{
  "abstract": "Background IBD is a chronic inflammatory condition driven by complex genetic and immune interactions, yet preclinical models often fail to fully recapitulate all aspects of the human disease. A systematic comparison of commonly used IBD models is essential to identify conserved molecular mechanisms and improve translational relevance.Objective We performed a multimodel transcriptomic analysis of 13 widely used IBD mouse models to uncover coregulatory gene networks conserved between preclinical colitis/ileitis and human IBD and to define model-specific and conserved cellular, subcellular and molecular signatures.Design We employed comparative transcriptomic analyses with curated and a priori statistical correlative methods between mouse models versus IBD patient datasets at both bulk and single-cell levels.Results We identify IBD-related pathways, ontologies and cellular compositions that are translatable between mouse models and patient cohorts. We further describe a conserved core inflammatory signature of IBD-associated genes governing T-cell homing, innate immunity and epithelial barrier that translates into the new mouse gut Molecular Inflammation Score (mMIS). Moreover, specific mouse IBD models have distinct signatures for B-cell, T-cell and enteric neurons. We discover that transcriptomic relatedness of models is a function of the mode of induction, not the canonical immunotype (Th1/Th2/Th17). Moreover, the model compendium database is made available as a web explorer ( http://trr241.hosting.rrze.uni-erlangen.de/SEPIA/).Conclusion This integrated multimodel approach provides a framework for systematically assessing the molecular landscape of intestinal inflammation. Our findings reveal conserved inflammatory circuits, refine model selection, offering a valuable resource for the IBD research community.",
  "authors": [
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Miguel Gonzalez-Acera"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Jay V Patankar"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Lena Erkert"
    },
    {
      "affiliations": [
        "Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany",
        "Deutsches Rheuma-Forschungszentrum, ein Institut der Leibniz-Gemeinschaft, Berlin, Germany"
      ],
      "name": "Roodline Cineus"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Reyes Gamez-Belmonte"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Tamara Leupold"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Marvin Bubeck"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Li-Li Bao"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Martin Dinkel"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Ru Wang"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Laura Schickedanz"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Heidi Limberger"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Iris Stolzer"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Katharina Gerlach"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Leonard Diemand"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Fabrizio Mascia"
    },
    {
      "affiliations": [
        "Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, Erlangen, Bayern, Germany"
      ],
      "name": "Pooja Gupta"
    },
    {
      "affiliations": [
        "Department of Surgery, Universitätsklinikum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany"
      ],
      "name": "Elisabeth Naschberger"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Kristina Koop"
    },
    {
      "affiliations": [
        "Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria"
      ],
      "name": "Christina Plattner"
    },
    {
      "affiliations": [
        "Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria"
      ],
      "name": "Gregor Sturm"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Benno Weigmann"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Claudia Günther"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Stefan Wirtz"
    },
    {
      "affiliations": [
        "Department of Surgery, Universitätsklinikum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany"
      ],
      "name": "Michael Stürzl"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Kai Hildner"
    },
    {
      "affiliations": [
        "iPATH.Berlin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany"
      ],
      "name": "Anja A Kühl"
    },
    {
      "affiliations": [
        "Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany"
      ],
      "name": "Britta Siegmund"
    },
    {
      "affiliations": [
        "Department of Ophthalmology, Universitätsklinikum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany"
      ],
      "name": "Andreas Gießl"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Raja Atreya"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany",
        "Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany",
        "Deutsches Rheuma-Forschungszentrum, ein Institut der Leibniz-Gemeinschaft, Berlin, Germany",
        "Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, Erlangen, Bayern, Germany",
        "Department of Surgery, Universitätsklinikum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany",
        "Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria",
        "iPATH.Berlin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany",
        "Department of Ophthalmology, Universitätsklinikum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany"
      ],
      "name": "TRR241 IBDome Consortium"
    },
    {
      "affiliations": [
        "Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany",
        "Deutsches Rheuma-Forschungszentrum, ein Institut der Leibniz-Gemeinschaft, Berlin, Germany"
      ],
      "name": "Ahmed N Hegazy"
    },
    {
      "affiliations": [
        "Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria"
      ],
      "name": "Zlatko Trajanoski"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Markus F Neurath"
    },
    {
      "affiliations": [
        "Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany",
        "Deutsche Zentrum Immuntherapie (DZI), Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany"
      ],
      "name": "Christoph Becker"
    }
  ],
  "title": "Integrated multimodel analysis of intestinal inflammation exposes key molecular features of preclinical and clinical IBD",
  "uid": "dc0637a3-89d2-5dc1-8e5a-bfb6d102cc5e"
}