Transcriptional profiling of the dose response: A more powerful approach for characterizing drug activities

PLoS Computational Biology

Volumn 5, Issue 9, 2009, Pages

  Ji, Rui Ru ^a   De Silva, Heshani ^a   Jin, Yisheng ^b   Bruccoleri, Robert E ^c   Cao, Jian ^a   He, Aiqing ^a   Huang, Wenjun ^a   Kayne, Paul S ^a   Neuhaus, Isaac M ^a   Ott, Karl Heinz ^a   Penhallow, Becky ^a   Cockett, Mark I ^a   Neubauer, Michael G ^a   Siemers, Nathan O ^a   Ross Macdonald, Petra ^a  

^a BRISTOL MYERS SQUIBB RESEARCH AND DEVELOPMENT   (United States)

^b Dyson School of Applied Economics and Management   (United States)

^c Congenomics ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEPTH PROFILING; DRUG DOSAGE; DRUG PRODUCTS;

ANALYTICAL METHOD; DOSE CALCULATE; DOSE RESPONSE; DOSE-DEPENDENT; DOSE-RESPONSE CURVES; DRUG ACTIVITIES; GENOMICS; GOLD STANDARDS; MICROARRAY DATA ANALYSIS; TRANSCRIPTIONAL PROFILING;

GENOME;

ADENOSINE TRIPHOSPHATE; CYCLIN DEPENDENT KINASE INHIBITOR 1A; CYTOCHROME P450 1A1; CYTOCHROME P450 1B1; DASATINIB; DNA; DUAL SPECIFICITY PHOSPHATASE 6; EPIDERMAL GROWTH FACTOR RECEPTOR; GAMMA INTERFERON RECEPTOR 1; GROWTH ARREST AND DNA DAMAGE INDUCIBLE PROTEIN 45; IMATINIB; INTERLEUKIN 15; JANUS KINASE; LEUKEMIA INHIBITORY FACTOR RECEPTOR; MITOGEN ACTIVATED PROTEIN KINASE KINASE; MITOGEN ACTIVATED PROTEIN KINASE P38; MITOGEN ACTIVATED PROTEIN KINASE PHOSPHATASE 1; MYC PROTEIN; N (2,3 DIHYDROXYPROPOXY) 3,4 DIFLUORO 2 (2 FLUORO 4 IODOANILINO)BENZAMIDE; NILOTINIB; PROTEIN BCL X; PROTEIN MDM2; RAF PROTEIN; RNA; STAT PROTEIN; STRATIFIN; TRANSCRIPTOME; TRANSFORMING GROWTH FACTOR ALPHA; TRANSFORMING GROWTH FACTOR BETA; X BOX BINDING PROTEIN 1; 4 METHYL N (3 (4 METHYLIMIDAZOL 1 YL) 5 (TRIFLUOROMETHYL)PHENYL) 3 ((4 PYRIDIN 3 YLPYRIMIDIN 2 YL)AMINO)BENZAMIDE; 4-METHYL-N-(3-(4-METHYLIMIDAZOL-1-YL)-5-(TRIFLUOROMETHYL)PHENYL)-3-((4-PYRIDIN-3-YLPYRIMIDIN-2-YL)AMINO)BENZAMIDE; BENZAMIDE DERIVATIVE; DIPHENYLAMINE; DRUG DERIVATIVE; PIPERAZINE DERIVATIVE; PROTEIN KINASE INHIBITOR; PYRIMIDINE DERIVATIVE; THIAZOLE DERIVATIVE;

ALGORITHM; ANALYTIC METHOD; ARTICLE; CELL CULTURE; CELL VIABILITY; DNA CONTENT; DOSE RESPONSE; DRUG ACTIVITY; FLUORESCENCE ACTIVATED CELL SORTING; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PATH ANALYSIS; QUANTITATIVE ANALYSIS; SIGMOIDAL DOSE RESPONSE SEARCH ALGORITHM; BIOLOGY; CELL CYCLE; CELL LINE; CLUSTER ANALYSIS; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION; METHODOLOGY; SIGNAL TRANSDUCTION;

