Identification of novel target genes by an epigenetic reactivation screen of renal cancer

Cancer Research

Volumn 66, Issue 10, 2006, Pages 5021-5028

  Ibanez De Caceres, Inmaculada ^a   Dulaimi, Essel ^a   Hoffman, Amanda M ^a   Al Saleem, Tahseen ^a   Uzzo, Robert G ^a   Cairns, Paul ^a  

^a FOX CHASE CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; DNA; GROWTH DIFFERENTIATION FACTOR 5; HISTONE; RAS ASSOCIATION DOMAIN FAMILY PROTEIN 1A; SOMATOMEDIN BINDING PROTEIN 1; SOMATOMEDIN BINDING PROTEIN 3; TRICHOSTATIN A;

ARTICLE; COL1A1 GENE; CONTROLLED STUDY; DEACETYLATION; DNA MICROARRAY; EPIGENETICS; GENE; GENE EXPRESSION; GENE FREQUENCY; GENE IDENTIFICATION; GENE SILENCING; GENE TARGETING; HUMAN; HUMAN CELL; KIDNEY CANCER; NUCLEOTIDE SEQUENCE; PLAU GENE; PRIORITY JOURNAL; UPREGULATION; VALIDATION PROCESS;

ADULT; AGED; AZACITIDINE; BASE SEQUENCE; CARCINOMA, RENAL CELL; CELL LINE, TUMOR; COLLAGEN TYPE I; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE SILENCING; HUMANS; HYDROXAMIC ACIDS; INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 1; INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 3; KIDNEY NEOPLASMS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, NEOPLASM; UP-REGULATION;

EID: 33744932953     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-05-3365     Document Type: Article

References (44)

