Critical role of endoplasmic reticulum aminopeptidase 1 in determining the length and sequence of peptides bound and presented by HLA-B27

OBJECTIVE

HLA-B27 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are the two strongest genetic factors predisposing to ankylosing spondylitis (AS). A key aminopeptidase in class I major histocompatibility complex presentation, ERAP1 potentially contributes to the pathogenesis of AS by altering HLA-B27 peptide presentation. The aim of this study was to analyze the effects of ERAP1 on the HLA-B27 peptide repertoire and peptide presentation to cytotoxic T lymphocytes (CTLs).

METHODS

ERAP1-silenced and -competent HeLa.B27 and C1R.B27 cells were isotope-labeled, mixed, lysed, and then immunoprecipitated using W6/32 or ME1 antibodies. Peptides bound to HLA-B27 were eluted and analyzed by tandem mass spectrometry. Selected peptides were synthesized and tested for HLA-B27 binding ability. The effect of ERAP1 silencing/mutation on presentation of an immunodominant viral HLA-B27 epitope, KK10, to CTLs was also studied.

RESULTS

In both HeLa.B27 and C1R.B27 cells, the proportion of 9-mer HLA-B27-bound peptides was decreased by ERAP1 silencing, whereas the percentages of longer peptides (11-13 mer) were increased. Surprisingly, following ERAP1 silencing, C-terminally extended peptides were readily identified. These were better able to bind to HLA-B27 than were N-terminally extended peptides lacking an arginine at position 2. In both HeLa.B27 cells and mouse fibroblasts expressing HLA-B27, the absence of ERAP1 reduced peptide recognition by HLA-B27-restricted KK10-specific CTLs following infection with recombinant vaccinia virus or transfection with minigenes expressing KK10 precursors. Presence of an AS-protective variant of ERAP1, K528R, as compared to wild-type ERAP1, reduced the peptide recognition by KK10 CTLs following transfection with extended KK10 minigenes.

CONCLUSION

These results show that ERAP1 directly alters peptide binding and presentation by HLA-B27, thus demonstrating a potential pathogenic mechanism in AS. Inhibition of ERAP1 could potentially be used for treatment of AS and other ERAP1-associated diseases.

Monitoring peptide processing for MHC class I molecules in the endoplasmic reticulum

Classical MHC class I molecules open a window into the cell by presenting intracellular peptides (pMHC I) on the surface. The peptides are used for immune surveillance by circulating CD8+ T and NK cells to detect and eliminate infected or tumor cells. Not surprisingly, viruses and tumor cells have evolved immune evasion mechanisms to keep the window shades down and the cytotoxic cells oblivious to their presence. Here, we review counter mechanisms that nevertheless allow the immune system to detect and eliminate cells unable to properly process antigenic peptides in the endoplasmic reticulum.

ERAAP and tapasin independently edit the amino and carboxyl termini of MHC class I peptides

Effective CD8(+) T cell responses depend on presentation of a stable peptide repertoire by MHC class I (MHC I) molecules on the cell surface. The overall quality of peptide-MHC I complexes (pMHC I) is determined by poorly understood mechanisms that generate and load peptides with appropriate consensus motifs onto MHC I. In this article, we show that both tapasin (Tpn), a key component of the peptide loading complex, and the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP) are quintessential editors of distinct structural features of the peptide repertoire. We carried out reciprocal immunization of wild-type mice with cells from Tpn- or ERAAP-deficient mice. Specificity analysis of T cell responses showed that absence of Tpn or ERAAP independently altered the peptide repertoire by causing loss as well as gain of new pMHC I. Changes in amino acid sequences of MHC-bound peptides revealed that ERAAP and Tpn, respectively, defined the characteristic amino and carboxy termini of canonical MHC I peptides. Thus, the optimal pMHC I repertoire is produced by two distinct peptide editing steps in the endoplasmic reticulum.

