that of 9-mers. Summarizing, the 9-mers used in MHC class I presentation tend to carry sufficient information to detect nonself peptides amongst self peptides.

Antigen bias in T cell cross-priming

Activated CD8+ T cells detect virally infected cells and tumor cells by recognition of major histocompatibility complex class I-bound peptides derived from degraded, endogenously produced proteins. In contrast, CD8+ T cell activation often occurs through interaction with specialized antigen-presenting cells displaying peptides acquired from an exogenous cellular source, a process termed cross-priming. Here, we observed a marked inefficiency in exogenous presentation of epitopes derived from signal sequences in mouse models. These data indicate that certain virus- and tumor-associated antigens may not be detected by CD8+ T cells because of impaired cross-priming. Such differences in the ability to cross-present antigens should form important considerations in vaccine design.

Messenger RNA-electroporated dendritic cells presenting MAGE-A3 simultaneously in HLA class I and class II molecules

An optimal anticancer vaccine probably requires the cooperation of both CD4(+) Th cells and CD8(+) CTLs. A promising tool in cancer immunotherapy is, therefore, the genetic modification of dendritic cells (DCs) by introducing the coding region of a tumor Ag, of which the antigenic peptides will be presented in both HLA class I and class II molecules. This can be achieved by linking the tumor Ag to the HLA class II-targeting sequence of an endosomal or lysosomal protein. In this study we compared the efficiency of the targeting signals of invariant chain, lysosome-associated membrane protein-1 (LAMP1) and DC-LAMP. Human DCs were electroporated before or after maturation with mRNA encoding unmodified enhanced green fluorescent protein (eGFP) or eGFP linked to various targeting signals. The lysosomal degradation inhibitor chloroquine was added, and eGFP expression was evaluated at different time points after electroporation. DCs were also electroporated with unmodified MAGE-A3 or MAGE-A3 linked to the targeting signals, and the presentation of MAGE-A3-derived epitopes in the context of HLA class I and class II molecules was investigated. Our data suggest that proteins linked to the different targeting signals are targeted to the lysosomes and are indeed presented in the context of HLA class I and class II molecules, but with different efficiencies. Proteins linked to the LAMP1 or DC-LAMP signal are more efficiently presented than proteins linked to the invariant chain-targeting signal. Furthermore, DCs electroporated after maturation are more efficient in Ag presentation than DCs electroporated before maturation.

A major role for TPPII in trimming proteasomal degradation products for MHC class I antigen presentation

Intracellular proteins are degraded by the proteasome, and resulting peptides surviving cytoplasmic peptidase activity can be presented by MHC class I molecules. Here, we show that intracellular aminopeptidases degrade peptides within seconds, almost irrespectively of amino acid sequence. N- but not C-terminal extension increases the half-life of peptides until they are 15 amino acids long. Beyond 15 amino acids, peptides are exclusively trimmed by the peptidase TPPII, which displays both exo- and endopeptidase activity. Surprisingly, most proteasomal degradation products are handled by TPPII before presentation by MHC class I molecules. We define three distinct proteolytic activities during antigen processing in vivo. Proteasome-generated peptides relevant for antigen presentation are mostly 15 amino acids or longer. These require TPPII activity for further trimming before becoming substrates for other peptidases and MHC class I. The heterogeneous pool of aminopeptidases will process TPPII products into MHC class I peptides and beyond.

Proteasomes Get By with Lots of Help from Their Friends

Proteasomes can't do it all. It was previously known that aminopeptidases frequently degrade proteasome-generated peptides. Now it appears that another protease, tripeptidyl peptidase II (TPP II), plays a critical role in cleaving proteasomal produced peptides into shorter peptides that can then be degraded by aminopeptidases.

Dendritic cell aggresome-like induced structures are dedicated areas for ubiquitination and storage of newly synthesized defective proteins

In response to inflammatory stimulation, dendritic cells (DCs) have a remarkable pattern of differentiation (maturation) that exhibits specific mechanisms to control antigen processing and presentation. One of these mechanisms is the sorting of polyubiquitinated proteins in large cytosolic aggregates called dendritic cell aggresome-like induced structures (DALIS). DALIS formation and maintenance are tightly linked to protein synthesis. Here, we took advantage of an antibody recognizing the antibiotic puromycin to follow the fate of improperly translated proteins, also called defective ribosomal products (DRiPs). We demonstrate that DRiPs are rapidly stored and protected from degradation in DALIS. In addition, we show that DALIS contain the ubiquitin-activating enzyme E1, the ubiquitin-conjugating enzyme E225K, and the COOH terminus of Hsp70-interacting protein ubiquitin ligase. The accumulation of these enzymes in the central area of DALIS defines specific functional sites where initial DRiP incorporation and ubiquitination occur. Therefore, DCs are able to regulate DRiP degradation in response to pathogen-associated motifs, a capacity likely to be important for their immune functions.

