A novel epigenetic signature for early diagnosis in lung cancer

Clinical Cancer Research

Volumn 22, Issue 13, 2016, Pages 3361-3371

  Diaz Lagares, Angel ^a   Mendez Gonzalez, Jesus ^a   Hervas, David ^b   Saigi, Maria ^c   Pajares, Maria J ^d,e   Garcia, Diana ^a   Crujerias, Ana B ^f   Pio, Ruben ^d,g   Montuenga, Luis M ^d,e   Zulueta, Javier ^h   Nadal, Ernest ^c   Rosell, Antoni ^a,i   Esteller, Manel ^a,j   Sandoval, Juan ^a  

^a BELLVITGE BIOMEDICAL RESEARCH INSTITUTE IDIBELL   (Spain)

^b HEALTH RESEARCH INSTITUTE LA FE   (Spain)

^c CATALAN INSTITUTE OF ONCOLOGY   (Spain)

^d UNIVERSITY OF NAVARRA   (Spain)

^e UNIVERSITY OF NAVARRA   (Spain)

^f UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^g UNIVERSITY OF NAVARRA   (Spain)

^h UNIVERSITY CLINIC OF NAVARRA   (Spain)

ⁱ INSTITUTO DE SALUD CARLOS III   (Spain)

^j INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

more..

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER; AMINOTRANSFERASE; BCAT1 PROTEIN, HUMAN; CYSTEINE DIOXYGENASE; CYSTEINE DIOXYGENASE, TYPE I, HUMAN; DNA BINDING PROTEIN; TRIPARTITE MOTIF PROTEIN; ZNF177 PROTEIN, HUMAN;

ADULT; AGED; ARTICLE; BCAT1 GENE; BRONCHIAL ASPIRATION PROCEDURE; CANCER CYTODIAGNOSIS; CANCER STAGING; CARCINOMA IN SITU; CDO1 GENE; COHORT ANALYSIS; CONTROLLED STUDY; CPG ISLAND; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; DNA METHYLATION; EARLY CANCER DIAGNOSIS; EPIGENETICS; FEMALE; GENE; GENE IDENTIFICATION; GENE SILENCING; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC REGULATION; HUMAN; HUMAN CELL; HUMAN TISSUE; INTERMETHOD COMPARISON; LUNG CANCER; LUNG LAVAGE; LUNG TUMOR; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; PYROSEQUENCING; RETROSPECTIVE STUDY; TRIM58 GENE; VALIDATION STUDY; ZNF177 GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; MIDDLE AGED; PROCEDURES; PROMOTER REGION; VERY ELDERLY;

ADULT; AGED; AGED, 80 AND OVER; BIOMARKERS, TUMOR; CPG ISLANDS; CYSTEINE DIOXYGENASE; DNA METHYLATION; DNA-BINDING PROTEINS; EARLY DETECTION OF CANCER; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; PROMOTER REGIONS, GENETIC; RETROSPECTIVE STUDIES; TRANSAMINASES; TRIPARTITE MOTIF PROTEINS;

EID: 84977117672     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-15-2346     Document Type: Article

References (49)

1. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2015. CA Cancer J Clin 2013;65:5-29.
2. International Early Lung Cancer Action Program Investigators, Henschke CI, Yankelevitz DF, Libby DM, Pasmantier MW, Smith JP, et al. Survival of patients with stage I lung cancer detected on CT screening. N Engl J Med 2006;355:1763-71.
3. Aberle DR, Adams AM, Berg CD, Black WC, Clapp JD, Fagerstrom RM, et al. Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med 2011;365:395-409.
4. Massion PP, Walker RC. Indeterminate pulmonary nodules: risk for having or for developing lung cancer?Cancer Prev Res 2014;7:1173-8.
5. Massion PP. Biomarkers to the rescue in a lung nodule epidemic. J Clin Oncol 2014;32:725-6.
6. Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet 2012;13:679-92.
7. Belinsky SA, Klinge DM, Dekker JD, Smith MW, Bocklage TJ, Gilliland FD, et al. Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clin Cancer Res 2005;11:6505-11.
8. Topaloglu O, Hoque MO, Tokumaru Y, Lee J, Ratovitski E, Sidransky D, 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.
9. Geng J, Sun J, Lin Q, Gu J, Zhao Y, Zhang H, et al. Methylation status of NEYROG2 and NID2 improves the diagnosis of stage I NSCLC. Oncol Lett 2012;3:901-6.
10. Schmidt B, Liebenberg V, Dietrich D, Schlegel T, Kneip C, Seegebarth A, et al. SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer based on bronchial aspirates. BMC Cancer 2010;10:600
11. Nikolaidis G, Raji OY, Markopoulou S, Gosney JR, Bryan J, Warburton C, et al. DNA methylation biomarkers offer improved diagnostic efficiency in lung cancer. Cancer Res 2012;72:5692-701.
12. Wrangle J, Machida EO, Danilova L, Hulbert A, Franco N, Zhang W, et al. Functional identification of cancer-specificmethylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer. Clin Cancer Res 2014;20:1856-64.
13. Sandoval J, Esteller M. Cancer epigenomics: beyond genomics. Curr Opin Genet Dev 2012;22:50-5.
14. Griffin JP, Zaman MK, Niell HB, Tolley EA, Cole FHJr, Weiman DS. Diagnosis of lung cancer: a bronchoscopist's perspective. J Bronchology Interv Pulmonol 2012;19:12-8.
15. Kaarteenaho R. The current position of surgical lung biopsy in the diagnosis of idiopathic pulmonary fibrosis. Respir Res 2013;14:43.
16. Liloglou T, Bediaga NG, Brown BR, Field JK, Davies MP. Epigenetic biomarkers in lung cancer. Cancer Lett 2014;342:200-12.
17. Silvestri GA, Vachani A, Whitney D, Elashoff M, Porta-Smith K, Ferguson JS, et al. A bronchial genomic classifier for the diagnostic evaluation of lung cancer. N Engl J Med 2015;373:243-51.
18. Lowrance WT, Scardino PT. Predictive models for newly diagnosed prostate cancer patients. Rev Urol 2009;11:117-26.
19. Sandoval J, Mendez-Gonzalez J, Nadal E, Chen G, Carmona FJ, Sayols S, et al. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. J Clin Oncol 2013;31:4140-7.
20. Belinsky SA. Gene-promoter hypermethylation as a biomarker in lung cancer. Nat Rev Cancer 2004;4:707-17.
21. Mikeska T, Bock C, Do H, Dobrovic A. DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Rev Mol Diagn 2012;12:473-87.
22. Sandoval J, Peiro-Chova L, Pallardo FV, García-Gimenez JL. Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Rev Mol Diagn 2013;13:457-71.
23. Esteller M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet 2007;16:R50-9.
24. Baxter E, Windloch K, Gannon F, Lee JS. Epigenetic regulation in cancer progression. Cell Biosci 2014;4:45.
25. Heitzer E, Ulz P, Geigl JB. Circulating tumor DNA as a liquid biopsy for cancer. Clin Chem 2015;61:112-23.
26. National Lung Screening Trial Research Team, Church TR, Black WC, Aberle DR, Berg CD, Clingan KL, et al. Results of initial low-dose computed tomographic screening for lung cancer. N Engl J Med 2013;368:1980-91.
27. Palmisano WA, Divine KK, Saccomanno G, Gilliland FD, Baylin SB, Herman JG, et al. Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Res 2000;60:5954-8.
28. 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 2012;18:3387-95.
29. Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, Vanaclocha V, et al. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 2000;343:1350-4.
30. Hegi ME, Diserens AC, Gorlia T, Hamou MF, de Tribolet N, Weller M, et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med 2005;352:997-1003.
31. Barault L, Amatu A, Bleeker FE, Moutinho C, Falcomata C, Fiano V, et al. Digital PCR quantification of MGMT methylation refines prediction of clinical benefit from alkylating agents in glioblastoma and metastatic colorectal cancer. Ann Oncol 2015;26:1994-9.
32. Jerónimo C, Usadel H, Henrique R, Oliveira J, Lopes C, Nelson WG, et al. Quantitation of GSTP1 methylation in non-neoplastic prostatic tissue and organ-confined prostate adenocarcinoma. J Natl Cancer Inst 2001;93:1747-52.
33. Hoque MO, Topaloglu O, Begum S, Henrique R, Rosenbaum E, Van Criekinge W, et al. Quantitative methylation-specific polymerase chain reaction gene patterns in urine sediment distinguish prostate cancer patients from control subjects. J Clin Oncol 2005;23:6569-75.
34. Licchesi JD, Westra WH, Hooker CM, Herman JG. Promoter hypermethylation of hallmark cancer genes in atypical adenomatous hyperplasia of the lung. Clin Cancer Res 2008;14:2570-8.
35. Dietrich D, Kneip C, Raji O, Liloglou T, Seegebarth A, Schlegel T, et al. Performance evaluation of the DNA methylation biomarker SHOX2 for the aid in diagnosis of lung cancer based on the analysis of bronchial aspirates. Int J Oncol 2012;40:825-32.
36. Belinsky SA. Silencing of genes by promoter hypermethylation: key event in rodent and human lung cancer. Carcinogenesis 2005;26:1481-7.
37. Kwon YJ, Lee SJ, Koh JS, Kim SH, Lee HW, Kang MC, et al. Genome-wide analysis of DNA methylation and the gene expression change in lung cancer. J Thorac Oncol 2012;7:20-33.
38. Brait M, Ling S, Nagpal JK, Chang X, Park HL, Lee J, et al. Cysteine dioxygenase 1 is a tumor suppressor gene silenced by promoter methylation in multiple human cancers. PLoS One 2012;7:e44951.
39. Tönjes M, Barbus S, Park YJ, Wang W, Schlotter M, Lindroth AM, et al. BCAT1 promotes cell proliferation through amino acid catabolism in gliomas carrying wild-type IDH1. Nat Med 2013;19:901-8.
40. Mitchell SM, Ross JP, Drew HR, Ho T, Brown GS, Saunders NF, et al. A panel of genes methylated with high frequency in colorectal cancer. BMC Cancer 2014;14:54.
41. Yamashita S, Tsujino Y, Moriguchi K, Tatematsu M, Ushijima T. Chemical genomic screening for methylation-silenced genes in gastric cancer cell lines using 5-aza-2′-deoxycytidine treatment and oligonucleotide microarray. Cancer Sci 2006;97:64-71.
42. Tao R, Li J, Xin J, Wu J, Guo J, Zhang L, et al. Methylation profile of single hepatocytes derived from hepatitis B virus-related hepatocellular carcinoma. PLoS One 2011;6:e19862.
43. Doyle B, O'Riain C, Appleton K. Pyrosequencing of DNA extracted from formalin-fixed paraffin-embedded tissue. Methods Mol Biol 2011;724:181-90
44. Dobler CC, Crawford AB. Bronchoscopic diagnosis of endoscopically visible lung malignancies: should cytological examinations be carried out routinely?Intern Med J 2009;39:806-11.
45. Van't Westeinde SC, van Klaveren RJ. Screening and early detection of lung cancer. Cancer J 2011;17:3-10.
46. Harrell FEJr. Regression modeling strategies 2nd edition. New York: Springer; 2015. p.4-6.
47. Dawid AP. Statistical Theory: The Prequential Approach. Journal of the Royal Statistical Society. Series A (General). The 150th Anniversary of the Royal Statistical Society; 1984;147:278-92.
48. Balachandran VP, Gonen M, Smith JJ, DeMatteo RP. Nomograms in oncology: more than meets the eye. Lancet Oncol 2015;16:e173-80.
49. Wiencke JK, Bracci PM, Hsuang G, Zheng S, Hansen H, Wrensch MR, et al. A comparison of DNA methylation specificdroplet digital PCR (ddPCR) and real time qPCR with flow cytometry in characterizing human T cells in peripheral blood. Epigenetics 2014;9:1360-5.