Differences in mRNA and microRNA microarray expression profiles in human colon adenocarcinoma HT-29 cells treated with either intensity-modulated radiation therapy (IMRT), or conventional radiation therapy (RT)

Cancer Genomics and Proteomics

Volumn 6, Issue 2, 2009, Pages 109-128

  Ahmed, Farid E ^a,d   Vos, Paul W ^a   Jeffries, Clark ^b   Wiley, John E ^c   Weidner, Douglas A ^c   Mota, Helvecio ^a   Bonnerup, Chris ^a   Sibata, Claudio ^a   Allison, Ron R ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

^b UNC Hamner Institute for Drug Safety Sciences   (United States)

^c EAST CAROLINA UNIVERSITY   (United States)

^d GEM Tox Consultants and Labs Inc   (United States)

Author keywords

Mismatch repair; Primers; Probes; Proteins; QC; RT qPCR; Statistics; Western blots

Indexed keywords

APOPTOSIS INDUCING FACTOR; ATM PROTEIN; CYCLIN D2; CYCLIN DEPENDENT KINASE INHIBITOR 2B; DAMAGE SPECIFIC DNA BINDING PROTEIN 2; DNA BINDING PROTEIN; ENDONUCLEASE; FLAP STRUCTURE SPECIFIC ENDONUCLEASE 1; GENE PRODUCT; MESSENGER RNA; MICRORNA; MITOGEN ACTIVATED PROTEIN KINASE 9; POSTMEIOTIC SEGREGATION INCREASED 1 PROTEIN; PROGRAMMED APOPTOSIS INDUCING CELL DEATH FACTOR 8; PROTEIN BAD; PROTEIN CASP 14; PROTEIN DDB2; PROTEIN FN1; PROTEIN MRE11A; PROTEIN MSH2; PROTEIN PDCCD8; PROTEIN PMS1; RNA METHYLTRANSFERASE; TRANSFORMING GROWTH FACTOR BETA RECEPTOR 1; UNCLASSIFIED DRUG;

ANALYZER; ARTICLE; CANCER RADIOTHERAPY; CAPILLARY ELECTROPHORESIS; CELL CYCLE G0 PHASE; CELL CYCLE G1 PHASE; CELL STRAIN HT29; CELL SURVIVAL; CELL VIABILITY; COMPUTER PROGRAM; CONTROLLED STUDY; DNA MICROARRAY; DNA REPAIR; EXTERNAL BEAM RADIOTHERAPY; GENE EXPRESSION PROFILING; GENETIC CORRELATION; HUMAN; HUMAN CELL; INTENSITY MODULATED RADIATION THERAPY; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; RADIATION DOSE; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; RNA PROBE; RNA TRANSCRIPTION; WESTERN BLOTTING;

EID: 65749089057     PISSN: 11096535     EISSN: 17906245     Source Type: Journal    
DOI: None     Document Type: Article

References (92)

