1
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Thurner L, Bewarder M, Fadle N, Regitz E, Poeschel V, Ziepert M, Schuck R, Altmeyer S, Kemele M, Bock T, Schormann C, Walter S, Szczepanowski M, Klapper W, Monoranu C, Rosenwald A, Moeller P, Kim Y, Buslei R, Kaddu-Mulindwa D, Neumann F, Roemer K, Bohle R, Illerhaus G, Schorb E, Schaefer H, Hansmann M, Hartmann S, Held G, Stilgenbauer S, Murawski N, Pfreundschuh M, Preuss K. SAMD14/NEURABIN-I AS BCR-ANTIGENS OF PRIMARY CENTRAL NERVOUS SYSTEM LYMPHOMA. Hematol Oncol 2019. [DOI: 10.1002/hon.9_2630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- L. Thurner
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - M. Bewarder
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - N. Fadle
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - E. Regitz
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - V. Poeschel
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - M. Ziepert
- Universität Leipzig; Institute for Medical Informatics, Statistics, and Epidemiology; Leipzig Germany
| | - R. Schuck
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - S. Altmeyer
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - M. Kemele
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - T. Bock
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - C. Schormann
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - S. Walter
- Saarland Medical School; Department of Neurology; Homburg/Saar Germany
| | - M. Szczepanowski
- University of Kiel; Institute of Pathology, Hematopathology Section and Lymph Node Registry; Kiel Germany
| | - W. Klapper
- University of Kiel; Institute of Pathology, Hematopathology Section and Lymph Node Registry; Kiel Germany
| | - C. Monoranu
- University of Würzburg; Institute of Pathology and Neuropathology; Würzburg Germany
| | - A. Rosenwald
- University of Würzburg; Institute of Pathology and Neuropathology; Würzburg Germany
| | - P. Moeller
- University of Ulm; Department of Pathology; Ulm Germany
| | - Y. Kim
- Saarland Medical school; Department of pathology; Homburg/Saar Germany
| | - R. Buslei
- SozialStiftung Bamberg; Institute of Pathology; Bamberg Germany
| | - D. Kaddu-Mulindwa
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - F. Neumann
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - K. Roemer
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - R. Bohle
- Saarland Medical school; Department of pathology; Homburg/Saar Germany
| | - G. Illerhaus
- Klinikum Stuttgart; Department Hematology and Oncology; Stuttgart Germany
| | - E. Schorb
- University Medical Center Freiburg; Department of Hematology and Oncology; Freiburg Germany
| | - H. Schaefer
- University Medical Center Freiburg; Department of Hematology and Oncology; Freiburg Germany
| | - M.L. Hansmann
- Goethe University Frankfurt; Senckenberg Institute of Pathology; Frankfurt Germany
| | - S. Hartmann
- Goethe University Frankfurt; Senckenberg Institute of Pathology; Frankfurt Germany
| | - G. Held
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - S. Stilgenbauer
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - N. Murawski
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - M. Pfreundschuh
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
| | - K.D. Preuss
- Saarland Medical School; Internal Medicine I, José Carreras Center; Homburg/Saar Germany
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2
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Altenbuchinger M, Schwarzfischer P, Rehberg T, Reinders J, Kohler CW, Gronwald W, Richter J, Szczepanowski M, Masqué-Soler N, Klapper W, Oefner PJ, Spang R. Molecular signatures that can be transferred across different omics platforms. Bioinformatics 2018; 33:i333-i340. [PMID: 28881975 PMCID: PMC5870545 DOI: 10.1093/bioinformatics/btx241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Motivation Molecular signatures for treatment recommendations are well researched. Still it is challenging to apply them to data generated by different protocols or technical platforms. Results We analyzed paired data for the same tumors (Burkitt lymphoma, diffuse large B-cell lymphoma) and features that had been generated by different experimental protocols and analytical platforms including the nanoString nCounter and Affymetrix Gene Chip transcriptomics as well as the SWATH and SRM proteomics platforms. A statistical model that assumes independent sample and feature effects accounted for 69–94% of technical variability. We analyzed how variability is propagated through linear signatures possibly affecting predictions and treatment recommendations. Linear signatures with feature weights adding to zero were substantially more robust than unbalanced signatures. They yielded consistent predictions across data from different platforms, both for transcriptomics and proteomics data. Similarly stable were their predictions across data from fresh frozen and matching formalin-fixed paraffin-embedded human tumor tissue. Availability and Implementation The R-package ‘zeroSum’ can be downloaded at https://github.com/rehbergT/zeroSum. Complete data and R codes necessary to reproduce all our results can be received from the authors upon request.
