Pharmacogenomics and its potential impact on drug and formulation development

Critical Reviews in Therapeutic Drug Carrier Systems

Volumn 22, Issue 5, 2005, Pages 465-492

  Regnström, Karin ^a   Burgess, Diane J ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Bioinformatics; Drug development; Drug target; Formulation; Pharmacogenomics; Toxicity disease classification

Indexed keywords

ANTICOAGULANT AGENT; ANTINEOPLASTIC AGENT; BETA ADRENERGIC RECEPTOR BLOCKING AGENT; BUCINDOLOL; LIPOXYGENASE INHIBITOR; NICOTINE; STATINE DERIVATIVE; SULFONYLUREA DERIVATIVE; TRASTUZUMAB; WARFARIN;

ADVERSE DRUG REACTION; BIOINFORMATICS; BREAST CANCER; CLINICAL TRIAL; DISEASE CLASSIFICATION; DNA SEQUENCE; DRUG DESIGN; DRUG EFFECT; DRUG EFFICACY; DRUG FORMULATION; DRUG METABOLISM; DRUG RESPONSE; EVALUATION; FOOD AND DRUG ADMINISTRATION; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC MARKER; GENOTYPE; HUMAN; HUMAN GENOME; NON INSULIN DEPENDENT DIABETES MELLITUS; NUCLEOTIDE SEQUENCE; PHARMACOGENOMICS; POSTMARKETING SURVEILLANCE; REVIEW; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TOXICITY TESTING;

EID: 29144437240     PISSN: 07434863     EISSN: None     Source Type: Journal    
DOI: 10.1615/CritRevTherDrugCarrierSyst.v22.i5.20     Document Type: Review

References (101)

