Variability in the measurement of the methylation status of lung cancer-related genes in bronchial secretions

Oncology Reports

Volumn 32, Issue 4, 2014, Pages 1435-1440

  Milares, Laura ^a,c   Rosel, Antoni ^b,d   Setó, Laia ^a,b,d,f   Sanz, José ^b,e   Andreo, Felipe ^b,e   Monsó, Eduard ^b,c,f  

^a Fundació Parc Taulí ^*  (Spain)

^b INSTITUTO DE SALUD CARLOS III   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^d HOSPITAL UNIVERSITARI DE BELLVITGE   (Spain)

^e HOSPITAL UNIVERSITARI GERMANS TRIAS I PUJOL   (Spain)

^f Servei de Pneumologia Hospital Universitari Parc Taulí   (Spain)

Author keywords

Bronchial washing; Methylation sensitive high resolution melting; Methylation sensitive pcr; Sputum

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; DEATH ASSOCIATED PROTEIN KINASE; RAS ASSOCIATION DOMAIN FAMILY PROTEIN 1A; DNA; RASSF1 PROTEIN, HUMAN; TUMOR SUPPRESSOR PROTEIN;

ADULT; ARTICLE; BRONCHUS SECRETION; CANCER PATIENT; CANCER RISK; CDKN2A GENE; CONTROLLED STUDY; CROSS-SECTIONAL STUDY; DAPK GENE; DIAGNOSTIC TEST ACCURACY STUDY; DNA DETERMINATION; DNA METHYLATION; EPITHELIUM CELL; GENE IDENTIFICATION; GENETIC VARIABILITY; HIGH RESOLUTION MELTING ANALYSIS; HUMAN; LUNG CANCER; MAJOR CLINICAL STUDY; MEASUREMENT; ONCOGENE; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE; PRIORITY JOURNAL; RASSF1A GENE; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SPUTUM ANALYSIS; AGED; CHEMISTRY; COMPARATIVE STUDY; CYTOLOGY; FEMALE; GENETICS; LUNG LAVAGE; LUNG TUMOR; MALE; MIDDLE AGED; SMOKING; SPUTUM; TUMOR SUPPRESSOR GENE;

AGED; BRONCHOALVEOLAR LAVAGE FLUID; CROSS-SECTIONAL STUDIES; DEATH-ASSOCIATED PROTEIN KINASES; DNA; DNA METHYLATION; FEMALE; GENES, P16; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; POLYMERASE CHAIN REACTION; SMOKING; SPUTUM; TUMOR SUPPRESSOR PROTEINS;

EID: 84923068176     PISSN: 1021335X     EISSN: 17912431     Source Type: Journal    
DOI: 10.3892/or.2014.3364     Document Type: Article

References (29)

