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Coupland SE, Du MQ, Ferry JA, de Jong D, Khoury JD, Leoncini L, Naresh KN, Ott G, Siebert R, Xerri L. The fifth edition of the WHO classification of mature B-cell neoplasms: open questions for research. J Pathol 2024; 262:255-270. [PMID: 38180354 DOI: 10.1002/path.6246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
The fifth edition of the World Health Organization Classification of Haematolymphoid Tumours (WHO-HAEM5) is the product of an evidence-based evolution of the revised fourth edition with wide multidisciplinary consultation. Nonetheless, while every classification incorporates scientific advances and aims to improve upon the prior version, medical knowledge remains incomplete and individual neoplasms may not be easily subclassified in a given scheme. Thus, optimal classification requires ongoing study, and there are certain aspects of some entities and subtypes that require further refinements. In this review, we highlight a selection of these challenging areas to prompt more research investigations. These include (1) a 'placeholder term' of splenic B-cell lymphoma/leukaemia with prominent nucleoli (SBLPN) to accommodate many of the splenic lymphomas previously classified as hairy cell leukaemia variant and B-prolymphocytic leukaemia, a clear new start to define their pathobiology; (2) how best to classify BCL2 rearrangement negative follicular lymphoma including those with BCL6 rearrangement, integrating the emerging new knowledge on various germinal centre B-cell subsets; (3) what is the spectrum of non-IG gene partners of MYC translocation in diffuse large B-cell lymphoma/high-grade B-cell lymphoma and how they impact MYC expression and clinical outcome; how best to investigate this in a routine clinical setting; and (4) how best to define high-grade B-cell lymphoma not otherwise specified and high-grade B-cell lymphoma with 11q aberrations to distinguish them from their mimics and characterise their molecular pathogenetic mechanism. Addressing these questions would provide more robust evidence to better define these entities/subtypes, improve their diagnosis and/or prognostic stratification, leading to better patient care. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sarah E Coupland
- Liverpool Clinical Laboratories, Liverpool University Hospitals Foundation Trust, Liverpool, UK
| | - Ming-Qing Du
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Judith A Ferry
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daphne de Jong
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joseph D Khoury
- Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lorenzo Leoncini
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Kikkeri N Naresh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Luc Xerri
- Institut Paoli-Calmettes, CRCM and Aix-Marseille University, Marseille, France
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2
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Hilton LK, Scott DW, Morin RD. Biological heterogeneity in diffuse large B-cell lymphoma. Semin Hematol 2023; 60:267-276. [PMID: 38151380 DOI: 10.1053/j.seminhematol.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/19/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is heterogeneous both in clinical outcomes and the underlying disease biology. Over the last 2 decades, several different approaches for dissecting biological heterogeneity have emerged. Gene expression profiling (GEP) stratifies DLBCL into 3 broad groups (ABC, GCB, and DZsig/MHG), each with parallels to different normal mature B cell developmental states and prognostic implications. More recently, several different genomic approaches have been developed to categorize DLBCL based on the co-occurrence of tumor somatic mutations, identifying more granular biologically unified subgroups that complement GEP-based approaches. We review the molecular approaches and clinical evidence supporting the stratification of DLBCL patients based on tumor biology. By offering a platform for subtype-guided therapy, these divisions remain a promising avenue for improving patient outcomes, especially in subgroups with inferior outcomes with current standard-of-care therapy.
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Affiliation(s)
- Laura K Hilton
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.; Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ryan D Morin
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, Canada
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3
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Davies JR, Hilton LK, Jiang A, Barrans S, Burton C, Johnson PWM, Davies AJ, Du MQ, Tooze R, Cucco F, Care MA, Morin RD, Steidl C, Sha C, Westhead DR, Scott DW. Comparison of MHG and DZsig reveals shared biology and a core overlap group with inferior prognosis in DLBCL. Blood Adv 2023; 7:6156-6162. [PMID: 37595057 PMCID: PMC10582343 DOI: 10.1182/bloodadvances.2023010673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 07/30/2023] [Indexed: 08/20/2023] Open
Affiliation(s)
- John R. Davies
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Laura K. Hilton
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Aixiang Jiang
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - Catherine Burton
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - Peter W. M. Johnson
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andrew J. Davies
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ming-Qing Du
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Reuben Tooze
- Section of Experimental Haematology, University of Leeds, Leeds, United Kingdom
| | - Francesco Cucco
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Institute of Clinical Physiology (IFC), Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Matthew A. Care
- Section of Experimental Haematology, University of Leeds, Leeds, United Kingdom
| | - Ryan D. Morin
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Christian Steidl
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chulin Sha
- Institute of Basic Medicine and Cancer, Chinese Academy of Science, Hangzhou, China
| | - David R. Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David W. Scott
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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4
