The diverse effects of complex chromosome rearrangements and chromothripsis in cancer development

Recent Results in Cancer Research

Volumn 200, Issue , 2015, Pages 165-193

  De Pagter, Mirjam S ^a   Kloosterman, Wigard P ^a  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

Chromosomal rearrangement; Chromothripsis; Mutation signatures; Next generation paired end sequencing

Indexed keywords

TUMOR MARKER;

AMINO ACID SUBSTITUTION; CANCER PROGNOSIS; CARCINOGENESIS; CARCINOGENICITY; CHROMOANASYNTHESIS; CHROMOPLEXY; CHROMOSOME REARRANGEMENT; CHROMOSOME SEGREGATION; CHROMOSOME TRANSLOCATION; CHROMOSOMES AND CHROMOSOMAL PHENOMENA; CHROMOTHRIPSIS; CHRONIC MYELOID LEUKEMIA; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; CYTOGENETICS; DNA DAMAGE; EPENDYMOMA; GENE AMPLIFICATION; GENE DELETION; GENE EXPRESSION REGULATION; GENE TARGETING; GENETIC ALGORITHM; GENETIC PREDISPOSITION; GENETIC VARIABILITY; GENOME; GLIOBLASTOMA; HETEROZYGOSITY LOSS; MICROARRAY ANALYSIS; MICRONUCLEUS; ONCOGENE; PREVALENCE; PRIORITY JOURNAL; PROSTATE CANCER; SINGLE NUCLEOTIDE POLYMORPHISM; TELOMERE HOMEOSTASIS;

EID: 84941927205     PISSN: 00800015     EISSN: 21976767     Source Type: Book Series    
DOI: 10.1007/978-3-319-20291-4_8     Document Type: Chapter

References (85)