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Affiliation(s)
- M Altenbuchinger
- Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
| | - P Schwarzfischer
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - T Rehberg
- Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
| | - J Reinders
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Ch W Kohler
- Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
| | - W Gronwald
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - J Richter
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - M Szczepanowski
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - N Masqué-Soler
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - W Klapper
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - P J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - R Spang
- Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
- To whom correspondence should be addressed.
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3
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Altenbuchinger M, Schwarzfischer P, Rehberg T, Reinders J, Kohler CW, Gronwald W, Richter J, Szczepanowski M, Masqué-Soler N, Klapper W, Oefner PJ, Spang R. Molecular signatures that can be transferred across different omics platforms. Bioinformatics 2017; 33:2790. [DOI: 10.1093/bioinformatics/btx488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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4
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Zamò A, Pischimarov J, Schlesner M, Rosenstiel P, Bomben R, Horn H, Grieb T, Nedeva T, López C, Haake A, Richter J, Trümper L, Lawerenz C, Klapper W, Möller P, Hummel M, Lenze D, Szczepanowski M, Flossbach L, Schreder M, Gattei V, Ott G, Siebert R, Rosenwald A, Leich E. Differences between BCL2-break positive and negative follicular lymphoma unraveled by whole-exome sequencing. Leukemia 2017; 32:685-693. [PMID: 28824170 DOI: 10.1038/leu.2017.270] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 08/08/2017] [Indexed: 12/25/2022]
Abstract
Depending on disease stage follicular lymphoma (FL) lack the t(14;18) in ~15-~50% of cases. Nevertheless, most of these cases express BCL2. To elucidate mechanisms triggering BCL2 expression and promoting pathogenesis in t(14;18)-negative FL, exonic single-nucleotide variant (SNV) profiles of 28 t(14;18)-positive and 13 t(14;18)-negative FL were analyzed, followed by the integration of copy-number changes, copy-neutral LOH and published gene-expression data as well as the assessment of immunoglobulin N-glycosylation sites. Typical FL mutations also affected t(14;18)-negative FL. Curated gene set/pathway annotation of genes mutated in either t(14;18)-positive or t(14;18)-negative FL revealed a strong enrichment of same or similar gene sets but also a more prominent or exclusive enrichment of immune response and N-glycosylation signatures in t(14;18)-negative FL. Mutated genes showed high BCL2 association in both subgroups. Among the genes mutated in t(14;18)-negative FL 555 were affected by copy-number alterations and/or copy-neutral LOH and 96 were differently expressed between t(14;18)-positive and t(14;18)-negative FL (P<0.01). N-glycosylation sites were detected considerably less frequently in t(14;18)-negative FL. These results suggest a diverse portfolio of genetic alterations that may induce or regulate BCL2 expression or promote pathogenesis of t(14;18)-negative FL as well as a less specific but increased crosstalk with the microenvironment that may compensate for the lack of N-glycosylation.
