Integrative Analysis Reveals Relationships of Genetic and Epigenetic Alterations in Osteosarcoma

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Kresse, Stine H ^a   Rydbeck, Halfdan ^a,b   Skårn, Magne ^a   Namløs, Heidi M ^a   Barragan Polania, Ana H ^a,b   Cleton Jansen, Anne Marie ^c   Serra, Massimo ^d   Liestøl, Knut ^b   Hogendoorn, Pancras C W ^c   Hovig, Eivind ^a,b   Myklebost, Ola ^a,b   Meza Zepeda, Leonardo A ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^d RIZZOLI ORTHOPAEDIC INSTITUTE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; EPITHELIAL DERIVED NEUTROPHIL ACTIVATING FACTOR 78; INTERLEUKIN 11 RECEPTOR ALPHA; MESSENGER RNA; TRANSCRIPTION FACTOR DLX5; TRANSCRIPTION FACTOR RUNX2;

1L11RA GENE; AKAP12 GENE; ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; CXCL5 GENE; DLX5 GENE; DNA METHYLATION; EFEMP1 GENE; GENE; GENE CONTROL; GENE EXPRESSION; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; OSTEOSARCOMA; OSTEOSARCOMA CELL; POLYMERASE CHAIN REACTION; RUNX2 GENE;

BONE NEOPLASMS; CELL LINE, TUMOR; CLUSTER ANALYSIS; DNA COPY NUMBER VARIATIONS; DNA METHYLATION; EPIGENESIS, GENETIC; GENE DOSAGE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; GENOME-WIDE ASSOCIATION STUDY; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OSTEOSARCOMA; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, MESSENGER;

EID: 84868128368     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048262     Document Type: Article

References (57)

