Application of a customized pathway-focused microarray for gene expression profiling of cellular homeostasis upon exposure to nicotine in PC12 cells

Molecular Brain Research

Volumn 121, Issue 1-2, 2004, Pages 102-113

  Konu, Özlen ^a,b   Xu, Xiaoyuan ^a   Ma, Jennie Z ^a   Kane, Justin ^a   Wang, Ju ^a   Shi, Shirley J ^a   Li, Ming D ^a  

^a UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

^b BILKENT UNIVERSITY   (Turkey)

Author keywords

AKT PKB signaling; Cellular homeostasis; Focused microarray; Gene networks; Nicotine; PC 12 cells

Indexed keywords

CALCIUM ION; NEUROTRANSMITTER; NICOTINE; NICOTINIC RECEPTOR; PHOSPHATIDYLINOSITOL; PROTEIN KINASE B;

ANIMAL CELL; ARTICLE; BIODIVERSITY; CALCIUM CELL LEVEL; CELL STRAIN; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION COEFFICIENT; DNA MICROARRAY; GENE EXPRESSION; GENE IDENTIFICATION; HOMEOSTASIS; MEASUREMENT; NEUROTRANSMITTER RELEASE; NONHUMAN; OXIDATIVE STRESS; PATHOGENESIS; PHEOCHROMOCYTOMA; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN SYNTHESIS; QUALITY CONTROL; RAT; REGRESSION ANALYSIS; SIGNAL TRANSDUCTION; STARVATION;

EID: 1242306279     PISSN: 0169328X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molbrainres.2003.11.012     Document Type: Article

References (43)

