401
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Abstract
Abstract
The application of high-throughput genomic approaches in lymphomas has generated a wealth of data regarding the molecular underpinnings of these cancers. In this review, key findings from recent studies are discussed, as well as the genetic heterogeneity that underlies common lymphomas including diffuse large B-cell lymphoma, Burkitt lymphoma, and chronic lymphocytic leukemia, and the implications for identifying new therapeutic opportunities and personalized medicine.
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402
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Whole-exome sequencing in splenic marginal zone lymphoma reveals mutations in genes involved in marginal zone differentiation. Leukemia 2013; 28:1334-40. [PMID: 24296945 DOI: 10.1038/leu.2013.365] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 01/12/2023]
Abstract
Splenic marginal zone lymphoma (SMZL) is a B-cell neoplasm whose molecular pathogenesis remains fundamentally unexplained, requiring more precise diagnostic markers. Previous molecular studies have revealed 7q loss and mutations of nuclear factor κB (NF-κB), B-cell receptor (BCR) and Notch signalling genes. We performed whole-exome sequencing in a series of SMZL cases. Results confirmed that SMZL is an entity distinct from other low-grade B-cell lymphomas, and identified mutations in multiple genes involved in marginal zone development, and others involved in NF-κB, BCR, chromatin remodelling and the cytoskeleton.
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403
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Yan HB, Wang XF, Zhang Q, Tang ZQ, Jiang YH, Fan HZ, Sun YH, Yang PY, Liu F. Reduced expression of the chromatin remodeling gene ARID1A enhances gastric cancer cell migration and invasion via downregulation of E-cadherin transcription. Carcinogenesis 2013; 35:867-76. [PMID: 24293408 DOI: 10.1093/carcin/bgt398] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The chromatin remodeling gene AT-rich interactive domain-containing protein 1A (ARID1A) encodes the protein BAF250a, a subunit of human SWI/SNF-related complexes. Recent studies have identified ARID1A as a tumor suppressor. Here, we show that ARID1A expression is reduced in gastric cancer (GC) tissues, which are significantly associated with local lymph node metastasis, tumor infiltration and poor patient prognosis. ARID1A silencing enforces the migration and invasion of GC cells, whereas ectopic expression of ARID1A inhibits migration. The adhesive protein E-cadherin is remarkably downregulated in response to ARID1A silencing, but it is upregulated by ARID1A overexpression. E-cadherin overexpression significantly inhibits GC cell migration and invasion, whereas CDH1 (coded E-cadherin) silencing promotes migration. Restored expression of CDH1 in ARID1A-silenced cell lines restores the inhibition of cell migration. Luciferase reporter assays and chromatin immunoprecipitation indicate that the ARID1A-associated SWI/SNF complex binds to the CDH1 promoter and modulates CDH1 transcription. ARID1A knockdown induces evident morphological changes of GC cells with increased expression of mesenchymal markers, indicating an epithelial-mesenchymal transition. ARID1A silencing does not alter the level of β-catenin but induces a subcellular redistribution of β-catenin from the plasma membrane to the cytoplasm and nucleus. Immunohistochemical studies demonstrate that reduced expression of E-cadherin is associated with local lymph node metastasis, tumor infiltration and poor clinical prognosis. ARID1A and E-cadherin expression show a strong correlation in 75.4% of the analyzed GC tissues. They are synergistically downregulated in 23.5% of analyzed GC tissues. In conclusion, ARID1A targets E-cadherin during the modulation of GC cell migration and invasion.
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Affiliation(s)
- Hai-Bo Yan
- School of Life Sciences and School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
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404
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Hassler MR, Schiefer AI, Egger G. Combating the epigenome: epigenetic drugs against non-Hodgkin's lymphoma. Epigenomics 2013; 5:397-415. [PMID: 23895653 DOI: 10.2217/epi.13.39] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Non-Hodgkin's lymphomas (NHLs) comprise a large and diverse group of neoplasms of lymphocyte origin with heterogeneous molecular features and clinical manifestations. Current therapies are based on standard chemotherapy, immunotherapy, radiation or stem cell transplantation. The discovery of recurrent mutations in epigenetic enzymes, such as chromatin modifiers and DNA methyltransferases, has provided researchers with a rationale to develop novel inhibitors targeting these enzymes. Several clinical and preclinical studies have demonstrated the efficacy of epigenetic drugs in NHL therapy and a few specific inhibitors have already been approved for clinical use. Here, we provide an overview of current NHL classification and a review of the present literature describing epigenetic alterations in NHL, including a summary of different epigenetic drugs, and their use in preclinical and clinical studies.
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Affiliation(s)
- Melanie R Hassler
- Clinical Institute of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
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405
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Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SMJ, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JGR, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res 2013; 42:D865-72. [PMID: 24217909 PMCID: PMC3965069 DOI: 10.1093/nar/gkt1059] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.
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Affiliation(s)
- Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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406
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Rosolowski M, Läuter J, Abramov D, Drexler HG, Hummel M, Klapper W, MacLeod RA, Pellissery S, Horn F, Siebert R, Loeffler M. Massive transcriptional perturbation in subgroups of diffuse large B-cell lymphomas. PLoS One 2013; 8:e76287. [PMID: 24223701 PMCID: PMC3817189 DOI: 10.1371/journal.pone.0076287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 08/22/2013] [Indexed: 11/19/2022] Open
Abstract
Based on the assumption that molecular mechanisms involved in cancerogenesis are characterized by groups of coordinately expressed genes, we developed and validated a novel method for analyzing transcriptional data called Correlated Gene Set Analysis (CGSA). Using 50 extracted gene sets we identified three different profiles of tumors in a cohort of 364 Diffuse large B-cell (DLBCL) and related mature aggressive B-cell lymphomas other than Burkitt lymphoma. The first profile had high level of expression of genes related to proliferation whereas the second profile exhibited a stromal and immune response phenotype. These two profiles were characterized by a large scale gene activation affecting genes which were recently shown to be epigenetically regulated, and which were enriched in oxidative phosphorylation, energy metabolism and nucleoside biosynthesis. The third and novel profile showed only low global gene activation similar to that found in normal B cells but not cell lines. Our study indicates novel levels of complexity of DLBCL with low or high large scale gene activation related to metabolism and biosynthesis and, within the group of highly activated DLBCLs, differential behavior leading to either a proliferative or a stromal and immune response phenotype.
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Affiliation(s)
- Maciej Rosolowski
- Institute of Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
- * E-mail:
| | - Jürgen Läuter
- Institute of Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
- Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Dmitriy Abramov
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University of Kiel, Kiel, Germany
- Department of Pathology, Russian Federal Research Center, Moscow, Russia
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Hummel
- Institute of Pathology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Germany
| | - Wolfram Klapper
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University of Kiel, Kiel, Germany
| | - Roderick A.F. MacLeod
- Department of Human and Animal Cell Lines, DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Shoji Pellissery
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/University of Kiel, Kiel, Germany
| | - Friedemann Horn
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/University of Kiel, Kiel, Germany
| | - Markus Loeffler
- Institute of Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
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407
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Levens D. Cellular MYCro economics: Balancing MYC function with MYC expression. Cold Spring Harb Perspect Med 2013; 3:3/11/a014233. [PMID: 24186489 DOI: 10.1101/cshperspect.a014233] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The expression levels of the MYC oncoprotein have long been recognized to be associated with the outputs of major cellular processes including proliferation, cell growth, apoptosis, differentiation, and metabolism. Therefore, to understand how MYC operates, it is important to define quantitatively the relationship between MYC input and expression output for its targets as well as the higher-order relationships between the expression levels of subnetwork components and the flow of information and materials through those networks. Two different views of MYC are considered, first as a molecular microeconomic manager orchestrating specific positive and negative responses at individual promoters in collaboration with other transcription and chromatin components, and second, as a macroeconomic czar imposing an overarching rule onto all active genes. In either case, c-myc promoter output requires multiple inputs and exploits diverse mechanisms to tune expression to the appropriate levels relative to the thresholds of expression that separate health and disease.