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Affiliation(s)
- A Zamò
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Department of Diagnostic and Public Health, University of Verona, Verona, Italy.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - J Pischimarov
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - M Schlesner
- Theoretical Bioinformatics (B080), Computational Oncology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - R Bomben
- Department of Translational Research, CRO, Aviano, Italy
| | - H Horn
- Dr Margarete Fischer-Bosch-Institute for Clinical Pharmacology, Stuttgart, Germany
| | - T Grieb
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - T Nedeva
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - C López
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany.,Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Haake
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - J Richter
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany.,Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - L Trümper
- Department of Hematology and Medical Oncology, University Hospital, Göttingen, Germany
| | - C Lawerenz
- Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - W Klapper
- Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - P Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - M Hummel
- Institute of Pathology, Charité-University Hospital Berlin, Germany
| | - D Lenze
- Institute of Pathology, Charité-University Hospital Berlin, Germany
| | - M Szczepanowski
- Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - L Flossbach
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - M Schreder
- Medizinische Klinik und Poliklinik II, University Hospital Würzburg, Würzburg, Germany
| | - V Gattei
- Department of Translational Research, CRO, Aviano, Italy
| | - G Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - R Siebert
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany.,Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - E Leich
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
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5
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Wagener R, Kretzmer H, Ammerpohl O, López C, Rohde M, Carillo-De-Santa-Pau E, Salaverria I, Szczepanowski M, Burkhardt B, Hummel M, Klapper W, Küppers R, Löffler M, Möller P, Neequaye J, Wößmann W, Lichter P, Stunnenberg H, Trümper L, Mbulaiteye S, Hoffman S, Siebert R. PROFILING OF DNA METHYLATION IN EPIDEMIOLOGICAL AND CLINICAL SUBGROUPS OF BURKITT LYMPHOMA IN THE FRAMEWORK OF THE MMML: ICGC AND BLUEPRINT CONSORTIA. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- R. Wagener
- University of Ulm; Institute of Human Genetics; Ulm Germany
| | - H. Kretzmer
- LIFE Research Center for Civilization Diseases, University of Leipzig; Transcriptome Bioinformatics Group; Leipzig Germany
| | - O. Ammerpohl
- Christian-Albrechts-University; Campus Kiel, Institute of Human Genetics; Kiel Germany
| | - C. López
- University of Ulm; Institute of Human Genetics; Ulm Germany
| | - M. Rohde
- Justus-Liebig-University Giessen; Department od Pediatric Hematology and Oncology; Giessen Germany
| | - E. Carillo-De-Santa-Pau
- Spanish National Cancer Research Centre (CNIO); Structural Biology and BioComputing Programme; Madrid Spain
| | - I. Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Hematopathology Unit, Hospital Clínic; Barcelona Spain
| | - M. Szczepanowski
- University Hospital Schleswig-Holstein Campus Kiel; Clinic of Internal Medicine II, Hematology Laboratory Section; Kiel Germany
| | - B. Burkhardt
- University Hospital Münster; Department of Pediatric Hematology and Oncology; Münster Germany
| | - M. Hummel
- Charité - University Medicine Berlin; Institute of Pathology; Berlin Germany
| | - W. Klapper
- University Hospital Schleswig-Holstein Campus Kiel/ Christian-Albrechts University Kiel; Institute of Hematopathology; Kiel Germany
| | - R. Küppers
- University of Duisburg-Essen; Institute of Cell Biology (Cancer Research); Essen Germany
| | - M. Löffler
- IMISE; Institute for Medical Informatics Statistics and Epidemiology; Leipzig Germany
| | - P. Möller
- Medical Faculty of the Ulm University; Institute of Pathology; Ulm Germany
| | - J. Neequaye
- University of Ghana Medical School; Department of Child Health; Accra Ghana
| | - W. Wößmann
- Justus-Liebig-University; 16 NHL-BFM Study Centre and Department of Paediatric Haematology and Oncology; Giessen Germany
| | - P. Lichter
- German Cancer Research Center; Division of Molecular Genetics; Heidelberg Germany
| | - H. Stunnenberg
- Radboud University; Molecular Biology, NCMLS, FNWI; Njimegen Netherlands
| | - L. Trümper
- Georg-August-University of Göttingen; Department of Hematology and Oncology; Göttingen Germany
| | - S.M. Mbulaiteye
