An omics strategy for discovering pulmonary biomarkers potentially relevant to the evaluation of tobacco products

Biomarkers in Medicine

Volumn 6, Issue 6, 2012, Pages 849-860

  Wang, Honggang ^a   Mattes, William B ^b   Richter, Patricia ^c   Mendrick, Donna L ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^b PharmPoint Consulting   (United States)

^c CENTER FOR TOBACCO PRODUCTS   (United States)

Author keywords

biomarker; genomics; lung; metabolomics; proteomics; smoking

Indexed keywords

ALPHA 1 ANTITRYPSIN; BIOLOGICAL MARKER; C REACTIVE PROTEIN; CARCINOEMBRYONIC ANTIGEN; FIBRINOGEN; INTERLEUKIN 6; RETINOL BINDING PROTEIN; SQUAMOUS CELL CARCINOMA ANTIGEN; SURFACTANT PROTEIN A; SURFACTANT PROTEIN D; TOBACCO SMOKE;

AMINO ACID METABOLISM; ASTHMA; BRONCHIECTASIS; BRONCHOSCOPY; CARCINOGENESIS; CHRONIC OBSTRUCTIVE LUNG DISEASE; COMPUTER ASSISTED TOMOGRAPHY; DISEASE MARKER; DISEASE SURVEILLANCE; DNA SEQUENCE; ENVIRONMENTAL EXPOSURE; EPIGENETICS; EVIDENCE BASED MEDICINE; FOOD AND DRUG ADMINISTRATION; GENE CLUSTER; GENOMICS; GLYCOLYSIS; GOVERNMENT; HEALTH PROMOTION; HUMAN; LIQUID CHROMATOGRAPHY; LUNG CANCER; LUNG DISEASE; METABOLOMICS; NONHUMAN; PROPHYLAXIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEOMICS; RESPIRATORY SYSTEM; REVIEW; RNA DEGRADATION; SEX DIFFERENCE; SMOKING; THORAX RADIOGRAPHY; TOBACCO; TUMOR GROWTH;

ANIMALS; BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; GOVERNMENT REGULATION; HUMANS; LUNG; TOBACCO PRODUCTS;

NICOTIANA TABACUM;

EID: 84870882114     PISSN: 17520363     EISSN: 17520371     Source Type: Journal    
DOI: 10.2217/bmm.12.78     Document Type: Review

References (154)

1. United States Department of Health and Human Services. Smoking and Health. United States. Public Health Service, Office of the Surgeon General, DC, USA(1964
2. United States Department of Health and Human Services. How Tobacco Smoke Causes Disease: The Biology and Behavioral Basis for Smoking-Attributable Disease. Public Health Service, Office of the Surgeon General, DC, USA (2010
3. Centers for Disease Control and Prevention. Smoking-Attributable mortality, years of potential life lost, and productivity losses -United States, 2000-2004. MMWR Morb. Mortal. Wkly Rep. 57(45), 1226-1228 (2008
4. Centers for Disease Control and Prevention. Vital signs: Current cigarette smoking among adults aged >or=18 years - United States, 2009. MMWR Morb. Mortal. Wkly Rep. 59(35), 1135-1140 (2010
5. Centers for Disease Control and Prevention, National Center for Chronic Disease Prevention and Health Promotion, Office on Smoking and Health. How Tobacco Smoke Causes Disease: The Biology and Behavioral Basis for Smoking-Attributable Disease: A Report of the Surgeon General. Centers for Disease Control and Prevention, GA, USA (2010
6. US FDA. Draft Guidance for Industry and FDA Staff "Harmful and Potentially Harmful Constituents" In Tobacco Products as Used in Section 904(e) of the Federal Food, Drug and Cosmetic Act. US FDA, MD, USA (2010
7. Carmines EL, Gaworski CL. Toxicological evaluation of glycerin as a cigarette ingredient. Food Chem. Toxicol. 43(10), 1521-1539 (2005
8. Leischow SJ, Zeller M, Backinger CL. Research priorities and infrastructure needs of the Family Smoking Prevention and Tobacco Control Act: Science to inform FDA policy. Nicotine Tob. Res. 14(1), 1-6 (2012
9. Burns DM, Anderson CM, Gray N. Do changes in cigarette design influence the rise in adenocarcinoma of the lung? Cancer Causes Control 22(1), 13-22 (2011
