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Journal of Translational Medicine
Published in: Journal of Translational Medicine 1/2010

Open Access 01-12-2010 | Research

Multiplexed methylation profiles of tumor suppressor genes and clinical outcome in lung cancer

Authors: Mónica Castro, Laura Grau, Patricia Puerta, Liliana Gimenez, Julio Venditti, Silvia Quadrelli, Marta Sánchez-Carbayo

Published in: Journal of Translational Medicine | Issue 1/2010

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Abstract

Background

Changes in DNA methylation of crucial cancer genes including tumor suppressors can occur early in carcinogenesis, being potentially important early indicators of cancer. The objective of this study was to examine a multiplexed approach to assess the methylation of tumor suppressor genes as tumor stratification and clinical outcome prognostic biomarkers for lung cancer.

Methods

A multicandidate probe panel interrogated DNA for aberrant methylation status in 18 tumor suppressor genes in lung cancer using a methylation-specific multiplex ligation-dependent probe amplification assay (MS-MLPA). Lung cancer cell lines (n = 7), and primary lung tumors (n = 54) were examined using MS-MLPA.

Results

Genes frequently methylated in lung cancer cell lines including SCGB3A1, ID4, CCND2 were found among the most commonly methylated in the lung tumors analyzed. HLTF, BNIP3, H2AFX, CACNA1G, TGIF, ID4 and CACNA1A were identified as novel tumor suppressor candidates methylated in lung tumors. The most frequently methylated genes in lung tumors were SCGB3A1 and DLC1 (both 50.0%). Methylation rates for ID4, DCL1, BNIP3, H2AFX, CACNA1G and TIMP3 were significantly different between squamous and adenocarcinomas. Methylation of RUNX3, SCGB3A1, SFRP4, and DLC1 was significantly associated with the extent of the disease when comparing localized versus metastatic tumors. Moreover, methylation of HTLF, SFRP5 and TIMP3 were significantly associated with overall survival.