ALGORITHMS; BENZAMIDES; CELL CYCLE; CELL LINE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DIPHENYLAMINE; DOSE-RESPONSE RELATIONSHIP, DRUG; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PIPERAZINES; PROTEIN KINASE INHIBITORS; PYRIMIDINES; SIGNAL TRANSDUCTION; THIAZOLES;

EID: 70349667211     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000512     Document Type: Article

References (56)

1. Paracelsus (1564) Dritte defensione, von der Beischreibung der neuen Rezepte. Sieben Defensiones, Verantwortung über etliche Verunglimpfungen seiner Mißgönner. Cologne: Arnold Byrckmann.
2. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161. (Pubitemid 44359727)
3. Stegmaier K, Ross KN, Colavito SA, O'Malley S, Stockwell BR, et al. (2004) Gene expression-based high-throughput screening(GE-HTS) and application to leukemia differentiation. Nat Genet 36: 257-263. (Pubitemid 38282750)
4. Parker RA, Flint OP, Mulvey R, Elosua C, Wang F, et al. (2005) Endoplasmic reticulum stress links dyslipidemia to inhibition of proteasome activity and glucose transport by HIV protease inhibitors. Mol Pharmacol 67: 1909-1919. (Pubitemid 41007773)
5. Boehm C, Newrzella D, Herberger S, Schramm N, Eisenhardt G, et al. (2006) Effects of antidepressant treatment on gene expression profile in mouse brain: cell type-specific transcription profiling using laser microdissection and microarray analysis. J Neurochem 97 Supplement 1: 44-49.
6. Fanton CP, Rowe MW, Moler EJ, Ison-Dugenny M, De Long SK, et al. (2006) Development of a screening assay for surrogate markers of CHK1 inhibitor-induced cell cycle release. J Biomol Screen 11: 792-806. (Pubitemid 44562320)
7. Kamb A, Wee S, Lengauer C (2007) Why is cancer drug discovery so difficult? Nat Rev Drug Discov 6: 115-120.
8. Wang XD, Reeves K, Luo FR, Xu LA, Lee F, et al. (2007) Identification of candidate predictive and surrogate molecular markers for dasatinib in prostate cancer: rationale for patient selection and efficacy monitoring. Genome Biol 8: R255. (Pubitemid 351917494)
9. Inglese J, Auld DS, Jadhav A, Johnson RL, Simeonov A, et al. (2006) Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries. Proceedings of the National Academy of Sciences 103: 11473-11478. (Pubitemid 44182476)
10. Tian H, Cao L, Tan Y, Williams S, Chen L, et al. (2004) Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis. Nucleic Acids Res 32: e126.
11. Muller PY, Netscher T, Frank J, Stoecklin E, Rimbach G, et al. (2005) Comparative quantification of pharmacodynamic parameters of chiral compounds (RRR- vs. all-rac-alpha tocopherol) by global gene expression profiling. J Plant Physiol 162: 811-817. (Pubitemid 40772097)
12. O'Grady M, Raha D, Hanson B, Bunting M, Hanson G (2005) Combining RNA interference and kinase inhibitors against cell signalling components involved in cancer. BMC Cancer 5: 125. (Pubitemid 41554904)
13. Balakrishnan N, ed (1991) Handbook of the Logistic Distribution: CRC Press. 601 p.
14. Varma R, Hector S, Greco WR, Clark K, Hawthorn L, et al. (2007) Platinum drug effects on the expression of genes in the polyamine pathway: time-course and concentration-effect analysis based on Affymetrix gene expression profiling of A2780 ovarian carcinoma cells. Cancer Chemother Pharmacol 59: 711-723. (Pubitemid 46440593)
