A method to improve selection of molecular targets by circumventing the ADME pharmacokinetic system utilizing PharmArray DNA microarrays

Biochemical and Biophysical Research Communications

Volumn 303, Issue 3, 2003, Pages 828-841

  Dooley, Thomas P ^a   Curto, Ernest V ^a   Reddy, Shanker P ^a   Davis, Richard L ^a   Lambert, Glenna ^a   Wilborn, Teresa W ^a  

^a IntegriDerm Inc   (United States)

Author keywords

786 O; Absorption distribution metabolism excretion; Bioinformatics; Biomarker; Brain; Caco 2; DNA microarray; HepG2; Molecular targets; Neuroblastoma

Indexed keywords

BIOLOGICAL MARKER; DNA; RNA;

ABSORPTION; ADULT; ANALYTIC METHOD; ARTICLE; BRAIN TISSUE; CELL TYPE; CONTROLLED STUDY; DNA MICROARRAY; EXCRETION; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; INTESTINE CELL; KIDNEY CELL; LIVER CELL; MALE; METABOLISM; MOLECULAR BIOLOGY; NEUROBLASTOMA CELL; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SAMPLING;

EID: 0037432664     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-291X(03)00438-8     Document Type: Article

References (58)

1. Hopkins A.L., Groom C.R. The druggable genome. Nat. Rev. Drug Disc. 1:2002;727-730.
2. Ekins S., Waller C.L., Swaan P.W., Cruciani G., Wrighton S.A., Wikel J.H. Progress in predicting human ADME parameters in silico. J. Pharmacol. Toxicol. Meth. 44:2000;251-272.
3. Gerhold D., Lu M., Xu J., Austin C., Caskey C.T., Rushmore T. Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays. Physiol. Genomics. 5:2001;161-170.
4. Ross J.A., Davies S.M. Screening for neuroblastoma: progress and pitfalls. Cancer Epidemiol. Biomarkers Prev. 8:1999;189-194.
5. Sawada T. Possibilities for early diagnosis by urinary screening for catecholamine metabolites. Pochedly C. Neuroblastoma: Tumor Biology and Therapy. 1990;349-368 CRC Press, Boca Raton.
6. Berthold F., Hero B. Neuroblastoma: current drug therapy recommendations as part of total treatment approach. Drugs. 59:2000;1261-1277.
7. Ara T., Fuuzawa M., Kusafuka T., Komota Y., Oue T., Inoue M., Okada A. Immunohistochemical expression of MMP-2, MMP-9 and TIMP-2 in neuroblastoma: association with tumor progression and clinical outcome. J. Pediatr. Surg. 33:1998;1271-1278.
8. Sardi I., Tintori V., Marchi C., Veltroni M., Lippi A., Tucci F., Tamburini A., Bernini G., Faulkner L. Molecular profiling of high-risk neuroblastoma by cDNA array. Int. J. Mol. Med. 9:2002;541-545.
9. Popko B., Pearl D.K., Walker D.M., Comas T.C., Baerwald K.D., Burger P.C., Scheithauer B.W., Yates A.J. Molecular markers that identify human astrocytomas and oligodendrogliomas. J. Neuropathol. Exp. Neurol. 61:2002;329-338.
10. Barrett T., Cheadle C., Wood W.B., Teichberg D., Donovan D.M., Freed W.J., Becker K.G., Vawter M.P. Assembly and use of a broadly applicable neural cDNA microarray. Restor. Neurol. Neurosci. 18:2001;127-135.
11. Curto E.V., Lambert G.W., Davis R.L., Wilborn T.W., Dooley T.P. Biomarkers of human skin cells identified using DermArray DNA arrays and new bioinformatics methods. Biochem. Biophys. Res. Commun. 291:2002;1052-1064.
