Networking of differentially expressed genes in human cancer cells resistant to methotrexate

Genome Medicine

Volumn 1, Issue 9, 2009, Pages

  Selga, Elisabet ^a   Oleaga, Carlota ^a   Ramírez, Sara ^a   de Almagro, M Cristina ^a   Noé, Véronique ^a   Ciudad, Carlos J ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DICKKOPF 1 PROTEIN; DIHYDROFOLATE REDUCTASE; ELONGATION FACTOR 1ALPHA; GLUCURONOSYLTRANSFERASE 1A1; MESSENGER RNA; METHOTREXATE; SMALL INTERFERING RNA; WNT PROTEIN;

ARTICLE; BREAST CANCER; CANCER CELL; CANCER CELL CULTURE; CHEMOSENSITIZATION; COLON CANCER; COMPUTER PROGRAM; CONTROLLED STUDY; DRUG SENSITIVITY; ERYTHROLEUKEMIA; GENE CLUSTER; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE OVEREXPRESSION; GENE REGULATORY NETWORK; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; OSTEOSARCOMA; PANCREAS CANCER; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA INTERFERENCE; UNINDEXED SEQUENCE;

EID: 77953413882     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm83     Document Type: Article

References (70)

1. Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA: Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC Bioinformatics 2007, 8:250.
2. Yu JX, Sieuwerts AM, Zhang Y, Martens JW, Smid M, Klijn JG, Wang Y, Foekens JA: Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer 2007, 7:182.
3. Kyoto Encyclopedia of Genes and Genomes [http://www. genome.jp/kegg/]
4. Dohr S, Klingenhoff A, Maier H, Hrabe de Angelis M, Werner T, Schneider R: Linking disease-associated genes to regulatory networks via promoter organization. Nucleic Acids Res 2005, 33:864-872.
5. Brazhnik P, de la Fuente A, Mendes P: Gene networks: how to put the function in genomics. Trends Biotechnol 2002, 20:467-472.
6. Natarajan J, Berrar D, Dubitzky W, Hack C, Zhang Y, DeSesa C, Van Brocklyn JR, Bremer EG: Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. BMC Bioinformatics 2006, 7:373.
7. Melera PW: Acquired versus intrinsic resistance to methotrexate: diversity of the drug-resistant phenotype in mammalian cells. Semin Cancer Biol 1991, 2:245-255.
8. Selga E, Noe V, Ciudad CJ: Transcriptional regulation of aldo-keto reductase 1C1 in HT29 human colon cancer cells resistant to methotrexate: role in the cell cycle and apoptosis. Biochem Pharmacol 2008, 75:414-426.
9. Rocke DM, Durbin B: A model for measurement error for gene expression arrays. J Comput Biol 2001, 8:557-569.
10. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW: BIND - The Biomolecular Interaction Network Database. Nucleic Acids Res 2001, 29:242-245.
11. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G: MINT: a Molecular INTeraction database. FEBS Lett 2002, 513:135-140.
12. Mosmann T: Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays. J Immunol Methods 1983, 65:55-63.
13. Selga E, Morales C, Noe V, Peinado MA, Ciudad CJ: Role of Caveolin 1, E-Cadherin, Enolase 2 and PKCalpha on resistance to methotrexate in human HT29 colon cancer cells. BMC Med Genomics 2008, 1:35.
14. Gene Expression Omnibus [http://www.ncbi.nlm.nih.gov/geo/]
15. Carman MD, Schornagel JH, Rivest RS, Srimatkandada S, Portlock CS, Duffy T, Bertino JR: Resistance to methotrexate due to gene amplification in a patient with acute leukemia. J Clin Oncol 1984, 2:16-20.
16. Curt GA, Cowan KH, Chabner BA: Gene amplification in drug resistance: of mice and men. J Clin Oncol 1984, 2:62-64.
17. Alt FW, Kellems RE, Schimke RT: Synthesis and degradation of folate reductase in sensitive and methotrexate-resistant lines of S-180 cells. J Biol Chem 1976, 251:3063-3074.