Fluorescent probes for proteolysis: tools for drug discovery

Our body contains many different protease and proteolytic systems that are involved in the recycling of proteins into amino acids, and also in a multitude of regulatory events inside and outside cells. Proteases are prominent drug targets because of their well-defined chemistry and their implication in a large number of diseases, such as cancer, neurodegeneration, arteriosclerosis, inflammation and infection.

Fluorescent reporter substrates can be used to directly probe the activities of proteases in their natural environment — that is, in cells and organisms. Conceptually different strategies have been used for this purpose depending on the location and the nature of the protease of interest.

Fluorescent reporters for the ubiquitin–proteasome system have been generated by linking constitutively active degradation signals to green fluorescent protein (GFP). These GFP-based substrates can be used for functional analysis of the ubiquitin–proteasome system in cells and transgenic animals.

A collection of different proteases is involved in degradation of small peptide fragments. This process can be followed in real time in living cells by confocal laser scanning microscopy after microinjection of internally quenched peptide substrates.

Extracellular and lysosomal proteases have the advantage that they are accessible for membrane-impermeable reporter substrates. Near-infrared fluorescence (NIRF) substrates are quenched fluorescent peptides that, because of their near-infrared excitation, can be readily detected in living animals and used for in vivo monitoring of, for example, lysosomal cathepsins or surface matrix metalloproteinases.

By combining specific pairs of fluorescent proteins (GFP and its variants with shifted excitation and emission spectra) in fusion proteins, fluorescence energy transfer (FRET) reporter substrates have been generated for initiator and effector caspases.

A fluorescent intracellular reporter for human immunodeficiency virus (HIV-1) protease activity was constructed by fusing a protease precursor protein composed of HIV-1 protease and GFP. Cells will only survive and emit fluorescence when the toxic protease activity is sufficiently blocked by drugs.

The diffusion rate of the endoplasmic reticulum-resident peptide transporter complex TAP correlates with activity and thus cytosolic peptide levels. By measuring the diffusion of TAP–GFP fusions with fluorescence recovery after photobleaching (FRAP), the kinetics of peptide generation can be followed in living cells.

Cells contain numerous proteases, which are found at many different locations. These proteases recognize an even larger number of different substrates and are involved in almost every process in the cell. Aberrations in proteolysis are linked to a plethora of diseases, such as cancer, inflammation, arteriosclerosis, neurodegeneration and infection. Because of their well-defined chemistry and key role in pathologies, proteases have been important targets for drug development. Recent progress in the development of fluorescent probes has opened up the possibility of visualizing protease activities in the natural environment of the cell. We will describe various strategies to follow protease activities in cells and organisms.

Immune recognition of a human renal cancer antigen through post-translational protein splicing

Cytotoxic T lymphocytes (CTLs) detect and destroy cells displaying class I molecules of the major histocompatibility complex (MHC) that present oligopeptides derived from aberrant self or foreign proteins. Most class I peptide ligands are created from proteins that are degraded by proteasomes and transported, by the transporter associated with antigen processing, from the cytosol into the endoplasmic reticulum, where peptides bind MHC class I molecules and are conveyed to the cell surface. C2 CTLs, cloned from human CTLs infiltrating a renal cell carcinoma, kill cancer cells overexpressing fibroblast growth factor-5 (FGF-5). Here we show that C2 cells recognize human leukocyte antigen-A3 MHC class I molecules presenting a nine-residue FGF-5 peptide generated by protein splicing. This process, previously described strictly in plants and unicellular organisms, entails post-translational excision of a polypeptide segment followed by ligation of the newly liberated carboxy-terminal and amino-terminal residues. The occurrence of protein splicing in vertebrates has important implications for the complexity of the vertebrate proteome and for the immune recognition of self and foreign peptides.