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Kouroukli AG, Fischer A, Kretzmer H, Chteinberg E, Rajaram N, Glaser S, Kolarova J, Bashtrykov P, Mathas S, Drexler HG, Ohno H, Ammerpohl O, Jeltsch A, Siebert R, Bens S. The DNA methylation status of the TERT promoter differs between subtypes of mature B-cell lymphomas. Blood Cancer J 2023; 13:98. [PMID: 37365157 DOI: 10.1038/s41408-023-00872-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/24/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Affiliation(s)
- Alexandra G Kouroukli
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Helene Kretzmer
- Computational Genomics, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Emil Chteinberg
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Nivethika Rajaram
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Stephan Mathas
- Charité - Universitätsmedizin Berlin, Hematology, Oncology and Tumor Immunology, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Group Biology of Malignant Lymphomas, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a cooperation between the MDC and the Charité, Berlin, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124, Braunschweig, Germany
| | - Hitoshi Ohno
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany.
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Bock T, Bewarder M, Cetin O, Fadle N, Regitz E, Schwarz EC, Held J, Roth S, Lohse S, Pfuhl T, Wagener R, Smola S, Becker SL, Bohle RM, Trümper L, Siebert R, Hansmann M, Pfreundschuh M, Drexler HG, Hoth M, Kubuschok B, Roemer K, Preuss K, Hartmann S, Thurner L. B‐cell receptors of EBV‐negative Burkitt lymphoma bind modified isoforms of autoantigens. eJHaem 2022; 3:739-747. [PMID: 36051037 PMCID: PMC9421956 DOI: 10.1002/jha2.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 11/08/2022]
Abstract
Burkitt lymphoma (BL) represents the most aggressive B‐cell‐lymphoma. Beside the hallmark of IG‐MYC‐translocation, surface B‐cell receptor (BCR) is expressed, and mutations in the BCR pathway are frequent. Coincidental infections in endemic BL, and specific extra‐nodal sites suggest antigenic triggers. To explore this hypothesis, BCRs of BL cell lines and cases were screened for reactivities against a panel of bacterial lysates, lysates of Plasmodium falciparum, a custom‐made virome array and against self‐antigens, including post‐translationally modified antigens. An atypically modified, SUMOylated isoform of Bystin, that is, SUMO1‐BYSL was identified as the antigen of the BCR of cell line CA46. SUMO1‐BYSL was exclusively expressed in CA46 cells with K139 as site of the SUMOylation. Secondly, an atypically acetylated isoform of HSP40 was identified as the antigen of the BCR of cell line BL41. K104 and K179 were the sites of immunogenic acetylation, and the acetylated HSP40 isoform was solely present in BL41 cells. Functionally, addition of SUMO1‐BYSL and acetylated HSP40 induced BCR pathway activation in CA46 and BL41 cells, respectively. Accordingly, SUMO1‐BYSL‐ETA’ immunotoxin, produced by a two‐step intein‐based conjugation, led to the specific killing of CA46 cells. Autoantibodies directed against SUMO1‐BYSL were found in 3 of 14 (21.4%), and autoantibodies against acetylated HSP40 in 1/14(7.1%) patients with sporadic Burkitt‐lymphoma. No reactivities against antigens of the infectious agent spectrum could be observed. These results indicate a pathogenic role of autoreactivity evoked by immunogenic post‐translational modifications in a subgroup of sporadic BL including two EBV‐negative BL cell lines.
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Affiliation(s)
- Theresa Bock
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Moritz Bewarder
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Onur Cetin
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Natalie Fadle
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Evi Regitz
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Eva C. Schwarz
- Center for Integrative Physiology and Molecular Medicine (CIPMM) School of Medicine Homburg Germany
| | - Jana Held
- Institute of Tropical Medicine Eberhard Karls Universität Tübingen Tübingen Germany
| | - Sophie Roth
- Institute of Medical Microbiology and Hygiene Saarland University Homburg/Saar Germany
| | - Stefan Lohse
- Institute of Virology University of Saarland Homburg Germany
| | - Thorsten Pfuhl
- Institute of Virology University of Saarland Homburg Germany
| | - Rabea Wagener
- Institute of Human Genetics Ulm University and Ulm University Medical Center Ulm Germany
| | - Sigrun Smola
- Institute of Virology University of Saarland Homburg Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Saarbrücken Germany
| | - Sören L. Becker
- Institute of Medical Microbiology and Hygiene Saarland University Homburg/Saar Germany
| | - Rainer Maria Bohle
- Institute of Pathology Saarland University Medical School Homburg/Saar Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology Georg August University Göttingen Göttingen Germany
| | - Reiner Siebert
- Institute of Human Genetics Ulm University and Ulm University Medical Center Ulm Germany
| | - Martin‐Leo Hansmann
- Dr. Senckenberg Institute of Pathology Goethe University Hospital of Frankfurt a. Main Frankfurt a. Main Germany
| | - Michael Pfreundschuh
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Hans G. Drexler
- Faculty of Life sciences Technical University of Braunschweig Braunschweig Germany
| | - Markus Hoth
- Center for Integrative Physiology and Molecular Medicine (CIPMM) School of Medicine Homburg Germany
| | - Boris Kubuschok
- Department of Internal Medicine II Augsburg University Medical Center Augsburg Germany
| | - Klaus Roemer
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Klaus‐Dieter Preuss
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology Goethe University Hospital of Frankfurt a. Main Frankfurt a. Main Germany
| | - Lorenz Thurner
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
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Nagel S, Pommerenke C, Meyer C, Drexler HG. NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells. Int J Mol Sci 2021; 22:ijms22115902. [PMID: 34072771 PMCID: PMC8198381 DOI: 10.3390/ijms22115902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/27/2021] [Indexed: 01/09/2023] Open
Abstract
Recently, we documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in human myelopoiesis including monocytes and their derived dendritic cells (DCs). Here, we enlarge this map to include normal NKL homeobox gene expressions in progenitor-derived DCs. Analysis of public gene expression profiling and RNA-seq datasets containing plasmacytoid and conventional dendritic cells (pDC and cDC) demonstrated HHEX activity in both entities while cDCs additionally expressed VENTX. The consequent aim of our study was to examine regulation and function of VENTX in DCs. We compared profiling data of VENTX-positive cDC and monocytes with VENTX-negative pDC and common myeloid progenitor entities and revealed several differentially expressed genes encoding transcription factors and pathway components, representing potential VENTX regulators. Screening of RNA-seq data for 100 leukemia/lymphoma cell lines identified prominent VENTX expression in an acute myelomonocytic leukemia cell line, MUTZ-3 containing inv(3)(q21q26) and t(12;22)(p13;q11) and representing a model for DC differentiation studies. Furthermore, extended gene analyses indicated that MUTZ-3 is associated with the subtype cDC2. In addition to analysis of public chromatin immune-precipitation data, subsequent knockdown experiments and modulations of signaling pathways in MUTZ-3 and control cell lines confirmed identified candidate transcription factors CEBPB, ETV6, EVI1, GATA2, IRF2, MN1, SPIB, and SPI1 and the CSF-, NOTCH-, and TNFa-pathways as VENTX regulators. Live-cell imaging analyses of MUTZ-3 cells treated for VENTX knockdown excluded impacts on apoptosis or induced alteration of differentiation-associated cell morphology. In contrast, target gene analysis performed by expression profiling of knockdown-treated MUTZ-3 cells revealed VENTX-mediated activation of several cDC-specific genes including CSFR1, EGR2, and MIR10A and inhibition of pDC-specific genes like RUNX2. Taken together, we added NKL homeobox gene activities for progenitor-derived DCs to the NKL-code, showing that VENTX is expressed in cDCs but not in pDCs and forms part of a cDC-specific gene regulatory network operating in DC differentiation and function.
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Drexler HG, Nagel S, Quentmeier H. Leukemia Cell Lines: In Vitro Models for the Study of Chronic Neutrophilic Leukemia. ACTA ACUST UNITED AC 2021; 28:1790-1794. [PMID: 34068566 PMCID: PMC8161829 DOI: 10.3390/curroncol28030166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022]
Abstract
Chronic neutrophilic leukemia (CNL) is a rare myeloproliferative neoplasm that is genetically characterized by the absence of both the Philadelphia chromosome and BCR-ABL1 fusion gene and the high prevalence of mutations in the colony-stimulating factor 3 receptor (CSF3R). Additional disease-modifying mutations have been recognized in CNL samples, portraying a distinct mutational landscape. Despite the growing knowledge base on genomic aberrations, further progress could be gained from the availability of representative models of CNL. To address this gap, we screened a large panel of available leukemia cell lines, followed by a detailed mutational investigation with focus on the CNL-associated candidate driver genes. The sister cell lines CNLBC-1 and MOLM-20 were derived from a patient with CNL and carry CNL-typical molecular hallmarks, namely mutations in several genes, such as CSF3R, ASXL1, EZH2, NRAS, and SETBP1. The use of these validated and comprehensively characterized models will benefit the understanding of the pathobiology of CNL and help inform therapeutic strategies.
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Affiliation(s)
- Hans G. Drexler
- Faculty of Life Sciences, Technical University of Braunschweig, 38106 Braunschweig, Germany
- Correspondence:
| | - Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.); (H.Q.)
| | - Hilmar Quentmeier
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.); (H.Q.)
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5
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Nagel S, Pommerenke C, Meyer C, MacLeod RAF, Drexler HG. Establishment of the TALE-code reveals aberrantly activated homeobox gene PBX1 in Hodgkin lymphoma. PLoS One 2021; 16:e0246603. [PMID: 33539429 PMCID: PMC7861379 DOI: 10.1371/journal.pone.0246603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Received: 12/08/2020] [Accepted: 01/21/2021] [Indexed: 12/26/2022] Open
Abstract
Homeobox genes encode transcription factors which regulate basic processes in development and cell differentiation and are grouped into classes and subclasses according to sequence similarities. Here, we analyzed the activities of the 20 members strong TALE homeobox gene class in early hematopoiesis and in lymphopoiesis including developing and mature B-cells, T-cells, natural killer (NK)-cells and innate lymphoid cells (ILC). The resultant expression pattern comprised eleven genes and which we termed TALE-code enables discrimination of normal and aberrant activities of TALE homeobox genes in lymphoid malignancies. Subsequent expression analysis of TALE homeobox genes in public datasets of Hodgkin lymphoma (HL) patients revealed overexpression of IRX3, IRX4, MEIS1, MEIS3, PBX1, PBX4 and TGIF1. As paradigm we focused on PBX1 which was deregulated in about 17% HL patients. Normal PBX1 expression was restricted to hematopoietic stem cells and progenitors of T-cells and ILCs but absent in B-cells, reflecting its roles in stemness and early differentiation. HL cell line SUP-HD1 expressed enhanced PBX1 levels and served as an in vitro model to identify upstream regulators and downstream targets in this malignancy. Genomic studies of this cell line therein showed a gain of the PBX1 locus at 1q23 which may underlie its aberrant expression. Comparative expression profiling analyses of HL patients and cell lines followed by knockdown experiments revealed NFIB and TLX2 as target genes activated by PBX1. HOX proteins operate as cofactors of PBX1. Accordingly, our data showed that HOXB9 overexpressed in HL coactivated TLX2 but not NFIB while activating TNFRSF9 without PBX1. Further downstream analyses showed that TLX2 activated TBX15 which operated anti-apoptotically. Taken together, we discovered a lymphoid TALE-code and identified an aberrant network around deregulated TALE homeobox gene PBX1 which may disturb B-cell differentiation in HL by reactivation of progenitor-specific genes. These findings may provide the framework for future studies to exploit possible vulnerabilities of malignant cells in therapeutic scenarios.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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6
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Yang Y, Zhang X, Zhang X, Wang Y, Wang X, Hu L, Zhao Y, Wang H, Wang Z, Wang H, Wang L, Dirks WG, Drexler HG, Xu X, Hu Z. Modulators of histone demethylase JMJD1C selectively target leukemic stem cells. FEBS Open Bio 2020; 11:265-277. [PMID: 33289299 PMCID: PMC7780120 DOI: 10.1002/2211-5463.13054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/19/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Leukemic stem cells (LSCs) comprise a very rare cell population that results in the development of acute myeloid leukemia. The selective targeting of drivers in LSCs with small molecule inhibitors holds promise for treatment of acute myeloid leukemia. Recently, we reported the identification of inhibitors of the histone lysine demethylase JMJD1C that preferentially kill MLL rearranged acute leukemia cells. Here, we report the identification of jumonji domain modulator #7 (JDM‐7). Surface plasmon resonance analysis showed that JDM‐7 binds to JMJD1C and its family homolog JMJD1B. JDM‐7 did not significantly suppress cell proliferation in liquid cell culture at higher doses, although it led to a significant decrease in semi‐solid colony formation experiments at lower concentrations. Moreover, low doses of JDM‐7 did not suppress the proliferation of erythroid progenitor cells. We identified that JDM‐7 downregulates the LSC self‐renewal gene HOXA9 in leukemia cells. We further found that the structure of JDM‐7 is similar to that of tadalafil, a drug approved by the US Food and Drug Administration. Molecular docking and surface plasmon resonance analysis showed that tadalafil binds to JMJD1C. Moreover, similar to JDM‐7, tadalafil suppressed colony formation of leukemia cells in semi‐solid cell culture at a concentration that did not affect primary umbilical cord blood cells. In summary, we have identified JDM‐7 and tadalafil as potential JMJD1C modulators that selectively inhibit the growth of LSCs.
