HLA Peptide Research Articles

HLA Ligandome Analysis in Primary Polycythemia Vera (PV) Samples Shows No Tumor-Association of Naturally Presented JAK2 Ligands but Reveals a Vast Array of Novel PV-Associated HLA Ligands

Polycythemia vera (PV) is a myeloproliferative disorder mainly driven by the JAK2V617F mutant kinase. Except allogeneic stem cell transplantation, the current standard therapies, including novel therapies aiming for specific inhibition of JAK2 that are presently under investigation, do not offer a chance for cure. Of note, clear clinical benefits of unspecific immunotherapy with pegylated IFN-α suggest that PV might also be targeted by specific peptide based vaccination. Here we aimed to identify tumor associated HLA ligands of PV with special focus on peptides derived from JAK2. Therefore we analyzed HLA class I and II ligands of primary PV samples using the approach of direct isolation and identification of naturally presented HLA peptides by affinity chromatography and mass spectrometry.We analyzed the HLA class I ligandomes of 7 PV patients with the JAK2V617F mutation as well as of 4 patients with secondary (JAK2V617F negative) polycythemia. As controls, we profiled the ligandomes of 40 healthy volunteers (30 blood and 10 bone marrow samples). We identified more than 7,000 unique HLA class I ligands representing 4,435 proteins on primary PV samples. Moreover, 3 different HLA ligands derived from JAK2 on PV (KYLINLETL, HLA-A*24; KIGDFGLTK, HLA-A*03; GQGTFTKIFK, HLA-A*11) were identified. None of these ligands was found to be PV-exclusive, with JAK2 being represented on 3/4 (75%) of PV samples (JAK2V617F positive) and 18/30 (60%) healthy controls. No JAK2-derived peptides were identified on JAK2V617F negative patients, and no peptides covering the JAK2V617F mutation were identified. Since our previous work strongly suggests that tumor exclusive representation of an antigen is a prerequisite for the immunogenicity of its corresponding T cell epitopes, JAK2-derived wild-type peptides are unlikely to constitute optimal vaccines in PV. On the other hand, comparative profiling of the HLA class I ligandomes identified 935 antigens to be exclusively presented in JAK2V617F positive PV with 12 ligandome-derived tumor-associated antigens (LiTAAs) representing 26 different HLA ligands with exclusive representation in ≥30% of PV patients. Overlap analysis of PV patients with and without JAK2V617F mutation revealed 92% of the exclusive antigens to be represented on both groups, while only 8% and 0% showed exclusive representation in JAK2V617F positive and negative PV patients, respectively.As CD4+ T cells play important indirect and direct roles in anti-tumor immunity, we further applied our approach to HLA class II ligandomes of 8 PV patients (6 with, 2 without JAK2V617F mutation) and 18 HV (13 blood and 5 bone marrow samples) Using this approach, we identified more than 7,700 different naturally presented HLA class II ligands (1,700 source proteins). Notably, no JAK2-derived HLA class II peptides were identified in PV patients and HV ligandomes. Applying the same antigen-ranking strategy as described for HLA class I, we identified 5 additional HLA class II LiTAAs (exclusive in >30% of PV ligandomes) represented by 19 corresponding LiTAPs (ligandome-derived tumor-associated peptides). Overlap analysis of PV-exclusive source proteins revealed 2 proteins (POLA1, polymerase (DNA directed), alpha 1 and RHOQ, ras homolog family member Q) to be exclusively represented both in HLA class I and II ligandomes of PV patients.The novel HLA class I and II ligandome-derived tumor associated antigens identified in this study may constitute prime candidates for peptide-based immunotherapy of PV. DisclosuresNo relevant conflicts of interest to declare.

Varicella-zoster virus-derived major histocompatibility complex class I-restricted peptide affinity is a determining factor in the HLA risk profile for the development of postherpetic neuralgia.

