Predictive properties of DNA methylation patterns in primary tumor samples for osteosarcoma relapse status

Epigenetics

Volumn 10, Issue 1, 2015, Pages 31-39

  Rosenblum, Jeremy M ^a   Ari Wijetunga, N A ^a   Fazzari, Melissa J ^a   Krailo, Mark ^b   Barkauskas, Donald A ^b   Gorlick, Richard ^a   Greally, John M ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

DNA methylation; Epigenetics; Osteosarcoma; Relapse

Indexed keywords

TOLL LIKE RECEPTOR 4; TLR4 PROTEIN, HUMAN; TUMOR MARKER;

ADOLESCENT; ARTICLE; CANCER RECURRENCE; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; DNA METHYLATION; EVENT FREE SURVIVAL; FEMALE; GENE LOCUS; GENETIC ASSOCIATION; HUMAN; HUMAN TISSUE; MALE; OSTEOSARCOMA; OVERALL SURVIVAL; PRIMARY TUMOR; PRINCIPAL COMPONENT ANALYSIS; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TUMOR BIOPSY; BONE TUMOR; GENETICS; PATHOLOGY;

ADOLESCENT; BIOMARKERS, TUMOR; BONE NEOPLASMS; CHILD; DNA METHYLATION; FEMALE; HUMANS; MALE; OSTEOSARCOMA; PROMOTER REGIONS, GENETIC; TOLL-LIKE RECEPTOR 4;

EID: 84924408124     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/15592294.2014.989084     Document Type: Article

References (51)