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Affiliation(s)
- Yong Yang
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
| | - Xinjing Zhang
- Department of Anesthesiology, Zibo Central Hospital, China
| | - Xiaoyan Zhang
- The Department of Obstetrics and Gynecology, The Affiliated Hospital of Weifang Medical University, China
| | - Yishu Wang
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
| | - Xintong Wang
- Beijing Beike Deyuan Bio-Pharm Technology Co. Ltd, China
| | - Linda Hu
- Upstate Medical University, Syracuse, NY, USA
| | - Yao Zhao
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
| | - Haihua Wang
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
| | - Zhanju Wang
- The Department of Hematology, the Affiliated Hospital of Weifang Medical University, China
| | - Haiying Wang
- The Department of Hematology, the Affiliated Hospital of Weifang Medical University, China
| | - Lin Wang
- The School of Physics and Optoelectronic Engineering, Weifang University, China
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Xin Xu
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China.,School of Life Science and Technology, Weifang Medical University, China
| | - Zhenbo Hu
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
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Nagel S, Pommerenke C, Meyer C, MacLeod RAF, Drexler HG. Aberrant expression of NKL homeobox genes HMX2 and HMX3 interferes with cell differentiation in acute myeloid leukemia. PLoS One 2020; 15:e0240120. [PMID: 33048949 PMCID: PMC7553312 DOI: 10.1371/journal.pone.0240120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Received: 06/22/2020] [Accepted: 09/18/2020] [Indexed: 12/30/2022] Open
Abstract
The NKL-code describes normal expression patterns of NKL homeobox genes in hematopoiesis. Aberrant expression of NKL homeobox gene subclass members have been reported in several hematopoietic malignancies including acute myeloid leukemia (AML). Here, we analyzed the oncogenic role of the HMX-group of NKL homeobox genes in AML. Public expression profiling data–available for HMX1 and HMX2—indicate aberrant activity of HMX2 in circa 2% AML patients overall, rising to 31% in those with KMT2A/MLL rearrangements whereas HMX1 expression remains inconspicuous. AML cell lines EOL-1, MV4-11 and MOLM-13 expressed both, HMX2 and neighboring HMX3 genes, and harbored KMT2A aberrations, suggesting their potential functional association. Surprisingly, knockdown experiments in these cell lines demonstrated that KMT2A inhibited HMX2/3 which, in turn, did not regulate KMT2A expression. Furthermore, karyotyping and genomic profiling analysis excluded rearrangements of the HMX2/3 locus in these cell lines. However, comparative expression profiling and subsequent functional analyses revealed that IRF8, IL7- and WNT-signalling activated HMX2/3 expression while TNFa/NFkB- signalling proved inhibitory. Whole genome sequencing of EOL-1 identified two mutations in the regulatory upstream regions of HMX2/3 resulting in generation of a consensus ETS-site and transformation of a former NFkB-site into an SP1-site. Reporter-gene assays demonstrated that both mutations contributed to HMX2/3 activation, modifying ETS1/ELK1- and TNFalpha-mediated gene regulation. Moreover, DMSO-induced eosinophilic differentiation of EOL-1 cells coincided with HMX2/3 downregulation while knockdown of HMX2 induced cell differentiation, collectively supporting a fundamental role for these genes in myeloid differentiation arrest. Finally, target genes of HMX2/3 were identified in EOL-1 and included suppression of differentiation gene EPX, and activation of fusion gene FIP1L1-PDGFRA and receptor-encoding gene HTR7, both of which enhanced oncogenic ERK-signalling. Taken together, our study documents a leukemic role for deregulated NKL homeobox genes HMX2 and HMX3 in AML, revealing molecular mechanisms of myeloid differentiation arrest.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Nagel S, Pommerenke C, MacLeod RAF, Meyer C, Kaufmann M, Drexler HG. The NKL-code for innate lymphoid cells reveals deregulated expression of NKL homeobox genes HHEX and HLX in anaplastic large cell lymphoma (ALCL). Oncotarget 2020; 11:3208-3226. [PMID: 32922661 PMCID: PMC7456612 DOI: 10.18632/oncotarget.27683] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/07/2020] [Indexed: 12/26/2022] Open
Abstract
NKL homeobox genes encode developmental transcription factors and display an NKL-code according to their physiological expression pattern in hematopoiesis. Here, we analyzed public transcriptome data from primary innate lymphoid cells (ILCs) for NKL homeobox gene activities and found that ILC3 expressed exclusively HHEX while in ILC1 and ILC2 these genes were silenced. Deregulation of the NKL-code promotes hematopoietic malignancies, including anaplastic large cell lymphoma (ALCL) which reportedly may derive from ILC3. Accordingly, we analyzed NKL homeobox gene activities in ALCL cell lines and investigated their role in this malignancy. Transcriptome analyses demonstrated low expression levels of HHEX but powerfully activated HLX. Forced expression of HHEX in ALCL cell lines induced genes involved in apoptosis and ILC3 differentiation, indicating tumor suppressor activity. ALCL associated NPM1-ALK and JAK-STAT3-signalling drove enhanced expression of HLX while discounting HHEX. Genomic profiling revealed copy number gains at the loci of HLX and STAT3 in addition to genes encoding both STAT3 regulators (AURKA, BCL3, JAK3, KPNB1, NAMPT, NFAT5, PIM3, ROCK1, SIX1, TPX2, WWOX) and targets (BATF3, IRF4, miR135b, miR21, RORC). Transcriptome data of ALCL cell lines showed absence of STAT3 mutations while MGA was mutated and downregulated, encoding a novel potential STAT3 repressor. Furthermore, enhanced IL17F-signalling activated HLX while TGFbeta-signalling inhibited HHEX expression. Taken together, our data extend the scope of the NKL-code for ILCs and spotlight aberrant expression of NKL homeobox gene HLX in ALCL. HLX represents a direct target of ALCL hallmark factor STAT3 and deregulates cell survival and differentiation in this malignancy.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Drexler HG, Quentmeier H. The LL-100 Cell Lines Panel: Tool for Molecular Leukemia-Lymphoma Research. Int J Mol Sci 2020; 21:ijms21165800. [PMID: 32823535 PMCID: PMC7461097 DOI: 10.3390/ijms21165800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Certified cell line models provide ideal experimental platforms to answer countless scientific questions. The LL-100 panel is a cohort of cell lines that are broadly representative of all leukemia–lymphoma entities (including multiple myeloma and related diseases), rigorously authenticated and validated, and comprehensively annotated. The process of the assembly of the LL-100 panel was based on evidence and experience. To expand the genetic characterization across all LL-100 cell lines, we performed whole-exome sequencing and RNA sequencing. Here, we describe the conception of the panel and showcase some exemplary applications with a focus on cancer genomics. Due diligence was paid to exclude cross-contaminated and non-representative cell lines. As the LL-100 cell lines are so well characterized and readily available, the panel will be a valuable resource for identifying cell lines with mutations in cancer genes, providing superior model systems. The data also add to the current knowledge of the molecular pathogenesis of leukemia–lymphoma. Additional efforts to expand the breadth of available high-quality cell lines are clearly warranted.
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Affiliation(s)
- Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
- Faculty of Life Sciences, Technical University of Braunschweig, 38124 Braunschweig, Germany
- Correspondence:
| | - Hilmar Quentmeier
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
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Quentmeier H, Pommerenke C, Hauer V, Uphoff CC, Zaborski M, Drexler HG. EZH2-activating mutation: no reliable indicator for efficacy of methyltransferase inhibitors. Leuk Lymphoma 2020; 61:2885-2893. [PMID: 32715799 DOI: 10.1080/10428194.2020.1795155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
EZH2 gain of function mutations (EZH2GOFmu) has been implicated in the pathogenesis of B-non-Hodgkin lymphoma. The EZH2-specific inhibitor GSK126 inhibits trimethylation of histone H3K27 and induces target gene expression. However, in 3/4 EZH2 GOFmu B-NHL lymphoma cell lines, GSK126 (400 nM) did not induce growth arrest. Only at high doses (10 µM), the inhibitor was effective as antiproliferative agent, comparably in EZH2 GOFmu, wild-type, and EZH2-negative cell lines, suggesting that at high concentrations, the antiproliferative effects of GSK126 are off-target effects. In sum, we could not confirm that B-NHL cell lines with EZH2 GOFmu show a higher sensitivity to GSK126 than EZH2 wild-type cell lines do. Only 1/4 EZH2 GOFmu B-NHL cell lines tested (PFEIFFER) were sensitive to GSK126 (400 nM) inducing growth arrest. If these results can be translated to patients, they raise the question of whether the presence of EZH2 activating mutations alone allows selection for targeted therapy with EZH2 inhibitors.
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Affiliation(s)
- Hilmar Quentmeier
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Bioinformatics and Databases, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vivien Hauer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cord C Uphoff
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Schnormeier AK, Pommerenke C, Kaufmann M, Drexler HG, Koeppel M. Genomic deregulation of PRMT5 supports growth and stress tolerance in chronic lymphocytic leukemia. Sci Rep 2020; 10:9775. [PMID: 32555249 PMCID: PMC7299935 DOI: 10.1038/s41598-020-66224-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/13/2020] [Indexed: 12/12/2022] Open
Abstract
Patients suffering from chronic lymphocytic leukemia (CLL) display highly diverse clinical courses ranging from indolent cases to aggressive disease, with genetic and epigenetic features resembling this diversity. Here, we developed a comprehensive approach combining a variety of molecular and clinical data to pinpoint translocation events disrupting long-range chromatin interactions and causing cancer-relevant transcriptional deregulation. Thereby, we discovered a B cell specific cis-regulatory element restricting the expression of genes in the associated locus, including PRMT5 and DAD1, two factors with oncogenic potential. Experimental PRMT5 inhibition identified transcriptional programs similar to those in patients with differences in PRMT5 abundance, especially MYC-driven and stress response pathways. In turn, such inhibition impairs factors involved in DNA repair, sensitizing cells for apoptosis. Moreover, we show that artificial deletion of the regulatory element from its endogenous context resulted in upregulation of corresponding genes, including PRMT5. Furthermore, such disruption renders PRMT5 transcription vulnerable to additional stimuli and subsequently alters the expression of downstream PRMT5 targets. These studies provide a mechanism of PRMT5 deregulation in CLL and the molecular dependencies identified might have therapeutic implementations.
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Affiliation(s)
- Ann-Kathrin Schnormeier
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany.,Institute for Cell Biology (Tumor Research), University of Duisburg-Essen, Medical School, Duisburg, Germany
| | - Claudia Pommerenke
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Maren Kaufmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Max Koeppel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany.
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Nagel S, Scherr M, MacLeod RAF, Pommerenke C, Koeppel M, Meyer C, Kaufmann M, Dallmann I, Drexler HG. NKL homeobox gene activities in normal and malignant myeloid cells. PLoS One 2019; 14:e0226212. [PMID: 31825998 PMCID: PMC6905564 DOI: 10.1371/journal.pone.0226212] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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] [Received: 09/02/2019] [Accepted: 11/21/2019] [Indexed: 12/30/2022] Open
Abstract
Recently, we have documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in early hematopoiesis and in lymphopoiesis, which spotlights genes deregulated in lymphoid malignancies. Here, we enlarge this map to include normal NKL homeobox gene expressions in myelopoiesis by analyzing public expression profiling data and primary samples from developing and mature myeloid cells. We thus uncovered differential activities of six NKL homeobox genes, namely DLX2, HHEX, HLX, HMX1, NKX3-1 and VENTX. We further examined public expression profiling data of 251 acute myeloid leukemia (AML) and 183 myelodysplastic syndrome (MDS) patients, thereby identifying 24 deregulated genes. These results revealed frequent deregulation of NKL homeobox genes in myeloid malignancies. For detailed analysis we focused on NKL homeobox gene NANOG, which acts as a stem cell factor and is correspondingly expressed alone in hematopoietic progenitor cells. We detected aberrant expression of NANOG in a small subset of AML patients and in AML cell line NOMO-1, which served as a model. Karyotyping and genomic profiling discounted rearrangements of the NANOG locus at 12p13. But gene expression analyses of AML patients and AML cell lines after knockdown and overexpression of NANOG revealed regulators and target genes. Accordingly, NKL homeobox genes HHEX, DLX5 and DLX6, stem cell factors STAT3 and TET2, and the NOTCH-pathway were located upstream of NANOG while NKL homeobox genes HLX and VENTX, transcription factors KLF4 and MYB, and anti-apoptosis-factor MIR17HG represented target genes. In conclusion, we have extended the NKL-code to the myeloid lineage and thus identified several NKL homeobox genes deregulated in AML and MDS. These data indicate a common oncogenic role of NKL homeobox genes in both lymphoid and myeloid malignancies. For misexpressed NANOG we identified an aberrant regulatory network, which contributes to the understanding of the oncogenic activity of NKL homeobox genes.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Michaela Scherr
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Max Koeppel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Iris Dallmann
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Quentmeier H, Pommerenke C, Dirks WG, Fähnrich S, Hauer V, Uphoff CC, Zaborski M, Drexler HG. DNMT3A R882H mutation in acute myeloid leukemia cell line SET-2. Leuk Res 2019; 88:106270. [PMID: 31739141 DOI: 10.1016/j.leukres.2019.106270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Hilmar Quentmeier
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silke Fähnrich
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vivien Hauer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cord C Uphoff
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Xu X, Wang L, Hu L, Dirks WG, Zhao Y, Wei Z, Chen D, Li Z, Wang Z, Han Y, Wei L, Drexler HG, Hu Z. Small molecular modulators of JMJD1C preferentially inhibit growth of leukemia cells. Int J Cancer 2019; 146:400-412. [PMID: 31271662 DOI: 10.1002/ijc.32552] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 01/08/2023]
Abstract
Histone demethylases are promising therapeutic targets as they play fundamental roles for survival of Mixed lineage leukemia rearranged acute leukemia (MLLr AL). Here we focused on the catalytic Jumonji domain of histone H3 lysine 9 (H3K9) demethylase JMJD1C to screen for potential small molecular modulators from 149,519 natural products and 33,765 Chinese medicine components via virtual screening. JMJD1C Jumonji domain inhibitor 4 (JDI-4) and JDI-12 that share a common structural backbone were detected within the top 15 compounds. Surface plasmon resonance analysis showed that JDI-4 and JDI-12 bind to JMJD1C and its family homolog KDM3B with modest affinity. In vitro demethylation assays showed that JDI-4 can reverse the H3K9 demethylation conferred by KDM3B. In vivo demethylation assays indicated that JDI-4 and JDI-12 could induce the global increase of H3K9 methylation. Cell proliferation and colony formation assays documented that JDI-4 and JDI-12 kill MLLr AL and other malignant hematopoietic cells, but not leukemia cells resistant to JMJD1C depletion or cord blood cells. Furthermore, JDI-16, among multiple compounds structurally akin to JDI-4/JDI-12, exhibits superior killing activities against malignant hematopoietic cells compared to JDI-4/JDI-12. Mechanistically, JDI-16 not only induces apoptosis but also differentiation of MLLr AL cells. RNA sequencing and quantitative PCR showed that JDI-16 induced gene expression associated with cell metabolism; targeted metabolomics revealed that JDI-16 downregulates lactic acids, NADP+ and other metabolites. Moreover, JDI-16 collaborates with all-trans retinoic acid to repress MLLr AML cells. In summary, we identified bona fide JMJD1C inhibitors that induce preferential death of MLLr AL cells.