1. Raymond AK, Ayala AG, Knuutila S (2002) Conventional osteosarcoma. In: Fletcher CDM, Unni KK, Mertens F, editors. World Health Organization Classification of Tumours Pathology and Genetics of Tumours of Soft Tissue and Bone. Lyon: IARC Press.
2. Aksnes LH, Hall KS, Folleraas G, Stenwig AE, Bjerkehagen B, et al. (2006) Management of high-grade bone sarcomas over two decades: the Norwegian Radium Hospital experience. Acta Oncol 45: 38-46.
3. PosthumaDeBoer J, Witlox MA, Kaspers GJ, van Royen BJ, (2011) Molecular alterations as target for therapy in metastatic osteosarcoma: a review of literature. Clin Exp Metastasis 28: 493-503.
4. Hattinger CM, Pasello M, Ferrari S, Picci P, Serra M, (2010) Emerging drugs for high-grade osteosarcoma. Expert Opin Emerg Drugs 15: 615-634.
5. Lewis IJ, Nooij MA, Whelan J, Sydes MR, Grimer R, et al. (2007) Improvement in histologic response but not survival in osteosarcoma patients treated with intensified chemotherapy: a randomized phase III trial of the European Osteosarcoma Intergroup. J Natl Cancer Inst 99: 112-128.
6. Bacci G, Briccoli A, Rocca M, Ferrari S, Donati D, et al. (2003) Neoadjuvant chemotherapy for osteosarcoma of the extremities with metastases at presentation: recent experience at the Rizzoli Institute in 57 patients treated with cisplatin, doxorubicin, and a high dose of methotrexate and ifosfamide. Ann Oncol 14: 1126-1134.
7. Kager L, Zoubek A, Potschger U, Kastner U, Flege S, et al. (2003) Primary metastatic osteosarcoma: presentation and outcome of patients treated on neoadjuvant Cooperative Osteosarcoma Study Group protocols. J Clin Oncol 21: 2011-2018.
8. Kresse SH, Szuhai K, Barragan-Polania AH, Rydbeck H, Cleton-Jansen AM, et al. (2010) Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours. BMC Res Notes 3: 223.
9. Smida J, Baumhoer D, Rosemann M, Walch A, Bielack S, et al. (2010) Genomic alterations and allelic imbalances are strong prognostic predictors in osteosarcoma. Clin Cancer Res 16: 4256-4267.
10. Yen CC, Chen WM, Chen TH, Chen WY, Chen PC, et al. (2009) Identification of chromosomal aberrations associated with disease progression and a novel 3q13.31 deletion involving LSAMP gene in osteosarcoma. Int J Oncol 35: 775-788.
11. Kresse SH, Ohnstad HO, Paulsen EB, Bjerkehagen B, Szuhai K, et al. (2009) LSAMP, a novel candidate tumor suppressor gene in human osteosarcomas, identified by array comparative genomic hybridization. Genes Chromosomes Cancer 48: 679-693.
12. Man TK, Lu XY, Jaeweon K, Perlaky L, Harris CP, et al. (2004) Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma. BMC Cancer 4: 45.
13. Lockwood WW, Stack D, Morris T, Grehan D, O'Keane C, et al. (2011) Cyclin E1 is amplified and overexpressed in osteosarcoma. J Mol Diagn 13: 289-296.
14. Lu XY, Lu Y, Zhao YJ, Jaeweon K, Kang J, et al. (2008) Cell cycle regulator gene CDC5L, a potential target for 6p12-p21 amplicon in osteosarcoma. Mol Cancer Res 6: 937-946.
15. Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, et al. (2012) A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature 481: 329-334.
16. Chari R, Coe BP, Vucic EA, Lockwood WW, Lam WL (2010) An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. BMC Syst Biol 4.
17. Hogan LE, Meyer JA, Yang J, Wang J, Wong N, et al. (2011) Integrated genomic analysis of relapsed childhood acute lymphoblastic leukemia reveals therapeutic strategies. Blood 118: 5218-5226.
18. Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, et al. (2011) Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A 109: 2802-2807.
19. Sadikovic B, Yoshimoto M, Al-Romaih K, Maire G, Zielenska M, et al. (2008) In vitro analysis of integrated global high-resolution DNA methylation profiling with genomic imbalance and gene expression in osteosarcoma. PloS ONE 3: e2834.
20. Sadikovic B, Yoshimoto M, Chilton-MacNeill S, Thorner P, Squire JA, et al. (2009) Identification of interactive networks of gene expression associated with osteosarcoma oncogenesis by integrated molecular profiling. Hum Mol Genet 18: 1962-1975.
21. Ottaviano L, Schaefer KL, Gajewski M, Huckenbeck W, Baldus S, et al. (2010) Molecular characterization of commonly used cell lines for bone tumor research: a trans-European EuroBoNet effort. Genes Chromosomes Cancer 49: 40-51.
22. Mohseny AB, Machado I, Cai Y, Schaefer KL, Serra M, et al. (2011) Functional characterization of osteosarcoma cell lines provides representative models to study the human disease. Lab Invest 91: 1195-1205.
23. Kuijjer ML, Namlos HM, Hauben EI, Machado I, Kresse SH, et al. (2011) mRNA expression profiles of primary high-grade central osteosarcoma are preserved in cell lines and xenografts. BMC Med Genomics 4: 66.
24. Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, et al. (2010) The Genomic HyperBrowser: inferential genomics at the sequence level. Genome Biol 11: R121.
25. Lau CC, Harris CP, Lu XY, Perlaky L, Gogineni S, et al. (2004) Frequent amplification and rearrangement of chromosomal bands 6p12-p21 and 17p11.2 in osteosarcoma. Genes Chromosomes Cancer 39: 11-21.