18. Yu M, Melera PW: Allelic variation in the dihydrofolate reductase gene at amino acid position 95 contributes to antifolate resistance in Chinese hamster cells. Cancer Res 1993, 53:6031-6035.
19. Srimatkandada S, Schweitzer BI, Moroson BA, Dube S, Bertino JR: Amplification of a polymorphic dihydrofolate reductase gene expressing an enzyme with decreased binding to methotrexate in a human colon carcinoma cell line, HCT-8R4, resistant to this drug. J Biol Chem 1989, 264:3524-3528.
20. Jansen G, Mauritz R, Drori S, Sprecher H, Kathmann I, Bunni M, Priest DG, Noordhuis P, Schornagel JH, Pinedo HM, Peters GJ, Assaraf YG: A structurally altered human reduced folate carrier with increased folic acid transport mediates a novel mechanism of antifolate resistance. J Biol Chem 1998, 273:30189-30198.
21. Roy K, Tolner B, Chiao JH, Sirotnak FM: A single amino acid difference within the folate transporter encoded by the murine RFC-1 gene selectively alters its interaction with folate analogues. Implications for intrinsic antifolate resistance and directional orientation of the transporter within the plasma membrane of tumor cells. J Biol Chem 1998, 273:2526-2531.
22. Zhao R, Sharina IG, Goldman ID: Pattern of mutations that results in loss of reduced folate carrier function under antifolate selective pressure augmented by chemical mutagenesis. Mol Pharmacol 1999, 56:68-76.
23. Gyorffy B, Surowiak P, Kiesslich O, Denkert C, Schafer R, Dietel M, Lage H: Gene expression profiling of 30 cancer cell lines predicts resistance towards 11 anticancer drugs at clinically achieved concentrations. Int J Cancer 2006, 118:1699-1712.
24. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D: Molecular portraits of human breast tumours. Nature 2000, 406:747-752.
25. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, et al.: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
26. Forget MA, Turcotte S, Beauseigle D, Godin-Ethier J, Pelletier S, Martin J, Tanguay S, Lapointe R: The Wnt pathway regulator DKK1 is preferentially expressed in hormone-resistant breast tumours and in some common cancer types. Br J Cancer 2007, 96:646-653.
27. Rothbacher U, Lemaire P: Creme de la Kremen of Wnt signalling inhibition. Nat Cell Biol 2002, 4:E172-173.
28. Nelson WJ, Nusse R: Convergence of Wnt, beta-catenin, and cadherin pathways. Science 2004, 303:1483-1487.
29. Polakis P: Wnt signaling and cancer. Genes Dev 2000, 14:1837-1851.
30. Gonzalez-Sancho JM, Aguilera O, Garcia JM, Pendas-Franco N, Pena C, Cal S, Garcia de Herreros A, Bonilla F, Munoz A: The Wnt antagonist DICKKOPF-1 gene is a downstream target of beta-catenin/TCF and is downregulated in human colon cancer. Oncogene 2005, 24:1098-1103.
31. Semenov MV, Tamai K, Brott BK, Kuhl M, Sokol S, He X: Head inducer Dickkopf-1 is a ligand for Wnt coreceptor LRP6. Curr Biol 2001, 11:951-961.
32. Mao B, Wu W, Davidson G, Marhold J, Li M, Mechler BM, Delius H, Hoppe D, Stannek P, Walter C, Glinka A, Niehrs C: Kremen proteins are Dickkopf receptors that regulate Wnt/beta-catenin signalling. Nature 2002, 417:664-667.
33. Koch A, Waha A, Hartmann W, Hrychyk A, Schuller U, Wharton KA Jr., Fuchs SY, von Schweinitz D, Pietsch T: Elevated expression of Wnt antagonists is a common event in hepatoblastomas. Clin Cancer Res 2005, 11:4295-4304.
34. Voorzanger-Rousselot N, Goehrig D, Journe F, Doriath V, Body JJ, Clezardin P, Garnero P: Increased Dickkopf-1 expression in breast cancer bone metastases. Br J Cancer 2007, 97:964-970.
35. Monaghan AP, Kioschis P, Wu W, Zuniga A, Bock D, Poustka A, Delius H, Niehrs C: Dickkopf genes are co-ordinately expressed in mesodermal lineages. Mech Dev 1999, 87:45-56.