1. Butcher SP. Target discovery and validation in the post-genomic era. Neurochem Res. 2003;28:367-71.
2. Emilien G, Ponchon M, Caldas C, Isacson O, Maloteaux JM. Impact of genomics on drug discovery and clinical medicine. Q J Med. 2000;93:391-423.
3. Couzin J. American Association for the Advancement of Science meeting. DNA tells story of heart drug failure. Science. 2005;307:1191.
4. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, et al. The sequence of the human genome. Science. 2001;291:1304-51.
5. Coleman RA, Clark KL. Target validation using human tissue: from gene expression to function. Targets. 2003;2:58-64.
6. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467-70.
7. Sander C. Genomic medicine and the future of health care. Science. 2000;287:1977-8.
8. Roses AD. Pharmacogenetics and drug development: the path to safer and more effective drugs. Nat Rev Genet. 2004;5:645-56.
9. Weinshilboum R, Wang L. Pharmacogenetics: inherited variation in amino acid sequence and altered protein quantity. Clin Pharmacol Ther. 2004;74:253-8.
10. Weinshilboum R, Wang L. Pharmacogenomics: bench to bedside. Nat Rev Drug Discov. 2004;3:739-48.
11. Buchanan A, Califano, A, Kahn J, McPherson E, Robertson J, Brody B. Pharmacogenetics: ethical issues and policy options. Kennedy Inst Ethics J. 2002;12:1-15.
12. Power A, Webb S, Seymour A, Milos P. The emergence of pharmacogenomics within the pharmaceutical industry. Drug Discovery World. 2002;3:47-52.
13. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High-density synthetic oligonucleotide arrays. Nat Genet. 1999;21(1 Suppl):20-4.
14. Hacia JG, Collins FS. Mutational analysis using oligonucleotide microarrays. J Med Genet. 1999;36:730-6.
15. Koch WH. Technology platforms for pharmacogenomic diagnostic assays. Nat Rev Drug Discov. 2004;3:749-61.
16. Reidhaar-Olson JF, Braxenthaler M, Hammer J. Process biology: integrated genomics and bioinformatics tools for improved target assessment. Targets. 2002;1:189-95.
17. Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug Discov. 2002;1:727-30.
18. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004;431:931-45.
19. Lockhardt DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotides arrays. Nat Biotechnol. 1996;14:1675-80.
20. Heid CA, Stevens J, Livak KJ, Williams PM. Real time quantitative PCR. Genome Res. 1996;6:986-94.
21. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 2001;411:494-8.
22. Mira MT, Alcais A, Nguyen VT, Moraes MO, Di Flumeri C, Vu HT, Mai CP, Nguyen TH, Nguyen NB, et al. Susceptibility to leprosy is associated with PARK2 and PACRG. Nature. 2004;427:636-40.
23. Allen, M, Heinzmann A, Noguchi E, Abecasis G, Broxholme J, Ponting CP, Bhattacharyya S, Tinsley J, Zhang Y, et al. Positional cloning of a novel gene influencing asthma from chromosome 2q14. Nature Genet. 2003;35:258-63.
24. Van de Vijer MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, et al. Gene expression signature as a predictor of survival in breast cancer. N Engl J Med. 2002;347:1999-2009.
25. Weigelt B, Glas AM, Wessels LF, Witteveen AT, Peterse JL, van't Veer LJ. Gene expression profiles of primary breast tumors maintained in distant metastases. Proc Natl Acad Sci USA. 2003;100:15901-5.
26. Wong YF, Selvanayagam ZE, Wei N, Porter J, Vittal R, Hu R, Lin Y, Liao J, Shih JW, et al. Expression genomics of cervical cancer: molecular classification and prediction of radiotherapy response by DNA microarray Clin Cancer Res. 2003;9:5486-92.
27. Ross ME, Zhou X, Song G, Shurtleff SA, Girtman K, Williams WK, Liu HC, Mahfouz R, Raimondi SC, et al. Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood. 2003;102:2951-9.
28. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, Mills GB, Simone C, Fishman DA, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet. 2002;359:572-7.
29. Bell GI, Polonsky KS. Diabetes mellitus and genetically programmed defects in β-cell function. Nature. 2001;414:788-91.