Postherpetic neuralgia (PHN) is the most common complication of herpes zoster and is typified by a lingering pain that can last months or years after the characteristic herpes zoster rash disappears. It is well known that there are risk factors for the development of PHN, such as its association with certain HLA alleles. In this study, previous HLA genotyping results were collected and subjected to a meta-analysis with increased statistical power. This work shows that the alleles HLA-A*33 and HLA-B*44 are significantly enriched in PHN patients, while HLA-A*02 and HLA-B*40 are significantly depleted. Prediction of the varicella-zoster virus (VZV) peptide affinity for these four HLA variants by using one in-house-developed and two existing state-of-the-art major histocompatibility complex (MHC) class I ligand prediction methods reveals that there is a great difference in their absolute and relative peptide binding repertoires. It was observed that HLA-A*02 displays a high affinity for an ∼7-fold-higher number of VZV peptides than HLA-B*44. Furthermore, after correction for HLA allele-specific limitations, the relative affinity of HLA-A*33 and HLA-B*44 for VZV peptides was found to be significantly lower than those of HLA-A*02 and HLA-B*40. In addition, HLA peptide affinity calculations indicate strong trends for VZV to avoid high-affinity peptides in some of its proteins, independent of the studied HLA allele. Varicella-zoster virus can cause two distinct diseases: chickenpox (varicella) and shingles (herpes zoster). Varicella is a common disease in young children, while herpes zoster is more frequent in older individuals. A common complication of herpes zoster is postherpetic neuralgia, a persistent and debilitating pain that can remain months up to years after the resolution of the rash. In this study, we show that the relative affinity of HLA variants associated with higher postherpetic neuralgia risk for varicella-zoster virus peptides is lower than that of variants with a lower risk. These results provide new insight into the development of postherpetic neuralgia and strongly support the hypothesis that one of its possible underlying causes is a suboptimal anti-VZV immune response due to weak HLA binding peptide affinity.

A25: The Association of Immunogenetic and Environmental Factors with Disease Course in Patients with Juvenile Idiopathic Inflammatory Myopathies

Background/Purpose:Three disease courses can be distinguished in patients with juvenile idiopathic inflammatory myopathies (JIIM): monocyclic (M), polycyclic (P), and chronic continuous (CC). Predictors of disease course could result in improved therapy and help focus research efforts. We examined the association of immunogenetic and environmental factors with disease course in a large JIIM cohort.Methods:We enrolled 240 Caucasian patients with JIIM (204 dermato‐, 21 poly‐, and 15 overlap myositis) diagnosed from 1980–2010 in the US and Canada into IRB‐approved studies. The ratio of girls to boys was 3:1. Median age at diagnosis was 7 years (IQR: 5–12). Physician questionnaires with clinical and demographic data and patient blood samples were obtained. Follow‐up was through medical record review. The disease course classification was as follows: M—no active disease and off medication within 2 years of diagnosis (n = 62); P—disease recurrence after definite remission (n = 62); and CC—persistent disease or continuation of medication for more than 2 years (n = 116). Genetic data included: high resolution HLA‐DRB1 and HLA‐DQA1 alleles, and peptide binding motifs; immunoglobulin gamma heavy and kappa light chain phenotypes and allotypes; and TNFα (−238, −308), IL‐1α (−889, +4845), and IL‐1β (−511, −3953) polymorphisms. Environmental data included: documentation of infections within 6 months prior to illness onset; average and highest ultraviolet (UV) index for the month prior to illness onset and prior to diagnosis based on residential location; season of illness onset; and geoclimatic regions and planting zones of residential location at illness onset.Results:HLA‐DRB1*1501 was present more frequently in the M group (22%) compared to the P (5%; OR [95% CI]=5.7 [1.1–29.0]; p=0.04) and CC groups (7%; OR=4.0 [12.4–1.3]; p=0.02). In patients with dermatomyositis only, the F25 peptide binding was present less frequently in the M group (18%) compared to the P (41%; OR = 0.3 [0.1–0.8]; p = 0.02) and CC groups (39%; OR = 0.3 [0.1–0.8]; p = 0.02). The other HLA alleles and peptide binding motifs, immunoglobulin gamma heavy and kappa light chain phenotypes and allotypes, and cytokine polymorphisms (including TNFα‐308) were not associated with disease course. Infections 6 months prior to illness onset were more often present in the P group (40%) compared to the M (18%; OR = 3.0 [1.3–7.2]; p = 0.01) and CC groups (21%; OR = 2.5 [1.2–5.2]; p = 0.01). Three‐quarter of these infections were respiratory. In girls, the average UV index in the month before diagnosis was higher in the P group (median [IQR] = 5.7 [4.0–6.6]) compared to the M group (median [IQR] = 4.3 [1.2–5.6]; p = 0.01). Season of illness onset, geoclimatic regions, and planting zones did not differ among the 3 disease courses.Conclusion:Immunogenetic factors, including HLA alleles, and environmental factors, including a history of preceding infections and the UV index at diagnosis, were significantly associated with disease course in this population of Caucasian patients with JIIM. Future studies are needed to confirm these associated factors and to identify the value of these factors in determining prognosis.