10. Hoffmann D, Djordjevic MV, Hoffmann I. The changing cigarette. Prev. Med. 26(4), 427-434 (1997
11. Biomarkers Definitions Working Group. Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 69(3), 89-95 (2001
12. Spitz MR, Bondy ML. Genetic susceptibility to cancer. Cancer 72(SUPPL3), S991-S995 (1993
13. Barrett JC, Vainio H, Peakall D, Goldstein BD. 12th meeting of the Scientific Group on methodologies for the safety evaluation of chemicals: Susceptibility to environmental hazards. Environ. Health Perspect. 105(SUPPL4), S699-S737 (1997
14. Hemminki K, Kumar R, Bykov VJ, Louhelainen J, Vodicka P. Future research directions in the use of biomarkers. Environ. Health Perspect. 104(SUPPL3), S459-S464 (1996
15. Shields PG. Tobacco smoking, harm reduction, and biomarkers. J. Natl Cancer Inst. 94(19), 1435-1444 (2002
16. Chung KF, Adcock IM. Multifaceted mechanisms in COPD: Inflammation, immunity, and tissue repair and destruction. Eur. Respir. J. 31(6), 1334-1356 (2008
17. Macnee W, Tuder RM. New paradigms in the pathogenesis of chronic obstructive pulmonary disease I. Proc. Am. Thorac. Soc. 6(6), 527-531 (2009
18. Sethi S, Mallia P, Johnston SL. New paradigms in the pathogenesis of chronic obstructive pulmonary disease II. Proc. Am. Thorac. Soc. 6(6), 532-534 (2009
19. Agusti A, Calverley PM, Celli B et al. Characterisation of COPD heterogeneity in the ECLIPSE cohort. Respir. Res. 11, 122 (2010
20. Cho MH, Castaldi PJ, Wan ES et al. A genome-Wide association study of COPD identifies a susceptibility locus on chromosome 19q13. Hum. Mol. Genet. 21(4), 947-957 (2012
21. Siedlinski M, Cho MH, Bakke P et al. Genome-Wide association study of smoking behaviours in patients with COPD. Thorax 66(10), 894-902 (2011
22. Pillai SG, Kong X, Edwards LD et al. Loci identified by genome-Wide association studies influence different disease-related phenotypes in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 182(12), 1498-1505 (2010
23. Murphy DM, O'Byrne PM. Recent advances in the pathophysiology of asthma. Chest 137(6), 1417-1426 (2010
24. Kim HY, Dekruyff RH, Umetsu DT. The many paths to asthma: Phenotype shaped by innate and adaptive immunity. Nat. Immunol. 11(7), 577-584 (2010
25. Bijanzadeh M, Mahesh PA, Ramachandra NB. An understanding of the genetic basis of asthma. Ind. J. Med. Res. 134, 149-161 (2011
26. Stapleton M, Howard-Thompson A, George C, Hoover RM, Self TH. Smoking and asthma. J. Am. Board Fam. Med. 24(3), 313-322 (2011
27. Gomperts BN, Spira A, Massion PP et al. Evolving concepts in lung carcinogenesis. Semin. Respir. Crit. Care Med. 32(1), 32-43 (2011
28. Kitamura H, Yazawa T, Okudela L, Shimoyamada H, Sato H. Molecular and genetic pathogenesis of lung cancer: Differences between small-cell and non-smallcell carcinomas. Open Pathol. J. 2, 106-114 (2008
29. Ridanpaa M, Karjalainen A, Anttila S, Vainio H, Husgafvelpursiainen K. Genetic alterations in p53 and k-ras in lung-cancer in relation to histopathology of the tumor and smoking history of the patient. Int. J. Oncol. 5(5), 1109-1117 (1994
30. Begum S. Molecular changes in smokingrelated lung cancer. Expert Rev. Mol. Diagn. 12(1), 93-106 (2012
31. Anglim PP, Galler JS, Koss MN et al. Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer. Mol. Cancer 7, 62 (2008
32. Brock MV, Hooker CM, Ota-Machida E et al. DNA methylation markers and early recurrence in stage I lung cancer. N. Engl. J. Med. 358(11), 1118-1128 (2008
