NetH2pan: A Computational Tool to Guide MHC Peptide Prediction on Murine Tumors

With the advancement of personalized cancer immunotherapies, new tools are needed to identify tumor antigens and evaluate T-cell responses in model systems, specifically those that exhibit clinically relevant tumor progression. Key transgenic mouse models of breast cancer are generated and maintained on the FVB genetic background, and one such model is the mouse mammary tumor virus-polyomavirus middle T antigen (MMTV-PyMT) mouse-an immunocompetent transgenic mouse that exhibits spontaneous mammary tumor development and metastasis with high penetrance. Backcrossing the MMTV-PyMT mouse from the FVB strain onto a C57BL/6 genetic background, in order to leverage well-developed C57BL/6 immunologic tools, results in delayed tumor development and variable metastatic phenotypes. Therefore, we initiated characterization of the FVB MHC class I H-2^q haplotype to establish useful immunologic tools for evaluating antigen specificity in the murine FVB strain. Our study provides the first detailed molecular and immunoproteomic characterization of the FVB H-2^q MHC class I alleles, including >8,500 unique peptide ligands, a multiallele murine MHC peptide prediction tool, and in vivo validation of these data using MMTV-PyMT primary tumors. This work allows researchers to rapidly predict H-2 peptide ligands for immune testing, including, but not limited to, the MMTV-PyMT model for metastatic breast cancer. Cancer Immunol Res; 6(6); 636-44. ©2018 AACR.

T cell recognition of Mycobacterium tuberculosis peptides presented by HLA-E derived from infected human cells

HLA-E is a non-conventional MHC Class I molecule that has been recently demonstrated to present pathogen-derived ligands, resulting in the TCR-dependent activation of αβ CD8+ T cells. The goal of this study was to characterize the ligandome displayed by HLA-E following infection with Mycobacterium tuberculosis (Mtb) using an in-depth mass spectrometry approach. Here we identified 28 Mtb ligands derived from 13 different source proteins, including the Esx family of proteins. When tested for activity with CD8+ T cells isolated from sixteen donors, nine of the ligands elicited an IFN-γ response from at least one donor, with fourteen of 16 donors responding to the Rv0634A19-29 peptide. Further evaluation of this immunodominant peptide response confirmed HLA-E restriction and the presence of Rv0634A19-29-reactive CD8+ T cells in the peripheral blood of human donors. The identification of an Mtb HLA-E ligand that is commonly recognized may provide a target for a non-traditional vaccine strategy.

Immunodominant West Nile Virus T Cell Epitopes Are Fewer in Number and Fashionably Late

Class I HLA molecules mark infected cells for immune targeting by presenting pathogen-encoded peptides on the cell surface. Characterization of viral peptides unique to infected cells is important for understanding CD8(+) T cell responses and for the development of T cell-based immunotherapies. Having previously reported a series of West Nile virus (WNV) epitopes that are naturally presented by HLA-A*02:01, in this study we generated TCR mimic (TCRm) mAbs to three of these peptide/HLA complexes-the immunodominant SVG9 (E protein), the subdominant SLF9 (NS4B protein), and the immunorecessive YTM9 (NS3 protein)-and used these TCRm mAbs to stain WNV-infected cell lines and primary APCs. TCRm staining of WNV-infected cells demonstrated that the immunorecessive YTM9 appeared several hours earlier and at 5- to 10-fold greater density than the more immunogenic SLF9 and SVG9 ligands, respectively. Moreover, staining following inhibition of the TAP demonstrated that all three viral ligands were presented in a TAP-dependent manner despite originating from different cellular compartments. To our knowledge, this study represents the first use of TCRm mAbs to define the kinetics and magnitude of HLA presentation for a series of epitopes encoded by one virus, and the results depict a pattern whereby individual epitopes differ considerably in abundance and availability. The observations that immunodominant ligands can be found at lower levels and at later time points after infection suggest that a reevaluation of the factors that combine to shape T cell reactivity may be warranted.

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T-cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we purify HLA-A*02:01 complexes from T. gondii infected cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen-derived peptides maintain a canonical N-terminal binding core yet exhibit a C-terminal extension of 1–30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F’ pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate that unrealized structural flexibility makes MHC class I receptive to parasite-derived ligands that exhibit unique C-terminal peptide extensions.