Antigenic peptide molecular recognition by the DRB1-DQB1 haplotype modulates multiple sclerosis susceptibility.

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system that has a notably high incidence in Sardinia. Our study focuses on two HLA class II haplotypes associated with the disease in Sardinia, the rare predisposing DRB1*15:01-DQB1*06:02 and the widespread protective DRB1*16:01-DQB1*05:02. This framework enabled the highlighting of HLA binding pocket specificity and peptide recognition mechanisms by employing molecular dynamics simulations of the whole DRB1-DQB1 haplotype interacting with MBP- and EBV-derived peptides. We analyzed peptide-protein interaction networks and temporal evolution of the original complexes and after key amino acid mutations. The mutation G86V of the protective DRB1 allele exerted its effect mainly in the presence of the EBV viral peptide, with local and long range outcomes. However, the V38A mutation of the protective DQB1 showed a long range effect only in the case of the MBP myelin peptide. Our findings also demonstrate a DRB1/DQB1 complementary molecular recognition of peptides. This mechanism could provide a robust synergistic action and a differential role of DRB1 and DQB1 in tissues and in the time-steps towards autoimmunity. In addition, we demonstrate that negatively charged residues in pockets 4 and 9 play a role in MS susceptibility. Our findings are supported by recent experiments using a closely related MS animal model. Overall, our analysis confirms the role of the DRB1-DQB1 haplotype in conferring disease predisposition and could provide a valuable aid in designing optimal therapeutic peptides for MS therapy.

HLA Ligandome Analysis Of Chronic Myeloid Leukemia (CML), Revealed Novel Tumor Associated Antigens For Peptide Based Immunotherapy

Despite the success of targeted therapy using tyrosine kinase inhibitors (TKIs), chronic myeloid leukemia (CML) remains largely incurable, most likely due to the treatment resistance of leukemic stem cells. Specific T-cell based immunotherapies for patients with CML might be able to eliminate these residual CML cells. For this goal the identification of tumor associated HLA-presented peptides, which are able to induce a tumor-specific T cell response, is indispensable. However, only few tumor associated antigens for CML are described till date. Thus the aim of this study was to identify for the first time naturally processed and presented HLA ligands from the cell surface of primary CML cells. HLA class I ligands from primary CML cells as well as from bone marrow mononuclear cell (BMNCs) and peripheral blood PBMCs of healthy donors were analyzed using the approach of direct isolation and identification of naturally presented HLA peptides by affinity chromatography and mass spectrometry (LC-MS/MS). LC-MS/MS peptide analysis provided qualitative and semi-quantitative information regarding the composition of the respective ligandomes. Comparative analysis of malignant and benign samples served to identify ligandome-derived tumor associated antigens (LiTAAs) and to select peptide vaccine candidates. So far 10 CML patients (8 chronic phase, 2 accelerated phase) and 30 healthy donors were analyzed within this study. We were able to identify a total of more than 8200 CML derived HLA ligands representing >4500 different source proteins, of which 734 were exclusively represented in CML, but not in healthy PBMCs/BMNCs. 55 of these CML exclusive antigens are presented on 3 or more of all examined CML patients, representing, as broadly represented LiTAAs, promising targets for peptide vaccination. For the first time, previously predicted CML tumor associated antigens for example Myeloperoxidase (10 peptide sequences on 7 CML patients) and Proteinase 3 (5 peptide sequences on 4 CML patients) were here confirmed by direct elution from primary CML cells, which also served to validate our methodological approach. Notably, beyond that we also identified a vast array of novel proteins (e.g. Carcinoembryonic antigen-related cell adhesion molecule 8, CEACAM8; Matrix metallopeptidase 8, MMP8; intracellular adhesion molecule 3, ICAM3) that are broadly and exclusively represented in the ligandome of CML cells.By providing for the first time HLA class I tumor associated antigens, directly obtained from the HLA ligandomes of CML patients, this study may pave the way for the future development of a multipeptide-based immunotherapy approach to eradicate residual CML cells after conventional TKI therapy. Disclosures:No relevant conflicts of interest to declare.

