Outcome prediction and risk assessment by quantitative pyrosequencing methylation analysis of the SFN gene in advanced stage, high-risk, neuroblastic tumor patients

International Journal of Cancer

Volumn 126, Issue 3, 2010, Pages 656-668

  Banelli, Barbara ^a   Bonassi, Stefano ^a   Casciano, Ida ^a   Mazzocco, Katia ^a   Di Vinci, Angela ^a   Scaruffi, Paola ^a   Brigati, Claudio ^a   Allemanni, Giorgio ^a   Borzì, Luana ^a   Tonini, Gian Paolo ^a   Romani, Massimo ^a  

^a UNIVERSITY OF GENOA   (Italy)

Author keywords

Dna methylation; Epigenetics; Neuroblastoma; Predictive oncology; Pyrosequencing

Indexed keywords

DNA;

ARTICLE; CANCER GROWTH; CANCER PATIENT; CANCER RISK; CANCER STAGING; CANCER SURVIVAL; CONTROLLED STUDY; CYP26C1 GENE; DCR2 GENE; DNA METHYLATION; GANGLIONEUROMA; GENE; GENE EXPRESSION; GENETIC ANALYSIS; HEALTH HAZARD; HIGH RISK POPULATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MAJOR CLINICAL STUDY; METHYLATION; NEUROBLASTOMA; OUTCOME ASSESSMENT; PRIORITY JOURNAL; PROGNOSIS; PYROSEQUENCING; QUANTITATIVE ANALYSIS; RASSF1A GENE; RECEIVER OPERATING CHARACTERISTIC; RISK ASSESSMENT; SFN GENE;

AZACITIDINE; CELL LINE, TUMOR; CHILD; CHILD, PRESCHOOL; COHORT STUDIES; CPG ISLANDS; DNA METHYLATION; DNA, NEOPLASM; EXONUCLEASES; FEMALE; GANGLIONEUROBLASTOMA; GANGLIONEUROMA; HUMANS; INFANT; KAPLAN-MEIERS ESTIMATE; MALE; NEOPLASM PROTEINS; NEUROBLASTOMA; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; RISK; RISK ASSESSMENT; SEQUENCE ANALYSIS, DNA; SOFT TISSUE NEOPLASMS; SURVIVORS; TUMOR MARKERS, BIOLOGICAL;

EID: 73449088389     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.24768     Document Type: Article

References (46)