DOI:http://dx.doi.org/10.7554/eLife.12556.001

Toxoplasma gondii is a parasite that can infect most warm-blooded animals and cause a disease called toxoplasmosis. In humans, toxoplasmosis generally does not cause any noticeable symptoms, but it can cause serious problems in pregnant women and individuals with weakened immune systems.

T. gondii is one of many parasites that hide within human cells in an attempt to avoid detection by the immune system. However, proteins called Human Leukocyte Antigens, or HLAs, can reveal hidden parasites by carrying small sections of them from the inside the infected cell to the cell’s surface. The immune system can then recognize the fragments as foreign and attack the parasite.

HLAs typically pick up parasite fragments of a certain length, which enables the immune system to recognize that what is being displayed is a piece of parasite. By purifying HLAs from cells that have been infected by T. gondii, McMurtrey et al. have now learned more about which fragments of the parasite are displayed to the immune system. This analysis revealed that the parasite somehow manipulates the HLAs to carry parasite fragments that are considerably longer than can be explained with our current knowledge of how HLAs work. By using a technique called X-ray crystallography, McMurtrey et al. also show that the structure of the HLA assumes a previously unseen configuration when interacting with fragments of T. gondii.

In the future, it will be important to understand how infected cells give rise to unusual structural configurations of HLAs and to unravel how these structures affect the immune system’s ability to fight infections.

DOI:http://dx.doi.org/10.7554/eLife.12556.002

The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference

HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8(+) T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8(+) T cell epitopes.

Human Leukocyte Antigen-Presented Macrophage Migration Inhibitory Factor Is a Surface Biomarker and Potential Therapeutic Target for Ovarian Cancer

T cells recognize cancer cells via HLA/peptide complexes, and when disease overtakes these immune mechanisms, immunotherapy can exogenously target these same HLA/peptide surface markers. We previously identified an HLA-A2-presented peptide derived from macrophage migration inhibitory factor (MIF) and generated antibody RL21A against this HLA-A2/MIF complex. The objective of the current study was to assess the potential for targeting the HLA-A2/MIF complex in ovarian cancer. First, MIF peptide FLSELTQQL was eluted from the HLA-A2 of the human cancerous ovarian cell lines SKOV3, A2780, OV90, and FHIOSE118hi and detected by mass spectrometry. By flow cytometry, RL21A was shown to specifically stain these four cell lines in the context of HLA-A2. Next, partially matched HLA-A*02:01+ ovarian cancer (n = 27) and normal fallopian tube (n = 24) tissues were stained with RL21A by immunohistochemistry to assess differential HLA-A2/MIF complex expression. Ovarian tumor tissues revealed significantly increased RL21A staining compared with normal fallopian tube epithelium (P < 0.0001), with minimal staining of normal stroma and blood vessels (P < 0.0001 and P < 0.001 compared with tumor cells) suggesting a therapeutic window. We then demonstrated the anticancer activity of toxin-bound RL21A via the dose-dependent killing of ovarian cancer cells. In summary, MIF-derived peptide FLSELTQQL is HLA-A2-presented and recognized by RL21A on ovarian cancer cell lines and patient tumor tissues, and targeting of this HLA-A2/MIF complex with toxin-bound RL21A can induce ovarian cancer cell death. These results suggest that the HLA-A2/MIF complex should be further explored as a cell-surface target for ovarian cancer immunotherapy.

A novel monoclonal antibody to the HLA of cisplatin resistant ovarian cancer cells (TUM2P.1018)

Cisplatin is widely used as a chemotherapeutic drug in the treatment of ovarian cancer. Resistance to cisplatin occurs in about one-third of women during the primary course of treatment. We hypothesized that the class I HLA of cisplatin-resistant ovarian cancer cells present peptides distinct to these cells as compared to sensitive cells and that HLA/peptide complexes unique to cisplatin-resistant cells would be valuable targets for immunotherapeutic intervention. To identify the peptides that are uniquely presented by cisplatin-resistant ovarian cancer cells, the intrinsic cisplatin-resistant cells (SKOV3) and sensitive cells (A2780, OV90, FHIOSE) were characterized by comparative mass spectrometry. Peptide sequences distinct to cisplatin-resistant cells include a peptide (VMF11) derived from thioredoxin interacting protein (TXNIP) that was in high abundance in SKOV3. Next a T cell receptor mimic monoclonal antibody (RL41A) against A*02:01/VMF11 complex was generated. The specificity and affinity of RL41A toward VMF11/A*02:01 complex was shown by staining peptide-pulsed T2 cells and surface plasmon resonance respectively. Staining of ovarian cancer cells by flow cytometry also demonstrates that RL41A stains cisplatin-resistant cells but not drug sensitive cells. We therefore report the successful development of a monoclonal antibody that represents an attractive candidate for further validation using cisplatin-resistant and sensitive primary ovary tissues.

