Identification of an epigenetic profile classifier that is associated with survival in head and neck cancer

Cancer Research

Volumn 72, Issue 11, 2012, Pages 2728-2737

  Poage, Graham M ^a,b   Butler, Rondi A ^c   Houseman, E Andrés ^c,e   McClean, Michael D ^f   Nelson, Heather H ^g,h   Christensen, Brock C ⁱ   Marsit, Carmen J ⁱ   Kelsey, Karl T ^c,d  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b BROWN UNIVERSITY   (United States)

^c BROWN UNIVERSITY   (United States)

^d BROWN UNIVERSITY   (United States)

^e OREGON STATE UNIVERSITY   (United States)

^f BOSTON UNIVERSITY   (United States)

^g UNIVERSITY OF MINNESOTA   (United States)

^h UNIVERSITY OF MINNESOTA   (United States)

ⁱ DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; DNA; POLYCOMB GROUP PROTEIN; TRANSCRIPTION FACTOR; TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1;

ADULT; AGED; ALDH3A1 GENE; ARTICLE; CANCER PATIENT; CANCER SURVIVAL; CLASSIFIER; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EPIGENETICS; FEMALE; GENE LOCUS; GENE SEQUENCE; HEAD AND NECK CANCER; HEAD AND NECK SQUAMOUS CELL CARCINOMA; HUMAN; HUMAN TISSUE; INTERSPERSED REPEAT; MAJOR CLINICAL STUDY; MALE; OVERALL SURVIVAL; PRIORITY JOURNAL; TAP1 GENE; TUMOR GENE;

ALDEHYDE DEHYDROGENASE; ATP-BINDING CASSETTE TRANSPORTERS; CARCINOMA, SQUAMOUS CELL; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; HEAD AND NECK NEOPLASMS; HUMANS; PROGNOSIS; PROPORTIONAL HAZARDS MODELS;

EID: 84861847134     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-11-4121-T     Document Type: Article

References (53)