26. Ozaki T, Schaefer KL, Wai D, Buerger H, Flege S, et al. (2002) Genetic imbalances revealed by comparative genomic hybridization in osteosarcomas. Int J Cancer 102: 355-365.
27. Kuijjer ML, Rydbeck H, Kresse SH, Buddingh EP, Lid AB, et al. (2012) Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data. Genes Chromosomes Cancer 51: 696-706.
28. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, et al. (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463: 899-905.
29. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, et al. (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144: 27-40.
30. Rao-Bindal K, Kleinerman ES, (2011) Epigenetic regulation of apoptosis and cell cycle in osteosarcoma. Sarcoma 2011: 679457.
31. Cui J, Wang W, Li Z, Zhang Z, Wu B, et al. (2011) Epigenetic changes in osteosarcoma. Bull Cancer 98: E62-68.
32. Baylin SB, Jones PA, (2011) A decade of exploring the cancer epigenome- biological and translational implications. Nat Rev Cancer 11: 726-734.
33. Lee MH, Surh YJ, (2009) eEF1A2 as a putative oncogene. Ann N Y Acad Sci 1171: 87-93.
34. Honma K, Iwao-Koizumi K, Takeshita F, Yamamoto Y, Yoshida T, et al. (2008) RPN2 gene confers docetaxel resistance in breast cancer. Nat Med 14: 939-948.
35. Martin JW, Zielenska M, Stein GS, van Wijnen AJ, Squire JA, (2011) The Role of RUNX2 in Osteosarcoma Oncogenesis. Sarcoma 2011: 282745.
36. Shah N, Sukumar S, (2010) The Hox genes and their roles in oncogenesis. Nat Rev Cancer 10: 361-371.
37. Nishimura R, Hata K, Matsubara T, Wakabayashi M, Yoneda T, (2012) Regulation of bone and cartilage development by network between BMP signalling and transcription factors. J Biochem 151: 247-254.
38. Pansuriya TC, van Eijk R, d'Adamo P, van Ruler MA, Kuijjer ML, et al. (2011) Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome. Nat Genet 43: 1256-1261.
39. Epping MT, Bernards R, (2006) A causal role for the human tumor antigen preferentially expressed antigen of melanoma in cancer. Cancer Res 66: 10639-10642.
40. Zou C, Shen J, Tang Q, Yang Z, Yin J, et al. (2011) Cancer-testis antigens expressed in osteosarcoma identified by gene microarray correlate with a poor patient prognosis. Cancer 118: 1845-1855.
41. Toledo SR, Zago MA, Oliveira ID, Proto-Siqueira R, Okamoto OK, et al. (2011) Insights on PRAME and osteosarcoma by means of gene expression profiling. J Orthop Sci 16: 458-466.
42. Schenk T, Stengel S, Goellner S, Steinbach D, Saluz HP, (2007) Hypomethylation of PRAME is responsible for its aberrant overexpression in human malignancies. Genes Chromosomes Cancer 46: 796-804.
43. Li Y, Meng G, Guo QN, (2008) Changes in genomic imprinting and gene expression associated with transformation in a model of human osteosarcoma. Exp Mol Pathol 84: 234-239.
44. Revill K, Dudley KJ, Clayton RN, McNicol AM, Farrell WE, (2009) Loss of neuronatin expression is associated with promoter hypermethylation in pituitary adenoma. Endocr Relat Cancer 16: 537-548.
45. Li A, King J, Moro A, Sugi MD, Dawson DW, et al. (2011) Overexpression of CXCL5 is associated with poor survival in patients with pancreatic cancer. Am J Pathol 178: 1340-1349.
46. Kawamura M, Toiyama Y, Tanaka K, Saigusa S, Okugawa Y, et al. (2011) CXCL5, a promoter of cell proliferation, migration and invasion, is a novel serum prognostic marker in patients with colorectal cancer. Eur J Cancer: In press.
47. Speetjens FM, Kuppen PJ, Sandel MH, Menon AG, Burg D, et al. (2008) Disrupted expression of CXCL5 in colorectal cancer is associated with rapid tumor formation in rats and poor prognosis in patients. Clin Cancer Res 14: 2276-2284.
48. Tessema M, Klinge DM, Yingling CM, Do K, Van Neste L, et al. (2010) Re-expression of CXCL14, a common target for epigenetic silencing in lung cancer, induces tumor necrosis. Oncogene 29: 5159-5170.
49. Flanagan JM, Cocciardi S, Waddell N, Johnstone CN, Marsh A, et al. (2010) DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status. Am J Hum Genet 86: 420-433.
50. Lauss M, Aine M, Sjodahl G, Veerla S, Patschan O, et al. (2012) DNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status. Epigenetics 7.
51. Schulz A, Battmann A, Heinrichs CM, Kern A, Tiedemann A, et al. (1993) Properties and reactivity of a new human osteosarcoma cell line (HOS 58). Calcif Tissue Int 52: 30.
52. Buddingh EP, Kuijjer ML, Duim RA, Burger H, Agelopoulos K, et al. (2011) Tumor-infiltrating macrophages are associated with metastasis suppression in high-grade osteosarcoma: a rationale for treatment with macrophage activating agents. Clin Cancer Res 17: 2110-2119.
53. Lin SM, Du P, Huber W, Kibbe WA, (2008) Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res 36: e11.
54. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
55. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.
56. Huang DW, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
57. Wu Q, Lothe RA, Ahlquist T, Silins I, Trope CG, et al. (2007) DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets. Mol Cancer 6: 45.