12. Borsani G., Bassi M.T., Sperando M.P., De Grandi A., Buoninconti A., Riboni M., Manzoni M., Inceri B., Pepe A., Andria G., Ballabio A., Sebastio G. SLC7A7, encoding a putative permease-related protein, is mutated in patients with lysinuric protein intolerance. Nat. Genet. 21:1999;297-301.
13. Fossar N., Chaouche M., Prochasson P., Rousset M., Brison O. Deregulated expression of the keratin18 gene in human colon carcinoma cells. Somat. Cell Mol. Genet. 25:1999;223-235.
14. Lawrence I.C., Fiocchi C., Chakravarti S. Ulcerative colitis and Crohn's disease: distinctive gene expression profiles and novel susceptibility candidate genes. Hum. Mol. Genet. 10:2001;445-456.
15. van Belzen N., Dinjens W.N., Diesveld M.P., Groen N.A., van der Made A.C., Nozawa Y., Vlietstra R., Trapman J., Bosman F.T. A novel gene which is up-regulated during colon epithelial cell differentiation and down-regulated in colorectal neoplasms. Lab Invest. 77:1997;85-92.
16. Witt H., Luck W., Hennies H.C., Classen M., Kage A., Lass U., Landt O., Becker M. Mutations in the gene encoding the serine protease inhibitor, Kazal type I associated with chronic pancreatitis. Nat. Genet. 25:2000;213-216.
17. Santamaria I., Velasco G., Cazorla M., Fueyo A., Campo E., Lopez-Otin C. Cathepsin L2, a novel human cysteine proteinase produced by breast and colorectal carcinomas. Cancer Res. 58:1998;1624-1630.
18. Xu X-R., Huang J., Xu Z-G., Qian B-Z., Zhu Z-D., Yan Q., Cai T., Zhang X., Xiao H-S., Qu J., Liu F., Huang Q-H., Cheng Z-H., Li N-G., Du J-J., Hu W., Shen K-T., Lu G., Zhong M., Xu S-H., Gu W-Y., Huang W., Zhao X-T., Hu G-X., Gu J.-R., Chen Z., Han Z.-G. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Proc. Natl. Acad. Sci. USA. 98:2001;15089-15094.
19. Lee J.-S., Thorgeirsson S.S. Functional and genomic implications of global gene expression profiles in cell lines from human hepatocellular cancer. Hepatology. 35:2002;1134-1143.
20. Loughnane N.K., Sabla G.E., Ley-Ebert C., Aronow B.J., Bezerra J.A. Independent and overlapping transcriptional activation during liver development and regeneration in mice. Hepatology. 35:2002;525-534.
21. Kawai H.F., Kaneko S., Honda M., Shirota Y., Kobayashi K. α-Fetoprotein producing hepatoma cell lines share common expression profiles of genes in various categories demonstrated by cDNA microarray analysis. Hepatology. 33:2001;676-691.
22. Castellani L.W., Goto A.M., Lusis A.J. Studies with apolipoprotein A-II transgenic mice indicate a role for HDLs in adiposity and insulin resistance. Diabetes. 50:2001;643-651.
23. Hsiao L.L., Stears R.L., Hong R.L., Gullans S.R. Prospective use of cDNA microarrays for evaluating renal function and disease. Curr. Opin. Nephrol. Hypertens. 9:2000;253-258.
24. Rae F.K., Stephenson S.A., Nicol D.L., Clements J.A. Novel association of diverse range of genes with renal cell carcinoma as identifed by differential display. Int. J. Cancer. 88:2000;726-732.
25. Engleman J.A., Zhang X.L., Lisanti M.P. Genes encoding human caveolin-1 and -2 are co-localized to the D7S522 locus (7q31.1), a known fragile site (FRA7G) that is frequently deleted in human cancers. FEBS Lett. 436:1998;403-410.
26. Yang G., Truong L.D., Wheeler T.M., Thompson T.C. Caveolin-1 expression in clinically confined human prostate cancer: a novel prognostic marker. Cancer Res. 59:1999;5719-5723.