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Affiliation(s)
- Xin Xu
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China.,College of Bioscience and Technology, Weifang, Shandong, China
| | - Lin Wang
- The School of Physics and Optoelectronic Engineering, Weifang University, Weifang, Shandong, China
| | - Linda Hu
- Upstate Medical University, Syracuse, NY
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Yao Zhao
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhishuai Wei
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Dexiang Chen
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Zhaoliang Li
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhanju Wang
- The Department of Hematology, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Yangyang Han
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Liuya Wei
- College of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Hans G Drexler
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Zhenbo Hu
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
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Quentmeier H, Pommerenke C, Dirks WG, Eberth S, Koeppel M, MacLeod RAF, Nagel S, Steube K, Uphoff CC, Drexler HG. The LL-100 panel: 100 cell lines for blood cancer studies. Sci Rep 2019; 9:8218. [PMID: 31160637 PMCID: PMC6547646 DOI: 10.1038/s41598-019-44491-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023] Open
Abstract
For many years, immortalized cell lines have been used as model systems for cancer research. Cell line panels were established for basic research and drug development, but did not cover the full spectrum of leukemia and lymphoma. Therefore, we now developed a novel panel (LL-100), 100 cell lines covering 22 entities of human leukemia and lymphoma including T-cell, B-cell and myeloid malignancies. Importantly, all cell lines are unequivocally authenticated and assigned to the correct tissue. Cell line samples were proven to be free of mycoplasma and non-inherent virus contamination. Whole exome sequencing and RNA-sequencing of the 100 cell lines were conducted with a uniform methodology to complement existing data on these publicly available cell lines. We show that such comprehensive sequencing data can be used to find lymphoma-subtype-characteristic copy number aberrations, mRNA isoforms, transcription factor activities and expression patterns of NKL homeobox genes. These exemplary studies confirm that the novel LL-100 panel will be useful for understanding the function of oncogenes and tumor suppressor genes and to develop targeted therapies.
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Affiliation(s)
- Hilmar Quentmeier
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany.
| | - Claudia Pommerenke
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Wilhelm G Dirks
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Sonja Eberth
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Max Koeppel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Roderick A F MacLeod
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Stefan Nagel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Klaus Steube
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Cord C Uphoff
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
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Nagel S, Pommerenke C, MacLeod RAF, Meyer C, Kaufmann M, Fähnrich S, Drexler HG. Deregulated expression of NKL homeobox genes in T-cell lymphomas. Oncotarget 2019; 10:3227-3247. [PMID: 31143370 PMCID: PMC6524933 DOI: 10.18632/oncotarget.26929] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/29/2019] [Indexed: 11/25/2022] Open
Abstract
Recently, we have presented a scheme, termed "NKL-code", which describes physiological expression patterns of NKL homeobox genes in early hematopoiesis and in lymphopoiesis including main stages of T-, B- and NK-cell development. Aberrant activity of these genes underlies the generation of hematological malignancies notably T-cell leukemia. Here, we searched for deregulated NKL homeobox genes in main entities of T-cell lymphomas comprising angioimmunoblastic T-cell lymphoma (AITL), anaplastic large cell lymphoma (ALCL), adult T-cell leukemia/lymphoma (ATLL), hepatosplenic T-cell lymphoma (HSTL), NK/T-cell lymphoma (NKTL) and peripheral T-cell lymphoma (PTCL). Our data revealed altogether 19 aberrantly overexpressed genes in these types, demonstrating deregulated NKL homeobox genes involvement in T-cell lymphomas as well. For detailed analysis we focused on NKL homeobox gene MSX1 which is normally expressed in NK-cells. MSX1 was overexpressed in subsets of HSTL patients and HSTL-derived sister cell lines DERL-2 and DERL-7 which served as models to characterize mechanisms of deregulation. We performed karyotyping, genomic and expression profiling, and whole genome sequencing to reveal mutated and deregulated gene candidates, including the fusion gene CD53-PDGFRB. Subsequent knockdown experiments allowed the reconstruction of an aberrant network involved in MSX1 deregulation, including chromatin factors AUTS2 and mutated histone HIST1H3B(K27M). The gene encoding AUTS2 is located at chromosome 7q11 and may represent a basic target of the HSTL hallmark aberration i(7q). Taken together, our findings highlight an oncogenic role for deregulated NKL homeobox genes in T-cell lymphoma and identify MSX1 as a novel player in HSTL, implicated in aberrant NK- and T-cell differentiation.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silke Fähnrich
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Abstract
Characteristic components of Hodgkin lymphoma (HL) tissue are the mono- or multinucleated Hodgkin-Reed-Sternberg (HRS) cells. Given the challenges of isolating these rare malignant cells and the difficulty in culturing cells from patients, many investigators have tried to establish cell lines in efforts to develop cellular tools for in vitro studies. A limited number of HL cell lines exist and have provided valuable insights into HL pathobiology. A literature survey indicated that 35 cell lines derived from HL patients have been published. To determine whether all these alleged HL cell lines hold up to scrutiny, we examined the available data and also put some of these cell lines to the test of hierarchical clustering, providing additional information regarding assignment to cell line type and tissue derivation. Hierarchical clustering separated the bona fide (classical) HL cell lines completely from cell lines derived from other lymphoma categories and proved conclusively that HL cell lines represent a distinct entity, irrespective of the cellular origin of the HRS cells. We conclude by pointing out the need for an intensified search for new cell culture avenues in order to develop a new generation of informative HL cell lines covering more widely the spectrum of HL stages and subtypes.
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Affiliation(s)
- Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Sonja Eberth
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
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Uphoff CC, Pommerenke C, Denkmann SA, Drexler HG. Screening human cell lines for viral infections applying RNA-Seq data analysis. PLoS One 2019; 14:e0210404. [PMID: 30629668 PMCID: PMC6328144 DOI: 10.1371/journal.pone.0210404] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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] [Received: 09/28/2018] [Accepted: 12/21/2018] [Indexed: 01/09/2023] Open
Abstract
Monitoring viral infections of cell cultures is largely neglected although the viruses may have an impact on the physiology of cells and may constitute a biohazard regarding laboratory safety and safety of bioactive agents produced by cell cultures. PCR, immunological assays, and enzyme activity tests represent common methods to detect virus infections. We have screened more than 300 Cancer Cell Line Encyclopedia RNA sequencing and 60 whole exome sequencing human cell lines data sets for specific viral sequences and general viral nucleotide and protein sequence assessment applying the Taxonomer bioinformatics tool developed by IDbyDNA. The results were compared with our previous findings from virus specific PCR analyses. Both, the results obtained from the direct alignment method and the Taxonomer alignment method revealed a complete concordance with the PCR results: twenty cell lines were found to be infected with five virus species. Taxonomer further uncovered a bovine polyomavirus infection in the breast cancer cell line SK-BR-3 most likely introduced by contaminated fetal bovine serum. RNA-Seq data sets were more sensitive for virus detection although a significant proportion of cell lines revealed low numbers of virus specific alignments attributable to low level nucleotide contamination during RNA preparation or sequencing procedure. Low quality reads leading to Taxonomer false positive results can be eliminated by trimming the sequence data before analysis. One further important result is that no viruses were detected that had never been shown to occur in cell cultures. The results prove that the currently applied testing of cell cultures is adequate for the detection of contamination and for the risk assessment of cell cultures. The results emphasize that next generation sequencing is an efficient tool to determine the viral infection status of human cells.
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Affiliation(s)
- Cord C. Uphoff
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine A. Denkmann
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Nagel S, MacLeod RAF, Meyer C, Kaufmann M, Drexler HG. NKL homeobox gene activities in B-cell development and lymphomas. PLoS One 2018; 13:e0205537. [PMID: 30308041 PMCID: PMC6181399 DOI: 10.1371/journal.pone.0205537] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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] [Received: 08/02/2018] [Accepted: 09/26/2018] [Indexed: 12/20/2022] Open
Abstract
Homeobox genes encode transcription factors which regulate basic processes in development and cell differentiation. Several members of the NKL subclass are deregulated in T-cell progenitors and support leukemogenesis. We have recently described particular expression patterns of nine NKL homeobox genes in early hematopoiesis and T-cell development. Here, we screened NKL homeobox gene activities in normal B-cell development and extended the NKL-code to include this lymphoid lineage. Analysis of public expression profiling datasets revealed that HHEX and NKX6-3 were the only members differentially active in naïve B-cells, germinal center B-cells, plasma cells and memory B-cells. Subsequent examination of different types of B-cell malignancies showed both aberrant overexpression of NKL-code members and ectopic activation of subclass members physiologically silent in lymphopoiesis including BARX2, DLX1, EMX2, NKX2-1, NKX2-2 and NKX3-2. Based on these findings we performed detailed studies of the B-cell specific NKL homeobox gene NKX6-3 which showed enhanced activity in patient subsets of follicular lymphoma, mantle cell lymphoma and diffuse large B-cell lymphoma (DLBCL), and in three DLBCL cell lines to serve as in vitro models. While excluding genomic and chromosomal rearrangements at the locus of NKX6-3 (8p11) promoter studies demonstrated that B-cell factors MYB and PAX5 activated NKX6-3 transcription. Furthermore, aberrant BMP7/SMAD1-signalling and deregulated expression of chromatin complex components AUTS2 and PCGF5 promoted NKX6-3 activation. Finally, NKL homeobox genes HHEX, HLX, MSX1 and NKX6-3 were expressed in B-cell progenitors and generated a regulatory gene network in cell lines which we propose may provide physiological support for NKL-code formation in early B-cell development. Together, we identified an NKL-code in B-cell development whose violation may deregulate differentiation and promote malignant transformation.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Quentmeier H, Pommerenke C, Bernhart SH, Dirks WG, Hauer V, Hoffmann S, Nagel S, Siebert R, Uphoff CC, Zaborski M, Drexler HG. RBFOX2 and alternative splicing in B-cell lymphoma. Blood Cancer J 2018; 8:77. [PMID: 30097561 PMCID: PMC6086906 DOI: 10.1038/s41408-018-0114-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/20/2018] [Accepted: 07/06/2018] [Indexed: 12/03/2022] Open
Affiliation(s)
- Hilmar Quentmeier
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group - Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vivien Hauer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Steve Hoffmann
- Computational Biology, Leibniz Institute on Aging - Fritz Lipmann Institute and Friedrich Schiller University Jena, Jena, Germany
| | - Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Cord C Uphoff
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Nagel S, Meyer C, Kaufmann M, Zaborski M, MacLeod RAF, Drexler HG. Aberrant activity of NKL homeobox gene NKX3-2 in a T-ALL subset. PLoS One 2018; 13:e0197194. [PMID: 29746601 PMCID: PMC5944955 DOI: 10.1371/journal.pone.0197194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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] [Received: 12/19/2017] [Accepted: 04/27/2018] [Indexed: 01/26/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a hematopoietic malignancy originating from T-cell progenitors in which differentiation is blocked at early stages. Physiological expression of specific NKL homeobox genes obeys a hematopoietic NKL-code implicated in the process of lymphopoiesis while in differentiated T-cells these genes are silenced. We propose that this developmental expression pattern underlies the observation that NKL homeobox genes are the most ubiquitous group of transcription factors deregulated in T-ALL, including TLX1, TLX3, NKX2-5 and NKX3-1. Here, we describe a novel member of the NKL homeobox gene subclass, NKX3-2 (BAPX1), which is aberrantly activated in 18% of pediatric T-ALL patients analyzed while being normally expressed in developing spleen. Identification of NKX3-2 expression in T-ALL cell line CCRF-CEM qualified these cells to model its deregulation and function in a leukemic context. Genomic and chromosomal analyses demonstrated normal configuration of the NKX3-2 locus at chromosome 4p15, thus excluding cytogenetic dysregulation. Comparative expression profiling analysis of NKX3-2 patient data revealed deregulated activity of BMP- and MAPK-signalling. These candidate pathways were experimentally confirmed to mediate aberrant NKX3-2 expression. We also show that homeobox gene SIX6, plus MIR17HG and GATA3 are downstream targets of NKX3-2 and plausibly contribute to the pathogenesis of this malignancy by suppressing T-cell differentiation. Finally, NKL homeobox gene NKX2-5 was activated by NKX3-2 in CCRF-CEM and by FOXG1 in PEER, representing mutually inhibitory activators of this translocated oncogene. Together, our findings reveal a novel oncogenic NKL homeobox gene subclass member which is aberrantly expressed in a large subset of T-ALL patients and participates in a deregulated gene network likely to arise in developing spleen.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Quentmeier H, Pommerenke C, Ammerpohl O, Geffers R, Hauer V, MacLeod RAF, Nagel S, Romani J, Rosati E, Rosén A, Uphoff CC, Zaborski M, Drexler HG. Subclones in B-lymphoma cell lines: isogenic models for the study of gene regulation. Oncotarget 2018; 7:63456-63465. [PMID: 27566572 PMCID: PMC5325377 DOI: 10.18632/oncotarget.11524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/15/2016] [Indexed: 11/25/2022] Open
Abstract
Genetic heterogeneity though common in tumors has been rarely documented in cell lines. To examine how often B-lymphoma cell lines are comprised of subclones, we performed immunoglobulin (IG) heavy chain hypermutation analysis. Revealing that subclones are not rare in B-cell lymphoma cell lines, 6/49 IG hypermutated cell lines (12%) consisted of subclones with individual IG mutations. Subclones were also identified in 2/284 leukemia/lymphoma cell lines exhibiting bimodal CD marker expression. We successfully isolated 10 subclones from four cell lines (HG3, SU-DHL-5, TMD-8, U-2932). Whole exome sequencing was performed to molecularly characterize these subclones. We describe in detail the clonal structure of cell line HG3, derived from chronic lymphocytic leukemia. HG3 consists of three subclones each bearing clone-specific aberrations, gene expression and DNA methylation patterns. While donor patient leukemic cells were CD5+, two of three HG3 subclones had independently lost this marker. CD5 on HG3 cells was regulated by epigenetic/transcriptional mechanisms rather than by alternative splicing as reported hitherto. In conclusion, we show that the presence of subclones in cell lines carrying individual mutations and characterized by sets of differentially expressed genes is not uncommon. We show also that these subclones can be useful isogenic models for regulatory and functional studies.