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Setiawan SA, Liu WZ, Weng PW, Lee CH, Yadav VK, Hardianti MS, Yeh CT, Chao TY. Synergistic disruption of BTK and BCL-2 causes apoptosis while inducing ferroptosis in double-hit lymphoma. Eur J Pharmacol 2023; 943:175526. [PMID: 36693553 DOI: 10.1016/j.ejphar.2023.175526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Double-hit lymphoma (DHL) is an aggressive subset of Diffuse Large B-cell Lymphoma (DLBCL) with poor outcomes and without satisfying treatment options. BTK inhibitor monotherapy is ineffective to suppress aggressive lymphoma. Hence, combination with other potential agents is warranted. Here, we demonstrated the second generation of BTK inhibitor, zanubrutinib, and a BCL-2 inhibitor, navitoclax, worked in synergistic manner to suppress DHL. Comprehensive in silico approach by interrogating single-cell to bulk-level profiling was employed along with in vitro and in vivo validation in DHL cell lines. Ablation of BTK enhanced sensitivity to navitoclax and suppressed proliferation of DHL cells. Combination of second generation of BTK inhibitor with navitoclax synergistically suppressed DLBCL cells with higher synergy score in DHL subset. The drug combination triggered apoptosis and ferroptosis, with the latter being characterized by reactive oxygen species (ROS) accumulation, extensive lipid peroxidation, and depletion of reduced glutathione. Moreover, ablation of BTK sensitized DHL cells to ferroptosis. Mechanistically, disruption of BTK and BCL-2 triggered ferroptosis by downregulating NRF2 and HMOX1, while deactivating GPX4. Combination of zanubrutinib and navitoclax effectively suppressed tumor growth in vivo. Our data suggest that zanubrutinib and navitoclax synergistically suppressed DHL by inducing apoptosis and ferroptosis.
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Affiliation(s)
- Syahru Agung Setiawan
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei City, 11031, Taiwan
| | | | - Pei-Wei Weng
- Department of Orthopaedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan; Department of Orthopaedics, Shuang Ho Hospital, Taipei Medical University, New Taipei City, 23561, Taiwan; Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
| | - Chia-Hwa Lee
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Vijesh Kumar Yadav
- Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, 23561, Taiwan
| | - Mardiah Suci Hardianti
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Chi-Tai Yeh
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei City, 11031, Taiwan; Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, 23561, Taiwan; Continuing Education Program of Food Biotechnology Applications, College of Science and Engineering, National Taitung University, Taitung, 95092, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei City, 11031, Taiwan.
| | - Tsu-Yi Chao
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei City, 11031, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei City, 11031, Taiwan; Department of Hematology & Oncology, Taipei Medical University-Shuang Ho Hospital, New Taipei City, 23561, Taiwan; Division of Medical Oncology and Hematology, Tri-Service General Hospital, National Defense Medical Centre, Taipei, 11409, Taiwan.
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5
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Tyryshkin K, Moore A, Good D, Popov J, Crocker S, Rauh MJ, Baetz T, LeBrun DP. Expression of TCF3 target genes defines a subclass of diffuse large B-cell lymphoma characterized by up-regulation of MYC target genes and poor clinical outcome following R-CHOP therapy. Leuk Lymphoma 2023; 64:119-129. [PMID: 36336953 DOI: 10.1080/10428194.2022.2136968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
TCF3 is a lymphopoietic transcription factor that acquires somatic driver mutations in diffuse large B-cell lymphoma (DLBCL). Hypothesizing that expression patterns of TCF3-regulated genes can inform clinical management, we found that unsupervised clustering analysis with 15 TCF3-regulated genes and eight additional ones resolved local DLBCL cases into two main clusters, denoted Groups A and B, of which Group A manifested inferior overall survival (OS, p = 0.0005). We trained a machine learning model to classify samples into the Groups based on expression of the 23 transcripts in an independent validation cohort of 569 R-CHOP-treated DLBCL cases. Group A overlapped with the ABC cell-of-origin subgroup but its prognostic power was superior. GSEA analysis demonstrated asymmetric expression of 30 gene sets between the Groups, pointing to biological differences. We present, validate and make available a novel method to assign DLBCL cases into biologically-distinct groups with divergent OS following R-CHOP therapy.
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Affiliation(s)
- Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada.,School of Computing, Queen's University, Kingston, Ontario, Canada
| | - Alison Moore
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - David Good
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Jesse Popov
- Department of Internal Medicine, Queen's University, Kingston, Ontario, Canada
| | - Susan Crocker
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Tara Baetz
- Department of Medical Oncology, Queen's University, Kingston, Ontario, Canada
| | - David P LeBrun
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
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6
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CAR T-cell Therapy in Highly-Aggressive B-Cell Lymphoma: Emerging Biological and Clinical Insights. Blood 2022; 140:1461-1469. [PMID: 35560330 DOI: 10.1182/blood.2022016226] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Recently, significant progress has been made in identifying novel therapies, beyond conventional immunochemotherapy strategies, with efficacy in B-cell lymphomas. One such approach involves targeting the CD19 antigen on B-cells with autologous-derived chimeric antigen receptor (CAR) cells. This strategy is highly effective in patients with relapsed and refractory diffuse large B-cell lymphoma (DLBCL) as evidenced by recent regulatory approvals. Recent reports suggest that this is an effective strategy for high-grade B-cell. The biological underpinnings of these entities and how they overlap with each other and DLBCL continue to be areas of intense investigation. Therefore, as more experience with CAR T-cell approaches is examined, it is interesting to consider how both tumor-cell specific and microenvironment factors that define these highly aggressive subsets influence susceptibility to this approach.
