XHypermutation of the inactive X chromosome is a frequent event in cancer

Cell

Volumn 155, Issue 3, 2013, Pages 567-

  Jäger, Natalie ^a   Schlesner, Matthias ^a   Jones, David T W ^a   Raffel, Simon ^a,b   Mallm, Jan Philipp ^a   Junge, Kristin M ^c   Weichenhan, Dieter ^a   Bauer, Tobias ^a   Ishaque, Naveed ^a   Kool, Marcel ^a   Northcott, Paul A ^a   Korshunov, Andrey ^a,d   Drews, Ruben M ^a   Koster, Jan ^e   Versteeg, Rogier ^e   Richter, Julia ^f   Hummel, Michael ^g   Mack, Stephen C ^h   Taylor, Michael D ^h   Witt, Hendrik ^a,i   Swartman, Benedict ^j   Schulte Bockholt, Dietrich ^j   Sultan, Marc ^k   Yaspo, Marie Laure ^k   Lehrach, Hans ^k   Hutter, Barbara ^a   Brors, Benedikt ^a   Wolf, Stephan ^a   Plass, Christoph ^a   Siebert, Reiner ^f   Trumpp, Andreas ^a,b   Rippe, Karsten ^a   Lehmann, Irina ^c   Lichter, Peter ^a   Pfister, Stefan M ^a,i   Eils, Roland ^a,d   more..

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI STEM)   (Germany)

^c HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^d UNIVERSITY OF HEIDELBERG   (Germany)

^e UNIVERSITY OF AMSTERDAM   (Netherlands)

^f UNIVERSITY OF KIEL   (Germany)

^g CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^h HOSPITAL FOR SICK CHILDREN   (Canada)

ⁱ UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^j BG Trauma Center   (Germany)

^k MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; CARCINOGENESIS; CONTROLLED STUDY; FEMALE; GENE SEQUENCE; HUMAN; HUMAN CELL; MALE; NEOPLASM; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SOMATIC HYPERMUTATION; SOMATIC MUTATION; X CHROMOSOME;

EID: 84886784734     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.09.042     Document Type: Article

References (40)