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Affiliation(s)
- Hilmar Quentmeier
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Robert Geffers
- Genome Analytics Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vivien Hauer
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Nagel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julia Romani
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Emanuela Rosati
- Department of Experimental Medicine, Bioscience and Medical Embryology Section, University of Perugia, Perugia, Italy
| | - Anders Rosén
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Linköping University, Linköping, Sweden
| | - Cord C Uphoff
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Nagel S, Pommerenke C, Meyer C, Kaufmann M, MacLeod RA, Drexler HG. Aberrant expression of NKL homeobox gene HLX in Hodgkin lymphoma. Oncotarget 2018; 9:14338-14353. [PMID: 29581848 PMCID: PMC5865674 DOI: 10.18632/oncotarget.24512] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/10/2018] [Indexed: 12/13/2022] Open
Abstract
NKL homeobox genes are basic regulators of cell and tissue differentiation, many acting as oncogenes in T-cell leukemia. Recently, we described an hematopoietic NKL-code comprising six particular NKL homeobox genes expressed in hematopoietic stem cells and lymphoid progenitors, unmasking their physiological roles in the development of these cell types. Hodgkin lymphoma (HL) is a B-cell malignancy showing aberrant activity of several developmental genes resulting in disturbed B-cell differentiation. To examine potential concordances in abnormal lymphoid differentiation of T- and B-cell malignancies we analyzed the expression of the hematopoietic NKL-code associated genes in HL, comprising HHEX, HLX, MSX1, NKX2-3, NKX3-1 and NKX6-3. Our approach revealed aberrant HLX activity in 8 % of classical HL patients and additionally in HL cell line L-540. Accordingly, to identify upstream regulators and downstream target genes of HLX we used L-540 cells as a model and performed chromosome and genome analyses, comparative expression profiling and functional assays via knockdown and overexpression experiments therein. These investigations excluded chromosomal rearrangements of the HLX locus at 1q41 and demonstrated that STAT3 operated directly as transcriptional activator of the HLX gene. Moreover, subcellular analyses showed highly enriched STAT3 protein in the nucleus of L-540 cells which underwent cytoplasmic translocation by repressing deacetylation. Finally, HLX inhibited transcription of B-cell differentiation factors MSX1, BCL11A and SPIB and of pro-apoptotic factor BCL2L11/BIM, thereby suppressing Etoposide-induced cell death. Collectively, we propose that aberrantly expressed NKL homeobox gene HLX is part of a pathological gene network in HL, driving deregulated B-cell differentiation and survival.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A.F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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24
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Ding C, Chen SN, Macleod RAF, Drexler HG, Nagel S, Wu DP, Sun AN, Dai HP. MiR-130a is aberrantly overexpressed in adult acute myeloid leukemia with t(8;21) and its suppression induces AML cell death. Ups J Med Sci 2018; 123:19-27. [PMID: 29493383 PMCID: PMC5901465 DOI: 10.1080/03009734.2018.1440037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Emerging evidence has revealed that miRNAs can function as oncogenes or tumor suppressor genes in leukemia. The ectopic expression of miR-130a has been reported in chronic leukemia, but our understanding of the biological implications of miR-130a expression remains incomplete. METHODS We quantified a cohort of de novo acute myeloid leukemia (AML) by bead-based miRNA and real-time quantitative PCR (Rq-PCR). The luciferase reporter gene assay was analyzed after the plasmid constructs which contain 5'-UTR of miR-130a and a Renilla luciferase reporter plasmid were transfected simultaneously into 293T cells. MTT and caspase 3/7 apoptosis assays were used to test cell viability and apoptosis. RESULTS We identified miR-130a as significantly overexpressed in t(8;21) AML. Expression of miR-130a decreased significantly once patients with t(8;21) achieved complete remission, but increased sharply at the time of relapse. In patients with t(8;21) AML, KIT mutational status was associated with miR-130a expression-with higher expression associated with KIT activating mutations. Increased miR-130a expression in t(8;21) AML was associated with slightly worse event-free survival; however, no impact on overall survival was observed. Knockdown of AML1/ETO protein in the SKNO-1 cell line resulted in decrease of expression of miR-130a. Direct binding of AML1/ETO fusion protein with the promoter sequence of miR-130a was detected with luciferase reporter gene assay. Following miR-130a knockdown, SKNO-1 demonstrated increased sensitivity to etoposide. CONCLUSIONS Our data suggest that miR-130a is directly activated by AML1/ETO, and may act as a factor which is associated with leukemia burden, event-free survival, and chemotherapy sensitivity in t(8;21) AML.
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MESH Headings
- Adult
- Apoptosis
- Cell Line, Tumor
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Core Binding Factor Alpha 2 Subunit/genetics
- Etoposide/therapeutic use
- Female
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Male
- MicroRNAs/analysis
- MicroRNAs/antagonists & inhibitors
- MicroRNAs/physiology
- Oncogene Proteins, Fusion/genetics
- RUNX1 Translocation Partner 1 Protein/genetics
- Translocation, Genetic
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Affiliation(s)
- Chao Ding
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Su-Ning Chen
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People’s Republic of China
| | - Roderick A. F. Macleod
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Nagel
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - De-Pei Wu
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People’s Republic of China
- Suzhou Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, People’s Republic of China
| | - Ai-Ning Sun
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People’s Republic of China
- Suzhou Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, People’s Republic of China
| | - Hai-Ping Dai
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People’s Republic of China
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- CONTACT Hai-ping Dai Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, 188, Shizi Street, Suzhou 215006, Jiangsu Province, P. R. China
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25
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Chen S, Nagel S, Schneider B, Dai H, Geffers R, Kaufmann M, Meyer C, Pommerenke C, Thress KS, Li J, Quentmeier H, Drexler HG, MacLeod RAF. A new ETV6-NTRK3 cell line model reveals MALAT1 as a novel therapeutic target - a short report. Cell Oncol (Dordr) 2017; 41:93-101. [PMID: 29119387 DOI: 10.1007/s13402-017-0356-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Previously, the chromosomal translocation t(12;15)(p13;q25) has been found to recurrently occur in both solid tumors and leukemias. This translocation leads to ETV6-NTRK3 (EN) gene fusions resulting in ectopic expression of the NTRK3 neurotropic tyrosine receptor kinase moiety as well as oligomerization through the donated ETV6-sterile alpha motif domain. As yet, no in vitro cell line model carrying this anomaly is available. Here we genetically characterized the acute promyelocytic leukemia (APL) cell line AP-1060 and, by doing so, revealed the presence of a t(12;15)(p13;q25). Subsequently, we evaluated its suitability as a model for this important clinical entity. METHODS Spectral karyotyping, fluorescence in situ hybridization (FISH), and genomic and transcriptomic microarray-based profiling were used to screen for the presence of EN fusions. qRT-PCR was used for quantitative expression analyses. Responses to AZ-23 (NTRK) and wortmannin (PI3K) inhibitors, as well as to arsenic trioxide (ATO), were assessed using colorimetric assays. An AZ-23 microarray screen was used to define the EN targetome, which was parsed bioinformatically. MAPK1 and MALAT1 activation were assayed using Western blotting and RNA-FISH, respectively, whereas an AML patient cohort was used to assess the clinical occurrence of MALAT1 activation. RESULTS An EN fusion was detected in AP1060 cells which, accordingly, turned out to be hypersensitive to AZ-23. We also found that AZ-23 can potentiate the effect of ATO and inhibit the phosphorylation of its canonical target MAPK1. The AZ-23 microarray screen highlighted a novel EN target, MALAT1, which also proved sensitive to wortmannin. Finally, we found that MALAT1 was massively up-regulated in a subset of AML patients. CONCLUSIONS From our data we conclude that AP-1060 may serve as a first publicly available preclinical model for EN. In addition, we conclude that these EN-positive cells are sensitive to the NTRK inhibitor AZ-23 and that this inhibitor may potentiate the therapeutic efficacy of ATO. Our data also highlight a novel AML EN target, MALAT1, which was so far only conspicuous in solid tumors.
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Affiliation(s)
- Suning Chen
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany.,Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Stefan Nagel
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany
| | - Bjoern Schneider
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany.,Institute of Pathology and Molecular Pathology, University of Rostock, Rostock, Germany
| | - Haiping Dai
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany.,Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Robert Geffers
- Genome Analytics Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany
| | | | - Jiao Li
- Department of Hematology, Yixing People's Hospital of Jiangsu Province, Yixing, People's Republic of China
| | - Hilmar Quentmeier
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124, Braunschweig, Germany.
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26
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Jawhar M, Naumann N, Knut M, Score J, Ghazzawi M, Schneider B, Kreuzer KA, Hallek M, Drexler HG, Chacko J, Wallis L, Fabarius A, Metzgeroth G, Hofmann WK, Chase A, Tapper W, Reiter A, Cross NCP. Cytogenetically cryptic ZMYM2-FLT3 and DIAPH1-PDGFRB gene fusions in myeloid neoplasms with eosinophilia. Leukemia 2017; 31:2271-2273. [PMID: 28751768 PMCID: PMC5630086 DOI: 10.1038/leu.2017.240] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- M Jawhar
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - N Naumann
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - M Knut
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - J Score
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Ghazzawi
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - B Schneider
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - K-A Kreuzer
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - M Hallek
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - H G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - J Chacko
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - L Wallis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - A Fabarius
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - G Metzgeroth
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - W-K Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - A Chase
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - W Tapper
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - A Reiter
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - N C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK
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27
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Ehrentraut S, Nagel S, Pommerenke C, Dirks WG, Quentmeier H, Kaufmann M, Meyer C, Zaborski M, Geffers R, Fujiwara H, Drexler HG, MacLeod RAF. Peripheral T-cell lymphoma cell line T8ML-1 highlights conspicuous targeting of PVRL2 by t(14;19)(q11.2;q13.3). Haematologica 2017; 102:e356-e359. [PMID: 28659334 DOI: 10.3324/haematol.2017.168203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Stefan Ehrentraut
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Stefan Nagel
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Claudia Pommerenke
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Wilhelm G Dirks
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Hilmar Quentmeier
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Maren Kaufmann
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Corinna Meyer
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Margarete Zaborski
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Robert Geffers
- Genome Analytics Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Hiroshi Fujiwara
- First Department of Internal Medicine, Ehime University Hospital, Ehime, Japan
| | - Hans G Drexler
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Roderick A F MacLeod
- DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
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28
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Aït Ghezali L, Arbabian A, Roudot H, Brouland JP, Baran-Marszak F, Salvaris E, Boyd A, Drexler HG, Enyedi A, Letestu R, Varin-Blank N, Papp B. Induction of endoplasmic reticulum calcium pump expression during early leukemic B cell differentiation. J Exp Clin Cancer Res 2017; 36:87. [PMID: 28651627 PMCID: PMC5485704 DOI: 10.1186/s13046-017-0556-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/18/2017] [Indexed: 11/15/2022] Open
Abstract
Background Endoplasmic reticulum (ER) calcium storage and release play important roles in B lymphocyte maturation, survival, antigen-dependent cell activation and immunoglobulin synthesis. Calcium is accumulated in the endoplasmic reticulum (ER) by Sarco/Endoplasmic Reticulum Calcium ATPases (SERCA enzymes). Because lymphocyte function is critically dependent on SERCA activity, it is important to understand qualitative and quantitative changes of SERCA protein expression that occur during B lymphoid differentiation and leukemogenesis. Methods In this work we investigated the modulation of SERCA expression during the pharmacologically induced differentiation of leukemic precursor B lymphoblast cell lines that carry the E2A-PBX1 fusion oncoprotein. Changes of SERCA levels during differentiation were determined and compared to those of established early B lymphoid differentiation markers. SERCA expression of the cells was compared to that of mature B cell lines as well, and the effect of the direct inhibition of SERCA-dependent calcium transport on the differentiation process was investigated. Results We show that E2A-PBX1+ leukemia cells simultaneously express SERCA2 and SERCA3-type calcium pumps; however, their SERCA3 expression is markedly inferior to that of mature B cells. Activation of protein kinase C enzymes by phorbol ester leads to phenotypic differentiation of the cells, and this is accompanied by the induction of SERCA3 expression. Direct pharmacological inhibition of SERCA-dependent calcium transport during phorbol ester treatment interferes with the differentiation process. Conclusion These data show that the calcium pump composition of the ER is concurrent with increased SERCA3 expression during the differentiation of precursor B acute lymphoblastic leukemia cells, that a cross-talk exists between SERCA function and the control of differentiation, and that SERCA3 may constitute an interesting new marker for the study of early B cell phenotype. Electronic supplementary material The online version of this article (doi:10.1186/s13046-017-0556-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lamia Aït Ghezali
- Institut National de la Santé et de la Recherche Médicale, U978, Bobigny, France.,Université Paris-13, PRES Sorbonne Paris-Cité, 74, rue Marcel Cachin 93017, Bobigny, France
| | | | - Hervé Roudot
- Institut National de la Santé et de la Recherche Médicale, U978, Bobigny, France.,Université Paris-13, PRES Sorbonne Paris-Cité, 74, rue Marcel Cachin 93017, Bobigny, France.,Service d'Hématologie Biologique, Hôpitaux Universitaires Paris Seine-Saint-Denis, AP-HP, Hôpital Avicenne, Bobigny, France
| | | | - Fanny Baran-Marszak
- Institut National de la Santé et de la Recherche Médicale, U978, Bobigny, France.,Université Paris-13, PRES Sorbonne Paris-Cité, 74, rue Marcel Cachin 93017, Bobigny, France.,Service d'Hématologie Biologique, Hôpitaux Universitaires Paris Seine-Saint-Denis, AP-HP, Hôpital Avicenne, Bobigny, France
| | - Evelyn Salvaris
- Immunology Research Centre, St Vincent's Hospital, Melbourne, VIC, Australia
| | - Andrew Boyd
- Department of Medicine, University of Queensland, Queensland, Australia
| | - Hans G Drexler
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Brauschweig, Germany
| | - Agnes Enyedi
- Second Institute of Pathology, Semmelweis University Medical School, Budapest, Hungary
| | - Remi Letestu
- Institut National de la Santé et de la Recherche Médicale, U978, Bobigny, France.,Université Paris-13, PRES Sorbonne Paris-Cité, 74, rue Marcel Cachin 93017, Bobigny, France.,Service d'Hématologie Biologique, Hôpitaux Universitaires Paris Seine-Saint-Denis, AP-HP, Hôpital Avicenne, Bobigny, France
| | - Nadine Varin-Blank
- Institut National de la Santé et de la Recherche Médicale, U978, Bobigny, France.,Université Paris-13, PRES Sorbonne Paris-Cité, 74, rue Marcel Cachin 93017, Bobigny, France
| | - Bela Papp
- Institut National de la Santé et de la Recherche Médicale, U978, Bobigny, France. .,Université Paris-13, PRES Sorbonne Paris-Cité, 74, rue Marcel Cachin 93017, Bobigny, France. .,U978 Inserm, UFR SMBH, Université Paris-13, 74, rue Marcel Cachin, 93017, Bobigny, France.
