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Jurmeister P, Glöß S, Roller R, Leitheiser M, Schmid S, Mochmann LH, Payá Capilla E, Fritz R, Dittmayer C, Friedrich C, Thieme A, Keyl P, Jarosch A, Schallenberg S, Bläker H, Hoffmann I, Vollbrecht C, Lehmann A, Hummel M, Heim D, Haji M, Harter P, Englert B, Frank S, Hench J, Paulus W, Hasselblatt M, Hartmann W, Dohmen H, Keber U, Jank P, Denkert C, Stadelmann C, Bremmer F, Richter A, Wefers A, Ribbat-Idel J, Perner S, Idel C, Chiariotti L, Della Monica R, Marinelli A, Schüller U, Bockmayr M, Liu J, Lund VJ, Forster M, Lechner M, Lorenzo-Guerra SL, Hermsen M, Johann PD, Agaimy A, Seegerer P, Koch A, Heppner F, Pfister SM, Jones DTW, Sill M, von Deimling A, Snuderl M, Müller KR, Forgó E, Howitt BE, Mertins P, Klauschen F, Capper D. DNA methylation-based classification of sinonasal tumors. Nat Commun 2022; 13:7148. [PMID: 36443295 PMCID: PMC9705411 DOI: 10.1038/s41467-022-34815-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
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.
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Affiliation(s)
- Philipp Jurmeister
- grid.411095.80000 0004 0477 2585Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany ,grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584 German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Glöß
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Renée Roller
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.484013.a0000 0004 6879 971XProteomics Platform, Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Maximilian Leitheiser
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simone Schmid
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Liliana H. Mochmann
- grid.411095.80000 0004 0477 2585Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Emma Payá Capilla
- grid.411095.80000 0004 0477 2585Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Rebecca Fritz
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carsten Dittmayer
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Corinna Friedrich
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.419491.00000 0001 1014 0849MDC Graduate School, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Humboldt Universität zu Berlin, Institute of Chemistry, Berlin, Germany
| | - Anne Thieme
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Philipp Keyl
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Armin Jarosch
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simon Schallenberg
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Hendrik Bläker
- grid.411339.d0000 0000 8517 9062Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Inga Hoffmann
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudia Vollbrecht
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika Lehmann
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Hummel
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Heim
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mohamed Haji
- grid.484013.a0000 0004 6879 971XProteomics Platform, Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Patrick Harter
- grid.7497.d0000 0004 0492 0584 German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7839.50000 0004 1936 9721Institute of Neurology (Edinger Institute), Goethe-University Frankfurt am Main, Frankfurt am Main, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Englert
- grid.411095.80000 0004 0477 2585Institute of Neuropathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Stephan Frank
- grid.410567.1Department of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | - Jürgen Hench
- grid.410567.1Department of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | - Werner Paulus
- grid.16149.3b0000 0004 0551 4246Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Martin Hasselblatt
- grid.16149.3b0000 0004 0551 4246Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Wolfgang Hartmann
- grid.16149.3b0000 0004 0551 4246Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Hildegard Dohmen
- grid.8664.c0000 0001 2165 8627Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Ursula Keber
- grid.10253.350000 0004 1936 9756Institute of Neuropathology, Philipps-University, Marburg, Germany
| | - Paul Jank
- grid.10253.350000 0004 1936 9756Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | - Carsten Denkert
- grid.10253.350000 0004 1936 9756Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | - Christine Stadelmann
- grid.411984.10000 0001 0482 5331Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Felix Bremmer
- grid.411984.10000 0001 0482 5331Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Annika Richter
- grid.411984.10000 0001 0482 5331Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Annika Wefers
- grid.5253.10000 0001 0328 4908Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.13648.380000 0001 2180 3484Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julika Ribbat-Idel
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sven Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany ,grid.418187.30000 0004 0493 9170Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany ,grid.452624.3German Center for Lung Research (DZL), Partner Site Luebeck, Luebeck, Germany
| | - Christian Idel
- grid.412468.d0000 0004 0646 2097Department of Otorhinolaryngology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Lorenzo Chiariotti
- grid.4691.a0000 0001 0790 385XDipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy ,grid.4691.a0000 0001 0790 385XCEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Rosa Della Monica
- grid.4691.a0000 0001 0790 385XCEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Alfredo Marinelli
- grid.4691.a0000 0001 0790 385XDepartment of Medicina Clinica e Chirurgia, University Federico II, Naples, Italy
| | - Ulrich Schüller
- grid.13648.380000 0001 2180 3484Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany ,grid.13648.380000 0001 2180 3484Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany ,grid.470174.1Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Michael Bockmayr
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.13648.380000 0001 2180 3484Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany ,grid.470174.1Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Jacklyn Liu