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Affiliation(s)
- David Levens
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-1500
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408
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Aukema SM, Kreuz M, Kohler CW, Rosolowski M, Hasenclever D, Hummel M, Küppers R, Lenze D, Ott G, Pott C, Richter J, Rosenwald A, Szczepanowski M, Schwaenen C, Stein H, Trautmann H, Wessendorf S, Trümper L, Loeffler M, Spang R, Kluin PM, Klapper W, Siebert R. Biological characterization of adult MYC-translocation-positive mature B-cell lymphomas other than molecular Burkitt lymphoma. Haematologica 2013; 99:726-35. [PMID: 24179151 DOI: 10.3324/haematol.2013.091827] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chromosomal translocations affecting the MYC oncogene are the biological hallmark of Burkitt lymphomas but also occur in a subset of other mature B-cell lymphomas. If accompanied by a chromosomal break targeting the BCL2 and/or BCL6 oncogene these MYC translocation-positive (MYC(+)) lymphomas are called double-hit lymphomas, otherwise the term single-hit lymphomas is applied. In order to characterize the biological features of these MYC(+) lymphomas other than Burkitt lymphoma we explored, after exclusion of molecular Burkitt lymphoma as defined by gene expression profiling, the molecular, pathological and clinical aspects of 80 MYC-translocation-positive lymphomas (31 single-hit, 46 double-hit and 3 MYC(+)-lymphomas with unknown BCL6 status). Comparison of single-hit and double-hit lymphomas revealed no difference in MYC partner (IG/non-IG), genomic complexity, MYC expression or gene expression profile. Double-hit lymphomas more frequently showed a germinal center B-cell-like gene expression profile and had higher IGH and MYC mutation frequencies. Gene expression profiling revealed 130 differentially expressed genes between BCL6(+)/MYC(+) and BCL2(+)/MYC(+) double-hit lymphomas. BCL2(+)/MYC(+) double-hit lymphomas more frequently showed a germinal center B-like gene expression profile. Analysis of all lymphomas according to MYC partner (IG/non-IG) revealed no substantial differences. In this series of lymphomas, in which immunochemotherapy was administered in only a minority of cases, single-hit and double-hit lymphomas had a similar poor outcome in contrast to the outcome of molecular Burkitt lymphoma and lymphomas without the MYC break. Our data suggest that, after excluding molecular Burkitt lymphoma and pediatric cases, MYC(+) lymphomas are biologically quite homogeneous with single-hit and double-hit lymphomas as well as IG-MYC and non-IG-MYC(+) lymphomas sharing various molecular characteristics.
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409
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Abstract
PURPOSE OF REVIEW Next-generation sequencing of whole genomes, exomes and DNA methylomes in chronic lymphocytic leukemia (CLL) has provided the first comprehensive view of somatic mutations and methylation changes in this disease. This review summarizes the recent findings in this field and their impact on our current understanding of this neoplasm. RECENT FINDINGS Genomic studies have revealed a remarkable molecular heterogeneity of the disease, with only few genes mutated in up to 10-15% of the patients and a relatively large number of genes recurrently mutated at low frequency. The mutated genes tend to cluster in different pathways that include NOTCH1 signaling, RNA splicing, processing and transport machinery, innate inflammatory response, and DNA damage and cell cycle control, among others. NOTCH1 and SF3B1 mutations are emerging as new drivers of aggressive forms of the disease. Genome-wide methylation studies have shown that CLL transformation is associated with a massive hypomethylation phenomenon frequently affecting the enhancer regions. This epigenetic reprogramming maintains an imprint of the putative cell of origin from naïve and memory B-cells. SUMMARY Genomic and epigenomic studies of CLL are reshaping our understanding of the disease and provide new perspective for a more individualized diagnosis and new potential therapeutic targets.
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410
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Plass C, Pfister SM, Lindroth AM, Bogatyrova O, Claus R, Lichter P. Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat Rev Genet 2013; 14:765-80. [DOI: 10.1038/nrg3554] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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411
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Morin RD, Gascoyne RD. Newly Identified Mechanisms in B-Cell Non-Hodgkin Lymphomas Uncovered by Next-Generation Sequencing. Semin Hematol 2013; 50:303-13. [DOI: 10.1053/j.seminhematol.2013.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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412
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Aquino G, Marra L, Cantile M, De Chiara A, Liguori G, Curcio MP, Sabatino R, Pannone G, Pinto A, Botti G, Franco R. MYC chromosomal aberration in differential diagnosis between Burkitt and other aggressive lymphomas. Infect Agent Cancer 2013; 8:37. [PMID: 24079473 PMCID: PMC3850004 DOI: 10.1186/1750-9378-8-37] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/17/2013] [Indexed: 11/10/2022] Open
Abstract
Myc oncogenetic deregulation is abundantly described in several solid human cancer and lymphomas. Particularly, Burkitt's lymphoma belongs to the family of B Non Hodgkin aggressive lymphomas. Although it is morphologically characterized, immunophenotypic and cytogenetic diagnosis remains complex. In 2008, the WHO has introduced a new diagnostic class of aggressive B-cell lymphomas with features intermediate between BL and DLBCL. This diagnostic class represents a temporary container of aggressive B-cell lymphomas, not completely belonging to the BL and DLBCL categories. The importance of establishing a correct diagnosis would allow a better prognostic classification and a better therapeutic approach. In this review, we summarize the main diagnostic approaches necessary for appropriate diagnoses and we emphasize the importance of cytogenetic analysis of the oncogene Myc in the histopathological diagnosis and the prognostic/predictive stratification. In this contest, Myc represents the more involved gene in the development of these lymphomas. Therefore, we analyze the genetic aberrations causing its over-expression and the concomitant deregulation of molecular pathways related to it. We also propose a FISH approach useful in the diagnosis of these lymphomas.
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Affiliation(s)
- Gabriella Aquino
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Laura Marra
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Monica Cantile
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Annarosaria De Chiara
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Giuseppina Liguori
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Maria Pia Curcio
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Rocco Sabatino
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Giuseppe Pannone
- Medicine and Surgery Department, Foggia University, Foggia, Italy
| | - Antonio Pinto
- Haematology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Gerardo Botti
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
| | - Renato Franco
- Pathology Unit, "Istituto Nazionale Tumori Fondazione G. Pascale" - Irccs, Naples, Italy
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413
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Soldini D, Georgis A, Montagna C, Schüffler PJ, Martin V, Curioni-Fontecedro A, Martinez A, Tinguely M. The combined expression of VPREB3 and ID3 represents a new helpful tool for the routine diagnosis of mature aggressive B-cell lymphomas. Hematol Oncol 2013; 32:120-5. [PMID: 24493312 DOI: 10.1002/hon.2094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 11/10/2022]
Abstract
Genomic studies, such as gene expression profiling and next-generation sequencing studies, have provided new insights into the phenotypic characteristics and pathogenesis of mature aggressive B-cell lymphomas. In particular, mutations in the transcription factors ID3 and TCF3, leading to overexpression of B-cell receptor components such as VPREB3, have been shown to be specific for Burkitt lymphoma (BL) and play an important tumourigenic role by mediating the activation of the pro-survival phosphatidylinositol-3-OH kinase pathway. We performed immunohistochemical analysis by applying commercially available anti-VPREB3 antibody to a large cohort of 185 genetically and immunophenotypically characterized mature aggressive B-cell lymphomas and analyzed these results together with recent data on ID3 expression. The combined expression of both VPREB3 and ID3 was associated with a diagnosis of BL with high sensitivity (0.77), high specificity (0.75) and high negative predictive values (0.96), however, with lower positive predictive value (0.30). Double negative cases were absent in the group of BLs but could be found in approximately one third of the remaining cases of mature aggressive B-cell lymphomas. Further, we could not identify a correlation with MYC, BCL2 or BCL6 aberrations with neither VPREB3 nor ID3 expression in each of the diagnostic groups analyzed. Our results, which are in line with recently discovered mutations in next-generation sequencing studies, suggest that the combined immunohistochemical detection of VPREB3 and ID3 is applicable to the routine diagnostic in case of mature aggressive B-cell lymphomas. In particular, it represents a useful and routinely applicable diagnostic tool to exclude BL diagnosis in case of single positive or double negative cases.
