Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma

BMC Cancer

Volumn 11, Issue , 2011, Pages

  Carén, Helena ^a   Djos, Anna ^a   Nethander, Maria ^a   Sjöberg, Rose Marie ^a   Kogner, Per ^b   Enström, Camilla ^c   Nilsson, Staffan ^d   Martinsson, Tommy ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^c UPPSALA UNIVERSITY   (Sweden)

^d CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; GENOMIC DNA; MESSENGER RNA; TRICHOSTATIN A; TUMOR MARKER;

ARTICLE; COLLAGEN TYPE 1A2 GENE; CONTROLLED STUDY; DHRS3 GENE; DISEASE COURSE; DNA METHYLATION; DUAL SPECIFICITY PHOSPHATASE 23 GENE; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENE FREQUENCY; GENE IDENTIFICATION; GENE SILENCING; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; KRT19 GENE; NEUROBLASTOMA; NEUROBLASTOMA CELL; ONCOGENE; POU2F2 GENE; PREDICTION; PRKCDBP GENE; PROGNOSIS; SCNN1A GENE; TRANSFORMING GROWTH FACTOR BETA 1 GENE; ALGORITHM; BRAIN TUMOR; GENE EXPRESSION PROFILING; GENETIC EPIGENESIS; GENETICS; MICROARRAY ANALYSIS; PHYSIOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TUMOR CELL LINE; TUMOR GENE; TUMOR SUPPRESSOR GENE; VALIDATION STUDY;

ALGORITHMS; BRAIN NEOPLASMS; CELL LINE, TUMOR; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENES, NEOPLASM; GENES, TUMOR SUPPRESSOR; GENETIC ASSOCIATION STUDIES; HUMANS; MICROARRAY ANALYSIS; NEUROBLASTOMA; PROGNOSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TUMOR MARKERS, BIOLOGICAL;

EID: 79751526520     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-11-66     Document Type: Article

References (45)