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7
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Plaça JR, Diepstra A, Los T, Mendeville M, Seitz A, Lugtenburg PJ, Zijlstra J, Lam K, da Silva WA, Ylstra B, de Jong D, van den Berg A, Nijland M. Reproducibility of Gene Expression Signatures in Diffuse Large B-Cell Lymphoma. Cancers (Basel) 2022; 14:cancers14051346. [PMID: 35267654 PMCID: PMC8909016 DOI: 10.3390/cancers14051346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 12/24/2022] Open
Abstract
Multiple gene expression profiles have been identified in diffuse large B-cell lymphoma (DLBCL). Besides the cell of origin (COO) classifier, no signatures have been reproduced in independent studies or evaluated for capturing distinct aspects of DLBCL biology. We reproduced 4 signatures in 175 samples of the HOVON-84 trial on a panel of 117 genes using the NanoString platform. The four gene signatures capture the COO, MYC activity, B-cell receptor signaling, oxidative phosphorylation, and immune response. Performance of our classification algorithms were confirmed in the original datasets. We were able to validate three of the four GEP signatures. The COO algorithm resulted in 94 (54%) germinal center B-cell (GCB) type, 58 (33%) activated B-cell (ABC) type, and 23 (13%) unclassified cases. The MYC-classifier revealed 77 cases with a high MYC-activity score (44%) and this MYC-high signature was observed more frequently in ABC as compared to GCB DLBCL (68% vs. 32%, p < 0.00001). The host response (HR) signature of the consensus clustering was present in 55 (31%) patients, while the B-cell receptor signaling, and oxidative phosphorylation clusters could not be reproduced. The overlap of COO, consensus cluster and MYC activity score differentiated six gene expression clusters: GCB/MYC-high (12%), GCB/HR (16%), GCB/non-HR (27%), COO-Unclassified (13%), ABC/MYC-high (25%), and ABC/MYC-low (7%). In conclusion, the three validated signatures identify distinct subgroups based on different aspects of DLBCL biology, emphasizing that each classifier captures distinct molecular profiles.
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Affiliation(s)
- Jessica Rodrigues Plaça
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands; (J.R.P.); (A.D.); (A.S.); (A.v.d.B.)
- Center for Cell-Based Therapy, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq), Ribeirão Preto 14051-060, Brazil;
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands; (J.R.P.); (A.D.); (A.S.); (A.v.d.B.)
| | - Tjitske Los
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, 1105 Amsterdam, The Netherlands; (T.L.); (M.M.); (B.Y.); (D.d.J.)
| | - Matías Mendeville
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, 1105 Amsterdam, The Netherlands; (T.L.); (M.M.); (B.Y.); (D.d.J.)
| | - Annika Seitz
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands; (J.R.P.); (A.D.); (A.S.); (A.v.d.B.)
| | - Pieternella J. Lugtenburg
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center, 3015 Rotterdam, The Netherlands;
| | - Josée Zijlstra
- Department of Hematology, Amsterdam UMC, 1105 Amsterdam, The Netherlands;
| | - King Lam
- Department of Pathology, Erasmus MC, 3015 Rotterdam, The Netherlands;
| | - Wilson Araújo da Silva
- Center for Cell-Based Therapy, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq), Ribeirão Preto 14051-060, Brazil;
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, 1105 Amsterdam, The Netherlands; (T.L.); (M.M.); (B.Y.); (D.d.J.)
| | - Daphne de Jong
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, 1105 Amsterdam, The Netherlands; (T.L.); (M.M.); (B.Y.); (D.d.J.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands; (J.R.P.); (A.D.); (A.S.); (A.v.d.B.)