HIV-1 NEF ligands predominate in the HLA class I of infected CD4+ T cells (APP2P.108)

Class I HLA reveal virus-derived ligands to cytotoxic T lymphocytes (CTL) whose function is to eliminate infected cells. The Los Alamos National Laboratory (LANL) database reports numerous HIV-1 CTL epitopes, none of which have elicited protective immunity in vaccine testing. The goal of this study was to determine the number and nature of HIV-1 ligands available for CTL targeting through presentation by the HLA class I of virus-infected cells. Class I presented peptides were recovered from immunoaffinity purified HLA-A*11:01 gathered from HIV-1 (NL4-3)-infected human CD4+ SUP-T1 T cells. These peptides were fractionated by RP-HPLC and mapped by tandem mass spectrometry (MS/MS). Seven HIV-derived peptides were confirmed by MS/MS as unique to infected cells. Twelve LANL HIV epitopes, including the well-studied Gag p24 epitope ACQGVGGPGHK (AK11), were clearly absent from the HLA-A*11:01 of infected cells. Of the 7 HIV-1 ligands found to be presented by A*11:01, 4 were derived from Nef, 2 from Gag, and 1 from Pol. When these 7 ligands were tested for T cell reactivity in a gamma interferon ELISPOT assay using PBMC from HIV-1 infected individuals (including elite controllers), the Nef-derived peptides were found to be highly reactive. These data demonstrate that the class I HLA of HIV-1 infected CD4+ T cells present a handful of viral peptide ligands for recognition by CTL and that reported HIV-1 CTL epitopes might not be presented by the HLA class I of infected cells.

Detection and validation of HLA Class I presented viral epitopes using T cell receptor mimics (APP2P.107)

Class I Human Leukocyte Antigens distinguish healthy cells from infected cells by presenting peptides at the cell surface. Viral epitopes confirmed as unique to infected cells can lead to successful development of vaccines and therapeutics, and a tool to validate viral epitope presentation on a variety of cell lineages is essential. Here, comparative mass spectrometry shows that the West Nile virus peptide epitopes SVGGVFTSV and ILRNPGYAL are presented by HLA-A*02:01 and HLA-B*07:02 of infected cells. To generate monoclonal antibodies against these HLA/WNV peptide epitopes, mice were immunized with peptide/HLA complexes, splenocytes were fused to myeloma cells, and single clones were picked and grown. Hybridoma supernatants were screened for recognition of the appropriate HLA/WNV peptide complex on peptide-pulsed cells with irrelevant HLA/peptides acting as a negative control. The T cell receptor mimic (TCRm) monoclonal antibodies RL15A and RL29A were found to be specific for A*02:01/SVG9 and B*07:02/ILR9, respectively. The RL15A and RL29A T cell receptor mimic mAb were then used to track viral epitope presentation on WNV infected cell lines and primary cells. In summary, we demonstrate the implementation of a mass spectrometry system for the direct discovery of class I HLA-presented viral epitopes from infected cells followed by the complementary use of TCRm mAb as a companion diagnostic for tracking epitope presentation during the course of a viral infection.

Peptide presentation by different HLA-Class I molecules during viral infection (APP2P.106)

Class I Human Leukocyte Antigens reveal intracellular viruses to the immune system by presenting viral epitopes at the cell surface. In this study we hypothesized that during infection particular HLA class I alleles consistently present more virus-derived peptide ligands to virus-specific CD8+ T cells than do other HLA class I. To test this hypothesis, we infected cells with West Nile virus (WNV) and directly identified and enumerated the virus specific peptides presented by various HLA class I molecules. Cells expressing a number of different HLA-A and HLA-B class I were cultured in bioreactors and infected with WNV. HLA/peptide complexes were harvested from infected and uninfected cells, peptides were eluted from affinity-purified HLA, comparatively mapped by mass spectroscopy, and sequenced. Twenty-four peptides, 20 eluted from HLA-A complexes (HLA-A*02:01, A*01:01, A*11:01 and A*24:02) and 4 from HLA-B complexes (HLA-B*27:05, B*07:02 and B*35:01), were identified as unique to infected cells. Ligands represented different parts of the viral polyprotein demonstrating that peptides sampled by class I HLA are distributed widely throughout the WNV proteome. These data indicate that, in WNV-infected cells, HLA-A present more virus-specific peptides than do HLA-B suggesting a potentially different role for HLA class I loci in developing immune responses that control WNV infection whereby HLA-A is responsible for diverse reactivity and HLA-B leads to more focused immunity.