1. Maris JM, Matthay KK. Molecular biology of neuroblastoma. J Clin Oncol 1999, 17:2264-2279.
2. Carén H, Erichsen J, Olsson L, Enerbäck C, Sjöberg RM, Abrahamsson J, Kogner P, Martinsson T. High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: Four cases of homozygous deletions of the CDKN2A gene. BMC Genomics 2008, 9:353. 2527340, 18664255.
3. Martinsson T, Sjöberg RM, Hedborg F, Kogner P. Homozygous deletion of the neurofibromatosis-1 gene in the tumor of a patient with neuroblastoma. Cancer Genet Cytogenet 1997, 95:183-189. 10.1016/S0165-4608(96)00259-2, 9169039.
4. Munoz J, Lazcoz P, Inda MM, Nistal M, Pestana A, Encio IJ, Castresana JS. Homozygous deletion and expression of PTEN and DMBT1 in human primary neuroblastoma and cell lines. Int J Cancer 2004, 109:673-679. 10.1002/ijc.20055, 14999773.
5. Origone P, Defferrari R, Mazzocco K, Lo Cunsolo C, De Bernardi B, Tonini GP. Homozygous inactivation of NF1 gene in a patient with familial NF1 and disseminated neuroblastoma. Am J Med Genet A 2003, 118:309-313.
6. Thompson PM, Maris JM, Hogarty MD, Seeger RC, Reynolds CP, Brodeur GM, White PS. Homozygous deletion of CDKN2A (p16INK4a/p14ARF) but not within 1p36 or at other tumor suppressor loci in neuroblastoma. Cancer Res 2001, 61:679-686.
7. Astuti D, Agathanggelou A, Honorio S, Dallol A, Martinsson T, Kogner P, Cummins C, Neumann HP, Voutilainen R, Dahia P, et al. RASSF1A promoter region CpG island hypermethylation in phaeochromocytomas and neuroblastoma tumours. Oncogene 2001, 20:7573-7577. 10.1038/sj.onc.1204968, 11709729.
8. Carén H, Ejeskär K, Fransson S, Hesson L, Latif F, Sjöberg RM, Krona C, Martinsson T. A cluster of genes located in 1p36 are down-regulated in neuroblastomas with poor prognosis, but not due to CpG island methylation. Mol Cancer 2005, 4:10. 554762, 15740626.
9. Carén H, Fransson S, Ejeskär K, Kogner P, Martinsson T. Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours. Br J Cancer 2007, 97:1416-1424. 2360241, 17940511.
10. Agathanggelou A, Dallol A, Zochbauer-Muller S, Morrissey C, Honorio S, Hesson L, Martinsson T, Fong KM, Kuo MJ, Yuen PW, et al. Epigenetic inactivation of the candidate 3p21.3 suppressor gene BLU in human cancers. Oncogene 2003, 22:1580-1588. 10.1038/sj.onc.1206243, 12629521.
11. 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, 24:5619-5628. 10.1038/sj.onc.1208722, 16044164.
12. Gonzalez-Gomez P, Bello MJ, Lomas J, Arjona D, Alonso ME, Aminoso C, Lopez-Marin I, Anselmo NP, Sarasa JL, Gutierrez M, et al. Aberrant methylation of multiple genes in neuroblastic tumours. relationship with MYCN amplification and allelic status at 1p. Eur J Cancer 2003, 39:1478-1485. 10.1016/S0959-8049(03)00312-5, 12826052.
13. Anderton JA, Lindsey JC, Lusher ME, Gilbertson RJ, Bailey S, Ellison DW, Clifford SC. Global analysis of the medulloblastoma epigenome identifies disease-subgroup-specific inactivation of COL1A2. Neuro Oncol 2008, 10:981-994. 10.1215/15228517-2008-048, 2719012, 18664619.
14. Becker J, Erdlenbruch B, Noskova I, Schramm A, Aumailley M, Schorderet DF, Schweigerer L. Keratoepithelin suppresses the progression of experimental human neuroblastomas. Cancer Res 2006, 66:5314-5321. 10.1158/0008-5472.CAN-05-3049, 16707457.
15. Becker J, Volland S, Noskova I, Schramm A, Schweigerer LL, Wilting J. Keratoepithelin reverts the suppression of tissue factor pathway inhibitor 2 by MYCN in human neuroblastoma: a mechanism to inhibit invasion. Int J Oncol 2008, 32:235-240.
16. Cerignoli F, Guo X, Cardinali B, Rinaldi C, Casaletto J, Frati L, Screpanti I, Gudas LJ, Gulino A, Thiele CJ, Giannini G. retSDR1, a short-chain retinol dehydrogenase/reductase, is retinoic acid-inducible and frequently deleted in human neuroblastoma cell lines. Cancer Res 2002, 62:1196-1204.
17. Furuta J, Nobeyama Y, Umebayashi Y, Otsuka F, Kikuchi K, Ushijima T. Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas. Cancer Res 2006, 66:6080-6086. 10.1158/0008-5472.CAN-06-0157, 16778180.
18. Haeseleer F, Huang J, Lebioda L, Saari JC, Palczewski K. Molecular characterization of a novel short-chain dehydrogenase/reductase that reduces all-trans-retinal. J Biol Chem 1998, 273:21790-21799. 10.1074/jbc.273.34.21790, 9705317.
19. Kamei N, Hiyama K, Yamaoka H, Kamimatsuse A, Onitake Y, Sueda T, Hiyama E. Evaluation of genes identified by microarray analysis in favorable neuroblastoma. Pediatr Surg Int 2009, 25:931-937. 10.1007/s00383-009-2448-1, 19701758.
20. Lee JH, Byun DS, Lee MG, Ryu BK, Kang MJ, Chae KS, Lee KY, Kim HJ, Park H, Chi SG. Frequent epigenetic inactivation of hSRBC in gastric cancer and its implication in attenuated p53 response to stresses. Int J Cancer 2008, 122:1573-1584. 10.1002/ijc.23166, 18059034.
21. Mori K, Enokida H, Kagara I, Kawakami K, Chiyomaru T, Tatarano S, Kawahara K, Nishiyama K, Seki N, Nakagawa M. CpG hypermethylation of collagen type I alpha 2 contributes to proliferation and migration activity of human bladder cancer. Int J Oncol 2009, 34:1593-1602. 10.3892/ijo_00000233, 19424577.
22. Roll JD, Rivenbark AG, Jones WD, Coleman WB. DNMT3b overexpression contributes to a hypermethylator phenotype in human breast cancer cell lines. Mol Cancer 2008, 7:15. 10.1186/1476-4598-7-15, 2246151, 18221536.
