title: Expitope: a web server for epitope expression.
abstract: BACKGROUND
  Adoptive T cell therapies based on introduction of new T cell receptors (TCRs) into patient recipient T cells is a promising new treatment for various kinds of cancers. A major challenge, however, is the choice of target antigens. If an engineered TCR can cross-react with self-antigens in healthy tissue, the side-effects can be devastating. We present the first web server for assessing epitope sharing when designing new potential lead targets. We enable the users to find all known proteins containing their peptide of interest. The web server returns not only exact matches, but also approximate ones, allowing a number of mismatches of the users choice. For the identified candidate proteins the expression values in various healthy tissues, representing all vital human organs, are extracted from RNA Sequencing (RNA-Seq) data as well as from some cancer tissues as control. All results are returned to the user sorted by a score, which is calculated using well-established methods and tools for immunological predictions. It depends on the probability that the epitope is created by proteasomal cleavage and its affinities to the transporter associated with antigen processing and the major histocompatibility complex class I alleles. With this framework, we hope to provide a helpful tool to exclude potential cross-reactivity in the early stage of TCR selection for use in design of adoptive T cell immunotherapy.
  
  
  METHODS
  The Expitope web server can be accessed via http://webclu.bio.wzw.tum.de/expitope.
authors: Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia.
authors: Kerstin
authors: K
authors: Haase
authors: Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia.
authors: Silke
authors: S
authors: Raffegerst
authors: Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia.
authors: Dolores J
authors: DJ
authors: Schendel
authors: Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia.
authors: Dmitrij
authors: D
authors: Frishman
mesh_terms: D017951:Antigen Presentation; D003429:Cross Reactions; D030562:Databases, Protein; D018984:Epitopes, T-Lymphocyte / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D020869:Gene Expression Profiling; D015395:Histocompatibility Antigens Class I / Q000235:genetics; D006801:Humans; D020407:Internet; D010455:Peptides / Q000276:immunology; D011506:Proteins / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D011948:Receptors, Antigen, T-Cell / Q000276:immunology; D017423:Sequence Analysis, RNA; D012984:Software; D013601:T-Lymphocytes / Q000276:immunology
chemical_list: D018984:Epitopes, T-Lymphocyte; D015395:Histocompatibility Antigens Class I; D010455:Peptides; D011506:Proteins; D011948:Receptors, Antigen, T-Cell