Characterization Of The HLA Class II Ligandome In Acute Myeloid Leukemia (AML) Reveals Novel Candidates For Peptide-Based Immunotherapy

CD4+ T cells are crucial for the induction and maintenance of cytotoxic T cell responses, but can also mediate direct tumor rejection. The therapeutic efficacy of peptide-based cancer vaccines may thus be improved by including HLA class II epitopes to stimulate T helper cells. In contrast to HLA class I ligands, only a small number of class II ligands of TAA has been described so far. We recently reported on the overexpression of HLA class II in AML cells as compared to autologous monocytes and granulocytes as well as on the first HLA class I leukemia associated antigens identified directly on the cell surface of primary AML cells (Stickel et. al. abstract in Blood 2012). In this study we characterized the HLA class II ligandome in AML to identify additional ligands for a peptide-based immunotherapy approach.HLA class II ligands from primary AML cells as well as bone marrow and peripheral blood mononuclear cell (BMNCs/PBMCs) of healthy donors were analyzed using the approach of direct isolation and identification of naturally presented HLA peptides by affinity chromatography and mass spectrometry (LC-MS/MS). LC-MS/MS peptide analysis provided qualitative and semi-quantitative information regarding the composition of the respective ligandomes. Comparative analysis of malignant and benign samples served to identify ligandome-derived tumor associated antigens (LiTAAs) and to select peptide vaccine candidates. Most abundantly detected peptides were functionally characterized with regard to their ability to induce a specific CD4+ T-cell response in healthy donors and in tumor patients using ELISpot. Samples from 10 AML patients (5 FLT3-ITD mutated) and 18 healthy donors were analyzed. We identified more than 2,100 AML-derived HLA class II ligands representing >1,000 different source proteins, of which 315 were exclusively represented in AML, but not in healthy PBMC/BMNC. Data mining for broadly represented LiTAAs pinpointed 26 HLA class II ligands from 8 source proteins that were presented exclusively on more than 40% of all analyzed AML samples as most promising targets. Amongst them were already described TAAs (e.g., RAB5A) as well as several so far understated proteins (e.g. calsyntenin 1, glycophorin A, mannose-binding lectin 2). Subset analysis revealed 58 LiTAAs presented exclusively on FLT3-ITD mutated AML cells. Additional screening for HLA class II ligands from described leukemia associated antigens showed positive results for NPM1 (1 peptide sequence) and MPO (13 peptide sequences). Peptides from calsyntenin 1 and RAB5A were able to elicit CD4+-T-cell response in 25% of tested AML patients (n=16). Thus, our study identified, for the first time, HLA class II tumor associated antigens directly obtained from the HLA ligandomes of AML patients and thereby represents a further step to our goal of developing a multipeptide vaccine for immunotherapy of AML. Disclosures:No relevant conflicts of interest to declare.

In silico Design of Discontinuous Peptides Representative of B and T-cell Epitopes from HER2-ECD as Potential Novel Cancer Peptide Vaccines

At present, the most common cause of cancer-related death in women is breast cancer. In a large proportion of breast cancers, there is the overexpression of human epidermal growth factor receptor 2 (HER2). This receptor is a 185 KDa growth factor glycoprotein, also known as the first tumor-associated antigen for different types of breast cancers. Moreover, HER2 is an appropriate cell-surface specific antigen for passive immunotherapy, which relies on the repeated application of monoclonal antibodies that are transferred to the patient. However, vaccination is preferable because it would stimulate a patient's own immune system to actively respond to a disease. In the current study, several bioinformatics tools were used for designing synthetic peptide vaccines. PEPOP was used to predict peptides from HER2 ECD subdomain III in the form of discontinuous-continuous B-cell epitopes. Then, T-cell epitope prediction web servers MHCPred, SYFPEITHI, HLA peptide motif search, Propred, and SVMHC were used to identify class-I and II MHC peptides. In this way, PEPOP selected 12 discontinuous peptides from the 3D structure of the HER2 ECD subdomain III. Furthermore, T-cell epitope prediction analyses identified four peptides containing the segments 77 (384-391) and 99 (495-503) for both B and T-cell epitopes. This work is the only study to our knowledge focusing on design of in silico potential novel cancer peptide vaccines of the HER2 ECD subdomain III that contain epitopes for both B and T-cells. These findings based on bioinformatics analyses may be used in vaccine design and cancer therapy; saving time and minimizing the number of tests needed to select the best possible epitopes.

