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Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the causative agent of one of the most important porcine diseases with a high impact on animal health, welfare, and production economy. PRRSV exhibits a multitude of immunoevasive strategies that, in combination with a very high mutation rate, has hampered the development of safe and broadly protective vaccines. Aiming at a vaccine inducing an effective cytotoxic T cell response, a bioinformatics approach was taken to identify conserved PRRSV-derived peptides predicted to react broadly with common swine leukocyte antigen (SLA) class I alleles. Briefly, all possible 9- and 10-mer peptides were generated from 104 complete PRRSV type 2 genomes of confirmed high quality, and peptides with high binding affinity to five common SLAs were identified combining the NetMHCpan and positional scanning combinatorial peptide libraries binding predictions. Predicted binders were prioritized according to genomic conservation and SLA coverage using the PopCover algorithm. From this, 53 peptides were acquired for further analysis. Binding affinity and stability of a subset of 101 peptide-SLA combinations were validated in vitro for 4 of the 5 SLAs. Eventually, 23% of the predicted peptide-SLA combinations showed to form complexes with a dissociation half-life ≥30 min. Additionally, combining the two prediction methods proved to be more robust across alleles than either method used alone in terms of predicted-to-observed correlations. In summary, our approach represents a finely tuned epitope prediction pipeline providing a rationally selected ensemble of peptides for future in vivo experiments with pigs expressing the included SLAs. Fil: Welner, Simon. Technical University of Denmark; Dinamarca Fil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina Fil: Rasmussen, Michael. Universidad de Copenhagen; Dinamarca Fil: Buus, Søren. Universidad de Copenhagen; Dinamarca Fil: Jungersen, Gregers. Technical University of Denmark; Dinamarca Fil: Larsen, Lars Erik. Technical University of Denmark; Dinamarca

Autoantibodies against centromere protein -F have been reported to be associated with various types of cancer with poor prognosis. The characterization of these autoantibody specificities is important in both diagnostics and basic research. In this study, we mapped the epitope (NELSRIRSEKA) of two monoclonal centromere protein F antibodies. The epitope was localized by screening of overlapping peptides followed by a fast and efficient estimation of the minimal peptide length required for antibody recognition, based on the screening of terminally truncated resin-bound peptide analogs. The epitope was determined through competitive inhibition assays of systematically truncated free peptides. In addition, the importance of the involved amino acid side chains of the identified epitope was determined through competitive inhibition assays using alanine-substituted analogs. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.

Quantitative and qualitative assessment of antigen-specific cytotoxic T cell (CTL) responses in pigs is not a straightforward process. Through the years we have developed a series of reagents, tools and protocols to characterize peptide-specific CTL responses in pigs.The most common recombinant SLA heavy chains were produced and peptide binding motifs were determined by assays measuring the affinity and stability of the peptide-SLA complex (pSLA) interaction. These results have been used to train neural networks to predict the binding of any pSLA (http://www.cbs.dtu.dk/services/). Recombinant SLA molecules complexed with verified binding peptides can be assembled to SLA multimers for staining of peptide-specific CTLs, and measured by flow cytometry, as we have shown with FMDV and influenza. This, however, requires SLA-matched pigs for which we have developed two methods: a sequence-based, high-resolution SLA genotyping method by standard PCR for specific detection of eight in-house SLA molecules; and a next-generation sequencing method for parallel detection of up to 50 samples of barcoded cDNA PCR products spanning exon 2 and 3. The latter for a wider characterization of expressed alleles in candidate pigs.The in vivo generation of CTL responses to antigens following peptide immunizations is thought to require cross-presentation in appropriate dendritic cells (DC). In mice this was linked to targeting of CD103+DCs recruited after intraperitoneal immunizations. We have therefore developed a protocol for intraperitoneal delivery of peptides formulated in poly(I:C)/MMG-decorated liposomes (CAF09) to investigate the influence of peptide dose on the generation of CTL vs. antibody responses. Finally, the induced CTL killing was assessed by an in vivo cytotoxicity assay, where purified autologous PBMCs, fluorescently labeled and pulsed with target peptides, were reinjected into the donor. The in vivo killing of peptide-pulsed cells was measured by flow cytometry relative to non-pulsed PBMCs at different time points after cell transfer.