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Affiliation(s)
- Davide Soldini
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
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414
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Abstract
Our understanding of the pathogenesis of lymphoid malignancies has been transformed by next-generation sequencing. The studies in this review have used whole-genome, exome, and transcriptome sequencing to identify recurring structural genetic alterations and sequence mutations that target key cellular pathways in acute lymphoblastic leukemia (ALL) and the lymphomas. Although each tumor type is characterized by a unique genomic landscape, several cellular pathways are mutated in multiple tumor types-transcriptional regulation of differentiation, antigen receptor signaling, tyrosine kinase and Ras signaling, and epigenetic modifications-and individual genes are mutated in multiple tumors, notably TCF3, NOTCH1, MYD88, and BRAF. In addition to providing fundamental insights into tumorigenesis, these studies have also identified potential new markers for diagnosis, risk stratification, and therapeutic intervention. Several genetic alterations are intuitively "druggable" with existing agents, for example, kinase-activating lesions in high-risk B-cell ALL, NOTCH1 in both leukemia and lymphoma, and BRAF in hairy cell leukemia. Future sequencing efforts are required to comprehensively define the genetic basis of all lymphoid malignancies, examine the relative roles of germline and somatic variation, dissect the genetic basis of clonal heterogeneity, and chart a course for clinical sequencing and translation to improved therapeutic outcomes.
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415
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Understanding MYC-driven aggressive B-cell lymphomas: pathogenesis and classification. Blood 2013; 122:3884-91. [PMID: 24009228 DOI: 10.1182/blood-2013-05-498329] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MYC is a potent oncogene initially identified as the target of the t(8;14)(q24;q32) chromosome translocation in Burkitt lymphoma. MYC gene alterations have been identified in other mature B-cell neoplasms that are usually associated with an aggressive clinical behavior. Most of these tumors originate in cells that do not normally express MYC protein. The oncogenic events leading to MYC up-regulation seem to overcome the inhibitory effect of physiological repressors such as BCL6 or BLIMP1. Aggressive lymphomas frequently carry additional oncogenic alterations that cooperate with MYC dysregulation, likely counteracting its proapoptotic function. The development of FISH probes and new reliable antibodies have facilitated the study of MYC gene alterations and protein expression in large series of patients, providing new clinical and biological perspectives regarding MYC dysregulation in aggressive lymphomas. MYC gene alterations in large B-cell lymphomas are frequently associated with BCL2 or BCL6 translocations conferring a very aggressive behavior. Conversely, MYC protein up-regulation may occur in tumors without apparent gene alterations, and its association with BCL2 overexpression also confers a poor prognosis. In this review, we integrate all of this new information and discuss perspectives, challenges, and open questions for the diagnosis and management of patients with MYC-driven aggressive B-cell lymphomas.
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416
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Worch J, Rohde M, Burkhardt B. Mature B-cell lymphoma and leukemia in children and adolescents-review of standard chemotherapy regimen and perspectives. Pediatr Hematol Oncol 2013; 30:465-83. [PMID: 23570584 DOI: 10.3109/08880018.2013.783891] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mature B-cell non-Hodgkin lymphoma (B-NHL) comprises more than 50% of all non-Hodgkin lymphoma (NHL) in children and adolescents. Many B-NHL subtypes frequently observed in adults are rarely diagnosed in children and adolescents. In this age group, Burkitt lymphoma (BL), Burkitt leukemia or FAB L3 leukemia (B-AL), diffuse large B-cell lymphoma (DLBCL), primary mediastinal large B-cell lymphoma (PMLBL), follicular lymphoma (FL), and aggressive mature B-NHL not further classifiable (B-NHL nfc) are the most common subtypes. Diverse clinical trials demonstrated similar results of current combination chemotherapy regimens succeeding in overall survival rates of more than 80%. However, treatment-related toxicity and the poor prognosis of relapse are serious concerns. Furthermore, specific histological B-NHL subtypes are rare in children and optimal treatment is not established. New treatment modalities are urgently needed for these patient groups. Rituximab, a monoclonal antibody that is already established in the treatment of adults with mature B-NHL, demonstrated promising results in pediatric patients. The definitive role of rituximab in the treatment of children and adolescents with B-NHL needs to be evaluated in prospective controlled clinical trials. This review provides a comprehensive overview of chemotherapy regimens and the perspectives for children and adolescents with mature B-cell lymphoma and leukemia.
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Affiliation(s)
- Jennifer Worch
- Department of Pediatric Hematology and Oncology, NHL-BFM Study Center, University Children's Hospital, Münster, Germany
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417
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Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL, Boyault S, Burkhardt B, Butler AP, Caldas C, Davies HR, Desmedt C, Eils R, Eyfjörd JE, Foekens JA, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinsk M, Jäger N, Jones DT, Jones D, Knappskog S, Kool M, Lakhani SR, López-Otín C, Martin S, Munshi NC, Nakamura H, Northcott PA, Pajic M, Papaemmanuil E, Paradiso A, Pearson JV, Puente XS, Raine K, Ramakrishna M, Richardson AL, Richter J, Rosenstiel P, Schlesner M, Schumacher TN, Span PN, Teague JW, Totoki Y, Tutt AN, Valdés-Mas R, van Buuren MM, van ’t Veer L, Vincent-Salomon A, Waddell N, Yates LR, Zucman-Rossi J, Futreal PA, McDermott U, Lichter P, Meyerson M, Grimmond SM, Siebert R, Campo E, Shibata T, Pfister SM, Campbell PJ, Stratton MR. Signatures of mutational processes in human cancer. Nature 2013; 500:415-421. [PMID: 23945592 PMCID: PMC3776390 DOI: 10.1038/nature12477 10.1038/nature12666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 07/19/2013] [Indexed: 09/19/2023]
Abstract
All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.