- National Cancer Institute; National Institutes of Health, Division of Cancer Epidemiology and Genetics; Rockville USA
| | - S. Hoffman
- LIFE Research Center for Civilization Diseases, University of Leipzig; Transcriptome Bioinformatics Group; Leipzig Germany
| | - R. Siebert
- University of Ulm; Institute of Human Genetics; Ulm Germany
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6
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Linke F, Harenberg M, Nietert MM, Zaunig S, von Bonin F, Arlt A, Szczepanowski M, Weich HA, Lutz S, Dullin C, Janovská P, Krafčíková M, Trantírek L, Ovesná P, Klapper W, Beissbarth T, Alves F, Bryja V, Trümper L, Wilting J, Kube D. Microenvironmental interactions between endothelial and lymphoma cells: a role for the canonical WNT pathway in Hodgkin lymphoma. Leukemia 2016; 31:361-372. [DOI: 10.1038/leu.2016.232] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/07/2016] [Accepted: 08/03/2016] [Indexed: 02/07/2023]
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7
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Dimitrova L, Seitz V, Hecht J, Lenze D, Hansen P, Szczepanowski M, Ma L, Oker E, Sommerfeld A, Jundt F, Klapper W, Hummel M. PAX5 overexpression is not enough to reestablish the mature B-cell phenotype in classical Hodgkin lymphoma. Leukemia 2013; 28:213-6. [PMID: 23842424 DOI: 10.1038/leu.2013.211] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- L Dimitrova
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - V Seitz
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - J Hecht
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - D Lenze
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - P Hansen
- 1] Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany [2] Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - M Szczepanowski
- Institute of Pathology, Kiel University (CAU), Kiel, Germany
| | - L Ma
- 1] Institute of Pathology, Kiel University (CAU), Kiel, Germany [2] Department of Hematology, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - E Oker
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - A Sommerfeld
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - F Jundt
- Department of Hematology, Oncology and Tumorimmunology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - W Klapper
- Institute of Pathology, Kiel University (CAU), Kiel, Germany
| | - M Hummel
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
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8
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Klapper W, Szczepanowski M, Heidorn K, Müschen M, Liedtke S, Sotnikova A, Andersen NS, Greeve J, Parwaresch R. Immunoglobulin class-switch recombination occurs in mantle cell lymphomas. J Pathol 2006; 209:250-7. [PMID: 16508921 DOI: 10.1002/path.1961] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Mantle cell lymphoma (MCL) is an IgM-expressing B cell lymphoma that originates from naive B cells and responds poorly to chemotherapy. We show here that several MCLs harbour isotype-switched subclones. Similar to the situation in normal B cells, in vitro stimulation of MCL cell lines with CD40 ligand (CD40L) and interleukin-4 induced expression of activation-induced cytidine deaminase (AID) and germline transcription at the immunoglobulin heavy chain gene locus. Additionally, the occurrence of switch-circle transcripts and mature IgG transcripts after stimulation indicated ongoing class-switch recombination in mantle cell lymphoma cell lines. Furthermore, stimulation of primary MCL cells in vitro induced expression of class-switched IgG mRNA in the tumour cells. Our data indicate that mantle cell lymphomas have retained the ability to undergo class-switch recombination if appropriate stimuli, such as the CD40 ligand, are provided.
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MESH Headings
- CD40 Antigens/immunology
- Cell Line, Tumor
- Cytidine Deaminase/immunology
- Dendritic Cells, Follicular/immunology
- Genes, Immunoglobulin Heavy Chain/genetics
- Genes, Immunoglobulin Heavy Chain/immunology
- Humans
- Immunoglobulin Class Switching/genetics
- Immunoglobulin Class Switching/immunology
- Immunoglobulin G/genetics
- Immunoglobulin G/immunology
- Immunohistochemistry/methods
- Interleukin-4/immunology
- Lymphoma, Mantle-Cell/genetics
- Lymphoma, Mantle-Cell/immunology
- Mutation/genetics
- Mutation/immunology
- RNA, Messenger/analysis
- RNA, Neoplasm/analysis
- Recombination, Genetic/genetics
- Recombination, Genetic/immunology
- Reverse Transcriptase Polymerase Chain Reaction/methods
- Transcription, Genetic/genetics
- Transcription, Genetic/immunology
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Affiliation(s)
- W Klapper
- Department of Haematopathology and Lymph Node Registry Kiel, Schleswig-Holstein University Hospitals, Campus Kiel, Niemannsweg 11, 24105 Kiel, Germany
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