Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas

Cancer Research

Volumn 66, Issue 18, 2006, Pages 8984-8993

  Meza Zepeda, Leonardo A ^a,b   Kresse, Stine H ^a,b   Barragan Polania, Ana H ^a,b   Bjerkehagen, Bodil ^a   Ohnstad, Hege O ^a   Namløs, Heidi M ^a   Wang, Junbai ^a   Kristiansen, Bjørn E ^a,b   Myklebost, Ola ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA;

ARTICLE; CHROMOSOME 10; CHROMOSOME 13Q; CHROMOSOME 14; CHROMOSOME 22; CHROMOSOME ABERRATION; CLONING; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA MICROARRAY; GASTROINTESTINAL STROMAL TUMOR; GENE EXPRESSION; HUMAN; LEIOMYOSARCOMA; MICROARRAY ANALYSIS; MUSCLE TUMOR; PRIORITY JOURNAL; SPINDLE CELL CARCINOMA; STATISTICAL ANALYSIS;

ADULT; AGED; ANIMALS; CHROMOSOME ABERRATIONS; CHROMOSOMES, HUMAN, PAIR 17; FEMALE; GASTROINTESTINAL STROMAL TUMORS; GENE DOSAGE; HUMANS; LEIOMYOSARCOMA; MALE; MICE; MIDDLE AGED; MULTIGENE FAMILY; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSPLANTATION, HETEROLOGOUS;

EID: 33749499031     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-06-1972     Document Type: Article

References (50)