Consequences of drug binding to immune receptors: Immune stimulation following pharmacological interaction with immune receptors (T-cell receptor for antigen or human leukocyte antigen) with altered peptide-human leukocyte antigen or peptide

Abstract Drugs may stimulate the immune system by forming hapten–carrier complexes or via their pharmacological features, namely by noncovalent binding to proteins such as immune receptors. The latter type of immune stimulation is called the p-i concept, meaning pharmacological interaction with immune receptors, which implies stimulation of the immune system by noncovalent binding of a drug to T-cell receptors for antigens (p-i TCR) or human leukocyte antigens (p-i HLA). The functional consequences of these interactions are heterogeneous: clinically, it can lead to T-cell mediated reactions such as Stevens–Johnson syndrome/toxic epidermal necrolysis, drug rash with eosinophilia and systemic symptoms, acute generalized exanthematous pustulosis, and maculopapular eruptions. If the drug binds to the TCR, it can become stimulatory, and an additional interaction with HLA/peptide complexes is necessary for full stimulation. The T-cell reaction can be oligoclonal or polyclonal. Binding of drugs to an HLA molecule can have two consequences: if the drug can modify the HLA molecule, a distinct repertoire of peptides might be presented: this is the altered peptide model. However, peptide exchange is not necessary to make the peptide-HLA complex immunogenic: if the drug binds to HLA, already the complex of altered HLA and normal peptide is immunogenic and able to stimulate T-cells (altered peptide-HLA model). The immunological and clinical consequences of different forms of the p-i concept are described with typical p-i binding drugs such as abacavir, carbamazepine, flucloxacillin, allopurinol, and sulfamethoxazole. Thereby the role of drug binding to HLA or TCR, the affinity of drug binding, additional TCR binding, and potential oligoclonality are described and compared.

HLA Peptide Length Preferences Control CD8+ T Cell Responses

Class I HLAs generally present peptides of 8-10 aa in length, although it is unclear whether peptide length preferences are affected by HLA polymorphism. In this study, we investigated the CD8(+) T cell response to the BZLF1 Ag of EBV, which includes overlapping sequences of different size that nevertheless conform to the binding motif of the large and abundant HLA-B*44 supertype. Whereas HLA-B*18:01(+) individuals responded strongly and exclusively to the octamer peptide (173)SELEIKRY(180), HLA-B*44:03(+) individuals responded to the atypically large dodecamer peptide (169)EECDSELEIKRY(180), which encompasses the octamer peptide. Moreover, the octamer peptide bound more stably to HLA-B*18:01 than did the dodecamer peptide, whereas, conversely, HLA-B*44:03 bound only the longer peptide. Furthermore, crystal structures of these viral peptide-HLA complexes showed that the Ag-binding cleft of HLA-B*18:01 was more ideally suited to bind shorter peptides, whereas HLA-B*44:03 exhibited characteristics that favored the presentation of longer peptides. Mass spectrometric identification of > 1000 naturally presented ligands revealed that HLA-B*18:01 was more biased toward presenting shorter peptides than was HLA-B*44:03. Collectively, these data highlight a mechanism through which polymorphism within an HLA class I supertype can diversify determinant selection and immune responses by varying peptide length preferences.

Immunodominant and subdominant WNV epitopes are differentially presented (P5005)

Abstract 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.

Human β-Cell Killing by Autoreactive Preproinsulin-Specific CD8 T Cells Is Predominantly Granule-Mediated With the Potency Dependent Upon T-Cell Receptor Avidity

The end-stage immunopathology of type 1 diabetes resulting in β-cell destruction appears to be strongly dominated by cytotoxic CD8 T lymphocytes (CD8 T cells). However, the mechanism of cytotoxicity used by autoreactive CD8 T cells in the human setting remains unknown. Using type 1 diabetes patient–derived preproinsulin-specific CD8 T-cell clones recognizing either an HLA-A2 (A*0201) or HLA-A24 (A*2402)-restricted epitope (peptide of preproinsulin [PPI]15–24, ALWGPDPAAA; or PPI3–11, LWMRLLPLL), we assessed the use of conventional mediators of cytotoxicity in the destruction of human β-cells in vitro compared with virus-specific cytotoxic CD8 T-cell clones. We show that PPI-specific CD8 T-cell clones are mainly reliant upon cytotoxic degranulation for inducing β-cell death. Furthermore, we find that in comparison with virus-specific CD8 T cells, there are differences in the killing potency of PPI-specific CD8 T cells that are not due to cell-intrinsic differences, but rather are mediated by differences in strength of signaling by peptide–HLA ligands. The study highlights the regulation of β-cell killing as a potential point for therapeutic control, including the possibility of blocking autoreactive CD8 T-cell function without impacting upon general immune competence.