1. T.S. Barakat, and J. Gribnau X chromosome inactivation in the cycle of life Development 139 2012 2085 2089
2. A.J. Bass, M.S. Lawrence, L.E. Brace, A.H. Ramos, Y. Drier, K. Cibulskis, C. Sougnez, D. Voet, G. Saksena, and A. Sivachenko Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion Nat. Genet. 43 2011 964 968
3. A.C. Bester, M. Roniger, Y.S. Oren, M.M. Im, D. Sarni, M. Chaoat, A. Bensimon, G. Zamir, D.S. Shewach, and B. Kerem Nucleotide deficiency promotes genomic instability in early stages of cancer development Cell 145 2011 435 446
4. C.J. Brown, B.D. Hendrich, J.L. Rupert, R.G. Lafrenière, Y. Xing, J. Lawrence, and H.F. Willard The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus Cell 71 1992 527 542
5. R.A. Burrell, S.E. McClelland, D. Endesfelder, P. Groth, M.-C. Weller, N. Shaikh, E. Domingo, N. Kanu, S.M. Dewhurst, and E. Gronroos Replication stress links structural and numerical cancer chromosomal instability Nature 494 2013 492 496
6. L. Carrel, and H.F. Willard X-inactivation profile reveals extensive variability in X-linked gene expression in females Nature 434 2005 400 404
7. M.A. Chapman, M.S. Lawrence, J.J. Keats, K. Cibulskis, C. Sougnez, A.C. Schinzel, C.L. Harview, J.-P. Brunet, G.J. Ahmann, and M. Adli Initial genome sequencing and analysis of multiple myeloma Nature 471 2011 467 472
8. J. Chow, and E. Heard X inactivation and the complexities of silencing a sex chromosome Curr. Opin. Cell Biol. 21 2009 359 366
9. H. Ellegren, N.G.C. Smith, and M.T. Webster Mutation rate variation in the mammalian genome Curr. Opin. Genet. Dev. 13 2003 562 568
10. C. Greenman, P. Stephens, R. Smith, G.L. Dalgliesh, C. Hunter, G. Bignell, H. Davies, J. Teague, A. Butler, and C. Stevens Patterns of somatic mutation in human cancer genomes Nature 446 2007 153 158
11. R.S. Hansen, T.K. Canfield, A.D. Fjeld, and S.M. Gartler Role of late replication timing in the silencing of X-linked genes Hum. Mol. Genet. 5 1996 1345 1353
12. A. Hodgkinson, and A. Eyre-Walker Variation in the mutation rate across mammalian genomes Nat. Rev. Genet. 12 2011 756 766
13. D.T.W. Jones, N. Jäger, M. Kool, T. Zichner, B. Hutter, M. Sultan, Y.-J. Cho, T.J. Pugh, V. Hovestadt, and A.M. Stütz Dissecting the genomic complexity underlying medulloblastoma Nature 488 2012 100 105
14. D.T.W. Jones, B. Hutter, N. Jäger, A. Korshunov, M. Kool, H.-J. Warnatz, T. Zichner, S.R. Lambert, M. Ryzhova, D.A.K. Quang International Cancer Genome Consortium PedBrain Tumor Project Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma Nat. Genet. 45 2013 927 932
15. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
16. L. Liu, S. De, and F. Michor DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes Nat Commun. 4 2013 1502
17. M.F. Lyon Gene action in the X-chromosome of the mouse (Mus musculus L.) Nature 190 1961 372 373
18. C.M. Malcom, G.J. Wyckoff, and B.T. Lahn Genic mutation rates in mammals: local similarity, chromosomal heterogeneity, and X-versus-autosome disparity Mol. Biol. Evol. 20 2003 1633 1641
19. F. Mietton, A.K. Sengupta, A. Molla, G. Picchi, S. Barral, L. Heliot, T. Grange, A. Wutz, and S. Dimitrov Weak but uniform enrichment of the histone variant macroH2A1 along the inactive X chromosome Mol. Cell. Biol. 29 2009 150 156
20. J.J. Molenaar, J. Koster, D.A. Zwijnenburg, P. van Sluis, L.J. Valentijn, I. van der Ploeg, M. Hamdi, J. van Nes, B.A. Westerman, and J. van Arkel Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes Nature 483 2012 589 593
21. A. Morishima, M.M. Grumbach, and J.H. Taylor Asynchronous duplication of human chromosomes and the origin of sex chromatin Proc. Natl. Acad. Sci. USA 48 1962 756 763
22. S. Nik-Zainal, L.B. Alexandrov, D.C. Wedge, P. Van Loo, C.D. Greenman, K. Raine, D. Jones, J. Hinton, J. Marshall, L.A. Stebbings Breast Cancer Working Group of the International Cancer Genome Consortium Mutational processes molding the genomes of 21 breast cancers Cell 149 2012 979 993
23. P.A. Northcott, D.T.W. Jones, M. Kool, G.W. Robinson, R.J. Gilbertson, Y.-J. Cho, S.L. Pomeroy, A. Korshunov, P. Lichter, M.D. Taylor, and S.M. Pfister Medulloblastomics: the end of the beginning Nat. Rev. Cancer 12 2012 818 834
24. K. Plath, S. Mlynarczyk-Evans, D.A. Nusinow, and B. Panning Xist RNA and the mechanism of X chromosome inactivation Annu. Rev. Genet. 36 2002 233 278
25. X.S. Puente, M. Pinyol, V. Quesada, L. Conde, G.R. Ordóñez, N. Villamor, G. Escaramis, P. Jares, S. Beà, and M. González- Díaz Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia Nature 475 2011 101 105
26. J. Richter, M. Schlesner, S. Hoffmann, M. Kreuz, E. Leich, B. Burkhardt, M. Rosolowski, O. Ammerpohl, R. Wagener, S.H. Bernhart ICGC MMML-Seq Project Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing Nat. Genet. 44 2012 1316 1320
27. B. Schuster-Böckler, and B. Lehner Chromatin organization is a major influence on regional mutation rates in human cancer cells Nature 488 2012 504 507
28. J.A. Stamatoyannopoulos, I. Adzhubei, R.E. Thurman, G.V. Kryukov, S.M. Mirkin, and S.R. Sunyaev Human mutation rate associated with DNA replication timing Nat. Genet. 41 2009 393 395
29. M.R. Stratton, P.J. Campbell, and P.A. Futreal The cancer genome Nature 458 2009 719 724
30. F. Tort, J. Bartkova, M. Sehested, T. Orntoft, J. Lukas, and J. Bartek Retinoblastoma pathway defects show differential ability to activate the constitutive DNA damage response in human tumorigenesis Cancer Res. 66 2006 10258 10263
31. J. Weischenfeldt, R. Simon, L. Feuerbach, K. Schlangen, D. Weichenhan, S. Minner, D. Wuttig, H.-J. Warnatz, H. Stehr, and T. Rausch Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer Cancer Cell 23 2013 159 170
32. K. Weisse, I. Lehmann, D. Heroux, T. Kohajda, G. Herberth, S. Röder, M. von Bergen, M. Borte, and J. Denburg The LINA cohort: indoor chemical exposure, circulating eosinophil/basophil (Eo/B) progenitors and early life skin manifestations Clin. Exp. Allergy 42 2012 1337 1346
33. J.S. Welch, T.J. Ley, D.C. Link, C.A. Miller, D.E. Larson, D.C. Koboldt, L.D. Wartman, T.L. Lamprecht, F. Liu, and J. Xia The origin and evolution of mutations in acute myeloid leukemia Cell 150 2012 264 278
34. J. Zhang, C.A. Benavente, J. McEvoy, J. Flores-Otero, L. Ding, X. Chen, A. Ulyanov, G. Wu, M. Wilson, and J. Wang A novel retinoblastoma therapy from genomic and epigenetic analyses Nature 481 2012 329 334
35. A. Adey, and J. Shendure Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing Genome Res. 22 2012 1139 1143
36. R.S. Hansen, S. Thomas, R. Sandstrom, T.K. Canfield, R.E. Thurman, M. Weaver, M.O. Dorschner, S.M. Gartler, and J.A. Stamatoyannopoulos Sequencing newly replicated DNA reveals widespread plasticity in human replication timing Proc. Natl. Acad. Sci. USA 107 2010 139 144
37. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
38. A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
39. Q. Wang, L. Gu, A. Adey, B. Radlwimmer, W. Wang, V. Hovestadt, M. Bähr, S. Wolf, J. Shendure, and R. Eils Tagmentation-based whole-genome bisulfite sequencing Nat. Protoc. 8 2013 2022 2032
40. Y. Zhang, T. Liu, C.A. Meyer, J. Eeckhoute, D.S. Johnson, B.E. Bernstein, C. Nusbaum, R.M. Myers, M. Brown, W. Li, and X.S. Liu Model-based analysis of ChIP-Seq (MACS) Genome Biol. 9 2008 R137