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29
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Nagel S, Pommerenke C, Meyer C, Kaufmann M, MacLeod RAF, Drexler HG. NKL homeobox gene MSX1 acts like a tumor suppressor in NK-cell leukemia. Oncotarget 2017; 8:66815-66832. [PMID: 28977998 PMCID: PMC5620138 DOI: 10.18632/oncotarget.18609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/29/2017] [Indexed: 12/17/2022] Open
Abstract
NKL homeobox gene MSX1 is physiologically expressed in lymphoid progenitors and subsequently downregulated in developing T- and B-cells. In contrast, elevated expression levels of MSX1 persist in mature natural killer (NK)-cells, indicating a functional role in this compartment. While T-cell acute lymphoblastic leukemia (T-ALL) subsets exhibit aberrant overexpression of MSX1, we show here that in malignant NK-cells the level of MSX1 transcripts is aberrantly downregulated. Chromosomal deletions at 4p16 hosting the MSX1 locus have been described in NK-cell leukemia patients. However, NK-cell lines analyzed here showed normal MSX1 gene configurations, indicating that this aberration might be uncommon. To identify alternative MSX1 regulatory mechanisms we compared expression profiling data of primary normal NK-cells and malignant NK-cell lines. This procedure revealed several deregulated genes including overexpressed IRF4, MIR155HG and MIR17HG and downregulated AUTS2, EP300, GATA3 and HHEX. As shown recently, chromatin-modulator AUTS2 is overexpressed in T-ALL subsets where it mediates aberrant transcriptional activation of MSX1. Here, our data demonstrate that in malignant NK-cell lines AUTS2 performed MSX1 activation as well, but in accordance with downregulated MSX1 transcription therein we detected reduced AUTS2 expression, a small genomic deletion at 7q11 removing exons 3 and 4, and truncating mutations in exon 1. Moreover, genomic profiling and chromosomal analyses of NK-cell lines demonstrated amplification of IRF4 at 6p25 and deletion of PRDM1 at 6q21, highlighting their potential oncogenic impact. Functional analyses performed via knockdown or forced expression of these genes revealed regulatory network disturbances effecting downregulation of MSX1 which may underlie malignant development in NK-cells.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
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30
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Xu X, Nagel S, Quentmeier H, Wang Z, Pommerenke C, Dirks WG, Macleod RAF, Drexler HG, Hu Z. KDM3B shows tumor-suppressive activity and transcriptionally regulates HOXA1 through retinoic acid response elements in acute myeloid leukemia. Leuk Lymphoma 2017; 59:204-213. [PMID: 28540746 DOI: 10.1080/10428194.2017.1324156] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
KDM3B reportedly shows both tumor-suppressive and tumor-promoting activities in leukemia. The function of KDM3B is likely cell-type dependent and its seeming functional discordance may reflect its phenotypic dependence on downstream targets. Here, we first showed the underexpression of KDM3B in acute myeloid leukemia (AML) patients and AML cell lines with MLL-AF6/9 or PML-RARA translocations. Overexpression of KDM3B repressed colony formation of AML cell line with 5q deletion. We then performed global microarray profiling to identify potential downstream targets of KDM3B, notably HOXA1, which was verified by real time PCR and Western blotting. We further showed KDM3B binding at retinoic acid response elements (RARE) but not at the promoter region of HOXA1 gene. KDM3B knockdown resulted in increased mono-methylation but decreased di-methylation of H3K9 at RARE while eschewing the promoter region of HOXA1. Collectively, we found that KDM3B exhibits potential tumor-suppressive activity and transcriptionally modulates HOXA1 expression via RARE in AML.
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Affiliation(s)
- Xin Xu
- a Laboratory for Stem Cell and Regenerative Medicine , The Affiliated Hospital of Weifang Medical University , Weifang , Shandong , China
| | - Stefan Nagel
- b Department of Human and Animal Cell Culture , Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Hilmar Quentmeier
- b Department of Human and Animal Cell Culture , Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Zhanju Wang
- c Department of Hematology , The Affiliated Hospital of Weifang Medical University , Weifang , Shandong , China
| | - Claudia Pommerenke
- b Department of Human and Animal Cell Culture , Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Wilhelm G Dirks
- b Department of Human and Animal Cell Culture , Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Roderick A F Macleod
- b Department of Human and Animal Cell Culture , Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Hans G Drexler
- b Department of Human and Animal Cell Culture , Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Zhenbo Hu
- a Laboratory for Stem Cell and Regenerative Medicine , The Affiliated Hospital of Weifang Medical University , Weifang , Shandong , China.,c Department of Hematology , The Affiliated Hospital of Weifang Medical University , Weifang , Shandong , China
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31
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Drexler HG, Dirks WG, MacLeod RAF, Uphoff CC. False and mycoplasma-contaminated leukemia-lymphoma cell lines: time for a reappraisal. Int J Cancer 2017; 140:1209-1214. [PMID: 27870004 DOI: 10.1002/ijc.30530] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 01/23/2023]
Abstract
Leukemia-lymphoma cell lines are important research tools in a variety of fields. To represent adequate model systems it is of utmost importance that cell lines faithfully model the primary tumor material and are not cross-contaminated with unrelated cell material (or contaminated with mycoplasma). As it has been previously reported that cross-contaminated cell lines represent a significant problem, it is of interest to know whether any improvement in the prevalence of such "false cell lines" had occurred since we called the alert in 1999. A retrospective review of our data archives covered 848 cell lines received from 1990 to 2014 from 290 laboratories in 23 countries spanning the spectrum of leukemia-lymphoma entities. Two variables were considered: authenticity and freedom from mycoplasma infection. Regarding provenance, we separately considered primary sources (original investigators having established the cell lines or reference repositories) and secondary sources. The percentages of mycoplasma-contaminated cell lines decreased significantly over the 25-year timespan. Among primary sourced material: mycoplasma-contamination fell from 23% to 0%; among secondary sourced: from 48% to 21%. The corresponding figures for cross-contamination declined from 15% to 6%, while among material obtained from secondary sources prevalence remained remarkably high, throughout the time periods at 14-18%. Taken together, our data indicate that using non-authenticated cell lines from secondary sources carries a risk of about 1:6 for obtaining a false cell line. The use of authentic leukemia-lymphoma cell lines holds important translational value for their model character and the reproducibility of the laboratory data in the clinical arena.
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Affiliation(s)
- Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cord C Uphoff
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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32
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Daniele G, Simonetti G, Fusilli C, Iacobucci I, Lonoce A, Palazzo A, Lomiento M, Mammoli F, Marsano RM, Marasco E, Mantovani V, Quentmeier H, Drexler HG, Ding J, Palumbo O, Carella M, Nadarajah N, Perricone M, Ottaviani E, Baldazzi C, Testoni N, Papayannidis C, Ferrari S, Mazza T, Martinelli G, Storlazzi CT. Epigenetically induced ectopic expression of UNCX impairs the proliferation and differentiation of myeloid cells. Haematologica 2017; 102:1204-1214. [PMID: 28411256 PMCID: PMC5566027 DOI: 10.3324/haematol.2016.163022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 04/12/2017] [Indexed: 11/09/2022] Open
Abstract
We here describe a leukemogenic role of the homeobox gene UNCX,
activated by epigenetic modifications in acute myeloid leukemia (AML). We found
the ectopic activation of UNCX in a leukemia patient harboring
a t(7;10)(p22;p14) translocation, in 22 of 61 of additional cases [a
total of 23 positive patients out of 62 (37.1%)], and in 6 of 75
(8%) of AML cell lines. UNCX is embedded within a
low-methylation region (canyon) and encodes for a transcription factor involved
in somitogenesis and neurogenesis, with specific expression in the eye, brain,
and kidney. UNCX expression turned out to be associated, and
significantly correlated, with DNA methylation increase at its canyon borders
based on data in our patients and in archived data of patients from The Cancer
Genome Atlas. UNCX-positive and -negative patients displayed
significant differences in their gene expression profiles. An enrichment of
genes involved in cell proliferation and differentiation, such as
MAP2K1 and CCNA1, was revealed. Similar
results were obtained in UNCX-transduced CD34+
cells, associated with low proliferation and differentiation arrest.
Accordingly, we showed that UNCX expression characterizes
leukemia cells at their early stage of differentiation, mainly M2 and M3
subtypes carrying wild-type NPM1. We also observed that
UNCX expression significantly associates with an increased
frequency of acute promyelocytic leukemia with PML-RARA and AML
with t(8;21)(q22;q22.1); RUNX1-RUNX1T1 classes, according to
the World Health Organization disease classification. In summary, our findings
suggest a novel leukemogenic role of UNCX, associated with
epigenetic modifications and with impaired cell proliferation and
differentiation in AML.
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Affiliation(s)
- Giulia Daniele
- Department of Biology, University of Bari "A. Moro", Italy
| | - Giorgia Simonetti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Caterina Fusilli
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, San Giovanni Rotondo, Italy
| | - Ilaria Iacobucci
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Angelo Lonoce
- Department of Biology, University of Bari "A. Moro", Italy
| | | | - Mariana Lomiento
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabiana Mammoli
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Vilma Mantovani
- Center for Applied Biomedical Research (CRBA), S. Orsola-Malpighi Hospital, Bologna, Italy.,Unit of Medical Genetics, Department of Medical and Surgical Sciences, S. Orsola-Malpighi Hospital University of Bologna, Italy
| | - Hilmar Quentmeier
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Jie Ding
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS "Casa Sollievo della Sofferenza (CSS)" Hospital, San Giovanni Rotondo, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS "Casa Sollievo della Sofferenza (CSS)" Hospital, San Giovanni Rotondo, Italy
| | | | - Margherita Perricone
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Emanuela Ottaviani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Carmen Baldazzi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Nicoletta Testoni
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Cristina Papayannidis
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Sergio Ferrari
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, San Giovanni Rotondo, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
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Abstract
To identify novel cancer-related genes targeted by copy number alterations, we performed genomic profiling of T-cell acute lymphoblastic leukemia (T-ALL) cell lines. In 3/8, we identified a shared deletion at chromosomal position 2p16.3-p21. Within the minimally deleted region, we recognized several candidate tumor suppressor (TS) genes, including FBXO11 and FOXN2. An additional deletion at chromosome 14q23.2-q32.11 included FOXN3, highlighting this class of FOX genes as potential TS. Quantitative expression analyses of FBXO11, FOXN2, and FOXN3 confirmed reduced transcript levels in the identified cell lines. Moreover, reduced expression of these genes was also observed in about 7% of T-ALL patients, showing their clinical relevance in this malignancy. Bioinformatic analyses revealed concurrent reduction of FOXN2 and/or FOXN3 together with homeobox gene ZHX1. Consistently, experiments demonstrated that both FOXN2 and FOXN3 directly activated transcription of ZHX1. Taken together, we identified novel TS genes forming a regulatory network in T-cell development and leukemogenesis.