| | - Marcel Nijland
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands
- Correspondence: ; Tel.: +31-50-361-2354
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Gong C, Krupka JA, Gao J, Grigoropoulos NF, Giotopoulos G, Asby R, Screen M, Usheva Z, Cucco F, Barrans S, Painter D, Zaini NBM, Haupl B, Bornelöv S, Ruiz De Los Mozos I, Meng W, Zhou P, Blain AE, Forde S, Matthews J, Khim Tan MG, Burke GAA, Sze SK, Beer P, Burton C, Campbell P, Rand V, Turner SD, Ule J, Roman E, Tooze R, Oellerich T, Huntly BJ, Turner M, Du MQ, Samarajiwa SA, Hodson DJ. Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis. Mol Cell 2021; 81:4059-4075.e11. [PMID: 34437837 DOI: 10.1016/j.molcel.2021.07.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/17/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022]
Abstract
DDX3X is a ubiquitously expressed RNA helicase involved in multiple stages of RNA biogenesis. DDX3X is frequently mutated in Burkitt lymphoma, but the functional basis for this is unknown. Here, we show that loss-of-function DDX3X mutations are also enriched in MYC-translocated diffuse large B cell lymphoma and reveal functional cooperation between mutant DDX3X and MYC. DDX3X promotes the translation of mRNA encoding components of the core translational machinery, thereby driving global protein synthesis. Loss-of-function DDX3X mutations moderate MYC-driven global protein synthesis, thereby buffering MYC-induced proteotoxic stress during early lymphomagenesis. Established lymphoma cells restore full protein synthetic capacity by aberrant expression of DDX3Y, a Y chromosome homolog, the expression of which is normally restricted to the testis. These findings show that DDX3X loss of function can buffer MYC-driven proteotoxic stress and highlight the capacity of male B cell lymphomas to then compensate for this loss by ectopic DDX3Y expression.
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Affiliation(s)
- Chun Gong
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | - Joanna A Krupka
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK; MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge CB2 0XZ, UK
| | - Jie Gao
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - George Giotopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | - Ryan Asby
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | - Michael Screen
- Immunology Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Zelvera Usheva
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | - Francesco Cucco
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, St. James's Institute of Oncology, Leeds LS9 7TF, UK
| | - Daniel Painter
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York YO10 5DD, UK
| | | | - Björn Haupl
- Department of Medicine II, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, 60596 Frankfurt, Germany
| | - Susanne Bornelöv
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Igor Ruiz De Los Mozos
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Wei Meng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore
| | - Peixun Zhou
- National Horizons Centre, Teesside University, 38 John Dixon Lane, Darlington DL1 1HG, UK; School of Health & Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
| | - Alex E Blain
- National Horizons Centre, Teesside University, 38 John Dixon Lane, Darlington DL1 1HG, UK; Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK; School of Health & Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
| | - Sorcha Forde
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK
| | - Jamie Matthews
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK
| | - Michelle Guet Khim Tan
- Department of Clinical Translational Research, Singapore General Hospital, Outram Road, Singapore 169856, Singapore
| | - G A Amos Burke
- Department of Paediatric Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore
| | - Philip Beer
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Cathy Burton
- Haematological Malignancy Diagnostic Service, St. James's Institute of Oncology, Leeds LS9 7TF, UK
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Vikki Rand
- National Horizons Centre, Teesside University, 38 John Dixon Lane, Darlington DL1 1HG, UK; School of Health & Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
| | - Suzanne D Turner
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK; CEITEC, Masaryk University, Brno, Czech Republic
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Eve Roman
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Reuben Tooze
- Haematological Malignancy Diagnostic Service, St. James's Institute of Oncology, Leeds LS9 7TF, UK; Section of Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, 60596 Frankfurt, Germany
| | - Brian J Huntly
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | - Martin Turner
- Immunology Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge CB2 0XZ, UK
| | - Daniel J Hodson
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK.
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9
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Pan M, Yang P, Wang F, Luo X, Li B, Ding Y, Lu H, Dong Y, Zhang W, Xiu B, Liang A. Whole Transcriptome Data Analysis Reveals Prognostic Signature Genes for Overall Survival Prediction in Diffuse Large B Cell Lymphoma. Front Genet 2021; 12:648800. [PMID: 34178023 PMCID: PMC8220154 DOI: 10.3389/fgene.2021.648800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Background With the improvement of clinical treatment outcomes in diffuse large B cell lymphoma (DLBCL), the high rate of relapse in DLBCL patients is still an established barrier, as the therapeutic strategy selection based on potential targets remains unsatisfactory. Therefore, there is an urgent need in further exploration of prognostic biomarkers so as to improve the prognosis of DLBCL. Methods The univariable and multivariable Cox regression models were employed to screen out gene signatures for DLBCL overall survival (OS) prediction. The differential expression analysis was used to identify representative genes in high-risk and low-risk groups, respectively, where student t test and fold change were implemented. The functional difference between the high-risk and low-risk groups was identified by the gene set enrichment analysis. Results We conducted a systematic data analysis to screen the candidate genes significantly associated with OS of DLBCL in three NCBI Gene Expression Omnibus (GEO) datasets. To construct a prognostic model, five genes (CEBPA, CYP27A1, LST1, MREG, and TARP) were then screened and tested using the multivariable Cox model and the stepwise regression method. Kaplan–Meier curve confirmed the good predictive performance of this five-gene Cox model. Thereafter, the prognostic model and the expression levels of the five genes were validated by means of an independent dataset. High expression levels of these five genes were significantly associated with favorable prognosis in DLBCL, both in training and validation datasets. Additionally, further analysis revealed the independent value and superiority of this prognostic model in risk prediction. Functional enrichment analysis revealed some vital pathways responsible for unfavorable outcome and potential therapeutic targets in DLBCL. Conclusion We developed a five-gene Cox model for the clinical outcome prediction of DLBCL patients. Meanwhile, potential drug selection using this model can help clinicians to improve the clinical practice for the benefit of patients.
