Literature DB >> 27846393

Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.

Ana C Queirós1, Renée Beekman2, Roser Vilarrasa-Blasi1, Martí Duran-Ferrer1, Guillem Clot2, Angelika Merkel3, Emanuele Raineri3, Nuria Russiñol4, Giancarlo Castellano2, Sílvia Beà2, Alba Navarro2, Marta Kulis1, Núria Verdaguer-Dot4, Pedro Jares5, Anna Enjuanes6, María José Calasanz7, Anke Bergmann8, Inga Vater9, Itziar Salaverría2, Harmen J G van de Werken10, Wyndham H Wilson11, Avik Datta12, Paul Flicek12, Romina Royo13, Joost Martens14, Eva Giné15, Armando Lopez-Guillermo15, Hendrik G Stunnenberg14, Wolfram Klapper16, Christiane Pott17, Simon Heath3, Ivo G Gut3, Reiner Siebert9, Elías Campo18, José I Martín-Subero19.   

Abstract

We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B cell lineage. We identified two MCL subgroups, respectively carrying epigenetic imprints of germinal-center-inexperienced and germinal-center-experienced B cells, and we found that DNA methylation profiles during lymphomagenesis are largely influenced by the methylation dynamics in normal B cells. An integrative epigenomic approach revealed 10,504 differentially methylated regions in regulatory elements marked by H3K27ac in MCL primary cases, including a distant enhancer showing de novo looping to the MCL oncogene SOX11. Finally, we observed that the magnitude of DNA methylation changes per case is highly variable and serves as an independent prognostic factor for MCL outcome.
Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  ChIP-seq; DNA looping; DNA methylation; SOX11; chromatin; enhancer; epigenomics; lymphoma; mantle cell lymphoma; whole-genome bisulfite sequencing

Mesh：

Substances：

Year:  2016        PMID： 27846393      PMCID： PMC5805090          DOI： 10.1016/j.ccell.2016.09.014

Source DB:  PubMed          Journal:  Cancer Cell        ISSN： 1535-6108            Impact factor:   31.743


  52 in total

1.  Mantle cell lymphoma displays a homogenous methylation profile: a comparative analysis with chronic lymphocytic leukemia.

Authors:  Anna Margrét Halldórsdóttir; Meena Kanduri; Millaray Marincevic; Larry Mansouri; Anders Isaksson; Hanna Göransson; Tomas Axelsson; Prasoon Agarwal; Helena Jernberg-Wiklund; Kostas Stamatopoulos; Birgitta Sander; Hans Ehrencrona; Richard Rosenquist
Journal:  Am J Hematol       Date:  2012-02-28       Impact factor: 10.047

2.  Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells.

Authors:  Zohar Shipony; Zohar Mukamel; Netta Mendelson Cohen; Gilad Landan; Elad Chomsky; Shlomit Reich Zeliger; Yael Chagit Fried; Elena Ainbinder; Nir Friedman; Amos Tanay
Journal:  Nature       Date:  2014-07-13       Impact factor: 49.962

3.  Prognostic impact of epigenetic classification in chronic lymphocytic leukemia: The case of subset #2.

Authors:  Sujata Bhoi; Viktor Ljungström; Panagiotis Baliakas; Mattias Mattsson; Karin E Smedby; Gunnar Juliusson; Richard Rosenquist; Larry Mansouri
Journal:  Epigenetics       Date:  2016-04-29       Impact factor: 4.528

4.  Chromatin organization is a major influence on regional mutation rates in human cancer cells.

Authors:  Benjamin Schuster-Böckler; Ben Lehner
Journal:  Nature       Date:  2012-08-23       Impact factor: 49.962

5.  Evidence for an instructive mechanism of de novo methylation in cancer cells.

Authors:  Ilana Keshet; Yeshayahu Schlesinger; Shlomit Farkash; Eyal Rand; Merav Hecht; Eran Segal; Eli Pikarski; Richard A Young; Alain Niveleau; Howard Cedar; Itamar Simon
Journal:  Nat Genet       Date:  2006-02       Impact factor: 38.330

6.  Identification and characterization of circulating human transitional B cells.

Authors:  Gary P Sims; Rachel Ettinger; Yuko Shirota; Cheryl H Yarboro; Gabor G Illei; Peter E Lipsky
Journal:  Blood       Date:  2005-02-08       Impact factor: 22.113

7.  Molecular subsets of mantle cell lymphoma defined by the IGHV mutational status and SOX11 expression have distinct biologic and clinical features.