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Affiliation(s)
- Stefan Nagel
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Claudia Pommerenke
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Corinna Meyer
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Maren Kaufmann
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Roderick A F MacLeod
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Hans G Drexler
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
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34
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Mansouri L, Noerenberg D, Young E, Mylonas E, Abdulla M, Frick M, Asmar F, Ljungström V, Schneider M, Yoshida K, Skaftason A, Pandzic T, Gonzalez B, Tasidou A, Waldhueter N, Rivas-Delgado A, Angelopoulou M, Ziepert M, Arends CM, Couronné L, Lenze D, Baldus CD, Bastard C, Okosun J, Fitzgibbon J, Dörken B, Drexler HG, Roos-Weil D, Schmitt CA, Munch-Petersen HD, Zenz T, Hansmann ML, Strefford JC, Enblad G, Bernard OA, Ralfkiaer E, Erlanson M, Korkolopoulou P, Hultdin M, Papadaki T, Grønbæk K, Lopez-Guillermo A, Ogawa S, Küppers R, Stamatopoulos K, Stavroyianni N, Kanellis G, Rosenwald A, Campo E, Amini RM, Ott G, Vassilakopoulos TP, Hummel M, Rosenquist R, Damm F. Frequent NFKBIE deletions are associated with poor outcome in primary mediastinal B-cell lymphoma. Blood 2016; 128:2666-2670. [PMID: 27670424 DOI: 10.1182/blood-2016-03-704528] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/16/2016] [Indexed: 12/19/2022] Open
Abstract
We recently reported a truncating deletion in the NFKBIE gene, which encodes IκBε, a negative feedback regulator of NF-κB, in clinically aggressive chronic lymphocytic leukemia (CLL). Because preliminary data indicate enrichment of NFKBIE aberrations in other lymphoid malignancies, we screened a large patient cohort (n = 1460) diagnosed with different lymphoid neoplasms. While NFKBIE deletions were infrequent in follicular lymphoma, splenic marginal zone lymphoma, and T-cell acute lymphoblastic leukemia (<2%), slightly higher frequencies were seen in diffuse large B-cell lymphoma, mantle cell lymphoma, and primary central nervous system lymphoma (3% to 4%). In contrast, a remarkably high frequency of NFKBIE aberrations (46/203 cases [22.7%]) was observed in primary mediastinal B-cell lymphoma (PMBL) and Hodgkin lymphoma (3/11 cases [27.3%]). NFKBIE-deleted PMBL patients were more often therapy refractory (P = .022) and displayed inferior outcome compared with wild-type patients (5-year survival, 59% vs 78%; P = .034); however, they appeared to benefit from radiotherapy (P =022) and rituximab-containing regimens (P = .074). NFKBIE aberrations remained an independent factor in multivariate analysis (P = .003) and when restricting the analysis to immunochemotherapy-treated patients (P = .008). Whole-exome sequencing and gene expression profiling verified the importance of NF-κB deregulation in PMBL. In summary, we identify NFKBIE aberrations as a common genetic event across B-cell malignancies and highlight NFKBIE deletions as a novel poor-prognostic marker in PMBL.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Daniel Noerenberg
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Emma Young
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elena Mylonas
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Maysaa Abdulla
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mareike Frick
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Fazila Asmar
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Viktor Ljungström
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Markus Schneider
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aron Skaftason
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Blanca Gonzalez
- Department of Pathology, Hospital Clinic and Institut d'Investigacions Biomediques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Anna Tasidou
- Hematopathology Department, Evangelismos Hospital, Athens, Greece
| | - Nils Waldhueter
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | | | - Maria Angelopoulou
- Department of Haematology, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - Marita Ziepert
- Institute for Medical Informatics, Statistics, and Epidemiology, University at Leipzig, Leipzig, Germany
| | | | - Lucile Couronné
- Service d'Hématologie Adulte, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Paris, France
| | - Dido Lenze
- Institute of Pathology, Charité, University Medical Center, Berlin, Germany
| | - Claudia D Baldus
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Christian Bastard
- INSERM U918, Université de Rouen, Centre Henri Becquerel, Rouen, France
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Bernd Dörken
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Damien Roos-Weil
- Université Paris-Sud, Orsay, France
- INSERM, U1170, Institut Gustave Roussy, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Clemens A Schmitt
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Helga D Munch-Petersen
- Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Thorsten Zenz
- Departments of Molecular Therapy in Haematology and Oncology and Translational Oncology, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Martin-Leo Hansmann
- Dr. Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - Jonathan C Strefford
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gunilla Enblad
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Olivier A Bernard
- Université Paris-Sud, Orsay, France
- INSERM, U1170, Institut Gustave Roussy, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Elisabeth Ralfkiaer
- Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Martin Erlanson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Penelope Korkolopoulou
- Department of Pathology, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | | | - Kirsten Grønbæk
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Niki Stavroyianni
- Hematology Department and Hematopoietic Cell Transplantation Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - George Kanellis
- Hematopathology Department, Evangelismos Hospital, Athens, Greece
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Elias Campo
- Department of Pathology, Hospital Clinic and Institut d'Investigacions Biomediques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Rose-Marie Amini
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany; and
| | - Theodoros P Vassilakopoulos
- Department of Haematology, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - Michael Hummel
- Institute of Pathology, Charité, University Medical Center, Berlin, Germany
| | - Richard Rosenquist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Frederik Damm
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
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35
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Quentmeier H, Drexler HG, Hauer V, MacLeod RAF, Pommerenke C, Uphoff CC, Zaborski M, Berglund M, Enblad G, Amini RM. Diffuse Large B Cell Lymphoma Cell Line U-2946: Model for MCL1 Inhibitor Testing. PLoS One 2016; 11:e0167599. [PMID: 27907212 PMCID: PMC5132233 DOI: 10.1371/journal.pone.0167599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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] [Received: 09/02/2016] [Accepted: 11/16/2016] [Indexed: 11/18/2022] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma worldwide. We describe the establishment and molecular characteristics of the DLBCL cell line U-2946. This cell line was derived from a 52-year-old male with DLBCL. U-2946 cells carried the chromosomal translocation t(8;14) and strongly expressed MYC, but not the mature B-cell lymphoma associated oncogenes BCL2 and BCL6. Instead, U-2946 cells expressed the antiapoptotic BCL2 family member MCL1 which was highly amplified genomically (14n). MCL1 amplification is recurrent in DLBCL, especially in the activated B cell (ABC) variant. Results of microarray expression cluster analysis placed U-2946 together with ABC-, but apart from germinal center (GC)-type DLBCL cell lines. The 1q21.3 region including MCL1 was focally coamplified with a short region of 17p11.2 (also present at 14n). The MCL1 inhibitor A-1210477 triggered apoptosis in U-2946 (MCL1pos/BCL2neg) cells. In contrast to BCL2pos DLBCL cell lines, U-2946 did not respond to the BCL2 inhibitor ABT-263. In conclusion, the novel characteristics of cell line U-2946 renders it a unique model system to test the function of small molecule inhibitors, especially when constructing a panel of DLBCL cell lines expressing broad combinations of antiapoptotic BCL2-family members.
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Affiliation(s)
- Hilmar Quentmeier
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vivien Hauer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cord C Uphoff
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Mattias Berglund
- Department of Immunology, Genetics and Pathology, Uppsala University and Uppsala University Hospital, Uppsala, Sweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala University and Uppsala University Hospital, Uppsala, Sweden
| | - Rose-Marie Amini
- Department of Immunology, Genetics and Pathology, Uppsala University and Uppsala University Hospital, Uppsala, Sweden
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36
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Palau A, Mallo M, Palomo L, Rodríguez-Hernández I, Diesch J, Campos D, Granada I, Juncà J, Drexler HG, Solé F, Buschbeck M. Immunophenotypic, cytogenetic, and mutational characterization of cell lines derived from myelodysplastic syndrome patients after progression to acute myeloid leukemia. Genes Chromosomes Cancer 2016; 56:243-252. [PMID: 27750403 DOI: 10.1002/gcc.22430] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 10/13/2016] [Accepted: 10/13/2016] [Indexed: 02/06/2023] Open
Abstract
Leukemia cell lines have been widely used in the hematology field to unravel mechanistic insights and to test new therapeutic strategies. Myelodysplastic syndromes (MDS) comprise a heterogeneous group of diseases that are characterized by ineffective hematopoiesis and frequent progress to acute myeloid leukemia (AML). A few cell lines have been established from MDS patients after progression to AML but their characterization is incomplete. Here we provide a detailed description of the immunophenotypic profile of the MDS-derived cell lines SKK-1, SKM-1, F-36P; and MOLM-13. Specifically, we analyzed a comprehensive panel of markers that are currently applied in the diagnostic routine for myeloid disorders. To provide high-resolution genetic data comprising copy number alterations and losses of heterozygosity we performed whole genome single nucleotide polymorphism-based arrays and included the cell line OHN-GM that harbors the frequent chromosome arm 5q deletion. Furthermore, we assessed the mutational status of 83 disease-relevant genes. Our results provide a resource to the MDS and AML field that allows researchers to choose the best-matching cell line for their functional studies. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Anna Palau
- Josep Carreras Leukaemia Research Institute, Campus ICO - Germans Trias i Pujol, Badalona, Spain
| | - Mar Mallo
- Josep Carreras Leukaemia Research Institute, Campus ICO - Germans Trias i Pujol, Badalona, Spain
| | - Laura Palomo
- Josep Carreras Leukaemia Research Institute, Campus ICO - Germans Trias i Pujol, Badalona, Spain
| | - Ines Rodríguez-Hernández
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Jeannine Diesch
- Josep Carreras Leukaemia Research Institute, Campus ICO - Germans Trias i Pujol, Badalona, Spain
| | - Diana Campos
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Isabel Granada
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Jordi Juncà
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Francesc Solé
- Josep Carreras Leukaemia Research Institute, Campus ICO - Germans Trias i Pujol, Badalona, Spain
| | - Marcus Buschbeck
- Josep Carreras Leukaemia Research Institute, Campus ICO - Germans Trias i Pujol, Badalona, Spain
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37
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Nagel S, Meyer C, Kaufmann M, Drexler HG, MacLeod RAF. Aberrant expression of homeobox gene SIX1 in Hodgkin lymphoma. Oncotarget 2016; 6:40112-26. [PMID: 26473286 PMCID: PMC4741883 DOI: 10.18632/oncotarget.5556] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/29/2015] [Indexed: 12/17/2022] Open
Abstract
In Hodgkin lymphoma (HL) we recently identified deregulated expression of homeobox genes MSX1 and OTX2 which are physiologically involved in development of the embryonal neural plate border region. Here, we examined in HL homeobox gene SIX1 an additional regulator of this embryonal region mediating differentiation of placodal precursors. SIX1 was aberrantly activated in 12 % of HL patient samples in silico, indicating a pathological role in a subset of this B-cell malignancy. In addition, SIX1 expression was detected in HL cell lines which were used as models to reveal upstream factors and target genes of this basic developmental regulator. We detected increased copy numbers of the SIX1 locus at chromosome 14q23 correlating with enhanced expression while chromosomal translocations were absent. Moreover, comparative expression profiling data and pertinent gene modulation experiments indicated that the WNT-signalling pathway and transcription factor MEF2C regulate SIX1 expression. Genes encoding the transcription factors GATA2, GATA3, MSX1 and SPIB – all basic lymphoid regulators - were identified as targets of SIX1 in HL. In addition, cofactors EYA1 and TLE4, respectively, contrastingly mediated activation and suppression of SIX1 target gene expression. Thus, the protein domain interfaces may represent therapeutic targets in SIX1-positive HL subsets. Collectively, our data reveal a gene regulatory network with SIX1 centrally deregulating lymphoid differentiation and support concordance of lymphopoiesis/lymphomagenesis and developmental processes in the neural plate border region.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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38
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Koning MT, Übelhart R, Cleven AH, Zoutman WH, van der Zeeuw SA, Kluin P, Griffioen M, Drexler HG, Tensen CP, Vermeer MH, Willemze R, Kielbasa SM, Navarrete MA, Jumaa H, Veelken H. Abstract LB-012: Autonomous, antigen-independent B-cell receptor signalling as a novel pathogenetic mechanism in non-GCB DLBCL. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The activated B-cell (ABC) type of diffuse large B-cell lymphoma (DLBCL) is clinically more aggressive than the germinal center (GCB) type. The gene expression profile of ABC DLBCL resembles that of mature B cells upon stimulation via their B-cell receptor (BCR). In up to 30% of ABC DLBCL cases, this signature can be explained by gain-of-function mutations in CD79A, CD79B, or CARD11. Antigen-independent, constitutively active (BCR) signaling is a general oncogenic mechanism of CLL (Dühren-von Minden, Nature 2012). We hypothesized that autonomous BCR signaling akin to CLL may operate in ABC DLBCL and could explain the characteristic ABC gene expression signature.
BCR transcripts were identified from fresh-frozen biopsies from 12 histologically confirmed, IgM-expressing DLBCL by ARTISAN PCR, a novel anchored RT-PCR for unbiased amplification of BCR transcripts facilitated by template switching. Clonal full-length BCR sequences were identified by PacBio next-generation sequencing. Triple KO (TKO) cells were transduced with functional DLBCL BCR. TKO cells are arrested at the pre-B-cell stage due to lack of the rag2 and lambda5 genes. In addition, TKO cells have their wild-type SLP65 adaptor replaced with a tamoxifen-dependent SLP65. When transduced with expression constructs encoding a functional BCR, autonomous or antigen-induced BCR signalling can be measured as calcium flux upon induction with tamoxifen.
TKO cells transduced with seven of the twelve DLBCL BCR (58%) showed robust calcium flux and proliferation upon activation of SLP65 by tamoxifen without additional BCR crosslinking. By histomorphology and immunohistochemistry for CD10, PAX5, MUM1, and Bcl-6, these cases were classified as non-GCB-type DLBCL, including one primary CNS DLBCL and two primary mediastinal (PM-)DLBCL. In accordance with our hypothesis, BCR from three DLBCL classified as GCB lacked an autonomous BCR signal. The remaining two negative cases were non-GCB-type and are currently being analyzed for activating CD79/CARD11 mutations.