1. Fletcher CDM, Unni KK, Mertens F. Pathology and genetics. Tumours of soft tissue and bone. Lyon: IARC Press; 2002.
2. Weiss SW, Goldblum J. Enzinger and Weiss's soft tissue tumors. 4th ed. St. Louis: Mosby; 2001.
3. Derre J, Lagace R, Nicolas A, et al. Leiomyosarcomas and most malignant fibrous histiocytomas share very similar comparative genomic hybridization imbalances: an analysis of a series of 27 leiomyosarcomas. Lab Invest 2001;81:211-5.
4. El-Rifai W, Sarlomo-Rikala M, Knuutila S, Miettinen M. DNA copy number changes in development and progression in leiomyosarcomas of soft tissues. Am J Pathol 1998;153:985-90.
5. Levy B, Mukherjee T, Hirschhorn K. Molecular cytogenetic analysis of uterine leiomyoma and leiomyosarcoma by comparative genomic hybridization. Cancer Genet Cytogenet 2000;121:1-8.
6. Packenham JP, du Manoir S, Schrock E, et al. Analysis of genetic alterations in uterine leiomyomas and leiomyosarcomas by comparative genomic hybridization. Mol Carcinog 1997;19:273-9.
7. Hu J, Khanna V, Jones M, Surti U. Genomic alterations in uterine leiomyosarcomas: potential markers for clinical diagnosis and prognosis. Genes Chromosomes Cancer 2001;31:117-24.
8. El-Rifai W, Sarlomo-Rikala M, Andersson LC, Knuutila S, Miettinen M. DNA sequence copy number changes in gastrointestinal stromal tumors: tumor progression and prognostic significance. Cancer Res 2000;60:3899-903.
9. El-Rifai W, Sarlomo-Rikala M, Andersson LC, Miettinen M, Knuutila S. High-resolution deletion mapping of chromosome 14 in stromal tumors of the gastrointestinal tract suggests two distinct tumor suppressor loci. Genes Chromosomes Cancer 2000;27:387-91.
10. Kim NG, Kim JJ, Ahn JY, et al. Putative chromosomal deletions on 9P, 9Q and 22Q occur preferentially in malignant gastrointestinal stromal tumors. Int J Cancer 2000;85:633-8.
11. Sabah M, Cummins R, Leader M, Kay E. Loss of heterozygosity of chromosome 9p and loss of p16INK4A expression are associated with malignant gastrointestinal stromal tumors. Mod Pathol 2004;17:1364-71.
12. Hirota S, Isozaki K, Moriyama Y, et al. Gain-of-function mutations of c-kit in human gastrointestinal stromal tumors. Science 1998;279:577-80.
13. Corless CL, Fletcher JA, Heinrich MC. Biology of gastrointestinal stromal tumors. J Clin Oncol 2004;22:3813-25.
14. Heinrich MC, Corless CL, Duensing A, et al. PDGFRA activating mutations in gastrointestinal stromal tumors. Science 2003;299:708-10.
15. Druker BJ, Tamura S, Buchdunger E, et al. Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat Med 1996;2:561-6.
16. Joensuu H, Roberts PJ, Sarlomo-Rikala M, et al. Effect of the tyrosine kinase inhibitor STI571 in a patient with a metastatic gastrointestinal stromal tumor. N Engl J Med 2001;344:1052-6.
17. Fiegler H, Carr P, Douglas EJ, et al. DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones [erratum appears in Genes Chromosomes Cancer 2003;37:223]. Genes Chromosomes Cancer 2003;36:361-74.
18. Wang J, Meza-Zepeda LA, Kresse SH, Myklebost O. M-CGH: analysing microarray-based CGH experiments. BMC Bioinformatics 2004;5:74.
19. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response [erratum appears in Proc Natl Acad Sci U S A 2001;98:10515]. Proc Natl Acad Sci U S A 2001;98:5116-21.
20. Dysvik B, Jonassen I. J-Express: exploring gene expression data using Java. Bioinformatics 2001;17:369-70.
21. Lingjaerde OC, Baumbusch LO, Liestol K, Glad IK, Borresen-Dale AL. CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics 2005;21:821-2.
22. Heinrich MC, Rubin BP, Longley BJ, Fletcher JA. Biology and genetic aspects of gastrointestinal stromal tumors: KIT activation and cytogenetic alterations. Hum Pathol 2002;33:484-95.
23. Bergmann F, Gunawan B, Hermanns B, Hoer J, Schumpelick V, Fuzesi L. Cytogenetic and morphologic characteristics of gastrointestinal stromal tumors. Recurrent rearrangement of chromosome 1 and losses of chromosomes 14 and 22 as common anomalies. Verh Dtsch Ges Pathol 1998;82:275-8.
24. Debiec-Rychter M, Sciot R, Pauwels P, Schoenmakers E, Dal Cin P, Hagemeijer A. Molecular cytogenetic definition of three distinct chromosome arm 14q deletion intervals in gastrointestinal stromal tumors. Genes Chromosomes Cancer 2001;32:26-32.
25. Fukasawa T, Chong JM, Sakurai S, et al. Allelic loss of 14q and 22q, NF2 mutation, and genetic instability occur independently of c-kit mutation in gastrointestinal stromal tumor. Jpn J Cancer Res 2000;91:1241-9.
26. El-Rifai W, Sarlomo-Rikala M, Miettinen M, Knuutila S, Andersson LC. DNA copy number losses in chromosome 14: an early change in gastrointestinal stromal tumors. Cancer Res 1996;56:3230-3.
