The Architecture and Evolution of Cancer Neochromosomes

Cancer Cell

Volumn 26, Issue 5, 2014, Pages 653-667

  Garsed, Dale W ^a,c,h   Marshall, Owen J ^e,m   Corbin, Vincent D A ^a,b,c   Hsu, Arthur ^b   DiStefano, Leon ^b   Schröder, Jan ^b,c   Li, Jason ^a   Feng, Zhi Ping ^b,c   Kim, Bo W ^e   Kowarsky, Mark ^b   Lansdell, Ben ^b   Brookwell, Ross ^f   Myklebost, Ola ⁱ   Meza Zepeda, Leonardo ⁱ   Holloway, Andrew J ^a   Pedeutour, Florence ^g   Choo, K H Andy ^e   Damore, Michael A ^j   Deans, Andrew J ^k   Papenfuss, Anthony T ^a,b,c,d   Thomas, David M ^a,c,l   more..

^a PETER MACCALLUM CANCER CENTRE   (Australia)

^b WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d UNIVERSITY OF MELBOURNE   (Australia)

^e ROYAL CHILDREN'S HOSPITAL   (Australia)

^f SULLIVAN NICOLAIDES PATHOLOGY   (Australia)

^g UNIVERSITY HOSPITAL OF NICE   (France)

^h UNIVERSITY OF MELBOURNE   (Australia)

ⁱ OSLO UNIVERSITY HOSPITAL   (Norway)

^j AMGEN INC   (United States)

^k ST VINCENT'S INSTITUTE OF MEDICAL RESEARCH   (Australia)

^l GARVAN INSTITUTE OF MEDICAL RESEARCH   (Australia)

^m WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CENTROMERE PROTEIN A;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CENTROMERE; CHROMOSOMAL INSTABILITY; CHROMOSOME; CHROMOSOME 12; CHROMOSOME 12Q; CHROMOSOME 17; CHROMOSOME 21; CHROMOSOME 22; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME 5P; CHROMOSOME 7; CHROMOSOME 7P; CHROMOSOME ANALYSIS; CONTROLLED STUDY; COPY NUMBER VARIATION; CYTOGENETICS; DERMATOFIBROSARCOMA PROTUBERANS; EPIGENETICS; FLUORESCENCE ACTIVATED CELL SORTING; GENE AMPLIFICATION; GENE MUTATION; GENE OVEREXPRESSION; GENE REARRANGEMENT; GENE SILENCING; GLIOBLASTOMA; HUMAN; HUMAN CELL; INDEL MUTATION; LIFE HISTORY; LIPOSARCOMA; METAPHASE; NEOCHROMOSOME; NEOPLASM; ONCOGENE; OSTEOSARCOMA; PRIMARY TUMOR; PROMOTER REGION; SUPERNUMERARY CHROMOSOME; TELOMERE; AGED; BIOLOGICAL MODEL; CARCINOGENESIS; CHROMOSOME ABERRATION; FEMALE; GENE TRANSLOCATION; GENETICS; HUMAN CHROMOSOME; MUTAGENESIS; PATHOLOGY; RETROPERITONEAL TUMOR; TUMOR CELL LINE;

AGED; CARCINOGENESIS; CELL LINE, TUMOR; CENTROMERE; CHROMOSOME ABERRATIONS; CHROMOSOMES, HUMAN; FEMALE; HUMANS; LIPOSARCOMA; MODELS, GENETIC; MUTAGENESIS; ONCOGENES; RETROPERITONEAL NEOPLASMS; TRANSLOCATION, GENETIC;

EID: 84912101773     PISSN: 15356108     EISSN: 18783686     Source Type: Journal    
DOI: 10.1016/j.ccell.2014.09.010     Document Type: Article

References (45)