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Affiliation(s)
- Mengmeng Pan
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pingping Yang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fangce Wang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiu Luo
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bing Li
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Ding
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huina Lu
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yan Dong
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenjun Zhang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bing Xiu
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Aibin Liang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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10
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Cucco F, Barrans S, Sha C, Clipson A, Crouch S, Dobson R, Chen Z, Thompson JS, Care MA, Cummin T, Caddy J, Liu H, Robinson A, Schuh A, Fitzgibbon J, Painter D, Smith A, Roman E, Tooze R, Burton C, Davies AJ, Westhead DR, Johnson PWM, Du MQ. Distinct genetic changes reveal evolutionary history and heterogeneous molecular grade of DLBCL with MYC/BCL2 double-hit. Leukemia 2020; 34:1329-1341. [PMID: 31844144 PMCID: PMC7192846 DOI: 10.1038/s41375-019-0691-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 11/22/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022]
Abstract
Using a Burkitt lymphoma-like gene expression signature, we recently defined a high-risk molecular high-grade (MHG) group mainly within germinal centre B-cell like diffuse large B-cell lymphomas (GCB-DLBCL), which was enriched for MYC/BCL2 double-hit (MYC/BCL2-DH). The genetic basis underlying MHG-DLBCL and their aggressive clinical behaviour remain unknown. We investigated 697 cases of DLBCL, particularly those with MYC/BCL2-DH (n = 62) by targeted sequencing and gene expression profiling. We showed that DLBCL with MYC/BCL2-DH, and those with BCL2 translocation, harbour the characteristic mutation signatures that are associated with follicular lymphoma and its high-grade transformation. We identified frequent MYC hotspot mutations that affect the phosphorylation site (T58) and its adjacent amino acids, which are important for MYC protein degradation. These MYC mutations were seen in a subset of cases with MYC translocation, but predominantly in those of MHG. The mutations were more frequent in double-hit lymphomas with IG as the MYC translocation partner, and were associated with higher MYC protein expression and poor patient survival. DLBCL with MYC/BCL2-DH and those with BCL2 translocation alone are most likely derived from follicular lymphoma or its precursor lesion, and acquisition of MYC pathogenic mutations may augment MYC function, resulting in aggressive clinical behaviour.
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Affiliation(s)
- Francesco Cucco
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Chulin Sha
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | - Simon Crouch
- Department of Health Sciences, University of York, York, UK
| | - Rachel Dobson
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zi Chen
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Matthew A Care
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Thomas Cummin
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Josh Caddy
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Hongxiang Liu
- Haematopathology and Oncology Diagnostics Service, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Anne Robinson
- Haematopathology and Oncology Diagnostics Service, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, UK
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, London, UK
| | - Daniel Painter
- Department of Health Sciences, University of York, York, UK
| | | | - Eve Roman
- Department of Health Sciences, University of York, York, UK
| | - Reuben Tooze
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Catherine Burton
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Andrew J Davies
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | - Peter W M Johnson
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Ming-Qing Du
- Department of Pathology, University of Cambridge, Cambridge, UK.
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11
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Yang AP, Liu LG, Chen MM, Liu F, You H, Liu L, Yang H, Xun Y, Liu J, Wang RX, Brand DD, Liu D, Zheng SG, Li WX. Integrated analysis of 10 lymphoma datasets identifies E2F8 as a key regulator in Burkitt's lymphoma and mantle cell lymphoma. Am J Transl Res 2019; 11:4382-4396. [PMID: 31396343 PMCID: PMC6684893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Burkitt's lymphoma (BURK), diffuse large B-cell lymphoma (DLBCL) and mantle cell lymphoma (MCL) are three main types of B-cell lymphomas. This study aimed to compare the differences of affected biological functions and pathways, as well as to explore the possible regulatory mechanisms and the potential therapeutic targets in BURK, DLBCL and MCL. We performed an integrated analysis of 10 lymphoma datasets including 352 BURK patients, 880 DLBCL patients, 216 MCL patients, and 33 controls. Our results showed that signaling pathways, amino acid metabolism and several lipid metabolism pathways varies considerably among these three types of lymphoma. Furthermore, we identified several key transcription factors (TFs) and their target genes that may promote these diseases by influencing multiple carcinogenic pathways. Among these TFs, we reported first that E2F8 displayed the most significant effects in BURK and MCL. Our results demonstrate that over-expression of E2F8 activates target genes that may promote cell cycle, mitosis, immune and other cancer related functions in BURK and MCL. Therefore, we suggest that E2F8 could be used as a biomarker and potential therapeutic target for BURK and MCL. These findings would be helpful in the study of pathogenesis, and drug discovery and also in the prognosis of B cell lymphomas.