30. Weatherall DJ. Phenotype-genotype relationships in monogenic disease: lessons from thalassaemias. Nature Rev Genet. 2001;2:245-55.
31. Ford D, Easton DF, Stratton M, Narod S, Goldgar D, Devilee P, Bishop DT, Weber B, Lenoir G, et al. Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. Am J Human Genet. 1998;62:676-89.
32. Keating MT, Sanguinetti MC. Molecular and cellular mechanisms of cardiac arrhythmias. Cell. 2001;104:569-80.
33. Watkins H. Sudden death in hypertrophic cardiomyopathy. N Engl J Med. 2000;342:422-44.
34. Mohler PJ, Schott JJ, Gramolini AO, Dilly KW, Guatimosim S, duBell WH, Song LS, Haurogne K, Kyndt F, et al. Ankyrin-B mutation causes type 4 long-QT cardia arrhythmia and sudden cardiac death. Nature. 2003;421:634-9.
35. Bell J. Predicting disease using genomics. Nature. 2004;429:453-7.
36. Liggett SB. Genetically modified mouse models for pharmacogenomic research. Nat Rev Genet. 2004;5:657-63.
37. Freund CL, Wilfond BS. Emerging ethical issues in pharmacogenomics: from research to clinical practice. Am J Pharmacogenomics. 2002;2:273-81.
38. Bredel M, Jacoby E. Chemogenomics: An emerging strategy for rapid target and drug discovery. Nat Rev Genet. 2004;5:262-75.
39. Freiberg C, Brotz-Oesterhelt H. Functional genomics in antibacterial drug discovery. Drug Discov Today. 2005;10:927-35.
40. Olson H, Betton G, Robinson G, Thomas K, Monro A, Kolaja G, Lilly P, Sanders J, Sippes G, et al. Concordance of the toxicity of pharmaceuticals in humans and in animals. Regul Toxicol Pharmacol. 2000;32:56-67.
41. Bugelski PJ. Gene expression profiling for pharmaceutical toxicology screening. Curr Opin Drug Disc Develop. 2002;5:79-89.
42. Steiner S, Anderson NL. Expression profiling in toxicology-potentials and limitations. Toxicol Lett. 2000;112-113:467-71.
43. Regnstrom K, Ragnarsson EGE, Fryknäs M, Köping- Höggård M, Artursson P. Differential gene expression profiles of mouse lung tissue after administration of PEI- and chitosan-based gene delivery systems wit focus on stress, toxicity and endocytosis. Pharm Res. 2005. [Submitted.]
44. Chan VSW, Theilade MV. The use of toxigenomic data in risk assessment: a regulatory Perspective. Clin Toxicol (Phila). 2005;43:121-6.
45. Cavalli V, Vilbois F, Corti M, Marcote MJ, Tamura K, Karin M, Arkinstall S, Gruenberg J. The stress-induced MAP kinase p38 regulates endocytic trafficking via the GDI:Rab5 complex, Mol Cell. 2001;7:421-32.
46. McLeish KR, Klein JB, Coxon PY, Head KZ, Ward RA. Bacterial phagocytosis activates extracellular signal-regulated kinase and p38 mitogen-activated protein kinase cascades in human neutrophils. J Leukoc Biol. 1998;64:835-44.
47. Arce A, Aicher L, Wahl D, Anderson NL, Meheus L, Raymackers J, Cordier A, Steiner S. Changes in the liver protein pattern of female Wistar rats treated with the hypoglycemic agent SDZ PGU 693. Life Sci. 1998;63(25):2243-50.
48. Norton RM. Clinical pharmacogenomics: applications in pharmaceutical R&D. Drug Discov Today. 2001;6:180-6.
49. Waring JF, Jolly RA, Ciurlionis R, Lum PY, Praestgaard JT, Morfitt DC, Buratto B, Roberts C, Schadt E, et al. Clustering of hepatoxins based on mechanisms of toxicity using gene expression profiles. Toxicol Appl Pharmacol. 2001;175:28-42.
50. Burczynski ME, McMillian M, Ciervo J, Li L, Parker JB, Dunn RT, Hicken S, Farr S, Hicken S, et al. Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells. Toxicol Sci. 2000;58:399-415.
51. Kang YJ. Molecular and cellular mechanisms of cardio toxicity. Environ Health Perspect. 2001;109:27-34.
52. Regnstrom K, Ragnarsson EGE, Köping-Höggårdh M, Torstensson E, Nyblom H, Artursson P. PEI-a potent, but not harmless, mucosal immuno-stimulator of mixed T-helper cell response and FasL-mediated cell death in mice. Gene Ther. 2003;10:1575-83.
53. 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;101:11809-14.
54. Bussiere JL, McCormick GC and Green JD. Preclinical safety assessment considerations in vaccine development. Pharm Biotechnol. 1995;6:61-79.