Conclusions

MS-MLPA can be used for classification of certain types of lung tumors and clinical outcome prediction. This latter is clinically relevant by offering an adjunct strategy for the clinical management of lung cancer patients.
Appendix
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Literature
1.
Jemal A, Siegel R, Ward E, Murray T, Xu J, Thun MJ: Cancer statistics. CA Cancer J Clin. 2009, 59 (4): 225-49. 10.3322/caac.20006.PubMedCrossRef
2.
Herbst RS, Heymach JV, Lippman SM: Lung Cancer. J Med N Engl. 2008, 359 (13): 1367-80. 10.1056/NEJMra0802714.CrossRef
3.
Pérez-Soler R: Individualized therapy in non-small-cell lung cancer: future versus current clinical practice. Oncogene. 2009, 28 (Suppl 1): S38-S45. 10.1038/onc.2009.200.PubMedCrossRef
4.
Heller G, Zielinski CC, Zöchbauer-Müller S: Lung cancer: From single-gene methylation to methylome profiling. Cancer Metastasis Rev. 2010, 29 (1): 95-107. 10.1007/s10555-010-9203-x.PubMedCrossRef
5.
Belinsky SA: Gene promoter hypermethylation as a biomarker in lung cancer. Nature Cancer Rev. 2004, 4 (9): 707-17. 10.1038/nrc1432.CrossRef
6.
7.
Costello JF, Fruhwald MC, Smiraglia DJ: Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet. 2000, 24 (2): 132-8. 10.1038/72785.PubMedCrossRef
8.
Esteller M: CpG island hypermethylation and tumor suppressor genes: A booming present, a brighter future. Oncogene. 2002, 21 (35): 5427-5440. 10.1038/sj.onc.1205600.PubMedCrossRef
9.
Jones PA, Baylin SB: The fundamental role of epigenetic events in cancer. Nat Rev Genet. 2003, 3 (6): 415-28.
10.
Herman JG, Baylin SB: Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003, 349 (21): 2042-2054. 10.1056/NEJMra023075.PubMedCrossRef
11.
Feinberg AP, Ohlsson R, Henikoff S: The epigenetic progenitor origin of human cancer. Nat Rev Genet. 2006, 7 (1): 21-33. 10.1038/nrg1748.PubMedCrossRef
12.
Hu YC, Sidransky D, Ahrendt SA: Molecular detection approaches for smoking associated tumors. Oncogene. 2002, 21 (48): 7289-97. 10.1038/sj.onc.1205805.PubMedCrossRef
13.
Rauch T, Wang Z, Zhang X, Zhong X, Wu X, Lau SK, Kernstine KH, Riggs AD, Pfeifer GP: Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci USA. 2007, 104 (13): 5527-32. 10.1073/pnas.0701059104.PubMedPubMedCentralCrossRef
14.
Wang Y, Zhang D, Zheng W, Luo J, Bai Y, Lu Z: Multiple gene methylation of nonsmall cell lung cancers evaluated with 3-dimensional microarray. Cancer. 2008, 112 (6): 1325-36. 10.1002/cncr.23312.PubMedCrossRef
15.
Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G: Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 2002, 30 (12): e57-10.1093/nar/gnf056.PubMedPubMedCentralCrossRef
16.
Nygren AO, Ameziane N, Duarte HM, Vijzelaar RN, Waisfisz Q, Hess CJ, Schouten JP, Errami A: Methylation-specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences. Nucleic Acids Res. 2005, 33 (14): e128-10.1093/nar/gni127.PubMedPubMedCentralCrossRef
17.
Worsham MJ, Chen KM, Meduri V, Nygren AO, Errami A, Schouten JP, Benninger MS: Epigenetic events of disease progression in head and neck squamous cell carcinoma. Arch Otolaryngol Head Neck Surg. 2006, 132 (6): 668-677. 10.1001/archotol.132.6.668.PubMedCrossRef
18.
Jeuken JW, Cornelissen SJ, Vriezen M, Dekkers MM, Errami A, Sijben A, Boots-Sprenger SH, Wesseling P: MS-MLPA: an attractive alternative laboratory assay for robust, reliable, and semiquantitative detection of MGMT promoter hypermethylation in gliomas. Lab Invest. 2007, 87 (10): 1055-65. 10.1038/labinvest.3700664.PubMedCrossRef