Immunotherapy has increased overall survival of metastatic cancer patients, and cancer antigens are promising vaccine targets. To fulfill the promise, appropriate tailoring of the vaccine formulations to mount in vivo cytotoxic T cell (CTL) responses toward co-delivered cancer antigens is essential. Previous development of therapeutic cancer vaccines has largely been based on studies in mice, and the majority of these candidate vaccines failed to induce therapeutic responses in the subsequent human clinical trials. Given that antigen dose and vaccine volume in pigs are translatable to humans and the porcine immunome is closer related to the human counterpart, we here introduce pigs as a supplementary large animal model for human cancer vaccine development. IDO and RhoC, both important in human cancer development and progression, were used as vaccine targets and 12 pigs were immunized with overlapping 20mer peptides spanning the entire porcine IDO and RhoC sequences formulated in CTL-inducing adjuvants: CAF09, CASAC, Montanide ISA 51 VG, or PBS. Taking advantage of recombinant swine MHC class I molecules (SLAs), the peptide-SLA complex stability was measured for 198 IDO- or RhoC-derived 9-11mer peptides predicted to bind to SLA-1(*)04:01, -1(*)07:02, -2(*)04:01, -2(*)05:02, and/or -3(*)04:01. This identified 89 stable (t½ ≥ 0.5 h) peptide-SLA complexes. By IFN-γ release in PBMC cultures we monitored the vaccine-induced peptide-specific CTL responses, and found responses to both IDO- and RhoC-derived peptides across all groups with no adjuvant being superior. These findings support the further use of pigs as a large animal model for vaccine development against human cancer.

Background Centromere protein-F (CENP-F) is a large nuclear protein of 367 kDa, which is involved in multiple mitosis-related events such as proper assembly of the kinetochores, stabilization of heterochromatin, chromosome alignment and mitotic checkpoint signaling. Several studies have shown a correlation between CENP-F and cancer, e.g. the expression of CENP-F has been described to be upregulated in cancer cells. Furthermore, several studies have described a significant correlation between the expression of autoantibodies to CENP-F and cancer. Methods Autoantibodies to CENP-F were detected in a small number of samples during routine indirect immunofluorescence (IIF) analysis for anti-nuclear antibodies (ANA) using HEp-2 cells as substrate. Using overlapping synthetic peptides covering a predicted structural maintenance of chromosomes (SMC) domain, we developed an enzyme-linked immunosorbent assay (ELISA) for detection of CENP-F antibodies. Results Analyzing the reactivity of the sera positive in IIF for CENP-F antibodies to overlapping CENP-F peptides, we showed that autoantibodies to several peptides correlate with the presence of antibodies to CENP-F and a diagnosis of cancer, as increased CENP-F antibody expression specific for malignant cancer patients to five peptides was found (A9, A12, A14, A16, A27). These antibodies to CENP-F in clinical samples submitted for ANA analysis were found to have a positive predictive value for cancer of 50%. Furthermore, the expression of cancer-correlated CENP-F antibodies seemed to increase as a function of time from diagnosis. Conclusion These results conform to previous findings that approximately 50% of those patients clinically tested for ANA analyses who express CENP-F antibodies are diagnosed with cancer, confirming that these antibodies may function as circulating tumor markers. Thus, a peptide-based CENP-F ELISA focused on the SMC domain may aid in identifying individuals with a potential cancer.

Autoantibodies against centromere protein -F have been reported to be associated with various types of cancer with poor prognosis. The characterization of these autoantibody specificities is important in both diagnostics and basic research. In this study, we mapped the epitope (NELSRIRSEKA) of two monoclonal centromere protein F antibodies. The epitope was localized by screening of overlapping peptides followed by a fast and efficient estimation of the minimal peptide length required for antibody recognition, based on the screening of terminally truncated resin-bound peptide analogs. The epitope was determined through competitive inhibition assays of systematically truncated free peptides. In addition, the importance of the involved amino acid side chains of the identified epitope was determined through competitive inhibition assays using alanine-substituted analogs.