55. Kabanov AV, Batrakova EV, Sriadibhatla S, Yang Z, Kelly DL, Alakov VY. Polymer genomics: shifting the gene and drug delivery paradigms. J Control Release. 2005;101:259-71.
56. Regnstrom K, Ragnarsson EGE, Rydell N, Sjöholm I, Artursson P. Tetanus antigen modulates the gene expression profile of aluminum phosphate adjuvant in spleen lymphocytes in vivo. Pharmacogenomics J. 2002;2:57-64.
57. Regnstrom K, Ragnarsson E, Artursson P. Gene expression after vaccination of mice with formulations of diphtheria toxoid or tetanus toxoid and different adjuvant: identification of shared and vaccine-specific genes in spleen lymphocytes. Vaccine. 2003;21:2307-17.
58. Preliminary guidelines for the manufacture and evaluation of DNA vaccines, Food and Drug Administration, Center for Biologies Evaluation and Research (1996), Docket No. 96N-0400.
59. Roses AD. Pharmacogenetics place in modern medical science and practice. Life Sci. 2002;70:1471-80.
60. Kabanov AV, Batrakova EV, Sriadibhatla S, Yang Z, Kelly DL, Alakov VY. Polymer genomics: shifting the gene and drug delivery paradigms. J Control Release. 2005;101:259-71.
61. Meyer UA. Pharmacogenetics and adverse drug reactions. Lancet. 2000;356:1667-71.
62. Nicholls H. Improving drug response with pharmacogenomics. Drug Discov Today. 2003;8:281-2.
63. Phillips KA, Veenstra DL, Oren E, Lee JK, Sadee W. Potential role of pharmacogenomics in reducing adverse drug reactions: a systematic review. JAMA. 2001;286:2270-79.
64. Rebbeck TR. More about: modification of clinical presentation of prostate tumors by a novel genetic variant in CYP3A4. J Natl Cancer Inst. 2000;92:76.
65. Walker AH, Jaffe JM, Gunasegaram S, Cummings SA, Huang CS, Chern HD, Olopade OI, Weber BL, Rebbeck TR. Characterization of an allelic variant in the nifepidine-specific element of CYP3A4: ethnic distribution and implication for prostate cancer risk. Human Mutat. 1998;12:289-93.
66. Bertilsson L, Aberg-Wistedt A, Gustafsson LL, Nordin C. Extremely rapid hydroxylation of debrisoquine: a case report with implication for treatment with nortryptoline and other tricyclic antidepressants. Ther Drug Monit. 1985;7:478-80.
67. De Morals SMF, Wilkinson GR, Blaisdell J, Nakamura K, Meyer UA, Goldstein JA. The major genetic defect responsible for the polymorphism of S-mephenytoin metabolism in humans. J Biol Chem. 1994;269:15419-22.
68. Chang M, Tybring G, Dahl ML, Gotharson E, Sagar M, Seensalu R, Bertilsson L. Interphenotype differences in disposition and effect on gastrin levels of omeprazole-suitability of omeprazole as a probe for CYP2C19. Br J Clin Pharmacol. 1995;39:511-8.
69. Harris BE, Carpenter JT, Diasio RB. Severe 5-fluorouracil toxicity secondary to dihydropyrimidme dehydrogenase deficiency. A potential more common pharmacogenetic syndrome. Cancer. 1991;68:499-501.
70. O'Kane DJ, Weinshilboum RL, Moyer TM. Pharmacogenomics and reducing the risk for adverse drug events. Pharmacogenomics. 2003;4:1-4.
71. Pirazzoli A, Recchia G. Pharmacogenetics and pharmacogenomics: are they still promising? Pharmacol Res. 2004;4:357-61.
72. Chung WH, Hung SI, Hong HS, Hsih MS, Yang LC, Ho HC, Wu JY, Chen YT. Medical genetics: a marker for Stevens-Johnson syndrome. Nature. 2004;428:486.
73. Slonim DK. Transcriptional profiling in cancer: the clinical pathway to pharmacogenomics. Pharmacogenomics. 2001;2:123-36.
74. Drazen JM, Yandava CN, Dube L, Szczerback N, Hippensteel R, Pillari A, Israel E, Schork N, Silverman ES, et al. Pharmacogenetic association between ALOX5 promoter genotype and the response to anti-asthma treatment. Nature Genet. 1999;22:168-70.
75. Johnstone EC, Yudkin PL, Hey K, Roberts SJ, Welch SJ, Murphy MF, Griffiths SE, Walton RT. Genetic variation in dopaminergic pathways and short-term effectiveness of the nicotine patch. Pharmacogenetics. 2004;14:83-90.