27. O'Leary T, Ernst S, Przygodzki R, Emory T, Sobin L. Loss of heterozygosity at 1p36 predicts poor prognosis in gastrointestinal stromal/smooth muscle tumors. Lab Invest 1999;79:1461-7.
28. Schneider-Stock R, Boltze C, Lasota J, et al. High prognostic value of p16INK4 alterations in gastrointestinal stromal tumors. J Clin Oncol 2003;21:1688-97.
29. Hu J, Rao UN, Jasani S, Khanna V, Yaw K, Surti U. Loss of DNA copy number of 10q is associated with aggressive behavior of leiomyosarcomas: a comparative genomic hybridization study. Cancer Genet Cytogenet 2005;161:20-7.
30. Busby V, Goossens S, Nowotny P, et al. α-T-catenin is expressed in human brain and interacts with the Wnt signaling pathway but is not responsible for linkage to chromosome 10 in Alzheimer's disease. Neuromolecular Med 2004;5:133-46.
31. Janssens B, Goossens S, Staes K, et al. αT-catenin: a novel tissue-specific β-catenin-binding protein mediating strong cell-cell adhesion. J Cell Sci 2001;114:3177-88.
32. Smith DI, Zhu Y, McAvoy S, Kuhn R. Common fragile sites, extremely large genes, neural development and cancer. Cancer Lett 2006;232:48-57.
33. Karpeh MS, Brennan MF, Cance WG, et al. Altered patterns of retinoblastoma gene product expression in adult soft-tissue sarcomas. Br J Cancer 1995;72:986-91.
34. Forus A, Weghuis DO, Smeets D, Fodstad O, Myklebost O, van Kessel AG. Comparative genomic hybridization analysis of human sarcomas: I. Occurrence of genomic unbalances and identification of a novel major amplicon at 1q21-22 in soft tissue sarcomas. Genes Chromosomes Cancer 1995;14:8-14.
35. Forus A, Berner JM, Meza-Zepeda LA, et al. Molecular characterization of a novel amplicon at 1q21-22 frequently observed in human sarcomas. Br J Cancer 1998;78:495-503.
36. Meza-Zepeda LA, Forus A, Lygren B, et al. Positional cloning identifies a novel cyclophilin as a candidate amplified oncogene in 1q21. Oncogene 2002;21:2261-9.
37. Zhang CC, Kaba M, Ge G, et al. Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells. Nat Med 2006;12:240-5.
38. Ettinger SL, Sobel R, Whitmore TG, et al. Dysregulation of sterol response element-binding proteins and downstream effectors in prostate cancer during progression to androgen independence. Cancer Res 2004;64:2212-21.
39. Li JN, Mahmoud MA, Han WF, Ripple M, Pizer ES. Sterol regulatory element-binding protein-1 participates in the regulation of fatty acid synthase expression in colorectal neoplasia. Exp Cell Res 2000;261:159-65.
40. Baird K, Davis S, Antonescu CR, et al. Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res 2005;65:9226-35.
41. Terada Y, Tatsuka M, Suzuki F, Yasuda Y, Fujita S, Otsu M. AIM-1: a mammalian midbody-associated protein required for cytokinesis. EMBOJ 1998;17:667-76.
42. Chieffi P, Cozzolino L, Kisslinger A, et al. Aurora B expression directly correlates with prostate cancer malignancy and influence prostate cell proliferation. Prostate 2006;66:326-33.
43. Smith SL, Bowers NL, Betticher DC, et al. Over-expression of aurora B kinase (AURKB) in primary non-small cell lung carcinoma is frequent, generally driven from one allele, and correlates with the level of genetic instability. Br J Cancer 2005;93:719-29.
44. Araki K, Nozaki K, Ueba T, Tatsuka M, Hashimoto N. High expression of Aurora-B/Aurora and Ip11-like midbody-associated protein (AIM-1) in astrocytomas. J Neurooncol 2004;67:53-64.
45. Kanda A, Kawai H, Suto S, et al. Aurora-B/AIM-1 kinase activity is involved in Ras-mediated cell transformation. Oncogene 2005;24:7266-72.
46. Forus A, Weghuis DO, Smeets D, Fodstad O, Myklebost O, van Kessel AG. Comparative genomic hybridization analysis of human sarcomas. II. Identification of novel amplicons at 6p and 17p in osteosarcomas. Genes Chromosomes Cancer 1995;14:15-21.
47. Tarkkanen M, Karhu R, Kallioniemi A, et al. Gains and losses of DNA sequences in osteosarcomas by comparative genomic hybridization. Cancer Res 1995;55:1334-8.
48. Henriksen J, Aagesen TH, Maelandsmo GM, Lothe RA, Myklebost O, Forus A. Amplification and over-expression of COPS3 in osteosarcomas potentially target TP53 for proteasome-mediated degradation. Oncogene 2003;22:5358-61.
49. van Dartel M, Cornelissen PW, Redeker S, et al. Amplification of 17p11.2 approximately p!2, including PMP22, TOP3A, and MAPK7, in high-grade osteosarcoma. Cancer Genet Cytogenet 2002;139:91-6.
50. van Dartel M, Redeker S, Bras J, Kool M, Hulsebos TJ. Overexpression through amplification of genes in chromosome region 17p11.2 approximately p12 in high-grade osteosarcoma. Cancer Genet Cytogenet 2004;152:8-14.