Validation of a blood protein signature for non-small cell lung cancer

Clinical Proteomics

Volumn 11, Issue 1, 2014, Pages

  Mehan, Michael R ^a   Williams, Stephen A ^a   Siegfried, Jill M ^b,c   Bigbee, William L ^b   Weissfeld, Joel L ^d   Wilson, David O ^b   Pass, Harvey I ^e   Rom, William N ^e   Muley, Thomas ^f   Meister, Michael ^f   Franklin, Wilbur ^g   Miller, York E ^g,h   Brody, Edward N ^a   Ostroff, Rachel M ^a  

^a SomaLogic Inc   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

^d UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

^e NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f UNIVERSITY OF HEIDELBERG   (Germany)

^g UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^h VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

Biomarker; Diagnosis; Lung cancer; Preanalytic variability; Proteomic; Sample bias; SOMAmer; Squamous cell carcinoma

Indexed keywords

APHA 1 ANTIPROTEINASE; C REACTIVE PROTEIN; CARBONIC ANHYDRASE VI; CARNOSINE DIPEPTIDASE 1; COMPLEMENT COMPONENT C9; HEAT SHOCK PROTEIN 90; MACROPHAGE ELASTASE; MATRILYSIN; PROTEIN; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; BLOOD ANALYSIS; CLASSIFIER; CONTROLLED STUDY; FEMALE; HUMAN; LUNG ADENOCARCINOMA; LUNG NODULE; MAJOR CLINICAL STUDY; MALE; NON SMALL CELL LUNG CANCER; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEOMICS; SMOKING; SQUAMOUS CELL LUNG CARCINOMA;

EID: 84912105423     PISSN: 15426416     EISSN: 15590275     Source Type: Journal    
DOI: 10.1186/1559-0275-11-32     Document Type: Article

References (55)