1. Purdy JA: Dose to normal tissues outside the radiation therapy patient's treated volume: a review of different radiation therapy techniques. Health Phys 95: 666-676, 2008.
2. Galvin JM, Chen XG and Smith RM: combining multileaf fields to modulate fluence distribution. Int J Radiat Oncol Biol Phys 27: 697-705, 1993.
3. Brahme A, Roos JE and Lax I: Solution of an integral equation encountered in radiation therapy. Phys Med Biol 27: 1221-1229, 1982.
4. Bortfeld T: IMRT: a review and preview. Phys Med Biol 51: R363-379, 2006.
5. Webb S: Intensity-modulated Radiation Therapy. Bristol, UK: Institute of Physics Publishing, pp. 1-19, 75-96, 2000.
6. Veldmann L, Madani I, Hulstaert F, De Merleer G, Marcel M and De Neve W: Evidence behind use of intensity-modulated radiotherapy: a systematic review of comparative clinical studies. Lancet Oncol 9: 367-375, 2008.
7. Jaffray DA, Siewerdsen JH, Wong JW and Martinez AA: Flat-panel cone-beam computed tomography for image-guided radiation therapy. Int J Radiat Oncol Biol Phys 53: 1337-1349, 2002.
8. Randall ME and Ibott GS: Intensity-modulated radiation therapy for gynecological cancers: pitfalls, hazards, and cautions to be considered. Semin Radiat Oncol 16: 138-142, 2006.
9. Hall EJ and Wuu CS: Radiation-induced second cancers: the impact of 3D-CRT and IMRT. Int J Radiat Oncol Biol Phys 56: 83-88, 2003.
10. Ling CC, York E and Fuks Z: From IMRT to IGRT: frontierland or neverland? Radiother Oncol 78: 119-122, 2006.
11. Tom BH, Rutzky LP, Jakstys MM, Oyasu R, Kaye CI and Kalhan BD: Human colonic adenocarcinoma cells. I. Establishment and description of a new line. In Vitro 12: 180-191, 1976.
12. Cooper S: Reanalysis of the protocol for in vitro synchronization of mammalian astrocytic cultures by serum deprivation. Brain Res Protocols 15: 115-118, 2005.
13. Davis PK, Ho A and Dowdy SF: Biological methods for cell-cell synchronization of mammalian cells. BioTechniques 30: 1322-1331, 2001.
14. Frantz DJ, Hughes BG, Nelson DR, Murray BK and Christensen MJ: Cell cycle arrest and differential gene expression in HT-29 cells exposed to an aqueous garlic extract. Nutr Cancer 38: 255-264, 2000.
15. Orfao A and Ruiz-Argüelles A: General concepts about cell sorting techniques. Clin Biochem 29: 5-9, 1996.
16. Pawlicki T, Yoo S, Court LE, McMillan SS, Rice RK, Russell JD, Pacyniak JM, Woo MK, Basran PS, Boyer AL and Bonilla G: Process control analysis of IMRT QA: implications for clinical trials. Phys Med Biol 53: 5193-5205, 2008.
17. Dobler B, Lorenz F, Wertz H, Polednik M, Wolff D, Steil V, Lohr F and Wenz F: Intensity-modulated radiation therapy (IMRT) with different combinations of treatment-planning systems and Linacs. Strahlenther Onkol 182: 481-488, 2006.
18. Kuecker SJ, Jin L, Kulig E, Oudrago GL, Roche PC and Lloyd RV: Analysis of PRL, PRL-R, TGFβ1 and TGFβ-RII gene expression in normal neoplastic breast tissue after laser capture microdissection. Appl Immunol Mol Morph 7: 193-200, 1999.
19. Ahmed FE: Microarray RNA transcriptional profiling: Part I. Platforms, experimental design and standardization. Exp Rev Mol Diag 6: 535-550, 2006.
20. Shannon W, Culverhouse R and Duncan J: Analyzing microarray data using cluster analysis. Pharmacogenomics 4: 41-51, 2003.
21. Drãghici S: Data Analysis Tools for DNA Microarrays. Boca Raton, FL, Chapman/CRC, 2003.
22. Stoyanova R, Querec TD, Brown TR and Parrioris C: Normalization of single channel DNA array data by principal component analysis. Bioinformatics 20: 1772-1748, 2004.
23. Liu CG, Callin GA, Meloon B, Gamliel N, Sevignani C, Ferracin M, Dumitru CD, Shimizu M, Zupos S, Dono M, Alder H, Bullrich F, Negrini M and Croce CM: An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA 101: 9740-9744, 2004.
24. Ahmed FE: Microarray RNA transcriptional profiling: Part II. Analytical considerations and annotations. Exp Rev Mol Diag 6: 736-750, 2006.
