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DNA methylation-based classification of sinonasal tumors

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  • Philipp Jurmeister

    (Ludwig Maximilians University Hospital Munich
    Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin
    Partner Site Berlin, and German Cancer Research Center (DKFZ)
    Partner Site Munich, and German Cancer Research Center (DKFZ))

  • Stefanie Glöß

    (Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology)

  • Renée Roller

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin
    Partner Site Berlin, and German Cancer Research Center (DKFZ)
    Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC))

  • Maximilian Leitheiser

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin)

  • Simone Schmid

    (Partner Site Berlin, and German Cancer Research Center (DKFZ)
    Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology)

  • Liliana H. Mochmann

    (Ludwig Maximilians University Hospital Munich)

  • Emma Payá Capilla

    (Ludwig Maximilians University Hospital Munich)

  • Rebecca Fritz

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin)

  • Carsten Dittmayer

    (Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology)

  • Corinna Friedrich

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin
    Partner Site Berlin, and German Cancer Research Center (DKFZ)
    MDC Graduate School, Max Delbrück Center for Molecular Medicine in the Helmholtz Association
    Humboldt Universität zu Berlin, Institute of Chemistry)

  • Anne Thieme

    (Partner Site Berlin, and German Cancer Research Center (DKFZ)
    Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology)

  • Philipp Keyl

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin)

  • Armin Jarosch

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin)

  • Simon Schallenberg

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin)

  • Hendrik Bläker

    (University Hospital Leipzig)

  • Inga Hoffmann

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin)

  • Claudia Vollbrecht

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin
    Partner Site Berlin, and German Cancer Research Center (DKFZ))

  • Annika Lehmann

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin)

  • Michael Hummel

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin
    Partner Site Berlin, and German Cancer Research Center (DKFZ))

  • Daniel Heim

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin)

  • Mohamed Haji

    (Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC))

  • Patrick Harter

    (Partner Site Munich, and German Cancer Research Center (DKFZ)
    Goethe-University Frankfurt am Main
    German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, German Cancer Research Center (DKFZ))

  • Benjamin Englert

    (Ludwig Maximilians University Hospital Munich)

  • Stephan Frank

    (Basel University Hospital)

  • Jürgen Hench

    (Basel University Hospital)

  • Werner Paulus

    (University Hospital Münster)

  • Martin Hasselblatt

    (University Hospital Münster)

  • Wolfgang Hartmann

    (University Hospital Münster)

  • Hildegard Dohmen

    (University of Giessen)

  • Ursula Keber

    (Philipps-University)

  • Paul Jank

    (Philipps-University Marburg and University Hospital Marburg)

  • Carsten Denkert

    (Philipps-University Marburg and University Hospital Marburg)

  • Christine Stadelmann

    (University Medical Centre Göttingen)

  • Felix Bremmer

    (University Medical Center)

  • Annika Richter

    (University Medical Center)

  • Annika Wefers

    (University Hospital Heidelberg
    German Cancer Research Center (DKFZ)
    University Medical Center Hamburg-Eppendorf)

  • Julika Ribbat-Idel

    (University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck)

  • Sven Perner

    (University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck
    Pathology, Research Center Borstel, Leibniz Lung Center
    German Center for Lung Research (DZL), Partner Site Luebeck)

  • Christian Idel

    (University Hospital Schleswig-Holstein, Campus Lübeck)

  • Lorenzo Chiariotti

    (Università degli Studi di Napoli Federico II
    CEINGE Biotecnologie Avanzate)

  • Rosa Monica

    (CEINGE Biotecnologie Avanzate)

  • Alfredo Marinelli

    (University Federico II)

  • Ulrich Schüller

    (University Medical Center Hamburg-Eppendorf
    University Medical Center Hamburg-Eppendorf
    Research Institute Children’s Cancer Center Hamburg)

  • Michael Bockmayr

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin
    University Medical Center Hamburg-Eppendorf
    Research Institute Children’s Cancer Center Hamburg)

  • Jacklyn Liu

    (University College London
    University College London)

