Analysis of polymorphisms and haplotype structure of the human thymidylate synthase genetic region: A tool for pharmacogenetic studies

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Ghosh, Soma ^a   Hossain, M Zulfiquer ^a   Borges, Michael ^b   Goggins, Michael G ^a,b   Ingersoll, Roxann G ^a   Eshleman, James R ^a,b   Klein, Alison P ^a,b   Kern, Scott E ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUOROURACIL; THYMIDYLATE SYNTHASE; ANTINEOPLASTIC ANTIMETABOLITE;

5' UNTRANSLATED REGION; ALLELE; ARTICLE; CANCER PATIENT; CONTROLLED STUDY; GENE; GENE FUNCTION; GENE LOCATION; GENE LOCUS; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HAPLOTYPE; HOMOPLASY; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; NUCLEOTIDE REPEAT; PHARMACOGENETICS; POPULATION RESEARCH; SINGLE NUCLEOTIDE POLYMORPHISM; TOXICOGENETICS; TYMS GENE; VARIABLE NUMBER OF TANDEM REPEAT; DRUG EFFECT; ENZYMOLOGY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PANCREAS; PANCREAS TUMOR; SEQUENCE HOMOLOGY; TANDEM REPEAT;

ANTIMETABOLITES, ANTINEOPLASTIC; BASE SEQUENCE; FLUOROURACIL; HAPLOTYPES; HUMANS; MINISATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PANCREAS; PANCREATIC NEOPLASMS; PHARMACOGENETICS; POLYMORPHISM, GENETIC; SEQUENCE HOMOLOGY, NUCLEIC ACID; TANDEM REPEAT SEQUENCES; THYMIDYLATE SYNTHASE;

EID: 84859332713     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034426     Document Type: Article

References (46)