27. Richmond E.J., Uzri A., Rogol A.D. The insulin-like growth factor system in kidney diseases. Nephron. 89:2001;5-9.
28. Coussens L.M., Fingleton B., Matrisian L.M. Matrix metalloproteinase inhibitors and cancer: trials and tribulations. Science. 295:2002;2387-2392.
29. Bittner M., Meltzer P., Chen Y., Jiang Y., Seftor E., Hendrix M., Radmacher M., Simon R., Yakhini Z., Ben-Dor A., Sampas N., Dougherty E., Wang E., Marincola F., Gooden C., Lueders J., Glatfelter A., Pollock P., Carpen J., Gillanders E., Leja D., Dietrich K., Beaudry C., Berens M., Alberts D., Sondak V., Hayward N., Trent J. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 406:2000;536-540.
30. Van den Berg J.S., Limburg M., Pals G., Arwert F., Westerveld A. Type III collagen deficiency in a family with intracranial aneurysms. Cerebrovasc. Dis. 11:2001;92-94.
31. Franzen R., Tanner S.L., Dashiell S.M., Rottkamp C.A., Hammer J.A., Quarles R.H. Microtubule-associated protein 1B: a neuronal binding partner for myelin-associated glycoprotein. J. Cell Biol. 155:2001;893-898.
32. Feng Y., Likos J.J., Zhu L., Woodward H., Munie G., McDonald J.J., Stevens A.M., Howard C.P., DeCrescenzo G.A., Welsch D., Shieh H.S., Stallings W.C. Solution structure and backbone dynamics of the catalytic domain of matrix metalloproteinase-2 complexed with a hydroxamic acid inhibitor. Biochim. Biophys. Acta. 1598:2002;10-23.
33. De Veas R.G., Schweigerer L., Medina M.A. Matrix metalloproteinase-2 and tissue inhibitor of metalloproteinase-2 expression in pediatric tumor cells. Effects of tumor cell proliferation modulators on gelatinolytic activity. J. Cancer Res. Clin. Oncol. 121:1995;275-278.
34. ′ -nucleotidase) in 165 glioblastomas by immunohistochemistry and electron microscopic histochemistry Anticancer Res. 19:1999;1747-1752.
35. ′ -nucleotidase activity indicates sites of synaptic plasticity and reactive synaptogenesis in the human brain J. Neuropathol. Exp. Neurol. 58:1999;451-458.
36. De la Fuente M., Hernanz A. Enzymes of mannose metabolism in murine and human lymphocytic leukemia. Br. J. Cancer. 58:1988;567-569.
37. Bolkenius F.N., Ganzhorn A.J. Peptidylglycine α-amidating mono-oxygenase: neuropeptide amidation as a target for drug design. Gen. Pharmacol. 31:1998;655-659.
38. Sullivan K.A., Castle V.P., Hanash S.M., Feldman E.L. Insulin-like growth factor-II in the pathogenesis of human neuroblastoma. Am. J. Pathol. 147:1995;1790-1798.
39. Mariani M., Corradi A., Baldessari D., Malgaretti N., Pozzoli O., Fesce R., Martinez S., Boncinelli E., Consalez G.G. Mab-21, the mouse homolog of a C. elegans cell-fate specification gene, participates in cerebellar, midbrain, and eye development. Mech. Dev. 79:1998;131-135.
40. Zhou J., Moroi K., Nishiyama M., Usui H., Seki N., Ishida J., Fukamizu A., Kimura S. Characterization of RGS5 in regulation of G-protein coupled receptor signaling. Life Sci. 68:2001;1457-1469.
41. Condon M.R., Hall A.K. Expression of thymosin β-4 and related genes in developing human brain. J. Mol. Neurosci. 3:1992;165-170.
42. Vartiainen N., Pyykonen I., Hokfelt T., Koistinaho J. Induction of thymosin β-4 mRNA folowing focal brain ischemia. Neuroreport. 7:1996;1613-1616.
