Quantitative analysis and modeling of glucocorticoid-controlled gene expression

Pharmacogenomics

Volumn 11, Issue 11, 2010, Pages 1545-1560

  Wei Chen Chen, Daphne ^a   Lynch, James T ^a   Demonacos, Constantinos ^a   Krstic Demonacos, Marija ^a   Schwartz, Jean Marc ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

dynamic model; gene expression; glucocorticoid receptor; systems biology

Indexed keywords

BH3 PROTEIN; BIM PROTEIN; CYCLOHEXIMIDE; DEXAMETHASONE; GLUCOCORTICOID INDUCED LEUCINE ZIPPER PROTEIN; GLUCOCORTICOID RECEPTOR; LEUCINE ZIPPER PROTEIN; MESSENGER RNA; PROTEIN BCL 2; PROTEIN BCL XL; UNCLASSIFIED DRUG;

ARTICLE; AUTOREGULATION; CANCER CELL CULTURE; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; START CODON; TRANSCRIPTION INITIATION; UPREGULATION; WESTERN BLOTTING;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; APOPTOSIS; BLOTTING, WESTERN; CELL CULTURE TECHNIQUES; CELL LINE, TUMOR; COMPUTER SIMULATION; DEXAMETHASONE; DRUG RESISTANCE, NEOPLASM; GENE EXPRESSION REGULATION, NEOPLASTIC; GLUCOCORTICOIDS; HUMANS; MODELS, BIOLOGICAL; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PROTEIN BINDING; PROTEIN TRANSPORT; RECEPTORS, GLUCOCORTICOID; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SYSTEMS BIOLOGY;

EID: 78649702770     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/pgs.10.125     Document Type: Article

References (54)