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Affiliation(s)
- Ludmil B. Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Medical Genetics, Box 134, Addenbrooke’s Hospital NHS Trust, Hills Road, Cambridge CB2 0QQ
| | - David C. Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Samuel A.J.R. Aparicio
- Molecular Oncology, Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada
- Centre for Translational and Applied Genomics, Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada
- Department of Pathology, University of British Columbia, G227-2211 Wesbrook Mall, British Columbia, Vancouver V6T 2B5, Canada
| | - Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Paediatrics, University of Cambridge, Hills Road, Cambridge, CB2 2XY
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland G4 0SF, United Kingdom
- The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Graham R. Bignell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Niccolo Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Ake Borg
- Department of Oncology, Lund University, SE-221 85 Lund, Sweden
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
- The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Sandrine Boyault
- Plateforme de Bioinformatique Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laennec, 69373 LYON CEDEX 08
| | - Birgit Burkhardt
- NHL-BFM Study Center and Department of Pediatric Hematology and Oncology, University Children’s Hospital, Münster, Germany
- NHL-BFM Study Center and Department of Pediatric Hematology and Oncology, University Children’s Hospital, Giessen, Germany
| | - Adam P. Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE
| | - Helen R. Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Christine Desmedt
- Breast Cancer Translational Res Lab - BCTL, Université Libre de Bruxelles - Institut Jules Bordet, Boulevard de Waterloo, 125, B-1000 Brussels
| | - Roland Eils
- Department of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Jórunn Erla Eyfjörd
- Cancer Research Laboratory, Faculty of Medicine, Biomedical Centre, University of Iceland, 101 Reykjavik, Iceland
| | - John A. Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mel Greaves
- Department of Haemato-oncology, Institute of Cancer Research, London
| | - Fumie Hosoda
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Barbara Hutter
- Department of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Tomislav Ilicic
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Sandrine Imbeaud
- INSERM, UMR-674, Génomique Fonctionnelle des Tumeurs Solides, Institut Universitaire d’Hematologie (IUH), Paris, France
- Université Paris Descartes, Labex Immuno-oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Marcin Imielinsk
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Natalie Jäger
- Department of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - David T.W. Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sunil R. Lakhani
- The University of Queensland Centre for Clinical Research, School of Medicine and Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston 4029,Brisbane, QLD, Australia
| | - Carlos López-Otín
- Dpt. Bioquímica y Biología Molecular, IUOPA-Universidad de Oviedo, 33006 Oviedo, Spain
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Nikhil C. Munshi
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Boston Veterans Administration Healthcare System, West Roxbury, MA
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Paul A. Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marina Pajic
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Angelo Paradiso
- Clinical Experimental Oncology Laboratory, National Cancer Institute, Via Amendola, 209, 70126, Bari, Italy
| | - John V. Pearson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Xose S. Puente
- Dpt. Bioquímica y Biología Molecular, IUOPA-Universidad de Oviedo, 33006 Oviedo, Spain
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Andrea L. Richardson
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital 75 Francis St. Boston, MA 02115, USA
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University,Kiel, Germany
| | - Matthias Schlesner
- Department of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Ton N. Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Paul N. Span
- Department of Radiation Oncology and department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500HB Nijmegen,the Netherlands
| | - Jon W. Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Andrew N.J. Tutt
- Breakthrough Breast Cancer Research Unit, King’s College London School of Medicine, London, UK
| | - Rafael Valdés-Mas
- Dpt. Bioquímica y Biología Molecular, IUOPA-Universidad de Oviedo, 33006 Oviedo, Spain
| | - Marit M. van Buuren
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Laura van ’t Veer
- The Netherlands Cancer Institute, 121 Plesmanlaan, 1066 CX Amsterdam, The Netherlands
| | - Anne Vincent-Salomon
- Institut Curie , Departement de Pathologie, INSERM U830, 26 rue d’Ulm 75248 PARIS CEDEX 05, France
| | - Nicola Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Lucy R. Yates
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | | | | | | | | | - Jessica Zucman-Rossi
- INSERM, UMR-674, Génomique Fonctionnelle des Tumeurs Solides, Institut Universitaire d’Hematologie (IUH), Paris, France
- Université Paris Descartes, Labex Immuno-oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - P. Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sean M. Grimmond
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Elías Campo
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, IDIBAPS, 08036 Barcelona, Spain
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Stefan M. Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg
| | - Peter J. Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
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418
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Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL, Boyault S, Burkhardt B, Butler AP, Caldas C, Davies HR, Desmedt C, Eils R, Eyfjörd JE, Foekens JA, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinsk M, Jäger N, Jones DT, Jones D, Knappskog S, Kool M, Lakhani SR, López-Otín C, Martin S, Munshi NC, Nakamura H, Northcott PA, Pajic M, Papaemmanuil E, Paradiso A, Pearson JV, Puente XS, Raine K, Ramakrishna M, Richardson AL, Richter J, Rosenstiel P, Schlesner M, Schumacher TN, Span PN, Teague JW, Totoki Y, Tutt AN, Valdés-Mas R, van Buuren MM, van ’t Veer L, Vincent-Salomon A, Waddell N, Yates LR, Zucman-Rossi J, Futreal PA, McDermott U, Lichter P, Meyerson M, Grimmond SM, Siebert R, Campo E, Shibata T, Pfister SM, Campbell PJ, Stratton MR. Signatures of mutational processes in human cancer. Nature 2013; 500:415-21. [PMID: 23945592 PMCID: PMC3776390 DOI: 10.1038/nature12477] [Citation(s) in RCA: 6885] [Impact Index Per Article: 625.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 07/19/2013] [Indexed: 02/06/2023]
Abstract
All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.
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Affiliation(s)
- Ludmil B. Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Medical Genetics, Box 134, Addenbrooke’s Hospital NHS Trust, Hills Road, Cambridge CB2 0QQ
| | - David C. Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Samuel A.J.R. Aparicio
- Molecular Oncology, Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada
- Centre for Translational and Applied Genomics, Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada
- Department of Pathology, University of British Columbia, G227-2211 Wesbrook Mall, British Columbia, Vancouver V6T 2B5, Canada
| | - Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Paediatrics, University of Cambridge, Hills Road, Cambridge, CB2 2XY
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland G4 0SF, United Kingdom
- The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Graham R. Bignell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Niccolo Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Ake Borg
- Department of Oncology, Lund University, SE-221 85 Lund, Sweden
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
- The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Sandrine Boyault
- Plateforme de Bioinformatique Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laennec, 69373 LYON CEDEX 08
| | - Birgit Burkhardt
- NHL-BFM Study Center and Department of Pediatric Hematology and Oncology, University Children’s Hospital, Münster, Germany
- NHL-BFM Study Center and Department of Pediatric Hematology and Oncology, University Children’s Hospital, Giessen, Germany
| | - Adam P. Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE
| | - Helen R. Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Christine Desmedt
- Breast Cancer Translational Res Lab - BCTL, Université Libre de Bruxelles - Institut Jules Bordet, Boulevard de Waterloo, 125, B-1000 Brussels
| | - Roland Eils
- Department of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Jórunn Erla Eyfjörd
- Cancer Research Laboratory, Faculty of Medicine, Biomedical Centre, University of Iceland, 101 Reykjavik, Iceland
| | - John A. Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mel Greaves
- Department of Haemato-oncology, Institute of Cancer Research, London
| | - Fumie Hosoda
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Barbara Hutter
- Department of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Tomislav Ilicic
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Sandrine Imbeaud
- INSERM, UMR-674, Génomique Fonctionnelle des Tumeurs Solides, Institut Universitaire d’Hematologie (IUH), Paris, France
- Université Paris Descartes, Labex Immuno-oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Marcin Imielinsk
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Natalie Jäger
- Department of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - David T.W. Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sunil R. Lakhani
- The University of Queensland Centre for Clinical Research, School of Medicine and Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston 4029,Brisbane, QLD, Australia
| | - Carlos López-Otín
- Dpt. Bioquímica y Biología Molecular, IUOPA-Universidad de Oviedo, 33006 Oviedo, Spain
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Nikhil C. Munshi
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Boston Veterans Administration Healthcare System, West Roxbury, MA
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Paul A. Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marina Pajic
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Angelo Paradiso
- Clinical Experimental Oncology Laboratory, National Cancer Institute, Via Amendola, 209, 70126, Bari, Italy
| | - John V. Pearson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Xose S. Puente
- Dpt. Bioquímica y Biología Molecular, IUOPA-Universidad de Oviedo, 33006 Oviedo, Spain
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Andrea L. Richardson
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital 75 Francis St. Boston, MA 02115, USA
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University,Kiel, Germany
| | - Matthias Schlesner
- Department of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Ton N. Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Paul N. Span
- Department of Radiation Oncology and department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500HB Nijmegen,the Netherlands
| | - Jon W. Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Andrew N.J. Tutt
- Breakthrough Breast Cancer Research Unit, King’s College London School of Medicine, London, UK
| | - Rafael Valdés-Mas
- Dpt. Bioquímica y Biología Molecular, IUOPA-Universidad de Oviedo, 33006 Oviedo, Spain
| | - Marit M. van Buuren
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Laura van ’t Veer
- The Netherlands Cancer Institute, 121 Plesmanlaan, 1066 CX Amsterdam, The Netherlands
| | - Anne Vincent-Salomon
- Institut Curie , Departement de Pathologie, INSERM U830, 26 rue d’Ulm 75248 PARIS CEDEX 05, France
| | - Nicola Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Lucy R. Yates
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | | | | | | | | | - Jessica Zucman-Rossi
- INSERM, UMR-674, Génomique Fonctionnelle des Tumeurs Solides, Institut Universitaire d’Hematologie (IUH), Paris, France
- Université Paris Descartes, Labex Immuno-oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - P. Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sean M. Grimmond
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Elías Campo
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, IDIBAPS, 08036 Barcelona, Spain
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Stefan M. Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg
| | - Peter J. Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
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419
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Gospodinov A, Herceg Z. Chromatin structure in double strand break repair. DNA Repair (Amst) 2013; 12:800-10. [PMID: 23919923 DOI: 10.1016/j.dnarep.2013.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 12/16/2022]
Abstract
Cells are under constant assault by endogenous and environmental DNA damaging agents. DNA double strand breaks (DSBs) sever entire chromosomes and pose a major threat to genome integrity as a result of chromosomal fragment loss or chromosomal rearrangements. Exogenous factors such as ionizing radiation, crosslinking agents, and topoisomerase poisons, contribute to break formation. DSBs are associated with oxidative metabolism, form during the normal S phase, when replication forks collapse and are generated during physiological processes such as V(D)J recombination, yeast mating type switching and meiosis. It is estimated that in mammalian cells ∼10 DSBs per cell are formed daily. If left unrepaired DSBs can lead to cell death or deregulated growth, and cancer development. Cellular response to DSB damage includes mechanisms to halt the progression of the cell cycle and to restore the structure of the broken chromosome. Changes in chromatin adjacent to DNA break sites are instrumental to the DNA damage response (DDR) with two apparent ends: to control compaction and to bind repair and signaling molecules to the lesion. Here, we review the key findings related to each of these functions and examine their cross-talk.