19.
Berkhout M, Nagtegaal ID, Cornelissen SJ, Dekkers MM, van de Molengraft FJ, Peters WH, Nagengast FM, van Krieken JH, Jeuken JW: Chromosomal and methylation alterations in sporadic and familial adenomatous polyposis-related duodenal carcinomas. Mod Pathol. 2007, 20 (12): 1253-62. 10.1038/modpathol.3800952.PubMedCrossRef
20.
Henken FE, Wilting SM, Overmeer RM, van Rietschoten JG, Nygren AO, Errami A, Schouten JP, Meijer CJ, Snijders PJ, Steenbergen RD: Sequential gene promoter methylation during HPV-induced cervical carcinogenesis. Br J Cancer. 2007, 97 (10): 1457-64. 10.1038/sj.bjc.6604055.PubMedPubMedCentralCrossRef
21.
Chen K, Sawhney R, Khan M, Benninger MS, Hou Z, Sethi S, Stephen JK, Worsham MJ: Methylation of multiple genes as diagnostic and therapeutic markers in primary head and neck squamous cell carcinoma. Arch Otolaryngol Head Neck Surg. 2007, 133 (11): 1131-8. 10.1001/archotol.133.11.1131.PubMedCrossRef
22.
Scott RH, Douglas J, Baskcomb L, Nygren AO, Birch JM, Cole TR, Cormier-Daire V, Eastwood DM, Garcia-Minaur S, Lapunzina P, Tatton-Brown K, Bliek J, Maher ER, Rahman N: Methylation-specific MLPA (MS-MLPA) robustly detects and distinguishes 11p15 abnormalities associated with overgrowth and growth retardation. J Med Genet. 2008, 45: 106-113. 10.1136/jmg.2007.053207.PubMedCrossRef
23.
Hess CJ, Errami A, Berkhof J, Denkers F, Ossenkoppele GJ, Nygren AO, Schuurhuis GJ, Waisfisz Q: Concurrent methylation of promoters from tumor associated genes predicts outcome in acute myeloid leukemia. Leuk Lymphoma. 2008, 49 (6): 1132-41. 10.1080/10428190802035990.PubMedCrossRef
24.
Ewald C, Hofmann T, Kuhn SA, Deufel T, Beetz C, Kalff R: Methylation-specific multiplex ligation-dependent probe amplification in meningiomas. J Neurooncol. 2008, 90 (3): 267-73. 10.1007/s11060-008-9672-8.PubMedCrossRef
25.
Gylling A, Ridanpää M, Vierimaa O, Aittomäki K, Avela K, Kääriäinen H, Laivuori H, Pöyhönen M, Sallinen SL, Wallgren-Pettersson C, Järvinen HJ, Mecklin JP, Peltomäki P: Large genomic rearrangements and germline epimutations in Lynch syndrome. Int J Cancer. 2009, 124 (10): 2333-40. 10.1002/ijc.24230.PubMedCrossRef
26.
Buyru N, Altinisik J, Ozdemir F, Demokan S, Dalay N: Methylation profiles in breast cancer. Cancer Invest. 2009, 27 (3): 307-12. 10.1080/07357900802350814.PubMedCrossRef
27.
Röhrs S, Dirks WG, Meyer C, Marschalek R, Scherr M, Slany R, Wallace A, Drexler HG, Quentmeier H: Hypomethylation and expression of BEX2, IGSF4 and TIMP3 are indicative of MLL translocations in acute myeloid leukemia. Mol Cancer. 2009, 8: 86-10.1186/1476-4598-8-86.PubMedPubMedCentralCrossRef
28.
Berginc G, Bracko M, Glavac D: MS-MLPA reveals progressive age-dependent promoter methylation of tumor suppressor genes and possible role of IGSF4 gene in colorectal carcinogenesis of microsatellite instable tumors. Cancer Invest J. 2010, 28 (1): 94-102. 10.3109/07357900902849673.CrossRef
29.
Brambilla E, Travis WD, Colby TV, Corrin B, Shimosato Y: The new World Health Organization classification of lung tumours. Eur Respir J. 2001, 18 (6): 1059-1068. 10.1183/09031936.01.00275301.PubMedCrossRef
30.