36. Gregory CA, Singh H, Perry AS, Prockop DJ: The Wnt signaling inhibitor dickkopf-1 is required for reentry into the cell cycle of human adult stem cells from bone marrow. J Biol Chem 2003, 278:28067-28078.
37. Katula KS, Heinloth AN, Paules RS: Folate deficiency in normal human fibroblasts leads to altered expression of genes primarily linked to cell signaling, the cytoskeleton and extracellular matrix. J Nutr Biochem 2007, 18:541-552.
38. Mackenzie PI, Owens IS, Burchell B, Bock KW, Bairoch A, Belanger A, Fournel-Gigleux S, Green M, Hum DW, Iyanagi T, Lancet D, Louisot P, Magdalou J, Chowdhury JR, Ritter JK, Schachter H, Tephly TR, Tipton KF, Nebert DW: The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence. Pharmacogenetics 1997, 7:255-269.
39. Guillemette C: Pharmacogenomics of human UDP-glucuronosyltransferase enzymes. Pharmacogenomics J 2003, 3:136-158.
40. Strassburg CP, Manns MP, Tukey RH: Expression of the UDP-glucuronosyltransferase 1A locus in human colon. Identification and characterization of the novel extrahepatic UGT1A8. J Biol Chem 1998, 273:8719-8726.
41. Kiang TK, Ensom MH, Chang TK: UDP-glucuronosyltransferases and clinical drug-drug interactions. Pharmacol Ther 2005, 106:97-132.
42. Nagar S, Remmel RP: Uridine diphosphoglucuronosyltransferase pharmacogenetics and cancer. Oncogene 2006, 25:1659-1672.
43. McCague R, Parr IB, Leclercq G, Leung OT, Jarman M: Metabolism of tamoxifen by isolated rat hepatocytes. Identification of the glucuronide of 4-hydroxytamoxifen. Biochem Pharmacol 1990, 39:1459-1465.
44. Platzer P, Schaden S, Thalhammer T, Hamilton G, Rosenberg B, Silgoner I, Jager W: Biotransformation of topotecan in the isolated perfusedrat liver: identification of three novel metabolites. Anticancer Res 1998, 18:2695-2700.
45. Rosing H, van Zomeren DM, Doyle E, Bult A, Beijnen JH: O-glucuronidation, a newly identified metabolic pathway for topotecan and N-desmethyl topotecan. Anticancer Drugs 1998, 9:587-592.
46. Andersen A, Holte H, Slordal L: Pharmacokinetics and metabolism of doxorubicin after short-term infusions in lymphoma patients. Cancer Chemother Pharmacol 1999, 44:422-426.
47. Iyer L, King CD, Whitington PF, Green MD, Roy SK, Tephly TR, Coffman BL, Ratain MJ: 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 1998, 101:847-854.
48. Cowan KH, Batist G, Tulpule A, Sinha BK, Myers CE: Similar biochemical changes associated with multidrug resistance in human breast cancer cells and carcinogen-induced resistance to xenobiotics in rats. Proc Natl Acad Sci U S A 1986, 83:9328-9332.
49. Gessner T, Vaughan LA, Beehler BC, Bartels CJ, Baker RM: Elevated pentose cycle and glucuronyltransferase in daunorubicin-resistant P388 cells. Cancer Res 1990, 50:3921-3927.
50. Franklin TJ, Jacobs V, Jones G, Ple P, Bruneau P: Glucuronidation associated with intrinsic resistance to mycophenolic acid in human colorectal carcinoma cells. Cancer Res 1996, 56:984-987.
51. Franklin TJ, Jacobs VN, Jones G, Ple P: Human colorectal carcinoma cells in vitro as a means to assess the metabolism of analogs of mycophenolic acid. Drug Metab Dispos 1997, 25:367-370.
52. Rekha GK, Sladek NE: Multienzyme-mediated stable and transient multidrug resistance and collateral sensitivity induced by xenobiotics. Cancer Chemother Pharmacol 1997, 40:215-224.
53. Takahashi T, Fujiwara Y, Yamakido M, Katoh O, Watanabe H, Mackenzie PI: The role of glucuronidation in 7-ethyl-10-hydroxycamptothecin resistance in vitro. Jpn J Cancer Res 1997, 88:1211-1217.