Consensus classification of human leukocyte antigen class II proteins

Class II human leukocyte antigens (HLA II) are proteins involved in the human immunological adaptive response by binding and exposing some pre-processed, non-self peptides in the extracellular domain in order to make them recognizable by the CD4+ T lymphocytes. However, the understanding of HLA–peptide binding interaction is a crucial step for designing a peptide-based vaccine because the high rate of polymorphisms in HLA class II molecules creates a big challenge, even though the HLA II proteins can be grouped into supertypes, where members of different class bind a similar pool of peptides. Hence, first we performed the supertype classification of 27 HLA II proteins using their binding affinities and structural-based linear motifs to create a stable group of supertypes. For this purpose, a well-known clustering method was used, and then, a consensus was built to find the stable groups and to show the functional and structural correlation of HLA II proteins. Thus, the overlap of the binding events was measured, confirming a large promiscuity within the HLA II–peptide interactions. Moreover, a very low rate of locus-specific binding events was observed for the HLA-DP genetic locus, suggesting a different binding selectivity of these proteins with respect to HLA-DR and HLA-DQ proteins. Secondly, a predictor based on a support vector machine (SVM) classifier was designed to recognize HLA II-binding peptides. The efficiency of prediction was estimated using precision, recall (sensitivity), specificity, accuracy, F-measure, and area under the ROC curve values of random subsampled dataset in comparison with other supervised classifiers. Also the leave-one-out cross-validation was performed to establish the efficiency of the predictor. The availability of HLA II–peptide interaction dataset, HLA II-binding motifs, high-quality amino acid indices, peptide dataset for SVM training, and MATLAB code of the predictor is available at http://sysbio.icm.edu.pl/HLA.Electronic supplementary materialThe online version of this article (doi:10.1007/s00251-012-0665-6) contains supplementary material, which is available to authorized users.

TCR Bias and HLA Cross-Restriction Are Strategies of Human Brain-Infiltrating JC Virus-Specific CD4+ T Cells during Viral Infection

Virus-specific CD4(+) T cells play a central role in control of viral pathogens including JC polyoma virus (JCV) infection. JCV is a ubiquitous small DNA virus that leads to persistent infection of humans with no clinical consequences. However, under circumstances of immunocompromise, it is able to cause an opportunistic and often fatal infection of the brain called progressive multifocal leukoencephalopathy (PML). PML has emerged as a serious adverse event in multiple sclerosis patients treated with the anti-VLA-4 mAb natalizumab, which selectively inhibits cell migration across the blood-brain barrier and the gut's vascular endothelium thus compromising immune surveillance in the CNS and gut. In a multiple sclerosis patient who developed PML under natalizumab treatment and a vigorous immune response against JCV after Ab washout, we had the unique opportunity to characterize in detail JCV-specific CD4(+) T cell clones from the infected tissue during acute viral infection. The in-depth analysis of 14 brain-infiltrating, JCV-specific CD4(+) T cell clones demonstrated that these cells use an unexpectedly broad spectrum of different strategies to mount an efficient JCV-specific immune response including TCR bias, HLA cross-restriction that increases avidity and influences in vivo expansion, and a combination of Th1 and Th1-2 functional phenotypes. The level of combinatorial diversity in TCR- and HLA-peptide interactions used by brain-infiltrating, JCV-specific CD4(+) T cells has not, to our knowledge, been reported before in humans for other viral infections and confirms the exceptional plasticity that characterizes virus-specific immune responses.