25. Huber W, von Heydebreck A, Sültmann M, Poustka A and Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18: S96-S104, 2002.
26. Pavlidis P: Using ANOVA for gene selection from microarray studies of the nervous system. Methods 31: 282-289, 2003.
27. Benjamini Y and Hochberger Y: Controlling false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B 57: 289-300, 1995.
28. Ahmed FE, Vos P, iJames S, Lysle DT, Allison RR, Flake G, Sinar DR, Naziri W, Marcuard ST and Pennigton R: Transcriptomic molecular markers for screening human colon cancer in stool and tissue. Cancer Genom Proteom 4: 1-20, 2007.
29. Kennedy B, Arar K, Reja V and Henry RJ: Locked nucleic acids for optimizing displacement probes for quantitative real-time PCR. Anal Bochem 348: 294-299, 2006.
30. de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, Swinkels DW and Span PN: Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest 85: 154-159, 2005.
31. Tellman G: The E-method: a highly accurate technique for gene-expression analysis. Nature Methods 3: 1-2, 2006.
32. LightCycler Software®, Version 3.5. Roche Molecular Biochemicals, Mannheim, Germany, pp. 64-79, 2001.
33. Pfaffl MW: Quantification strategies in real-time PCR. In: A-Z of Quantitative PCR. Bustin SA (ed). La Jolla, CA, USA, International University Line, pp. 89-120, 2004.
34. ΔΔCT method. Methods 25: 402-408, 2001.
35. Tichopad A, Dilger M, Schwarz G and Pfaffl MW: Standardised determination of real-time PCR efficiency from a single reaction setup. Nucleic Acids Res 31: 21-33, 2003.
36. Ahmed FE: qRT-PCR: application to carcinogenesis. Cancer Genom Proteom 2: 317-332, 2005.
37. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ and Guegler KJ: Real-time quantification of microRNAs by stem-loop RT-OCR. Nucleic Acids Res 33: e179, 2005.
38. Lee EJ and Schmittgen TD: Comparison of RNA assay methods used to normalize cDNA for quantitative real-time PCR. Anal Biochem 357: 299-301, 2006.
39. Lanza G, Ferracin M, Gafà R, Veronese R, Spizzo R, Pichiorri F, Liu C, Calin GA, Croce CM and Negrini M: mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer. Molecular Cancer 6: 54, 2007.
40. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP and Burge CB: Prediction of mammalian microRNA targets. Cell 115: 787-798, 2003.
41. Ahmed FE: The role of microRNA in carcinogenesis and biomarker selection: a methodological perspective. Exp Rev Mol Diag 7: 569-603, 2007.
42. Thompson D and Larson G: Western blots using stained protein gels. BioTechniques 12: 656-658, 1992.
43. Edgar R, Domrachev M and Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 270-210, 2002.
44. Ding LA, Shingyoji M, Chen F, Hwang JJ, Burma S, Lee C, Cheng JF and Chen DJ: Gene expression profiles of normal human fibroblasts after exposure to ionizing radiation: a comparative study of low and high doses. Radiat Res 164: 17-26, 2005.
45. Prtilo A, Leach FS, Murkwalder R, Kappeler A, Burkhard FC, Cecchini MG, Studer UE and Thalmann GN: Tissue microarray analysis of hMSH2 expression predicts outcome in men with prostate cancer. J Urol 174: 1814-1818, 2005.
46. Bartek J and Lukas J: DNA damage checkpoints: from initiation to recovery or adaptation. Curr Opin Cell Biol 19: 238-245, 2007.
47. Choudhury A, Cuddihy A and Bristow RG: Radiation and molecular agents. Part I: targeting ATM-ATR checkpoints, DNA repair and the proteasome. Semin Radiat Oncol 16: 51-58, 2006.
48. Bristow RG, Ozcelik H, Jalali F, Chan N and Vesprini D: Homologous recombination and prostate cancer: A model for normal DNA repair targets and therapies. Radiotherap Oncol 83: 220-230, 2007.
49. Elshaikh M, Ljungman M, Haken RT and Lichter A: Advances in radiation oncology. Ann Rev Med 57: 19-31, 2006.