Location of the CD8 T cell epitope within the antigenic precursor determines immunogenicity and protection against the Toxoplasma gondii parasite

CD8 T cells protect the host from disease caused by intracellular pathogens, such as the Toxoplasma gondii (T. gondii) protozoan parasite. Despite the complexity of the T. gondii proteome, CD8 T cell responses are restricted to only a small number of peptide epitopes derived from a limited set of antigenic precursors. This phenomenon is known as immunodominance and is key to effective vaccine design. However, the mechanisms that determine the immunogenicity and immunodominance hierarchy of parasite antigens are not well understood. Here, using genetically modified parasites, we show that parasite burden is controlled by the immunodominant GRA6-specific CD8 T cell response but not by responses to the subdominant GRA4- and ROP7-derived epitopes. Remarkably, optimal processing and immunodominance were determined by the location of the peptide epitope at the C-terminus of the GRA6 antigenic precursor. In contrast, immunodominance could not be explained by the peptide affinity for the MHC I molecule or the frequency of T cell precursors in the naive animals. Our results reveal the molecular requirements for optimal presentation of an intracellular parasite antigen and for eliciting protective CD8 T cells.

Brain microvessel cross-presentation is a hallmark of experimental cerebral malaria

Cerebral malaria is a devastating complication of Plasmodium falciparum infection. Its pathogenesis is complex, involving both parasite- and immune-mediated events. CD8⁺ T cells play an effector role in murine experimental cerebral malaria (ECM) induced by Plasmodium berghei ANKA (PbA) infection. We have identified a highly immunogenic CD8 epitope in glideosome-associated protein 50 that is conserved across rodent malaria species. Epitope-specific CD8⁺ T cells are induced during PbA infection, migrating to the brain just before neurological signs manifest. They are functional, cytotoxic and can damage the blood–brain barrier in vivo. Such CD8⁺ T cells are also found in the brain during infection with parasite strains/species that do not induce neuropathology. We demonstrate here that PbA infection causes brain microvessels to cross-present parasite antigen, while non-ECM-causing parasites do not. Further, treatment with fast-acting anti-malarial drugs before the onset of ECM reduces parasite load and thus antigen presentation in the brain, preventing ECM death. Thus our data suggest that combined therapies targeting both the parasite and host antigen-presenting cells may improve the outcome of CM patients.

Presentation of cryptic peptides by MHC I molecules is enhanced by inflammatory stimuli. (P5003)

Cytolytic T cells eliminate infected cells by recognizing intracellular peptides presented by MHC class I molecules. The antigenic peptides are derived primarily from newly synthesized proteins including those produced by cryptic translation. Previous studies have shown that in addition to the canonical AUG codon, translation can be initiated at non-AUG codons . Furthermore, translation initiation at non-AUG codons such as CUG is mechanistically distinct from canonical translation initiation as it is resistant to protein synthesis inhibitors that cause global translation shutdown. Here, we show that Toll-like receptor (TLR) signaling pathways involved in pathogen recognition enhance presentation of the cryptic peptides. Moreover, infection of bone-marrow derived macrophages with MCMV, influenza viruses or pro-inflammatory cytokines also enhances cryptic peptide presentation. Thus, translation and presentation of cryptic peptides may allow the immune system to detect intracellular pathogens that inhibit host translation and presentation of peptides from conventional sources.