33. Jin Y, Xu H, Zhang C et al. Combined effects of cigarette smoking, gene polymorphisms and methylations of tumor suppressor genes on non small cell lung cancer: A hospitalbased case-control study in China. BMC Cancer 10, 422 (2010
34. Vaissiere T, Hung RJ, Zaridze D et al. Quantitative analysis of DNA methylation profiles in lung cancer identifies aberrant DNA methylation of specific genes and its association with gender and cancer risk factors. Cancer Res. 69(1), 243-252 (2009
35. Belinsky SA, Nikula KJ, Palmisano WA et al. Aberrant methylation of p16(INK4a) is an early event in lung cancer and a potential biomarker for early diagnosis. Proc. Natl Acad. Sci. USA 95(20), 11891-11896 (1998
36. Shinjo K, Kondo Y. Clinical implications of epigenetic alterations in human thoracic malignancies: Epigenetic alterations in lung cancer. Methods Mol. Biol. 863, 221-239 (2012
37. Tekpli X, Zienolddiny S, Skaug V, Stangeland L, Haugen A, Mollerup S. DNA methylation of the CYP1A1 enhancer is associated with smoking-Induced genetic alterations in human lung. Int. J. Cancer 131(7), 1509-1516 (2012
38. Zhang B, Zhu W, Yang P et al. Cigarette smoking and p16INK4a gene promoter hypermethylation in non-small cell lung carcinoma patients: A meta-Analysis. Plos One 6(12), e28882 (2011
39. Miller RL, Ho SM. Environmental epigenetics and asthma: Current concepts and call for studies. Am. J. Respir. Crit. Care Med. 177(6), 567-573 (2008
40. Sakao S, Tatsumi K. The importance of epigenetics in the development of chronic obstructive pulmonary disease. Respirology 16(7), 1056-1063 (2011
41. Yang IV, Schwartz DA. Epigenetic control of gene expression in the lung. Am. J. Respir. Crit. Care Med. 183(10), 1295-1301 (2011
42. Tomankova T, Petrek M, Kriegova E. Involvement of microRNAs in physiological and pathological processes in the lung. Respir. Res. 11, 159 (2010
43. Hudder A, Novak RF. miRNAs: Effectors of environmental influences on gene expression and disease. Toxicol. Sci. 103(2), 228-240 (2008
44. Sinha AU, Kaimal V, Chen J, Jegga AG. Dissecting microregulation of a master regulatory network. BMC Genomics 9, 88 (2008
45. Cho WC. Role of miRNAs in lung cancer. Expert Rev. Mol. Diagn. 9(8), 773-776 (2009
46. Yanaihara N, Caplen N, Bowman E et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9(3), 189-198 (2006
47. Maccani MA, Knopik VS. Cigarette smoke exposure-Associated alterations to non-coding RNA. Front. Genet. 3, 53 (2012
48. Broekhuizen BD, Sachs AP, Hoes AW, Verheij TJ, Moons KG. Diagnostic management of chronic obstructive pulmonary disease. Neth. J. Med. 70(1), 6-11 (2012
49. Reddy C, Chilla D, Boltax J. Lung cancer screening: A review of available data and current guidelines. Hosp. Pract. (Minneap.) 39(4), 107-112 (2011
50. Szefler SJ, Wenzel S, Brown R et al. Asthma outcomes: Biomarkers. J. Allergy Clin. Immunol. 129(SUPPL3), S9-S23 (2012
51. Louhelainen N, Myllarniemi M, Rahman I, Kinnula VL. Airway biomarkers of the oxidant burden in asthma and chronic obstructive pulmonary disease: Current and future perspectives. Int. J. Chron. Obstruct. Pulmon. Dis. 3(4), 585-603 (2008
52. Chung KF. Inflammatory biomarkers in severe asthma. Curr. Opin. Pulm. Med. 18(1), 35-41 (2012
53. Hillas G, Loukides S, Kostikas K, Bakakos P. Biomarkers obtained by non-Invasive methods in patients with COPD: Where do we stand, what do we expect? Curr. Med. Chem. 16(22), 2824-2838 (2009