1. Janeway K, Gorlick R, Bernstein M. Osteosarcoma. Oncology of Infancy and Childhood Philadelphia: Saunders Elsevier 2009:871-910.
2. Bielack SS, Kempf-Bielack B, Delling G, Exner GU, Flege S, Helmke K, Kotz R, Salzer-Kuntschik M, Werner M, Winkelmann W, et al. Prognostic factors in high-grade osteosarcoma of the extremities or trunk: an analysis of 1,702 patients treated on neoadjuvant cooperative osteosarcoma study group protocols. J Clin Oncol 2002; 20:776-90; PMID:11821461; http://dx.doi.org/10.1200/JCO.20.3.776
3. Bramer JA, van Linge JH, Grimer RJ, Scholten RJ. Prognostic factors in localized extremity osteosarcoma: a systematic review. Eur J Surg Oncol 2009; 35:1030-6; PMID:19232880; http://dx.doi.org/10.1016/j.ejso.2009.01.011
4. Clark JC, Dass CR, Choong PF. A review of clinical and molecular prognostic factors in osteosarcoma. J Cancer Res Clin Oncol 2008; 134:281-97; PMID:17965883; http://dx.doi.org/10.1007/s00432-007-0330-x
5. Yang R, Li WW, Hoang BH, Kim H, Banerjee D, Kheradpour A, Healey JH, Meyers PA, Bertino JR, Gorlick R. Quantitative correlation between promoter methylation and messenger RNA levels of the reduced folate carrier. BMC Cancer 2008; 8:124; PMID:18452618; http://dx.doi.org/10.1186/1471-2407-8-124
6. Yang R, Qin J, Hoang BH, Healey JH, Gorlick R. Polymorphisms and methylation of the reduced folate carrier in osteosarcoma. Clin Orthop Relat Res 2008; 466:2046-51; PMID:18528741; http://dx.doi.org/10.1007/s11999-008-0323-3
7. Patino-Garcia A, Pineiro ES, Diez MZ, Iturriagagoitia LG, Klussmann FA, Ariznabarreta LS. Genetic and epigenetic alterations of the cell cycle regulators and tumor suppressor genes in pediatric osteosarcomas. J Pediatr Hematol Oncol 2003; 25:362-7; PMID:12759621; http://dx.doi.org/10.1097/00043426-200305000-00003
8. Hou P, Ji M, Yang B, Chen Z, Qiu J, Shi X, Lu Z. Quantitative analysis of promoter hypermethylation in multiple genes in osteosarcoma. Cancer 2006; 106:1602-9; PMID:16502411; http://dx.doi.org/10.1002/cncr.21762
9. Oh JH, Kim HS, Kim HH, Kim WH, Lee SH. Aberrant methylation of p14ARF gene correlates with poor survival in osteosarcoma. Clin Orthop Relat Res 2006; 442:216-22; PMID:16394764; http://dx.doi.org/10.1097/01.blo.0000188063.56091.69
10. Sadikovic B, Yoshimoto M, Al-Romaih K, Maire G, Zielenska M, Squire JA. In vitro analysis of integrated global high-resolution DNA methylation profiling with genomic imbalance and gene expression in osteosarcoma. PLoS One 2008; 3:e2834; PMID:18698372; http://dx.doi.org/10.1371/journal.pone.0002834
11. Kresse SH, Rydbeck H, Skarn M, Namlos HM, Barragan-Polania AH, Cleton-Jansen AM, Serra M, Liestol K, Hogendoorn PC, Hovig E, et al. Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma. PLos One 2012; 7:e48262; PMID:23144859; http://dx.doi.org/10.1371/journal.pone.0048262
12. Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM. Optimized design and data analysis of tagbased cytosine methylation assays. Genome Biol 2010; 11:R36; PMID:20359321; http://dx.doi.org/10.1186/gb-2010-11-4-r36
13. Rauch TA, Wu X, Zhong X, Riggs AD, Pfeifer GP. A human B cell methylome at 100-base pair resolution. Proc Natl Acad Sci U S A 2009; 106:671-8; PMID:19139413; http://dx.doi.org/10.1073/pnas.0812399106
14. Esteller M. Epigenetics in cancer. N Engl J Med 2008; 358:1148-59; PMID:18337604; http://dx.doi.org/10.1056/NEJMra072067
15. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, et al. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009; 41:178-86; PMID:19151715; http://dx.doi.org/10.1038/ng.298
16. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM. Targeted and genomescale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 2009; 27:361-8; PMID:19329998; http://dx.doi.org/10.1038/nbt.1533
17. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011; 473:43-9; PMID:21441907; http://dx.doi.org/10.1038/nature09906
18. Mutsaers AJ, Walkley CR. Cells of origin in osteosarcoma: mesenchymal stem cells or osteoblast committed cells? Bone 2014; 62:56-63; PMID:24530473; http://dx.doi.org/10.1016/j.bone.2014.02.003
