Development of transcriptomic biomarker signature in human saliva to detect lung cancer

Cellular and Molecular Life Sciences

Volumn 69, Issue 19, 2012, Pages 3341-3350

  Zhang, Lei ^a   Xiao, Hua ^a   Zhou, Hui ^a,b   Santiago, Silverio ^c   Lee, Jay M ^c   Garon, Edward B ^c   Yang, Jieping ^a   Brinkmann, Ole ^a   Yan, Xinmin ^a   Akin, David ^a   Chia, David ^c   Elashoff, David ^c   Park, No Hee ^a,c   Wong, David T W ^a,c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Department of Civil and Environmental Engineering   (United States)

Author keywords

Biomarker signature; Early detection; Human saliva; Lung cancer; Transcriptomic

Indexed keywords

B RAF KINASE; CYCLIN I; FIBROBLAST GROWTH FACTOR 19; MESSENGER RNA; PROTEIN EGRF; PROTEIN FRS2; PROTEIN GREB1; PROTEIN LZTS1; TRANSCRIPTOME; TUMOR MARKER; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; BREAST CANCER; CANCER PATIENT; CHRONIC OBSTRUCTIVE LUNG DISEASE; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; FEMALE; HUMAN; LUNG CANCER; MALE; NON INSULIN DEPENDENT DIABETES MELLITUS; NUCLEOTIDE SEQUENCE; OVARY CANCER; PANCREAS CANCER; PROTEIN ANALYSIS; SALIVA ANALYSIS; SENSITIVITY AND SPECIFICITY; TRANSCRIPTOMICS; TUMOR DIFFERENTIATION; VALIDATION STUDY;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; AGED; CASE-CONTROL STUDIES; CYSTEINE-RICH PROTEIN 61; DNA-BINDING PROTEINS; FEMALE; FIBROBLAST GROWTH FACTORS; HUMANS; LUNG NEOPLASMS; MALE; MEMBRANE PROTEINS; MIDDLE AGED; NEOPLASM PROTEINS; PREDICTIVE VALUE OF TESTS; PROTO-ONCOGENE PROTEINS B-RAF; REGRESSION ANALYSIS; SALIVA; SMOKING; TRANSCRIPTOME; TUMOR MARKERS, BIOLOGICAL; TUMOR SUPPRESSOR PROTEINS;

EID: 84866398779     PISSN: 1420682X     EISSN: 14209071     Source Type: Journal    
DOI: 10.1007/s00018-012-1027-0     Document Type: Article

References (52)