Identification of class I HLA T cell control epitopes for West Nile virus

The recent West Nile virus (WNV) outbreak in the United States underscores the importance of understanding human immune responses to this pathogen. Via the presentation of viral peptide ligands at the cell surface, class I HLA mediate the T cell recognition and killing of WNV infected cells. At this time, there are two key unknowns in regards to understanding protective T cell immunity: 1) the number of viral ligands presented by the HLA of infected cells, and 2) the distribution of T cell responses to these available HLA/viral complexes. Here, comparative mass spectroscopy was applied to determine the number of WNV peptides presented by the HLA-A*11:01 of infected cells after which T cell responses to these HLA/WNV complexes were assessed. Six viral peptides derived from capsid, NS3, NS4b, and NS5 were presented. When T cells from infected individuals were tested for reactivity to these six viral ligands, polyfunctional T cells were focused on the GTL9 WNV capsid peptide, ligands from NS3, NS4b, and NS5 were less immunogenic, and two ligands were largely inert, demonstrating that class I HLA reduce the WNV polyprotein to a handful of immune targets and that polyfunctional T cells recognize infections by zeroing in on particular HLA/WNV epitopes. Such dominant HLA/peptide epitopes are poised to drive the development of WNV vaccines that elicit protective T cells as well as providing key antigens for immunoassays that establish correlates of viral immunity.

Profiling class II HLA alloantibodies in transplant patient sera (P2222)

Allogeneic immunizing events including pregnancy, blood transfusion, and transplantation promote strong antibody responses to HLA. Such anti-HLA antibodies preclude organ transplantation, foster hyperacute rejection, and contribute to chronic transplant failure. Diagnostic antibody-screening assays can detect alloreactive antibodies and determine their HLA specificity, yet a number of key antibody attributes remain unexplored. The goal here was to provide the first detailed profile of antibodies directed to allogeneic HLA. Methodologically, sixteen sensitized patients were identified with alloantibodies to HLA-DR11, antibodies reactive with this class II HLA antigen were purified using a novel immunoaffinity column constructed with milligram quantities of native DR11, and these purified DR11 specific antibodies were categorized. Results show that allogeneic antibodies to DR11 were found in the serum at a median concentration of 2.3ug/ml and consisted of the IgM, IgG, IgA, and IgE isotypes. IgG2, IgM, and IgE were elevated while IgG1 was decreased in sensitized patients and, in most patients, these antibodies fixed complement. In conclusion, we show that HLA alloantibody responses are consistently comprised of multiple isotypes, that these alloantibodies reach an appreciable serum concentration, and that these alloantibodies fix complement.

Immunodominant and subdominant WNV epitopes are differentially presented (P5005)

There are many factors that are thought to contribute to T-cell immunodominance hierarchies including timing and levels of antigen presentation to T-cells. One of the most potent tools for studying antigen presentation for a specific determinant are monoclonal antibodies that are specific for not only MHC but a specific ligand, similar to a T cell receptor. In this study we utilize these antibodies to study levels and timing of antigen presentation of immunodominant (SVG9), sub-dominant (SLF9), and super sub-dominant (YTM9) T-cell epitopes during West Nile virus (WNV) infection. In this study, we demonstrate that these ligands are differentially expressed on the surface of a cell infected with WNV. Specifically, the super sub-dominant ligand (YTM9) was presented earlier and at 20 times the levels of the immunodominant (SVG9) and subdominant (SLF9) ligands. Transfection of ICP47 in the infected cells show that all three epitopes are TAP dependent. Using these highly specific reagents we show that there is differential ligand presentation within the restrictive allele. High levels of peptide HLA complexes on the surface of an infected do not correspond with immunodominance hierarchies as the super subdominant epitope YTM9 was presented at higher levels than the most dominant epitope SVG9. This differential in presentation was not due the TAP dependence of the ligands.