50. Willers H, Daphi-Dahm J and Powell SN: Repair of radiation damage to DNA. Br J Cancer 90: 1297-1301, 2004.
51. Wang JZ, Li A. D'Souza WD and Steward RD: Impact of prolonged fraction of delivery times on tumor control: a note of caution for intensity-modulated radiation therapy (IMRT). Int J Radiat Oncol Biol Phys 57: 543-552, 2003.
52. Elkind MM: Cell-cycle sensitivity, recovery from radiation damage and a new paradigm for risk assessment. Int J Radiat Biol 71: 657-665, 1997.
53. Mu X, Löfroth PO, Karlsson M and Zackrisson B: The effect of fraction time in intensity-modulated radiotherapy: theoretical and experimental evaluation of an optimization problem. Radiotherap Oncol 68: 181-187, 2003.
54. Guerrero M, Stewart RD, Wang JZ and Li XA: Equivalence of the linear-quadratic and tumor lesion kinetic models. Phys Med Biol 47: 3197-3209, 2002.
55. Wang JZ, Guerrero M and Li XA: How low is the α/β ratio for prostate cancer? Int J Radiat Oncol Biol Phys 55: 194-203, 2003.
56. Paganetti H: Changes in tumor cell response due to prolonged dose delivery times in fractionated radiation therapy. Int J Radiat Oncol Biol Phys 63: 892-900, 2005.
57. Fowler JF, Welsh JS and Howard SP: Loss of biological effect in prolonged fraction delivery. Int J Radiat Oncol Biol Phys 59: 242-249.
58. Brenner D, Armour E, Cory P and Hall E: Sublethal damage repair times for a late-responding tissue relevant to brachytherapy (and external-beam radiotherapy): Implications for new brachytherapy protocols. Int J Radiat Oncol Biol Phys 41: 135-138, 1998.
59. Crooks SM, McAven LF, Robinson DF and Xing X: Minimizing delivery time and monitor units in static IMRT by leaf-sequencing. Phys Med Biol 47: 3105-3116, 2002.
60. Shepard DM, Earl MA, Li A and Naqvi S: Direct aperture optimization: A turnkey solution for step-and-shoot IMRT. Med Phys 29: 1007-1018, 2002.
61. Shibamoto Y, Ito M, Sugie C, Ogino H and Hara M: Recovery from sublethal damage during intermittent exposure in cultured tumor cells: implications for dose modification in radiosurgery and IMRT. Int J Radiat Oncol Biol Phys 59: 1484-1490, 2004.
62. Ogino H, Shibamoto Y, Sugie C and Ito M: Biological effects of intermittent radiation in cultured tumor cells: influence of fraction number and dose per fraction. J Radiat Res 46: 401-406, 2005.
63. Sugie C, Shibamoto Y, Ito M, Ogino H, Miyamoto A, Fukaya N, Nimi H and Hasizume T: Radiobiologic effect of intermittent radiation exposure in murine tumors. Int J Radiat Oncol Biol Phys 64: 619-624, 2006.
64. Tomita N, Shibamoto Y, Ito M, Ogino H, Sugie C, Ayakawa S and Iwata H: Biological effect of intermittent radiation exposure in vivo: Recovery from sublethal damage versus reoxygenation. Radiotherapy Oncol 86: 369-374, 2008.
65. Lewis BP, Burge CB and Bartel DP: Conserved seed paring, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20, 2005.
66. Ruby JG, Jan CH and Bartel DP: Intronic microRNA precursors that bypass Drosha processing. Nature 448: 83-86, 2007.
67. Reinhart BJ, Slack FJ, Basson M, Pasquinell AE, Bettinger JC, Rougvie AE, Horvitz HR and Ruvkun G: RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906, 2000.
68. Xu P, Guo M and Hay BA: MicroRNAs and the regulation of cell death. Trend Genet 20: 617-624, 2004.
69. Gregory RI and Shiekhattar R: MicroRNA biogenesis and cancer. Cancer Res 65: 3509-3512, 2005.
70. Cummins JM and Velculescu VE: Implication of microRNA profiling for cancer diagnosis. Oncogene 15: 6220-6227, 2006.
71. Lee EJ, Gusev Y, Jiang J, Nuovo GJ, Lerner M, Frankel WL, Morgan DL, Positer RG, Campiglio M, Menard S, Palazzo JP, Rosenberg A, Musiani P, Volinia S, Neaci T, Calin GA, Querzoli P, Negrini M and Croce CM: Expression profiling identifies distinct microRNA signature in pancreatic cancer. Int J Cancer 120: 1046-1054, 2007.
72. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamota A, Yokota J, Tanaka T, Galin GA, Liu CG, Groce CM and Harris CC: Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9: 189-198, 2006.
73. Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S, Margri E, Pedriali M and Fabbri M: MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65: 7065-7070, 2005.
74. Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O, Benturch Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Kinzler KW, Juhl H, Vogelstein B and Velculescu VE: The colorectal microRNome. Proc Natl Acad Sci USA 103: 3687-3692, 2006.
75. Calin GA, Ferracin M, Cimmino A, Dileva G, Shimiz M, Wojcik SE, Iorio MV, Visone R, Sever NI, Fabbri M, Ludiano R, Palumbo T, Pichiorri F, Roldo C, Garzon R, Sevignani C, Rassenti L, Adler H, Volinia S, Liu CG, Kipps TJ, Negrini M and Croce CM: A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Eng J Med 353: 1793-1801, 2005.
76. Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF, Lund E and Dahlberg JE: Accumulation of miR- 155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci USA 102: 3627-3632, 2005.
77. Chang-Zheng C: MicroRNAs as oncogenes and tumor supressors. N Eng J Med 353: 1768-1771, 2005.
78. Schepler T, Reinert JT, Oslenfeld MS, Christensen LL, Silahtaroglu AN, Dyrskjøt L, Wiuf C, Sørensen FJ, Kruhøffer M, Laurberg S, Kauppinen S, Ørntoft T and Andersen CL: Diagnostic and prognostic microRNAs in Stage II colon cancer. Cancer Res 68: 6416-6424, 2008.
79. Barbarotto E, Schmittgen TD and Calin GA: MicroRNAs and cancer: Profile, profile, profile. Int J Cancer 122: 969-977, 2008.
80. Schetter AJ, Leung SY, Sohn JJ, Zanetti KA, Bowman ED, Yanaihara N, Yuen ST, Chan TS, Kwong DLW, Au GKH, Liu CG, Calin GA and Harris CC: MicroRNA expression profile associated with progression and therapeutic outcome in colon adenocarcinoma. J Am Med Assoc 299: 425-436, 2006.
81. Chen X, Ba Y, Ma L, Cai X, Yin Y, Wang K, Guo J, Zhang Y, Chen J, Guo X, Li Q, Li X, Wang W, Zhang Y, Wang I, Jiang X, Xiang Y, Xu C, Zheng P, Zhang J, Li R, Zhang H, Shang X, Ning G, Wang J, Zen K, Zhang J and Zhang CY: Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18: 997-1006, 2008.
82. Gusev Y: Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. Methods 44: 61-72, 2008.
83. Bhattacharyya S, Habermacher R, Martine U, Closs EI and Filipowicz W: Relief of microRNA-mediated translational repression in human cells subjected to stress. Cells 125: 111-124, 2006.
84. Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H and Dahiya R: Small ds RNA induce transcriptional activation in human cells. Proc Natl Acad Sci USA 103: 17337-17342, 2006.
85. Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W and Cui Q: An analysis of human microRNA and disease associations. PLoS ONE 3: e3420, 2008.
86. Rutherford SL: Between genotype and phenotype: protein chaperones and evolvability. Nat Rev Genet 4: 263-274, 2003,
87. Brodersen P and Voinnet O: Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 10: 141-148, 2009.
88. He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C, Lowe SW, Cleary MA and Hannon GJ: A microRNA component of the p53 tumor suppressor network. Nature 447: 1130-1134, 2007.
89. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyiokos C, Mourelatos Z and Hatzigeorgiou A: A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18: 1165-1178, 2004.
90. John BB, Enright AJ, Aravin A, Tuschl T, Sander C and Marks DS: Human microRNA target. PloS Biol 2: e363, 2004.
91. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedale I, Gunsalus KC, Stoffel M and Rajewsky N: Combinational microRNA target predictions. Nature Genet 37: 495-500, 2005.
92. Sethupathy P, Megraw M and Hatzigeorgiou AG: A guide through present computation approaches for identification of mammalian microRNA target. Nature Methods 3: 881-888, 2006.