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