Classical antigen presentation by HLA-A2 of Mycobacterium tuberculosis derived ligands (106.40)

Mycobacterium tuberculosis (Mtb) remains a world health threat, with 8.8 million cases reported in 2010, 65% of which were new and recurrent cases of tuberculosis . Cellular immunity is critical for controlling Mtb and recent studies identify CD8+ T cells as important players in controlling infection. Cytotoxic T lymphocytes (CTLs) recognize peptide antigen presented by Major Histocompatibility Complex (MHC) Class I molecules and destroy infected cells, therefore discovery of CTL epitopes is of high importance. Using a method of soluble HLA production, we were able to generate soluble HLA-A2 from THP-1 monocyte cell lines transfected with a soluble form of HLA A*02:01. Transfected cells were seeded into a hollow fiber bioreactor and were infected with Mtb or left uninfected. Following production of 25 mgs of HLA-A2 from infected and uninfected cells, peptides were eluted from the supernatants of uninfected and infected cells. Peptides from each group were fractionated using HPLC and analyzed by mass spectrometry. We were able to identify six Mtb derived ligands presented by the MHC Class I molecule HLA-A*0201, two of which reacted well with donor PBMC from patients with both active and latent Mtb infection. Identifying new vaccine candidates is a top priority in the TB field and the reactive Mtb ligands identified here demonstrate that multiple Mtb proteins are processed for presentation by Class I HLA and a fraction of these ligands are immunologically reactive.

The role of MHC class I allele Mamu-A*07 during SIV(mac)239 infection

Virus-specific CD8(+) T cells play an important role in controlling HIV/SIV replication. These T cells recognize intracellular pathogen-derived peptides displayed on the cell surface by individual MHC class I molecules. In the SIV-infected rhesus macaque model, five Mamu class I alleles have been thoroughly characterized with regard to peptide binding, and a sixth was shown to be uninvolved. In this study, we describe the peptide binding of Mamu-A1*007:01 (formerly Mamu-A*07), an allele present in roughly 5.08% of Indian-origin rhesus macaques (n = 63 of 1,240). We determined a preliminary binding motif by eluting and sequencing endogenously bound ligands. Subsequently, we used a positional scanning combinatorial library and panels of single amino acid substitution analogs to further characterize peptide binding of this allele and derive a quantitative motif. Using this motif, we selected and tested 200 peptides derived from SIV(mac)239 for their capacity to bind Mamu-A1*007:01; 33 were found to bind with an affinity of 500 nM or better. We then used PBMC from SIV-infected or vaccinated but uninfected, A1*007:01-positive rhesus macaques in IFN-γ Elispot assays to screen the peptides for T-cell reactivity. In all, 11 of the peptides elicited IFN-γ(+) T-cell responses. Six represent novel A1*007:01-restricted epitopes. Furthermore, both Sanger and ultradeep pyrosequencing demonstrated the accumulation of amino acid substitutions within four of these six regions, suggestive of selective pressure on the virus by antigen-specific CD8(+) T cells. Thus, it appears that Mamu-A1*007:01 presents SIV-derived peptides to antigen-specific CD8(+) T cells and is part of the immune response to SIV(mac)239.

Immune cross recognition of a conserved Flavivirus epitope (130.28)

We previously characterized an immunodomiant, HLA-A*0201 restricted, West Nile virus (WNV) peptide determinant. This dominant WNV peptide epitope, termed SVG9, lies within a highly conserved region of the envelope glycoprotein and demonstrates 100% homology among contemporary WNV strains. This region of the virus envelope is also highly conserved among other Flaviviruses such as Japanese encephalitis virus and Dengue virus (DV). Since immune cross reactivity has been reported within the Dengue virus serogroup, we hypothesized that T cells specific for this A*0201 restricted WNV stretch of envelope would cross-recognize different flaviviruses due to epitope conservation. As an initial test of this hypothesis we synthesized the corresponding envelope peptide for WNV (SVG9) and DV type 1 (SIG9). We utilized a competitive peptide binding assay to demonstrate that SVG9 and SIG9 have comparable and high A*0201 binding affinities. We then utilized PBMC from WNV and DV1 seropositive donors to assess T cell cross recognition of SVG9 and SIG9. T cells specific for the WNV SVG9 were cross-reactive for their DV1 Flaviviral counterpart SIG 9 and vice versa. These data demonstrate that cellular immunity is cross-reactive among different Flaviviruses. This observation has implications for vaccine development and for unraveling the immunopathology associated with infection.