19. Ziller MJ, Gu H, Muller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 2013; 500:477-81; PMID:23925113; http://dx.doi.org/10.1038/nature12433
20. Kempf-Bielack B, Bielack S, Jürgens H, Branscheid D, Berdel W, Exner G, Göbel U, Helmke K, Jundt G, Kabisch H, et al. Osteosarcoma relapse after combined modality therapy: an analysis of unselected patients in the Cooperative Osteosarcoma Study Group (COSS). J Clin Oncol 2005; 23:559-627; PMID:15659502; http://dx.doi.org/10.1200/JCO.2005.04.063
21. Cui Q, Jiang W, Guo J, Liu C, Li D, Wang X, Zeng Y. Relationship between hypermethylated MGMT gene and osteosarcoma necrosis rate after chemotherapy. Pathol Oncol Res 2011; 17:587-91; PMID:21424568; http://dx.doi.org/10.1007/s12253-010-9354-7
22. Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, van Putten W, Skrabanek L, et al. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell 2010; 17:13-27; PMID:20060365; http://dx.doi.org/10.1016/j.ccr.2009.11.020
23. Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP. CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A 1999; 96:8681-6; PMID:10411935; http://dx.doi.org/10.1073/pnas.96.15.8681
24. Man TK, Chintagumpala M, Visvanathan J, Shen J, Perlaky L, Hicks J, Johnson M, Davino N, Murray J, Helman L, et al. Expression profiles of osteosarcoma that can predict response to chemotherapy. Cancer Res 2005; 65:8142-50; PMID:16166288; http://dx.doi.org/10.1158/0008-5472.CAN-05-0985
25. Mintz MB, Sowers R, Brown KM, Hilmer SC, Mazza B, Huvos AG, Meyers PA, Lafleur B, McDonough WS, Henry MM, et al. An expression signature classifies chemotherapy-resistant pediatric osteosarcoma. Cancer Res 2005; 65:1748-54; PMID:15753370; http://dx.doi.org/10.1158/0008-5472.CAN-04-2463
26. Eden A, Gaudet F, Waghmare A, Jaenisch R. Chromosomal instability and tumors promoted byDNA hypomethylation. Science 2003; 300:455; PMID:12702868; http://dx.doi.org/10.1126/science.1083557
27. Gaudet F, Hodgson JG, Eden A, Jackson-Grusby L, Dausman J, Gray JW, Leonhardt H, Jaenisch R. Induction of tumors in mice by genomic hypomethylation. Science 2003; 300:489-92; PMID:12702876; http://dx.doi.org/10.1126/science.1083558
28. Chen X, Bahrami A, Pappo A, Easton J, Dalton J, Hedlund E, Ellison D, Shurtleff S, Wu G, Wei L, et al. Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Cell Rep 2014; 7:104-12; PMID:24703847; http://dx.doi.org/10.1016/j.celrep.2014.03.003
29. Bridge JA, Nelson M, McComb E, McGuire MH, Rosenthal H, Vergara G, Maale GE, Spanier S, Neff JR. Cytogenetic findings in 73 osteosarcoma specimens and a review of the literature. Cancer Genet Cytogenet 1997; 95:74-87; PMID:9140456; http://dx.doi.org/10.1016/S0165-4608(96)00306-8
30. Smida J, Baumhoer D, Rosemann M, Walch A, Bielack S, Poremba C, Remberger K, Korsching E, Scheurlen W, Dierkes C, et al. Genomic alterations and allelic imbalances are strong prognostic predictors in osteosarcoma. Clin Cancer Res 2010; 16:4256-67; PMID:20610556; http://dx.doi.org/10.1158/1078-0432.CCR-10-0284
31. Bork S, Pfister S, Witt H, Horn P, Korn B, Ho AD, Wagner W. DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells. Aging Cell 2010; 9:54-63; PMID:19895632; http://dx.doi.org/10.1111/j.1474-9726.2009.00535.x
32. Yu L, Wang L, Chen S. Endogenous toll-like receptor ligands and their biological significance. J Cell Mol Med 2010; 14:2592-603; PMID:20629986; http://dx.doi.org/10.1111/j.1582-4934.2010.01127.x
33. Yang H, Zhou H, Feng P, Zhou X, Wen H, Xie X, Shen H, Zhu X. Reduced expression of Toll-like receptor 4 inhibits human breast cancer cells proliferation and inflammatory cytokines secretion. J Exp Clin Cancer Res 2010; 29:92; http://dx.doi.org/10.1186/1756-9966-29-92
34. Simiantonaki N, Kurzik-Dumke U, Karyofylli G, Jayasinghe C, Michel-Schmidt R, Kirkpatrick CJ. Reduced expression of TLR4 is associated with the metastatic status of human colorectal cancer. Int J Mol Med 2007; 20:21-9; PMID:17549384
35. Waterman RS, Tomchuck SL, Henkle SL, Betancourt AM. A new mesenchymal stem cell (MSC) paradigm: polarization into a pro-inflammatory MSC1 or an Immunosuppressive MSC2 phenotype. PLoS One 2010; 5:e10088; PMID:20436665; http://dx.doi.org/10.1371/journal.pone.0010088
