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Loeffler-Wirth H, Kreuz M, Hopp L, Arakelyan A, Haake A, Cogliatti SB, Feller AC, Hansmann ML, Lenze D, Möller P, Müller-Hermelink HK, Fortenbacher E, Willscher E, Ott G, Rosenwald A, Pott C, Schwaenen C, Trautmann H, Wessendorf S, Stein H, Szczepanowski M, Trümper L, Hummel M, Klapper W, Siebert R, Loeffler M, Binder H, for the German Cancer Aid consortium Molecular Mechanisms for Malignant Lymphoma. A modular transcriptome map of mature B cell lymphomas. Genome Med 2019; 11:27. [PMID: 31039827 PMCID: PMC6492344 DOI: 10.1186/s13073-019-0637-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/04/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Germinal center-derived B cell lymphomas are tumors of the lymphoid tissues representing one of the most heterogeneous malignancies. Here we characterize the variety of transcriptomic phenotypes of this disease based on 873 biopsy specimens collected in the German Cancer Aid MMML (Molecular Mechanisms in Malignant Lymphoma) consortium. They include diffuse large B cell lymphoma (DLBCL), follicular lymphoma (FL), Burkitt's lymphoma, mixed FL/DLBCL lymphomas, primary mediastinal large B cell lymphoma, multiple myeloma, IRF4-rearranged large cell lymphoma, MYC-negative Burkitt-like lymphoma with chr. 11q aberration and mantle cell lymphoma. METHODS We apply self-organizing map (SOM) machine learning to microarray-derived expression data to generate a holistic view on the transcriptome landscape of lymphomas, to describe the multidimensional nature of gene regulation and to pursue a modular view on co-expression. Expression data were complemented by pathological, genetic and clinical characteristics. RESULTS We present a transcriptome map of B cell lymphomas that allows visual comparison between the SOM portraits of different lymphoma strata and individual cases. It decomposes into one dozen modules of co-expressed genes related to different functional categories, to genetic defects and to the pathogenesis of lymphomas. On a molecular level, this disease rather forms a continuum of expression states than clearly separated phenotypes. We introduced the concept of combinatorial pattern types (PATs) that stratifies the lymphomas into nine PAT groups and, on a coarser level, into five prominent cancer hallmark types with proliferation, inflammation and stroma signatures. Inflammation signatures in combination with healthy B cell and tonsil characteristics associate with better overall survival rates, while proliferation in combination with inflammation and plasma cell characteristics worsens it. A phenotypic similarity tree is presented that reveals possible progression paths along the transcriptional dimensions. Our analysis provided a novel look on the transition range between FL and DLBCL, on DLBCL with poor prognosis showing expression patterns resembling that of Burkitt's lymphoma and particularly on 'double-hit' MYC and BCL2 transformed lymphomas. CONCLUSIONS The transcriptome map provides a tool that aggregates, refines and visualizes the data collected in the MMML study and interprets them in the light of previous knowledge to provide orientation and support in current and future studies on lymphomas and on other cancer entities.
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Affiliation(s)
- Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Markus Kreuz
- Institute for Medical Informatics, Statistics and Epidemiology, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Lydia Hopp
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Arsen Arakelyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, 7 Hasratyan str, 0014 Yerevan, Armenia
| | - Andrea Haake
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
| | - Sergio B. Cogliatti
- Institute of Pathology, Kantonal Hospital St. Gallen, Rorschacher Str. 95, 9007 St. Gallen, Switzerland
| | - Alfred C. Feller
- Hematopathology Lübeck, Maria-Goeppert-Str. 9a, 23562 Lübeck, Germany
| | - Martin-Leo Hansmann
- Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Dido Lenze
- AstraZeneca, Tinsdaler Weg 183, 22880 Wedel, Germany
| | - Peter Möller
- Institute of Pathology, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | | | - Erik Fortenbacher
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Edith Willscher
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - German Ott
- Department of Pathology, Robert-Bosch-Hospital, Auerbachstr. 110, 70376 Stuttgart, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
| | - Carsten Schwaenen
- Ortenau Hospital Offenburg-Gengenbach, Ebertpl. 12, 77654 Offenburg, Germany
- Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Heiko Trautmann
- Second Medical Department, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
| | - Swen Wessendorf
- Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
- Hospital Esslingen, Hirschlandstr. 97, 73730 Esslingen a. N, Germany
| | - Harald Stein
- Pathodiagnostik, Komturstr. 58-62, 12099 Berlin, Germany
| | - Monika Szczepanowski
- Second Medical Department, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August University, Robert-Koch-Str. 42, 37077 Göttingen, Germany