54. Lacoma A, Prat C, Andreo F, Dominguez J. Biomarkers in the management of COPD. Eur. Respir. Rev. 18(112), 96-104 (2009
55. Snell N, Newbold P. The clinical utility of biomarkers in asthma and COPD. Curr. Opin. Pharmacol. 8(3), 222-235 (2008
56. Cazzola M, Novelli G. Biomarkers in COPD. Pulm. Pharmacol. Ther. 23(6), 493-500 (2010
57. Patz EF Jr, Campa MJ, Gottlin EB, Kusmartseva I, Guan XR, Herndon JE 2nd. Panel of serum biomarkers for the diagnosis of lung cancer. J. Clin. Oncol. 25(35), 5578-5583 (2007
58. Cho WC. Potentially useful biomarkers for the diagnosis, treatment and prognosis of lung cancer. Biomed. Pharmacother. 61(9), 515-519 (2007
59. Song WA, Liu X, Tian XD et al. Utility of squamous cell carcinoma antigen, carcinoembryonic antigen, Cyfra 21-1 and neuron specific enolase in lung cancer diagnosis: A prospective study from China. Chin. Med. J. (Engl.) 124(20), 3244-3248 (2011
60. Topic A, Ljujic M, Petrovic-Stanojevic N, Dopudja-Pantic V, Radojkovic D. Phenotypes and serum level of alpha-1-Antitrypsin in lung cancer. J. BUON 16(4), 672-676 (2011
61. Agusti A, Edwards LD, Rennard SI et al. Persistent systemic inflammation is associated with poor clinical outcomes in COPD: A novel phenotype. Plos One 7(5), e37483 (2012).
62. Dahl M, Vestbo J, Lange P, Bojesen SE, Tybjaerg-Hansen A, Nordestgaard BG. C-reactive protein as a predictor of prognosis in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 175(3), 250-255 (2007
63. Franciosi LG, Page CP, Celli BR et al. Markers of disease severity in chronic obstructive pulmonary disease. Pulm. Pharmacol. Ther. 19(3), 189-199 (2006
64. Gan WQ, Man SF, Senthilselvan A, Sin DD. Association between chronic obstructive pulmonary disease and systemic inflammation: A systematic review and a meta-Analysis. Thorax 59(7), 574-580 (2004
65. Pinto-Plata V, Toso J, Lee K et al. Profiling serum biomarkers in patients with COPD: Associations with clinical parameters. Thorax 62(7), 595-601 (2007
66. Luisetti M, Ma S, Iadarola P et al. Desmosine as a biomarker of elastin degradation in COPD: Current status and future directions. Eur. Respir. J. 32(5), 1146-1157 (2008
67. Turino GM, Ma S, Lin YY, Cantor JO, Luisetti M. Matrix elastin: A promising biomarker for chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 184(6), 637-641 (2011
68. Ilumets H, Mazur W, Toljamo T et al. Ageing and smoking contribute to plasma surfactant proteins and protease imbalance with correlations to airway obstruction. BMC Pulm. Med. 11, 19 (2011
69. Jaw JE, Sin DD. Unifying thoracic biomarkers: Surfactant protein-D and beyond. Expert Rev. Respir. Med. 6(2), 147-154 (2012
70. Lomas DA, Silverman EK, Edwards LD et al. Serum surfactant protein D is steroid sensitive and associated with exacerbations of COPD. Eur. Respir. J. 34(1), 95-102 (2009
71. More JM, Voelker DR, Silveira LJ, Edwards MG, Chan ED, Bowler RP. Smoking reduces surfactant protein D and phospholipids in patients with and without chronic obstructive pulmonary disease. BMC Pulm. Med. 10, 53 (2010
72. Winkler C, Atochina-Vasserman EN, Holz O et al. Comprehensive characterisation of pulmonary and serum surfactant protein D in COPD. Respir. Res. 12, 29 (2011
73. Poliska S, Csanky E, Szanto A et al. Chronic obstructive pulmonary disease-specific gene expression signatures of alveolar macrophages as well as peripheral blood monocytes overlap and correlate with lung function. Respiration 81(6), 499-510 (2011).