Immune surveillance for ERAAP dysfunction

The ER aminopeptidase associated with antigen processing, ERAAP (or ERAP1), is essential for trimming peptides that are presented by MHC class I molecules. ERAP1 is inhibited by human cytomegalovirus, and ERAP1 polymorphisms are associated with autoimmune diseases. How the immune system detects ERAAP dysfunction, however, is unknown. We have shown previously that ERAAP-deficient cells present an immunogenic pMHC I repertoire, that elicits CD8+ T cell response in WT mice. Additionally, we discovered that the WT CD8+ T cells recognized novel peptides presented by non-classical, or MHC class Ib, molecules on ERAAP-deficient cells. The MHC Ib restricted WT CD8 T cells eliminated ERAAP-deficient cells in vitro and in vivo. We identified the FL9 peptide, presented by Qa-1(b), a MHC class Ib molecule exclusively on ERAAP-deficient cells. Remarkably, T cells specific for the FL9-Qa-1(b) complex were frequent in naïve WT mice, and had an antigen-experienced phenotype. Thus, novel non-classical pQa-1(b) complexes direct cytotoxic T cells to target cells with defective peptide processing in the endoplasmic reticulum. Here, we discuss the implications of our findings, and the possible roles of pMHC Ib-specific T cells in immune surveillance for ERAAP dysfunction.

Biochemical analysis of naturally processed antigenic peptides presented by MHC class I molecules

Immune surveillance of infected or tumor cells by CD8(+) T cells requires that MHC class I molecules present a diverse repertoire of peptides on the cell surface. Even a few copies of individual peptides among this mixture are sufficient for recognition by the antigen receptors of appropriate CD8(+) T cells. Here we describe a method for biochemical analysis of the naturally processed peptides in living cells. The peptide mixture in cell extracts is fractionated using reverse phase high performance liquid chromatography and detected by the activation of CD8(+) T cell hybridomas. The results provide information on the structure and amount of the peptides and yield insights into the mechanisms that generate the naturally processed peptides.

Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I

Effective immune surveillance by cytotoxic T cells requires newly synthesized polypeptides for presentation by major histocompatibility complex (MHC) class I molecules. These polypeptides are produced not only from conventional AUG-initiated, but also from cryptic non-AUG-initiated, reading frames by distinct translational mechanisms. Biochemical analysis of ribosomal initiation complexes at CUG versus AUG initiation codons revealed that cells use an elongator leucine-bound transfer RNA (Leu-tRNA) to initiate translation at cryptic CUG start codons. CUG/Leu-tRNA initiation was independent of the canonical initiator tRNA (AUG/Met-tRNA(i)(Met)) pathway but required expression of eukaryotic initiation factor 2A. Thus, a tRNA-based translation initiation mechanism allows non-AUG-initiated protein synthesis and supplies peptides for presentation by MHC class I molecules.

Equal Immune Rights For All Polypeptides (106.38)

Effective immune surveillance requires that MHC class I molecules display a peptide repertoire on the surface representing all cellular proteins. How the peptide repertoire can be comprehensive despite large differences in abundance and stability of individual proteins is not known. We show here that peptide presentation by MHC I molecules is strongly influenced by the pioneer round of translation (PRT) associated with nonsense mediated decay (NMD) of mRNAs. The PRT allows cells to detect and eliminate aberrant mRNAs containing premature stop codons. Inhibition of PRT by knock-down of CBP80, a unique cap-binding protein reduced peptide presentation by MHC class I molecules on the cell surface without affecting global protein synthesis. On the other hand, introduction of premature stop codons changed mRNA stability without affecting peptide presentation by MHC I on the cell surface. Thus, the pioneer round of translation could be used to derive peptides presentation by MHC I molecules to generate a comprehensive display of virtually all endogenous proteins.

The mechanism of resistance to parasite infection. (100.14)

The parasite, Toxoplasma gondii (T. gondii) can cause severe disease in immunocompromised humans. Susceptibility to T. gondii is also linked to the MHC haplotype: B10.D2 (H-2d) mice are relatively resistant to T. gondii infection than C57Bl/6 mice (B6, H-2b). CD8 T cells, activated by MHC molecules, are known to be that primary mediators of protection from T. gondii, and it is possible that differences in their responses might determine susceptibility to infection. Indeed, in H-2d mice, we recently identified the key immunodominant peptide, HF10, contained in the GRA6 protein that elicited protective CD8 T cell responses. In contrast, we show here that the CD8 T cell response to T. gondii in susceptible B6 mice is weaker and specific for a distinct peptide derived from the ROP5 protein. Furthermore, unlike the HF10 peptide that generated protective CD8 T cells in H-2d mice, immunization with the ROP5 peptide failed to diminish the parasite burden in chronically infected H-2b mice. Thus, susceptibility to T. gondii correlates with MHC-linked processing of specific parasite proteins that elicit differential CD8 T cell responses in mice.