1. Musante CJ, Lewis AK, Hall K: Small- and large-scale biosimulation applied to drug discovery and development. Drug Discov. Today 7(20), S192-S196 (2002).
2. Rajasethupathy P, Vayttaden SJ, Bhalla US: Systems modeling: a pathway to drug discovery. Curr. Opin Chem. Biol. 9(4), 400-406 (2005).
3. Materi W, Wishart DS: Computational systems biology in drug discovery and development: methods and applications. Drug Discov. Today 12(7-8), 295-303 (2007).
4. Hoffmann A, Levchenko A, Scott ML, Baltimore D: The IK B-NF-K B signaling module: temporal control and selective gene activation. Science 298(5596), 1241-1245 (2002).
5. Faratian D, Goltsov A, Lebedeva G et al.: Systems biology reveals new strategies for personalizing cancer medicine and confrms the role of PTEN in resistance to Trastuzumab. Cancer Res. 69, 6713-6720 (2009).
6. Gilchrist M, Thorsson V, Li B et al.: Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441(7090), 173-178 (2006).
7. Yamamoto KR: Steroid receptor regulated transcription of specifc genes and gene networks. Ann. Rev. Gen. 19(1), 209-252 (1985).
8. Krstic MD, Rogatsky I, Yamamoto KR, Garabedian MJ: Mitogen-activated and cyclin-dependent protein kinases selectively and differentially modulate transcriptional enhancement by the glucocorticoid receptor. Mol. Cell Biol. 17(7), 3947-3954 (1997).
9. Wang JC, Derynck MK, Nonaka DF, Khodabakhsh DB, Haqq C, Yamamoto KR: Chromatin immunoprecipitation (ChIP) scanning identifes primary glucocorticoid receptor target genes. PNAS 101(44), 15603-15608 (2004).
10. Lonard DM, O'Malley BW: Nuclear receptor coregulators: Judges, juries, and executioners of cellular regulation. Mol. Cell 27(5), 691-700 (2007).
11. Davies L, Karthikeyan N, Lynch JT et al.: Cross talk of signaling pathways in the regulation of the glucocorticoid receptor function. Mol. Endocrinol. 22(6), 1331-1344 (2008).
12. So AY-L, Chaivorapol C, Bolton EC, Li H, Yamamoto KR: Determinants of cell- and gene-specifc transcriptional regulation by the glucocorticoid receptor. PLoS Genetics 3(6), e94 (2007).
13. Miller A, Komak S, Webb MS, Leiter E, Thompson EB: Gene expression profling of leukemic cells and primary thymocytes predicts a signature for apoptotic sensitivity to glucocorticoids. Cancer Cell Int. 7(1), 18 (2007).
14. Ploner C, Rainer J, Niederegger H et al.: The BCL2 rheostat in glucocorticoid-induced apoptosis of acute lymphoblastic leukemia. Leukemia 22(2), 370-377 (2007).
15. Reddy T, Pauli F, Sprouse R et al.: Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res. 12, 2163-2171 (2009).
16. Wang Z, Malone MH, He H, McColl KS, Distelhorst CW: Microarray ana lysis uncovers the induction of the proapoptotic BH3-only protein Bim in multiple models of glucocorticoid-induced apoptosis. J. Biol Chem. 278, 23861-23867 (2003).
17. Gascoyne DM, Kypta RM, ViVanco MDM: Glucocorticoids inhibit apoptosis during fbrosarcoma development by transcriptionally activating Bcl-xL*. J. Biol. Chem. 278(20), 18022-18029 (2003).
18. Rocha-Viegas L, Vicent GP, Barañao JL, Beato M, Pecci A: Steroid hormones induce bcl-X gene expression through direct activation of distal promoter P4. J. Biol. Chem. 279, 9831-9839 (2004).
19. Almawi WY, Melemedjian OK, Jaoude MMA: On the link between Bcl-2 family proteins and glucocorticoid-induced apoptosis. J. Leukocyte Biol. 76(1), 7-14 (2004).
20. Thompson E, Webb M, Miller A, Fofanov Y, Johnson B: Identifcation of genes leading to glucocorticoid-induced leukemic cell death. Lipids 39, 821-825 (2004).
21. Ayroldi E, Riccardi C: Glucocorticoid-induced leucine zipper (GILZ), a new important mediator of glucocorticoid action. FASEB J. 23(11), 3649-3658 (2009).
22. Jin JY, Almon RR, DuBois DC, Jusko WJ: Modeling of corticosteroid pharmacogenomics in rat liver using gene microarrays. J. Pharmacol. Exp. Ther. 307(1), 93-109 (2003).
23. Thompson EB: Stepping stones in the path of glucocorticoid-driven apoptosis of lymphoid cells. Acta Biochim. Biophys. Sin. (Shanghai) 40(7), 595-600 (2008).
24. Schmidt S, Rainer J, Ploner C, Presul E, Riml S, Kofer R: Glucocorticoid-induced apoptosis and glucocorticoid resistance: molecular mechanisms and clinical releVance. Cell Death Differ. 11(S1), S45-S55 (2004).
25. Schoneveld OJ, Gaemers IC, Lamers WH: Mechanisms of glucocorticoid signalling. Biochim. Biophys. Acta. 1680(2), 114-128 (2004).
26. Ramdas J, Liu W, Harmon JM: Glucocorticoid-induced cell death requires autoinduction of glucocorticoid receptor expression in human leukemic T cells. Cancer Res. 59(6), 1378-1385 (1999).
27. Schmidt S, Irving JAE, Minto L et al.: Glucocorticoid resistance in two key models of acute lymphoblastic leukemia occurs at the level of the glucocorticoid receptor. FASEB J. 20(14), 2600-2602 (2006).
28. Geng C-D, Vedeckis WV: c-Myb and members of the c-Ets family of transcription factors act as molecular switches to mediate opposite steroid regulation of the human glucocorticoid receptor 1A promoter. J. Biol. Chem. 280(52), 43264-43271 (2005).