23. Sengupta PK, Smith EM, Kim K, Murnane MJ, Smith BD. DNA hypermethylation near the transcription start site of collagen alpha2(I) gene occurs in both cancer cell lines and primary colorectal cancers. Cancer Res 2003, 63:1789-1797.
24. Shao G, Berenguer J, Borczuk AC, Powell CA, Hei TK, Zhao Y. Epigenetic inactivation of Betaig-h3 gene in human cancer cells. Cancer Res 2006, 66:4566-4573. 10.1158/0008-5472.CAN-05-2130, 16651406.
25. Tonks NK, Neel BG. Combinatorial control of the specificity of protein tyrosine phosphatases. Curr Opin Cell Biol 2001, 13:182-195. 10.1016/S0955-0674(00)00196-4, 11248552.
26. Wu Q, Li Y, Gu S, Li N, Zheng D, Li D, Zheng Z, Ji C, Xie Y, Mao Y. Molecular cloning and characterization of a novel dual-specificity phosphatase 23 gene from human fetal brain. Int J Biochem Cell Biol 2004, 36:1542-1553. 10.1016/j.biocel.2003.12.014, 15147733.
27. Dahlman T, Lammerts E, Bergstrom D, Franzen A, Westermark K, Heldin NE, Rubin K. Collagen type I expression in experimental anaplastic thyroid carcinoma: regulation and relevance for tumorigenicity. Int J Cancer 2002, 98:186-192. 10.1002/ijc.10181, 11857406.
28. Hendrix MJ, Seftor EA, Chu YW, Trevor KT, Seftor RE. Role of intermediate filaments in migration, invasion and metastasis. Cancer Metastasis Rev 1996, 15:507-525. 10.1007/BF00054016, 9034607.
29. Koga Y, Pelizzola M, Cheng E, Krauthammer M, Sznol M, Ariyan S, Narayan D, Molinaro AM, Halaban R, Weissman SM. Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res 2009, 19:1462-1470. 10.1101/gr.091447.109, 2720187, 19491193.
30. Margetts CD, Morris M, Astuti D, Gentle DC, Cascon A, McRonald FE, Catchpoole D, Robledo M, Neumann HP, Latif F, Maher ER. Evaluation of a functional epigenetic approach to identify promoter region methylation in phaeochromocytoma and neuroblastoma. Endocr Relat Cancer 2008, 15:777-786. 10.1677/ERC-08-0072, 2519165, 18499731.
31. Martinez R, Martin-Subero JI, Rohde V, Kirsch M, Alaminos M, Fernandez AF, Ropero S, Schackert G, Esteller M. A microarray-based DNA methylation study of glioblastoma multiforme. Epigenetics 2009, 4:255-264.
32. Schramm A, Schulte JH, Klein-Hitpass L, Havers W, Sieverts H, Berwanger B, Christiansen H, Warnat P, Brors B, Eils J, et al. Prediction of clinical outcome and biological characterization of neuroblastoma by expression profiling. Oncogene 2005, 24:7902-7912. 10.1038/sj.onc.1208936, 16103881.
33. Stathopoulos EN, Sanidas E, Kafousi M, Mavroudis D, Askoxylakis J, Bozionelou V, Perraki M, Tsiftsis D, Georgoulias V. Detection of CK-19 mRNA-positive cells in the peripheral blood of breast cancer patients with histologically and immunohistochemically negative axillary lymph nodes. Ann Oncol 2005, 16:240-246. 10.1093/annonc/mdi043, 15668277.
34. Theodorou E, Dalembert G, Heffelfinger C, White E, Weissman S, Corcoran L, Snyder M. A high throughput embryonic stem cell screen identifies Oct-2 as a bifunctional regulator of neuronal differentiation. Genes Dev 2009, 23:575-588. 10.1101/gad.1772509, 2658525, 19270158.
35. Tong SY, Ki KD, Lee JM, Kang MJ, Ha TK, Chung SI, Chi SG, Lee SK. Frequent inactivation of hSRBC in ovarian cancers by promoter CpG island hypermethylation. Acta Obstet Gynecol Scand 2010, 89:629-635. 10.3109/00016341003678443, 20423276.
36. Xu XL, Wu LC, Du F, Davis A, Peyton M, Tomizawa Y, Maitra A, Tomlinson G, Gazdar AF, Weissman BE, et al. Inactivation of human SRBC, located within the 11p15.5-p15.4 tumor suppressor region, in breast and lung cancers. Cancer Res 2001, 61:7943-7949.
37. Zochbauer-Muller S, Fong KM, Geradts J, Xu X, Seidl S, End-Pfutzenreuter A, Lang G, Heller G, Zielinski CC, Gazdar AF, Minna JD. Expression of the candidate tumor suppressor gene hSRBC is frequently lost in primary lung cancers with and without DNA methylation. Oncogene 2005, 24:6249-6255. 10.1038/sj.onc.1208775, 15940253.
38. Morris MR, Gentle D, Abdulrahman M, Clarke N, Brown M, Kishida T, Yao M, Teh BT, Latif F, Maher ER. Functional epigenomics approach to identify methylated candidate tumour suppressor genes in renal cell carcinoma. Br J Cancer 2008, 98:496-501. 10.1038/sj.bjc.6604180, 2361461, 18195710.
39. Crowe DL, Milo GE, Shuler CF. Keratin 19 downregulation by oral squamous cell carcinoma lines increases invasive potential. J Dent Res 1999, 78:1256-1263. 10.1177/00220345990780061001, 10371250.
40. Schultze JL, Eggle D. IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform. Bioinformatics 2007, 23:1431-1433. 10.1093/bioinformatics/btm101, 17384020.
41. Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, Doucet D, Thomas NJ, Wang Y, Vollmer E, et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res 2006, 16:383-393. 10.1101/gr.4410706, 1415217, 16449502.
42. Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 2002, 99:3740-3745. 10.1073/pnas.052410099, 122594, 11891299.
43. Tusnady GE, Simon I, Varadi A, Aranyi T. BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes. Nucleic Acids Res 2005, 33:e9. 10.1093/nar/gni012, 546182, 15653630.
44. Han W, Cauchi S, Herman JG, Spivack SD. DNA methylation mapping by tag-modified bisulfite genomic sequencing. Anal Biochem 2006, 355:50-61. 10.1016/j.ab.2006.05.010, 16797472.
45. Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 2005, 21:4067-4068. 10.1093/bioinformatics/bti652, 16141249.