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Affiliation(s)
- Anastas Gospodinov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. 21, 1113 Sofia, Bulgaria.
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420
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Oike T, Ogiwara H, Nakano T, Yokota J, Kohno T. Inactivating Mutations in SWI/SNF Chromatin Remodeling Genes in Human Cancer. Jpn J Clin Oncol 2013; 43:849-55. [DOI: 10.1093/jjco/hyt101] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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421
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Knoechel B, Lohr JG. Genomics of lymphoid malignancies reveal major activation pathways in lymphocytes. J Autoimmun 2013; 45:15-23. [PMID: 23880067 DOI: 10.1016/j.jaut.2013.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 06/19/2013] [Indexed: 01/21/2023]
Abstract
Breakdown of tolerance leads to autoimmunity due to emergence of autoreactive T or B cell clones. Autoimmune diseases predispose to lymphoid malignancies and lymphoid malignancies, conversely, can manifest as autoimmune diseases. While it has been clear for a long time that a competitive advantage and uncontrolled growth of lymphocytes contribute to the pathogenesis of both lymphoid malignancies as well as autoimmune diseases, the overlap of the underlying mechanisms has been less well described. Next generation sequencing has led to massive expansion of the available genomic data in many diseases over the last five years. These data allow for comparison of the molecular pathogenesis between autoimmune diseases and lymphoid malignancies. Here, we review the similarities between autoimmune diseases and lymphoid malignancies: 1) Both, autoimmune diseases and lymphoid malignancies are characterized by activation of the same T and B cell signaling pathways, and dysregulation of these pathways can occur through genetic or epigenetic events. 2) In both scenarios, clonal and subclonal evolution of lymphocytes contribute to disease. 3) Development of both diseases not only depends on T or B cell intrinsic factors, such as germline or somatic mutations, but also on environmental factors. These include infections, the presence of other immune cells in the microenvironment, and the cytokine milieu. A better mechanistic understanding of the parallels between lymphomagenesis and autoimmunity may help the development of precision treatment strategies with rationally designed therapeutic agents.
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Affiliation(s)
- Birgit Knoechel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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422
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Oike T, Ogiwara H, Tominaga Y, Ito K, Ando O, Tsuta K, Mizukami T, Shimada Y, Isomura H, Komachi M, Furuta K, Watanabe SI, Nakano T, Yokota J, Kohno T. A synthetic lethality-based strategy to treat cancers harboring a genetic deficiency in the chromatin remodeling factor BRG1. Cancer Res 2013; 73:5508-18. [PMID: 23872584 DOI: 10.1158/0008-5472.can-12-4593] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The occurrence of inactivating mutations in SWI/SNF chromatin-remodeling genes in common cancers has attracted a great deal of interest. However, mechanistic strategies to target tumor cells carrying such mutations are yet to be developed. This study proposes a synthetic-lethality therapy for treating cancers deficient in the SWI/SNF catalytic (ATPase) subunit, BRG1/SMARCA4. The strategy relies upon inhibition of BRM/SMARCA2, another catalytic SWI/SNF subunit with a BRG1-related activity. Immunohistochemical analysis of a cohort of non-small-cell lung carcinomas (NSCLC) indicated that 15.5% (16 of 103) of the cohort, corresponding to preferentially undifferentiated tumors, was deficient in BRG1 expression. All BRG1-deficient cases were negative for alterations in known therapeutic target genes, for example, EGFR and DDR2 gene mutations, ALK gene fusions, or FGFR1 gene amplifications. RNA interference (RNAi)-mediated silencing of BRM suppressed the growth of BRG1-deficient cancer cells relative to BRG1-proficient cancer cells, inducing senescence via activation of p21/CDKN1A. This growth suppression was reversed by transduction of wild-type but not ATPase-deficient BRG1. In support of these in vitro results, a conditional RNAi study conducted in vivo revealed that BRM depletion suppressed the growth of BRG1-deficient tumor xenografts. Our results offer a rationale to develop BRM-ATPase inhibitors as a strategy to treat BRG1/SMARCA4-deficient cancers, including NSCLCs that lack mutations in presently known therapeutic target genes.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Adenocarcinoma/therapy
- Adult
- Aged
- Aged, 80 and over
- Anaplastic Lymphoma Kinase
- Animals
- Apoptosis
- Blotting, Western
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/therapy
- Cell Cycle
- Cell Differentiation
- Cell Proliferation
- Cellular Senescence
- DNA Helicases/antagonists & inhibitors
- DNA Helicases/genetics
- DNA Helicases/metabolism
- Discoidin Domain Receptors
- Female
- Fluorescent Antibody Technique
- Genes, Lethal
- Humans
- Immunoenzyme Techniques
- Kinesins/genetics
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/therapy
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Microscopy, Fluorescence
- Middle Aged
- Mutation/genetics
- Neoplasm Staging
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Oncogene Proteins, Fusion/genetics
- RNA, Small Interfering/genetics
- Receptor Protein-Tyrosine Kinases/genetics
- Receptors, Mitogen/genetics
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Takahiro Oike
- Divisions of Genome Biology and Multistep Carcinogenesis, National Cancer Center Research Institute, Tokyo, Japan, USA
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423
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Braggio E, Egan JB, Fonseca R, Stewart AK. Lessons from next-generation sequencing analysis in hematological malignancies. Blood Cancer J 2013; 3:e127. [PMID: 23872706 PMCID: PMC3730204 DOI: 10.1038/bcj.2013.26] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/14/2013] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing has led to a revolution in the study of hematological malignancies with a substantial number of publications and discoveries in the last few years. Significant discoveries associated with disease diagnosis, risk stratification, clonal evolution and therapeutic intervention have been generated by this powerful technology. As part of the post-genomic era, sequencing analysis will likely become part of routine clinical testing and the challenge will ultimately be successfully transitioning from gene discovery to preventive and therapeutic intervention as part of individualized medicine strategies. In this report, we review recent advances in the understanding of hematological malignancies derived through genome-wide sequence analysis.