1. Edwards BK, Ward E, Kohler BA, Eheman C, Zauber AG, Anderson RN, et al. Annual report to the nation on the status of cancer, 1975-2006, featuring colorectal cancer trends and impact of interventions (risk factors, screening, and treatment) to reduce future rates. Cancer 2010;116:544-73.
2. Adelstein DJ, Ridge JA, Gillison ML, Chaturvedi AK, D'Souza G, Gravitt PE, et al. Head and neck squamous cell cancer and the human papillomavirus: summary of a National Cancer Institute State of the Science Meeting, November. 9-10, 2008, Washington, D.C. Head Neck 2009;31:1393-422.
3. Avissar M, McClean MD, Kelsey KT, Marsit CJ. MicroRNA expression in head and neck cancer associates with alcohol consumption and survival. Carcinogenesis 2009;30:2059-63.
4. Vlatkovic N, El-Fert A, Devling T, Ray-Sinha A, Gore DM, Rubbi CP, et al. Loss of MTBP expression is associated with reduced survival in a biomarker-defined subset of patients with squamous cell carcinoma of the head and neck. Cancer 2011;13:2939-50.
5. Chang KP, Wu CC, Chen HC, Chen SJ, Peng PH, Tsang NM, et al. Identification of candidate nasopharyngeal carcinoma serum biomarkers by cancer cell secretome and tissue transcriptome analysis: potential usage of cystatin A for predicting nodal stage and poor prognosis. Proteomics 2010;10:2644-60.
6. Rosas SL, Koch W, da Costa Carvalho MG, Wu L, Califano J, Westra W, et al. Promoter hypermethylation patterns of p16, O6-methylguanine-DNA- methyltransferase, and death-associated protein kinase in tumors and saliva of head and neck cancer patients. Cancer Res 2001;61:939-42. (Pubitemid 32174408)
7. Ha PK, Califano JA. Promoter methylation and inactivation of tumour-suppressor genes in oral squamous-cell carcinoma. Lancet Oncol 2006;7:77-82. (Pubitemid 43025396)
8. Hasegawa M, Nelson HH, Peters E, Ringstrom E, Posner M, Kelsey KT. Patterns of gene promoter methylation in squamous cell cancer of the head and neck. Oncogene 2002;21:4231-6. (Pubitemid 34753829)
9. Bennett KL, Romigh T, Eng C. Disruption of transforming growth factor-beta signaling by five frequently methylated genes leads to head and neck squamous cell carcinoma pathogenesis. Cancer Res 2009;69:9301-5.
10. Langevin SM, Stone RA, Bunker CH, Lyons-Weiler MA, Laframboise WA, Kelly L, et al. MicroRNA-137 promoter methylation is associated with poorer overall survival in patients with squamous cell carcinoma of the head and neck. Cancer 2011;117:1454-62.
11. Misawa K, Ueda Y, Kanazawa T, Misawa Y, Jang I, Brenner JC, et al. Epigenetic inactivation of galanin receptor. 1 in head and neck cancer. Clin Cancer Res 2008;14:7604-13.
12. Estilo CL, O-Charoenrat P, Ngai I, Patel SG, Reddy PG, Dao S, et al. The role of novel oncogenes squamous cell carcinoma-related oncogene and phosphatidylinositol. 3-kinase p110alpha in squamous cell carcinoma of the oral tongue. Clin Cancer Res 2003;9:2300-6.
13. Calmon MF, Rodrigues RV, Kaneto CM, Moura RP, Silva SD, Mota LD, et al. Epigenetic silencing of CRABP2 and MX1 in head and neck tumors. Neoplasia 2009;11:1329-39.
14. Estecio MR, Gallegos J, Vallot C, Castoro RJ, Chung W, Maegawa S, et al. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res 2010;20: 1369-82.
15. Wolff EM, Chihara Y, Pan F, Weisenberger DJ, Siegmund KD, Sugano K, et al. Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res 2010;70:8169-78.
16. Poage GM, Houseman EA, Christensen BC, Butler RA, Avissar-Whiting M, McClean MD, et al. Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer. Clin Cancer Res 2011;17:3579-89.
17. Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schubeler D. Identification of genetic elements that autonomously determine DNA methylation states. Nat Genet 2011;43:1091-7.
18. Marsit CJ, McClean MD, Furniss CS, Kelsey KT. Epigenetic inactivation of the SFRP genes is associated with drinking, smoking and HPV in head and neck squamous cell carcinoma. Int J Cancer 2006;119: 1761-6. (Pubitemid 44356831)
19. Furniss CS, McClean MD, Smith JF, Bryan J, Nelson HH, Peters ES, et al. Human papillomavirus. 16 and head and neck squamous cell carcinoma. Int J Cancer 2007;120:2386-92. (Pubitemid 46642125)
20. Marsit CJ, Christensen BC, Houseman EA, Karagas MR, Wrensch MR, Yeh RF, et al. Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma. Carcinogenesis 2009;30:416-22.
21. Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, et al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 2009;1:177-200.
22. Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A 2002;99:3740-5. (Pubitemid 34252176)
23. Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev 2006;20:1123-36.
24. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006;125:301-13. (Pubitemid 44313811)
25. Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 2007;39:232-6. (Pubitemid 46184355)
26. Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, et al. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res 2006;16:890-900. (Pubitemid 43992913)
27. Bollati V, Baccarelli A, Hou L, Bonzini M, Fustinoni S, Cavallo D, et al. Changes in DNA methylation patterns in subjects exposed to low-dose benzene. Cancer Res 2007;67:876-80.
28. Kong KL, Kwong DL, Fu L, Chan TH, Chen L, Liu H, et al. Characterization of a candidate tumor suppressor gene uroplakin 1A in esophageal squamous cell carcinoma. Cancer Res 2010;70:8832-41.
29. Hoque MO, Begum S, Brait M, Jeronimo C, Zahurak M, Ostrow KL, et al. Tissue inhibitor of metalloproteinases-3 promoter methylation is an independent prognostic factor for bladder cancer. J Urol 2008;179: 743-7.