1. Lozano R, Naghavi M, Foreman K, Lim S, Shibuya K, Aboyans V, Abraham J, Adair T, Aggarwal R, Ahn SY, Alvarado M, Anderson HR, Anderson LM, Andrews KG, Atkinson C, Baddour LM, Barker-Collo S, Bartels DH, Bell ML, Benjamin EJ, Bennett D, Bhalla K, Bikbov B, Bin AA, Birbeck G, Blyth F, Bolliger I, Boufous S, Bucello C, Burch M, et al.: Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 2012, 380:2095-2128.
2. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D: Global cancer statistics. CA Cancer J Clin 2011, 61:69-90.
3. She J, Yang P, Hong Q, Bai C: Lung cancer in China: challenges and interventions. Chest 2013, 143:1117-1126.
4. DeAngelis R, Sant M, Coleman MP, Francisci S, Baili P, Pierannunzio D, Trama A, Visser O, Brenner H, Ardanaz E, Bielska-Lasota M, Engholm G, Nennecke A, Siesling S, Berrino F, Capocaccia R: Cancer survival in Europe 1999-2007 by country and age: results of EUROCARE-5-a population-based study. Lancet Oncol 2013, 15:23-34.
5. American Cancer Society: Cancer Facts & Figures 2013. Atlanta: American Cancer Society; 2013.
6. Aberle DR, Adams AM, Berg CD, Black WC, Clapp JD, Fagerstrom RM, Gareen IF, Gatsonis C, Marcus PM, Sicks JD: Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med 2011, 365:395-409.
7. Wilson DO, Weissfeld JL, Fuhrman CR, Fisher SN, Balogh P, Landreneau RJ, Luketich JD, Siegfried JM: The Pittsburgh Lung Screening Study (PLuSS): outcomes within 3 years of a first computed tomography scan. Am J Respir Crit Care Med 2008, 178:956-961.
8. Horeweg N, van der Aalst CM, Vliegenthart R, Zhao Y, Xie X, Scholten ET, Mali W, Thunnissen E, Weenink C, Groen HJ, Lammers JW, Nackaerts K, Van Rosmalen J, Oudkerk M, De Koning HJ: Volumetric computed tomography screening for lung cancer: three rounds of the NELSON trial. Eur Respir J 2013, 42:1659-1667.
9. van Klaveren RJ, Oudkerk M, Prokop M, Scholten ET, Nackaerts K, Vernhout R, van Iersel CA, van den Bergh KA, van 't Westeinde S, van der Aalst C, Thunnissen E, Xu DM, Wang Y, Zhao Y, Gietema HA, de Hoop BJ, Groen HJ, de Bock GH, van OP, Weenink C, Verschakelen J, Lammers JW, Timens W, Willebrand D, Vink A, Mali W, de Koning HJ: Management of lung nodules detected by volume CT scanning. N Engl J Med 2009, 361:2221-2229.
10. Heist RS, Sequist LV, Engelman JA: Genetic changes in squamous cell lung cancer: a review. J Thorac Oncol 2012, 7:924-933.
11. Aberle DR, DeMello S, Berg CD, Black WC, Brewer B, Church TR, Clingan KL, Duan F, Fagerstrom RM, Gareen IF, Gatsonis CA, Gierada DS, Jain A, Jones GC, Mahon I, Marcus PM, Rathmell JM, Sicks J: Results of the two incidence screenings in the National Lung Screening Trial. N Engl J Med 2013, 369:920-931.
12. Horeweg N, van der Aalst CM, Thunnissen E, Nackaerts K, Weenink C, Groen HJ, Lammers JW, Aerts JG, Scholten ET, van Rosmalen J, Mali W, Oudkerk M, De Koning HJ: Characteristics of lung cancers detected by computer tomography screening in the randomized NELSON trial. Am J Respir Crit Care Med 2013, 187:848-854.
13. Lopes PA, Picozzi G, Falaschi F, Carrozzi L, Falchini M, Carozzi FM, Pistelli F, Comin C, Deliperi A, Grazzini M, Innocenti F, Maddau C, Vella A, Vaggelli L, Paci E, Mascalchi M: Four-year results of low-dose CT screening and nodule management in the ITALUNG trial. J Thorac Oncol 2013, 8:866-875.
14. Reck M, Heigener DF, Mok T, Soria JC, Rabe KF: Management of non-small-cell lung cancer: recent developments. Lancet 2013, 382:709-719.
15. Detterbeck FC, Gibson CJ: Turning gray: the natural history of lung cancer over time. J Thorac Oncol 2008, 3:781-792.
16. Wang BY, Huang JY, Cheng CY, Lin CH, Ko J, Liaw YP: Lung cancer and prognosis in Taiwan: a population-based cancer registry. J Thorac Oncol 2013, 8:1128-1135.
17. Bach PB, Mirkin JN, Oliver TK, Azzoli CG, Berry DA, Brawley OW, Byers T, Colditz GA, Gould MK, Jett JR, Sabichi AL, Smith-Bindman R, Wood DE, Qaseem A, Detterbeck FC: Benefits and harms of CT screening for lung cancer: a systematic review. JAMA 2012, 307:2418-2429.
