Global gene expression as a function of germline genetic variation

Human Molecular Genetics

Volumn 14, Issue 12, 2005, Pages 1621-1629

  French, Deborah ^a   Wilkinson, Mark R ^a   Yang, Wenjian ^a   de Chaisemartin, Luc ^a   Cook, Edwin H ^c   Das, Soma ^c   Ratain, Mark J ^c   Evans, William E ^a,b   Downing, James R ^a   Pui, Ching Hon ^a   Relling, Mary V ^a,b  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^b UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; GENE PRODUCT; GLUCURONOSYLTRANSFERASE 1A1; GLUTATHIONE TRANSFERASE M1; HISTONE DEACETYLASE 1; NIBRIN; PRKR PROTEIN; SLC 2A1 PROTEIN; THYMINE; TRANSCRIPTION FACTOR RELA; UNCLASSIFIED DRUG; XENOBIOTIC AGENT;

ACUTE LYMPHOBLASTIC LEUKEMIA; ANALYSIS OF VARIANCE; ARTICLE; BLAST CELL; CHILD; CLINICAL ARTICLE; CONJUGATION; CONTROLLED STUDY; FISHER EXACT TEST; GENE CLUSTER; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; GERM LINE; HUMAN; LIPOPHILICITY; PHENOTYPIC VARIATION; PRIORITY JOURNAL; PROMOTER REGION;

CHILD; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOTYPE; GERM-LINE MUTATION; GLUCURONOSYLTRANSFERASE; GLUTATHIONE TRANSFERASE; HUMANS; LEUKEMIA, LYMPHOCYTIC, ACUTE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); SEQUENCE DELETION; VARIATION (GENETICS);

EID: 21244475088     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddi170     Document Type: Article

References (63)