The role of ERAAP polymorphisms in the autoimmune disease Ankylosing Spondylitis (100.17)

Ankylosing spondylitis (AS) is a chronic inflammatory joint disease of the axial skeleton, ultimately leading to fusion of the spine. For over three decades it has been known that the MHC class I molecule HLA-B27 is strongly associated with AS. In addition, the ER-resident aminopeptidase ERAAP (or ERAP1) was recently shown to be associated with as much as 26% of the risk for developing AS in HLA-B27 positive individuals. Multiple non-synonymous SNPs have been identified in the ERAAP gene that increase the risk of AS, but the functional significance of these polymorphisms is not known. The ERAAP protease is an essential component of the MHC class I pathway where it trims antigenic peptides in the ER. The significant association of both HLA-B27 and ERAAP with AS suggests that an altered MHC class I antigen processing pathway could play an important role in this partially T cell-mediated disease. To test this hypothesis we have analyzed the antigen processing capacity of several polymorphic forms of human ERAAP in ERAAP-deficient cells. All the polymorphic ERAAP constructs tested were enzymatically active and able to trim model antigenic peptides in different cell lines, with either no or minor differences in the quantity of total epitopes generated. We will discuss the implications of these findings.

A novel MHC class Ib-mediated immune surveillance mechanism detects the absence of ERAAP (100.16)

Immune surveillance mechanisms detect failures in vital parts of the host immune system, such as in the antigen processing pathway. The ER aminopeptidase associated with antigen processing, ERAAP, is an essential component of the antigen processing pathway, and is required to generate the final peptides presented by MHC class I molecules. It has been unclear how the immune system detects deficiencies in ERAAP function, and here we describe a potential mechanism to do so. Non-classical MHC class I, or MHC class Ib, molecules present novel peptides in ERAAP-deficient cells, and elicit potent CD8 T cell responses in wild-type mice. Using these CD8 T cells as a probe, we identified a novel peptide presented by Qa-1b. FL9-Qa-1b-specific CD8 T cells can be readily detected in naïve mice and constitute a substantial fraction of the anti-ERAAP-/- immune response in wild-type mice. Additionally, WT CD8 T cells detect and eliminate MHC class Ib-expressing ERAAP-deficient cells. Therefore, we suggest that presentation of the FL9 peptide by Qa-1b molecules is a surveillance mechanism for detecting inhibition of ERAAP function.

ERAAP-deficiency differentially affects peptide presentation across multiple MHC I (100.15)

Genome-wide association studies in humans have linked polymorphisms in the ER aminopeptidase associated with antigen processing (ERAAP) as well as particular MHC class I molecules to autoimmune diseases. How ERAAP polymorphisms affect function of different MHC I molecules is not known. ERAAP normally trims antigenic precursor peptides to generate potential peptide-MHC I ligands that can be recognized by CD8 T cells. To detect changes in the peptide repertoires displayed by different MHC I molecules, we immunized wild-type B10.D2 (H-2d) mice with ERAAP-deficient (ERAAP-KO) cells and analyzed the specificity of the CD8 T cell response. In wild-type mice, anti-ERAAP KO T cells responded primarily to peptides presented by Kd, and not the other two MHC I molecules, Dd and Ld of the H-2d haplotype. We also assessed the MHC I bound peptide repertoire by mass spectrometry. This analysis revealed that Dd and Kd molecules were bound to large number of shared as well as unique peptides, some with N-terminal extensions. Remarkably, Ld bound peptides were not detected in ERAAP-deficient mice. Thus, changes in ERAAP expression can have a major influence on the peptide repertoire presented by different MHC I molecules as well as on CD8 T cell responses.