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Affiliation(s)
- E Braggio
- Mayo Clinic in Arizona, 13400 East Shea Boulevard, Scottsdale, AZ, USA
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424
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Emadali A, Rousseaux S, Bruder-Costa J, Rome C, Duley S, Hamaidia S, Betton P, Debernardi A, Leroux D, Bernay B, Kieffer-Jaquinod S, Combes F, Ferri E, McKenna CE, Petosa C, Bruley C, Garin J, Ferro M, Gressin R, Callanan MB, Khochbin S. Identification of a novel BET bromodomain inhibitor-sensitive, gene regulatory circuit that controls Rituximab response and tumour growth in aggressive lymphoid cancers. EMBO Mol Med 2013; 5:1180-95. [PMID: 23828858 PMCID: PMC3944460 DOI: 10.1002/emmm.201202034] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 12/13/2022] Open
Abstract
Immuno-chemotherapy elicit high response rates in B-cell non-Hodgkin lymphoma but heterogeneity in response duration is observed, with some patients achieving cure and others showing refractory disease or relapse. Using a transcriptome-powered targeted proteomics screen, we discovered a gene regulatory circuit involving the nuclear factor CYCLON which characterizes aggressive disease and resistance to the anti-CD20 monoclonal antibody, Rituximab, in high-risk B-cell lymphoma. CYCLON knockdown was found to inhibit the aggressivity of MYC-overexpressing tumours in mice and to modulate gene expression programs of biological relevance to lymphoma. Furthermore, CYCLON knockdown increased the sensitivity of human lymphoma B cells to Rituximab in vitro and in vivo. Strikingly, this effect could be mimicked by in vitro treatment of lymphoma B cells with a small molecule inhibitor for BET bromodomain proteins (JQ1). In summary, this work has identified CYCLON as a new MYC cooperating factor that autonomously drives aggressive tumour growth and Rituximab resistance in lymphoma. This resistance mechanism is amenable to next-generation epigenetic therapy by BET bromodomain inhibition, thereby providing a new combination therapy rationale for high-risk lymphoma. The nuclear factor CYCLON is a new MYC cooperating factor that drives tumor growth and Rituximab resistance in lymphoma. This resistance mechanism can be targeted by next-generation epigenetic therapy by BET bromodomain inhibition downstream of MYC.
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Affiliation(s)
- Anouk Emadali
- CEA, iRTSV, Biologie à Grande Echelle, Grenoble, France
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425
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Treatment of Adolescents with Aggressive B-Cell Malignancies: The Pediatric Experience. Curr Hematol Malig Rep 2013; 8:226-35. [DOI: 10.1007/s11899-013-0166-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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426
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Soldini D, Campo E. Genetic sequencing studies in Burkitt's lymphoma: what can we learn about tumorigenesis? Expert Rev Hematol 2013; 6:219-21. [PMID: 23782073 DOI: 10.1586/ehm.13.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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427
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The SWI/SNF genetic blockade: effects in cell differentiation, cancer and developmental diseases. Oncogene 2013; 33:2681-9. [PMID: 23752187 DOI: 10.1038/onc.2013.227] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 12/26/2022]
Abstract
Our rapidly growing knowledge about cancer genetics attests to the widespread occurrence of alterations at genes encoding different components of the SWI/SNF complex. This reveals an important new feature that sustains cancer development: the blockade of chromatin remodeling. Here, we provide an overview of our current knowledge on the gene alterations of chromatin-remodeling factors, and how they relate to cancer and human developmental diseases. We also consider the functional repercussions, particularly how the inactivation of the SWI/SNF complex impairs the appropriate cell response to nuclear receptor signaling, which, in turn, prevents cell differentiation and sustains cell growth independently of the environment.
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428
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Dykhuizen EC, Hargreaves DC, Miller EL, Cui K, Korshunov A, Kool M, Pfister S, Cho YJ, Zhao K, Crabtree GR. BAF complexes facilitate decatenation of DNA by topoisomerase IIα. Nature 2013; 497:624-7. [PMID: 23698369 PMCID: PMC3668793 DOI: 10.1038/nature12146] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 04/03/2013] [Indexed: 12/19/2022]
Abstract
Recent exon-sequencing studies of human tumours have revealed that subunits of BAF (mammalian SWI/SNF) complexes are mutated in more than 20% of all human malignancies, but the mechanisms involved in tumour suppression are unclear. BAF chromatin-remodelling complexes are polymorphic assemblies that use energy provided by ATP hydrolysis to regulate transcription through the control of chromatin structure and the placement of Polycomb repressive complex 2 (PRC2) across the genome. Several proteins dedicated to this multisubunit complex, including BRG1 (also known as SMARCA4) and BAF250a (also known as ARID1A), are mutated at frequencies similar to those of recognized tumour suppressors. In particular, the core ATPase BRG1 is mutated in 5-10% of childhood medulloblastomas and more than 15% of Burkitt's lymphomas. Here we show a previously unknown function of BAF complexes in decatenating newly replicated sister chromatids, a requirement for proper chromosome segregation during mitosis. We find that deletion of Brg1 in mouse cells, as well as the expression of BRG1 point mutants identified in human tumours, leads to anaphase bridge formation (in which sister chromatids are linked by catenated strands of DNA) and a G2/M-phase block characteristic of the decatenation checkpoint. Endogenous BAF complexes interact directly with endogenous topoisomerase IIα (TOP2A) through BAF250a and are required for the binding of TOP2A to approximately 12,000 sites across the genome. Our results demonstrate that TOP2A chromatin binding is dependent on the ATPase activity of BRG1, which is compromised in oncogenic BRG1 mutants. These studies indicate that the ability of TOP2A to prevent DNA entanglement at mitosis requires BAF complexes and suggest that this activity contributes to the role of BAF subunits as tumour suppressors.
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Affiliation(s)
- Emily C Dykhuizen
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
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429
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Abstract
Cancer arises as a consequence of cumulative disruptions to cellular growth control with Darwinian selection for those heritable changes that provide the greatest clonal advantage. These traits can be acquired and stably maintained by either genetic or epigenetic means. Here, we explore the ways in which alterations in the genome and epigenome influence each other and cooperate to promote oncogenic transformation. Disruption of epigenomic control is pervasive in malignancy and can be classified as an enabling characteristic of cancer cells, akin to genome instability and mutation.
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Affiliation(s)
- Hui Shen
- USC Epigenome Center, University of Southern California, Room G511B, 1450 Biggy Street, Los Angeles, CA 90089-9061, USA
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430
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Blombery PA, Dickinson M, Westerman DA. Molecular lesions in B-cell lymphoproliferative disorders: recent contributions from studies utilizing high-throughput sequencing techniques. Leuk Lymphoma 2013; 55:19-30. [DOI: 10.3109/10428194.2013.792112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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431
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Rossi D, Ciardullo C, Gaidano G. Genetic aberrations of signaling pathways in lymphomagenesis: revelations from next generation sequencing studies. Semin Cancer Biol 2013; 23:422-30. [PMID: 23665546 DOI: 10.1016/j.semcancer.2013.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/24/2013] [Accepted: 04/29/2013] [Indexed: 11/17/2022]
Abstract
Next generation sequencing (NGS) technology has led to a burst of disease-relevant molecular information in a variety of lymphoid tumors, including chronic lymphocytic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, mantle cell lymphoma, Burkitt lymphoma, Waldenström macroglobulinemia, hairy cell leukemia, and splenic marginal zone lymphoma. Beside disclosing comprehensive catalogs of somatic mutations and new insights into the genes that contribute to cellular transformation, NGS has also provided molecular clues useful for addressing a number of unmet clinical needs in the field of B-cell tumor management, including biomarkers for disease diagnosis and classification improvement (i.e. mutations of BRAF, MYD88 and NOTCH2), and new targets to be translated into therapeutic interventions (i.e. BCR, TLR, NOTCH, NF-κB and MAPK signaling pathways). This review summarizes the molecular lesions of signaling pathways that have been discovered in B-cell lymphoproliferative disorders by NGS studies.
