Expression of housekeeping and immunoproteasome subunit genes is differentially regulated in positively and negatively selecting thymic stroma subsets

The expression of housekeeping and/or immunoproteasomes in isolated thymic stroma subsets has so far not been analyzed but may have important consequences for self peptide repertoires presented by MHC class I molecules during positive and negative thymic selection. Here we determined the expression of housekeeping and immunoproteasome beta subunits and of PA28 in positively and negatively selecting stroma subsets. Positively selecting cortical thymic epithelial cells (cTEC) expressed only housekeeping but no immunoproteasome beta subunit mRNA and proteins. However, immunoproteasome beta subunits could be induced in cTEC by infection with Listeria monocytogenes or injection of IFN-gamma. In negatively selecting stroma including medullary epithelial cells and dendritic cells, incomplete and low representation of housekeeping beta subunit proteins but high and complete expression of immunoproteasome beta subunit proteins suggests absence of proper housekeeping proteasomes and predominance of immunoproteasomes. Expression of immunoproteasome beta subunits in negatively selecting stroma was independent of IFN-gamma receptor as shown in knockout (KO) mice. Absence of LMP2 altered thymic selection of the MHC class I-restricted transgenic P14 TCR in KO mice. The data suggest that negative selection may primarily involve immunoproteasome peptide repertoires and that peripheral infection may influence peptide repertoires involved in positive selection.     

Proteasome and peptidase function in MHC-class-I-mediated antigen presentation

MHC-class-I-presented peptides are predominantly generated by the proteasome system. IFN-gamma strongly influences the processing efficiency by inducing immunoproteasome formation and proteasome activator PA28 synthesis. Depending on the protein substrate, the presence of immunoproteasomes and PA28 influence epitope liberation either positively or negatively. Abundantly occurring defective ribosomal products are a major source for proteasome-dependent antigen processing; however, antigen presentation is relatively inefficient. This is in part due to the existence of a panel of cytosolic aminopeptidases, such as bleomycin hydrolase (BH), puromycin-sensitive aminopeptidase (PSA) and thimet oligoendopeptidase (TOP), that can destroy epitopes or their precursors. Other aminopeptidases, such as leucine aminopeptidase (LAP) and endoplasmic reticulum aminopeptidase 1 (ERAP 1), can trim epitope precursors from the amino terminus to their correct size for MHC class I binding to enhance antigen presentation. Recent evidence suggests that tripeptidyl peptidase II (TPPII), a large peptidase with exo-and endo-proteolytic activities, is also involved in antigen processing and may generate a specific set of MHC class I epitopes.     

Interferon-γ, the functional plasticity of the ubiquitin–proteasome system, and MHC class I antigen processing

Summary: The proteasome system is a central component of a cascade of proteolytic processing steps required to generate antigenic peptides presented at the cell surface to cytotoxic T lymphocytes by major histocompatibility complex (MHC) class I molecules. The nascent protein pool or DRiPs (defective ribosomal products) appear to represent an important source for MHC class I epitopes. Owing to the destructive activities of aminopeptidases in the cytosol, at most 1% of the peptides generated by the ubiquitin–proteasome system seems to be made available to the immune system. Interferon‐γ (IFN‐γ) helps to override these limitations by the formation of immunoproteasomes, the activator complex PA28, and the induction of several aminopeptidases. Both immunoproteasomes and PA28 use cleavage sites already used by constitutive proteasomes but with altered and in some cases dramatically enhanced frequency. Therefore, two proteolytic cascades appear to have evolved to provide MHC class I epitopes. The ‘constitutive proteolytic cascade’ is designed to efficiently degrade proteins to single amino acid residues, allowing only a small percentage of peptides to be presented at the cell surface. In contrast, the IFN‐γ‐controlled proteolytic cascade generates larger amounts of appropriate antigenic peptides, assuring more peptides to overcome the proteolytic restrictions of the constitutive system, thereby enhancing MHC class I antigen presentation.     