54. Cummings J, Ethell BT, Jardine L, Boyd G, Macpherson JS, Burchell B, Smyth JF, Jodrell DI: Glucuronidation as a mechanism of intrinsic drug resistance in human colon cancer: reversal of resistance by food additives. Cancer Res 2003, 63:8443-8450.
55. Brangi M, Litman T, Ciotti M, Nishiyama K, Kohlhagen G, Takimoto C, Robey R, Pommier Y, Fojo T, Bates SE: Camptothecin resistance: role of the ATP-binding cassette (ABC), mitoxantrone-resistance half-transporter (MXR), and potential for glucuronidation in MXRexpressing cells. Cancer Res 1999, 59:5938-5946.
56. Meijerman I, Beijnen JH, Schellens JH: Combined action and regulation of phase II enzymes and multidrug resistance proteins in multidrug resistance in cancer. Cancer Treat Rev 2008, 34:505-520.
57. Zembutsu H, Ohnishi Y, Tsunoda T, Furukawa Y, Katagiri T, Ueyama Y, Tamaoki N, Nomura T, Kitahara O, Yanagawa R, Hirata K, Nakamura Y: Genome-wide cDNA microarray screening to correlate gene expression profiles with sensitivity of 85 human cancer xenografts to anticancer drugs. Cancer Res 2002, 62:518-527.
58. Hanioka N, Obika N, Nishimura M, Jinno H, Tanaka-Kagawa T, Saito K, Kiryu K, Naito S, Narimatsu S: Inducibility of UDP-glucuronosyltransferase 1As by beta-naphthoflavone in HepG2 cells. Food Chem Toxicol 2006, 44:1251-1260.
59. Thornton S, Anand N, Purcell D, Lee J: Not just for housekeeping: protein initiation and elongation factors in cell growth and tumorigenesis. J Mol Med 2003, 81:536-548.
60. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A 1999, 96:6745-6750.
61. Hassell JA, Engelhardt DL: The regulation of protein synthesis in animal cells by serum factors. Biochemistry 1976, 15:1375-1381.
62. Grassi G, Scaggiante B, Farra R, Dapas B, Agostini F, Baiz D, Rosso N, Tiribelli C: The expression levels of the translational factors eEF1A 1/2 correlate with cell growth but not apoptosis in hepatocellular carcinoma cell lines with different differentiation grade. Biochimie 2007, 89:1544-1552.
63. Tatsuka M, Mitsui H, Wada M, Nagata A, Nojima H, Okayama H: Elongation factor-1 alpha gene determines susceptibility to transformation. Nature 1992, 359:333-336.
64. Shepherd JC, Walldorf U, Hug P, Gehring WJ: Fruit flies with additional expression of the elongation factor EF-1 alpha live longer. Proc Natl Acad Sci U S A 1989, 86:7520-7521.
65. Edmonds BT, Wyckoff J, Yeung YG, Wang Y, Stanley ER, Jones J, Segall J, Condeelis J: Elongation factor-1 alpha is an overexpressedactin binding protein in metastatic rat mammary adenocarcinoma. J Cell Sci 1996, 109:2705-2714.
66. Johnsson A, Zeelenberg I, Min Y, Hilinski J, Berry C, Howell SB, Los G: Identification of genes differentially expressed in association with acquired cisplatin resistance. Br J Cancer 2000, 83:1047-1054.
67. Bertram J, Palfner K, Hiddemann W, Kneba M: Overexpression of ribosomal proteins L4 and L5 and the putative alternative elongation factor PTI-1 in the doxorubicin resistant human colon cancer cell line LoVoDxR. Eur J Cancer 1998, 34:731-736.
68. Beyer-Sehlmeyer G, Hiddemann W, Wormann B, Bertram J: Suppressive subtractive hybridisation reveals differential expression of serglycin, sorcin, bone marrow proteoglycan and prostate-tumourinducing gene I (PTI-1) in drug-resistant and sensitive tumour cell lines of haematopoetic origin. Eur J Cancer 1999, 35:1735-1742.
69. Talapatra S, Wagner JD, Thompson CB: Elongation factor-1 alpha is a selective regulator of growth factor withdrawal and ER stressinduced apoptosis. Cell Death Differ 2002, 9:856-861.
70. Su Z, Goldstein NI, Fisher PB: Antisense inhibition of the PTI-1 oncogene reverses cancer phenotypes. Proc Natl Acad Sci U S A 1998, 95:1764-1769.