- grid.83440.3b0000000121901201UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK ,grid.83440.3b0000000121901201UCL Academic Head and Neck Centre, Division of Surgery and Interventional Science, University College London, London, UK
| | - Valerie J. Lund
- grid.83440.3b0000000121901201UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK ,grid.83440.3b0000000121901201UCL Academic Head and Neck Centre, Division of Surgery and Interventional Science, University College London, London, UK
| | - Martin Forster
- grid.83440.3b0000000121901201UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK ,grid.83440.3b0000000121901201UCL Academic Head and Neck Centre, Division of Surgery and Interventional Science, University College London, London, UK
| | - Matt Lechner
- grid.83440.3b0000000121901201UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK ,grid.83440.3b0000000121901201UCL Academic Head and Neck Centre, Division of Surgery and Interventional Science, University College London, London, UK
| | - Sara L. Lorenzo-Guerra
- grid.511562.4Department of Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Mario Hermsen
- grid.511562.4Department of Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pascal D. Johann
- Swabian Childrens’ Cancer Center, University Childrens’ Hospital Augsburg and EU-RHAB Registry, Augsburg, Germany
| | - Abbas Agaimy
- grid.411668.c0000 0000 9935 6525Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Philipp Seegerer
- grid.6734.60000 0001 2292 8254Machine-Learning Group, Department of Software Engineering and Theoretical Computer Science, Technical University of Berlin, Berlin, Germany
| | - Arend Koch
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Frank Heppner
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Stefan M. Pfister
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T. W. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Andreas von Deimling
- grid.5253.10000 0001 0328 4908Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matija Snuderl
- grid.240324.30000 0001 2109 4251Division of Neuropathology, NYU Langone Health, New York, USA ,grid.240324.30000 0001 2109 4251Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, USA ,grid.240324.30000 0001 2109 4251Division of Molecular Pathology and Diagnostics, NYU Langone Health, New York, USA
| | - Klaus-Robert Müller
- grid.6734.60000 0001 2292 8254Machine-Learning Group, Department of Software Engineering and Theoretical Computer Science, Technical University of Berlin, Berlin, Germany ,grid.222754.40000 0001 0840 2678Department of Artificial Intelligence, Korea University, Seoul, South Korea ,grid.419528.30000 0004 0491 9823Max-Planck-Institute for Informatics, Saarbrücken, Germany ,BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Erna Forgó
- grid.168010.e0000000419368956Stanford University School of Medicine, Stanford, CA USA
| | - Brooke E. Howitt
- grid.168010.e0000000419368956Stanford University School of Medicine, Stanford, CA USA
| | - Philipp Mertins
- grid.484013.a0000 0004 6879 971XProteomics Platform, Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Frederick Klauschen
- grid.411095.80000 0004 0477 2585Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany ,grid.7497.d0000 0004 0492 0584 German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - David Capper
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
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López-Hernández A, Vivanco B, Franchi A, Bloemena E, Cabal VN, Potes S, Riobello C, García-Inclán C, López F, Llorente JL, Hermsen M. Genetic profiling of poorly differentiated sinonasal tumours. Sci Rep 2018; 8:3998. [PMID: 29507386 PMCID: PMC5838253 DOI: 10.1038/s41598-018-21690-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/08/2018] [Indexed: 01/26/2023] Open
Abstract
The sinonasal cavities harbour a variety of rare tumour types. Many carry a poor prognosis while therapeutic options are limited. Histopathological classification can be difficult, especially for poorly differentiated tumours such as olfactory neuroblastoma (ONB), sinonasal neuroendocrine carcinoma (SNEC) and sinonasal undifferentiated carcinoma (SNUC). We analysed Affymetrix OncoScan genome-wide copy number profiles of these three tumour types, both as originally diagnosed and as regrouped by their cytokeratin (Ck) and neuroendocrine (Ne) expression pattern, aiming to find a relation between phenotype and genotype. According to the original histopathological classification our series consisted of 24 ONB, 11 SNEC and 19 SNUC, while immunohistochemistry indicated 11 Ck−Ne+/ONB, 18 Ck+Ne+/SNEC, 24 Ck+Ne−/SNUC, and 1 Ck−Ne−/unclassified. As originally diagnosed, the three tumour types showed similar copy number profiles. However, when regrouped by Ck/Ne immunostaining we found a distinct set of gains and losses; Ck−Ne+/ONB harboured few and predominantly whole chromosomes abnormalities, Ck+Ne+/SNEC carried both gains and losses in high frequency, and Ck+Ne−/SNUC showed mostly gains. In addition, each tumour carried a number of unique chromosomal deletions. Genome-wide copy number profiling supports the value of immunohistochemical CkNe staining of ONB, SNEC and SNUC for tumour classification, which is important for prognosis and therapeutic decision-making.
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Affiliation(s)
- Alejandro López-Hernández
- Department Otolaryngology, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - Blanca Vivanco
- Department Pathology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Alessandro Franchi
- Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Virginia N Cabal
- Department Otolaryngology, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - Sira Potes
- Department Otolaryngology, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - Cristina Riobello
- Department Otolaryngology, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - Cristina García-Inclán
- Department Otolaryngology, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - Fernando López
- Department Otolaryngology, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - José L Llorente
- Department Otolaryngology, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - Mario Hermsen
- Department Otolaryngology, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain.
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