1. Angelastro J.M., Torocsik B., Greene L.A. Nerve growth factor selectively regulates expression of transcripts encoding ribosomal proteins. BMC Neurosci. 3:2002;3.
2. Black M.A., Doerge R.W. Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. Bioinformatics. 18:2002;1609-1616.
3. Bourbon N.A., Sandirasegarane L., Kester M. Ceramide-induced inhibition of Akt is mediated through protein kinase Czeta: implications for growth arrest. J. Biol. Chem. 277:2002;3286-3292.
4. Bustin S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25:2000;169-193.
5. Chung C.H., Bernard P.S., Perou C.M. Molecular portraits and the family tree of cancer. Nat. Genet. 32:2002;533-540. (Suppl).
6. Churchill G.A. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32(Suppl. 2):2002;490-495.
7. Colangelo V., Schurr J., Ball M.J., Pelaez R.P., Bazan N.G., Lukiw W.J. Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: transcription and neurotrophic factor down-regulation and up-regulation of apoptotic and pro-inflammatory signaling. J. Neurosci. Res. 70:2002;462-473.
8. Doornbos R.P., Theelen M., van der Hoeven P.C., van Blitterswijk W.J., Verkleij A.J., van Bergen en Henegouwen P.M. Protein kinase Czeta is a negative regulator of protein kinase B activity. J. Biol. Chem. 274:1999;8589-8596.
9. 2+ and cAMP in nicotine-elicited elevation of tyrosine hydroxylase mRNA. Am. J. Physiol. 276:1999;C54-C65.
10. Halgren R.G., Fielden M.R., Fong C.J., Zacharewski T.R. Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones. Nucleic Acids Res. 29:2001;582-588.
11. Heeschen C., Weis M., Aicher A., Dimmeler S., Cooke J.P. A novel angiogenic pathway mediated by non-neuronal nicotinic acetylcholine receptors. J. Clin. Invest. 110:2002;527-536.
12. Hoege C., Pfander B., Moldovan G.L., Pyrowolakis G., Jentsch S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature. 419:2002;135-141.
13. Holloway A.J., van Laar R.K., Tothill R.W., Bowtell D.D. Options available - from start to finish - for obtaining data from DNA microarrays II. Nat. Genet. 32:2002;481-489. (Suppl.).
14. Jorgensen M.S., Wagner P.G., Arden W.A., Jackson B.A. Modulation of stimulus-secretion coupling in porcine adrenal chromaffin cells by receptor-mediated increases in protein kinase C activity. J. Neurosci. Res. 59:2000;760-766.
15. Kerr M.K., Churchill G.A. Statistical design and the analysis of gene expression microarray data. Genet. Res. 77:2001;123-128.
16. Kihara T., Shimohama S., Sawada H., Honda K., Nakamizo T., Shibasaki H., Kume T., Akaike A. Alpha 7 nicotinic receptor transduces signals to phosphatidylinositol 3-kinase to block A beta-amyloid-induced neurotoxicity. J. Biol. Chem. 276:2001;13541-13546.
17. Konu O., Kane J.K., Barrett T., Vawter M.P., Chang R., Ma J.Z., Donovan D.M., Sharp B., Becker K.G., Li M.D. Region-specific transcriptional response to chronic nicotine in rat brain. Brain Res. 909:2001;194-203.
18. Lee M.L., Kuo F.C., Whitmore G.A., Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. U. S. A. 97:2000;9834-9839.
19. Li M.D., MacDonald G.J., Ford J.J. Breed differences in expression of inhibin/activin subunits in porcine anterior pituitary glands. Endocrinology. 138:1997;712-718.
20. Li M.D., Konu O., Kane J.K., Becker K.G. Microarray technology and its application on nicotine research. Mol. Neurobiol. 25:2002;265-285.
21. Li M.D., Kane J.K., Konu O. Nicotine, body weight and potential implications in the treatment of obesity. Curr. Top. Med. Chem. 3:2003;899-919.
22. 2+ signaling in rat chromaffin cells. J. Neurosci. Res. 66:2001;559-564.
23. Meyuhas O. Synthesis of the translational apparatus is regulated at the translational level. Eur. J. Biochem. 267:2000;6321-6330.
24. Miller S.J., Lou D.Y., Seldin D.C., Lane W.S., Neel B.G. Direct identification of PTEN phosphorylation sites. FEBS Lett. 528:2002;145-153.
25. Neri L.M., Borgatti P., Capitani S., Martelli A.M. The nuclear phosphoinositide 3-kinase/AKT pathway: a new second messenger system. Biochim. Biophys. Acta. 1584:2002;73-80.
26. Persad S., Attwell S., Gray V., Delcommenne M., Troussard A., Sanghera J., Dedhar S. Inhibition of integrin-linked kinase (ILK) suppresses activation of protein kinase B/Akt and induces cell cycle arrest and apoptosis of PTEN-mutant prostate cancer cells. Proc. Natl. Acad. Sci. U. S. A. 97:2000;3207-3212.
27. Persad S., Attwell S., Gray V., Mawji N., Deng J.T., Leung D., Yan J., Sanghera J., Walsh M.P., Dedhar S. Regulation of protein kinase B/Akt-serine 473 phosphorylation by integrin-linked kinase: critical roles for kinase activity and amino acids arginine 211 and serine 343. J. Biol. Chem. 276:2001;27462-27469.
28. Romieu-Mourez R., Landesman-Bollag E., Seldin D.C., Sonenshein G.E. Protein kinase CK2 promotes aberrant activation of nuclear factor-kappaB, transformed phenotype, and survival of breast cancer cells. Cancer Res. 62:2002;6770-6778.
29. Saito M., Smiley J., Toth R., Vadas C. Microarray analysis of gene expression in rat hippocampus after chronic ethanol treatment. Neurochem. Res. 27:2002;1221-1229.
30. Sawiris G.P., Sherman-Baust C.A., Becker K.G., Cheadle C., Teichberg D., Morin P.J. Development of a highly specialized cDNA array for the study and diagnosis of epithelial ovarian cancer. Cancer Res. 62:2002;2923-2928.
31. Stolovich M., Tang H., Hornstein E., Levy G., Cohen R., Bae S.S., Birnbaum M.J., Meyuhas O. Transduction of growth or mitogenic signals into translational activation of TOP mRNAs is fully reliant on the phosphatidylinositol 3-kinase-mediated pathway but requires neither S6K1 nor rpS6 phosphorylation. Mol. Cell. Biol. 22:2002;8101-8113.
32. Tanaka T.S., Jaradat S.A., Lim M.K., Kargul G.J., Wang X., Grahovac M.J., Pantano S., Sano Y., Piao Y., Nagaraja R., Doi H., Wood W.H. 3rd, Becker K.G., Ko M.S. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Proc. Natl. Acad. Sci. U. S. A. 97:2000;9127-9132.
33. Tang K., Wu H., Mahata S.K., Mahata M., Gill B.M., Parmer R.J., O'Connor D.T. Stimulus coupling to transcription versus secretion in pheochromocytoma cells. Convergent and divergent signal transduction pathways and the crucial roles for route of cytosolic calcium entry and protein kinase C. J. Clin. Invest. 100:1997;1180-1192.
34. Tang H., Hornstein E., Stolovich M., Levy G., Livingstone M., Templeton D., Avruch J., Meyuhas O. Amino acid-induced translation of TOP mRNAs is fully dependent on phosphatidylinositol 3-kinase-mediated signaling, is partially inhibited by rapamycin, and is independent of S6K1 and rpS6 phosphorylation. Mol. Cell. Biol. 21:2001;8671-8683.
35. Tremblay F., Marette A. Amino acid and insulin signaling via the mTOR/ p70 S6 kinase pathway. A negative feedback mechanism leading to insulin resistance in skeletal muscle cells. J. Biol. Chem. 276:2001;38052-38060.
36. Tseng G.C., Oh M.K., Rohlin L., Liao J.C., Wong W.H. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29:2001;2549-2557.
37. Van Gelder R.N., von Zastrow M.E., Yool A., Dement W.C., Barchas J.D., Eberwine J.H. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. U. S. A. 87:1990;1663-1667.
38. Walder K., Segal D., Chehab S., Augert G., Cameron-Smith D., Hargreaves M., Collier G.R. A custom-built insulin resistance gene chip. Ann N.Y. Acad. Sci. 967:2002;274-282.
39. Wen H.C., Huang W.C., Ali A., Woodgett J.R., Lin W.W. Negative regulation of phosphatidylinositol 3-kinase and Akt signalling pathway by PKC. Cell. Signal. 15:2003;37-45.
40. West K.A., Brognard J., Clark A.S., Linnoila I.R., Yang X., Swain S.M., Harris C., Belinsky S., Dennis P.A. Rapid Akt activation by nicotine and a tobacco carcinogen modulates the phenotype of normal human airway epithelial cells. J. Clin. Invest. 111:2003;81-90.
41. Winer J., Jung C.K., Shackel I., Williams P.M. Development and validation of real-time quantitative reverse transcriptase-polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro. Anal. Biochem. 270:1999;41-49.
42. Wurmbach E., Yuen T., Ebersole B.J., Sealfon S.C. Gonadotropin-releasing hormone receptor-coupled gene network organization. J. Biol. Chem. 276:2001;47195-47201.
43. Zick Y. Insulin resistance: a phosphorylation-based uncoupling of insulin signaling. Trends Cell Biol. 11:2001;437-441.