Two Distinct Categories of Focal Deletions in Cancer Genomes

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Rajaram, Megha ^a   Zhang, Jianping ^a   Wang, Tim ^a   Li, Jinyu ^a   Kuscu, Cem ^a   Qi, Huan ^a   Kato, Mamoru ^a   Grubor, Vladimir ^a   Weil, Robert J ^b   Helland, Aslaug ^c   Borrenson Dale, Anne Lise ^c   Cho, Kathleen R ^d   Levine, Douglas A ^e   Houghton, Alan N ^e   Wolchok, Jedd D ^e   Myeroff, Lois ^f   Markowitz, Sanford D ^f   Lowe, Scott W ^a   Zhang, Michael ^a   Krasnitz, Alex ^a   Lucito, Robert ^a   Mu, David ^a   Powers, R Scott ^a   more..

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b LERNER RESEARCH INSTITUTE   (United States)

^c OSLO UNIVERSITY HOSPITAL   (Norway)

^d UNIVERSITY OF MICHIGAN   (United States)

^e MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^f CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; DNA LIGASE; HYDROLASE; MACROD2 PROTEIN, HUMAN; RBFOX1 PROTEIN, HUMAN; RNA SPLICING FACTOR;

A2BP1 GENE; ARTICLE; CANCER INHIBITION; CELL LINE; CHROMOSOME 16P; CHROMOSOME 20P; COMPUTER ANALYSIS; CONTROLLED STUDY; FEMALE; GENE DELETION; GENE DOSAGE; GENE EXPRESSION; GENE FREQUENCY; GENE FUNCTION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC STABILITY; HUMAN; HUMAN CELL; HUMAN TISSUE; MACROD2 GENE; MALE; PRIMARY TUMOR; TUMOR GENE; TUMOR SUPPRESSOR GENE; ANIMAL; CHROMOSOMAL MAPPING; CHROMOSOME; CHROMOSOME FRAGILE SITE; COMPARATIVE GENOMIC HYBRIDIZATION; GENETICS; GENOME; METABOLISM; MOUSE; NEOPLASM; PATHOPHYSIOLOGY; REAL TIME POLYMERASE CHAIN REACTION; TUMOR CELL LINE; XENOGRAFT;

ANIMALS; CELL LINE, TUMOR; CHROMOSOME FRAGILE SITES; CHROMOSOME MAPPING; CHROMOSOMES; COMPARATIVE GENOMIC HYBRIDIZATION; DNA REPAIR ENZYMES; GENOME; HUMANS; HYDROLASES; MICE; NEOPLASMS; REAL-TIME POLYMERASE CHAIN REACTION; RNA SPLICING FACTORS; SEQUENCE DELETION; TRANSPLANTATION, HETEROLOGOUS;

EID: 84879256573     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0066264     Document Type: Article

References (38)