The proteasome regulator PA28alpha/beta can enhance antigen presentation without affecting 20S proteasome subunit composition

PA28alpha/beta is a regulatory complex of the 20S proteasome which consists of two IFN-gamma inducible subunits. Both subunits, alpha and beta, contribute equally to the formation of hexa- or heptameric rings which can associate with the 20S proteasome. Previously, we have shown that overexpression of the PA28alpha subunit enhanced the MHC class I-restricted presentation of two viral epitopes and that purified PA28alpha/beta accelerated T cell epitope generation by the 20S proteasome in vitro, indicating a role for PA28alpha/beta in antigen presentation. This conclusion was recently confirmed in PA28beta gene targeted mice which were severely deficient in MHC class I-restricted antigen presentation. These mice displayed a defect in the assembly of immunoproteasomes, suggesting that a lack of the proteasome subunits LMP2, LMP7, and MECL-1 may account for the deficiency in antigen presentation. In this study we investigated whether the effect of PA28alpha/beta on antigen presentation is dependent on a change of proteasome subunit composition. We have analyzed the assembly and subunit composition of proteasomes in fibroblast transfectants overexpressing both, alpha and beta subunits of PA28. In these transfectants we found a marked enhancement in the presentation of the immunodominant H-2Ld-restricted pp89 epitope of murine cytomegalovirus, although the 20S proteasome composition was the same as in recipient cells. We, therefore, conclude that PA28alpha/beta can enhance antigen processing independently of changes in 20S proteasome subunit composition or assembly.     

Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells

By stimulating human lymphocytes with an autologous renal carcinoma, we obtained CTL recognizing an antigen derived from a novel, ubiquitous protein. The CTL failed to lyse autologous EBV-transformed B cells, even though the latter express the protein. This is due to the presence in these cells of immunoproteasomes, which, unlike standard proteasomes, cannot produce the antigenic peptide. We show that dendritic cells also carry immunoproteasomes and fail to present this antigen. This may explain why the relevant CTL escape thymic deletion and are not regularly activated in the periphery. Lack of cleavage by the immunoproteasome was also observed for melanoma differentiation antigen Melan-A26-35/HLA-A2, currently used for antitumoral vaccination. For immunization with such antigens, proteins should be less suitable than peptides, which do not require proteasome digestion in dendritic cells.     

Immunoproteasomes and immunosenescence

Aging is a complex process which is accompanied with the decline and the reshaping of different functions of the body. In particular the immune system is characterized, during ageing (immunosenescence) by a remodeling of innate immunity (well preserved, up-regulated) and clonotypical immunity (severely altered) and by the occurrence of a chronic inflammatory process (inflammaging) which are, at least in part, genetically controlled. In this scenario, it can be anticipated that a crucial role is played by age-related structural and functional alterations and modifications of proteasomes and immunoproteasomes, the last being a key component of antigen processing and MHC class I antigen presentation. A variety of experimental data are available, suggesting that proteasomes are affected by age, and that in centenarians they are relatively preserved. On the contrary, few data are available on immunoproteasomes, likely as a consequence of the poverty of suitable cellular models. Lymphoblastoid cell lines from EBV immortalized B cells from old donors is envisaged as a possible model for the study of immunoproteasomes in humans and their changes with age. Thus, basic questions such as those related to possible consequences, for immune responses in infectious diseases and cancer, of age-related alterations of antigen processing and presenting, change with age of self-antigen repertoire, and the genetic basis of immunoproteasome activity and its change with age, remain largely unanswered.     

Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation

Immunoproteasomes are considered to be optimised to process Ags and to alter the peptide repertoire by generating a qualitatively different set of MHC class I epitopes. Whether the immunoproteasome at the biochemical level, influence the quality rather than the quantity of the immuno‐genic peptide pool is still unclear. Here, we quantified the cleavage‐site usage by human standard‐ and immunoproteasomes, and proteasomes from immuno‐subunit‐deficient mice, as well as the peptides generated from model polypeptides. We show in this study that the different proteasome isoforms can exert significant quantitative differences in the cleavage‐site usage and MHC class I restricted epitope production. However, independent of the proteasome isoform and substrates studied, no evidence was obtained for the abolishment of the specific cleavage‐site usage, or for differences in the quality of the peptides generated. Thus, we conclude that the observed differences in MHC class I restricted Ag presentation between standard‐ and immunoproteasomes are due to quantitative differences in the proteasome‐generated antigenic peptides.     