1. Jemal A, Siegel R, Xu JQ, Ward E (2010) Cancer Statistics, 2010. CA Cancer J Clin 60:277-300
2. Hecht SS (2002) Cigarette smoking and lung cancer: chemical mechanisms and approaches to prevention. Lancet Oncol 3:461-469
3. Spira A, Beane J, Shah V, Liu G, Schembri F, Yang XM, Palma J, Brody JS (2004) Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci USA 101:10143-10148
4. Spira A, Beane JE, Shah V, Steiling K, Liu G, Schembri F, Gilman S, Dumas YM, Calner P, Sebastiani P, Sridhar S, Beamis J, Lamb C, Anderson T, Gerry N, Keane J, Lenburg ME, Brody JS (2007) Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat Med 13:361-366
5. Petty TL (2000) The early identification of lung carcinoma by sputum cytology. Cancer 89:2461-2464
6. Gohagan JK, Marcus PM, Fagerstrom RM, Pinsky PF, Kramer BS, Prorok PC, Ascher S, Bailey W, Brewer B, Church T, Engelhard D, Ford M, Fouad M, Freedman M, Gelmann E, Gierada D, Hocking W, Inampudi S, Irons B, Johnson CC, Jones A, Kucera G, Kvale P, Lappe K, Manor W, Moore A, Nath H, Neff S, Oken M, Plunkett M, Price H, Reding D, Riley T, Schwartz M, Spizarny D, Yoffie R, Zylak C (2005) Final results of the Lung Screening Study, a randomized feasibility study of spiral CT versus chest X-ray screening for lung cancer. Lung Cancer 47:9-15
7. Singh S, Pinsky P, Fineberg NS, Gierada DS, Garg K, Sun YH, Nath PH (2011) Evaluation of reader variability in the interpretation of follow-up CT scans at lung cancer screening. Radiology 259:263-270
8. Gray RD, Duncan A, Noble D, Imrie M, O'Reilly DSJ, Innes A, Porteous DJ, Greening AP, Boyd AC (2010) Sputum trace metals are biomarkers of inflammatory and suppurative lung disease. Chest 137:635-641
9. Fliss MS, Usadel H, Caballero OL, Wu L, Buta MR, Eleff SM, Jen J, Sidransky D (2000) Facile detection of mitochondrial DNA mutations in tumors and bodily fluids. Science 287:2017-2019
10. Gessner C, Rechner B, Hammerschmidt S, Kuhn H, Hoheisel G, Sack U, Ruschpler P, Wirtz H (2010) Angiogenic markers in breath condensate identify non-small cell lung cancer. Lung Cancer 68:177-184
11. Lacroix J, Becker HD, Woerner SM, Rittgen W, Drings P, von Knebel Doeberitz M (2001) Sensitive detection of rare cancer cells in sputum and peripheral blood samples of patients with lung cancer by preproGRP-specific RT-PCR. Int J Cancer 92:1-8
12. Taylor MD, Smith PW, Brix WK, Wick MR, Theodosakis N, Swenson BR, Kozower BD, Lau CL, Jones DR (2009) Fluorodeoxyglucose positron emission tomography and tumor marker expression in non-small cell lung cancer. J Thorac Cardiovasc Surg 137:43-48
13. Miller YE, Vu KO, Kennedy TC, Hirsch FR, Petty TL, Bunn PA, Keith RL, Franklin WA, Wolf HJ, Prindiville S, Byers T (2006) Lack of association between sputum atypia and chronic obstructive pulmonary disease mortality. J Thorac Oncol 1:302-307
14. Xiao H, Wong DT (2011) Proteomics and its applications for biomarker discovery in human saliva. Bioinformation 5:294-296
15. Zhang L, Farrell JJ, Zhou H, Elashoff D, Akin D, Park NH, Chia D, Wong DT (2010) Salivary transcriptomic biomarkers for detection of resectable pancreatic cancer. Gastroenterology 138:949-957
16. Gonzalez-Begne M, Lu BW, Han XM, Hagen FK, Hand AR, Melvin JE, Yates JR (2009) Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). J Proteome Res 8:1304-1314
17. Wong DT (2006) Salivary diagnostics powered by nanotechnologies, proteomics and genomics. J Am Dent Assoc 137:313-321
18. Pfaffe T, Cooper-White J, Beyerlein P, Kostner K, Punyadeera C (2008) Diagnostic potential of saliva: current state and future applications. Clin Chem 57:675-687
