Taiwanese Journal of Obstetrics and Gynecology
Volume 46, Issue 4 , Pages 363-373 , December 2007

Overview of Microarray Analysis of Gene Expression and its Applications to Cervical Cancer Investigation

  • Angel Chao

      Affiliations

    • Department of Obstetrics and Gynecology, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Chang Gung University, Tao-Yuan, Taiwan
    • Corresponding Author InformationCorrespondence to: Dr Angel Chao, Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Chang Gung University, Tao-Yuan 333, Taiwan
    • ,
  • Tzu-Hao Wang

      Affiliations

    • Department of Obstetrics and Gynecology, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Chang Gung University, Tao-Yuan, Taiwan
    • Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
    • ,
  • Chyong-Huey Lai

      Affiliations

    • Department of Obstetrics and Gynecology, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Chang Gung University, Tao-Yuan, Taiwan

,Accepted 19 September 2007.

References 

  1. Brazma A , Hingamp P , Quackenbush J , et al.   Minimum information about a microarray experiment (MIAME)-toward standards for microarray data . Nat Genet . 2001;29:365–371
  2. Cancer Registration Annual Report in Taiwan . Taiwan: Department of Health, Executive Yuan; 2002;
  3. Munoz N , Bosch FX , de Sanjose S , et al.   Epidemiologic classification of human papillomavirus types associated with cervical cancer . N Engl J Med . 2003;348:518–527
  4. Bosch FX , Manos MM , Munoz N , et al.   Prevalence of human papillomavirus in cervical cancer: a worldwide perspective. International Biological Study on Cervical Cancer (IBSCC) Study Group . J Natl Cancer Inst . 1995;87:796–802
  5. zur Hausen H . Papillomaviruses causing cancer: evasion from host-cell control in early events in carcinogenesis . J Natl Cancer Inst . 2000;92:690–698
  6. Chao A , Wang TH , Lee YS , et al.   Molecular characterization of adenocarcinoma and squamous carcinoma of the uterine cervix using microarray analysis of gene expression . Int J Cancer . 2006;119:91–98
  7. Lai CH , Huang HJ , Hsueh S , et al.   Human papillomavirus genotype in cervical cancer: a population-based study . Int J Cancer . 2007;120:1999–2006
  8. Hacker NF . Cervical Cancer . In:  Berek JS ,  Hacker NF editor. Practical Gynecologic Oncology . 3rd edition. Philadelphia: Lippincott Williams & Wilkins; 2000;p. 345–405
  9. Green JA, Kirwan JM, Tierney JF, Symonds P, Fresco L, Collingwood M, et al. Survival and recurrence after concomitant chemotherapy and radiotherapy for cancer of the uterine cervix: a systematic review and meta-analysis . Lancet . 2001;358:781–786
  10. Snyder AR , Morgan WF . Gene expression profiling after irradiation: clues to understanding acute and persistent responses? . Cancer Metastasis Rev . 2004;23:259–268
  11. Fodor SP , Read JL , Pirrung MC , Stryer L , Lu AT , Solas D . Light-directed, spatially addressable parallel chemical synthesis . Science . 1991;251:767–773
  12. Fodor SP , Rava RP , Huang XC , Pease AC , Holmes CP , Adams CL . Multiplexed biochemical assays with biological chips . Nature . 1993;364:555–556
  13. Schena M , Shalon D , Davis RW , Brown PO . Quantitative monitoring of gene expression patterns with a complementary DNA microarray . Science . 1995;270:467–470
  14. Wang TH , Chao A . Microarray analysis of gene expression of cancer to guide the use of chemotherapeutics . Taiwan J Obstet Gynecol . 2007;46:222–229
  15. Stekel D . Microarray Bioinformatics . Cambridge: Cambridge University Press; 2003;
  16. Duggan DJ , Bittner M , Chen Y , Meltzer P , Trent JM . Expression profiling using cDNA microarrays . Nat Genet . 1999;21:10–14
  17. Wang TH , Lee YS , Chen ES , et al.   Establishment of cDNA microarray analysis at the Genomic Medicine Research Core Laboratory (GMRCL) of Chang Gung Memorial Hospital . Chang Gung Med J . 2004;27:243–260
  18. Yang YH , Speed T . Design issues for cDNA microarray experiments . Nat Rev Genet . 2002;3:579–588
  19. Witmer JA , Samuels ML . Statistics for the Life Sciences . 3rd edition. New Jersey: Prentice Hall; 2002;
  20. Chao A, Wang TH, Lee YS, et al. Analysis of functional groups of differentially expressed genes in the peripheral blood of patients with cervical cancer undergoing concurrent chemoradiation. Radiat Res (In press).