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Affiliation(s)
- An-Ping Yang
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - Leyna G Liu
- Portola High School1001 Cadence, Irvine 92618, CA, USA
| | - Min-Min Chen
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - Fang Liu
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - Hua You
- Affiliated Cancer Hospital and Institute of Guangzhou Medical UniversityGuangzhou 510095, Guangdong, China
| | - Lian Liu
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - Hua Yang
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - Yang Xun
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - Jing Liu
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - Rui-Xue Wang
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - David D Brand
- Research Service, Memphis VA Medical CenterMemphis 38104, TN, USA
| | - Dahai Liu
- School of Stomatology and Medicine, Foshan UniversityFoshan 528000, Guangdong, China
| | - Song Guo Zheng
- Department of Internal Medicine, Ohio State University College of Medicine and Wexner Medical CenterColumbus 43210, USA
| | - Wen-Xing Li
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of SciencesKunming 650223, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of SciencesKunming 650204, Yunnan, China
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12
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Sha C, Barrans S, Cucco F, Bentley MA, Care MA, Cummin T, Kennedy H, Thompson JS, Uddin R, Worrillow L, Chalkley R, van Hoppe M, Ahmed S, Maishman T, Caddy J, Schuh A, Mamot C, Burton C, Tooze R, Davies A, Du MQ, Johnson PW, Westhead DR. Molecular High-Grade B-Cell Lymphoma: Defining a Poor-Risk Group That Requires Different Approaches to Therapy. J Clin Oncol 2019; 37:202-212. [PMID: 30523719 PMCID: PMC6338391 DOI: 10.1200/jco.18.01314] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Biologic heterogeneity is a feature of diffuse large B-cell lymphoma (DLBCL), and the existence of a subgroup with poor prognosis and phenotypic proximity to Burkitt lymphoma is well known. Conventional cytogenetics identifies some patients with rearrangements of MYC and BCL2 and/or BCL6 (double-hit lymphomas) who are increasingly treated with more intensive chemotherapy, but a more biologically coherent and clinically useful definition of this group is required. PATIENTS AND METHODS We defined a molecular high-grade (MHG) group by applying a gene expression-based classifier to 928 patients with DLBCL from a clinical trial that investigated the addition of bortezomib to standard rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) therapy. The prognostic significance of MHG was compared with existing biomarkers. We performed targeted sequencing of 70 genes in 400 patients and explored molecular pathology using gene expression signature databases. Findings were validated in an independent data set. RESULTS The MHG group comprised 83 patients (9%), with 75 in the cell-of-origin germinal center B-cell-like group. MYC rearranged and double-hit groups were strongly over-represented in MHG but comprised only one half of the total. Gene expression analysis revealed a proliferative phenotype with a relationship to centroblasts. Progression-free survival rate at 36 months after R-CHOP in the MHG group was 37% (95% CI, 24% to 55%) compared with 72% (95% CI, 68% to 77%) for others, and an analysis of treatment effects suggested a possible positive effect of bortezomib. Double-hit lymphomas lacking the MHG signature showed no evidence of worse outcome than other germinal center B-cell-like cases. CONCLUSION MHG defines a biologically coherent high-grade B-cell lymphoma group with distinct molecular features and clinical outcomes that effectively doubles the size of the poor-prognosis, double-hit group. Patients with MHG may benefit from intensified chemotherapy or novel targeted therapies.