43. Sapp E., Kegel K.B., Aronin N., Hashikawa T., Uchiyama Y., Tohyama K., Bhinde P.G., Vonsattel J.P., DiFiglia M. Early and progressive accumulation of reactive microglia in the Huntington disease brain. J. Neuropathol. Exp. Neurol. 60:2001;161-172.
44. Siu I-M., Lal A., Riggins G.J. A database for regional gene expression in the human brain. Gene Expr. Pattern. 1:2001;33-38.
45. Garbern J.Y., Yool D.A., Moore G.J., Wilds I.B., Faulk M.W., Klugmann M., Nave K.A., Sistermans E.A., van der Knapp M.S., Bird T.D., Shy M.E., Kamholz J.A., Griffiths I.R. Patients lacking the major CNS myelin protein, proteolipid protein1, develop length-dependent axonal degeneration in the absence of demyelination and inflammation. Brain. 125:2002;551-561.
46. Werner H., Dimou L., Klugmann M., Pfeiffer S., Nave K.A. Multiple splice isoforms of proteolipid M6B in neurons and oligodendrocytes. Mol. Cell Neurosci. 18:2001;593-605.
47. Dong J.M., Smith P., Hall C., Lim L. Promoter region of the transcriptional unit for human α-1-chimaerin, a neuron specific GTPase-activating protein for p21rac. Eur. J. Biochem. 227:1995;636-646.
48. Roth B.L., Chuang D.M. Multiple mechanisms of serotonergic signal transduction. Life Sci. 41:1987;1051-1064.
49. Gurevich I., Tamir H., Arango V., Dwork A.J., Mann J.J., Schmauss C. Altered editing of serotonin 2C receptor pre-mRNA in the prefrontal cortex of depressed suicide victims. Neuron. 34:2002;349-356.
50. Chang J.W., Schmacher E., Coulter P.M., Vinters H.V., Watson J.B. Dendritic translocation of RC3/neurogranin mRNA in normal aging, Alzheimer disease and fronto-temporal dementia. J. Neuropathol. Exp. Neurol. 56:1997;1105-1118.
51. Birnbaumer L., Qin N., Olcese R., Tareilus E., Platano D., Constantin J., Stefani E. Structures and functions of calcium channel β subunits. J. Bioenerg. Biomembr. 30:1998;357-375.
52. Kanai Y., Okada Y., Tanaka Y., Harada A., Terada S., Hirokawa N. KIF5C, a novel neuronal kinesin enriched in motor neurons. J. Neurosci. 20:2000;6374-6384.
53. Gonzalez B-C., Engelke M., Jimenez M., Wandosell F., Caceros A., Avila J. Participation of structural microtubule-associated proteins (MAPs) in the development of neuronal polarity. J. Neurosci. Res. 67:2002;713-719.
54. Matsubara S., Bourdeau A., derBrugge K.G., Wallace C., Letarte M. Analysis of endoglin expression in normal brain tissue and in cerebral arteriovenous malformations. Stroke. 31:2000;2653-2660.
55. Darves F., Szabo I., Karancsi T., Slegel P., Dorman G., Urge L., Krajcsi P. Drug discovery: dual uses of in silico and in vitro metabolism data in lead discovery. Genet. Eng. News. 22:2002;32-34.
56. Mueller G.P., Driscoll W.J., Eipper B.A. In vivo inhibition of peptidylglycine-α-hydroxylating monooxygenase by 4-phenyl-3-butenoic acid. J. Pharmacol. Exp. Ther. 290:1999;1331-1336.
57. Pritchard C.C., Hsu L., Delrow J., Nelson P.S. Project normal: defining normal variance in mouse gene expression. Proc. Natl. Acad. Sci. USA. 98:2001;13266-13271.
58. Tanaka S., Mito T., Takashima S. Progress of myelination in the human fetal spinal nerve roots, spinal cord and brainstem with myelin basic protein immunohistochemistry. Early Hum. Dev. 41:1995;49-59.