15. Brun YF, Varma R, Hector SM, Pendyala L, Tummala R, et al. (2008) Simultaneous modeling of concentration-effect and time-course patterns in gene expression data from microarrays. Cancer Genomics Proteomics 5: 43-53.
16. Black JW, Leff P (1983) Operational models of pharmacological agonism. Proc R Soc Lond B Biol Sci 220: 141-162.
17. Lamb J (2007) The Connectivity Map: a new tool for biomedical research. Nat Rev Cancer 7: 54-60. (Pubitemid 46020847)
18. Fabian MA, Biggs WH 3rd, Treiber DK, Atteridge CE, Azimioara MD, et al. (2005) A small molecule-kinase interaction map for clinical kinase inhibitors. Nat Biotechnol 23: 329-336.
19. Quintas-Cardama A, Kantarjian H, Cortes J (2007) Flying under the radar: the new wave of BCR-ABL inhibitors. Nat Rev Drug Discov 6: 834-1348 (Pubitemid 47500507)
20. Lombardo LJ, Lee FY, Chen P, Norris D, Barrish JC, et al. (2004) Discovery of N- (2-chloro-6-methyl-phenyl)-2-(6-(4-(2-hydroxyethyl)-piperazin-1- yl)-2-methylpyrimidin- 4-ylamino)thiazole-5-carboxamide (BMS-354825), a dual Src/Abl kinase inhibitor with potent antitumor activity in preclinical assays. J Med Chem 47: 6658-6661. (Pubitemid 40053752)
21. zKaraman MW, Herrgard S, Treiber DK, Gallant P, Atteridge CE, et al. (2008) A quantitative analysis of kinase inhibitor selectivity. Nat Biotechnol 26: 127-132.
22. Wang JY, Wilcoxen KM, Nomoto K, Wu S (2007) Recent advances of MEK inhibitors and their clinical progress. Curr Top Med Chem 7: 1364-1378. (Pubitemid 47471235)
23. Rix U, Hantschel O, Durnberger G, Remsing Rix LL, Planyavsky M, et al. (2007) Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib and dasatinib reveal novel kinase and non-kinase targets. Blood: pp 4055-4063. (Pubitemid 350248462)
24. Smith CK, Windsor WT (2007) Thermodynamics of Nucleotide and Non-ATP-Competitive Inhibitor Binding to MEK1 by Circular Dichroism and Isothermal Titration Calorimetry. Biochemistry 46: 1358-1367.
25. Akhmetshina A, Dees C, Pileckyte M, Maurer B, Axmann R, et al. (2008) Dual inhibition of c-abl and PDGF receptor signaling by dasatinib and nilotinib for the treatment of dermal fibrosis. FASEB J 22: 2214-2222. (Pubitemid 351948641)
26. Brown A, Carlson T, Loi C-M, Graziano M (2007) Pharmacodynamic and toxicokinetic evaluation of the novel MEK inhibitor, PD0325901, in the rat following oral and intravenous administration. Cancer Chemotherapy and Pharmacology 59: 671-679. (Pubitemid 46295133)
27. Xie S, Wang Y, Liu J, Sun T, Wilson MB, et al. (2001) Involvement of Jak2 tyrosine phosphorylation in Bcr-Abl transformation. Oncogene 20: 6188-6195. (Pubitemid 32964431)
28. Lam L, Pickeral O, Peng A, Rosenwald A, Hurt E, et al. (2001) Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anticancer drug flavopiridol. Genome Biology 2: research0041.0041-research0041. 0011.
29. Marquardt DW (1963) An Algorithm for Least-Squares Estimation of Nonlinear Parameters. SIAM Journal on Applied Mathematics 11: 431-441.
30. Khatri P, Draghici S (2005) Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21: 3587-3595. (Pubitemid 41264092)
31. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucl Acids Res 36: D480-484. (Pubitemid 351149770)
32. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
33. Solit DB, Garraway LA, Pratilas CA, Sawai A, Getz G, et al. (2006) BRAF mutation predicts sensitivity to MEK inhibition. Nature 439: 358-362. (Pubitemid 43128863)
34. Decker T, Kovarik P (2000) Serine phosphorylation of STATs. Oncogene 19: 2628-2637.