1. Davies, S.M., Bhatia, S., Ross, J.A., Kiffmeyer, W.R., Gaynon, P.S., Radloff, G.A., Robison, L.L. and Perentesis, J.P. (2002) Glutathione S-transferase genotypes, genetic susceptibility, and outcome of therapy in childhood acute lymphoblastic leukemia. Blood, 100, 67-71.
2. Krajinovic, M., Lemieux-Blanchard, E., Chiasson, S., Primeau, M., Costea, I. and Moghrabi, A. (2004) Role of polymorphisms in MTHFR and MTHFD1 genes in the outcome of childhood acute lymphoblastic leukemia. Pharmacogenomics. J., 4, 66-72.
3. Relling, M.V. and Dervieux, T. (2001) Pharmacogenetics and cancer therapy. Nat. Rev. Cancer, 1, 99-108.
4. Desai, A.A., Innocenti, F. and Ratain, M.J. (2003) Pharmacogenomics: road to anticancer therapeutics nirvana? Oncogene, 22, 6621-6628.
5. de Jong, F.A., Marsh, S., Mathijssen, R.H., King, C., Verweij, J., Sparreboom, A. and McLeod, H.L. (2004) ABCG2 pharmacogenetics: ethnic differences in allele frequency and assessment of influence on irinotecan disposition. Clin. Cancer Res., 10, 5889-5894.
6. Bertucci, F., Nasser, V., Granjeaud, S., Eisinger, F., Adelaide, J., Tagett, R., Loriod, B., Giaconia, A., Benziane, A. Devilard, E. et al. (2002) Gene expression profiles of poor-prognosis primary breast cancer correlate with survival. Hum. Mol. Genet., 11, 863-872.
7. Yeoh, E.J., Ross, M.E., Shurtleff, S.A., Williams, W.K., Patel, D., Mahfouz, R., Behm, F.G., Raimondi, S.C., Relling, M.V., Patel, A. et al. (2002) Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell, 1, 133-143.
8. Edick, M.J., Cheng, C., Yang, W, Cheok, M., Wilkinson, M., Pei, D., Evans, W.E., Kun, L.E., Pui, C.H. and Relling, M.V. (2005) Lymphoid gene expression as a predictor of risk of secondary brain tumors. Genes Chromosomes Cancer, 42, 107-116.
9. Shmueli, O., Horn-Saban, S., Chalifa-Caspi, V., Shmoish, M., Ophir, R., Benjamin-Rodrig, H., Safran, M., Domany, E. and Lancet, D. (2003) GeneNote: whole genome expression profiles in normal human tissues. C. R. Biol., 326, 1067-1072.
10. Cheung, V.G., Conlin, L.K., Weber, T.M., Arcaro, M., Jen, K.Y., Morley, M. and Spielman, R.S. (2003) Natural variation in human gene expression assessed in lymphoblastoid cells. Nat. Genet., 33, 422-425.
11. Cheung, V.G., Jen, K.Y., Weber, T., Morley, M., Devlin, J.L., Ewens, K.G. and Spielman, R.S. (2003) Genetics of quantitative variation in human gene expression. Cold Spring Harb. Symp. Quant. Biol., 68, 403-407.
12. Enard, W., Khaitovich, P., Klose, J., Zollner, S., Heissig, F., Giavalisco, P., Nieselt-Struwe, K., Muchmore, E., Varki, A., Ravid, R. et al. (2002) Intra- and interspecific variation in primate gene expression patterns. Science, 296, 340-343.
13. Kishi, S., Yang, W., Boureau, B., Morand, S., Das, S., Chen, P., Cook, E.H., Rosner, G.L., Schuetz, E., Pui, C.H., and Relling, M.V. (2004) Effects of prednisone and genetic polymorphisms on etoposide disposition in children with acute lymphoblastic leukemia. Blood, 103, 67-72.
14. Cario, G., Stanulla, M., Fine, B.M., Teuffel, O., Neuhoff, V., Schrauder, A., Flohr, T., Schafer, B.W., Bartram, C.R., Welte, K. et al. (2005) Distinct gene expression profiles determine molecular treatment response in childhood acute lymphoblastic leukemia. Blood, 105, 821-826.
15. Fine, B.M., Stanulla, M., Schrappe, M., Ho, M., Viehmann, S., Harbott, J. and Boxer, L.M. (2004) Gene expression patterns associated with recurrent chromosomal translocations in acute lymphoblastic leukemia. Blood, 103, 1043-1049.
16. Holleman, A., Cheok, M.H., den Boer, M.L., Yang, W., Veerman, A.J., Kazemier, K.M., Pei, D., Cheng, C., Pui, C.H., Relling, M.V. et al. (2004) Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment. N. Engl. J. Med., 351, 533-542.
17. Golub, T.R., Slonim, D.K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J.P., Coller, H., Loh, M.L., Downing, J.R., Caligiuri, M.A. et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
18. Ferrando, A.A., Neuberg, D.S., Staunton, J., Loh, M.L., Huard, C., Raimondi, S.C., Behm, F.G., Pui, C.H., Downing, J.R., Gilliland, D.G. et al. (2002) Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell, 1, 75-87.
19. Szakacs, G., Annereau, J.P., Lababidi, S., Shankavaram, U., Arciello, A., Bussey, K.J., Reinhold, W., Guo, Y., Kruh, G.D., Reimers, M. et al. (2004) Predicting drug sensitivity and resistance: profiling ABC transporter genes in cancer cells. Cancer Cell, 6, 129-137.
20. van de Vijver, M.J., He, Y.D., van't Veer, L.J., Dai, H., Hart, A.A., Voskuil, D.W., Schreiber, G.J., Peterse, J.L., Roberts, C., Marton, M.J. et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med., 347, 1999-2009.