  • Valerie J. Lund

    (University College London
    University College London)

  • Martin Forster

    (University College London
    University College London)

  • Matt Lechner

    (University College London
    University College London)

  • Sara L. Lorenzo-Guerra

    (Instituto de Investigación Sanitaria del Principado de Asturias (ISPA))

  • Mario Hermsen

    (Instituto de Investigación Sanitaria del Principado de Asturias (ISPA))

  • Pascal D. Johann

    (University Childrens’ Hospital Augsburg and EU-RHAB Registry)

  • Abbas Agaimy

    (Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital)

  • Philipp Seegerer

    (Technical University of Berlin)

  • Arend Koch

    (Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology)

  • Frank Heppner

    (Partner Site Berlin, and German Cancer Research Center (DKFZ)
    Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology)

  • Stefan M. Pfister

    (Hopp Children’s Cancer Center Heidelberg (KiTZ)
    German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)
    Heidelberg University Hospital)

  • David T. W. Jones

    (Hopp Children’s Cancer Center Heidelberg (KiTZ)
    German Cancer Research Center (DKFZ))

  • Martin Sill

    (Hopp Children’s Cancer Center Heidelberg (KiTZ))

  • Andreas Deimling

    (University Hospital Heidelberg
    German Cancer Research Center (DKFZ))

  • Matija Snuderl

    (Division of Neuropathology, NYU Langone Health
    Laura and Isaac Perlmutter Cancer Center, NYU Langone Health
    Division of Molecular Pathology and Diagnostics, NYU Langone Health)

  • Klaus-Robert Müller

    (Technical University of Berlin
    Korea University
    Max-Planck-Institute for Informatics
    BIFOLD – Berlin Institute for the Foundations of Learning and Data)

  • Erna Forgó

    (Stanford University School of Medicine)

  • Brooke E. Howitt

    (Stanford University School of Medicine)

  • Philipp Mertins

    (Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC))

  • Frederick Klauschen

    (Ludwig Maximilians University Hospital Munich
    Partner Site Munich, and German Cancer Research Center (DKFZ)
    BIFOLD – Berlin Institute for the Foundations of Learning and Data)

  • David Capper

    (Partner Site Berlin, and German Cancer Research Center (DKFZ)
    Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology)

Abstract

The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply a machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, one class composed of highly aggressive SMARCB1-deficient carcinomas and another class with tumors that represent potentially previously misclassified adenoid cystic carcinomas. Our findings can aid in improving the diagnostic classification of sinonasal tumors and could help to change the current perception of SNUCs.

Suggested Citation

  • Philipp Jurmeister & Stefanie Glöß & Renée Roller & Maximilian Leitheiser & Simone Schmid & Liliana H. Mochmann & Emma Payá Capilla & Rebecca Fritz & Carsten Dittmayer & Corinna Friedrich & Anne Thiem, 2022. "DNA methylation-based classification of sinonasal tumors," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34815-3
    DOI: 10.1038/s41467-022-34815-3
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    as
    1. David Capper & David T. W. Jones & Martin Sill & Volker Hovestadt & Daniel Schrimpf & Dominik Sturm & Christian Koelsche & Felix Sahm & Lukas Chavez & David E. Reuss & Annekathrin Kratz & Annika K. We, 2018. "DNA methylation-based classification of central nervous system tumours," Nature, Nature, vol. 555(7697), pages 469-474, March.
    2. Corinna Friedrich & Simon Schallenberg & Marieluise Kirchner & Matthias Ziehm & Sylvia Niquet & Mohamed Haji & Christin Beier & Jens Neudecker & Frederick Klauschen & Philipp Mertins, 2021. "Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    3. Christian Koelsche & Daniel Schrimpf & Damian Stichel & Martin Sill & Felix Sahm & David E. Reuss & Mirjam Blattner & Barbara Worst & Christoph E. Heilig & Katja Beck & Peter Horak & Simon Kreutzfeldt, 2021. "Sarcoma classification by DNA methylation profiling," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    Full references (including those not matched with items on IDEAS)

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