Authors:  Alba Navarro; Guillem Clot; Cristina Royo; Pedro Jares; Anastasia Hadzidimitriou; Andreas Agathangelidis; Vasilis Bikos; Nikos Darzentas; Theodora Papadaki; Itziar Salaverria; Magda Pinyol; Xavier Puig; Jara Palomero; Maria Carmela Vegliante; Virgina Amador; Alejandra Martinez-Trillos; Lenka Stefancikova; Adrian Wiestner; Wyndham Wilson; Christiane Pott; Maria Jose Calasanz; Nicola Trim; Wendy Erber; Birgitta Sander; German Ott; Andreas Rosenwald; Dolors Colomer; Eva Giné; Reiner Siebert; Armando Lopez-Guillermo; Kostas Stamatopoulos; Sílvia Beà; Elías Campo
Journal:  Cancer Res       Date:  2012-08-20       Impact factor: 12.701

8.  Genome-wide methylation analyses identify a subset of mantle cell lymphoma with a high number of methylated CpGs and aggressive clinicopathological features.

Authors:  Anna Enjuanes; Robert Albero; Guillem Clot; Alba Navarro; Sílvia Beà; Magda Pinyol; José I Martín-Subero; Wolfram Klapper; Louis M Staudt; Elaine S Jaffe; Lisa Rimsza; Rita M Braziel; Jan Delabie; James R Cook; Raymond R Tubbs; Randy Gascoyne; Joseph M Connors; Dennis D Weisenburger; Timothy C Greiner; Wing-Chung Chan; Armando López-Guillermo; Andreas Rosenwald; German Ott; Elías Campo; Pedro Jares
Journal:  Int J Cancer       Date:  2013-07-16       Impact factor: 7.396

9.  BLUEPRINT to decode the epigenetic signature written in blood.

Authors:  David Adams; Lucia Altucci; Stylianos E Antonarakis; Juan Ballesteros; Stephan Beck; Adrian Bird; Christoph Bock; Bernhard Boehm; Elias Campo; Andrea Caricasole; Fredrik Dahl; Emmanouil T Dermitzakis; Tariq Enver; Manel Esteller; Xavier Estivill; Anne Ferguson-Smith; Jude Fitzgibbon; Paul Flicek; Claudia Giehl; Thomas Graf; Frank Grosveld; Roderic Guigo; Ivo Gut; Kristian Helin; Jonas Jarvius; Ralf Küppers; Hans Lehrach; Thomas Lengauer; Åke Lernmark; David Leslie; Markus Loeffler; Elizabeth Macintyre; Antonello Mai; Joost H A Martens; Saverio Minucci; Willem H Ouwehand; Pier Giuseppe Pelicci; Hèléne Pendeville; Bo Porse; Vardhman Rakyan; Wolf Reik; Martin Schrappe; Dirk Schübeler; Martin Seifert; Reiner Siebert; David Simmons; Nicole Soranzo; Salvatore Spicuglia; Michael Stratton; Hendrik G Stunnenberg; Amos Tanay; David Torrents; Alfonso Valencia; Edo Vellenga; Martin Vingron; Jörn Walter; Spike Willcocks
Journal:  Nat Biotechnol       Date:  2012-03-07       Impact factor: 54.908

10.  Increased methylation variation in epigenetic domains across cancer types.

Authors:  Kasper Daniel Hansen; Winston Timp; Héctor Corrada Bravo; Sarven Sabunciyan; Benjamin Langmead; Oliver G McDonald; Bo Wen; Hao Wu; Yun Liu; Dinh Diep; Eirikur Briem; Kun Zhang; Rafael A Irizarry; Andrew P Feinberg
Journal:  Nat Genet       Date:  2011-06-26       Impact factor: 38.330
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  35 in total

1.  Molecular signatures for CCN1, p21 and p27 in progressive mantle cell lymphoma.

Authors:  Afak Rasheed Salman Zaidi; Sadie Dresman; Charlotte Burt; Simon Rule; Lynn McCallum
Journal:  J Cell Commun Signal       Date:  2018-11-21       Impact factor: 5.782

2.  Molecular profiling and management of mantle cell lymphoma.

Authors:  Jia Ruan
Journal:  Hematology Am Soc Hematol Educ Program       Date:  2019-12-06

3.  Genomic and epigenomic insights into the origin, pathogenesis, and clinical behavior of mantle cell lymphoma subtypes.