1. Agudo D., Gómez-Esquer F., Martínez-Arribas F., Núñez-Villar M.J., Pollán M., Schneider J. Nup88 mRNA overexpression is associated with high aggressiveness of breast cancer. Int. J. Cancer 2004, 109:717-720.
2. Amor D.J., Bentley K., Ryan J., Perry J., Wong L., Slater H., Choo K.H. Human centromere repositioning "in progress". Proc. Natl. Acad. Sci. USA 2004, 101:6542-6547.
3. Baird D.M., Farr C.J. The organization and function of chromosomes. EMBO Rep. 2006, 7:372-376.
4. Banerjee H.N., Gibbs J., Jordan T., Blackshear M. Depletion of a single nucleoporin, Nup107, induces apoptosis in eukaryotic cells. Mol. Cell. Biochem. 2010, 343:21-25.
5. Barretina J., Taylor B.S., Banerji S., Ramos A.H., Lagos-Quintana M., Decarolis P.L., Shah K., Socci N.D., Weir B.A., Ho A., et al. Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat. Genet. 2010, 42:715-721.
6. Bignell G.R., Santarius T., Pole J.C., Butler A.P., Perry J., Pleasance E., Greenman C., Menzies A., Taylor S., Edkins S., et al. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res. 2007, 17:1296-1303.
7. Buoen L.C., Brand K.G. Double-minute chromosomes in plastic film-induced sarcomas in mice. Naturwissenschaften 1968, 55:135-136.
8. Cahilly-Snyder L., Yang-Feng T., Francke U., George D.L. Molecular analysis and chromosomal mapping of amplified genes isolated from a transformed mouse 3T3 cell line. Somat. Cell Mol. Genet. 1987, 13:235-244.
9. Dahlback H.S., Brandal P., Meling T.R., Gorunova L., Scheie D., Heim S. Genomic aberrations in 80 cases of primary glioblastoma multiforme: Pathogenetic heterogeneity and putative cytogenetic pathways. Genes Chromosomes Cancer 2009, 48:908-924.
10. Forus A., Larramendy M.L., Meza-Zepeda L.A., Bjerkehagen B., Godager L.H., Dahlberg A.B., Saeter G., Knuutila S., Myklebost O. Dedifferentiation of a well-differentiated liposarcoma to a highly malignant metastatic osteosarcoma: amplification of 12q14 at all stages and gain of1q22-q24 associated with metastases. Cancer Genet. Cytogenet. 2001, 125:100-111.
11. Garsed D.W., Holloway A.J., Thomas D.M. Cancer-associated neochromosomes: a novel mechanism of oncogenesis. BioEssays 2009, 31:1191-1200.
12. Gisselsson D., Pettersson L., Höglund M., Heidenblad M., Gorunova L., Wiegant J., Mertens F., Dal Cin P., Mitelman F., Mandahl N. Chromosomal breakage-fusion-bridge events cause genetic intratumor heterogeneity. Proc. Natl. Acad. Sci. USA 2000, 97:5357-5362.
13. Italiano A., Bianchini L., Keslair F., Bonnafous S., Cardot-Leccia N., Coindre J.M., Dumollard J.M., Hofman P., Leroux A., Mainguené C., et al. HMGA2 is the partner of MDM2 in well-differentiated and dedifferentiated liposarcomas whereas CDK4 belongs to a distinct inconsistent amplicon. Int. J. Cancer 2008, 122:2233-2241.
14. Kansara M., Tsang M., Kodjabachian L., Sims N.A., Trivett M.K., Ehrich M., Dobrovic A., Slavin J., Choong P.F., Simmons P.J., et al. Wnt inhibitory factor 1 is epigenetically silenced in human osteosarcoma, and targeted disruption accelerates osteosarcomagenesis in mice. J.Clin. Invest. 2009, 119:837-851.
15. Korbel J.O., Campbell P.J. Criteria for inference of chromothripsis in cancer genomes. Cell 2013, 152:1226-1236.
16. Levan A., Levan G., Mandahl N. A new chromosome type replacing the double minutes in a mouse tumor. Cytogenet. Cell Genet. 1978, 20:12-23.
