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      Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy

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          Abstract

          There are limitations in pre-clinical settings using mice as a basis for clinical development in humans. In cancer, similarities exist between humans and dogs; thus, the dog patient can be a link in the transition from laboratory research on mouse models to clinical trials in humans. Knowledge of the peptides presented on MHC molecules is fundamental for the development of highly specific T cell-based immunotherapies. This information is available for human MHC molecules but is absent for the canine MHC. In the present study, we characterized the binding motif of dog leukocyte antigen (DLA) class I allele DLA-88*50101, using human C1R and K562 transfected cells expressing the DLA-88*50101 heavy chain. MHC class I immunoaffinity-purification revealed 3720 DLA-88*50101 derived peptides, which enabled the determination of major anchor positions. The characterized binding motif of DLA-88*50101 was similar to HLA-A*02:01. Peptide binding analyses on HLA-A*02:01 and DLA-88*50101 via flow cytometry showed weak binding of DLA-88*50101 derived peptides to HLA-A*02:01, and vice versa. Our results present for the first time a detailed peptide binding motif of the canine MHC class I allelic product DLA-88*50101. These data support the goal of establishing dogs as a suitable animal model for the evaluation and development of T cell-based cancer immunotherapies, benefiting both dog and human patients.

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          Most cited references50

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          Gapped sequence alignment using artificial neural networks: application to the MHC class I system.

          Many biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to peptides of length 8-11 amino acids. On this relatively simple system, we developed a sequence alignment method based on artificial neural networks that allows insertions and deletions in the alignment.
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            Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.

            In this paper we describe an improved neural network method to predict T-cell class I epitopes. A novel input representation has been developed consisting of a combination of sparse encoding, Blosum encoding, and input derived from hidden Markov models. We demonstrate that the combination of several neural networks derived using different sequence-encoding schemes has a performance superior to neural networks derived using a single sequence-encoding scheme. The new method is shown to have a performance that is substantially higher than that of other methods. By use of mutual information calculations we show that peptides that bind to the HLA A*0204 complex display signal of higher order sequence correlations. Neural networks are ideally suited to integrate such higher order correlations when predicting the binding affinity. It is this feature combined with the use of several neural networks derived from different and novel sequence-encoding schemes and the ability of the neural network to be trained on data consisting of continuous binding affinities that gives the new method an improved performance. The difference in predictive performance between the neural network methods and that of the matrix-driven methods is found to be most significant for peptides that bind strongly to the HLA molecule, confirming that the signal of higher order sequence correlation is most strongly present in high-binding peptides. Finally, we use the method to predict T-cell epitopes for the genome of hepatitis C virus and discuss possible applications of the prediction method to guide the process of rational vaccine design.
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              Structure of the human class I histocompatibility antigen, HLA-A2.

              The class I histocompatibility antigen from human cell membranes has two structural motifs: the membrane-proximal end of the glycoprotein contains two domains with immunoglobulin-folds that are paired in a novel manner, and the region distal from the membrane is a platform of eight antiparallel beta-strands topped by alpha-helices. A large groove between the alpha-helices provides a binding site for processed foreign antigens. An unknown 'antigen' is found in this site in crystals of purified HLA-A2.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                28 November 2016
                2016
                : 11
                : 11
                : e0167017
                Affiliations
                [1 ]Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
                [2 ]Institute for Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
                [3 ]Immatics, Biotechnologies GmbH, Tuebingen, Germany
                [4 ]Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
                [5 ]Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
                [6 ]Applied Bioinformatics, Center of Bioinformatics and Department of Computer Science, University of Tuebingen, Tuebingen, Germany
                Centro Nacional de Biotecnologia, SPAIN
                Author notes

                Competing Interests: The commercial affiliations Immatics, Biotechnologies GmbH, Biomolecular Mass Spectrometry and Proteomics do not alter our adherence to PLOS ONE policies on sharing data and materials.

                • Conceptualization: OP HGR SB.

                • Data curation: SB DK.

                • Formal analysis: LB HS DK CS SB.

                • Funding acquisition: OP SB CS.

                • Investigation: OP SB FP CS KO LL.

                • Methodology: OP HS SS KO.

                • Project administration: OP.

                • Resources: HGR OP.

                • Software: LB TS.

                • Supervision: OP SB CS.

                • Validation: OP SB FP HS DK MDM.

                • Visualization: SB CS.

                • Writing – original draft: OP SB.

                • Writing – review & editing: SB CS FP KO LL DK MDM TS LB HS SS HGR OP.

                Article
                PONE-D-16-34325
                10.1371/journal.pone.0167017
                5125661
                27893789
                cd237994-f5c8-4d0b-8344-c1a4fef7cd01
                © 2016 Barth et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 26 August 2016
                : 7 November 2016
                Page count
                Figures: 5, Tables: 3, Pages: 19
                Funding
                Funded by: Dres. Bruns Stiftung
                Award Recipient :
                The funders Immatics, Biotechnologies GmbH, Biomolecular Mass Spectrometry and Proteomics provided no support in the form of salaries for authors [D.K., H.S. and T.S], and did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.
                Categories
                Research Article
                Medicine and Health Sciences
                Clinical Medicine
                Clinical Immunology
                Major Histocompatibility Complex
                Biology and Life Sciences
                Immunology
                Clinical Immunology
                Major Histocompatibility Complex
                Medicine and Health Sciences
                Immunology
                Clinical Immunology
                Major Histocompatibility Complex
                Biology and Life Sciences
                Immunology
                Major Histocompatibility Complex
                Medicine and Health Sciences
                Immunology
                Major Histocompatibility Complex
                Research and Analysis Methods
                Chemical Characterization
                Binding Analysis
                Research and Analysis Methods
                Spectrum Analysis Techniques
                Spectrophotometry
                Cytophotometry
                Flow Cytometry
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Sequence Analysis
                Sequence Motif Analysis
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Sequence Analysis
                Sequence Motif Analysis
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Sequence Analysis
                Sequence Alignment
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Sequence Analysis
                Sequence Alignment
                Biology and Life Sciences
                Organisms
                Animals
                Vertebrates
                Amniotes
                Mammals
                Dogs
                Biology and Life Sciences
                Biochemistry
                Peptides
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Protein Sequencing
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Protein Sequencing
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

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