21. Davis, R.E. and Staudt, L.M. (2002) Molecular diagnosis of lymphoid malignancies by gene expression profiling. Curr. Opin. Hematol., 9, 333-338.
22. Kakiuchi, S., Daigo, Y., Ishikawa, N., Furukawa, C., Tsunoda, T., Yano, S., Nakagawa, K., Tsuruo, T., Kohno, N., Fukuoka, M. et al. (2004) Prediction of sensitivity of advanced non-small cell lung cancers to gefitinib (Iressa, ZD1839). Hum. Mol. Genet., 13, 3029-3043.
23. Huang, J.Z., Sanger, W.G., Greiner, T.C., Staudt, L.M., Weisenburger, D.D., Pickering, D.L., Lynch, J.C., Armitage, J.O., Warnke, R.A., Alizadeh, A.A. et al. (2002) The t(14;18) defines a unique subset of diffuse large B-cell lymphoma with a germinal center B-cell gene expression profile. Blood, 99, 2285-2290.
24. Armstrong, S.A., Golub, T.R. and Korsmeyer, S.J. (2003) MLL-rearranged leukemias: insights from gene expression profiling. Semin. Hematol., 40, 268-273.
25. Bosma, P.J., Chowdhury, J.R., Bakker, C., Gantla, S., de Boer, A., Oostra, B.A., Lindhout, D., Tytgat, G.N., Jansen, P.L. and Oude Elferink, R.P. (1995) The genetic basis of the reduced expression of bilirubin UDP-glucuronosyltransferase 1 in Gilbert's syndrome. N. Engl. J. Med., 333, 1171-1175.
26. Duguay, Y., McGrath, M., Lepine, J., Gagne, J.F., Hankinson, S.E., Colditz, G.A., Hunter, D.J., Plante, M., Tetu, B., Belanger, A. et al. (2004) The functional UGT1A1 promoter polymorphism decreases endometrial cancer risk. Cancer Res., 64, 1202-1207.
27. Miners, J.O., McKinnon, R.A. and MacKenzie, P.I. (2002) Genetic polymorphisms of UDP-glucuronosyltransferases and their functional significance. Toxicology, 181-182, 453-456.
28. Iyer, L., King, C.D., Whitington, P.F., Green, M.D., Roy, S.K., Tephly, T.R., Coffman, B.L. and Ratain, M.J. (1998) Genetic predisposition to the metabolism of irinotecan (CPT-11). Role of uridine diphosphate glucuronosyltransferase isoform 1A1 in the glucuronidation of its active metabolite (SN-38) in human liver microsomes. J. Clin. Invest., 101, 847-854.
29. Cheng, Z., Rios, G.R., King, C.D., Coffman, B.L., Green, M.D., Mojarrabi, B., MacKenzie, P.I. and Tephly, T.R. (1998) Glucuronidation of catechol estrogens by expressed human UDP-glucuronosyltransferases (UGTs) 1A1, 1A3, and 2B7. Toxicol. Sci., 45, 52-57.
30. McDonnell, D.P. and Norris, J.D. (2002) Connections and regulation of the human estrogen receptor. Science, 296, 1642-1644.
31. Guillemette, C., Deivo, VI., Hankinson, S.E., Haiman, C.A., Spiegelman, D., Housman, D.E. and Hunter, D.J. (2001) Association of genetic polymorphisms in UGT1A1 with breast cancer and plasma hormone levels. Cancer Epidemiol. Biomarkers Prev., 10, 711-714.
32. Sparks, R., Ulrich, C.M., Bigler, J., Tworoger, S.S., Yasui, Y., Rajan, K.B., Porter, P., Stanczyk, F.Z., Ballard-Barbash, R., Yuan, X. et al. (2004) UDP-glucuronosyltransferase and sulfotransferase polymorphisms, sex hormone concentrations, and tumor receptor status in breast cancer patients. Breast Cancer Res., 6, R488-R498.
33. Valentine, J.E., Kalkhoven, E., White, R., Hoare, S. and Parker, M.G. (2000) Mutations in the estrogen receptor ligand binding domain discriminate between hormone-dependent transactivation and transrepression. J. Biol. Chem., 275, 25322-25329.
34. Kawai, H., Li, H., Avraham, S., Jiang, S. and Avraham, H.K. (2003) Overexpression of histone deacetylase HDAC1 modulates breast cancer progression by negative regulation of estrogen receptor alpha. Int. J. Cancer, 107, 353-358.
35. Wang, D.Y., Fulthorpe, R., Liss, S.N. and Edwards, E.A. (2004) Identification of estrogen-responsive genes by complementary deoxyribonucleic acid microarray and characterization of a novel early estrogen-induced gene: EEIG1. Mol. Endocrinol., 18, 402-411.
36. Shi, J. and Simpkins, J.W. (1997) 17 beta-Estradiol modulation of glucose transporter 1 expression in blood-brain barrier. Am. J. Physiol., 272, E1016-E1022.
37. Findlay, K.A., Kaptein, E., Visser, T.J. and Burchell, B. (2000) Characterization of the uridine diphosphate-glucuronosyltransferase-catalyzing thyroid hormone glucuronidation in man. J. Clin. Endocrinol. Metab., 85, 2879-2883.
38. Bocher, V., Pineda-Torra, I., Fruchart, J.C. and Staels, B. (2002) PPARs: transcription factors controlling lipid and lipoprotein metabolism. Ann. N Y Acad. Sci., 967, 7-18.
39. Turgeon, D., Chouinard, S., Belanger, P., Picard, S., Labbe, J.F., Borgeat, P. and Belanger, A. (2003) Glucuronidation of arachidonic and linoleic acid metabolites by human UDP-glucuronosyltransferases. J. Lipid Res., 44, 1182-1191.
40. Garcia-Silva, S. and Aranda, A. (2004) The thyroid hormone receptor is a suppressor of ras-mediated transcription, proliferation, and transformation. Mol. Cell Biol., 24, 7514-7523.