1. Shimada H, Ambros IM, Dehner LP, Hata J, Joshi VV, Roald B. Terminology and morphologic criteria of neuroblastic tumors: recommendations by the International Neuroblastoma Pathology Committee. Cancer 1999;86:349-63.
2. Brodeur GM. Neuroblastoma: biological insights into a clinical enigma. Nat Rev Cancer 2003;3:203-16.
3. Castleberry RP, Pritchard J, Ambros P, Berthold F, Brodeur GM, Castel V, Cohn SL, De Bernardi B, Dicks-Mireaux C, Frappaz D, Haase GM, Haber M, et al. The International Neuroblastoma Risk Groups (INRG): a preliminary report. Eur J Cancer 1997;33:2113-6.
4. Maris JM, Hogarty MD, Bagatell R, Cohn SL. Neuroblastoma. Lancet 2007;369:2106-20.
5. Brodeur GM, Pritchard J, Berthold F, Carlsen NL, Castel V, Castelberry RP, De Bernardi B, Evans AE, Favrot M, Hedborg F. Revisions of the international criteria for neuroblastoma diagnosis, staging, and response to treatment. J Clin Oncol 1993;11:1466-77.
6. Cohn SL, Pearson AD, London WB, Monclair T, Ambros PF, Brodeur GM, Faldum A, Hero B, Iehara T, Machin D, Mosseri V, Simon T, et al. The International Neuroblastoma Risk Group (INRG) classification system: an INRG Task Force report. J Clin Oncol 2009;27:289-97.
7. London WB, Castleberry RP, Matthay KK, Look AT, Seeger RC, Shimada H, Thorner P, Brodeur G, Maris JM, Reynolds CP, Cohn SL. Evidence for an age cutoff greater than 365 days for neuroblastoma risk group stratification in the Children's Oncology Group. J Clin Oncol 2005;23:6459-65.
8. London WB, Boni L, Simon T, Berthold F, Twist C, Schmidt ML, Castleberry RP, Matthay KK, Cohn SL, De Bernardi B. The role of age in neuroblastoma risk stratification: the German. Italian, and children's oncology group perspectives. Cancer Lett 2005;228:257-66.
9. Mora J, Gerald WL, Cheung NK. Evolving significance of prognostic markers associated with new treatment strategies in neuroblastoma. Cancer Lett 2003;197:119-24.
10. Maris JM. The biologic basis for neuroblastoma heterogeneity and risk stratification. Curr Opin Pediatr 2005;17:7-13.
11. Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer 2003;3:253-66.
12. Ushijima T. Detection and interpretation of altered methylation patterns in cancer cells. Nat Rev Cancer 2005;5:223-31.
13. Alaminos M, Davalos V, Cheung NK, Gerald WL, Esteller M. Clustering of gene hypermethylation associated with clinical risk groups in neuroblastoma. J Natl Cancer Inst 2004;96:1208-19.
14. Yang Q, Zage P, Kagan D, Tian Y, Seshadri R, Salwen HR, Liu S, Chlenski A, Cohn SL. Association of epigenetic inactivation of RASSF1A with poor outcome in human neuroblastoma. Clin Cancer Res 2004;10:8493-500.
15. Abe M, Ohira M, Kaneda A, Yagi Y, Yamamoto S, Kitano Y, Takato T, Nakagawara A, Ushijima T. CpG island methylator phenotype is a strong determinant of poor prognosis in neuroblastomas. Cancer Res 2005;65:828-34.
16. Banelli B, Gelvi I, Di Vinci A, Scaruffi P, Casciano I, Allemanni G, Bonassi S, Tonini GP, Romani M. Distinct CpG methylation profiles characterize different clinical groups of neuroblastic tumors. Oncogene 2005;24:5619-28.
17. Yang Q, Kiernan CM, Tian Y, Salwen HR, Chlenski A, Brumback BA, London WB, Cohn SL. Methylation of CASP8. DCR2, and. HIN-1 in neuroblastoma is associated with poor outcome. Clin Cancer Res 2007;13:3191-7.
18. Abe M, Westermann F, Nakagawara A, Takato T, Schwab M, Ushijima T. Marked and independent prognostic significance of the CpG island methylator phenotype in neuroblastomas. Cancer Lett 2007;247:253-8.
19. Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP. CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci USA 1999;96:8681-6.
20. Fraga MF, Esteller M. DNA methylation: a profile of methods and applications. Biotechniques 2002;33:632,4,6-49.
21. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 1996;93:9821-6.
22. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 1992;89:1827-31.
23. Di Vinci A, Perdelli L, Banelli B, Salvi S, Casciano I, Gelvi I, Allemanni G, Margallo E, Gatteschi B, Romani M. p16(INK4a) promoter methylation and protein expression in breast fibroadenoma and carcinoma. Int J Cancer 2005;114:414-21.
24. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suner D, Cigudosa JC, Urioste M, Benitez J, Boix-Chornet M, Sanchez-Aguilera A, et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 2005;102:10604-9.
25. Korshunova Y, Maloney RK, Lakey N, Citek RW, Bacher B, Budiman A, Ordway JM, McCombie WR, Leon J, Jeddeloh JA, McPherson JD. Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancerassociated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Res 2008;18:19-29.
26. Lehmann U, Langer F, Feist H, Glockner S, Hasemeier B, Kreipe H. Quantitative assessment of promoter hypermethylation during breast cancer development. Am J Pathol 2002;160:605-12.
27. Hermeking H. The 14-3-3 cancer connection. Nat Rev Cancer 2003;3:931-43.
28. Agathanggelou A, Cooper WN, Latif F. Role of the Ras-association domain family 1 tumor suppressor gene in human cancers. Cancer Res 2005;65:3497-508.
29. Taimi M, Helvig C, Wisniewski J, Ramshaw H, White J, Amad M, Korczak B, Petkovich M. A novel human cytochrome P450. CYP26C1, involved in metabolism of 9-cis and all-trans isomers of retinoic acid. J Biol Chem 2004;279:77-85.
30. Degli-Esposti MA, Dougall WC, Smolak PJ, Waugh JY, Smith CA, Goodwin RG. The novel receptor TRAIL-R4 induces NF-kappaB and protects against TRAILmediated apoptosis, yet retains an incomplete death domain. Immunity 1997;7:813-20.
31. Tonini GP. Neuroblastoma: a multiple biological disease. Eur J Cancer29A:802-4,1993.
32. Dupont JM, Tost J, Jammes H, Gut IG. De novo quantitative bisulfite sequencing using the pyrosequencing technology. Anal Biochem 2004;333:119-27.
33. Akahira J, Sugihashi Y, Suzuki T, Ito K, Niikura H, Moriya T, Nitta M, Okamura H, Inoue S, Sasano H, Okamura K, Yaegashi N. Decreased expression of 14-3-3 sigma is associated with advanced disease in human epithelial ovarian cancer: its correlation with aberrant DNA methylation. Clin Cancer Res 2004;10:2687-93.
34. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009;55:611-22.
35. Hanley JA, McNeil BJ. A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology 1983;148:839-43.
36. Kaplan EL, Maier P. Nonparametric estimation from incomplete observations. J Am Stat Assoc 1958;53:457-81.
37. Abe M, Watanabe N, McDonell N, Takato T, Ohira M, Nakagawara A, Ushijima T. Identification of genes targeted by CpG island methylator phenotype in neuroblastomas, and their possible integrative involvement in poor prognosis. Oncology 2008;74:50-60.
38. Seeger RC, Brodeur GM, Sather H, Dalton A, Siegel SE, Wong KY, Hammond D. Association of multiple copies of the Nmyc oncogene with rapid progression of neuroblastomas. N Engl J Med 1985;313:1111-6.
39. Fiegl H, Elmasry K. Cancer diagnosis, risk assessment and prediction of therapeutic response by means of DNA methylation markers. Dis Markers 2007;23:89-96.
40. Zhu J, Yao X. Use of DNA methylation for cancer detection and molecular classification. J Biochem Mol Biol 2007;40:135-41.
41. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV,Laird PW MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 2000;28:E32.
42. Yang H, Wen YY, Zhao R, Lin YL, Fournier K, Yang HY, Qiu Y, Diaz J, Laronga C, Lee MH. DNA damageinduced protein 14-3-3 sigma inhibits protein kinase B/Akt activation and suppresses Akt-activated cancer. Cancer Res 2006;66:3096-105.
43. Schramm A, Schulte JH, Astrahantseff K, Apostolov O, Limpt V, Sieverts H, Kuhfittig-Kulle S, Pfeiffer P, Versteeg R, Eggert A. Biological effects of TrkA and TrkB receptor signaling in neuroblastoma. Cancer Lett 2005;228:143-53.
44. Zhu J, Jiang J, Zhou W, Chen X. The potential tumor suppressor p73 differentially regulates cellular p53 target genes. Cancer Res 1998;58:5061-5.
45. Westfall MD, Mays DJ, Sniezek JC, Pietenpol JA. The delta Np63 alpha phosphoprotein binds the p21 and 14-3-3 sigma promoters in vivo and has transcriptional repressor activity that is reduced by Hay-Wells syndrome-derived mutations. Mol Cell Biol 2003;23:2264-76.
46. Casciano I, Mazzocco K, Boni L, Pagnan G, Banelli B, Allemanni G, Ponzoni M, Tonini GP, Romani M. Expression of deltaNp73 is a molecular marker for adverse outcome in neuroblastoma patients. Cell Death Differ 2002;9:246-51.