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MESH Headings
- Antibodies, Monoclonal, Murine-Derived/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Bortezomib/administration & dosage
- Cyclophosphamide/administration & dosage
- Databases, Genetic
- Doxorubicin/administration & dosage
- Female
- Humans
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Neoplasm Grading
- Prednisone/administration & dosage
- Proportional Hazards Models
- Randomized Controlled Trials as Topic
- Retrospective Studies
- Rituximab/administration & dosage
- Transcriptome
- Vincristine/administration & dosage
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Affiliation(s)
- Chulin Sha
- University of Leeds, Leeds, United Kingdom
| | | | | | | | | | - Thomas Cummin
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | | | | | | | | | | | | | | | - Tom Maishman
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Josh Caddy
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Anna Schuh
- University of Oxford, Oxford, United Kingdom
| | - Christoph Mamot
- Cantonal Hospital Aarau, Aarau/Swiss Group for Clinical Cancer Research, Switzerland
| | | | | | - Andrew Davies
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Ming-Qing Du
- University of Cambridge, Cambridge, United Kingdom
| | - Peter W.M. Johnson
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
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13
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Chan WC. Using Gene Expression Profiling to Move Beyond MYC/BCL2 Rearrangements in High-Grade Lymphoma. J Clin Oncol 2018; 37:175-177. [PMID: 30523718 DOI: 10.1200/jco.18.01910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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14
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Painter D, Barrans S, Lacy S, Smith A, Crouch S, Westhead D, Sha C, Patmore R, Tooze R, Burton C, Roman E. Cell-of-origin in diffuse large B-cell lymphoma: findings from the UK's population-based Haematological Malignancy Research Network. Br J Haematol 2018; 185:781-784. [PMID: 30408148 DOI: 10.1111/bjh.15619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Daniel Painter
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Stuart Lacy
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Alexandra Smith
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Simon Crouch
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - David Westhead
- Bioinfomatics Group, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Chulin Sha
- Bioinfomatics Group, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Russell Patmore
- Queen's Centre for Oncology and Haematology, Hull and East Yorkshire Hospitals, Cottingham, UK
| | - Reuben Tooze
- Section of Experimental Haematology, University of Leeds, Leeds, UK
| | - Cathy Burton
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Eve Roman
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
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15
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Altenbuchinger M, Schwarzfischer P, Rehberg T, Reinders J, Kohler CW, Gronwald W, Richter J, Szczepanowski M, Masqué-Soler N, Klapper W, Oefner PJ, Spang R. Molecular signatures that can be transferred across different omics platforms. Bioinformatics 2018; 33:i333-i340. [PMID: 28881975 PMCID: PMC5870545 DOI: 10.1093/bioinformatics/btx241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Motivation Molecular signatures for treatment recommendations are well researched. Still it is challenging to apply them to data generated by different protocols or technical platforms. Results We analyzed paired data for the same tumors (Burkitt lymphoma, diffuse large B-cell lymphoma) and features that had been generated by different experimental protocols and analytical platforms including the nanoString nCounter and Affymetrix Gene Chip transcriptomics as well as the SWATH and SRM proteomics platforms. A statistical model that assumes independent sample and feature effects accounted for 69–94% of technical variability. We analyzed how variability is propagated through linear signatures possibly affecting predictions and treatment recommendations. Linear signatures with feature weights adding to zero were substantially more robust than unbalanced signatures. They yielded consistent predictions across data from different platforms, both for transcriptomics and proteomics data. Similarly stable were their predictions across data from fresh frozen and matching formalin-fixed paraffin-embedded human tumor tissue. Availability and Implementation The R-package ‘zeroSum’ can be downloaded at https://github.com/rehbergT/zeroSum. Complete data and R codes necessary to reproduce all our results can be received from the authors upon request.
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Affiliation(s)
- M Altenbuchinger
- Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
| | - P Schwarzfischer
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - T Rehberg
- Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
| | - J Reinders
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Ch W Kohler
- Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
| | - W Gronwald
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - J Richter
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - M Szczepanowski
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - N Masqué-Soler
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - W Klapper
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - P J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - R Spang
- Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
- To whom correspondence should be addressed.
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16
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Guo L, Lin P, Xiong H, Tu S, Chen G. Molecular heterogeneity in diffuse large B-cell lymphoma and its implications in clinical diagnosis and treatment. Biochim Biophys Acta Rev Cancer 2018; 1869:85-96. [PMID: 29337112 DOI: 10.1016/j.bbcan.2018.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over half of patients with diffuse large B-cell lymphoma (DLBCL) can be cured by standard R-CHOP treatment (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone). However, the remaining patients are refractory and ultimately succumb to progressive or relapsed disease. During the past decade, there has been significant progress in the understanding of molecular mechanisms in DLBCL, largely owing to collaborative efforts in large-scale gene expression profiling and deep sequencing, which have identified genetic alterations critical in lymphomagenesis through activation of key signaling transduction pathways in DLBCL. These discoveries have not only led to the development of targeted therapies, including several currently in clinical trials, but also laid a solid foundation for the future identification of more effective therapies for patients not curable by R-CHOP. This review summarizes the recent advances in our understanding of the molecular characterization and pathogenesis of DLBCL and new treatment directions.
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Affiliation(s)
- Lingchuan Guo
- Department of Pathology, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou, Jiangsu 215000, China.
| | - Pei Lin
- Department of Hematopathology, MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 72, Houston, TX 77030, USA.
| | - Hui Xiong
- Shanghai Righton Biotechnology Co., Ltd, 1698 Wangyuan Road, Building 12, Fengxian District, Shanghai 201403, China.
| | - Shichun Tu
- Shanghai Righton Biotechnology Co., Ltd, 1698 Wangyuan Road, Building 12, Fengxian District, Shanghai 201403, China; Scintillon Institute for Biomedical and Bioenergy Research, 6888 Nancy Ridge Dr., San Diego, CA 92121, USA; Allele Biotechnology & Pharmaceuticals, Inc., 6404 Nancy Ridge Drive, San Diego, CA 92121, USA.
| | - Gang Chen
- Department of Pathology of Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, 420 Fuma Road, Fuzhou, Fujian 350014, China.