76. Kuivenhoven JA, Jukema JW, Zwinderman AH, de Knijff P, McPherson R, Bruschke AV, Lie KI, Kastelein JJ. The role of a common variant of the cholesterylester transfer protein gene in the progression of coronary atherosclerosis. N Engl J Med. 1998;338:86-93.
77. Miller L. Pitfalls in the drug approval process: dose effect, experimental design and risk-benefit issues. Drug Inf J. 1992;26:251-60.
78. Roden DM, George AL Jr. The genetic basis of variability in drug responses. Nat Rev Drug Disc. 2001;1:37-44.
79. Hara H, Adachi T. Contribution of hepatocyte nuclear factor 4 to down-regulation of CYP2D6 gene expression by nitric oxide. Mol Pharmacol. 2002;61:194-200.
80. Wang L, Sullivan W, Toft D, Weinshilboum R. Thiopurine S-methyltransferase pharmacogenetics: chaperone protein association and allozyme degradation. Pharmacogenetics. 2003;13:555-64.
81. Tai HL, Krynetski EY, Schuetz EG, Yanishevski Y, Evans WE. Enhanced proteolysis of thiopurine S-methyltransferase (TPMT) encoded by mutant alleles in humans (TPMT*3A, TPMT*2): mechanisms for the genetic polymorphism of TPMT activity. Proc Natl Acad Sci U S A. 1997;94:6444-9.
82. Acuna G, Foernzler D, Leong D, Rabbia M, Smit R, Dorflinger E, Gasser R, Hoh J, Ott J, et al. Pharmacogenetic analysis of adverse drug effect reveals genetic variant for susceptibility to liver toxicity. Pharmacogenomics J. 2002;2(5):327-34.
83. Alvarado I, Wong ML, Licinio J. Advances in the pharmacogenomics of adverse drug reactions. Pharmacogenomics J. 2002;2(5):273.
84. Jain KK. Applied neurogenomics. Pharmacogenomics. 2001;2:143-52.
85. Peroutka SJ. The medical utility of genomics data in neuropsychiatry: mutational genetics versus association genetics. Curr Opin Biotechnol. 1997;8:688-91.
86. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999;286:531-7.
87. Welsh JB, Zarrinkar PP, Sapinoso LM, Kern SG, Behling CA, Monk BJ, Lockhart DJ, Burger RA, Hampton GM. Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci U S A. 2001;98:1176-81.
88. Chin KV, Kong ANT. Application of DNA microarrays in pharmacogenomics and toxicogenomics. Pharm Res. 2002;19:1773-78.
89. Van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Bernards R, Friend SH. Expression profiling predicts outcome in breast cancer. Breast Cancer Res. 2003;5:57-8.
90. Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, et al. A gene expression data base for the molecular pharmacology of cancer. Nat Genet. 2000;24:236-44.
91. Lazarou J, Pomeranz B, Corey P. Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies. JAMA. 1998;279:1200-5.
92. Higashi MK, Veenstra DL, Kondo LM, Wittkowsky AK, Srinouanprachanh SL, Farin FM, Rettie AE. Association between CYP2C9 genetic variants and anticoagulation-related outcomes during warfarin therapy. JAMA. 2002;287:1690-8.
93. Pearson ER, Starkey BJ, Powell RJ, Gribble FM, Clark PM, Hattersley AT. Genetic cause of hyperglycaemia in response to treatment in diabetes. Lancet. 2003;362:1275-81.
94. Former M, Risio M, Van Poznak C, Siedman A. HER2 testing and correlation with efficacy of trastuzumab therapy. Oncology. 2002;16:1340-58.
95. Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, Vanaclocha V, Baylin SB, Herman JG. Inactivation of the DNA repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med. 2000;343:1350-4.
96. Kemp DM, Habener JF. Functional genomics in the clinic: a path toward personalized medicine. Preclinica.2004;2:388-92.
97. Lesko LJ, Woodcock J. Translation of pharmacogenomics and pharmacogenetics: a regulatory perspective. Nat Rev Drug Discov. 2004;3:763-9.
98. Young D. Scientists focus on pharmacogenomics at FDA Science Forum. Am J Health Syst Pharm. 2005;62:1226.
99. Need AC, Motulsky AG, Goldstein DB. Principles and standards in pharmacogenetic research. Nat Genetics. 2005;37:671-81.
100. FDA, Draft Guidance for Industry, Pharmacogenomic Data Submissions November. 2003 http://www.fda.gov/cder/guidance/5900dft.pdf.
101. FDA, Guidance for Industry, Pharmacogenomics Data Submissions, http://www.fda.gov/cber/gdlns/pharmdtasub.htm March 31st. 2005.