Genetic association with overall survival of taxane-treated lung cancer patients a genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study

BMC Cancer

Volumn 12, Issue , 2012, Pages

  Niu, Nifang ^a   Schaid, Daniel J ^b   Abo, Ryan P ^c   Kalari, Krishna ^b   Fridley, Brooke L ^b   Feng, Qiping ^d   Jenkins, Gregory ^b   Batzler, Anthony ^b   Brisbin, Abra G ^b   Cunningham, Julie M ^b   Li, Liang ^a   Sun, Zhifu ^b   Yang, Ping ^b   Wang, Liewei ^a  

^a MAYO GRADUATE SCHOOL   (United States)

^b MAYO CLINIC   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Genome wide association; Lung cancer; Lymphoblastoid cell line; Overall survival; Taxane

Indexed keywords

DOCETAXEL; EPIDERMAL GROWTH FACTOR RECEPTOR KINASE INHIBITOR; ETOPOSIDE; GEMCITABINE; MESSENGER RNA; MICRORNA; MICRORNA 1468; MICRORNA 584; PACLITAXEL; PLATINUM COMPLEX; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ADULT; AFRICAN AMERICAN; AGED; ARTICLE; ASIAN AMERICAN; CANCER RADIOTHERAPY; CCT5 GENE; CELL PROLIFERATION; CHEMOSENSITIVITY; CMBL GENE; CONTROLLED STUDY; DESENSITIZATION; DRUG CYTOTOXICITY; EUROPEAN AMERICAN; EXO1 GENE; FEMALE; GENE; GENE EXPRESSION; GENE SILENCING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN CELL; KMO GENE; LUNG NON SMALL CELL CANCER; LUNG SMALL CELL CANCER; LUNG SURGERY; LYMPHOBLASTOID CELL LINE; MAJOR CLINICAL STUDY; MALE; NUCLEOTIDE SEQUENCE; OPN3 GENE; OVERALL SURVIVAL; PIP4K2A GENE; PROPORTIONAL HAZARDS MODEL; RNA INTERFERENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; AGED; AGED, 80 AND OVER; ANTINEOPLASTIC AGENTS; BRIDGED COMPOUNDS; CARCINOMA, NON-SMALL-CELL LUNG; CELL LINE, TUMOR; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; SMALL CELL LUNG CARCINOMA; SURVIVAL ANALYSIS; TAXOIDS; TUMOR MARKERS, BIOLOGICAL;

EID: 84866515205     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-12-422     Document Type: Article

References (51)