1. Heidelberger C, Chaudhuri NK, Danneberg P, Mooren D, Griesbach L, et al. (1957) Fluorinated pyrimidines, a new class of tumour-inhibitory compounds. Nature 179: 663-666.
2. Noordhuis P, Holwerda U, Van der Wilt CL, Van Groeningen CJ, Smid K, et al. (2004) 5-Fluorouracil incorporation into RNA and DNA in relation to thymidylate synthase inhibition of human colorectal cancers. Ann Oncol 15: 1025-1032.
3. Brody JR, Hucl T, Costantino CL, Eshleman JR, Gallmeier E, et al. (2009) Limits to thymidylate synthase and TP53 genes as predictive determinants for fluoropyrimidine sensitivity and further evidence for RNA-based toxicity as a major influence. Cancer Res 69: 984-991.
4. Parker WB, Cheng YC, (1990) Metabolism and mechanism of action of 5-fluorouracil. Pharmacol Ther 48: 381-395.
5. Longley DB, Harkin DP, Johnston PG, (2003) 5-fluorouracil: mechanisms of action and clinical strategies. Nat Rev Cancer 3: 330-338.
6. Lum PY, Armour CD, Stepaniants SB, Cavet G, Wolf MK, et al. (2004) Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116: 121-137.
7. Saif MW, Choma A, Salamone SJ, Chu E, (2009) Pharmacokinetically guided dose adjustment of 5-fluorouracil: a rational approach to improving therapeutic outcomes. J Natl Cancer Inst 101: 1543-1552.
8. Kline CL, Sheikh HS, Scicchitano A, Gingrich R, Beachler C, et al. (2011) Preliminary observations indicate variable patterns of plasma 5-fluorouracil (5-FU) levels during dose optimization of infusional 5-FU in colorectal cancer patients. Cancer Biol Ther 12: 557-568.
9. Gamelin E, Delva R, Jacob J, Merrouche Y, Raoul JL, et al. (2008) Individual fluorouracil dose adjustment based on pharmacokinetic follow-up compared with conventional dosage: results of a multicenter randomized trial of patients with metastatic colorectal cancer. J Clin Oncol 26: 2099-2105.
10. Kaneda S, Takeishi K, Ayusawa D, Shimizu K, Seno T, et al. (1987) Role in translation of a triple tandemly repeated sequence in the 5′-untranslated region of human thymidylate synthase mRNA. Nucleic Acids Res 15: 1259-1270.
11. Horie N, Aiba H, Oguro K, Hojo H, Takeishi K, (1995) Functional analysis and DNA polymorphism of the tandemly repeated sequences in the 5′-terminal regulatory region of the human gene for thymidylate synthase. Cell Struct Funct 20: 191-197.
12. Ulrich CM, Bigler J, Velicer CM, Greene EA, Farin FM, et al. (2000) Searching expressed sequence tag databases: discovery and confirmation of a common polymorphism in the thymidylate synthase gene. Cancer Epidemiol Biomarkers Prev 9: 1381-1385.
13. Kakimoto M, Uetake H, Osanai T, Shirota Y, Takagi Y, et al. (2005) Thymidylate synthase and dihydropyrimidine dehydrogenase gene expression in breast cancer predicts 5-FU sensitivity by a histocultural drug sensitivity test. Cancer Lett 223: 103-111.
14. Kawakami K, Watanabe G, (2003) Identification and functional analysis of single nucleotide polymorphism in the tandem repeat sequence of thymidylate synthase gene. Cancer Res 63: 6004-6007.
15. Yawata A, Kim SR, Miyajima A, Kubo T, Ishida S, et al. (2005) Polymorphic tandem repeat sequences of the thymidylate synthase gene correlates with cellular-based sensitivity to fluoropyrimidine antitumor agents. Cancer Chemother Pharmacol 56: 465-472.
16. Ghosh S, Winter JM, Patel K, Kern SE, (2011) Reexamining a proposal: Thymidylate synthase 5′-untranslated region as a regulator of translation efficiency. Cancer Biol Ther 12: 750-755.
17. Pullarkat ST, Stoehlmacher J, Ghaderi V, Xiong YP, Ingles SA, et al. (2001) Thymidylate synthase gene polymorphism determines response and toxicity of 5-FU chemotherapy. Pharmacogenomics J 1: 65-70.
18. Lecomte T, Ferraz JM, Zinzindohoue F, Loriot MA, Tregouet DA, et al. (2004) Thymidylate synthase gene polymorphism predicts toxicity in colorectal cancer patients receiving 5-fluorouracil-based chemotherapy. Clin Cancer Res 10: 5880-5888.
19. Ichikawa W, Takahashi T, Suto K, Sasaki Y, Hirayama R, (2006) Orotate phosphoribosyltransferase gene polymorphism predicts toxicity in patients treated with bolus 5-fluorouracil regimen. Clin Cancer Res 12: 3928-3934.
20. Schwab M, Zanger UM, Marx C, Schaeffeler E, Klein K, et al. (2008) Role of genetic and nongenetic factors for fluorouracil treatment-related severe toxicity: a prospective clinical trial by the German 5-FU Toxicity Study Group. J Clin Oncol 26: 2131-2138.