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Affiliation(s)
- Davide Rossi
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy
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432
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Kadoch C, Hargreaves DC, Hodges C, Elias L, Ho L, Ranish J, Crabtree GR. Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nat Genet 2013; 45:592-601. [PMID: 23644491 DOI: 10.1038/ng.2628] [Citation(s) in RCA: 997] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 04/08/2013] [Indexed: 12/13/2022]
Abstract
Subunits of mammalian SWI/SNF (mSWI/SNF or BAF) complexes have recently been implicated as tumor suppressors in human malignancies. To understand the full extent of their involvement, we conducted a proteomic analysis of endogenous mSWI/SNF complexes, which identified several new dedicated, stable subunits not found in yeast SWI/SNF complexes, including BCL7A, BCL7B and BCL7C, BCL11A and BCL11B, BRD9 and SS18. Incorporating these new members, we determined mSWI/SNF subunit mutation frequency in exome and whole-genome sequencing studies of primary human tumors. Notably, mSWI/SNF subunits are mutated in 19.6% of all human tumors reported in 44 studies. Our analysis suggests that specific subunits protect against cancer in specific tissues. In addition, mutations affecting more than one subunit, defined here as compound heterozygosity, are prevalent in certain cancers. Our studies demonstrate that mSWI/SNF is the most frequently mutated chromatin-regulatory complex (CRC) in human cancer, exhibiting a broad mutation pattern, similar to that of TP53. Thus, proper functioning of polymorphic BAF complexes may constitute a major mechanism of tumor suppression.
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Affiliation(s)
- Cigall Kadoch
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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433
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Balbás-Martínez C, Rodríguez-Pinilla M, Casanova A, Domínguez O, Pisano DG, Gómez G, Lloreta J, Lorente JA, Malats N, Real FX. ARID1A alterations are associated with FGFR3-wild type, poor-prognosis, urothelial bladder tumors. PLoS One 2013; 8:e62483. [PMID: 23650517 PMCID: PMC3641081 DOI: 10.1371/journal.pone.0062483] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 03/20/2013] [Indexed: 02/06/2023] Open
Abstract
Urothelial bladder cancer (UBC) is heterogeneous at the clinical, pathological, genetic, and epigenetic levels. Exome sequencing has identified ARID1A as a novel tumor suppressor gene coding for a chromatin remodeling protein that is mutated in UBC. Here, we assess ARID1A alterations in two series of patients with UBC. In the first tumor series, we analyze exons 2–20 in 52 primary UBC and find that all mutant tumors belong to the aggressive UBC phenotype (high grade non-muscle invasive and muscle invasive tumors) (P = 0.05). In a second series (n = 84), we assess ARID1A expression using immunohistochemistry, a surrogate for mutation analysis, and find that loss of expression increases with higher stage/grade, it is inversely associated with FGFR3 overexpression (P = 0.03) but it is not correlated with p53 overexpression (P = 0.30). We also analyzed the expression of cytokeratins in the same set of tumor and find, using unsupervised clustering, that tumors with ARID1A loss of expression are generally KRT5/6-low. In this patient series, loss of ARID1A expression is also associated with worse prognosis, likely reflecting the higher prevalence of losses found in tumors of higher stage and grade. The independent findings in these two sets of patients strongly support the notion that ARID1A inactivation is a key player in bladder carcinogenesis occurring predominantly in FGFR3 wild type tumors.
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MESH Headings
- Aged
- Aged, 80 and over
- Base Sequence
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/mortality
- Carcinoma, Transitional Cell/pathology
- Cell Line, Tumor
- DNA Mutational Analysis
- DNA-Binding Proteins
- Female
- HEK293 Cells
- Humans
- Kaplan-Meier Estimate
- Male
- Middle Aged
- Mutation, Missense
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Prognosis
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/mortality
- Urinary Bladder Neoplasms/pathology
- Urothelium/pathology
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Affiliation(s)
- Cristina Balbás-Martínez
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - María Rodríguez-Pinilla
- Lymphoma Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Ariel Casanova
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Orlando Domínguez
- Genomics Unit, Biotechnology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - David G. Pisano
- Bioinformatics Unit, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Gonzalo Gómez
- Bioinformatics Unit, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Josep Lloreta
- Department of Pathology, Hospital del Mar, Barcelona, Spain
- Departament de Ciències Experimentals de i la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Núria Malats
- Genetic and Molecular Epidemiology Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Francisco X. Real
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Departament de Ciències Experimentals de i la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail:
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434
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Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, Moore RA, Mungall KL, Qian J, Tam A, Thiessen N, Zhao Y, Cole KA, Diamond M, Diskin SJ, Mosse YP, Wood AC, Ji L, Sposto R, Badgett T, London WB, Moyer Y, Gastier-Foster JM, Smith MA, Auvil JMG, Gerhard DS, Hogarty MD, Jones SJM, Lander ES, Gabriel SB, Getz G, Seeger RC, Khan J, Marra MA, Meyerson M, Maris JM. The genetic landscape of high-risk neuroblastoma. Nat Genet 2013; 45:279-84. [PMID: 23334666 PMCID: PMC3682833 DOI: 10.1038/ng.2529] [Citation(s) in RCA: 827] [Impact Index Per Article: 75.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/20/2012] [Indexed: 12/11/2022]
Abstract
Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 affected individuals (cases) using a combination of whole-exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per Mb (0.48 nonsilent) and notably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, and an additional 7.1% had focal deletions), MYCN (1.7%, causing a recurrent p.Pro44Leu alteration) and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1 and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies that rely on frequently altered oncogenic drivers.
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Affiliation(s)
- Trevor J. Pugh
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Olena Morozova
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
- University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Edward F. Attiyeh
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shahab Asgharzadeh
- Division of Hematology/Oncology, The Children’s Hospital Los Angeles, CA, 90027
- Saban Research Institute, The Children’s Hospital Los Angeles, CA, 90027
- Keck School of Medicine, University of Southern California; Los Angeles, CA, 90007, USA
| | - Jun S. Wei
- Pediatric Oncology Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Gaithersburg, MD, 20877, USA
| | - Daniel Auclair
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Scott L. Carter
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Megan Hanna
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Adam Kiezun
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Lee Lichenstein
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Aaron McKenna
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Chandra Sekhar Pedamallu
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Alex H. Ramos
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Erica Shefler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Adrian Ally
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Inanc Birol
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Richard D. Corbett
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Martin Hirst
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Shaun D. Jackman
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Baljit Kamoh
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Alireza Hadj Khodabakshi
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Martin Krzywinski
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Allan Lo
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A. Moore
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Karen L. Mungall
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Jenny Qian
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Angela Tam
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Nina Thiessen
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Kristina A. Cole
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maura Diamond
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sharon J. Diskin
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yael P. Mosse
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew C. Wood
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lingyun Ji
- Division of Hematology/Oncology, The Children’s Hospital Los Angeles, CA, 90027
- Saban Research Institute, The Children’s Hospital Los Angeles, CA, 90027
- Keck School of Medicine, University of Southern California; Los Angeles, CA, 90007, USA
| | - Richard Sposto
- Division of Hematology/Oncology, The Children’s Hospital Los Angeles, CA, 90027
- Saban Research Institute, The Children’s Hospital Los Angeles, CA, 90027
- Keck School of Medicine, University of Southern California; Los Angeles, CA, 90007, USA
| | - Thomas Badgett
- Pediatric Oncology Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Gaithersburg, MD, 20877, USA
| | - Wendy B. London
- Harvard Medical School, Boston, MA, 02115, USA
- Children’s Hospital Boston / Dana-Farber Cancer Institute and Children’s Oncology Group, Boston, MA, 02215, USA
| | - Yvonne Moyer
- Nationwide Children’s Hospital, Columbus, OH, 43205, USA
- The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Julie M. Gastier-Foster
- Nationwide Children’s Hospital, Columbus, OH, 43205, USA
- The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, 20892, USA
| | | | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michael D. Hogarty
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven J. M. Jones
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| | - Eric S. Lander
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Robert C. Seeger
- Division of Hematology/Oncology, The Children’s Hospital Los Angeles, CA, 90027
- Saban Research Institute, The Children’s Hospital Los Angeles, CA, 90027
- Keck School of Medicine, University of Southern California; Los Angeles, CA, 90007, USA
| | - Javed Khan
- Pediatric Oncology Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Gaithersburg, MD, 20877, USA
| | - Marco A. Marra
- Genome Sciences Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
- University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - John M. Maris
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Philadelphia, PA, 19104, USA
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435
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Abstract
Two studies in this issue identify the landscape of somatic mutations in Burkitt lymphoma and highlight the pathogenic and clinical relevance of inactivating mutations of ID3, an inhibitor of the TCF3 transcription factor.