Authors:  Ferran Nadeu; David Martin-Garcia; Guillem Clot; Ander Díaz-Navarro; Martí Duran-Ferrer; Alba Navarro; Roser Vilarrasa-Blasi; Marta Kulis; Romina Royo; Jesús Gutiérrez-Abril; Rafael Valdés-Mas; Cristina López; Vicente Chapaprieta; Montserrat Puiggros; Giancarlo Castellano; Dolors Costa; Marta Aymerich; Pedro Jares; Blanca Espinet; Ana Muntañola; Inmaculada Ribera-Cortada; Reiner Siebert; Dolors Colomer; David Torrents; Eva Gine; Armando López-Guillermo; Ralf Küppers; Jose I Martin-Subero; Xose S Puente; Sílvia Beà; Elias Campo
Journal:  Blood       Date:  2020-09-17       Impact factor: 22.113

4.  Genome-wide promoter methylation of hairy cell leukemia.

Authors:  Alberto J Arribas; Andrea Rinaldi; Giorgia Chiodin; Ivo Kwee; Afua Adjeiwaa Mensah; Luciano Cascione; Davide Rossi; Meena Kanduri; Richard Rosenquist; Emanuele Zucca; Peter W Johnson; Gianluca Gaidano; Christopher C Oakes; Francesco Bertoni; Francesco Forconi
Journal:  Blood Adv       Date:  2019-02-12

Review 5.  Molecular Pathogenesis of Mantle Cell Lymphoma.

Authors:  Alba Navarro; Sílvia Beà; Pedro Jares; Elías Campo
Journal:  Hematol Oncol Clin North Am       Date:  2020-07-22       Impact factor: 3.722

Review 6.  Epigenetic dynamics in normal and malignant B cells: die a hero or live to become a villain.

Authors:  Jared M Andrews; Jacqueline E Payton
Journal:  Curr Opin Immunol       Date:  2018-10-17       Impact factor: 7.486

7.  SOX11 augments BCR signaling to drive MCL-like tumor development.

Authors:  Pei-Yu Kuo; Shashidhar S Jatiani; Adeeb H Rahman; Donna Edwards; Zewei Jiang; Katya Ahr; Deepak Perumal; Violetta V Leshchenko; Joshua Brody; Rita Shaknovich; B Hilda Ye; Samir Parekh
Journal:  Blood       Date:  2018-04-03       Impact factor: 22.113

8.  Cyclin D1 overexpression induces global transcriptional downregulation in lymphoid neoplasms.

Authors:  Robert Albero; Anna Enjuanes; Santiago Demajo; Giancarlo Castellano; Magda Pinyol; Noelia García; Cristina Capdevila; Guillem Clot; Helena Suárez-Cisneros; Mariko Shimada; Kennosuke Karube; Mónica López-Guerra; Dolors Colomer; Sílvia Beà; José Ignacio Martin-Subero; Elías Campo; Pedro Jares
Journal:  J Clin Invest       Date:  2018-08-20       Impact factor: 14.808

9.  The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.

Authors:  Renée Beekman; Vicente Chapaprieta; Núria Russiñol; Roser Vilarrasa-Blasi; Núria Verdaguer-Dot; Joost H A Martens; Martí Duran-Ferrer; Marta Kulis; François Serra; Biola M Javierre; Steven W Wingett; Guillem Clot; Ana C Queirós; Giancarlo Castellano; Julie Blanc; Marta Gut; Angelika Merkel; Simon Heath; Anna Vlasova; Sebastian Ullrich; Emilio Palumbo; Anna Enjuanes; David Martín-García; Sílvia Beà; Magda Pinyol; Marta Aymerich; Romina Royo; Montserrat Puiggros; David Torrents; Avik Datta; Ernesto Lowy; Myrto Kostadima; Maša Roller; Laura Clarke; Paul Flicek; Xabier Agirre; Felipe Prosper; Tycho Baumann; Julio Delgado; Armando López-Guillermo; Peter Fraser; Marie-Laure Yaspo; Roderic Guigó; Reiner Siebert; Marc A Martí-Renom; Xose S Puente; Carlos López-Otín; Ivo Gut; Hendrik G Stunnenberg; Elias Campo; Jose I Martin-Subero
Journal:  Nat Med       Date:  2018-05-21       Impact factor: 53.440

10.  Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM.

Authors:  Jerry Fong; Jacob R Gardner; Jared M Andrews; Amanda F Cashen; Jacqueline E Payton; Kilian Q Weinberger; John R Edwards
Journal:  Nucleic Acids Res       Date:  2021-09-20       Impact factor: 16.971
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