41. Yen, P.M. (2001) Physiological and molecular basis of thyroid hormone action. Physiol. Rev., 81, 1097-1142.
42. Board, P., Coggan, M., Johnston, P., Ross, V., Suzuki, T. and Webb, G. (1990) Genetic heterogeneity of the human glutathione transferases: a complex of gene families. Pharmacol. Ther., 48, 357-369.
43. Daly, A.K., Thomas, D.J., Cooper, J., Pearson, W.R., Neal, D.E. and Idle, J.R. (1993) Homozygous deletion of gene for glutathione S-transferase M1 in bladder cancer. Br. Med. J., 307, 481-482.
44. Townsend, D.M. and Tew, K.D. (2003) The role of glutathione-S-transferase in anti-cancer drug resistance. Oncogene, 22, 7369-7375.
45. Xu, S., Wang, Y., Roe, B. and Pearson, W.R. (1998) Characterization of the human class Mu glutathione S-transferase gene cluster and the GSTM1 deletion. J. Biol. Chem., 273, 3517-3527.
46. Matsuura, S., Kobayashi, J., Tauchi, H. and Komatsu, K. (2004) Nijmegen breakage syndrome and DNA double strand break repair by NBS1 complex. Adv. Biophys., 38, 65-80.
47. Demuth, I., Frappart, P.O., Hildebrand, G., Melchers, A., Lobitz, S., Stockl, L., Varon, R., Herceg, Z., Sperling, K., Wang, Z.Q. and Digweed, M. (2004) An inducible null mutant murine model of Nijmegen breakage syndrome proves the essential function of NBS1 in chromosomal stability and cell viability. Hum. Mol. Genet., 13, 2385-2397.
48. Williams, B.R. (1999) PKR; a sentinel kinase for cellular stress. Oncogene, 18, 6112-6120.
49. Morley, M., Molony, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S. and Cheung, V.G. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature, 430, 743-747.
50. Pastinen, T., Sladek, R., Gurd, S., Sammak, A., Ge, B., Lepage, P., Lavergne, K., Villeneuve, A., Gaudin, T., Brandstrom, H. et al. (2004) A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genomics, 16, 184-193.
51. Whitney, A.R., Diehn, M., Popper, S.J., Alizadeh, A.A., Boldrick, J.C., Relman, D.A. and Brown, P.O. (2003) Individuality and variation in gene expression patterns in human blood. Proc. Natl Acad. Sci. U S A, 100, 1896-1901.
52. Krynetski, E.Y., Schuetz, J.D., Galpin, A.J., Part, C.H., Relling, M.V. and Evans, W.E. (1995) A single point mutation leading to loss of catalytic activity in human thiopurine S-methyltransferase. Proc. Natl Acad. Sci. USA, 92, 949-953.
53. Tai, H.L., Krynetski, E.Y., Yates, C.R., Loennechen, T., Fessing, M.Y., Krynetskaia, N.F. and Evans, W.E. (1996) Thiopurine S-methyltransferase deficiency: two nucleotide transitions define the most prevalent mutant allele associated with loss of catalytic activity in Caucasians. Am. J. Hum. Genet., 58, 694-702.
54. Blanco, J.G., Edick, M.J., Hancock, M.L., Winick, N.J., Dervieux, T., Amylon, M.D., Bash, R.O., Behm, F.G., Camitta, B.M., Pui, C.H. et al. (2002) Genetic polymorphisms in CYP3A5, CYP3A4 and NQO1 in children who developed therapy-related myeloid malignancies. Pharmacogenetics, 12, 605-611.
55. Marsh, S., Ameyaw, M.M., Githang'a, J., Indalo, A., Ofori-Adjei, D. and McLeod, H.L. (2000) Novel thymidylate synthase enhancer region alleles in African populations. Hum. Mutat., 16, 528.
56. Relling, M.V., Yang, W., Das, S., Cook, E.H., Rosner, G.L., Neel, M., Howard, S., Ribeiro, R., Sandlund, J.T., Pui, C.H. and Kaste, S.C. (2004) Pharmacogenetic risk factors for osteonecrosis of the hip among children with leukemia. J. Clin. Oncol., 22, 3930-3936.
57. Koper, J.W. (1997) Lack of association between five polymorphisms in the human glucocorticoid receptor gene and glucocorticoid resistance. Hum. Genet., 99, 663-668.
58. Kishi, S., Griener, J.C., Cheng, C., Das, S., Yang, P., Cook, E.H., Hudson, M., Rubnitz, J., Sandlund, J.T., Pui, C.H. and Relling, M.V. (2003) Homocysteine, pharmacogenetics, and neurotoxicity in children with leukemia. J. Clin. Oncol., 21, 3084-3091.
59. Cheok, M.H., Yang, W., Pui, C.H., Downing, J.R., Cheng, C., Naeve, C.W., Relling, M.V. and Evans, W.E. (2003) Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells. Nat. Genet., 34, 85-90.
60. Kohlmann, A., Schoch, C., Schnittger, S., Dugas, M., Hiddemann, W., Kern, W. and Haferlach, T. (2003) Molecular characterization of acute leukemias by use of microarray technology. Genes Chromosomes Cancer, 37, 396-405.
61. Ross, M.E., Zhou, X., Song, G., Shurtleff, S.A., Girtman, K., Williams, W.K., Liu, H.C., Mahfouz, R., Raimondi, S.C., Lenny, N. et al. (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood, 102, 2951-2959.
62. Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genome-wide studies. Proc. Natl Acad. Sci. U S A, 100, 9440-9445.
63. Ripley, B.D. (1996) Pattern Recognition and Neural Networks. Cambridge University Press, Section 3.1, p. 92.