1. Durkin SG, Glover TW, (2007) Chromosome fragile sites. Annu Rev Genet 41: 169-192.
2. Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD, (2012) A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? Genome Res 22: 993-1005.
3. Huebner K, Croce CM, (2001) FRA3B and other common fragile sites: the weakest links. Nat Rev Cancer 1: 214-221.
4. Abdeen SK, Salah Z, Maly B, Smith Y, Tufail R, et al. (2011) Wwox inactivation enhances mammary tumorigenesis. Oncogene 30: 3900-3906.
5. Poulogiannis G, McIntyre RE, Dimitriadi M, Apps JR, Wilson CH, et al. (2010) PARK2 deletions occur frequently in sporadic colorectal cancer and accelerate adenoma development in Apc mutant mice. Proc Natl Acad Sci U S A 107: 15145-15150.
6. Je EM, Yoo NJ, Lee SH (2012) Somatic Mutation of PARK2 Tumor Suppressor Gene is not Common in Common Solid Cancers. Pathol Oncol Res.
7. Thiagalingam S, Lisitsyn NA, Hamaguchi M, Wigler MH, Willson JK, et al. (1996) Evaluation of the FHIT gene in colorectal cancers. Cancer Res 56: 2936-2939.
8. Watanabe A, Hippo Y, Taniguchi H, Iwanari H, Yashiro M, et al. (2003) An opposing view on WWOX protein function as a tumor suppressor. Cancer Res 63: 8629-8633.
9. Kendall J, Liu Q, Bakleh A, Krasnitz A, Nguyen KC, et al. (2007) Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer. Proc Natl Acad Sci U S A 104: 16663-16668.
10. Mu D, Chen L, Zhang X, See LH, Koch CM, et al. (2003) Genomic amplification and oncogenic properties of the KCNK9 potassium channel gene. Cancer Cell 3: 297-302.
11. Zender L, Spector MS, Xue W, Flemming P, Cordon-Cardo C, et al. (2006) Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 125: 1253-1267.
12. Li J, Yang Y, Peng Y, Austin RJ, van Eyndhoven WG, et al. (2002) Oncogenic properties of PPM1D located within a breast cancer amplification epicenter at 17q23. Nat Genet 31: 133-134.
13. van der Horst EH, Degenhardt YY, Strelow A, Slavin A, Chinn L, et al. (2005) Metastatic properties and genomic amplification of the tyrosine kinase gene ACK1. Proc Natl Acad Sci U S A 102: 15901-15906.
14. Sawey ET, Chanrion M, Cai C, Wu G, Zhang J, et al. (2011) Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening. Cancer Cell 19: 347-358.
15. Zender L, Xue W, Zuber J, Semighini CP, Krasnitz A, et al. (2008) An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell 135: 852-864.
16. Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, et al. (2010) Signatures of mutation and selection in the cancer genome. Nature 463: 893-898.
17. Cancer Genome Atlast Network, (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487: 330-337.
18. Andersen CL, Lamy P, Thorsen K, Kjeldsen E, Wikman F, et al. (2011) Frequent genomic loss at chr16p13.2 is associated with poor prognosis in colorectal cancer. Int J Cancer 129: 1848-1858.
19. Kuroyanagi H, (2009) Fox-1 family of RNA-binding proteins. Cell Mol Life Sci 66: 3895-3907.
20. Forbes SA, Tang G, Bindal N, Bamford S, Dawson E, et al. (2010) COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res 38: D652-657.
21. McAvoy S, Ganapathiraju SC, Ducharme-Smith AL, Pritchett JR, Kosari F, et al. (2007) Non-random inactivation of large common fragile site genes in different cancers. Cytogenet Genome Res 118: 260-269.
22. Arlt MF, Mulle JG, Schaibley VM, Ragland RL, Durkin SG, et al. (2009) Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants. Am J Hum Genet 84: 339-350.
23. Raschke S, Balz V, Efferth T, Schulz WA, Florl AR, (2005) Homozygous deletions of CDKN2A caused by alternative mechanisms in various human cancer cell lines. Genes Chromosomes Cancer 42: 58-67.
24. Murano I, Kuwano A, Kajii T, (1989) Fibroblast-specific common fragile sites induced by aphidicolin. Hum Genet 83: 45-48.
25. Teng DH, Perry WL 3rd, Hogan JK, Baumgard M, Bell R, et al (1997) Human mitogen-activated protein kinase kinase 4 as a candidate tumor suppressor. Cancer Res 57: 4177-4182.
26. Agarwal SK, Kester MB, Debelenko LV, Heppner C, Emmert-Buck MR, et al. (1997) Germline mutations of the MEN1 gene in familial multiple endocrine neoplasia type 1 and related states. Hum Mol Genet 6: 1169-1175.
27. Farrell C, Crimm H, Meeh P, Croshaw R, Barbar T, et al. (2008) Somatic mutations to CSMD1 in colorectal adenocarcinomas. Cancer Biol Ther 7: 609-613.
28. Hasan K, Cheung C, Kaul Z, Shah N, Sakaushi S, et al. (2009) CARF Is a vital dual regulator of cellular senescence and apoptosis. J Biol Chem 284: 1664-1672.
29. Chi YH, Ward JM, Cheng LI, Yasunaga J, Jeang KT, (2009) Spindle assembly checkpoint and p53 deficiencies cooperate for tumorigenesis in mice. Int J Cancer 124: 1483-1489.
30. Suzuki M, Toyooka S, Shivapurkar N, Shigematsu H, Miyajima K, et al. (2005) Aberrant methylation profile of human malignant mesotheliomas and its relationship to SV40 infection. Oncogene 24: 1302-1308.
31. Nancarrow DJ, Handoko HY, Smithers BM, Gotley DC, Drew PA, et al. (2008) Genome-wide copy number analysis in esophageal adenocarcinoma using high-density single-nucleotide polymorphism arrays. Cancer Res 68: 4163-4172.
32. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, et al. (2008) Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455: 1069-1075.
33. Komuro H, Valentine MB, Rubnitz JE, Saito M, Raimondi SC, et al. (1999) p27KIP1 deletions in childhood acute lymphoblastic leukemia. Neoplasia 1: 253-261.
34. Letessier A, Millot GA, Koundrioukoff S, Lachages AM, Vogt N, et al. (2011) Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site. Nature 470: 120-123.
35. Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, et al. (2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 16: 1465-1479.
36. Chen S, Auletta T, Dovirak O, Hutter C, Kuntz K, et al. (2008) Copy number alterations in pancreatic cancer identify recurrent PAK4 amplification. Cancer Biol Ther 7.
37. Venkatraman ES, Olshen AB, (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
38. Zhang C, Zhang Z, Castle J, Sun S, Johnson J, et al. (2008) Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev 22: 2550-2563.