18. Greenberg AK, Lu F, Goldberg JD, Eylers E, Tsay JC, Yie TA, Naidich D, McGuinness G, Pass H, Tchou-Wong KM, Addrizzo-Harris D, Chachoua A, Crawford B, Rom WN: CT scan screening for lung cancer: risk factors for nodules and malignancy in a high-risk urban cohort. PloS One 2012, 7:e39403.
19. Patz EF Jr, Pinsky P, Gatsonis C, Sicks JD, Kramer BS, Tammemagi MC, Chiles C, Black WC, Aberle DR, for the NOMWT: Overdiagnosis in low-dose computed tomography screening for lung cancer. JAMA Inter Med 2014, 174:269-274.
20. Ostroff RM, Bigbee WL, Franklin W, Gold L, Mehan M, Miller YE, Pass HI, Rom WN, Siegfried JM, Stewart A, Walker JJ, Weissfeld JL, Williams S, Zichi D, Brody EN: Unlocking biomarker discovery: large scale application of aptamer proteomic technology for early detection of lung cancer. PLoS One 2010, 5:e15003.
21. Fuzery AK, Levin J, Chan MM, Chan DW: Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin Proteomics 2013, 10:13.
22. Brody E, Gold L, Mehan M, Ostroff R, Rohloff J, Walker J, Zichi D: Life's simple measures: unlocking the proteome. J Mol Biol 2012, 422:595-606.
23. Mehan MR, Ostroff R, Wilcox SK, Steele F, Schneider D, Jarvis TC, Baird GS, Gold L, Janjic N: Highly multiplexed proteomic platform for biomarker discovery, diagnostics, and therapeutics. Adv Exp Med Biol 2013, 735:283-300.
24. Ostroff R, Foreman T, Keeney TR, Stratford S, Walker JJ, Zichi D: The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. J Proteomics 2010, 73:649-666.
25. Gold L, Ayers D, Bertino J, Bock C, Bock A, Brody EN, Carter J, Dalby AB, Eaton BE, Fitzwater T, Flather D, Forbes A, Foreman T, Fowler C, Gawande B, Goss M, Gunn M, Gupta S, Halladay D, Heil J, Heilig J, Hicke B, Husar G, Janjic N, Jarvis T, Jennings S, Katilius E, Keeney TR, Kim N, Koch TH, et al.: Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One 2010, 5:e15004.
26. Vaught JD, Bock C, Carter J, Fitzwater T, Otis M, Schneider D, Rolando J, Waugh S, Wilcox SK, Eaton BE: Expanding the chemistry of DNA for in vitro selection. J Am Chem Soc 2010, 132:4141-4151.
27. Pinsky PF, Church TR, Izmirlian G, Kramer BS: The national lung screening trial: results stratified by demographics, smoking history, and lung cancer histology. Cancer 2013, 119:3976-3983.
28. Li XJ, Hayward C, Fong PY, Dominguez M, Hunsucker SW, Lee LW, McLean M, Law S, Butler H, Schirm M, Gingras O, Lamontagne J, Allard R, Chelsky D, Price ND, Lam S, Massion PP, Pass H, Rom WN, Vachani A, Fang KC, Hood L, Kearney P: A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med 2013, 5:207ra142.
29. Daly S, Rinewalt D, Fhied C, Basu S, Mahon B, Liptay MJ, Hong E, Chmielewski G, Yoder MA, Shah PN, Edell ES, Maldonado F, Bungum AO, Borgia JA: Development and validation of a plasma biomarker panel for discerning clinical significance of indeterminate pulmonary nodules. J Thorac Oncol 2013, 8:31-36.
30. Pine SR, Mechanic LE, Enewold L, Chaturvedi AK, Katki HA, Zheng YL, Bowman ED, Engels EA, Caporaso NE, Harris CC: Increased levels of circulating interleukin 6, interleukin 8, C-reactive protein, and risk of lung cancer. JNCI 2011, 103:1112-1122.
31. Cancer Genome Atlas Research Network: Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012, 489:519-525.
32. Roy R, Yang J, Moses MA: Matrix metalloproteinases as novel biomarkers and potential therapeutic targets in human cancer. J Clin Oncol 2009, 27:5287-5297.
33. Liu D, Nakano J, Ishikawa S, Yokomise H, Ueno M, Kadota K, Urushihara M, Huang CL: Overexpression of matrix metalloproteinase-7 (MMP-7) correlates with tumor proliferation, and a poor prognosis in non-small cell lung cancer. Lung Cancer 2007, 58:384-391.
34. Qu P, Du H, Wang X, Yan C: Matrix metalloproteinase 12 overexpression in lung epithelial cells plays a key role in emphysema to lung bronchioalveolar adenocarcinoma transition. Cancer Res 2009, 69:7252-7261.