74. Malerba M, Montuschi P. Non-Invasive biomarkers of lung inflammation in smoking subjects. Curr. Med. Chem. 19(2), 187-196 (2012
75. Lee W, Thomas PS. Oxidative stress in COPD and its measurement through exhaled breath condensate. Clin. Transl. Sci. 2(2), 150-155 (2009
76. Koczulla AR, Noeske S, Herr C et al. Alpha-1 antitrypsin is elevated in exhaled breath condensate and serum in exacerbated COPD patients. Respir. Med. 106(1), 120-126 (2012
77. Fens N, Zwinderman AH, Van Der Schee MP et al. Exhaled breath profiling enables discrimination of chronic obstructive pulmonary disease and asthma. Am. J. Respir. Crit. Care Med. 180(11), 1076-1082 (2009
78. Celli BR, Locantore N, Yates J et al. Inflammatory biomarkers improve clinical prediction of mortality in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 185(10), 1065-1072 (2012
79. Hecht SS. Tobacco carcinogens, their biomarkers and tobacco-Induced cancer. Nat. Rev. Cancer 3(10), 733-744 (2003
80. Lodovici M, Bigagli E. Biomarkers of induced active and passive smoking damage. Int. J. Environ. Res. Public Health 6(3), 874-888 (2009
81. Hecht SS, Yuan JM, Hatsukami D. Applying tobacco carcinogen and toxicant biomarkers in product regulation and cancer prevention. Chem. Res. Toxicol. 23(6), 1001-1008 (2010
82. Hecht SS. Research opportunities related to establishing standards for tobacco products under the Family Smoking Prevention and Tobacco Control Act. Nicotine Tob. Res. 14(1), 18-28 (2012
83. Gregg EO, Fisher AL, Lowe F, Mcewan M, Massey ED. An approach to the validation of biomarkers of harm for use in a tobacco context. Regul. Toxicol. Pharmacol. 44(3), 262-267 (2006
84. Stratton K, Shetty P, Wallace R, Bondurant S. Clearing the smoke: The science base for tobacco harm reduction - executive summary. Tob. Control 10(2), 189-195 (2001
85. Dahl M, Nordestgaard BG. Markers of early disease and prognosis in COPD. Int. J. Chron. Obstruct. Pulmon. Dis. 4, 157-167 (2009
86. Glaab T, Vogelmeier C, Buhl R. Outcome measures in chronic obstructive pulmonary disease (COPD): Strengths and limitations. Respir. Res. 11, 79 (2010
87. Sin DD, Vestbo J. Biomarkers in chronic obstructive pulmonary disease. Proc. Am. Thorac. Soc. 6(6), 543-545 (2009
88. Devanarayan V, Scholand MB, Hoidal J et al. Identification of distinct plasma biomarker signatures in patients with rapid and slow declining forms of COPD. COPD 7(1), 51-58 (2010
89. Huertas A, Palange P. COPD: A multifactorial systemic disease. Ther. Adv. Respir. Dis. 5(3), 217-224 (2011
90. Aardema MJ, MacGregor JT. Toxicology and genetic toxicology in the new era of 'toxicogenomics': Impact of '-omics' technologies. Mutat. Res. 499(1), 13-25 (2002
91. Van Leeuwen DM, Gottschalk RW, Van Herwijnen MH, Moonen EJ, Kleinjans JC, Van Delft JH. Differential gene expression in human peripheral blood mononuclear cells induced by cigarette smoke and its constituents. Toxicol. Sci. 86(1), 200-210 (2005
92. Suter L, Haiker M, De Vera MC, Albertini S. Effect of two 5-HT6 receptor antagonists on the rat liver: A molecular approach. Pharmacogenom. J. 3(6), 320-334 (2003
93. Allison DB, Cui X, Page GP, Sabripour M. Microarray data analysis: From disarray to consolidation and consensus. Nat. Rev. Genet. 7(1), 55-65 (2006
94. Miller JA, Horvath S, Geschwind DH. Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc. Natl Acad. Sci. USA 107(28), 12698-12703 (2010