To further explore the detection of autonomous BCR signaling in DLBCL, PM-DLBCL and ABC DLBCL cell lines were tested in vitro by comparing calcium flux with and without blockade of Syk signaling by the tyrosine kinase inhibitor R406. All four PM-DLBCL and two of five ABC DLBCL cell lines had higher calcium flux in the absence of R406, indicating autonomous signaling activity without antigenic stimulation or artificial BCR crosslinking.
In summary, we demonstrate autonomous BCR activity in a substantial fraction (72%) of non-GCB DLBCL (including PM-DLBCL). These results point to an oncogenic role of structurally normal BCR in non-GCB DLBCL akin to CLL. Autonomous BCR signaling is a candidate alternative mechanism to the previously described activating mutations of components of the BCR signaling cascade to induce the characteristic gene expression signature of ABC DLBCL. Formal delineation of autonomous BCR signalling to activating mutations in the BCR signalling cascade is ongoing.
Citation Format: Marvyn T. Koning, Rudolf Übelhart, Arjen H.G. Cleven, Willem H. Zoutman, Sander A.J. van der Zeeuw, Philip Kluin, Marieke Griffioen, Hans G. Drexler, Cornelis P. Tensen, Maarten H. Vermeer, Rein Willemze, Szymon M. Kielbasa, Marcelo A. Navarrete, Hassan Jumaa, Hendrik Veelken. Autonomous, antigen-independent B-cell receptor signalling as a novel pathogenetic mechanism in non-GCB DLBCL. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-012.
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Affiliation(s)
- Marvyn T. Koning
- 1Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Rudolf Übelhart
- 2Department of Immunology, University Medical Center Ulm, Ulm, Germany
| | - Arjen H.G. Cleven
- 3Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Willem H. Zoutman
- 4Department of Dermatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Philip Kluin
- 6Pathology and Laboratory Medicine, University Medical Center Groningen, Leiden, Netherlands
| | - Marieke Griffioen
- 1Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Cornelis P. Tensen
- 4Department of Dermatology, Leiden University Medical Center, Leiden, Netherlands
| | - Maarten H. Vermeer
- 4Department of Dermatology, Leiden University Medical Center, Leiden, Netherlands
| | - Rein Willemze
- 4Department of Dermatology, Leiden University Medical Center, Leiden, Netherlands
| | - Szymon M. Kielbasa
- 5Sequence Analysis Support Core, Leiden University Medical Center, Leiden, Netherlands
| | - Marcelo A. Navarrete
- 1Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Hassan Jumaa
- 2Department of Immunology, University Medical Center Ulm, Ulm, Germany
| | - Hendrik Veelken
- 1Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
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39
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Hezaveh K, Kloetgen A, Bernhart SH, Mahapatra KD, Lenze D, Richter J, Haake A, Bergmann AK, Brors B, Burkhardt B, Claviez A, Drexler HG, Eils R, Haas S, Hoffmann S, Karsch D, Klapper W, Kleinheinz K, Korbel J, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Leich E, Loeffler M, Mantovani-Loeffler L, López C, McHardy AC, Möller P, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schlesner M, Scholz I, Stadler PF, Stilgenbauer S, Sungalee S, Szczepanowski M, Trümper L, Weniger MA, Siebert R, Borkhardt A, Hummel M, Hoell JI. Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. Haematologica 2016; 101:1380-1389. [PMID: 27390358 DOI: 10.3324/haematol.2016.143891] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/01/2016] [Indexed: 12/22/2022] Open
Abstract
MicroRNA are well-established players in post-transcriptional gene regulation. However, information on the effects of microRNA deregulation mainly relies on bioinformatic prediction of potential targets, whereas proof of the direct physical microRNA/target messenger RNA interaction is mostly lacking. Within the International Cancer Genome Consortium Project "Determining Molecular Mechanisms in Malignant Lymphoma by Sequencing", we performed miRnome sequencing from 16 Burkitt lymphomas, 19 diffuse large B-cell lymphomas, and 21 follicular lymphomas. Twenty-two miRNA separated Burkitt lymphomas from diffuse large B-cell lymphomas/follicular lymphomas, of which 13 have shown regulation by MYC. Moreover, we found expression of three hitherto unreported microRNA. Additionally, we detected recurrent mutations of hsa-miR-142 in diffuse large B-cell lymphomas and follicular lymphomas, and editing of the hsa-miR-376 cluster, providing evidence for microRNA editing in lymphomagenesis. To interrogate the direct physical interactions of microRNA with messenger RNA, we performed Argonaute-2 photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation experiments. MicroRNA directly targeted 208 messsenger RNA in the Burkitt lymphomas and 328 messenger RNA in the non-Burkitt lymphoma models. This integrative analysis discovered several regulatory pathways of relevance in lymphomagenesis including Ras, PI3K-Akt and MAPK signaling pathways, also recurrently deregulated in lymphomas by mutations. Our dataset reveals that messenger RNA deregulation through microRNA is a highly relevant mechanism in lymphomagenesis.
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Affiliation(s)
- Kebria Hezaveh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Andreas Kloetgen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany.,Department of Algorithmic Bioinformatics, Heinrich-Heine University, Duesseldorf, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
| | - Kunal Das Mahapatra
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Dido Lenze
- Institute of Pathology, Charité - University Medicine Berlin, Germany
| | - Julia Richter
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Andrea Haake
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Anke K Bergmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Benedikt Brors
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Birgit Burkhardt
- Department of Pediatric Hematology and Oncology, University Hospital Münster, Germany
| | - Alexander Claviez
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Cultures, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology and Bioquant, Heidelberg University, Germany
| | - Siegfried Haas
- Friedrich-Ebert Hospital Neumünster, Clinics for Hematology, Oncology and Nephrology, Neumünster, Germany
| | - Steve Hoffmann
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany
| | - Dennis Karsch
- Department of Internal Medicine II: Hematology and Oncology, University Medical Centre, Campus Kiel, Germany
| | - Wolfram Klapper
- Hematopathology Section, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- EMBL Heidelberg, Genome Biology, Heidelberg, Germany
| | - Helene Kretzmer
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Chris Lawerenz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ellen Leich
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Markus Loeffler
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | | | - Cristina López
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Alice C McHardy
- Department of Algorithmic Bioinformatics, Heinrich-Heine University, Duesseldorf, Germany.,Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Peter Möller
- Institute of Pathology, Medical Faculty of the Ulm University, Germany
| | - Marius Rohde
- Department of Pediatric Hematology and Oncology University Hospital Giessen, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Markus Schilhabel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ingrid Scholz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter F Stadler
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany.,RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany.,Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany.,Santa Fe Institute, NM, USA
| | | | | | - Monika Szczepanowski
- Hematopathology Section, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, Germany
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - University Medicine Berlin, Germany
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Ehrentraut S, Schneider B, Nagel S, Pommerenke C, Quentmeier H, Geffers R, Feist M, Kaufmann M, Meyer C, Kadin ME, Drexler HG, MacLeod RAF. Th17 cytokine differentiation and loss of plasticity after SOCS1 inactivation in a cutaneous T-cell lymphoma. Oncotarget 2016; 7:34201-16. [PMID: 27144517 PMCID: PMC5085149 DOI: 10.18632/oncotarget.9077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/10/2016] [Indexed: 12/02/2022] Open
Abstract
We propose that deregulated T-helper-cell (Th) signaling underlies evolving Th17 cytokine expression seen during progression of cutaneous T-cell lymphoma (CTCL). Accordingly, we developed a lymphoma progression model comprising cell lines established at indolent (MAC-1) and aggressive (MAC-2A) CTCL stages. We discovered activating JAK3 (V722I) mutations present at indolent disease, reinforced in aggressive disease by novel compound heterozygous SOCS1 (G78R/D105N) JAK-binding domain inactivating mutations. Though isogenic, indolent and aggressive-stage cell lines had diverged phenotypically, the latter expressing multiple Th17 related cytokines, the former a narrower profile. Importantly, indolent stage cells remained poised for Th17 cytokine expression, readily inducible by treatment with IL-2 - a cytokine which mitigates Th17 differentiation in mice. In indolent stage cells JAK3 expression was boosted by IL-2 treatment. Th17 conversion of MAC-1 cells by IL-2 was blocked by pharmacological inhibition of JAK3 or STAT5, implicating IL2RG - JAK3 - STAT5 signaling in plasticity responses. Like IL-2 treatment, SOCS1 knockdown drove indolent stage cells to mimic key aggressive stage properties, notably IL17F upregulation. Co-immunoprecipitation experiments showed that SOCS1 mutations abolished JAK3 binding, revealing a key role for SOCS1 in regulating JAK3/STAT5 signaling. Collectively, our results show how JAK/STAT pathway mutations contribute to disease progression in CTCL cells by potentiating inflammatory cytokine signaling, widening the potential therapeutic target range for this intractable entity. MAC-1/2A cells also provide a candidate human Th17 laboratory model for identifying potentally actionable CTCL markers or targets and testing their druggability in vitro.
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Affiliation(s)
- Stefan Ehrentraut
- Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany
| | - Björn Schneider
- University of Rostock, Institute of Pathology and Molecular Pathology, Rostock, Germany
| | - Stefan Nagel
- Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany
| | - Hilmar Quentmeier
- Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany
| | - Robert Geffers
- HZI - Helmholtz Center for Infection Research, Genome Analytics Research Group, Braunschweig, Germany
| | - Maren Feist
- University Medical Center Goettingen, Department of Haematology and Medical Oncology, Goettingen, Germany
| | - Maren Kaufmann
- Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany
| | - Marshall E Kadin
- Department of Dermatology and Skin Surgery, Roger Williams Medical Center, Boston University School of Medicine, Providence, RI, USA
| | - Hans G Drexler
- Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany
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Abstract
Mature B-cell lymphomas with concurrent rearrangements of MYC and BCL2 (more rarely BCL6), "double-hit lymphomas" (DHLs), form a heterogeneous group. Recent studies have shown that DHLs often present with an aggressive clinical course and a poor prognosis with standard therapy. This distinct clinical entity would benefit from more detailed pathobiological characterization to develop improved treatment options. Lymphoma cell lines are important and informative research tools. Several cell lines have been established from B-cell lymphoma patients harboring MYC rearrangements combined with either (double-hit) or both (triple-hit) BCL2 or BCL6 translocations. All rearrangements have been detected by cytogenetics and validated by FISH. These cell lines provide preclinical models for basic and translational research which speed development of effective treatment strategies.
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Affiliation(s)
- Hans G Drexler
- a Department Human and Animal Cell Lines , Leibniz-Institute DSMZ-German Collection of Microorganisms & Cell Cultures , Braunschweig , Germany
| | - Sonja Eberth
- a Department Human and Animal Cell Lines , Leibniz-Institute DSMZ-German Collection of Microorganisms & Cell Cultures , Braunschweig , Germany
| | - Stefan Nagel
- a Department Human and Animal Cell Lines , Leibniz-Institute DSMZ-German Collection of Microorganisms & Cell Cultures , Braunschweig , Germany
| | - Roderick A F MacLeod
- a Department Human and Animal Cell Lines , Leibniz-Institute DSMZ-German Collection of Microorganisms & Cell Cultures , Braunschweig , Germany
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Dai H, Ehrentraut S, Nagel S, Eberth S, Pommerenke C, Dirks WG, Geffers R, Kalavalapalli S, Kaufmann M, Meyer C, Faehnrich S, Chen S, Drexler HG, MacLeod RAF. Genomic Landscape of Primary Mediastinal B-Cell Lymphoma Cell Lines. PLoS One 2015; 10:e0139663. [PMID: 26599546 PMCID: PMC4657880 DOI: 10.1371/journal.pone.0139663] [Citation(s) in RCA: 16] [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] [Received: 08/04/2015] [Accepted: 09/15/2015] [Indexed: 12/02/2022] Open
Abstract
Primary mediastinal B-Cell lymphoma (PMBL) is a recently defined entity comprising ~2–10% non-Hodgkin lymphomas (NHL). Unlike most NHL subtypes, PMBL lacks recurrent gene rearrangements to serve as biomarkers or betray target genes. While druggable, late chemotherapeutic complications warrant the search for new targets and models. Well characterized tumor cell lines provide unlimited material to serve as preclinical resources for verifiable analyses directed at the discovery of new biomarkers and pathological targets using high throughput microarray technologies. The same cells may then be used to seek intelligent therapies directed at clinically validated targets. Four cell lines have emerged as potential PMBL models: FARAGE, KARPAS-1106P, MEDB-1 and U-2940. Transcriptionally, PMBL cell lines cluster near c(lassical)-HL and B-NHL examples showing they are related but separate entities. Here we document genomic alterations therein, by cytogenetics and high density oligonucleotide/SNP microarrays and parse their impact by integrated global expression profiling. PMBL cell lines were distinguished by moderate chromosome rearrangement levels undercutting cHL, while lacking oncogene translocations seen in B-NHL. In total 61 deletions were shared by two or more cell lines, together with 12 amplifications (≥4x) and 72 homozygous regions. Integrated genomic and transcriptional profiling showed deletions to be the most important class of chromosome rearrangement. Lesions were mapped to several loci associated with PMBL, e.g. 2p15 (REL/COMMD1), 9p24 (JAK2, CD274), 16p13 (SOCS1, LITAF, CIITA); plus new or tenuously associated loci: 2p16 (MSH6), 6q23 (TNFAIP3), 9p22 (CDKN2A/B), 20p12 (PTPN1). Discrete homozygous regions sometimes substituted focal deletions accompanied by gene silencing implying a role for epigenetic or mutational inactivation. Genomic amplifications increasing gene expression or gene-activating rearrangements were respectively rare or absent. Our findings highlight biallelic deletions as a major class of chromosomal lesion in PMBL cell lines, while endorsing the latter as preclinical models for hunting and testing new biomarkers and actionable targets.
