MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells

Cancer Research

Volumn 66, Issue 16, 2006, Pages 7939-7947

  Rauch, Tibor ^a   Li, Hongwei ^a   Wu, Xiwei ^a   Pfeifer, Gerd P ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HOMEODOMAIN PROTEIN; METHYL CPG BINDING PROTEIN 2; TRANSCRIPTION FACTOR PAX7; TRANSCRIPTION FACTOR PAX9;

ARTICLE; BINDING AFFINITY; CANCER CELL; CELL DIFFERENTIATION; CELL TYPE; CHROMOSOME; CHROMOSOME 3P; CONTROLLED STUDY; CPG ISLAND; DLEC1 GENE; DLX1 GENE; DNA METHYLATION; GENE; GENE LOCATION; GENE TARGETING; GENOME; HOXB13 GENE; HOXD1 GENE; HOXD3 GENE; HUMAN; HUMAN CELL; LBX1 GENE; LHX2 GENE; LHX4 GENE; LUNG CANCER; MELANOMA; MICROARRAY ANALYSIS; ONECUT2 GENE; PRIORITY JOURNAL; SIX2 GENE; TUMOR SUPPRESSOR GENE;

CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 3; DINUCLEOSIDE PHOSPHATES; DNA; DNA METHYLATION; DNA, NEOPLASM; FALSE POSITIVE REACTIONS; HUMANS; LUNG NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMIDS; TUMOR SUPPRESSOR PROTEINS;

EID: 33748055105     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-06-1888     Document Type: Article

References (50)