17. Li Y., Schwab C., Ryan S.L., Papaemmanuil E., Robinson H.M., Jacobs P., Moorman A.V., Dyer S., Borrow J., Griffiths M., et al. Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 2014, 508:98-102.
18. Liehr T., Mrasek K., Weise A., Dufke A., Rodríguez L., Martínez Guardia N., Sanchís A., Vermeesch J.R., Ramel C., Polityko A., et al. Small supernumerary marker chromosomes-progress towards a genotype-phenotype correlation. Cytogenet. Genome Res. 2006, 112:23-34.
19. Lo A.W., Sabatier L., Fouladi B., Pottier G., Ricoul M., Murnane J.P. DNA amplification by breakage/fusion/bridge cycles initiated by spontaneous telomere loss in a human cancer cell line. Neoplasia 2002, 4:531-538.
20. Lo A.W., Sprung C.N., Fouladi B., Pedram M., Sabatier L., Ricoul M., Reynolds G.E., Murnane J.P. Chromosome instability as a result of double-strand breaks near telomeres in mouse embryonic stem cells. Mol. Cell. Biol. 2002, 22:4836-4850.
21. Marshall O.J., Chueh A.C., Wong L.H., Choo K.H. Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution. Am. J. Hum. Genet. 2008, 82:261-282.
22. Marshall O.J., Marshall A.T., Choo K.H. Three-dimensional localization of CENP-A suggests a complex higher order structure of centromeric chromatin. J.Cell Biol. 2008, 183:1193-1202.
23. McClintock B. The stability of broken ends of chromosomes in Zea Mays. Genetics 1941, 26:234-282.
24. Meltzer P.S., Guan X.Y., Trent J.M. Telomere capture stabilizes chromosome breakage. Nat. Genet. 1993, 4:252-255.
25. Nagai S., Dubrana K., Tsai-Pflugfelder M., Davidson M.B., Roberts T.M., Brown G.W., Varela E., Hediger F., Gasser S.M., Krogan N.J. Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science 2008, 322:597-602.
26. Nakayama R., Nemoto T., Takahashi H., Ohta T., Kawai A., Seki K., Yoshida T., Toyama Y., Ichikawa H., Hasegawa T. Gene expression analysis of soft tissue sarcomas: characterization and reclassification of malignant fibrous histiocytoma. Mod. Pathol. 2007, 20:749-759.
27. Nik-Zainal S., Alexandrov L.B., Wedge D.C., Van Loo P., Greenman C.D., Raine K., Jones D., Hinton J., Marshall J., Stebbings L.A., et al. Mutational processes molding the genomes of 21 breast cancers. Cell 2012, 149:979-993. Breast Cancer Working Group of the International Cancer Genome Consortium.
28. Nilsson M., Meza-Zepeda L.A., Mertens F., Forus A., Myklebost O., Mandahl N. Amplification of chromosome 1 sequences in lipomatous tumors and other sarcomas. Int. J. Cancer 2004, 109:363-369.
29. Nord K.H., Macchia G., Tayebwa J., Nilsson J., Vult von Steyern F., Brosjo O., Mandahl N., Mertens F. Integrative genome and transcriptome analyses reveal two distinct types of ring chromosome in soft tissue sarcomas. Hum. Mol. Genet. 2013, 23:878-888.
30. Palancade B., Liu X., Garcia-Rubio M., Aguilera A., Zhao X., Doye V. Nucleoporins prevent DNA damage accumulation by modulating Ulp1-dependent sumoylation processes. Mol. Biol. Cell 2007, 18:2912-2923.
31. Park J.H., Roeder R.G. GAS41 is required for repression of thep53 tumor suppressor pathway during normal cellular proliferation. Mol. Cell. Biol. 2006, 26:4006-4016.
32. Paux E., Sourdille P., Salse J., Saintenac C., Choulet F., Leroy P., Korol A., Michalak M., Kianian S., Spielmeyer W., et al. A physical map of the 1-gigabase bread wheat chromosome 3B. Science 2008, 322:101-104.