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Affiliation(s)
- Haiping Dai
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Stefan Ehrentraut
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Nagel
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sonja Eberth
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wilhelm G. Dirks
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Robert Geffers
- Department of Genome Analysis, HZI, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Maren Kaufmann
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corrina Meyer
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silke Faehnrich
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Suning Chen
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Hans G. Drexler
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A. F. MacLeod
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
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Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Humme M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenzek D, Loeffler M, López C, MacLeod RA, Martens JH, Kulis M, Martín-Subero JI, Möller P, Nage I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat Genet 2015; 47:1316-1325. [PMID: 26437030 PMCID: PMC5444523 DOI: 10.1038/ng.3413] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/08/2015] [Indexed: 12/14/2022]
Abstract
Although Burkitt lymphomas and follicular lymphomas both have features of germinal center B cells, they are biologically and clinically quite distinct. Here we performed whole-genome bisulfite, genome and transcriptome sequencing in 13 IG-MYC translocation-positive Burkitt lymphoma, nine BCL2 translocation-positive follicular lymphoma and four normal germinal center B cell samples. Comparison of Burkitt and follicular lymphoma samples showed differential methylation of intragenic regions that strongly correlated with expression of associated genes, for example, genes active in germinal center dark-zone and light-zone B cells. Integrative pathway analyses of regions differentially methylated in Burkitt and follicular lymphomas implicated DNA methylation as cooperating with somatic mutation of sphingosine phosphate signaling, as well as the TCF3-ID3 and SWI/SNF complexes, in a large fraction of Burkitt lymphomas. Taken together, our results demonstrate a tight connection between somatic mutation, DNA methylation and transcriptional control in key B cell pathways deregulated differentially in Burkitt lymphoma and other germinal center B cell lymphomas.
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Affiliation(s)
- Helene Kretzmer
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Stephan H. Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Wei Wang
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Andrea Haake
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Marc A. Weniger
- German ICGC MMML-Seq-project
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Anke K. Bergmann
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- BLUEPRINT project
| | - Matthew J. Betts
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Enrique Carrillo-de-Santa-Pau
- BLUEPRINT project
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Gero Doose
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Jana Gutwein
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Julia Richter
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Volker Hovestadt
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Bingding Huang
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Daniel Rico
- BLUEPRINT project
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Frank Jühling
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Qianhao Lu
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Christian Otto
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Rabea Wagener
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Judith Arnolds
- Department of Otorhinolaryngology, University of Duisburg-Essen, Essen, Germany
| | - Birgit Burkhardt
- German ICGC MMML-Seq-project
- University Hospital Muenster - Pediatric Hematology and Oncology, Münster Germany
| | - Alexander Claviez
- German ICGC MMML-Seq-project
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Hans G. Drexler
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sonja Eberth
- German ICGC MMML-Seq-project
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Department of Hematology and Oncology, Georg-Augusts-University of Göttingen, Göttingen, Germany
| | - Roland Eils
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Paul Flicek
- BLUEPRINT project
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Siegfried Haas
- German ICGC MMML-Seq-project
- Friedrich-Ebert Hospital Neumuenster, Clinics for Haematology, Oncology and Nephrology, Neumünster, Germany
| | - Michael Humme
- German ICGC MMML-Seq-project
- Institute of Pathology, Charité – University Medicine Berlin, Berlin, Germany
| | - Dennis Karsch
- German ICGC MMML-Seq-project
- Department of Internal Medicine II: Hematology and Oncology, University Medical Centre, Campus Kiel, Kiel, Germany
| | - Hinrik H.D. Kerstens
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Wolfram Klapper
- German ICGC MMML-Seq-project
- Hematopathology Section, Christian-Albrechts-University, Kiel, Germany
| | - Markus Kreuz
- German ICGC MMML-Seq-project
- BLUEPRINT project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Chris Lawerenz
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Dido Lenzek
- German ICGC MMML-Seq-project
- Institute of Pathology, Charité – University Medicine Berlin, Berlin, Germany
| | - Markus Loeffler
- German ICGC MMML-Seq-project
- BLUEPRINT project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Cristina López
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Roderick A.F. MacLeod
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Joost H.A. Martens
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Marta Kulis
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - José Ignacio Martín-Subero
- BLUEPRINT project
- Departamento de Anatomía Patológica, Farmacología y Microbiología, Universitat de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Peter Möller
- German ICGC MMML-Seq-project
- Institute of Pathology, Medical Faculty of the Ulm University, Ulm, Germany
| | - Inga Nage
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Simone Picelli
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Inga Vater
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Marius Rohde
- German ICGC MMML-Seq-project
- University Hospital Giessen, Pediatric Hematology and Oncology, Giessen, Germany
| | - Philip Rosenstiel
- German ICGC MMML-Seq-project
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Maciej Rosolowski
- German ICGC MMML-Seq-project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Robert B. Russell
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Markus Schilhabel
- German ICGC MMML-Seq-project
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Matthias Schlesner
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Peter F. Stadler
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
- RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany
| | | | - Lorenz Trümper
- German ICGC MMML-Seq-project
- Department of Hematology and Oncology, Georg-Augusts-University of Göttingen, Göttingen, Germany
| | - Hendrik G. Stunnenberg
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Ralf Küppers
- German ICGC MMML-Seq-project
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
- BLUEPRINT project
| | - Ole Ammerpohl
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Peter Lichter
- German ICGC MMML-Seq-project
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Reiner Siebert
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
- BLUEPRINT project
| | - Steve Hoffmann
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
- BLUEPRINT project
| | - Bernhard Radlwimmer
- German ICGC MMML-Seq-project
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
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Ehrentraut S, Schneider B, Nagel S, Eberth S, Kaufmann M, Meyer C, Kadin ME, Drexler HG, MacLeod RA. ID: 142. Cytokine 2015. [DOI: 10.1016/j.cyto.2015.08.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Wagener R, Aukema SM, Schlesner M, Haake A, Burkhardt B, Claviez A, Drexler HG, Hummel M, Kreuz M, Loeffler M, Rosolowski M, López C, Möller P, Richter J, Rohde M, Betts MJ, Russell RB, Bernhart SH, Hoffmann S, Rosenstiel P, Schilhabel M, Szczepanowski M, Trümper L, Klapper W, Siebert R. ThePCBP1gene encoding poly(rc) binding protein i is recurrently mutated in Burkitt lymphoma. Genes Chromosomes Cancer 2015; 54:555-64. [DOI: 10.1002/gcc.22268] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 05/11/2015] [Indexed: 12/19/2022] Open
Affiliation(s)
- Rabea Wagener
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Sietse M. Aukema
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Matthias Schlesner
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics; Heidelberg Germany
| | - Andrea Haake
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Birgit Burkhardt
- Non-Hodgkin Lymphoma Berlin-Frankfurt-Münster Group Study Center, Department of Pediatric Hematology and Oncology, University Children's Hospital; Münster Germany
| | - Alexander Claviez
- Department of Pediatrics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University; Kiel Germany
| | - Hans G. Drexler
- Leibniz-Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH; Braunschweig Germany
| | - Michael Hummel
- Institute of Pathology, Campus Benjamin Franklin, Charité-Universitätsmedizin; Berlin Germany
| | - Markus Kreuz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Maciej Rosolowski
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Cristina López
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Peter Möller
- Institute of Pathology, Universitätsklinikum Ulm; Ulm Germany
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Marius Rohde
- Department of Pediatric Hematology and Oncology; Justus Liebig University; Giessen Germany
| | - Matthew J. Betts
- Cell Networks, Bioquant, University of Heidelberg; Heidelberg Germany
| | - Robert B. Russell
- Cell Networks, Bioquant, University of Heidelberg; Heidelberg Germany
| | - Stephan H. Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig; Leipzig Germany
| | - Steve Hoffmann
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig; Leipzig Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Markus Schilhabel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Monika Szczepanowski
- Institute of Hematopathology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology; Georg-August University of Göttingen; Germany
| | - Wolfram Klapper
- Institute of Hematopathology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
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Nagel S, Ehrentraut S, Meyer C, Kaufmann M, Drexler HG, MacLeod RA. NFkB is activated by multiple mechanisms in hairy cell leukemia. Genes Chromosomes Cancer 2015; 54:418-32. [DOI: 10.1002/gcc.22253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/04/2015] [Indexed: 12/12/2022] Open
Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines; Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Stefan Ehrentraut
- Department of Human and Animal Cell Lines; Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines; Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines; Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines; Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Roderick A.F. MacLeod
- Department of Human and Animal Cell Lines; Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
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47
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Ding J, Dirks WG, Ehrentraut S, Geffers R, MacLeod RAF, Nagel S, Pommerenke C, Romani J, Scherr M, Vaas LAI, Zaborski M, Drexler HG, Quentmeier H. BCL6--regulated by AhR/ARNT and wild-type MEF2B--drives expression of germinal center markers MYBL1 and LMO2. Haematologica 2015; 100:801-9. [PMID: 25769544 DOI: 10.3324/haematol.2014.120048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/04/2015] [Indexed: 12/28/2022] Open
Abstract
Genetic heterogeneity is widespread in tumors, but poorly documented in cell lines. According to immunoglobulin hypermutation analysis, the diffuse large B-cell lymphoma cell line U-2932 comprises two subpopulations faithfully representing original tumor subclones. We set out to identify molecular causes underlying subclone-specific expression affecting 221 genes including surface markers and the germinal center oncogenes BCL6 and MYC. Genomic copy number variations explained 58/221 genes differentially expressed in the two U-2932 clones. Subclone-specific expression of the aryl-hydrocarbon receptor (AhR) and the resulting activity of the AhR/ARNT complex underlaid differential regulation of 11 genes including MEF2B. Knock-down and inhibitor experiments confirmed that AhR/ARNT regulates MEF2B, a key transcription factor for BCL6. AhR, MEF2B and BCL6 levels correlated not only in the U-2932 subclones but in the majority of 23 cell lines tested, indicting overexpression of AhR as a novel mechanism behind BCL6 diffuse large B-cell lymphoma. Enforced modulation of BCL6 affected 48/221 signature genes. Although BCL6 is known as a transcriptional repressor, 28 genes were up-regulated, including LMO2 and MYBL1 which, like BCL6, signify germinal center diffuse large B-cell lymphoma. Supporting the notion that BCL6 can induce gene expression, BCL6 and the majority of potential targets were co-regulated in a series of B-cell lines. In conclusion, genomic copy number aberrations, activation of AhR/ARNT, and overexpression of BCL6 are collectively responsible for differential expression of more than 100 genes in subclones of the U-2932 cell line. It is particularly interesting that BCL6 - regulated by AhR/ARNT and wild-type MEF2B - may drive expression of germinal center markers in diffuse large B-cell lymphoma.
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Affiliation(s)
- Jie Ding
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Wilhelm G Dirks
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Stefan Ehrentraut
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Robert Geffers
- Helmholtz Centre for Infection Research, Genome Analysis Research Group, Braunschweig
| | - Roderick A F MacLeod
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Stefan Nagel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Claudia Pommerenke
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Julia Romani
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Michaela Scherr
- Medical School Hannover, Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Germany
| | - Lea A I Vaas
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Margarete Zaborski
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
| | - Hilmar Quentmeier
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig
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48
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Wu L, Xu Y, Wang Q, Ruan C, Drexler HG, Wu D, MacLeod RAF, Chen S. High frequency of cryptic chromosomal rearrangements involving the LMO2 gene in T-cell acute lymphoblastic leukemia. Haematologica 2015; 100:e233-6. [PMID: 25682596 DOI: 10.3324/haematol.2014.120089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Lili Wu
- Jiangsu Institute of Hematology (JIH), Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Yang Xu
- Jiangsu Institute of Hematology (JIH), Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Qian Wang
- Jiangsu Institute of Hematology (JIH), Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Changgeng Ruan
- Jiangsu Institute of Hematology (JIH), Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Hans G Drexler
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Depei Wu
- Jiangsu Institute of Hematology (JIH), Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Roderick A F MacLeod
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Suning Chen
- Jiangsu Institute of Hematology (JIH), Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
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49
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Wagener R, Alexandrov LB, Montesinos-Rongen M, Schlesner M, Haake A, Drexler HG, Richter J, Bignell GR, McDermott U, Siebert R. Analysis of mutational signatures in exomes from B-cell lymphoma cell lines suggest APOBEC3 family members to be involved in the pathogenesis of primary effusion lymphoma. Leukemia 2015; 29:1612-5. [DOI: 10.1038/leu.2015.22] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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50
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Jones AV, Ward D, Lyon M, Leung W, Callaway A, Chase A, Dent CL, White HE, Drexler HG, Nangalia J, Mattocks C, Cross NCP. Evaluation of methods to detect CALR mutations in myeloproliferative neoplasms. Leuk Res 2014; 39:82-7. [PMID: 25499808 DOI: 10.1016/j.leukres.2014.11.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/19/2014] [Accepted: 11/22/2014] [Indexed: 12/30/2022]
Abstract
The recent discovery of somatically acquired CALR mutations in a substantial proportion of patients with myeloproliferative neoplasms has provided a new marker of clonal disease, advancing both diagnosis and prognosis in these previously difficult to characterise disorders. The mutations, which can be challenging to detect on a routine basis, are heterogeneous insertions/deletions (indels) in exon 9 with mutant allele burden that vary substantially between patients. We evaluated four genetic screening methods for their ability to detect a series of different CALR mutations; Sanger sequencing, fragment analysis PCR, high resolution melt (HRM) and targeted next generation sequencing (NGS). The limit of detection (LoD) of each assay was tested using serial dilution series made with DNA from CALR positive sample DNA and a cell line, MARIMO, found to carry a heterozygous 61 nucleotide CALR deletion. All methods were capable of detecting each mutation; HRM and fragment analysis PCR were better at detecting low mutation levels compared to Sanger sequencing but targeted NGS had the lowest LoD at a 1% mutation burden.
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Affiliation(s)
- Amy V Jones
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Daniel Ward
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Matthew Lyon
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - William Leung
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Andrew Chase
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Carolyn L Dent
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Helen E White
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Hans G Drexler
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Jyoti Nangalia
- Cambridge Institute for Medical Research and Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Chris Mattocks
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Nicholas C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK.
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