131-P

Aim As part of work evaluating peptide contribution to alloreactivity we have sought to assess the binding of candidate HLA peptides into HLA∗02:01 molecules. Methods HLA derived peptides predicted to be capable of being bound by HLA-A∗02:01 were defined using the SYFPEITHI database and commercially synthesised. A TAP deficient,HLA-A∗02:01 positive cell line (T2) was utilised in assessment of peptide binding via measurement of surface expression of HLA-A∗02:01 using a flow cytometric approach. 100 μg/ml β-2-microglobulin and 25 μg/ml (saturating concentration) of HLA derived candidate peptides were incubated overnight with T2. HLA-A∗02:01 stabilisation was assessed using PE conjugated anti W6/32 mab. A HLA class II binding peptide was used as a negative control and a HLA-A∗02 restricted HA-2 peptide was a positive control. A competitive binding assay was also established using HA-2 directly conjugated to FAM (HA-2-FAM). Competitive binding consisted of 22hr culture with low affinity peptide followed by 2 hr incubation with high affinity peptide to compete with bound low affinity peptides. Results HLA-CII neg control peptide and no peptide control showed similar HLA class I expression (FL2 MFI shown), CII = 924, No peptide = 1099. HA-2 pos control showed increased HLA class I expression, HA-2 = 3004. 2 of 10 synthsized HLA peptides demonstrated positive binding, with a lower affinity than HA-2, pep 1 = 1500, pep 2 = 1777 Peptide competitive binding assay (showing FL1 and FL2 MFI respectively), pep 1 (low affinity) = 106 and 1701, pep 1+2hr with HA-2-FAM = 448 and 1715, 2hr HA-2-FAM = 368 and 691. Conclusions Consistent levels of HLA on the cell surface were seen for low affinity peptide and +2hr high affinity peptide as assessed via W6/32. However FAM high affinity peptide was clearly bound in the pep 1 +2hr HA-2FAM competitive binding assay, suggesting either loss of pep 1 HLA stabilized molecules being replaced with equal HA-1-FAM peptide stabilized molecules, or exchange of pep 1 for HA-2-FAM at the cell surface.

58-OR

Aim 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. Methods High avidity antibodies specific for peptide/HLA-A∗02:01 complexes, SVG9, SLF9, and YTM9 were generated by mouse immunization with peptide/HLA complexes. Specific antibody producing hybridomas were expanded and the antibodies were purified from the cell supernatant. The purified antibodies were then used to stain WNV infected HeLa cells transfected with HLA-A∗02:01. Relative number of complexes was measured using flow cytometry. TAP inhibition studies were performed using TAP inhibitor protein ICP47. Results In this study, we demonstrate that viral peptide ligands are differentially expressed by A∗02:01 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 infected cells show that all three epitopes are TAP dependent. Conclusions Using these highly specific reagents we show that there is differential ligand presentation within the restrictive allele A∗02:01. 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 immune dominant epitope SVG9. We then show that this differential presentation was not due the TAP dependence of the ligands.

Harmonization of the intracellular cytokine staining assay

Active immunotherapy for cancer is an accepted treatment modality aiming to reinforce the T-cell response to cancer. T-cell reactivity is measured by various assays and used to guide the clinical development of immunotherapeutics. However, data obtained across different institutions may vary substantially making comparative conclusions difficult. The Cancer Immunotherapy Immunoguiding Program organizes proficiency panels to identify key parameters influencing the outcome of commonly used T-cell assays followed by harmonization. Our successes with IFNγ-ELISPOT and peptide HLA multimer analysis have led to the current study on intracellular cytokine staining (ICS). We report the results of three successive panels evaluating this assay. At the beginning, 3 out of 9 participants (33 %) were able to detect >6 out of 8 known virus-specific T-cell responses in peripheral blood of healthy individuals. This increased to 50 % of the laboratories in the second phase. The reported percentages of cytokine-producing T cells by the different laboratories were highly variable with coefficients of variation well over 60 %. Variability could partially be explained by protocol-related differences in background cytokine production leading to sub-optimal signal-to-noise ratios. The large number of protocol variables prohibited identification of prime guidelines to harmonize the assays. In addition, the gating strategy used to identify reactive T cells had a major impact on assay outcome. Subsequent harmonization of the gating strategy considerably reduced the variability within the group of participants. In conclusion, we propose that first basic guidelines should be applied for gating in ICS experiments before harmonizing assay protocol variables.Electronic supplementary materialThe online version of this article (doi:10.1007/s00262-012-1282-9) contains supplementary material, which is available to authorized users.

Stability of peptide–HLA-I complexes and tapasin folding facilitation – tools to define immunogenic peptides

Only a small fraction of the peptides generated inside the cell end up being presented by HLA-I on the cell surface. High stability of peptide–HLA-I complexes and a low HLA-I tapasin-facilitation have been proposed to predict immunogenicity. We here set out to investigate if these parameters correlated and defined immunogenic peptides. Both peptide–HLA–B∗08:01 and peptide–HLA–A∗02:01 complexes showed small differences in tapasin-facilitation and larger differences in stability. This suggests that the stability of immunogenic peptide–HLA-I complexes vary above an HLA-I allomorph dependent lower limit (e.g. >2h for HLA–A∗02:01), immunogenicity predicted by tapasin-facilitation may be defined by an equally allomorph unique upper value (e.g. tapasin-facilitation <1.5 for HLA–A∗02:01), and variation above the stability-threshold does not directly reflect a variation in tapasin-facilitation.