Direct discovery of an influenza B peptide displayed by HLA-B*0702. (92.15)

Annual influenza epidemics caused by influenza A and B viruses substantially impact global public health. The proportion of infections due to influenza B fluctuates from season to season, but on average accounts for 20% of influenza cases each year. We used a direct discovery method to screen for influenza B epitopes presented by HLA-B*0702. We identified epitope TIRLVTEEL (TL9) that lies within the influenza B non-structural protein 2 (NS2) also known as nuclear export protein (NEP). The TIRLVTEEL sequence is found in 86% of influenza B strains (38 out of 44 sequences) and it is a high-affinity binder to HLA-B*0702. To test the immunogenicity of this peptide, we isolated splenocytes from influenza B-infected HLA-B*0702 transgenic mice and found that TIRLVTEEL generated a strong IFN-gamma production by ELISPOT. As three variants of this epitope occur in nature, each differing from TIRLVTEEL by a single amino acid, we tested each variant for B*0702 binding and for cross-recognition by ELISPOT. Each variant is a high affinity HLA-B*0702 binder and each stimulates IFN-gamma production. In summary, we discovered a conserved epitope within the influenza B non-structural protein 2 (NS2) or nuclear export protein (NEP) which may be a candidate for future CTL-based therapies directed towards the influenza B virus.

Origin and number of viral peptides sampled by class I MHC following West Nile Virus infection (130.27)

West Nile Virus (WNV) was introduced into the United States in 1999 and it has emerged as the most common cause of arboviral neuroinvasive disease in the U.S. An estimated 1.65 million infections occurred between 1999 and 2008 and there is no specific treatment or vaccine available. WNV-infected cells can be detected and destroyed by the CD8+ cytotoxic lymphocytes via the presentation of viral peptides by major histocompatability complex class I molecules. Currently, no one knows how many WNV derived peptides decorate the MHC of infected cells, nor do we know which viral proteins MHC molecules sample. Understanding the number and origin of viral peptides available for immune recognition is a key prerequisite in the development of antiviral immunotherapeutics. Using an HLA-A and an HLA-B molecule, we previously reported that a given class I MHC molecule samples 2-6 viral peptides. Here we test this observation with additional HLA-A and HLA-B by secreting A*0101 and B*2705 from uninfected cells and then from WNV infected cells. Peptides eluted from the infected and uninfected class I molecules were compared by mass spectrometry, and peptides unique to infected cells were sequenced by tandem mass spectrometry. The resulting data demonstrate that different class I MHC molecules consistently present a like number of WNV peptides for immune recognition and that the viral peptides originate from clusters or “hot spots” within the viral polyprotein.

HLA class I molecules reflect an altered host proteome after influenza virus infection

Class I HLA sample and display peptides from thousands of endogenous proteins at the cell surface. During infection, the influenza virus modifies the host cell proteome by triggering host antiviral responses, hijacking host processes, and inhibiting host mRNA processing. In turn, the catalog of HLA class I peptides that decorate the surface of an infected cell is positioned to reflect an altered host cell proteome. To understand the host-encoded peptides presented by class I molecules after influenza infection, we compared by mass spectrometry (MS) the peptides eluted from the HLA of naive and infected cells. We identified 20 peptide ligands unique to infected cells and 347 peptides with increased presentation after infection. Infection with different influenza strains demonstrated that proteome changes are predominantly strain-specific, with few individual cellular interactions observed for multiple viral strains. Modeling by pathway analysis, however, revealed that strain specific host peptide changes represent different routes to the same destination; host changes mediated by influenza are found predominantly clustered around HLA-B, ACTB, HSP90AB1, CDK2, and ANXA2. The class I HLA proteome scanning of influenza-infected cells therefore indicates how divergent strains of influenza pursue alternate routes to access the same host cell processes.

T-cell tolerance for variability in an HLA class I-presented influenza A virus epitope

To escape immune recognition, viruses acquire amino acid substitutions in class I human leukocyte antigen (HLA)-presented cytotoxic T-lymphocyte (CTL) epitopes. Such viral escape mutations may (i) prevent peptide processing, (ii) diminish class I HLA binding, or (iii) alter T-cell recognition. Because residues 418 to 426 of the hypervariable influenza A virus nucleoprotein (NP(418-426)) epitope are consistently bound by class I HLA and presented to CTL, we assessed the impact that intraepitope sequence variability has upon T-cell recognition. CTL elicited by intranasal influenza virus infection were tested for their cross-recognition of 20 natural NP(418-426) epitope variants. Six of the variant epitopes, of both H1N1 and H3N2 origin, were cross-recognized by CTL while the remaining NP(418-426) epitope variants escaped targeting. A pattern emerged whereby variability at position 5 (P5) within the epitope reduced T-cell recognition, changes at P4 or P6 enabled CTL escape, and a mutation at P8 enhanced T-cell recognition. These data demonstrate that substitutions at P4 and/or P6 facilitate influenza virus escape from T-cell recognition and provide a model for the number, nature, and location of viral mutations that influence T-cell cross-recognition.

Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B*08 and HLA-B*2705, bind peptides with sequence similarity

HLA-B27- and -B57-positive HIV-infected humans have long been associated with control of HIV replication, implying that CD8(+) T cell responses contribute to control of viral replication. In a similar fashion, 50% of Mamu-B*08-positive Indian rhesus macaques control SIVmac239 replication and become elite controllers with chronic-phase viremia <1000 viral RNA copies/ml. Interestingly, Mamu-B*08-restricted SIV-derived epitopes appeared to match the peptide binding profile for HLA-B*2705 in humans. We therefore defined a detailed peptide-binding motif for Mamu-B*08 and investigated binding similarities between the macaque and human MHC class I molecules. Analysis of a panel of approximately 900 peptides revealed that despite substantial sequence differences between Mamu-B*08 and HLA-B*2705, the peptide-binding repertoires of these two MHC class I molecules share a remarkable degree of overlap. Detailed knowledge of the Mamu-B*08 peptide-binding motif enabled us to identify six additional novel Mamu-B*08-restricted SIV-specific CD8(+) T cell immune responses directed against epitopes in Gag, Vpr, and Env. All 13 Mamu-B*08-restricted epitopes contain an R at the position 2 primary anchor and 10 also possess either R or K at the N terminus. Such dibasic peptides are less prone to cellular degradation. This work highlights the relevance of the Mamu-B*08-positive SIV-infected Indian rhesus macaque as a model to examine elite control of immunodeficiency virus replication. The remarkable similarity of the peptide-binding motifs and repertoires for Mamu-B*08 and HLA-B*2705 suggests that the nature of the peptide bound by the MHC class I molecule may play an important role in control of immunodeficiency virus replication.

Mauritian cynomolgus macaques share two exceptionally common major histocompatibility complex class I alleles that restrict simian immunodeficiency virus-specific CD8+ T cells

Vaccines that elicit CD8(+) T-cell responses are routinely tested for immunogenicity in nonhuman primates before advancement to clinical trials. Unfortunately, the magnitude and specificity of vaccine-elicited T-cell responses are variable in currently utilized nonhuman primate populations, owing to heterogeneity in major histocompatibility (MHC) class I genetics. We recently showed that Mauritian cynomolgus macaques (MCM) have unusually simple MHC genetics, with three common haplotypes encoding a shared pair of MHC class IA alleles, Mafa-A*25 and Mafa-A*29. Based on haplotype frequency, we hypothesized that CD8(+) T-cell responses restricted by these MHC class I alleles would be detected in nearly all MCM. We examine here the frequency and functionality of these two alleles, showing that 88% of MCM express Mafa-A*25 and Mafa-A*29 and that animals carrying these alleles mount three newly defined simian immunodeficiency virus-specific CD8(+) T-cell responses. The epitopes recognized by each of these responses accumulated substitutions consistent with immunologic escape, suggesting these responses exert antiviral selective pressure. The demonstration that Mafa-A*25 and Mafa-A*29 restrict CD8(+) T-cell responses that are shared among nearly all MCM indicates that these animals are an advantageous nonhuman primate model for comparing the immunogenicity of vaccines that elicit CD8(+) T-cell responses.

Determination of cellular lipids bound to human CD1d molecules

CD1 molecules are glycoproteins that present lipid antigens at the cell surface for immunological recognition by specialized populations of T lymphocytes. Prior experimental data suggest a wide variety of lipid species can bind to CD1 molecules, but little is known about the characteristics of cellular ligands that are selected for presentation. Here we have molecularly characterized lipids bound to the human CD1d isoform. Ligands were eluted from secreted CD1d molecules and separated by normal phase HPLC, then characterized by mass spectroscopy. A total of 177 lipid species were molecularly identified, comprising glycerophospholipids and sphingolipids. The glycerophospholipids included common diacylglycerol species, reduced forms known as plasmalogens, lyso-phospholipids (monoacyl species), and cardiolipins (tetraacyl species). The sphingolipids included sphingomyelins and glycosylated forms, such as the ganglioside GM3. These results demonstrate that human CD1d molecules bind a surprising diversity of lipid structures within the secretory pathway, including compounds that have been reported to play roles in cancer, autoimmune diseases, lipid signaling, and cell death.