1. McGrogan BT, Gilmartin B, Carney DN, McCann A. Taxanes, microtubules and chemoresistant breast cancer. Biochim Biophys Acta 2008, 1785(2):96-132.
2. Zhao J, Kim JE, Reed E, Li QQ. Molecular mechanism of antitumor activity of taxanes in lung cancer (Review). Int J Oncol 2005, 27(1):247-256.
3. Cancer Facts & Figures 2012 2012, Atlanta: American Cancer Society, Cancer Facts & Figures 2012.
4. Goffin J, Lacchetti C, Ellis PM, Ung YC, Evans WK. First-line systemic chemotherapy in the treatment of advanced non-small cell lung cancer: a systematic review. J Thorac Oncol 2010, 5(2):260-274. 10.1097/JTO.0b013e3181c6f035, 20101151.
5. Rodriguez E, Lilenbaum RC. Small cell lung cancer: past, present, and future. Curr Oncol Rep 2010, 12(5):327-334. 10.1007/s11912-010-0120-5, 20632219.
6. Lee JJ, Swain SM. Peripheral neuropathy induced by microtubule-stabilizing agents. J Clin Oncol 2006, 24(10):1633-1642. 10.1200/JCO.2005.04.0543, 16575015.
7. Rowinsky EK, Donehower RC. Paclitaxel (taxol). N Engl J Med 1995, 332(15):1004-1014. 10.1056/NEJM199504133321507, 7885406.
8. Rigas JR. Taxane-platinum combinations in advanced non-small cell lung cancer: a review. Oncologist 2004, 9(Suppl 2):16-23.
9. Rosell R, Taron M, Alberola V, Massuti B, Felip E. Genetic testing for chemotherapy in non-small cell lung cancer. Lung Cancer 2003, 41(Suppl 1):S97-102.
10. Isla D, Sarries C, Rosell R, Alonso G, Domine M, Taron M, Lopez-Vivanco G, Camps C, Botia M, Nunez L, et al. Single nucleotide polymorphisms and outcome in docetaxel-cisplatin-treated advanced non-small-cell lung cancer. Ann Oncol 2004, 15(8):1194-1203. 10.1093/annonc/mdh319, 15277258.
11. Gandara DR, Kawaguchi T, Crowley J, Moon J, Furuse K, Kawahara M, Teramukai S, Ohe Y, Kubota K, Williamson SK, et al. Japanese-US common-arm analysis of paclitaxel plus carboplatin in advanced non-small-cell lung cancer: a model for assessing population-related pharmacogenomics. J Clin Oncol 2009, 27(21):3540-3546. 10.1200/JCO.2008.20.8793, 2717760, 19470925.
12. Leskela S, Jara C, Leandro-Garcia LJ, Martinez A, Garcia-Donas J, Hernando S, Hurtado A, Vicario JC, Montero-Conde C, Landa I, et al. Polymorphisms in cytochromes P450 2C8 and 3A5 are associated with paclitaxel neurotoxicity. Pharmacogenomics J 2010, [Epub ahead of print].
13. Sissung TM, Mross K, Steinberg SM, Behringer D, Figg WD, Sparreboom A, Mielke S. Association of ABCB1 genotypes with paclitaxel-mediated peripheral neuropathy and neutropenia. Eur J Cancer 2006, 42(17):2893-2896. 10.1016/j.ejca.2006.06.017, 1647318, 16950614.
14. Rochat B. Role of cytochrome P450 activity in the fate of anticancer agents and in drug resistance: focus on tamoxifen, paclitaxel and imatinib metabolism. Clin Pharmacokinet 2005, 44(4):349-366. 10.2165/00003088-200544040-00002, 15828850.
15. Spratlin J, Sawyer MB. Pharmacogenetics of paclitaxel metabolism. Crit Rev Oncol Hematol 2007, 61(3):222-229. 10.1016/j.critrevonc.2006.09.006, 17092739.
16. Watters JW, Kraja A, Meucci MA, Province MA, McLeod HL. Genome-wide discovery of loci influencing chemotherapy cytotoxicity. Proc Natl Acad Sci U S A 2004, 101(32):11809-11814. 10.1073/pnas.0404580101, 511056, 15282376.
17. O'Brien C, Cavet G, Pandita A, Hu X, Haydu L, Mohan S, Toy K, Rivers CS, Modrusan Z, Amler LC, et al. Functional genomics identifies ABCC3 as a mediator of taxane resistance in HER2-amplified breast cancer. Cancer Res 2008, 68(13):5380-5389. 10.1158/0008-5472.CAN-08-0234, 18593940.