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17
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Adult high-grade B-cell lymphoma with Burkitt lymphoma signature: genomic features and potential therapeutic targets. Blood 2017; 130:1819-1831. [PMID: 28801451 DOI: 10.1182/blood-2017-02-767335] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/22/2017] [Indexed: 12/15/2022] Open
Abstract
The adult high-grade B-cell lymphomas sharing molecular features with Burkitt lymphoma (BL) are highly aggressive lymphomas with poor clinical outcome. High-resolution structural and functional genomic analysis of adult Burkitt lymphoma (BL) and high-grade B-cell lymphoma with BL gene signature (adult-molecularly defined BL [mBL]) revealed the MYC-ARF-p53 axis as the primary deregulated pathway. Adult-mBL had either unique or more frequent genomic aberrations (del13q14, del17p, gain8q24, and gain18q21) compared with pediatric-mBL, but shared commonly mutated genes. Mutations in genes promoting the tonic B-cell receptor (BCR)→PI3K pathway (TCF3 and ID3) did not differ by age, whereas effectors of chronic BCR→NF-κB signaling were associated with adult-mBL. A subset of adult-mBL had BCL2 translocation and mutation and elevated BCL2 mRNA and protein expression, but had a mutation profile similar to mBL. These double-hit lymphomas may have arisen from a tumor precursor that acquired both BCL2 and MYC translocations and/or KMT2D (MLL2) mutation. Gain/amplification of MIR17HG and its paralogue loci was observed in 50% of adult-mBL. In vitro studies suggested miR-17∼92's role in constitutive activation of BCR signaling and sensitivity to ibrutinib. Overall integrative analysis identified an interrelated gene network affected by copy number and mutation, leading to disruption of the p53 pathway and the BCR→PI3K or NF-κB activation, which can be further exploited in vivo by small-molecule inhibitors for effective therapy in adult-mBL.
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18
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Binder H, Kurz T, Teschner S, Kreutz C, Geyer M, Donauer J, Kraemer-Guth A, Timmer J, Schumacher M, Walz G. Dealing with prognostic signature instability: a strategy illustrated for cardiovascular events in patients with end-stage renal disease. BMC Med Genomics 2016; 9:43. [PMID: 27439789 PMCID: PMC4955222 DOI: 10.1186/s12920-016-0210-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 07/14/2016] [Indexed: 11/13/2022] Open
Abstract
Background Identification of prognostic gene expression markers from clinical cohorts might help to better understand disease etiology. A set of potentially important markers can be automatically selected when linking gene expression covariates to a clinical endpoint by multivariable regression models and regularized parameter estimation. However, this is hampered by instability due to selection from many measurements. Stability can be assessed by resampling techniques, which might guide modeling decisions, such as choice of the model class or the specific endpoint definition. Methods We specifically propose a strategy for judging the impact of different endpoint definitions, endpoint updates, different approaches for marker selection, and exclusion of outliers. This strategy is illustrated for a study with end-stage renal disease patients, who experience a yearly mortality of more than 20 %, with almost 50 % sudden cardiac death or myocardial infarction. The underlying etiology is poorly understood, and we specifically point out how our strategy can help to identify novel prognostic markers and targets for therapeutic interventions. Results For markers such as the potentially prognostic platelet glycoprotein IIb, the endpoint definition, in combination with the signature building approach is seen to have the largest impact. Removal of outliers, as identified by the proposed strategy, is also seen to considerably improve stability. Conclusions As the proposed strategy allowed us to precisely quantify the impact of modeling choices on the stability of marker identification, we suggest routine use also in other applications to prevent analysis-specific results, which are unstable, i.e. not reproducible.
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Affiliation(s)
- Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center Mainz, Obere Zahlbacher Str. 69, Mainz, 55131, Germany.
| | - Thorsten Kurz
- Core Facility Genomics, Centre for Systems Biology, University Freiburg, Freiburg, Germany
| | - Sven Teschner
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Clemens Kreutz
- Institute of Physics, University Freiburg, Freiburg, Germany
| | - Marcel Geyer
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg, Germany
| | | | | | - Jens Timmer
- Institute of Physics, University Freiburg, Freiburg, Germany.,BIOSS Center for Biological Signalling Studies, University Freiburg, Germany, Freiburg, Germany
| | - Martin Schumacher
- Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Freiburg, Germany
| | - Gerd Walz
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg, Germany.,BIOSS Center for Biological Signalling Studies, University Freiburg, Germany, Freiburg, Germany
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19
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Han van Krieken J. New developments in the pathology of malignant lymphoma: a review of the literature published from May 2015-September 2015. J Hematop 2015; 8:225-234. [PMID: 26640600 PMCID: PMC4659846 DOI: 10.1007/s12308-015-0262-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- J Han van Krieken
- Department of Pathology, Radboud University Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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