Identification of breast cancer peptide epitopes presented by HLA-A*0201

Cellular immune mechanisms detect and destroy cancerous and infected cells via the human leukocyte antigen (HLA) class I molecules that present peptides of intracellular origin on the surface of all nucleated cells. The identification of novel, tumor-specific epitopes is a critical step in the development of immunotherapeutics for breast cancer. To directly identify peptide epitopes unique to cancerous cells, secreted human class I HLA molecules (sHLA) were constructed by deletion of the transmembrane and cytoplasmic domain of HLA A*0201. The resulting sHLA-A*0201 was transferred and expressed in breast cancer cell lines MCF-7, MDA-MB-231, and BT-20 as well as in the immortal, nontumorigenic cell line MCF10A. Stable transfectants were seeded into bioreactors for production of > 25 mg of sHLA-A*0201. Peptides eluted from affinity purified sHLA were analyzed by mass spectroscopy. Comparative analysis of HLA-A*0201 peptides revealed 5 previously uncharacterized epitopes uniquely presented on breast cancer cells. These peptides were derived from intracellular proteins with either well-defined or putative roles in breast cancer development and progression: Cyclin Dependent Kinase 2 (Cdk2), Ornithine Decarboxylase (ODC1), Kinetochore Associated 2 (KNTC2 or HEC1), Macrophage Migration Inhibitory Factor (MIF), and Exosome Component 6 (EXOSC6). Cellular recognition of the MIF, KNTC2, EXOSC6, and Cdk2 peptides by circulating CD8+ cells was demonstrated by tetramer staining and IFN-gamma ELISPOT. The identification and characterization of peptides unique to the class I of breast cancer cells provide putative targets for the development of immune diagnostic tools and therapeutics.

Viral and Self HLA Class I Peptides Mark the Surface of Influenza Infected Cells (93.2)

The influenza virus attacks epithelial cells of the lower and upper respiratory tracts. Following infection, the virus alters the proteome of the infected cell and triggers anti-viral cellular immune responses. The infected cell’s altered proteome is reflected at the cell surface by the HLA (Human Leukocyte Antigen) class I molecule. Class I HLA sample and display endogenously loaded peptides at the surface of all nucleated cells so that CTL can distinguish infected from uninfected cells. To identify class I ligands that mark infected cells, we collect soluble HLA B*0702 and A*0201 molecules from influenza infected and uninfected cells. Peptide ligands and their class I carriers are size separated, uninfected and infected peptide pools are fractionated by RP-HPLC, and peptides are comparatively mapped via mass spectrometry. Thus far, we have identified B*0702 peptides derived from the Influenza A/PR/8 hemagglutinin and nucleoprotein molecules and multiple B*0702 and A*0201 host-derived peptides that are either uniquely expressed or up-regulated on the surface of influenza infected cells. The identification of viral peptides unique to the class I of influenza infected cells indicates a route for eliciting CTL via vaccination whilst changes in class I HLA presented self peptide epitopes indicate “danger” signals that demark the infected cell.

Breast Cancer Peptide Epitopes Presented by HLA-A*0201 (48.6)

Cellular immune mechanisms detect and destroy cancerous and infected cells via the human leukocyte antigen (HLA) class I molecules that present peptides of intracellular origin on the surface of all nucleated cells. The identification of novel, tumor-specific epitopes is a critical step in the development of TCR mediated immunotherapeutics. In order to directly identify peptide epitopes unique to cancerous cells, secreted human class I HLA molecules were constructed by deletion of the transmembrane and cytoplasmic domain of HLA A*0201. The resulting sHLA-A*0201 was transferred and expressed in breast cancer cell lines MCF-7, MDA-MB-231, and BT-20 as well as in the immortal, non-tumorigenic cell line MCF10A. Stable transfectants producing sHLA-A*0201 were seeded into Bioreactors for production of &gt; 25 mg of sHLA-A*0201. Peptides eluted from affinity purified sHLA were analyzed by mass spectroscopy and peptides derived from proteins with reported cancer association have been identified; BAP31, Cytokeratin 19, KIAA0336, and UGT1 peptide epitopes have been found on cancer cells. The identification of peptides unique to the class I of cancerous breast cells provides putative targets for immune diagnostics and therapeutics.

OH is supported by NSF Graduate Fellowship 2006036207