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436
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Base-pair resolution DNA methylome of the EBV-positive Endemic Burkitt lymphoma cell line DAUDI determined by SOLiD bisulfite-sequencing. Leukemia 2013; 27:1751-3. [PMID: 23307032 PMCID: PMC3740476 DOI: 10.1038/leu.2013.4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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437
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Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common form of lymphoma in adults. The disease exhibits a striking heterogeneity in gene expression profiles and clinical outcomes, but its genetic causes remain to be fully defined. Through whole genome and exome sequencing, we characterized the genetic diversity of DLBCL. In all, we sequenced 73 DLBCL primary tumors (34 with matched normal DNA). Separately, we sequenced the exomes of 21 DLBCL cell lines. We identified 322 DLBCL cancer genes that were recurrently mutated in primary DLBCLs. We identified recurrent mutations implicating a number of known and not previously identified genes and pathways in DLBCL including those related to chromatin modification (ARID1A and MEF2B), NF-κB (CARD11 and TNFAIP3), PI3 kinase (PIK3CD, PIK3R1, and MTOR), B-cell lineage (IRF8, POU2F2, and GNA13), and WNT signaling (WIF1). We also experimentally validated a mutation in PIK3CD, a gene not previously implicated in lymphomas. The patterns of mutation demonstrated a classic long tail distribution with substantial variation of mutated genes from patient to patient and also between published studies. Thus, our study reveals the tremendous genetic heterogeneity that underlies lymphomas and highlights the need for personalized medicine approaches to treating these patients.
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438
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Ott G, Rosenwald A, Campo E. Understanding MYC-driven aggressive B-cell lymphomas: pathogenesis and classification. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2013; 2013:575-583. [PMID: 24319234 DOI: 10.1182/asheducation-2013.1.575] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
MYC is a potent oncogene initially identified as the target of the t(8;14)(q24;q32) chromosome translocation in Burkitt lymphoma. MYC gene alterations have been identified in other mature B-cell neoplasms that are usually associated with an aggressive clinical behavior. Most of these tumors originate in cells that do not normally express MYC protein. The oncogenic events leading to MYC up-regulation seem to overcome the inhibitory effect of physiological repressors such as BCL6 or BLIMP1. Aggressive lymphomas frequently carry additional oncogenic alterations that cooperate with MYC dysregulation, likely counteracting its proapoptotic function. The development of FISH probes and new reliable antibodies have facilitated the study of MYC gene alterations and protein expression in large series of patients, providing new clinical and biological perspectives regarding MYC dysregulation in aggressive lymphomas. MYC gene alterations in large B-cell lymphomas are frequently associated with BCL2 or BCL6 translocations conferring a very aggressive behavior. Conversely, MYC protein up-regulation may occur in tumors without apparent gene alterations, and its association with BCL2 overexpression also confers a poor prognosis. In this review, we integrate all of this new information and discuss perspectives, challenges, and open questions for the diagnosis and management of patients with MYC-driven aggressive B-cell lymphomas.
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Affiliation(s)
- German Ott
- 1Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
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439
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FISH in Burkitt lymphoma diagnosis: a single Romanian center experience. REV ROMANA MED LAB 2013. [DOI: 10.2478/rrlm-2013-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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440
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Gonzalez-Perez A, Jene-Sanz A, Lopez-Bigas N. The mutational landscape of chromatin regulatory factors across 4,623 tumor samples. Genome Biol 2013; 14:r106. [PMID: 24063517 PMCID: PMC4054018 DOI: 10.1186/gb-2013-14-9-r106] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 09/24/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chromatin regulatory factors are emerging as important genes in cancer development and are regarded as interesting candidates for novel targets for cancer treatment. However, we lack a comprehensive understanding of the role of this group of genes in different cancer types. RESULTS We have analyzed 4,623 tumor samples from thirteen anatomical sites to determine which chromatin regulatory factors are candidate drivers in these different sites. We identify 34 chromatin regulatory factors that are likely drivers in tumors from at least one site, all with relatively low mutational frequency. We also analyze the relative importance of mutations in this group of genes for the development of tumorigenesis in each site, and indifferent tumor types from the same site. CONCLUSIONS We find that, although tumors from all thirteen sites show mutations in likely driver chromatin regulatory factors, these are more prevalent in tumors arising from certain tissues. With the exception of hematopoietic, liver and kidney tumors, as a median, the mutated factors are less than one fifth of all mutated drivers across all sites analyzed. We also show that mutations in two of these genes, MLL and EP300, correlate with broad expression changes across cancer cell lines, thus presenting at least one mechanism through which these mutations could contribute to tumorigenesis in cells of the corresponding tissues.
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Affiliation(s)
- Abel Gonzalez-Perez
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
| | - Alba Jene-Sanz
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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441
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Martínez-Trillos A, Quesada V, Villamor N, Puente XS, López-Otín C, Campo E. Recurrent gene mutations in CLL. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 792:87-107. [PMID: 24014293 DOI: 10.1007/978-1-4614-8051-8_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing of whole genomes and exomes in chronic lymphocytic leukemia (CLL) has provided the first comprehensive view of somatic mutations in this disease. Subsequent studies have characterized the oncogenic pathways and clinical implications of a number of these mutations. The global number of somatic mutations per case is lower than those described in solid tumors but is in agreement with previous estimates of less than one mutation per megabase in hematological neoplasms. The number and pattern of somatic mutations differ in tumors with unmutated and mutated IGHV, extending at the genomic level the clinical differences observed in these two CLL subtypes. One of the striking conclusions of these studies has been the marked genetic heterogeneity of the disease, with a relatively large number of genes recurrently mutated at low frequency and only a few genes mutated in up to 10-15 % of the patients. The mutated genes tend to cluster in different pathways that include NOTCH1 signaling, RNA splicing and processing machinery, innate inflammatory response, Wnt signaling, and DNA damage and cell cycle control, among others. These results highlight the molecular heterogeneity of CLL and may provide new biomarkers and potential therapeutic targets for the diagnosis and management of the disease.
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Affiliation(s)
- Alejandra Martínez-Trillos
- Unidad de Hematopatologia, Departamento de Anatomía Patológica, Hospital Clinic, Institut d'Investigació Biomèdica August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
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