19. Zhang L, Xiao H, Wong DT (2009) Salivary biomarkers for clinical applications. Mol Diagn Ther 13:245-259
20. Hu S, Arellano M, Boontheung P, Wang J, Zhou H, Jiang J, Elashoff D, Wei R, Loo JA, Wong DT (2008) Salivary proteomics for oral cancer biomarker discovery. Clin Cancer Res 14:6246-6252
21. Li Y, St John MAR, Zhou X, Kim Y, Sinha U, Jordan RCK, Eisele D, Abemayor E, Elashoff D, Park N-H, Wong DT (2004) Salivary transcriptome diagnostics for oral cancer detection. Clin Cancer Res 10:8442-8450
22. Mager DL, Haffajee AD, Devlin PM, Norris CM, Posner MR, Goodson JM (2005) The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects. J Transl Med 3:27
23. Wei F, Patel P, Liao W, Chaudhry K, Zhang L, Arellano-Garcia M, Hu S, Elashoff D, Zhou H, Shukla S, Shah F, Ho C-M, Wong DT (2009) Electrochemical sensor for multiplex biomarkers detection. Clin Cancer Res 15:4446-4452
24. Hu S, Wang J, Meijer J, Ieong S, Xie Y, Yu T, Zhou H, Henry S, Vissink A, Pijpe J, Kallenberg C, Elashoff D, Loo JA, Wong DT (2007) Salivary proteomic and genomic biomarkers for primary Sjögren's syndrome. Arthritis Rheum 56:3588-3600
25. Zhang L, Xiao H, Karlan S, Zhou H, Gross J, Elashoff D, Akin D, Yan X, Chia D, Karlan B, Wong DT (2010) Discovery and preclinical validation of salivary transcriptomic and proteomic biomarkers for the non-invasive detection of breast cancer. PLoS One 5:e15573
26. Xiao H, Zhang L, Zhou H, Lee JM, Garon EB, Wong DT (2012) Proteomic analysis of human saliva from lung cancer patients using two-dimensional difference gel electrophoresis and mass spectrometry. Mol Cell Proteomics 11:M111.012112
27. Edgar R, Barrett T (2006) NCBI GEO standards and services for microarray data. Nat Biotechnol 24:1471-1472
28. Therneau TM, Ballman KV (2008) What does PLIER really do? Cancer Inf 6:423-431
29. Hu ZZ, Zimmermann BG, Zhou H, Wang JH, Henson BS, Yu WX, Elashoff D, Krupp G, Wong DT (2008) Exon-level expression profiling: a comprehensive transcriptome analysis of oral fluids. Clin Chem 54:824-832
30. Jessie K, Pang WW, Rahim ZHA, Hashim OH (2010) Proteomic analysis of whole human saliva detects enhanced expression of interleukin-1 receptor antagonist, thioredoxin and lipocalin-1 in cigarette smokers compared to non-smokers. Int J Mol Sci 11:4488-4505
31. Vanni H, Kazeros A, Wang R, Harvey BG, Ferris B, De BP, Carolan BJ, Hubner RH, O'Connor TP, Crystal RG (2009) Cigarette smoking induces overexpression of a fat-depleting gene AZGP1 in the human. Chest 135:1197-1208
32. Molina R, Auge JM, Escudero JM, Marrades R, Vinolas N, Carcereny E, Ramirez J, Filella X (2008) Mucins CA 125, CA 19.9, CA 15.3 and TAG-72.3 as tumor markers in patients with lung cancer: comparison with CYFRA 21-1, CEA, SCC and NSE. Tumor Biol 29:371-380
33. Molina R, Filella X, Auge JM, Fuentes R, Bover I, Rifa J, Moreno V, Canals E, Vinolas N, Marquez A, Barreiro E, Borras J, Viladiuc P (2003) Tumor markers (CEA, CA 125, CYFRA 21-1, SCC and NSE) in patients with non-small cell lung cancer as an aid in histological diagnosis and prognosis-comparison with the main clinical and pathological prognostic factors. Tumor Biol 24:209-218
34. Shitrit D, Zingerman B, Shitrit ABG, Shlomi D, Kramer MR (2005) Diagnostic value of CYFRA 21-1, CEA, CA 19-9, CA 15-3, and CA 125 assays in pleural effusions: analysis of 116 cases and review of the literature. Oncologist 10:501-507
35. Li Y, Zhou X, John M, Wong DTW (2004) RNA profiling of cellfree saliva using microarray technology. J Dent Res 83:199-203