The importance of the proteasome and subsequent proteolytic steps in the generation of antigenic peptides

Three different proteolytic processes have been shown to be important in the generation of antigenic peptides displayed on MHC-class I molecules. The great majority of these peoptides are derived from oligopeptides produced during the degradation of intracellular proteins by the ubiquitin-proteasome pathway. Novel methods were developed to follow this process in vitro. When pure 26S proteasomes degrade the model substrate, ovalbumin, they produce the immunodominant peptide, SIINFEKL, occasionally, but more often an N-extended form of SIINFEKL. Interferon-gamma stimulates antigen presentation in part by inducing new forms of the proteasome that are more efficient in antigen presentation, and in vitro these immunoproteasomes specifically produce more of the N-extended versions of SIINFEKL. In addition, gamma-interferon induces a novel 26S complex containing the 19S and 20S particles and the proteasome activator, PA28, which we show cleaves proteins in distinct ways. In vivo studies established that proteasomal cleavages produce the C-termini of antigenic peptides, but not their N-termini, which can be formed efficiently by aminopeptidases that trim longer proteasomal products to the presented epitopes. gamma-interferon stimulates this trimming process by inducing in the cytosol leucine aminopeptidase and a novel aminopeptidase in the ER. Peptides released by proteasomes, including antigenic peptides, are labile in cytosolic extracts, and most of the longer proteasome products are rapidly cleaved by the cytosolic enzyme, thymet oligopeptidase (TOP). If cells express large amounts of TOP, class I presentation decreases, and if TOP is inhibited, presentation increases. Thus, peptide degradation in the cytosol appears to limit the efficiency of antigen presentation.     

The proteasome immunosubunits,PA28 and ER‐aminopeptidase 1 protect melanoma cells from efficient MART‐126‐35‐specific T‐cell recognition

The immunodominant MART‐1_26(27)‐35 epitope, liberated from the differentiation antigen melanoma antigen recognized by T cells/melanoma antigen A (MART‐1/Melan‐A), has been frequently targeted in melanoma immunotherapy, but with limited clinical success. Previous studies suggested that this is in part due to an insufficient peptide supply and epitope presentation, since proteasomes containing the immunosubunits β5i/LMP7 (LMP, low molecular weight protein) or β1i/LMP2 and β5i/LMP7 interfere with MART‐1_26‐35 epitope generation in tumor cells. Here, we demonstrate that in addition the IFN‐γ‐inducible proteasome subunit β2i/MECL‐1 (multicatalytic endopeptidase complex‐like 1), proteasome activator 28 (PA28), and ER‐resident aminopeptidase 1 (ERAP1) impair MART‐1_26‐35 epitope generation. β2i/MECL‐1 and PA28 negatively affect C‐ and N‐terminal cleavage and therefore epitope liberation from the proteasome, whereas ERAP1 destroys the MART‐1_26‐35 epitope by overtrimming activity. Constitutive expression of PA28 and ERAP1 in melanoma cells indicate that both interfere with MART‐1_26‐35 epitope generation even in the absence of IFN‐γ. In summary, our results provide first evidence that activities of different antigen‐processing components contribute to an inefficient MART‐1_26‐35 epitope presentation, suggesting the tumor cell's proteolytic machinery might have an important impact on the outcome of epitope‐specific immunotherapies.     

Differences in the production of spliced antigenic peptides by the standard proteasome and the immunoproteasome

Peptide splicing allows the production of antigenic peptides composed of two fragments initially non-contiguous in the parental protein. The proposed mechanism of splicing is a transpeptidation occurring within the proteasome. Three spliced peptides, derived from FGF-5, melanoma protein gp100 and nuclear protein SP110, have been described. Here, we compared the production of these spliced peptides by the standard proteasome and the immunoproteasome. Differential isotope labelling was used to quantify (by mass spectrometry) the fragments contained in digests obtained with precursor peptides and purified proteasomes. The results show that both the standard and the immunoproteasomes can produce spliced peptides although they differ in their efficiency of production of each peptide. The FGF-5 and gp100 peptides are more efficiently produced by the standard proteasome, whereas the SP110 peptide is more efficiently produced by the immunoproteasome. This seems to result from differences in the production of the two splicing partners, which depends on a balance between cleavages liberating or destroying those fragments. By showing that splicing depends on the efficiency of production of the splicing partners, these results also support the transpeptidation model of peptide splicing. Furthermore, given the presence of immunoproteasomes in dendritic cells and cells exposed to IFN-γ, the findings may be relevant for vaccine design.     