Aleman A, Adrien L, Lopez-Serra L, Cordon-Cardo C, Esteller M, Belbin TJ, Sanchez-Carbayo M: Identification of DNA hypermethylation of SOX9 in association with bladder cancer progression using CpG microarrays. Br J Cancer. 2008, 98 (2): 466-73. 10.1038/sj.bjc.6604143.PubMedPubMedCentralCrossRef
31.
Dawson-Saunders B, Trapp RG: Basic & Clinical Biostatistics. 1994, Norwalk, Connecticut, Appleton & Lange, 2
32.
Du Y, Carling T, Fang W, Piao Z, Sheu JC, Huang S: Hypermethylation in human cancers of the RIZ1 tumor suppressor gene, a member of a histone/protein methyltransferase superfamily. Cancer Res. 2001, 61 (22): 8094-9.PubMed
33.
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 (7): 589-92. 10.1111/j.1349-7006.2003.tb01487.x.PubMedCrossRef
34.
Li QL, Kim HR, Kim WJ, Choi JK, Lee YH, Kim HM, Li LS, Kim H, Chang J, Ito Y, YoulLee K, Bae SC: Transcriptional silencing of the RUNX3 gene by CpG hypermethylation is associated with lung cancer. Biochem Biophys Res Commun. 2004, 314 (1): 223-8. 10.1016/j.bbrc.2003.12.079.PubMedCrossRef
35.
Sato K, Tomizawa Y, Iijima H, Saito R, Ishizuka T, Nakajima T, Mori M: Epigenetic inactivation of the RUNX3 gene in lung cancer. Oncol Rep. 2006, 15 (1): 129-35.PubMed
36.
Licchesi JD, Westra WH, Hooker CM, Machida EO, Baylin SB, Herman JG: Epigenetic alteration of Wnt pathway antagonists in progressive glandular neoplasia of the lung. Carcinogenesis. 2008, 29 (5): 895-904. 10.1093/carcin/bgn017.PubMedPubMedCentralCrossRef
37.
Jin M, Kawakami K, Fukui Y, Tsukioka S, Oda M, Watanabe G, Takechi T, Oka T, Minamoto T: Different histological types of non-small cell lung cancer have distinct folate and DNA methylation levels. Cancer Sci. 2009, 100 (12): 2325-30. 10.1111/j.1349-7006.2009.01321.x.PubMedCrossRef
38.
Yoshino M, Suzuki M, Tian L, Moriya Y, Hoshino H, Okamoto T, Yoshida S, Shibuya K, Yoshino I: Promoter hypermethylation of the p16 and Wif-1 genes as an independent prognostic marker in stage IA non-small cell lung cancers. Int J Oncol. 2009, 35 (5): 1201-9.PubMed
39.
Chan EC, Lam SY, Fu KH, Kwong YL: Polymorphisms of the GSTM1, GSTP1, MPO, XRCC1, and NQO1 genes in Chinese patients with non-small cell lung cancers: relationship with aberrant promoter methylation of the CDKN2A and RARB genes. Cancer Genet Cytogenet. 2005, 162 (1): 10-20. 10.1016/j.cancergencyto.2005.03.008.PubMedCrossRef
40.
Feng Q, Hawes SE, Stern JE, Wiens L, Lu H, Dong ZM, Jordan CD, Kiviat NB, Vesselle H: DNA methylation in tumor and matched normal tissues from non-small cell lung cancer patients. Cancer Epidemiol Biomarkers Prev. 2008, 17 (3): 645-54. 10.1158/1055-9965.EPI-07-2518.PubMedPubMedCentralCrossRef
41.
Hawes SE, Stern JE, Feng Q, Wiens LW, Rasey JS, Lu H, Kiviat NB, Vesselle H: DNA hypermethylation of tumors from non-small cell lung cancer (NSCLC) patients is associated with gender and histologic type. Lung Cancer. 2009, PMID: 19945765,
42.
Krop I, Player A, Tablante A, Taylor-Parker M, Lahti-Domenici J, Fukuoka J, Batra SK, Papadopoulos N, Richards WG, Sugarbaker DJ, Wright RL, Shim J, Stamey TA, Sellers WR, Loda M, Meyerson M, Hruban R, Jen J, Polyak K: Frequent HIN-1 promoter methylation and lack of expression in multiple human tumor types. Mol Cancer Res. 2004, 2 (9): 489-94.PubMed
43.
Shigematsu H, Suzuki M, Takahashi T, Miyajima K, Toyooka S, Shivapurkar N, Tomlinson GE, Mastrangelo D, Pass HI, Brambilla E, Sathyanarayana UG, Czerniak B, Fujisawa T, Shimizu N, Gazdar AF: Aberrant methylation of HIN-1 (high in normal-1) is a frequent event in many human malignancies. Int J Cancer. 2005, 113 (4): 600-4. 10.1002/ijc.20622.PubMedCrossRef