36. Park NJ, Li Y, Yu TW, Brinkman BMN, Wong DT (2006) Characterization of RNA in saliva. Clin Chem 52:988-994
37. Balko JM, Potti A, Saunders C, Stromberg A, Haura EB, Black EP (2006) Gene expression patterns that predict sensitivity to epidermal growth factor receptor tyrosine kinase inhibitors in lung cancer cell lines and human lung tumors. BMC Genomics 7:289
38. Shibata T, Hanada S, Kokubu A, Matsuno Y, Asamura H, Ohta T, Sakamoto M, Hirohashi S (2007) Gene expression profiling of epidermal growth factor receptor/KRAS pathway activation in lung adenocarcinoma. Cancer Sci 98:985-991
39. Nonaka D, Fabbri A, Roz L, Mariani L, Vecchione A, Moore GW, Tavecchio L, Croce CM, Sozzi G (2005) Reduced FEZ1/ LZTS1 expression and outcome prediction in lung cancer. Cancer Res 65:1207-1212
40. Kobayashi S, Boggon TJ, Dayaram T, Janne PA, Kocher O, Meyerson M, Johnson BE, Eck MJ, Tenen DG, Halmos B (2005) EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. N Engl J Med 352:786-792
41. Sordella R, Bell DW, Haber DA, Settleman J (2004) Gefitinibsensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways. Science 305:1163-1167
42. Paez JG, Janne PA, Lee JC, Tracy S, Greulich H, Gabriel S, Herman P, Kaye FJ, Lindeman N, Boggon TJ, Naoki K, Sasaki H, Fujii Y, Eck MJ, Sellers WR, Johnson BE, Meyerson M (2004) EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 304:1497-1500
43. Herbst RS, Heymach JV, Lippman SM (2008) Molecular origins of cancer: lung cancer. N Engl J Med 359:1367-1380
44. Schmid K, Oehl N, Wrba F, Pirker R, Pirker C, Filipits M (2009) EGFR/KRAS/BRAF mutations in primary lung adenocarcinomas and corresponding locoregional lymph node metastases. Clin Cancer Res 15:4554-4560
45. Desnoyers LR, Pai R, Ferrando RE, Hotzel K, Le T, Ross J, Carano R, D'Souza A, Qing J, Mohtashemi I, Ashkenazi A, French DM (2008) Targeting FGF19 inhibits tumor growth in colon cancer xenograft and FGF19 transgenic hepatocellular carcinoma models. Oncogene 27:85-97
46. Sato T, Gotoh N (2009) The FRS2 family of docking/scaffolding adaptor proteins as therapeutic targets of cancer treatment. Expert Opin Ther Targets 13:689-700
47. Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik- Zainal S, Davies HR, Ordonez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen LN, Jia MM, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, Costa GL, Lee CC, Minna JD, Gazdar A, Birney E, Rhodes MD, McKernan KJ, Stratton MR, Futreal PA, Campbell PJ (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463:184-190
48. Church TR, Anderson KE, Caporaso NE, Geisser MS, Le CT, Zhang Y, Benoit AR, Carmella SG, Hecht SS (2009) A prospectively measured serum biomarker for a tobacco-specific carcinogen and lung cancer in smokers. Cancer Epidemiol Biomarkers Prev 18:260-266
49. Gao K, Zhou H, Zhang L, Lee JW, Zhou Q, Hu S, Wolinsky LE, Farrell J, Eibl G, Wong DT (2009) Systemic disease-induced salivary biomarker profiles in mouse models of melanoma and non-small cell lung cancer. PLoS One 4:e5875
50. Pepe MS, Feng Z, Janes H, Bossuyt PM, Potter JD (2008) Pivotal evaluation of the accuracy of a biomarker used for classification or prediction: standards for study design. J Natl Cancer Inst 100:1432-1438
51. Landberg G, Nilsson K, Jirstrom K, Ryden L, Kitching R, Burger AM, Seth A (2005) Cyclin I is expressed in human breast cancer and closely associated with VEGF and KDR expression. Breast Cancer Res Treat 89:313-316
52. Ghosh MG, Thompson DA, Weigel RJ (2000) PDZK1 and GREB1 are estrogen-regulated genes expressed in hormoneresponsive breast cancer. Cancer Res 60:6367-6375