Cryptic tRNAi shapes the pMHC I repertoire (100.5)

MHC class I molecules present peptides on the cell surface for immune surveillance of viruses and cancer. Interestingly, the peptides are encoded not only in conventional AUG-initiated translational reading frames but also in non-AUG initiated cryptic reading frames. Whether the same or distinct translational machinery is used to produce cryptic peptides at non-AUG start codons, such as CUG, is not known. Here, we show that translational initiation of antigenic precursors at cryptic CUG codons is differentially regulated by ribosomal initiation complexes that contain novel initiator tRNAs. This tRNA is distinct from Met-initiator tRNA and enhances initiation at CUG start codons. Thus, a novel tRNA -based mechanism can supply peptides for presentation by MHC I.

Non-conventional sources of peptides presented by MHC class I

Effectiveness of immune surveillance of intracellular viruses and bacteria depends upon a functioning antigen presentation pathway that allows infected cells to reveal the presence of an intracellular pathogen. The antigen presentation pathway uses virtually all endogenous polypeptides as a source to produce antigenic peptides that are eventually chaperoned to the cell surface by MHC class I molecules. Intriguingly, MHC I molecules present peptides encoded not only in the primary open reading frames but also those encoded in alternate reading frames. Here, we review recent studies on the generation of cryptic pMHC I. We focus on the immunological significance of cryptic pMHC I, and the novel translational mechanisms that allow production of these antigenic peptides from unconventional sources.

Topological journey of parasite-derived antigens for presentation by MHC class I molecules

Within cells of their host, many bacteria and parasites inhabit specialized compartments, such as a modified phagosome for Mycobacterium tuberculosis or a parasitophorous vacuole for Toxoplasma gondii. These locations could exclude microbial material from entry into the MHC class I surveillance pathway. Remarkably, however, under these circumstances, cells can still signal the presence of invading pathogens to circulating CD8(+) T cells, which typically play a key role in protection against such intracellular organisms. Here, we review MHC I presentation pathways in various contexts, ranging from model antigens in non-infectious settings to pathogen-infected cells. We suggest that presentation of intracellular pathogens can be described as not just one, but several distinct pathways; perhaps because diverse pathogens have evolved different strategies to interact with host cells.

Editing the pMHCI repertoire in the ER by tapasin and ERAAP (130.24)

The peptide/MHC class I complexes (pMHCI) displayed on the cell surface are essential for eliciting CD8+ T cell responses for adaptive immunity. How appropriate pMHCI are assembled within the peptide loading complex (PLC) in the endoplasmic reticulum (ER) is unclear. Here we show that tapasin, the core component of the PLC, edits the pMHCI repertoire in vivo. Compared to cells from wild-type mice, cells from tapasin-deficient mice express an immunologically distinct pMHCI repertoire. Tapasin-deficient cells lack many normal pMHCI and also express a set of novel pMHCI on the surface. Thus, CD8+ T cells responses are elicited in reciprocal immunizations between wild-type and tapasin-deficient mice. Interestingly, this set of pMHCI ligands is distinct from that found earlier in mice lacking ERAAP, the ER aminopeptidase associated with antigen processing. Taken together these findings suggest that the pMHC I repertore is edited independently by tapasin and ERAAP in the ER.