29. Funahashi A, Morohashi M, Kitano H, Tanimura N: CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1(5), 159-162 (2003).
30. Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H: CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proceedings of the IEEE 96(8), 1254-1265 (2008).
31. Zi Z, Klipp E: SBML-PET: A systems biology markup language-based parameter estimation tool. Bio informatics 22(21), 2704-2705 (2006).
32. Medh RD, Webb MS, Miller AL et al.: Gene expression profle of human lymphoid CEM cells sensitive and resistant to glucocorticoid-evoked apoptosis. Genomics 81, 543-555 (2003).
33. Samorodnitsky E, Pugh BF: Genome-wide modeling of transcription preinitiation complex disassembly mechanisms using ChIP-chip data. PLoS Comput. Biol. 6(4), e1000733 (2010).
34. Yao Z, Hoffman EP, Ghimbovschi S, DuBois DC, Almon RR, Jusko WJ: Mathematical modeling of corticosteroid pharmacogenomics in rat muscle following acute and chronic methylprednisolone dosing. Mol. Pharm. 5(2), 328-339 (2008).
35. Wei G, Twomey D, Lamb J et al.: Gene expression-based chemical genomics identifes rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell Int. 10, 331-342 (2006).
36. Eisen LP, Elsasser MS, Harmon JM: Positive regulation of the glucocorticoid receptor in human T-cells sensitive to the cytolytic effects of glucocorticoids. J. Biol. Chem. 263(24), 12044-12048 (1988).
37. Hargrove JL, Schmidt FH: The role of mRNA and protein stability in gene expression. FASEB J. 3(12), 2360-2370 (1989).
38. Ing NH: Steroid hormones regulate gene expression posttranscriptionally by altering the stabilities of messenger RNAs. Biol. Reprod. 72(6), 1290-1296 (2005).
39. Staton JM, Thomson AM, Leedman PJ: Hormonal regulation of mRNA stability and RNA-protein interactions in the pituitary. J. Mol. Endocrinol. 25(1), 17-34 (2000).
40. Garcia-Gras EA, Chi P, Thompson EA: Glucocorticoid-mediated destabilization of cyclin D3 mRNA involves RNA-protein interactions in the 3́-untranslated region of the mRNA*. J. Biol. Chem. 275(29), 22001-22008 (2000).
41. Schaaf MJM, Cidlowski JA: Molecular mechanisms of glucocorticoid action and resistance. J. Steroid Biochem. Mol. Biol. 83(1-5), 37-48 (2002).
42. Zawydiwski R, Harmon JM, Thompson EB: Glucocorticoid-resistant human acute lymphoblastic leukemic cell line with functional receptor. Cancer Res. 43(8), 3865-3873 (1983).
43. Geley S, Hartmann BL, Hala M, Strasser-Wozak EMC, Kapelari K, Kofer R: Resistance to glucocorticoid-induced apoptosis in human T-cell acute lymphoblastic leukemia CEM-C1 cells is due to insuffcient glucocorticoid receptor expression. Cancer Res. 56(21), 5033-5038 (1996).
44. Thompson EB, Johnson BH: Regulation of a distinctive set of genes in glucocorticoid-evoked apoptosis in CEM human lymphoid cells. Recent Prog. Horm. Res. 58, 175-197 (2003).
45. Tissing WJE, Meijerink JPP, Brinkhof B et al.: Glucocorticoid-induced glucocorticoid-receptor expression and promoter usage is not linked to glucocorticoid resistance in childhood ALL. Blood 108(3), 1045-1049 (2006).
46. Lynch J, Rajendran R, Xenaki G, Berrou I, Demonacos C, Krstic-Demonacos M: The role of glucocorticoid receptor phosphorylation in Mcl-1 and NOXA gene expression. Mol. Cancer 9(1), 38 (2010).
47. Riml S, Schmidt S, Ausserlechner MJ, Geley S, Kofer R: Glucocorticoid receptor heterozygosity combined with lack of receptor auto-induction causes glucocorticoid resistance in Jurkat acute lymphoblastic leukemia cells. Cell Death Differ. 11(S1), S65-S72 (2004).
48. Cannarile L, Zollo O, D'Adamio F et al.: Cloning, chromosomal assignment and tissue distribution of human GILZ, a glucocorticoid hormone-induced gene. Cell Death Differ. 8, 201-203 (2001).
49. Ito K, Barnes PJ, Adcock IM: Glucocorticoid receptor recruitment of histone deacetylase 2 inhibits interleukin-1b -induced histone H4 acetylation on lysines 8 and 12. Mol. Cell Biol. 20(18), 6891-6903 (2000).
50. Zhang Y, Adachi M, Kawamura R, Imai K: Bmf is a possible mediator in histone deacetylase inhibitors FK228 and CBHA-induced apoptosis. Cell Death Differ. 13(1), 129-140 (2005).
51. Holleman A, Cheok MH, den Boer ML et al.: Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment. N. Engl. J. Med. 351(6), 533-542 (2004).
52. Laane E, Panaretakis T, Pokrovskaja K et al.: Dexamethasone-induced apoptosis in acute lymphoblastic leukemia involves differential regulation of Bcl-2 family members. Haematologica 92(11), 1460-1469 (2007).
53. Klipp E, Herwig R, Kowald A, Wierling C, Lehrach H: Systems Biology In Practice. In: Concepts, Implementation, And Application (1st Edition). WILEY-VCH Verlag GmbH & Co. KGaA, Berlin, Germany (2005).
54. Singh H, Singh JR, Dhillon VS, Bali D, Paul H: In vitro and in vivo genetoxicity evaluation of hormonal drugs. II. Dexamethasone. Mutat. Res. 308(1), 89-97 (1994). (Pubitemid 2104673)