1. Jemal A, Tiwari HC, Murray T, et al. Cancer statistics, 2004. CA Cancer J Clin 2004;54:8-29.
2. Kovacs G, Akhtar M, Beckwith BJ, et al. The Heidelberg classification of renal cell tumours. J Pathol 1997;183: 131-3.
3. Storkel S, Eble JN, Adlakha K, et al. Classification of renal cell carcinoma: Workgroup No. 1. Union Internationale Contre le Cancer (UICC) and the American Joint Committee on Cancer (AJCC). Cancer 1997;80:987-9.
4. Zambrano NR, Lubensky IA, Merino MJ, Linehan WM, Walther MM. Histopathology and molecular genetics of renal tumors: toward unification of a classification system. J Urol 1999;162:1246-58.
5. Baylin SB, Herman JG, Graff JR, Vertino PM, Issa JP. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res 1998;72:141-96.
6. Jones PA, Laird PW. Cancer epigenetics comes of age. Nat Genet 1999;21:163-7.
7. Herman JG, Latif F, Weng Y, et al. Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma. Proc Natl Acad Sci U S A 1994;91:9700-4.
8. Herman JG, Merlo A, Mao L, et al. Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers. Cancer Res 1995;55:4525-30.
9. Morrissey C, Martinez A, Zatyka M, et al. Epigenetic inactivation of the RASSF1A 3p21.3 tumor suppressor gene in both clear cell and papillary renal cell carcinoma. Cancer Res 2001;61:7277-81.
10. Yoon JH, Dammann R, Pfeifer GP. Hypermethylation of the CpG island of the RASSF1A gene in ovarian and renal cell carcinomas. Int J Cancer 2001;94:212-7.
11. Dulaimi E, Ibanez De Caceres I, Uzzo RG, et al. Promoter hypermethylation profile of kidney cancer. Clin Cancer Res 2004;10:3972-9.
12. Bachman KE, Herman JG, Cora PG, et al. Methylation-associated silencing of the tissue inhibitor of metalloproteinase-3 gene suggests a suppressor role in kidney, brain, and other human cancers. Cancer Res 1999;59:798-802.
13. Marks PA, Richon VM, Miller T, Kelly WK. Histone deacetylase inhibitors. Adv Cancer Res 2004;91:137-68.
14. Cameron EE, Bachman KE, Myohanen S, Herman JG, Baylin SB. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet 1999;21:103-7.
15. Liang G, Gonzales FA, Jones PA, Orntoft TF, Thykjaer T. Analysis of gene induction in human fibroblasts and bladder cancer cells exposed to the methylation inhibitor 5-aza-2′-deoxycytidine. Cancer Res 2002;62:961-6.
16. Suzuki H, Gabrielson E, Chen W, et al. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 2002;31:141-9.
17. Yamashita K, Upadhyay S, Osada M, et al. Pharmacologic unmasking of epigenetically silenced tumor suppressor genes in esophageal squamous cell carcinoma. Cancer Cell 2002;2:485-95.
18. Sato N, Fukushima N, Maitra A, et al. Discovery of novel targets for aberrant methylation in pancreatic carcinoma using high-throughput microarrays. Cancer Res 2003;63:3735-42.
19. Tokumaru Y, Yamashita K, Osada M, et al. Inverse correlation between cyclin A1 hypermethylation and p53 mutation in head and neck cancer identified by reversal of epigenetic silencing. Cancer Res 2004;64: 5982-7.
20. Lodygin D, Epanchintsev A, Menssen A, Diebold J, Hermeking H. Functional epigenomics identifies genes frequently silenced in prostate cancer. Cancer Res 2005; 65:4218-27.
21. Battagli C, Uzzo RG, Dulaimi E, et al. Promoter hypermethylation of tumor suppressor genes in urine from kidney cancer patients. Cancer Res 2003;63:8695-9.
22. Sambrook J, Russell DW. Molecular cloning. A laboratory manual. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2001.
23. 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.
24. Wheeler JM, Beck NE, Kim HC, Tomlinson IP, Mortensen NJ, Bodmer WF. Mechanisms of inactivation of mismatch repair genes in human colorectal cancer cell lines: the predominant role of hMLH1. Proc Natl Acad Sci U S A 1999;96:10296-301.
25. 6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia. Cancer Res 1999;59:793-7.
26. Paz MF, Fraga MF, Avila S, et al. A systematic profile of DNA methylation in human cancer cell lines. Cancer Res 2003;63:1114-21.
27. Wade PA. Methyl CpG binding proteins: coupling chromatin architecture to gene regulation. Oncogene 2001;20:3166-73.
28. Bender CM, Gonzalgo ML, Gonzales FA, Nguyen CT, Robertson KD, Jones PA. Roles of cell division and gene transcription in the methylation of CpG islands. Mol Cell Biol 1999;19:6690-8.
29. Hoque MO, Begum S, Topaloglu O, et al. Quantitative detection of promoter hypermethylation of multiple genes in the tumor, urine, and serum DNA of patients with renal cancer. Cancer Res 2004;64:5511-7.
30. Monta R, Ishikawa J, Tsutsumi M, et al. Allelotype of renal cell carcinoma. Cancer Res 1991;51:820-3.
31. Thrash-Bingham CA, Greenberg RE, Howard S, et al. Comprehensive allelotyping of human renal cell carcinomas using microsatellite DNA probes. Proc Natl Acad Sci U S A 1995;92:2854-8.
32. Chang YS, Kong G, Sun S, et al. Clinical significance of insulin-like growth factor-binding protein-3 expression in stage I non-small cell lung cancer. Clin Cancer Res 2002;8:3796-802.
33. Chan JM, Stampfer MJ, Giovannucci E, et al. Plasma insulin-like growth factor-I and prostate cancer risk: a prospective study. Science 1998;279:563-6.
34. Gong Y, Cui L, Minuk GY. The expression of insulin-like growth factor binding proteins in human hepatocellular carcinoma. Mol Cell Biochem 2000;207:101-4.
35. Hanafusa T, Yumoto Y, Nouso K, et al. Reduced expression of insulin-like growth factor binding protein-3 and its promoter hypermethylation in human hepatocellular carcinoma Cancer Lett 2002;176:149-58.
36. Fraga MF, Herranz M, Espada J, et al. A mouse skin multistage carcinogenesis model reflects the aberrant DNA methylation patterns of human tumors. Cancer Res 2004;64:5527-34.
37. 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; 63:1789-97.
38. Paz MF, Wei S, Cigudosa JC, et al. Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases. Hum Mol Genet 2003;12:2209-19.
39. Ahuja N, Li Q, Mohan AL, Baylin SB, Issa JP. Aging and DNA methylation in colorectal mucosa and cancer. Cancer Res 1998;58:5489-94.
40. Agathanggelou A, Bieche I, Ahmed-Choudhury J, et al. Identification of novel gene expression targets for the Ras association domain family 1 (RASSF1A) tumor suppressor gene in non-small cell lung cancer and neuroblastoma. Cancer Res 2003;63:5344-51.
41. Merlo A, Herman JG, Mao L, et al. 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nat Med 1995;1:686-92.
42. Costello JF, Fruhwald MC, Smiraglia DJ, et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet 2000;24:132-8.
43. Wei SH, Chen CM, Strathdee G, et al. Methylation micro-array analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. Clin Cancer Res 2002;8:2246-52.
44. Morris MR, Gentle D, Abdulrahman M, et al. Tumor suppressor activity and epigenetic inactivation of hepatocyte growth factor activator inhibitor type 2/SPINT2 in papillary and clear cell renal cell carcinoma. Cancer Res 2005;65:4598-606.