18. Kroetz DL, Baldwin RM, Owzar K, Jiang C, Zembutsu H, Kubo M, Nakamura Y, Shulman LN, Ratain MJ. Inherited genetic variation in EPHA5, FGD4, and NRDG1 and paclitaxel (P)-induced peripheral neuropathy (PN): results from a genome-wide association study (GWAS) in CALGB 40101. J Clin Oncol 2010, 28:15s.
19. Li L, Fridley B, Kalari K, Jenkins G, Batzler A, Safgren S, Hildebrandt M, Ames M, Schaid D, Wang L. Gemcitabine and cytosine arabinoside cytotoxicity: association with lymphoblastoid cell expression. Cancer Res 2008, 68(17):7050-7058. 10.1158/0008-5472.CAN-08-0405, 2562356, 18757419.
20. Li L, Fridley BL, Kalari K, Jenkins G, Batzler A, Weinshilboum RM, Wang L. Gemcitabine and arabinosylcytosin pharmacogenomics: genome-wide association and drug response biomarkers. PLoS One 2009, 4(11):e7765. 10.1371/journal.pone.0007765, 2770319, 19898621.
21. Niu N, Qin Y, Fridley BL, Hou J, Kalari KR, Zhu M, Wu TY, Jenkins GD, Batzler A, Wang L. Radiation pharmacogenomics: a genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines. Genome Res 2010, 20(11):1482-1492. 10.1101/gr.107672.110, 2963812, 20923822.
22. Yang P, Sun Z, Krowka MJ, Aubry MC, Bamlet WR, Wampfler JA, Thibodeau SN, Katzmann JA, Allen MS, Midthun DE, et al. Alpha1-antitrypsin deficiency carriers, tobacco smoke, chronic obstructive pulmonary disease, and lung cancer risk. Arch Intern Med 2008, 168(10):1097-1103. 10.1001/archinte.168.10.1097, 2562773, 18504338.
23. Moyer AM, Sun Z, Batzler AJ, Li L, Schaid DJ, Yang P, Weinshilboum RM. Glutathione pathway genetic polymorphisms and lung cancer survival after platinum-based chemotherapy. Cancer Epidemiol Biomarkers Prev 2010, 19(3):811-821. 10.1158/1055-9965.EPI-09-0871, 2837367, 20200426.
24. Wigginton JE, Cutler DJ, Abecasis GR. A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet 2005, 76(5):887-893. 10.1086/429864, 1199378, 15789306.
25. Schaid DJ, Batzler AJ, Jenkins GD, Hildebrandt MA. Exact tests of Hardy-Weinberg equilibrium and homogeneity of disequilibrium across strata. Am J Hum Genet 2006, 79(6):1071-1080. 10.1086/510257, 1698709, 17186465.
26. Cunningham JM, Oberg AL, Borralho PM, Kren BT, French AJ, Wang L, Bot BM, Morlan BW, Silverstein KA, Staggs R, et al. Evaluation of a new high-dimensional miRNA profiling platform. BMC Med Genomics 2009, 2:57. 10.1186/1755-8794-2-57, 2744682, 19712457.
27. Brain P, Cousens R. An equation to describe dose responses where there is stimulation of growth at low doses. Weed Res 1989, 29(2):93-96.
28. Van Ewijk PH, Hoekstra JA. Calculation of the EC50 and its confidence interval when subtoxic stimulus is present. Ecotoxicol Environ Saf 1993, 25(1):25-32. 10.1006/eesa.1993.1003, 7682915.
29. Wu ZJ, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 2004, 99(468):909-917.
30. Li YAG. Mach 1.0: Rapid Haplotype Reconstruction and Missing Genotype Inference. Am J Hum Genet 2006, S79:2290.
31. Bandiera S, Hatem E, Lyonnet S, Henrion-Caude A. microRNAs in diseases: from candidate to modifier genes. Clin Genet 2010, 77(4):306-313. 10.1111/j.1399-0004.2010.01370.x, 20132241.
32. Gligorov J, Lotz JP. Preclinical pharmacology of the taxanes: implications of the differences. Oncologist 2004, 9(Suppl 2):3-8.
33. Mielke S, Sparreboom A, Mross K. Peripheral neuropathy: a persisting challenge in paclitaxel-based regimes. Eur J Cancer 2006, 42(1):24-30. 10.1016/j.ejca.2005.06.030, 16293411.
34. Stewart DJ. Tumor and host factors that may limit efficacy of chemotherapy in non-small cell and small cell lung cancer. Crit Rev Oncol Hematol 2010, 75(3):173-234. 10.1016/j.critrevonc.2009.11.006, 2888634, 20047843.
35. Sie L, Loong S, Tan EK. Utility of lymphoblastoid cell lines. J Neurosci Res 2009, 87(9):1953-1959. 10.1002/jnr.22000, 19224581.
36. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, et al. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 2008, 4(11):e1000287. 10.1371/journal.pgen.1000287, 2583954, 19043577.
37. Stark AL, Zhang W, Zhou T, O'Donnell PH, Beiswanger CM, Huang RS, Cox NJ, Dolan ME. Population differences in the rate of proliferation of international HapMap cell lines. Am J Hum Genet 2010, 87(6):829-833. 10.1016/j.ajhg.2010.10.018, 2997375, 21109222.
38. Cai Y, Yu X, Hu S, Yu J. A brief review on the mechanisms of miRNA regulation. Genomics Proteomics Bioinformatics 2009, 7(4):147-154. 10.1016/S1672-0229(08)60044-3, 20172487.
39. Mishra PJ, Mishra PJ, Banerjee D, Bertino JR. MiRSNPs or MiR-polymorphisms, new players in microRNA mediated regulation of the cell: introducing microRNA pharmacogenomics. Cell Cycle 2008, 7(7):853-858. 10.4161/cc.7.7.5666, 18414050.
40. Mishra PJ, Humeniuk R, Mishra PJ, Longo-Sorbello GS, Banerjee D, Bertino JR. A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc Natl Acad Sci U S A 2007, 104(33):13513-13518. 10.1073/pnas.0706217104, 1948927, 17686970.
41. Ishizuka T, Fujimori I, Kato M, Noji-Sakikawa C, Saito M, Yoshigae Y, Kubota K, Kurihara A, Izumi T, Ikeda T, et al. Human carboxymethylenebutenolidase as a bioactivating hydrolase of olmesartan medoxomil in liver and intestine. J Biol Chem 2010, 285(16):11892-11902. 10.1074/jbc.M109.072629, 2852926, 20177059.
42. Yang X, Zou P, Yao J, Yun D, Bao H, Du R, Long J, Chen X. Proteomic dissection of cell type-specific H2AX-interacting protein complex associated with hepatocellular carcinoma. J Proteome Res 2010, 9(3):1402-1415. 10.1021/pr900932y, 20000738.
43. Clarke JH, Irvine RF. The activity, evolution and association of phosphatidylinositol 5-phosphate 4-kinases. Adv Enzyme Regul 2011, Epub ahead of print.
44. van den Bout I, Divecha N. PIP5K-driven PtdIns(4,5)P2 synthesis: regulation and cellular functions. J Cell Sci 2009, 122(Pt 21):3837-3850.
45. Clarke JH, Wang M, Irvine RF. Localization, regulation and function of type II phosphatidylinositol 5-phosphate 4-kinases. Adv Enzyme Regul 2010, 50(1):12-18. 10.1016/j.advenzreg.2009.10.006, 2877797, 19896968.
46. Clarke JH, Richardson JP, Hinchliffe KA, Irvine RF. Type II PtdInsP kinases: location, regulation and function. Biochem Soc Symp 2007, 74:149-159. 10.1042/BSS0740149, 17233588.
47. Bultsma Y, Keune WJ, Divecha N. PIP4Kbeta interacts with and modulates nuclear localization of the high-activity PtdIns5P-4-kinase isoform PIP4Kalpha. Biochem J 2010, 430(2):223-235. 10.1042/BJ20100341, 20583997.
48. Wilcox A, Hinchliffe KA. Regulation of extranuclear PtdIns5P production by phosphatidylinositol phosphate 4-kinase 2alpha. FEBS Lett 2008, 582(9):1391-1394. 10.1016/j.febslet.2008.03.022, 18364242.
49. Carricaburu V, Lamia KA, Lo E, Favereaux L, Payrastre B, Cantley LC, Rameh LE. The phosphatidylinositol (PI)-5-phosphate 4-kinase type II enzyme controls insulin signaling by regulating PI-3,4,5-trisphosphate degradation. Proc Natl Acad Sci U S A 2003, 100(17):9867-9872. 10.1073/pnas.1734038100, 187868, 12897244.
50. Ramel D, Lagarrigue F, Dupuis-Coronas S, Chicanne G, Leslie N, Gaits-Iacovoni F, Payrastre B, Tronchere H. PtdIns5P protects Akt from dephosphorylation through PP2A inhibition. Biochem Biophys Res Commun 2009, 387(1):127-131. 10.1016/j.bbrc.2009.06.139, 19576174.
51. Jones DR, Bultsma Y, Keune WJ, Halstead JR, Elouarrat D, Mohammed S, Heck AJ, D'Santos CS, Divecha N. Nuclear PtdIns5P as a transducer of stress signaling: an in vivo role for PIP4Kbeta. Mol Cell 2006, 23(5):685-695. 10.1016/j.molcel.2006.07.014, 16949365.