95. Miklos GL, Maleszka R. Microarray reality checks in the context of a complex disease. Nat. Biotechnol. 22(5), 615-621 (2004
96. Segal E, Friedman N, Kaminski N, Regev A, Koller D. From signatures to models: Understanding cancer using microarrays. Nat. Genet. 37(Suppl.), S38-S45 (2005
97. Ross JS, Hatzis C, Symmans WF, Pusztai L, Hortobagyi GN. Commercialized multigene predictors of clinical outcome for breast cancer. Oncologist 13(5), 477-493 (2008
98. Toh SH, Prathipati P, Motakis E, Kwoh CK, Yenamandra SP, Kuznetsov VA. A robust tool for discriminative analysis and feature selection in paired samples impacts the identification of the genes essential for reprogramming lung tissue to adenocarcinoma. BMC Genom. 12(SUPPL3), S24 (2011
99. Shi I, Hashemi Sadraei N, Duan ZH, Shi T. Aberrant signaling pathways in squamous cell lung carcinoma. Cancer Inform. 10, 273-285 (2011
100. Borczuk AC, Toonkel RL, Powell CA. Genomics of lung cancer. Proc. Am. Thorac. Soc. 6(2), 152-158 (2009
101. Masuda K, Takano A, Oshita H et al. Chondrolectin is a novel diagnostic biomarker and a therapeutic target for lung cancer. Clin. Cancer Res. 17(24), 7712-7722 (2011
102. Zhu CQ, Pintilie M, John T et al. Understanding prognostic gene expression signatures in lung cancer. Clin. Lung Cancer 10(5), 331-340 (2009
103. Suzuki K, Kachala SS, Kadota K et al. Prognostic immune markers in non-small cell lung cancer. Clin. Cancer Res. 17(16), 5247-5256 (2011
104. Singh D, Fox SM, Tal-Singer R et al. Induced sputum genes associated with spirometric and radiological disease severity in COPD ex-smokers. Thorax 66(6), 489-495 (2011
105. Pottelberge GR, Mestdagh P, Bracke KR et al. MicroRNA expression in induced sputum of smokers and patients with chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 183(7), 898-906 (2011
106. Shaykhiev R, Krause A, Salit J et al. Smoking-dependent reprogramming of alveolar macrophage polarization: Implication for pathogenesis of chronic obstructive pulmonary disease. J. Immunol. 183(4), 2867-2883 (2009
107. Spira A, Beane J, Shah V et al. Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc. Natl Acad. Sci. USA 101(27), 10143-10148 (2004
108. Gelbman BD, Heguy A, O'Connor TP, Zabner J, Crystal RG. Upregulation of pirin expression by chronic cigarette smoking is associated with bronchial epithelial cell apoptosis. Respir. Res. 8, 10 (2007
109. Beane J, Sebastiani P, Liu G, Brody JS, Lenburg ME, Spira A. Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol. 8(9), R201 (2007
110. Cully M, Downward J. Translational responses to growth factors and stress. Biochem. Soc. Trans. 37(PT1), 284-288 (2009
111. Hetz C. The unfolded protein response: Controlling cell fate decisions under ER stress and beyond. Nat. Rev. Mol. Cell. Biol. 13(2), 89-102 (2012
112. Vadasz I, Weiss CH, Sznajder JI. Ubiquitination and proteolysis in acute lung injury. Chest 141(3), 763-771 (2012
113. Cho JY, Sung HJ. Proteomic approaches in lung cancer biomarker development. Expert Rev. Proteomics 6(1), 27-42 (2009
114. Sin DD, Man SF. Systemic inflammation and mortality in chronic obstructive pulmonary disease. Can. J. Physiol. Pharmacol. 85(1), 141-147 (2007
115. Shaker SB, Von Wachenfeldt KA, Larsson S et al. Identification of patients with chronic obstructive pulmonary disease (COPD) by measurement of plasma biomarkers. Clin. Respir. J. 2(1), 17-25 (2008