Coeliac disease: the showcase of interaction between genes, environment and immunology in chronic tissue inflammation

Coeliac disease is a multifactorial disease controlled by multiple genes and environmental factors. Gluten proteins of grains are a key environmental factor as the disease goes in compete remission when gluten proteins are eliminated from the diet of the patients. The disease can be categorised as both a food hypersensitivity disorder as well as an autoimmune disease. Autoantibodies to the enzyme transglutaminase 2 (TG2) typical of coeliac disease have higher disease specificity and sensitivity than autoantibodies for any other disorder. Both the autoantibodies and the disease lesion of the small intestine, characterised by villous blunting, lamina propriaplasmacytosis and intraepithelial lymphocytosis, are reversibly dependent gastrointestinal exposure to cereal gluten proteins. There is strong association of coeliac disease with HLA-DQ2.5 and HLA-DQ8, and the presence of antibodies to TG2 is also completely dependent on carriage of DQ2.5 or DQ8. In addition to HLA genes, genome wide association studies have so far identified 39 non-loci implicated in the disease. Most of the coeliac disease susceptibility genes are related to the function of antigen presenting cells and T cells, and many risk genes are shared with organ specific autoimmune diseases. Research in our laboratory has demonstrated that gluten reactive CD4 T cells can be found in the lamina propria of coeliac disease patients, but not healthy controls. These T cells recognise proline-rich gluten peptides that have become deamidated by TG2 in the context of DQ2.5 or DQ8 suggesting that preferential antigen presentation of as the reason for the HLA association. DQ2.5 and DQ8 is necessary but not sufficient for coeliac disease development, suggesting that activation of gluten reactive CD4 T cells is a key step in the pathogenesis. Many similar, yet distinct T-cell epitopes exist. The selection of gluten T-cell epitopes depends on gastrointestinal proteolysis, TG2 specificity and HLA peptide binding. Intraepithelial CD8 that bear NK cell receptors are involved in killing of stressed enterocytes. Although the mechanisms still have to be elucidated, this process seems to involve the gluten reactive CD4 T cells. A strong anti-gluten T cell response require high HLA binding stability of gluten peptides, and the disparate HLA association between two closely related HLA molecules, HLA-DQ2.5 and HLA-DQ2.2, seems to relate to this phenomenon. Finally, among the plasma cells of the lesion, many of them (10%) are specific for TG2. The TG2 specific plasma cells utilise a limited repertoire of variable genes with low degree of somatic mutation. Thus this antibody response, despite being part of a chronic condition, bears signs of a primary response. Together, these findings highlight that coeliac disease offers unique opportunities for dissection of T cell and B cell responses that lead to an autoimmune disease.

The Human Immunopeptidome Project, a Suggestion for yet another Postgenome Next Big Thing

The time is ripe for staging the Human Immunopeptidome Project, whose goal is to analyze the full repertoires of peptides bound to the HLA molecules, in both health and disease. Mass spectrometry technologies have matured to enable comprehensive analyses of both the membrane-bound and the plasma soluble immunopeptidomes associated with each of the HLA allomorphs and the different diseases. The expected outcomes of such project will include basic understanding of the molecular mechanisms involved with formation of immunopeptidomes, correlating them with their source cellular proteomes, definition of both the consensus motifs and the scope of each allomorphs-specific immunopeptidomes, and most importantly, identification of disease-related HLA peptides, which may eventually serve as biomarkers or immunotherapeutics. Ideally, the Human Immunopeptidome Project will become public and the gathered data will be shared, as soon as possible. Other immunopeptidome projects, of other animals, will follow suit.

Immune system simulation online

The recognition of antigenic peptides is a major event of an immune response. In current mesoscopic-scale simulators of the immune system, this crucial step has been modeled in a very approximated way. We have equipped an agent-based model of the immune system with immuno-informatics methods to allow the simulation of the cardinal events of the antigenic recognition, going from single peptides to whole proteomes. The recognition process accounts for B cell-epitopes prediction through Parker-scale affinity estimation, class I and II HLA peptide prediction and binding through position-specific scoring matrices based on information from known HLA epitopes prediction tools, and TCR binding to HLA-peptide complex calculated as the averaged sum of a residue-residue contact potential. These steps are executed for all lymphocytes agents encountering the antigen in a wide-reaching Monte Carlo simulation. http://www.cbs.dtu.dk/services/C-ImmSim-10.1/