36. He G, Luo W, Li P, Remmers C, Netzer WJ, Hendrick J, Bettayeb K, Flajolet M, Gorelick F, Wennogle LP, et al. Gamma-secretase activating protein is a therapeutic target for Alzheimer’s disease. Nature 2010; 467:95-8; PMID:20811458; http://dx.doi.org/10.1038/nature09325
37. Ho WL, Che MI, Chou CH, Chang HH, Jeng YM, Hsu WM, Lin KH, Huang MC. B3GNT3 expression suppresses cell migration and invasion and predicts favorable outcomes in neuroblastoma. Cancer Sci 2013; 104:1600-8; PMID:24118321; http://dx.doi.org/10.1111/cas.12294
38. Lu CH, Wu WY, Lai YJ, Yang CM, Yu LC. Suppression of B3GNT7 gene expression in colon adenocarcinoma and its potential effect in the metastasis of colon cancer cells. Glycobiology 2014; 24:359-67; PMID:24418929; http://dx.doi.org/10.1093/glycob/cwu002
39. Ni J, Jiang Z, Shen L, Gao L, Yu M, Xu X, Zou S, Hua D, Wu S. beta3GnT8 regulates the metastatic potential of colorectal carcinoma cells by altering the glycosylation of CD147. Oncol Rep 2014; 31:1795-801; PMID:24573103
40. Shan SW, Lee DY, Deng Z, Shatseva T, Jeyapalan Z, Du WW, Zhang Y, Xuan JW, Yee SP, Siragam V, et al. MicroRNA MiR-17 retards tissue growth and represses fibronectin expression. Nat Cell Biol 2009; 11:1031-8; PMID:19633662; http://dx.doi.org/10.1038/ncb1917
41. Meyers PA, Schwartz CL, Krailo M, Kleinerman ES, Betcher D, Bernstein ML, Conrad E, Ferguson W, Gebhardt M, Goorin AM, et al. Osteosarcoma: a randomized, prospective trial of the addition of ifosfamide and/or muramyl tripeptide to cisplatin, doxorubicin, and high-dose methotrexate. J Clin Oncol 2005; 23:2004-11; PMID:15774791; http://dx.doi.org/10.1200/JCO.2005.06.031
42. Schwartz CL, Wexler LH, Devidas M, Goorin A, Grier H, Meyers P, Bernstein M. P9754 therapeutic intensification in non-metastatic osteosarcoma: a COG trial. J Clin Oncol 2004; 22:802; http://dx.doi.org/10.1200/JCO.2004.04.086
43. Ebb D, Meyers P, Grier H, Bernstein M, Gorlick R, Lipshultz SE, Krailo M, Devidas M, Barkauskas DA, Siegal GP, et al. Phase II trial of trastuzumab in combination with cytotoxic chemotherapy for treatment of metastatic osteosarcoma with human epidermal growth factor receptor 2 overexpression: a report from the children’s oncology group. J Clin Oncol 2012; 30:2545-51; PMID:22665540; http://dx.doi.org/10.1200/JCO.2011.37.4546
44. Kager L, Zoubek A, Potschger U, Kastner U, Flege S, Kempf-Bielack B, Branscheid D, Kotz R, Salzer-Kuntschik M, Winkelmann W, et al. Primary metastatic osteosarcoma: presentation and outcome of patients treated on neoadjuvant cooperative osteosarcoma study group protocols. J Clin Oncol 2003; 21:2011-8; PMID:12743156; http://dx.doi.org/10.1200/JCO.2003.08.132
45. Ozaki T, Schaefer KL, Wai D, Buerger H, Flege S, Lindner N, Kevric M, Diallo R, Bankfalvi A, Brinkschmidt C, et al. Genetic imbalances revealed by comparative genomic hybridization in osteosarcomas. Int J Cancer 2002; 102:355-65; PMID:12402305; http://dx.doi.org/10.1002/ijc.10709
46. Bayani J, Zielenska M, Pandita A, Al-Romaih K, Karaskova J, Harrison K, Bridge JA, Sorensen P, Thorner P, Squire JA. Spectral karyotyping identifies recurrent complex rearrangements of chromosomes 8, 17, and 20 in osteosarcomas. Genes Chromosomes Cancer 2003; 36:7-16; PMID:12461745; http://dx.doi.org/10.1002/gcc.10132
47. Atiye J, Wolf M, Kaur S, Monni O, Bohling T, Kivioja A, Tas E, Serra M, Tarkkanen M, Knuutila S. Gene amplifications in osteosarcoma-CGH microarray analysis. Genes Chromosomes Cancer 2005; 42:158-63; PMID:15540165; http://dx.doi.org/10.1002/gcc.20120
48. Li LC, Dahiya R. MethPrimer: designing primers for methylation PCRs. Bioinformatics 2002; 18:1427-31; PMID:12424112; http://dx.doi.org/10.1093/bioinformatics/18.11.1427
49. Thompson RF, Suzuki M, Lau KW, Greally JM. A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics 2009; 25:2164-70; PMID:19561019; http://dx.doi.org/10.1093/bioinformatics/btp382
50. Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res 2009; 37:3829-39; PMID:19386619; http://dx.doi.org/10.1093/nar/gkp260
51. Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 2009; 25:1952-8; PMID:19505939; http://dx.doi.org/10.1093/bioinformatics/btp340