35. Li H, Gade P, Xiao W, Kalvakolanu DV (2007) The interferon signaling network and transcription factor C/EBP-beta. Cell Mol Immunol 4: 407-418.
36. O'Neill LA (2006) Targeting signal transduction as a strategy to treat inflammatory diseases. Nat Rev Drug Discov 5: 549-563.
37. Jeffrey KL, Camps M, Rommel C, Mackay CR (2007) Targeting dual-specificity phosphatases: manipulating MAP kinase signalling and immune responses. Nat Rev Drug Discov 6: 391-403. (Pubitemid 46705202)
38. Hebenstreit D, Horejs-Hoeck J, Duschl A (2005) JAK/STAT-dependent gene regulation by cytokines. Drug News Perspect 18: 243-249.
39. Murray PJ (2007) The JAK-STAT signaling pathway: input and output integration. J Immunol 178: 2623-2629.
40. Xu Y, Ikegami M, Wang Y, Matsuzaki Y, Whitsett JA (2007) Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells. BMC Genomics 8: 455-460. (Pubitemid 351228656)
41. Bantscheff M, Eberhard D, Abraham Y, Bastuck S, Boesche M, et al. (2007) Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol 25: 1035-1044. (Pubitemid 47517638)
42. Buettner R, Mesa T, Vultur A, Lee F, Jove R (2008) Inhibition of Src Family Kinases with Dasatinib Blocks Migration and Invasion of Human Melanoma Cells. Mol Cancer Res 6: 1766-1774.
43. Han MS, Chung KW, Cheon HG, Rhee SD, Yoon C-H, et al. (2009) Imatinib Mesylate Reduces Endoplasmic Reticulum Stress and Induces Remission of Diabetes in db/db Mice. Diabetes 58: 329-336.
44. Picard S, Titier K, Etienne G, Teilhet E, Ducint D, et al. (2007) Trough imatinib plasma levels are associated with both cytogenetic and molecular responses to standard-dose imatinib in chronic myeloid leukemia. Blood 109: 3496-3499. (Pubitemid 46572540)
45. Kerkela R, Grazette L, Yacobi R, Iliescu C, Patten R, et al. (2006) Cardiotoxicity of the cancer therapeutic agent imatinib mesylate. Nat Med 12: 908-916. (Pubitemid 44175142)
46. Taylor WR, Stark GR (2001) Regulation of the G2/M transition by p53. Oncogene 20: 1803-1815.
47. Berkson J (1953) A statistically precise and relatively simple method of estimating the bio-assay with quantal response, based upon the logistic function. Journal of the American Statistical Association 48: 565-599.
48. Neubauer M, Ross-Macdonald P (2007) The Application of Transcriptional Profiling in Model Connectivity and Lead Assessment in Drug Discovery. In: Macor J , ed. Annual Reports in Medicinal Chemistry: Academic Press. pp 417-430.
49. Luo FR, Yang Z, Camuso A, Smykla R, McGlinchey K, et al. (2006) Dasatinib (BMS-354825) Pharmacokinetics and Pharmacodynamic Biomarkers in Animal Models Predict Optimal Clinical Exposure. Clin Cancer Res 12: 7180-7186. (Pubitemid 44974520)
50. Kantarjian H, Giles F, Wunderle L, Bhalla K, O'Brien S, et al. (2006) Nilotinib in Imatinib-Resistant CML and Philadelphia Chromosome-Positive ALL. N Engl J Med 354: 2542-2551. (Pubitemid 43882350)
51. Bindslev N (2004) A homotropic two-state model and auto-antagonism. BMC Pharmacol 4: 11.
52. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
53. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
54. Simes RJ (1986) An improved Bonferroni procedure for multiple tests of significance. Biometrika 73: 751-754.
55. Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society B 57: 289-300.
56. Agresti A (1992) A Survey of Exact Inference for Contingency Tables. Statist Sci 7: 131-153.