PA28 and the proteasome immunosubunits play a central and independent role in the production of MHC class I-binding peptides in vivo

Proteasomes play a fundamental role in the processing of intracellular antigens into peptides that bind to MHC class I molecules for the presentation of CD8(+) T cells. Three IFN-γ-inducible catalytic proteasome (immuno)subunits as well as the IFN-γ-inducible proteasome activator PA28 dramatically accelerate the generation of a subset of MHC class I-presented antigenic peptides. To determine whether these IFN-γ-inducible proteasome components play a compounded role in antigen processing, we generated mice lacking both PA28 and immunosubunits β5i/LMP7 and β2i/MECL-1. Analyses of MHC class I cell-surface levels ex vivo demonstrated that PA28 deficiency reduced the production of MHC class I-binding peptides both in cells with and without immunosubunits, in the latter cells further decreasing an already diminished production of MHC ligands in the absence of immunoproteasomes. In contrast, the immunosubunits but not PA28 appeared to be of critical importance for the induction of CD8(+) T-cell responses to multiple dominant Influenza and Listeria-derived epitopes. Taken together, our data demonstrate that PA28 and the proteasome immunosubunits use fundamentally different mechanisms to enhance the supply of MHC class I-binding peptides; however, only the immunosubunit-imposed effects on proteolytic epitope processing appear to have substantial influence on the specificity of pathogen-specific CD8(+) T-cell responses.     

Immunoproteasomes edit tumors,which then escapes immune recognition

In 1985, John Monaco—the discoverer of LMP‐2 and ‐7, the inducible components of the immunoproteasome—asked his advanced immunology class as to why the MHC region contained not only structural genes, but several others as well, whose functions were then unknown. As we drew a blank, he quipped: perchance because many of the MHC genes are induced by IFN‐γ! The ensuing three decades have witnessed the unveiling of the profound fundamental and clinical implications of that classroom tête–à–tête. Amongst its multitudinous effects, IFN‐γ induces genes enhancing antigen processing and presentation to T cells; such as those encoding cellular proteases and activators of proteases. In this issue, Keller et al. [Eur. J. Immunol. 2015. 45 : 3257–3268] demonstrate that the limited success of MART‐1/Melan‐A‐targeted immunotherapy in melanoma patients could be due to inefficient MART‐1_26—35 presentation, owing to the proteolytic activities of IFN‐γ‐inducible β2i/MECL‐1, proteasome activator 28 (PA28), and endoplasmic reticulum‐associated aminopeptidase‐associated with antigen processing (ERAP). Specifically, whilst β2i and PA28 impede MART‐1_26—35 liberation from its precursor protein, ERAP‐1 degrades this epitope. Hence, critical to effective cancer immunotherapy is deep knowledge of T‐cell‐targeted tumor antigens and how cellular proteases generate protective epitope(s) from them, or destroy them.     

Bipartite regulation of different components of the MHC class I antigen-processing machinery during dendritic cell maturation.

Dendritic cells (DC) are professional antigen-presenting cells (APC) which proceed from immature to a mature stage during their final differentiation. Immature DC are highly effective in terms of antigen uptake and processing, whereas mature DC become potent immunostimulatory cells. Until now, the expression profiles of the major components of the MHC class I antigen-processing machinery (APM) during DC development have not been well characterized. In this study, the mRNA and protein expression levels of the IFN-gamma inducible proteasome subunits, of the proteasome activators PA28, and of key components required for peptide transport and MHC class I-peptide complex assembly have been evaluated in immature and mature stages of human monocyte-derived DC using semiquantitative RT-PCR and Western blot analyses. The IFN-gamma-responsive immunoproteasome subunits LMP2, LMP7 and MECL1 are up-regulated in immature DC, whereas the other components of the MHC class I presentation machinery, such as PA28, TAP, tapasin, and HLA heavy and light chains, were found to be more abundant in mature DC. These findings support the hypothesis that immature DC produced by the differentiation of monocytes in response to IL-4 and granulocyte macrophage colony stimulating factor first increase their capacity to capture antigens and process them into peptides, thereby switching from housekeeping to immunoproteasomes, while mature DC rather up-regulate the components required for peptide translocation and MHC class I-peptide complex formation, and thus specialize in antigen presentation. Our results establish that MHC class I, like MHC class II surface expression, is markedly regulated during DC development and maturation.     