1. Adhvaryu SG et al (1988) Complex translocation involving chromosomes #1, #9, and #22 in a patient with chronic myelogenous leukemia. Cancer Genet Cytogenet 32(2):277–280
2. Alexandrov LB et al (2013) Signatures of mutational processes in human cancer. Nature 500 (7463):415–421
3. Alves IT et al (2013) Gene fusions by chromothripsis of chromosome 5q in the VCaP prostate cancer cell line. Hum Genet 132(6):709–713
4. Baca SC et al (2013) Punctuated evolution of prostate cancer genomes. Cell 153(3):666–677
5. Bass AJ et al (2011) Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet 43(10):964–968
6. Bassaganyas L et al (2013) Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis. Leukemia 27(12):2376–2379
7. Bayani J et al (2003) Spectral karyotyping identifies recurrent complex rearrangements of chromosomes 8, 17, and 20 in osteosarcomas. Genes Chromosomes Cancer 36(1):7–16
8. Berger MF et al (2011) The genomic complexity of primary human prostate cancer. Nature 470 (7333):214–220
9. Beroukhim R et al (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci USA 104(50):20007–20012
10. Beroukhim R et al (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463(7283):899–905
11. Bignell GR et al (2007) Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res 17(9):1296–1303
12. Cai H et al (2014) Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genom 15:82
13. Campbell PJ et al (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40(6):722–729
14. Campbell PJ et al (2010) The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467(7319):1109–1113
15. Carter SL et al (2006) A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet 38(9):1043–1048
16. Carter SL et al (2012) Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol 30(5):413–421
17. Carvalho CM et al (2009) Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching. Hum Mol Genet 18(12):2188–2203
18. Chiang C et al (2012) Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet 44(4):390–397, S1
19. Conlin LK et al (2010) Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum Mol Genet 19(7):1263–1275
20. Cowell JK (1982) Double minutes and homogeneously staining regions: gene amplification in mammalian cells. Annu Rev Genet 16:21–59
21. Cowell JK, Miller OJ (1983) Occurrence and evolution of homogeneously staining regions may be due to breakage-fusion-bridge cycles following telomere loss. Chromosoma 88(3):216–221
22. Crasta K et al (2012) DNA breaks and chromosome pulverization from errors in mitosis. Nature 482(7383):53–58
23. Ding L et al (2010) Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464(7291):999–1005
24. Donley N, Thayer MJ (2013) DNA replication timing, genome stability and cancer: late and/or delayed DNA replication timing is associated with increased genomic instability. Semin Cancer Biol 23(2):80–89
25. Fitzgerald PH, Morris CM (1991) Complex chromosomal translocations in the Philadelphia chromosome leukemias. Serial translocations or a concerted genomic rearrangement? Cancer Genet Cytogenet 57(2):143–151
26. Forment JV, Kaidi A, Jackson SP (2012) Chromothripsis and cancer: causes and consequences of chromosome shattering. Nat Rev Cancer 12(10):663–670
27. Govind SK et al (2014) Shatter Proof: operational detection and quantification of chromothripsis. BMC Bioinformatics 15:78
28. Hastings PJ, Ira G, Lupski JR (2009) A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5(1):e1000327
29. Hatch EM et al (2013) Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell 154 (1):47–60
30. Hillmer AM et al (2011) Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res 21(5):665–675
31. Holland AJ, Cleveland DW (2012) Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements. Nat Med 18(11):1630–1638
32. Hoogstraat M et al (2014) Genomic and transcriptomic plasticity in treatment-naive ovarian cancer. Genome Res 24(2):200–211
33. Johnson RT, Rao PN (1970) Mammalian cell fusion: induction of premature chromosome condensation in interphase nuclei. Nature 226(5247):717–722
34. Kadam PR, Nanjangud GJ, Advani SH (1990) The occurrence of variant Ph translocations in chronic myeloid leukemia (CML): a report of six cases. Hematol Oncol 8(6):303–312
35. Kim TM et al (2013) Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res 23(2):217–227
36. Kloosterman WP, Cuppen E (2013) Chromothripsis in congenital disorders and cancer: similarities and differences. Curr Opin Cell Biol 25(3):341–348
37. Kloosterman WP et al (2011a) Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biol 12(10):R103
38. Kloosterman WP et al (2011b) Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum Mol Genet 20(10):1916–1924
39. Kloosterman WP et al (2012) Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Rep 1(6):648–655
40. Kloosterman WP, Koster J, Molenaar JJ (2014) Prevalence and clinical implications of chromothripsis in cancer genomes. Curr Opin Oncol 26(1):64–72
41. Korbel JO, Campbell PJ (2013) Criteria for inference of chromothripsis in cancer genomes. Cell 152(6):1226–1236
42. Korbel JO et al (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318(5849):420–426
43. Leary RJ et al (2010) Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med 2(20):20ra14
44. Leary RJ et al (2012) Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 4(162):162ra154
45. Li Y et al (2014) Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 508(7494):98–102
46. Liu P et al (2011) Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146(6):889–903
47. Magrangeas F et al (2011) Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients. Blood 118(3):675–678
48. Maher CA, Wilson RK (2012) Chromothripsis and human disease: piecing together the shattering process. Cell 148(1–2):29–32
49. Malhotra A et al (2013) Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res 23(5):762–776
50. Mardis ER (2009) New strategies and emerging technologies for massively parallel sequencing: applications in medical research. Genome Med 1(4):40
51. McBride DJ et al (2010) Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Genes Chromosomes Cancer 49(11):1062–1069
52. McBride DJ et al (2012) Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes. J Pathol 227(4):446–455
53. McEvoy J et al (2014) RB1 gene inactivation by chromothripsis in human retinoblastoma. Oncotarget 5(2):438–450
54. Mehine M et al (2013) Characterization of uterine leiomyomas by whole-genome sequencing. N Engl J Med 369(1):43–53
55. Mitelman F, Johansson B, Mertens F (2007) The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7(4):233–245
56. Molenaar JJ et al (2012) Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature 483(7391):589–593
57. Moore JK, Haber JE (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 16(5):2164–2173
58. Moorman AV et al (2007) Prognosis of children with acute lymphoblastic leukemia (ALL) and intrachromosomal amplification of chromosome 21 (iAMP21). Blood 109(6):2327–2330
59. Morin RD et al (2013) Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood 122(7):1256–1265
60. Morrison CD et al (2014) Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer. Proc Natl Acad Sci USA 111(6):E672–E681
61. Nik-Zainal S et al (2012) Mutational processes molding the genomes of 21 breast cancers. Cell 149(5):979–993
62. Nilbert M et al (1989) Complex karyotypic anomalies in a bizarre leiomyoma of the uterus. Genes Chromosomes Cancer 1(2):131–134
63. Nishi Y, Akiyama K, Korf BR (1992) Characterization of N-myc amplification in a human neuroblastoma cell line by clones isolated following the phenol emulsion reassociation technique and by hexagonal field gel electrophoresis. Mamm Genome 2(1):11–20
64. Northcott PA et al (2012) Subgroup-specific structural variation across 1000 medulloblastoma genomes. Nature 488(7409):49–56
65. Parker M et al (2014) C11orf95-RELA fusions drive oncogenic NF-kappaB signalling in ependymoma. Nature 506(7489):451–455
66. Rausch T et al (2012) Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell 148(1–2):59–71
67. Rosson D, Reddy EP (1988) Activation of the abl oncogene and its involvement in chromosomal translocations in human leukemia. Mutat Res 195(3):231–243
68. Rowley JD (1973) Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243(5405):290–293
69. Shimizu N (2009) Extrachromosomal double minutes and chromosomal homogeneously staining regions as probes for chromosome research. Cytogenet Genome Res 124(3–4):312–326
70. Shimizu N et al (2005) When, where and how the bridge breaks: anaphase bridge breakage plays a crucial role in gene amplification and HSR generation. Exp Cell Res 302(2):233–243
71. Shtivelman E et al (1985) Fused transcript of abl and bcr genes in chronic myelogenous leukaemia. Nature 315(6020):550–554
72. Solinas-Toldo S et al (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20(4):399–407
73. Sorzano CO et al (2013) Chromothripsis: breakage-fusion-bridge over and over again. Cell Cycle 12(13):2016–2023
74. Sperling K, Rao PN (1974) Mammalian cell fusion. V. Replication behaviour of heterochromatin as observed by premature chromosome condensation. Chromosoma 45(2):121–131
75. Stephens PJ et al (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462(7276):1005–1010
76. Stephens PJ et al (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144(1):27–40
77. Taylor BJ et al (2013) DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. E life 2:e00534
78. Terradas M et al (2009) DNA lesions sequestered in micronuclei induce a local defective-damage response. DNA Repair (Amst) 8(10):1225–1234
79. Vogelstein B et al (2013) Cancer genome landscapes. Science 339(6127):1546–1558
80. Yang L et al (2013) Diverse mechanisms of somatic structural variations in human cancer genomes. Cell 153(4):919–929
81. Zack TI et al (2013) Pan-cancer patterns of somatic copy number alteration. Nat Genet 45 (10):1134–1140
82. Zhang F et al (2009) The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat Genet 41(7):849–853
83. Zhang W et al (2011) DNA damage response is suppressed by the high cyclin-dependent kinase 1 activity in mitotic mammalian cells. J Biol Chem 286(41):35899–35905
84. Zhang CZ, Leibowitz ML, Pellman D (2013) Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements. Genes Dev 27(23):2513–2530
85. Zhang CZ et al (2015) Chromothripsis from DNA damage in micronuclei. Nature 522 (7555):179–184