1. 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.
2. Esteller M, Corn PG, Baylin SB, Herman JG. A gene hypermethylation profile of human cancer. Cancer Res 2001;61:3225-9.
3. Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet 2002;3:415-28.
4. Issa JP. CpG island methylator phenotype in cancer. Nat Rev Cancer 2004;4:988-93.
5. Baylin S, Bestor TH. Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell 2002;1:299-305.
6. Keshet I, Schlesinger Y, Farkash S, et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 2006;38:149-53.
7. Ushijima T. Detection and interpretation of altered methylation patterns in cancer cells. Nat Rev Cancer 2005;5:223-31.
8. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002;16:6-21.
9. Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet 2006; 7:21-33.
10. Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. Predicting aberrant CpG island methylation. Proc Natl Acad Sci U S A 2003;100:12253-8.
11. Shiraishi M, Sekiguchi A, Terry MJ, et al. A comprehensive catalog of CpG islands methylated in human lung adenocarcinomas for the identification of tumor suppressor genes. Oncogene 2002;21:3804-13.
12. Dammann R, Strunnikova M, Schagdarsurengin U, et al. CpG island methylation and expression of tumour-associated genes in lung carcinoma. Eur J Cancer 2005; 41:1223-36.
13. Topaloglu O, Hoque MO, Tokumaru Y, et al. Detection of promoter hypermethylation of multiple genes in the tumor and bronchoalveolar lavage of patients with lung cancer. Clin Cancer Res 2004;10: 2284-8.
14. Yanagawa N, Tamura G, Oizumi H, Takahashi N, Shimazaki Y, Motoyama T. Promoter hypermethylation of tumor suppressor and tumor-related genes in non-small cell lung cancers. Cancer Sci 2003;94:589-92.
15. Zochbauer-Muller S, Fong KM, Virmani AK, Geradts J, Gazdar AF, Minna JD. Aberrant promoter methylation of multiple genes in non-small cell lung cancers. Cancer Res 2001;61:249-55.
16. Dammann R, Li C, Yoon JH, Chin PL, Bates S, Pfeifer GP. Epigenetic inactivation of a RAS association domain family protein from the lung tumour suppressor locus 3p21.3. Nat Genet 2000;25:315-9.
17. Belinsky SA. Gene-promoter hypermethylation as a biomarker in lung cancer. Nat Rev Cancer 2004;4:707-17.
18. Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer 2003;3:253-66.
19. Shi H, Wei SH, Leu YW, et al. Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation. Cancer Res 2003;63:2164-71.
20. Suzuki H, Gabrielson E, Chen W, et al. A genomic screen for genes up-regulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 2002;31:141-9.
21. Yamashita K, Upadhyay S, Osada M, et al. Pharmacologic unmasking of epigeneticaUy silenced tumor suppressor genes in esophageal squamous cell carcinoma. Cancer Cell 2002;2:485-95.
22. Ching TT, Maunakea AK, Jun P, et al. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet 2005;37:645-51.
23. Weber M, Davies JJ, Wittig D, et al. Chromosomewide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005;37:853-62.
24. Rauch T, Pfeifer GP. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 2005;85: 1172-80.
25. Jiang CL, Jin SG, Pfeifer GP. MBD3L1 is a transcriptional repressor that interacts with MBD2 and components of the NuRD complex. J Biol Chem 2004;279: 52456-64.
26. Cross SH, Charlton JA, Nan X Bird AP. Purification of CpG islands using a methylated DNA binding column. Nat Genet 1994;6:236-44.
27. Heisler LE, Torti D, Boutros PC, et al. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res 2005;33:2952-61.
28. Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 1997;25:2532-4.
29. Fraga MF, Ballestar E, Montoya G, Taysavang P, Wade PA, Esteller M. The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties. Nucleic Acids Res 2003;31:1765-74.
30. Klose RJ, Sarraf SA, Schmiedeberg L, McDermott SM, Stancheva I, Bird AP. DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG. Mol Cell 2005;19:667-78.
31. Jiang CL, Jin SG, Lee DH, et al. MBD3L1 and MBD3L2, two new proteins homologous to the methyl-CpG-binding proteins MBD2 and MBD3: characterization of MBD3L1 as a testis-specific transcriptional repressor. Genomics 2002;80:621-9.
32. Daigo Y, Nishiwaki T, Kawasoe T, Tamari M, Tsuchiya E, Nakamura Y. Molecular cloning of a candidate tumor suppressor gene, DLC1, from chromosome 3p21.3. Cancer Res 1999;59:1966-72.
33. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994;22:2990-7.
34. Wistuba II, Behrens C, Virmani AK, et al. High resolution chromosome 3p allelotyping of human lung cancer and preneoplastic/preinvasive bronchial epithelium reveals multiple, discontinuous sites of 3p allele loss and three regions of frequent breakpoints. Cancer Res 2000;60:1949-60.
35. Tomizawa Y, Sekido Y, Kondo M, et al. Inhibition of lung cancer cell growth and induction of apoptosis after reexpression of 3p21.3 candidate tumor suppressor gene SEMA3B. Proc Natl Acad Sci U S A 2001;98: 13954-9.
36. Grier DG, Thompson A, Kwasniewska A, McGonigle GJ, Halliday HL, Lappin TR. The pathophysiology of HOX genes and their role in cancer. J Pathol 2005;205: 154-71.
37. Samuel S, Naora H. Homeobox gene expression in cancer: insights from developmental regulation and deregulation. Eur J Cancer 2005;41:2428-37.
38. Okuda H, Toyota M, Ishida W, et al. Epigenetic inactivation of the candidate tumor suppressor gene HOXB13 in human renal cell carcinoma. Oncogene 2006; 25:1733-42.
39. Shiraishi M, Sekiguchi A, Oates AJ, Terry MJ, Miyamoto Y. HOX gene clusters are hotspots of de novo methylation in CpG islands of human lung adenocarcinomas. Oncogene 2002;21:3659-62.
40. Raman V, Martensen SA, Reisman D, et al. Compromised HOXA5 function can limit p53 expression in human breast tumours. Nature 2000;405:974-8.
41. Asatiani E, Huang WX, Wang A, et al. Deletion, methylation, and expression of the NKX3.1 suppressor gene in primary human prostate cancer. Cancer Res 2005;65:1164-73.
42. Sharma K, Sheng HZ, Lettieri K, et al. LIM homeodomain factors Lhx3 and Lhx4 assign subtype identities for motor neurons. Cell 1998;95:817-28.
43. Porter FD, Drago J, Xu Y, et al. Lhx2, a LIM homeobox gene, is required for eye, forebrain, and definitive erythrocyte development Development 1997;124:2935-44.
44. Cao R, Zhang Y. SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol Cell 2004;15:57-67.
45. Boyer LA, Plath K, Zeitlinger J, et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006;441:349-53.
46. Lee TI, Jenner RG, Boyer LA, et al. Control of developmental regulators by polycomb in human embryonic stem cells. Cell 2006;125:301-13.
47. Vire E, Brenner C, Deplus R, et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2006;439:871-4.
48. Hernandez-Munoz I, Taghavi P, Kuijl C, Neefjes J, van Lohuizen M. Association of BMI1 with polycomb bodies is dynamic and requires PRC2/EZH2 and the maintenance DNA methyltransferase DNMT1. Mol Cell Biol 2005;25:11047-58.
49. Ding L, Erdmann C, Chinnaiyan AM, Merajver SD, Kleer CG. Identification of EZH2 as a molecular marker for a precancerous state in morphologically normal breast tissues. Cancer Res 2006;66:4095-9.
50. Varambally S, Dhanasekaran SM, Zhou M, et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 2002;419:624-9.