Identity of Toxoplasma gondii antigens that elicit CD4 T cells and their protective potential (130.13)

Toxoplasma gondii (Toxo) can cause severe disease in immunocompromised individuals. Previous studies in various strains of mice have shown that genetic resistance to disease is linked to the MHC locus and protection is largely mediated by Toxo-specific CD8 T cells. In B10.D2 (H-2d) mice, CD8 T cells recognize an immunodominant peptide derived from the Toxo-protein, GRA6. However, a GRA6-specific response is not detected in C57BL/6 (B6, H-2b) mice. Instead, Toxo immunization of B6 mice elicits primarily a CD4 T cell response to unknown Toxo antigens. To identify the CD4 T cell stimulating antigens, we generated a Toxo-specific, lacZ inducible, CD4 T cell hybridoma and used it as a probe to screen a Toxo-cDNA library in bone marrow derived dendritic cells. The results reveal that CD4 T cells can be elicited by a hypothetical protein in the Toxo sequence database. We have defined the minimal peptide presented by MHC class II molecules and we will discuss the protective potential of this peptide-specific CD4 T cells in Toxo infected mice.

Cross-presentation of peptides from intracellular pathogens by MHC class I molecules

Many prokaryotic and eukaryotic parasites multiply in specialized subcellular niches in the host cell. The invading microbes hijack key cellular functions to establish the intracellular niches but, unlike viruses, do not need the protein synthesis machinery of host cells to replicate. Circulating CD8+ T cells provide protective immunity by recognizing pathogen-derived peptide major histocompatibility complex class I molecules (pMHC I) expressed by infected cells. Here, we review studies on the complex and varied pathways that produce the appropriate pMHC I as ligands for the CD8+ T cells. We also discuss possible explanations for the curious observations that CD8+ T cells are specific for fewer pMHC I ligands in parasite infections compared to the diversity of pMHC I ligands in viral infections.

Endoplasmic reticulum aminopeptidase associated with antigen processing defines the composition and structure of MHC class I peptide repertoire in normal and virus-infected cells

The MHC class I (MHC-I) molecules ferry a cargo of peptides to the cell surface as potential ligands for CD8(+) cytotoxic T cells. For nearly 20 years, the cargo has been described as a collection of short 8-9 mer peptides, whose length and sequences were believed to be primarily determined by the peptide-binding groove of MHC-I molecules. Yet the mechanisms for producing peptides of such optimal length and composition have remained unclear. In this study, using mass spectrometry, we determined the amino acid sequences of a large number of naturally processed peptides in mice lacking the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP). We find that ERAAP-deficiency changed the oeuvre and caused a marked increase in the length of peptides normally presented by MHC-I. Furthermore, we observed similar changes in the length of viral peptides recognized by CD8(+) T cells in mouse CMV-infected ERAAP-deficient mice. In these mice, a distinct CD8(+) T cell population was elicited with specificity for an N-terminally extended epitope. Thus, the characteristic length, as well as the composition of MHC-I peptide cargo, is determined not only by the MHC-I peptide-binding groove but also by ERAAP proteolysis in the endoplasmic reticulum.

Mousepox detected in a research facility: case report and failure of mouse antibody production testing to identify Ectromelia virus in contaminated mouse serum

An outbreak of mousepox in a research institution was caused by Ectromelia-contaminated mouse serum that had been used for bone marrow cell culture and the cells subsequently injected into the footpads of mice. The disease initially was diagnosed by identification of gross and microscopic lesions typical for Ectromelia infection, including foci of necrosis in the liver and spleen and eosinophilic intracytoplasmic inclusion bodies in the skin. The source of infection was determined by PCR analysis to be serum obtained from a commercial vendor. To determine whether viral growth in tissue culture was required to induce viral infection, 36 mice (BALB/cJ, C57BL/6J) were experimentally exposed intraperitoneally, intradermally (footpad), or intranasally to contaminated serum or bone marrow cell cultures using the contaminated serum in the culture medium. Mice were euthanized when clinical signs developed or after 12 wk. Necropsy, PCR of spleen, and serum ELISA were performed on all mice. Mice injected with cell cultures and their cage contacts developed mousepox, antibodies to Ectromelia, and lesions, whereas mice injected with serum without cells did not. Mouse antibody production, a tool commonly used to screen biologic materials for viral contamination, failed to detect active Ectromelia contamination in mouse serum.