1. Adcock IM, Tsaprouni L, Bhavsar P and Ito K: Epigenetic regulation of airway inflammation. Curr Opin Immunol 19: 694-700, 2007. (Pubitemid 350236802)
2. Barlesi F, Giaccone G, Gallegos-Ruiz MI, Loundou A, Span SW, Lefesvre P, et al: Global histone modifications predict prognosis of resected non small-cell lung cancer. J Clin Oncol 25: 4358-4364, 2007.
3. Leng S, Do K, Yingling CM, Picchi MA, Wolf HJ, Kennedy TC, et al: Defining a gene promoter methylation signature in sputum for lung cancer risk assessment. Clin Cancer Res 18: 3387-3395, 2012.
4. Malentacchi F, Forni G, Vinci S and Orlando C: Quantitative evaluation of DNA methylation by optimization of a differential?high resolution melt analysis protocol. Nucleic Acids Res 37: e86, 2009.
5. Mikeska T, Bock C, Do H and Dobrovic A: DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Rev Mol Diagn 12: 473-487, 2012.
6. Anglim PP, Alonzo TA and Laird-Offringa IA: DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update. Mol Cancer 7: 81, 2008.
7. Kim H, Kwon YM, Kim JS, Lee H, Park JH, Shim YM, et al: Tumor?specific methylation in bronchial lavage for the early detection of non-small-cell lung cancer. J Clin Oncol 22: 2363-2370, 2004.
8. Hubers AJ, van der Drift MA, Prinsen CF, Witte BI, Wang Y, Shivapurkar N, et al: Methylation analysis in spontaneous sputum for lung cancer diagnosis. Lung Cancer 84: 127-133, 2014.
9. Fahy JV, Wong H, Liu J and Boushey HA: Comparison of samples collected by sputum induction and bronchoscopy from asthmatic and healthy subjects. Am J Respir Crit Care Med 152: 53-58, 1995.
10. Kristensen LS and Hansen LL: PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment. Clin Chem 55: 1471-1483, 2009.
11. Mikeska T, Candiloro IL and Dobrovic A: The implications of heterogeneous DNA methylation for the accurate quantification of methylation. Epigenomics 2: 561-573, 2010.
12. Warnecke PM, Stirzaker C, Song J, Grunau C, Melki JR and Clark SJ: Identification and resolution of artifacts in bisulfite sequencing. Methods 27: 101-107, 2002. (Pubitemid 34757119)
13. Lorente A, Mueller W, Urdangarin E, Lazcoz P, von Deimling A and Castresana JS: Detection of methylation in promoter sequences by melting curve analysis-based semiquantitative real time PCR. BMC Cancer 8: 61, 2008.
14. Kristensen LS, Mikeska T, Krypuy M and Dobrovic A: Sensitive melting analysis after real time-methylation specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection. Nucleic Acids Res 36: e42, 2008.
15. Kristensen LS, Wojdacz TK, Thestrup BB, Wiuf C, Hager H and Hansen LL: Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM. BMC Cancer 9: 453, 2009.
16. Do H, Krypuy M, Mitchell PL, Fox SB and Dobrovic A: High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies. BMC Cancer 8: 142, 2008.
17. Wojdacz TK, Dobrovic A and Hansen LL: Methylation-sensitive high-resolution melting. Nat Protoc 3: 1903-1908, 2008.
18. Pin I, Gibson PG, Kolendowicz R, Girgis-Gabardo A, Denburg JA, Hargreave FE and Dolovich J: Use of induced sputum cell counts to investigate airway inflammation in asthma. Thorax 47: 25-29, 1992.
19. Pizzichini E, Pizzichini MM, Efthimiadis A, Evans S, Morris MM, Squillace D, et al: Indices of airway inflammation in induced sputum: reproducibility and validity of cell and fluid?phase measurements. Am J Respir Crit Care Med 154: 308-317, 1996. (Pubitemid 26269096)
20. Du Rand IA, Blaikley J, Booton R, Chaudhuri N, Gupta V, Khalid S, et al: British Thoracic Society guideline for diagnostic flexible bronchoscopy in adults. Thorax 68: i1-i44, 2013.
21. Reed AP: Preparation of the patient for awake flexible fiberoptic bronchoscopy. Chest 101: 244-253, 1992.
22. Herman JG, Graff JR, Myohanen S, Nelkin BD and Baylin SB: Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 93: 9821-9826, 1996. (Pubitemid 26296693)
23. Belinsky SA, Palmisano WA, Gilliland FD, Crooks LA, Divine KK, Winters SA, et al: Aberrant promoter methylation in bronchial epithelium and sputum from current and former smokers. Cancer Res 62: 2370-2377, 2002. (Pubitemid 34411720)
24. Smith E, Jones ME and Drew PA: Quantitation of DNA methylation by melt curve analysis. BMC Cancer 9: 123, 2009.
25. Belinsky SA, Liechty KC, Gentry FD, Wolf HJ, Rogers J, Vu K, et al: Promoter hypermethylation of multiple genes in sputum precedes lung cancer incidence in a high-risk cohort. Cancer Res 66: 3338-3344, 2006.
26. Belinsky SA, Grimes MJ, Casas E, Stidley CA, Franklin WA, Bocklage TJ, et al: Predicting gene promoter methylation in non-small-cell lung cancer by evaluating sputum and serum. Br J Cancer 96: 1278-1283, 2007. (Pubitemid 46625083)
27. Candiloro IL, Mikeska T and Dobrovic A: Assessing combined methylation-sensitive high resolution melting and pyrosequencing for the analysis of heterogeneous DNA methylation. Epigenetics 6: 500-507, 2011.
28. Wojdacz TK and Dobrovic A: Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 35: e41, 2007.
29. Shen L, Guo Y, Chen X, Ahmed S and Issa JP: Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis. Biotechniques 42: 48-58, 2007. University of Illinois at Urbana-Champaign