35. Hipkiss AR, Cartwright SP, Bromley C, Gross SR, Bill RM: Carnosine: can understanding its actions on energy metabolism and protein homeostasis inform its therapeutic potential? Chem Cent J 2013, 7:38.
36. Supuran CT: Carbonic anhydrases: novel therapeutic applications for inhibitors and activators. Nat Rev Drug Discov 2008, 7:168-181.
37. Warburg O: On the origin of cancer cells. Science 1956, 123:309-314.
38. Walser T, Cui X, Yanagawa J, Lee JM, Heinrich E, Lee G, Sharma S, Dubinett SM: Smoking and lung cancer: the role of inflammation. Proc Am Thorac Soc 2008, 5:811-815.
39. Gao WM, Kuick R, Orchekowski RP, Misek DE, Qiu J, Greenberg AK, Rom WN, Brenner DE, Omenn GS, Haab BB, Hanash SM: Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer 2005, 5:110.
40. Chaturvedi AK, Caporaso NE, Katki HA, Wong HL, Chatterjee N, Pine SR, Chanock SJ, Goedert JJ, Engels EA: C-reactive protein and risk of lung cancer. J Clin Oncol 2010, 28:2719-2726.
41. Shiels MS, Pfeiffer RM, Hildesheim A, Engels EA, Kemp TJ, Park JH, Katki HA, Koshiol J, Shelton G, Caporaso NE, Pinto LA, Chaturvedi AK: Circulating inflammation markers and prospective risk for lung cancer. JNCI 2013, 105:1871-1880.
42. Rutkowski MJ, Sughrue ME, Kane AJ, Mills SA, Parsa AT: Cancer and the complement cascade. Mol Cancer Res 2010, 8:1453-1465.
43. 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 2007, 25:5578-5583.
44. Sin DD, Tammemagi CM, Lam S, Barnett MJ, Duan X, Tam A, Auman H, Feng Z, Goodman GE, Hanash S, Taguchi A: Pro-surfactant protein B as a biomarker for lung cancer prediction. J Clin Oncol 2013, 31:4536-4543.
45. Pecot CV, Li M, Zhang XJ, Rajanbabu R, Calitri C, Bungum A, Jett JR, Putnam JB, Callaway-Lane C, Deppen S, Grogan EL, Carbone DP, Worrell JA, Moons KG, Shyr Y, Massion PP: Added value of a serum proteomic signature in the diagnostic evaluation of lung nodules. Cancer Epidemiol Biomarkers Prev 2012, 21:786-792.
46. Patz EF Jr, Campa MJ, Gottlin EB, Trotter PR, Herndon JE 2nd, Kafader D, Grant RP, Eisenberg M: Biomarkers to help guide management of patients with pulmonary nodules. Am J Respir Crit Care Med 2013, 188:461-465.
47. Lung Cancer Biomarkers Group: Blood repository for the validation of lung cancer biomarkers. [ http://edrn.nci.nih.gov/resources/sample-reference-sets ]
48. Church TR, Black WC, Aberle DR, Berg CD, Clingan KL, Duan F, Fagerstrom RM, Gareen IF, Gierada DS, Jones GC, Mahon I, Marcus PM, Sicks JD, Jain A, Baum S, National Lung Screening Trial Research Team: Results of initial low-dose computed tomographic screening for lung cancer. NEJM 2013, 368:1980-1991.
49. Tuck MK, Chan DW, Chia D, Godwin AK, Grizzle WE, Krueger KE, Rom W, Sanda M, Sorbara L, Stass S, Wang W, Brenner DE: Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group. J Proteome Res 2009, 8:113-117.
50. Ostroff RM, Mehan MR, Stewart A, Ayers D, Brody EN, Williams SA, Levin S, Black B, Harbut M, Carbone M, Goparaju C, Pass HI: Early detection of malignant pleural mesothelioma in asbestos-exposed individuals with a noninvasive proteomics-based surveillance tool. PLoS One 2012, 7:e46091.
51. Kraemer S, Vaught JD, Bock C, Gold L, Katilius E, Keeney TR, Kim N, Saccomano NA, Wilcox SK, Zichi D, Sanders GM: From SOMAmer-based biomarker discovery to diagnostic and clinical applications: a SOMAmer-based, streamlined multiplex proteomic assay. PLoS One 2011, 6:e26332.
52. Breiman L: Machine learning. Mach Learn 2001, 45:5-32.
53. Hastie T, Tibshirani R, Friedman JH: The Elements of Statistical Learning: Data Mining, Inference, and Prediction. 2nd edition. New York, NY: Springer; 2009.
54. Pepe MS, Etzioni R, Feng Z, Potter JD, Thompson ML, Thornquist M, Winget M, Yasui Y: Phases of biomarker development for early detection of cancer. JNCI 2001, 93:1054-1061.
55. Huang dW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.