30. Wang J, Lee JJ, Wang L, Liu DD, Lu C, Fan YH, et al. Value of p16INK4a and RASSF1A promoter hypermethylation in prognosis of patients with resectable non-small cell lung cancer. Clin Cancer Res 2004; 10:6119-25. (Pubitemid 39287517)
31. Marsit CJ, Liu M, Nelson HH, Posner M, Suzuki M, Kelsey KT. Inactivation of the Fanconi anemia/BRCA pathway in lung and oral cancers: implications for treatment and survival. Oncogene 2004;23: 1000-4. (Pubitemid 38250946)
32. Ghosh A, Ghosh S, Maiti GP, Sabbir MG, Zabarovsky ER, Roy A, et al. Frequent alterations of the candidate genes hMLH1, ITGA9 and RBSP3 in early dysplastic lesions of head and neck: clinical and prognostic significance. Cancer Sci 2010;101:1511-20.
33. Marsit CJ, Posner MR, McClean MD, Kelsey KT. Hypermethylation of E-cadherin is an independent predictor of improved survival in head and neck squamous cell carcinoma. Cancer 2008;113: 1566-71.
34. Huang KH, Huang SF, Chen IH, Liao CT, Wang HM, Hsieh LL. Methylation of RASSF1A, RASSF2A, and HIN-1 is associated with poor outcome after radiotherapy, but not surgery, in oral squamous cell carcinoma. Clin Cancer Res 2009;15:4174-80.
35. Long NK, Kato K, Yamashita T, Makita H, Toida M, Hatakeyama D, et al. Hypermethylation of the RECK gene predicts poor prognosis in oral squamous cell carcinomas. Oral Oncol 2008;44:1052-8.
36. Puri SK, Si L, Fan CY, Hanna E. Aberrant promoter hypermethylation of multiple genes in head and neck squamous cell carcinoma. Am J Otolaryngol 2005;26:12-7. (Pubitemid 40038069)
37. Langevin SM, Houseman EA, Christensen BC, Wiencke JK, Nelson HH, Karagas MR, et al. The influence of aging, environmental exposures and local sequence features on the variation of DNA methylation in blood. Epigenetics 2011;6:908-19.
38. Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 2008;30:755-66.
39. Baylin SB. Stem cells, cancer, and epigenetics (October 31, 2009), StemBook, ed. The Stem Cell Research Community, StemBook, doi/10.3824/stembook. 1.50.1, http://www.stembook.org.
40. Crabb DW, Matsumoto M, Chang D, You M. Overview of the role of alcohol dehydrogenase and aldehyde dehydrogenase and their variants in the genesis of alcohol-related pathology. Proc Nutr Soc 2004;63:49-63. (Pubitemid 38543873)
41. Pappa A, Brown D, Koutalos Y, DeGregori J, White C, Vasiliou V. Human aldehyde dehydrogenase 3A1 inhibits proliferation and promotes survival of human corneal epithelial cells. J Biol Chem 2005;280:27998-8006. (Pubitemid 41076917)
42. Afsar NA, Haenisch S, Mateen A, Usman A, Ufer M, Ahmed KZ, et al. Genotype frequencies of selected drug metabolizing enzymes and ABC drug transporters among breast cancer patients on FAC chemotherapy. Basic Clin Pharmacol Toxicol 2010;107:570-6.
43. Banh A, Xiao N, Cao H, Chen CH, Kuo P, Krakow T, et al. A novel aldehyde dehydrogenase-3 activator leads to adult salivary stem cell enrichment in vivo. Clin Cancer Res 2011;17:7265-72.
44. Leibowitz MS, Andrade Filho PA, Ferrone S, Ferris RL. Deficiency of activated STAT1 in head and neck cancer cells mediates TAP1-dependent escape from cytotoxic T lymphocytes. Cancer Immunol Immunother 2011;60:525-35.
45. Bandoh N, Ogino T, Katayama A, Takahara M, Katada A, Hayashi T, et al. HLA class I antigen and transporter associated with antigen processing downregulation in metastatic lesions of head and neck squamous cell carcinoma as a marker of poor prognosis. Oncol Rep 2010;23:933-9.
46. Lou Y, Vitalis TZ, Basha G, Cai B, Chen SS, Choi KB, et al. Restoration of the expression of transporters associated with antigen processing in lung carcinoma increases tumor-specific immune responses and survival. Cancer Res 2005;65:7926-33. (Pubitemid 41297271)
47. Meissner M, Reichert TE, Kunkel M, Gooding W, Whiteside TL, Ferrone S, et al. Defects in the human leukocyte antigen class I antigen processing machinery in head and neck squamous cell carcinoma: association with clinical outcome. Clin Cancer Res 2005;11:2552-60. (Pubitemid 40569453)
48. Ogino T, Shigyo H, Ishii H, Katayama A, Miyokawa N, Harabuchi Y, et al. HLA class I antigen down-regulation in primary laryngeal squamous cell carcinoma lesions as a poor prognostic marker. Cancer Res 2006;66:9281-9. (Pubitemid 44521150)
49. Lopez-Albaitero A, Nayak JV, Ogino T, Machandia A, Gooding W, DeLeo AB, et al. Role of antigen-processing machinery in the in vitro resistance of squamous cell carcinoma of the head and neck cells to recognition by CTL. J Immunol 2006;176:3402-9. (Pubitemid 43363987)
50. Nie L, Zhao Y, Wu W, Yang YZ, Wang HC, Sun XH. Notch-induced Asb2 expression promotes protein ubiquitination by forming noncanonical E3 ligase complexes. Cell Res 2011;21:754-69.
51. Guibal FC, Moog-Lutz C, Smolewski P, Di Gioia Y, Darzynkiewicz Z, Lutz PG, et al. ASB-2 inhibits growth and promotes commitment in myeloid leukemia cells. J Biol Chem 2002;277:218-24. (Pubitemid 34952048)
52. Chung W, Kwabi-Addo B, Ittmann M, Jelinek J, Shen L, Yu Y, et al. Identification of novel tumor markers in prostate, colon and breast cancer by unbiased methylation profiling. PLoS One 2008;3:e2079.
53. Taylor KH, Pena-Hernandez KE, Davis JW, Arthur GL, Duff DJ, Shi H, et al. Large-scale CpG methylation analysis identifies novel candidate genes and reveals methylation hotspots in acute lymphoblastic leukemia. Cancer Res 2007;67:2617-25. (Pubitemid 46548948)