| | - Michael Hummel
- Institute of Pathology, Charité Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany
| | - Wolfram Klapper
- Hematopathology Section, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
- Institute of Human Genetics, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Markus Loeffler
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - for the German Cancer Aid consortium Molecular Mechanisms for Malignant Lymphoma
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, 7 Hasratyan str, 0014 Yerevan, Armenia
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
- Institute of Pathology, Kantonal Hospital St. Gallen, Rorschacher Str. 95, 9007 St. Gallen, Switzerland
- Hematopathology Lübeck, Maria-Goeppert-Str. 9a, 23562 Lübeck, Germany
- Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- AstraZeneca, Tinsdaler Weg 183, 22880 Wedel, Germany
- Institute of Pathology, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
- Institute of Pathology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
- Department of Pathology, Robert-Bosch-Hospital, Auerbachstr. 110, 70376 Stuttgart, Germany
- Second Medical Department, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
- Ortenau Hospital Offenburg-Gengenbach, Ebertpl. 12, 77654 Offenburg, Germany
- Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
- Hospital Esslingen, Hirschlandstr. 97, 73730 Esslingen a. N, Germany
- Pathodiagnostik, Komturstr. 58-62, 12099 Berlin, Germany
- Department of Hematology and Oncology, Georg-August University, Robert-Koch-Str. 42, 37077 Göttingen, Germany
- Institute of Pathology, Charité Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany
- Hematopathology Section, University Hospital Schleswig-Holstein, Arnold-Heller Str. 3, 24105 Kiel, Germany
- Institute of Human Genetics, University Hospital of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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Luanpitpong S, Chanthra N, Janan M, Poohadsuan J, Samart P, U-Pratya Y, Rojanasakul Y, Issaragrisil S. Inhibition of O-GlcNAcase Sensitizes Apoptosis and Reverses Bortezomib Resistance in Mantle Cell Lymphoma through Modification of Truncated Bid. Mol Cancer Ther 2017; 17:484-496. [PMID: 29167312 DOI: 10.1158/1535-7163.mct-17-0390] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/29/2017] [Accepted: 11/14/2017] [Indexed: 01/10/2023]
Abstract
Aberrant energy metabolism represents a hallmark of cancer and contributes to numerous aggressive behaviors of cancer cells, including cell death and survival. Despite the poor prognosis of mantle cell lymphoma (MCL), due to the inevitable development of drug resistance, metabolic reprograming of MCL cells remains an unexplored area. Posttranslational modification of proteins via O-GlcNAcylation is an ideal sensor for nutritional changes mediated by O-GlcNAc transferase (OGT) and is removed by O-GlcNAcase (OGA). Using various small-molecule inhibitors of OGT and OGA, we found for the first time that O-GlcNAcylation potentiates MCL response to bortezomib. CRISPR interference of MGEA5 (encoding OGA) validated the apoptosis sensitization by O-GlcNAcylation and OGA inhibition. To identify the potential clinical candidates, we tested MCL response to drug-like OGA inhibitor, ketoconazole, and verified that it exerts similar sensitizing effect on bortezomib-induced apoptosis. Investigations into the underlying molecular mechanisms reveal that bortezomib and ketoconazole act in concert to cause the accumulation of truncated Bid (tBid). Not only does ketoconazole potentiate tBid induction, but also increases tBid stability through O-GlcNAcylation that interferes with tBid ubiquitination and proteasomal degradation. Remarkably, ketoconazole strongly enhances bortezomib-induced apoptosis in de novo bortezomib-resistant MCL cells and in patient-derived primary cells with minimal cytotoxic effect on normal peripheral blood mononuclear cells and hepatocytes, suggesting its potential utility as a safe and effective adjuvant for MCL. Together, our findings provide novel evidence that combination of bortezomib and ketoconazole or other OGA inhibitors may present a promising strategy for the treatment of drug-resistant MCL. Mol Cancer Ther; 17(2); 484-96. ©2017 AACR.
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Affiliation(s)
- Sudjit Luanpitpong
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nawin Chanthra
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Montira Janan
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jirarat Poohadsuan
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Parinya Samart
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yaowalak U-Pratya
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yon Rojanasakul
- WVU Cancer Institute, West Virginia University, Morgantown, West Virginia
| | - Surapol Issaragrisil
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. .,Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Bangkok Hematology Center, Wattanosoth Hospital, BDMS Center of Excellence for Cancer, Bangkok, Thailand
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