  21. Adams R , Bischof L . Seeded region growing . IEEE Trans Pattern Anal Mach Intell . 1994;16:641–647
  22. Kamberova G , Shah S . DNA Array Image Analysis: Nuts and Bolts . Eagleville: DNA Press; 2002;
  23. Quackenbush J . Microarray data normalization and transformation . Nat Genet . 2002;32:496–501
  24. Kooperberg C , Fazzio TG , Delrow JJ , Tsukiyama T . Improved background correction for spotted DNA micro-arrays . J Comput Biol . 2002;9:55–66
  25. Huber W , von Heydebreck A , Sultmann H , Poustka A , Vingron M . Variance stabilization applied to microarray data calibration and to the quantification of differential expression . Bioinformatics . 2002;18(Suppl 1):S96–S104
  26. Everitt BS . Cluster Analysis . 3rd edition. London: Edward Arnold; 1993;
  27. Chatfield C , Collins AJ . Introduction to Multivariate Analysis . London: Chapman & Hall; 1980;
  28. Dysvik B , Jonassen I . J-Express: exploring gene expression data using Java . Bioinformatics . 2001;17:369–370
  29. Raychaudhuri S , Stuart JM , Altman RB . Principal components analysis to summarize microarray experiments: application to sporulation time series . Pac Symp Biocomput . 2000;455–466
  30. Xia X , Xie Z . AMADA: analysis of microarray data . Bioinformatics . 2001;17:569–570
  31. Kohonen T . Self Organized Maps . Berlin: Springer; 2000;
  32. Microarray standards at last . Nature . 2002;419:323
  33. Rainen L , Oelmueller U , Jurgensen S , et al.   Stabilization of mRNA expression in whole blood samples . Clin Chem . 2002;48:1883–1890
  34. Thach DC, Lin B, Walter E, Kruzelock R, Rowley RK, Tibbetts C, et al. Assessment of two methods for handling blood in collection tubes with RNA stabilizing agent for surveillance of gene expression profiles with high density microarrays . J Immunol Methods . 2003;283:269–279
  35. Chai V , Vassilakos A , Lee Y , Wright JA , Young AH . Optimization of the PAXgene blood RNA extraction system for gene expression analysis of clinical samples . J Clin Lab Anal . 2005;19:182–188
  36. Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, et al. Individuality and variation in gene expression patterns in human blood . Proc Natl Acad Sci USA . 2003;100:1896–1901
  37. Lee YS , Chen CH , Chao A , et al.   Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome coronavirus (SARS-CoV) . BMC Genomics . 2005;6:132
  38. Tsuang MT , Nossova N , Yager T , et al.   Assessing the validity of blood-based gene expression profiles for the classification of schizophrenia and bipolar disorder: a preliminary report . Am J Med Genet B Neuropsychiatr Genet . 2005;133:1–5
  39. Hamaoui K , Butt A , Powrie J , Swaminathan R . Concentration of circulating rhodopsin mRNA in diabetic retinopathy . Clin Chem . 2004;50:2152–2155
  40. Li D , Butt A , Clarke S , Swaminathana R . Real-time quantitative PCR measurement of thyroglobulin mRNA in peripheral blood of thyroid cancer patients and healthy subjects . Ann N Y Acad Sci . 2004;1022:147–151
  41. Muller MC, Merx K, Weisser A, Kreil S, Lahaye T, Hehlmann R, et al. Improvement of molecular monitoring of residual disease in leukemias by bedside RNA stabilization . Leukemia . 2002;16:2395–2399
  42. Livak KJ , Schmittgen TD . Analysis of relative gene expression data using real-time quantitative PCR and the 2 method . Methods . 2001;25:402–408
  43. Fujimoto T , Nishikawa A , Iwasaki M , Akutagawa N , Teramoto M , Kudo R . Gene expression profiling in two morphologically different uterine cervical carcinoma cell lines derived from a single donor using a human cancer cDNA array . Gynecol Oncol . 2004;93:446–453
  44. Kitahara O , Katagiri T , Tsunoda T , Harima Y , Nakamura Y . Classification of sensitivity or resistance of cervical cancers to ionizing radiation according to expression profiles of 62 genes selected by cDNA microarray analysis . Neoplasia . 2002;4:295–303
  45. Wong YF , Selvanayagam ZE , Wei N , et al.   Expression genomics of cervical cancer: molecular classification and prediction of radiotherapy response by DNA microarray . Clin Cancer Res . 2003;9:5486–5492
  46. Harima Y , Togashi A , Horikoshi K , et al.   Prediction of outcome of advanced cervical cancer to thermoradiotherapy according to expression profiles of 35 genes selected by cDNA microarray analysis . Int J Radiat Oncol Biol Phys . 2004;60:237–248