116. Bortner JD Jr, Richie JP Jr, Das A et al. Proteomic profiling of human plasma by iTRAQ reveals down-regulation of ITI-HC3 and VDBP by cigarette smoking. J. Proteome Res. 10(3), 1151-1159 (2011
117. Ohlmeier S, Mazur W, Linja-Aho A et al. Sputum proteomics identifies elevated PIGR levels in smokers and mild-To-moderate COPD. J. Proteome Res. 11(2), 599-608 (2012
118. Merkel D, Rist W, Seither P, Weith A, Lenter MC. Proteomic study of human bronchoalveolar lavage fluids from smokers with chronic obstructive pulmonary disease by combining surface-enhanced laser desorption/ ionization-mass spectrometry profiling with mass spectrometric protein identification. Proteomics 5(11), 2972-2980 (2005
119. Tewari AK, Popova-Butler A, El-Mahdy MA, Zweier JL. Identification of differentially expressed proteins in blood plasma of control and cigarette smoke-exposed mice by 2-D DIGE/MS. Proteomics 11(10), 2051-2062 (2011
120. Sexton K, Balharry D, Brennan P, Mclaren J, Brewis IA, Berube KA. Proteomic profiling of human respiratory epithelia by iTRAQ reveals biomarkers of exposure and harm by tobacco smoke components. Biomarkers 16(7), 567-576 (2011
121. Spratlin JL, Serkova NJ, Eckhardt SG. Clinical applications of metabolomics in oncology: A review. Clin. Cancer Res. 15(2), 431-440 (2009
122. Wishart DS, Knox C, Guo AC et al. HMDB: A knowledgebase for the human metabolome. Nucleic Acids Res. 37(Database issue), D603-D610 (2009
123. Breault CD, Hathcock D, Beaver C, Cairns C, Kraft C. Metabolomic and inflammatory profiling in patients with chronic obstructive pulmonary disease (COPD). Am. J. Respir. Crit. Care Med. 183, A4107 (2011
124. Vulimiri SV, Misra M, Hamm JT, Mitchell M, Berger A. Effects of mainstream cigarette smoke on the global metabolome of human lung epithelial cells. Chem. Res. Toxicol. 22(3), 492-503 (2009
125. Miyagi Y, Higashiyama M, Gochi A et al. Plasma free amino acid profiling of five types of cancer patients and its application for early detection. Plos One 6(9), e24143 (2011
126. Hori S, Nishiumi S, Kobayashi K et al. A metabolomic approach to lung cancer. Lung Cancer 74(2), 284-292 (2011
127. Ubhi BK, Riley JH, Shaw PA et al. Metabolic profiling detects biomarkers of protein degradation in COPD patients. Eur. Respir. J. 40(2), 345-355 (2012
128. Rocha CM, Carrola J, Barros AS et al. Metabolic signatures of lung cancer in biofluids: NMR-based metabonomics of blood plasma. J. Proteome Res. 10(9), 4314-4324 (2011
129. Forey BA, Thornton AJ, Lee PN. Systematic review with meta-Analysis of the epidemiological evidence relating smoking to COPD, chronic bronchitis and emphysema. BMC Pulm. Med. 11, 36 (2011
130. Anthonisen NR, Skeans MA, Wise RA, Manfreda J, Kanner RE, Connett JE. The effects of a smoking cessation intervention on 14.5-year mortality: A randomized clinical trial. Ann. Intern. Med. 142(4), 233-239 (2005
131. Balkissoon R, Lommatzsch S, Carolan B, Make B. Chronic obstructive pulmonary disease: A concise review. Med. Clin. North Am. 95(6), 1125-1141 (2011
132. Faught BE, Flouris AD, Cairney J. Epidemiological evidence associating second hand smoke exposure with cardiovascular disease. Inflamm. Allergy Drug Targets 8(5), 321-327 (2009