33. Pedeutour F., Suijkerbuijk R.F., Forus A., Van Gaal J., Van de Klundert W., Coindre J.M., Nicolo G., Collin F., Van Haelst U., Huffermann K., et al. Complex composition and co-amplification of SAS and MDM2 in ringand giant rod marker chromosomes in well-differentiated liposarcoma. Genes Chromosomes Cancer 1994, 10:85-94.
34. Pedeutour F., Maire G., Pierron A., Thomas D.M., Garsed D.W., Bianchini L., Duranton-Tanneur V., Cortes-Maurel A., Italiano A., Squire J.A., et al. A newly characterized human well-differentiated liposarcoma cell line contains amplifications of the 12q12-21 and 10p11-14 regions. Virchows Arch. 2012, 461:67-78.
35. Persson F., Olofsson A., Sjögren H., Chebbo N., Nilsson B., Stenman G., Aman P. Characterization of the 12q amplicons by high-resolution, oligonucleotide array CGH and expression analyses of a novel liposarcoma cell line. Cancer Lett. 2008, 260:37-47.
36. Pilotti S., Della Torre G., Lavarino C., Sozzi G., Minoletti F., Vergani B., Azzarelli A., Rilke F., Pierotti M.A. Molecular abnormalities in liposarcoma: role of MDM2 and CDK4-containing amplicons at 12q13-22. J.Pathol. 1998, 185:188-190.
37. Sanborn J.Z., Salama S.R., Grifford M., Brennan C.W., Mikkelsen T., Jhanwar S., Katzman S., Chin L., Haussler D. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Res. 2013, 73:6036-6045.
38. Sirvent N., Forus A., Lescaut W., Burel F., Benzaken S., Chazal M., Bourgeon A., Vermeesch J.R., Myklebost O., Turc-Carel C., et al. Characterization of centromere alterations in liposarcomas. Genes Chromosomes Cancer 2000, 29:117-129.
39. Snyder E.L., Sandstrom D.J., Law K., Fiore C., Sicinska E., Brito J., Bailey D., Fletcher J.A., Loda M., Rodig S.J., et al. c-Jun amplification and overexpression are oncogenic in liposarcoma but not always sufficient to inhibit the adipocytic differentiation programme. J.Pathol. 2009, 218:292-300.
40. Stephens P.J., Greenman C.D., Fu B., Yang F., Bignell G.R., Mudie L.J., Pleasance E.D., Lau K.W., Beare D., Stebbings L.A., et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 2011, 144:27-40.
41. Stratford E.W., Castro R., Daffinrud J., Skårn M., Lauvrak S., Munthe E., Myklebost O. Characterization of liposarcoma cell lines for preclinical and biological studies. Sarcoma 2012, 2012:148614.
42. Su Y.A., Hutter C.M., Trent J.M., Meltzer P.S. Complete sequence analysis of a gene (OS-9) ubiquitously expressed in human tissues and amplified in sarcomas. Mol. Carcinog. 1996, 15:270-275.
43. Tap W.D., Eilber F.C., Ginther C., Dry S.M., Reese N., Barzan-Smith K., Chen H.W., Wu H., Eilber F.R., Slamon D.J., Anderson L. Evaluation of well-differentiated/de-differentiated liposarcomas by high-resolution oligonucleotide array-based comparative genomic hybridization. Genes Chromosomes Cancer 2011, 50:95-112.
44. Therizols P., Fairhead C., Cabal G.G., Genovesio A., Olivo-Marin J.C., Dujon B., Fabre E. Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region. J.Cell Biol. 2006, 172:189-199.
45. Tyler-Smith C., Gimelli G., Giglio S., Floridia G., Pandya A., Terzoli G., Warburton P.E., Earnshaw W.C., Zuffardi O. Transmission of a fully functional human neocentromere through three generations. Am. J. Hum. Genet. 1999, 64:1440-1444.