  47. Chung YM , Kim BG , Park CS , et al.   Increased expression of ICAM-3 is associated with radiation resistance in cervical cancer . Int J Cancer . 2005;117:194–201
  48. Wong YF , Sahota DS , Cheung TH , et al.   Gene expression pattern associated with radiotherapy sensitivity in cervical cancer . Cancer J . 2006;12:189–193
  49. Achary MP , Jaggernauth W , Gross E , Alfieri A , Klinger HP , Vikram B . Cell lines from the same cervical carcinoma but with different radiosensitivities exhibit different cDNA microarray patterns of gene expression . Cytogenet Cell Genet . 2000;91:39–43
  50. Chaudhry MA , Chodosh LA , McKenna WG , Muschel RJ . Gene expression profile of human cells irradiated in G1 and G2 phases of cell cycle . Cancer Lett . 2003;195:221–233
  51. Chen X, Shen B, Xia L, Khaletzkiy A, Chu D, Wong JY, et al. Activation of nuclear factor kappaB in radioresistance of TP53-inactive human keratinocytes . Cancer Res . 2002;62:1213–1221
  52. Chopra V , Dinh TV , Hannigan EV . Circulating serum levels of cytokines and angiogenic factors in patients with cervical cancer . Cancer Invest . 1998;16:152–159
  53. Comerci JT, Runowicz CD, Flanders KC, De Victoria C, Fields AL, Kadish AS, et al. Altered expression of transforming growth factor-beta 1 in cervical neoplasia as an early biomarker in carcinogenesis of the uterine cervix . Cancer . 1996;77:1107–1114
  54. Kloth JN , Fleuren GJ , Oosting J , et al.   Substantial changes in gene expression of Wnt, MAPK and TNFalpha pathways induced by TGF-beta1 in cervical cancer cell lines . Carcinogenesis . 2005;26:1493–1502
  55. Hudelist G , Czerwenka K , Singer C , Pischinger K , Kubista E , Manavi M . cDNA array analysis of cytobrush-collected normal and malignant cervical epithelial cells: a feasibility study . Cancer Genet Cytogenet . 2005;158:35–42
  56. Cheng Q , Lau WM , Tay SK , Chew SH , Ho TH , Hui KM . Identification and characterization of genes involved in the carcinogenesis of human squamous cell cervical carcinoma . Int J Cancer . 2002;98:419–426
  57. Shim C , Zhang W , Rhee CH , Lee JH . Profiling of differentially expressed genes in human primary cervical cancer by complementary DNA expression array . Clin Cancer Res . 1998;4:3045–3050
  58. Chen Y , Miller C , Mosher R , et al.   Identification of cervical cancer markers by cDNA and tissue microarrays . Cancer Res . 2003;63:1927–1935
  59. Pappa KI , Anagnou NP . Emerging issues of the expression profiling technologies for the study of gynecologic cancer . Am J Obstet Gynecol . 2005;193:908–918
  60. Kendrick JE , Conner MG , Huh WK . Gene expression profiling of women with varying degrees of cervical intraepithe-lial neoplasia . J Low Genit Tract Dis . 2007;11:25–28
  61. Contag SA , Gostout BS , Clayton AC , Dixon MH , McGovern RM , Calhoun ES . Comparison of gene expression in squamous cell carcinoma and adenocarcinoma of the uterine cervix . Gynecol Oncol . 2004;95:610–617
  62. Wong YF , Cheung TH , Tsao GS , et al.   Genome-wide gene expression profiling of cervical cancer in Hong Kong women by oligonucleotide microarray . Int J Cancer . 2006;118:2461–2469
  63. Harima Y , Sawada S , Miyazaki Y , et al.   Expression of Ku80 in cervical cancer correlates with response to radiotherapy and survival . Am J Clin Oncol . 2003;26:e80–e85
  64. Thomas G . The effect of hemoglobin level on radiotherapy outcomes: the Canadian experience . Semin Oncol . 2001;28:60–65
  65. Grogan M , Thomas GM , Melamed I , et al.   The importance of hemoglobin levels during radiotherapy for carcinoma of the cervix . Cancer . 1999;86:1528–1536
  66. Tewari D, Monk BJ, Al-Ghazi MS, Parker R, Heck JD, Burger RA, et al. Gene expression profiling of in vitro radiation resistance in cervical carcinoma: a feasibility study . Gynecol Oncol . 2005;99:84–91
  67. Kruse JJ , te Poele JA , Russell NS , Boersma LJ , Stewart FA . Microarray analysis to identify molecular mechanisms of radiation-induced microvascular damage in normal tissues . Int J Radiat Oncol Biol Phys . 2004;58:420–426
  68. Narayan G , Bourdon V , Chaganti S , et al.   Gene dosage alterations revealed by cDNA microarray analysis in cervical cancer: identification of candidate amplified and overexpressed genes . Genes Chromosomes Cancer . 2007;46:373–384

PII: S1028-4559(08)60005-4

doi: 10.1016/S1028-4559(08)60005-4

Taiwanese Journal of Obstetrics and Gynecology
Volume 46, Issue 4 , Pages 363-373 , December 2007

Article Tools