133. Johnson MD, Schilz J, Djordjevic MV, Rice JR, Shields PG. Evaluation of in vitro assays for assessing the toxicity of cigarette smoke and smokeless tobacco. Cancer Epidemiol. Biomarkers Prev. 18(12), 3263-3304 (2009
134. Pate Capps N, Stewart A, Burns C. The interplay between second hand cigarette smoke, genetics, and cervical cancer: A review of the literature. Biol. Res. Nurs. 10(4), 392-399 (2009
135. Patel RR, Ryu JH, Vassallo R. Cigarette smoking and diffuse lung disease. Drugs 68(11), 1511-1527 (2008
136. Sarkar P, Hayes BE. Proteomic profiling of rat lung epithelial cells induced by acrolein. Life Sci. 85(5-6), 188-195 (2009
137. Westbrook DG, Anderson PG, Pinkerton KE, Ballinger SW. Perinatal tobacco smoke exposure increases vascular oxidative stress and mitochondrial damage in non-human primates. Cardiovasc. Toxicol. 10(3), 216-226 (2010
138. Gao Y, Schug J, Mckenna LB, Le Lay J, Kaestner KH, Greenbaum LE. Tissue-specific regulation of mouse microRNA genes in endoderm-derived tissues. Nucleic Acids Res. 39(2), 454-463 (2011
139. Wang X, Elling AA, Li X et al. Genome-Wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21(4), 1053-1069 (2009
140. Chen Y, Zhang Y, Yin Y et al. SPD - A web-based secreted protein database. Nucleic Acids Res. 33(Database issue), D169-D173 (2005
141. Anderson NL, Polanski M, Pieper R et al. The human plasma proteome: A nonredundant list developed by combination of four separate sources. Mol. Cell Proteomics 3(4), 311-326 (2004
142. Anderson NL. The clinical plasma proteome: A survey of clinical assays for proteins in plasma and serum. Clin. Chem. 56(2), 177-185 (2010
143. Indovina P, Marcelli E, Maranta P, Tarro G. Lung cancer proteomics: Recent advances in biomarker discovery. Int. J. Proteomics 726869 (2011
144. Lescuyer P, Hochstrasser D, Rabilloud T. How shall we use the proteomics toolbox for biomarker discovery? J. Proteome Res. 6(9), 3371-3376 (2007
145. Semenuk MA, Veenstra TD, Gradimir G et al. Translating cancer biomarker discoveries to clinical tests: What should be considered? Recent Patents Biomarkers 1, 222-240 (2011
146. Mann M. Comparative analysis to guide quality improvements in proteomics. Nat. Methods 6(10), 717-719 (2009
147. Goodsaid FM, Mendrick DL. Translational medicine and the value of biomarker qualification. Sci. Transl. Med. 2(47), 47ps44 (2010
148. Mattes WB, Walker EG, Abadie E et al. Research at the interface of industry, academia and regulatory science. Nat. Biotechnol. 28(5), 432-433 (2010
149. Goodsaid F, Frueh F. Biomarker qualification pilot process at the US Food and Drug Administration. AAPS J. 9(1), E105-E108 (2007
150. Wagner JA, Williams SA, Webster CJ. Biomarkers and surrogate end points for fit-for-purpose development and regulatory evaluation of new drugs. Clin. Pharmacol. Ther. 81(1), 104-107 (2007
151. Altar CA, Amakye D, Bounos D et al. A prototypical process for creating evidentiary standards for biomarkers and diagnostics. Clin. Pharmacol. Ther. 83(2), 368-371 (2008
152. Mendrick DL. Transcriptional profiling to identify biomarkers of disease and drug response. Pharmacogenomics 12(2), 235-249 (2011
153. Zatloukal K, Hainaut P. Human tissue biobanks as instruments for drug discovery and development: Impact on personalized medicine. Biomarkers Med. 4(6), 895-903 (2010
154. Irgon J, Huang CC, Zhang Y, Talantov D, Bhanot G, Szalma S. Robust multi-Tissue gene panel for cancer detection. BMC Cancer 10, 319 (2010