21. Gusella M, Frigo AC, Bolzonella C, Marinelli R, Barile C, et al. (2009) Predictors of survival and toxicity in patients on adjuvant therapy with 5-fluorouracil for colorectal cancer. Br J Cancer 100: 1549-1557.
22. Mandola MV, Stoehlmacher J, Muller-Weeks S, Cesarone G, Yu MC, et al. (2003) A novel single nucleotide polymorphism within the 5′ tandem repeat polymorphism of the thymidylate synthase gene abolishes USF-1 binding and alters transcriptional activity. Cancer Res 63: 2898-2904.
23. de Bock CE, Garg MB, Scott N, Sakoff JA, Scorgie FE, et al. (2011) Association of thymidylate synthase enhancer region polymorphisms with thymidylate synthase activity in vivo. Pharmacogenomics J 11: 307-314.
24. Wenz H, Robertson JM, Menchen S, Oaks F, Demorest DM, et al. (1998) High-precision genotyping by denaturing capillary electrophoresis. Genome Res 8: 69-80.
25. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, et al. (2002) The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
26. Taylor JS, Breden F, (2000) Slipped-strand mispairing at noncontiguous repeats in Poecilia reticulata: a model for minisatellite birth. Genetics 155: 1313-1320.
27. Taylor JS, Sanny JS, Breden F, (1999) Microsatellite allele size homoplasy in the guppy (Poecilia reticulata). J Mol Evol 48: 245-247.
28. Olsen KM, (1999) Minisatellite variation in a single-copy nuclear gene: phylogenetic assessment of repeat length homoplasy and mutational mechanism. Mol Biol Evol 16: 1406-1409.
29. Kristensen MH, Weidinger M, Bzorek M, Pedersen PL, Mejer J, (2010) Correlation between thymidylate synthase gene variants, RNA and protein levels in primary colorectal adenocarcinomas. J Int Med Res 38: 484-497.
30. Fujishima M, Inui H, Hashimoto Y, Azumi T, Yamamoto N, et al. (2010) Relationship between thymidylate synthase (TYMS) gene polymorphism and TYMS protein levels in patients with high-risk breast cancer. Anticancer Res 30: 4373-4379.
31. Kim SR, Park CH, Park S, Park JO, Lee J, et al. (2010) Genetic polymorphisms associated with 5-Fluorouracil-induced neurotoxicity. Chemotherapy 56: 313-317.
32. Li WH, eds. (1997) Molecular Evolution Sunderland, Mass.
33. Ohta T, Kimura M, (2007) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population*. Genet Res 89: 367-370.
34. Schwartz S Jr, Yamamoto H, Navarro M, Maestro M, Reventos J, et al. (1999) Frameshift mutations at mononucleotide repeats in caspase-5 and other target genes in endometrial and gastrointestinal cancer of the microsatellite mutator phenotype. Cancer Res 59: 2995-3002.
35. Aitman TJ, Hearne CM, McAleer MA, Todd JA, (1991) Mononucleotide repeats are an abundant source of length variants in mouse genomic DNA. Mamm Genome 1: 206-210.
36. Kufe DW, Major PP, Egan EM, Loh E, (1981) 5-Fluoro-2′-deoxyuridine incorporation in L1210 DNA. J Biol Chem 256: 8885-8888.
37. Major PP, Egan E, Herrick D, Kufe DW, (1982) 5-Fluorouracil incorporation in DNA of human breast carcinoma cells. Cancer Res 42: 3005-3009.
38. Showalter SL, Showalter TN, Witkiewicz A, Havens R, Kennedy EP, et al. (2008) Evaluating the drug-target relationship between thymidylate synthase expression and tumor response to 5-fluorouracil. Is it time to move forward? Cancer Biol Ther 7: 986-994.
39. Vignoli M, Nobili S, Napoli C, Putignano AL, Morganti M, et al. (2011) Thymidylate synthase expression and genotype have no major impact on the clinical outcome of colorectal cancer patients treated with 5-fluorouracil. Pharmacol Res 64: 242-248.
40. Lyss AP, Lilenbaum RC, Harris BE, Diasio RB, (1993) Severe 5-fluorouracil toxicity in a patient with decreased dihydropyrimidine dehydrogenase activity. Cancer Invest 11: 239-240.
41. Santi DV, McHenry CS, (1972) 5-Fluoro-2′-deoxyuridylate: covalent complex with thymidylate synthetase. Proc Natl Acad Sci U S A 69: 1855-1857.
42. Fujii R, Seshimo A, Kameoka S, (2003) Relationships between the expression of thymidylate synthase, dihydropyrimidine dehydrogenase, and orotate phosphoribosyltransferase and cell proliferative activity and 5-fluorouracil sensitivity in colorectal carcinoma. Int J Clin Oncol 8: 72-78.
43. Brody JR, Calhoun ES, Gallmeier E, Creavalle TD, Kern SE, (2004) Ultra-fast high-resolution agarose electrophoresis of DNA and RNA using low-molarity conductive media. Biotechniques 37: 598, 600, 602.
44. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
45. Barrett JC, Fry B, Maller J, Daly MJ, (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
46. Stephens M, Scheet P, (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet 76: 449-462.