Immunotherapy against cancer has shown increased overall survival of metastatic cancer patients and is a promising new vaccine target. For this to succeed, appropriate tailoring of vaccine formulations to mount in vivo cytotoxic T cell (CTL) responses towards co-delivered cancer antigens is important. Previous development of therapeutic cancer vaccines has largely been based on studies in mice and the majority of these candidate vaccines failed to establish therapeutic responses in subsequent human clinical trials. Since the porcine immunome is more closely related to the human counterpart, we here introduce pigs as a superior large animal model for human cancer vaccine development via the use of our unique technology for swine leukocyte antigen (SLA) production. IDO and RhoC, both known to be important in human cancer development and progression, were used as vaccine targets. Pigs were immunized with overlapping 20-mer peptides spanning the entire porcine IDO and RhoC sequences formulated in a panel of CTL-inducing adjuvants. 198 candidate IDO- and RhoC-derived 9-11mer peptides potentially binding to SLA- 1*04:01, -1*07:02, -2*04:01, -2*05:02 and/or -3*04:01 were identified in silico, and peptide-SLA complex stability measurements revealed 89 stable (t½ ≥ 0.5 hour) complexes. Vaccine-induced peptide-specific CTL responses were monitored using IFN-γ release as a read out. We found responses to IDO- and RhoC-derived peptides across all groups; surprisingly non-stably binding peptides also induced responses. None of the adjuvants was found to be superior as they were all capable of generating CTL responses to IDO and RhoC hence supporting the further use of pigs as a large animal model for vaccine development against human cancer.

The development of vaccines against porcine reproductive and respiratory syndrome virus (PRRSV) has been hampered by the high mutation rate and the multiple immunoevasive strategies of the virus.With the overall aim of designing a broad coverage vaccine that induces an effective CTL response against PRRSV, we have used a bioinformatics approach to identify common PRRSV type 2 epitopes predicted to react broadly with predominant swine MHC (SLA) alleles.All possible 9- and 10-mer peptides derived from 104 wild-type strains were analyzed in silico for their predicted binding affinity to 3 common SLA class I alleles and ranked according to genomic conservation and SLA binding coverage. Of the 53 top-ranked peptides, 33 were verified in vitro as high affinity binders. Polyepitope gene cassettes of these peptides, flanked by an upstream ubiquitin sequence and a downstream FLAG tag, were cloned into a classical swine fever virus (CSFV)-derived replicon vector. Virus replicon particles (VRP) were rescued by transfection of a complementing cell line with replicon RNA. Polyepitope expression and subsequent proteasomal degradation was confirmed indirectly by increased FLAG-tagged protein detection in the presence of a proteasome inhibitor.Finally, a vaccination-challenge experiment using 18 SLA-matched pigs is currently being conducted until July 2016 in which a test group and a control group are being vaccinated twice with VRPs expressing PRRSV epitopes and non-sense control epitopes, respectively, before challenged with live wild type PRRSV. The induced epitope specific cell-mediated immune responses are being monitored by ELISPOT, flow cytometry and cytotoxicity assays, and the degree of protection against infection will be characterized by qPCR and antibody analysis. The results will be available for IVIS.This study exemplifies how bioinformatics epitope prediction, recombinant SLA molecules and RNA virus replicon design can be used to engineer a replicating non-propagating vaccine tailored to deliver conserved and immunogenic CTL epitopes.

Immune therapy of cancer has recently experienced a great breakthrough with prolonged overall survival in patients with metastatic disease following the use of checkpoint inhibitors and T cell therapy with ex vivo expanded CD8+ cytotoxic T cells (CTLs). In the further development of immune therapies against cancer, vaccine formulations tailored to mount in vivo CTL responses towards co-delivered cancer antigens will be an important hallmark. Recognition of antigen-derived peptides presented in the context of major histocompatibility complex (MHC) class I molecules on cancer cells is a requirement for activation of CTLs. Previously, the development of therapeutic anti-cancer vaccines have largely been based on rodent models, in particular mice; however the majority of these fail to establish a therapeutic response once put into clinical trials. Pigs have the potential of serving as a model superior to rodents as they are more closely related to humans in terms of immunology and physiology. Here, we introduce pigs as a supplementary large animal model for human cancer vaccine development via the use of our unique technology for swine leukocyte antigen (SLA) production. IDO and RhoC, two tumor antigens previously identified as important players in human cancer development and progression, were used as vaccine targets. Using peptide-MHC-I binding predictors we identified IDO-derived and RhoC-derived candidate peptides potentially binding to five different broadly distributed SLA molecules. We measured the peptide-SLA complex stability of these and found a total of 89 stable (t½ ≥ 0.5 hours) peptide-MHC complexes with SLA-1*04:01, -1*07:02, -2*04:01, -2*05:02 and/or -3*04:01. For a pilot study, 12 pigs were immunized with overlapping 20-mer peptides spanning the entire IDO and RhoC sequences formulated in a panel of CTL-inducing adjuvants. Vaccine and adjuvant efficacy will be evaluated through immunological assays among others including ex vivo stimulation of whole blood with identified stable SLA-binding peptides and quantification of peptide-specific CTLs. Hence, these data elucidate the potential in using pigs as a large animal model for human anti-cancer vaccine development.