44.
Tsou JA, Galler JS, Siegmund KD, Laird PW, Turla S, Cozen W, Hagen JA, Koss MN, Laird-Offringa IA: Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma. Mol Cancer. 2007, 6: 70-10.1186/1476-4598-6-70.PubMedPubMedCentralCrossRef
45.
Yuan BZ, Jefferson AM, Baldwin KT, Thorgeirsson SS, Popescu NC, Reynolds SH: DLC-1 operates as a tumor suppressor gene in human non-small cell lung carcinomas. Oncogene. 2004, 23 (7): 1405-11. 10.1038/sj.onc.1207291.PubMedCrossRef
46.
Dammann R, Strunnikova M, Schagdarsurengin U, Rastetter M, Papritz M, Hattenhorst UE, Hofmann HS, Silber RE, Burdach S, Hansen G: CpG island methylation and expression of tumour-associated genes in lung carcinoma. Eur J Cancer. 2005, 41 (8): 1223-36. 10.1016/j.ejca.2005.02.020.PubMedCrossRef
47.
Suzuki M, Wada H, Yoshino M, Tian L, Shigematsu H, Suzuki H, Alaa M, Tamura H, Fujiwara T, Nagato K, Motohashi S, Moriya Y, Hoshino H, Yoshida S, Shibuya K, Hiroshima K, Nakatani Y, Yoshino I: Molecular characterization of chronic obstructive pulmonary disease-related non-small cell lung cancer through aberrant methylation and alterations of EGFR signaling. Ann Surg Oncol. 2010, 17 (3): 878-88. 10.1245/s10434-009-0739-3.PubMedCrossRef
48.
Virmani A, Rathi A, Heda S, Sugio K, Lewis C, Tonk V, Takahashi T, Roth JA, Minna JD, Euhus DM, Gazdar AF: Aberrant methylation of the cyclin D2 promoter in primary small cell, nonsmall cell lung and breast cancers. Int J Cancer. 2003, 107 (3): 341-5. 10.1002/ijc.11393.PubMedCrossRef
49.
Kubo T, Yamamoto H, Ichimura K, Jida M, Hayashi T, Otani H, Tsukuda K, Sano Y, Kiura K, Toyooka S: DNA methylation in small lung adenocarcinoma with bronchioloalveolar carcinoma components. Lung Cancer. 2009, 65 (3): 328-32. 10.1016/j.lungcan.2008.12.001.PubMedCrossRef
50.
Nagatake M, Osada H, Kondo M, Uchida K, Nishio M, Shimokata K, Takahashi T, Takahashi T: Aberrant hypermethylation at the bcl-2 locus at 18q21 in human lung cancers. Cancer Res. 1996, 56 (8): 1886-91.PubMed
51.
Gu J, Berman D, Lu C, Wistuba II, Roth JA, Frazier M, Spitz MR, Wu X: Aberrant promoter methylation profile and association with survival in patients with non-small cell lung cancer. Clin Cancer Res. 2006, 12 (24): 7329-38. 10.1158/1078-0432.CCR-06-0894.PubMedCrossRef
52.
Herbst A, Wallner M, Rahmig K, Stieber P, Crispin A, Lamerz R, Kolligs FT: Methylation of helicase-like transcription factor in serum of patients with colorectal cancer is an independent predictor of disease recurrence. Eur J Gastroenterol Hepatol. 2009, 21 (5): 565-9. 10.1097/MEG.0b013e328318ecf2.PubMedCrossRef
53.
Friedrich MG, Chandrasoma S, Siegmund KD, Weisenberger DJ, Cheng JC, Toma MI, Huland H, Jones PA, Liang G: Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma. Eur J Cancer. 2005, 41 (17): 2769-78. 10.1016/j.ejca.2005.07.019.PubMedCrossRef
Metadata
Title
Multiplexed methylation profiles of tumor suppressor genes and clinical outcome in lung cancer
Authors
Mónica Castro
Laura Grau
Patricia Puerta
Liliana Gimenez
Julio Venditti
Silvia Quadrelli
Marta Sánchez-Carbayo
Publication date
01-12-2010
Publisher
BioMed Central
Published in
Journal of Translational Medicine / Issue 1/2010
Electronic ISSN: 1479-5876
DOI
https://doi.org/10.1186/1479-5876-8-86

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