Adenovirus E1A interacts directly with, and regulates the level of expression of, the immunoproteasome component MECL1

Proteasomes represent the major non-lysosomal mechanism responsible for the degradation of proteins. Following interferon γ treatment 3 proteasome subunits are replaced producing immunoproteasomes. Adenovirus E1A interacts with components of the 20S and 26S proteasome and can affect presentation of peptides. In light of these observations we investigated the relationship of AdE1A to the immunoproteasome. AdE1A interacts with the immunoproteasome subunit, MECL1. In contrast, AdE1A binds poorly to the proteasome β2 subunit which is replaced by MECL1 in the conversion of proteasomes to immunoproteasomes. Binding sites on E1A for MECL1 correspond to the N-terminal region and conserved region 3. Furthermore, AdE1A causes down-regulation of MECL1 expression, as well as LMP2 and LMP7, induced by interferon γ treatment during Ad infections or following transient transfection. Consistent with previous reports AdE1A reduced IFNγ-stimulated STAT1 phosphorylation which appeared to be responsible for its ability to reduce expression of immunoproteasome subunits.     

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.     

Dendritic cells up-regulate immunoproteasomes and the proteasome regulator PA28 during maturation

Dendritic cells (DC) are highly specialized professional antigen presenting cells which are pivotal for the initiation and control of the cytotoxic T cell response. Upon stimulation by cytokines, bacteria, or CD40L DC undergo a maturation process from an antigen-receptive state to a state of optimal stimulation of T cells. We investigated the composition of proteasomes of DC derived from human peripheral blood monocytes before and after stimulation by CD40L, LPS, or proinflammatory cytokines (TNF-alpha + IL-6 + IL-1beta). Immunoprecipitation of proteasomes and analysis on two-dimensional gels revealed that during maturation the inducible proteasome subunits LMP2, LMP7, and MECL-1 are up-regulated and that the neosynthesis of proteasomes is switched exclusively to the production of immunoproteasomes containing these subunits. The proteasome regulator PA28 is markedly up-regulated in mature DC and in addition a so - far unidentified 21-kDa protein co-precipitates with the proteasome in LPS - stimulated DC. These changes in proteasome composition may be functionally linked to special properties of DC like MHC class I up-regulation or cross-priming. Our findings imply that the spectrum of class I-bound peptides may change after DC maturation which could be relevant for the design of DC - based vaccines.     

Proteasome composition in immune cells implies special immune-cell-specific immunoproteasome function

Immunoproteasomes are a special class of proteasomes, which can be induced with IFN-γ in an inflammatory environment. In recent years, it became evident that certain immune cell types constitutively express high levels of immunoproteasomes. However, information regarding the basal expression of proteolytically active immunoproteasome subunits in different types of immune cells is still rare. Hence, we quantified standard proteasome subunits (β1c, β2c, β5c) and immunoproteasome subunits (LMP2, MECL-1, LMP7) in the major murine (CD4⁺ T cells, CD8⁺ T cells, CD19⁺ B cells, CD11c⁺ dendritic cells, CD49d⁺ natural killer cells, Ly-6G⁺ neutrophils) and human immune cell (CD4⁺ T cells, CD8⁺ T cells, CD19⁺ B cells, CD1c⁺CD141⁺ myeloid dendritic cells, CD56⁺ natural killer cells, granulocytes) subsets. The different human immune cell types were isolated from peripheral blood and the murine immune cell subsets from spleen. We found that proteasomes of most immune cell subsets mainly consist of immunoproteasome subunits. Our data will serve as a reference and guideline for immunoproteasome expression and imply a special role of immunoproteasomes in immune cells.     

Immunoproteasomes at the interface of innate and adaptive immune responses: two faces of one enzyme

The immunoproteasome is a specific proteasome isoform induced by interferons. Its proteolytic function has been almost exclusively connected with the adaptive immune response and improved MHC class I antigen presentation. However, IFN-signaling also exposes cells to oxidative stress with concomitant production of nascent-oxidant damaged poly-ubiquitylated proteins. Here we discuss how immunoproteasomes protect cells against accumulation of toxic protein-aggregates and how i-proteasomes dysfunction associates with different diseases. We propose that the immunoproteasome has a central function at the interface between the innate and adaptive immune response and that its predominant protective innate function determines its favorable role in the adaptive immune response.