Biomedical Science Letters (대한의생명과학회지)

The Korean Society for Biomedical Laboratory Sciences (대한의생명과학회)
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Microarray Approaches in Clinical Oncology: Potential and Perspectives

  • Kang, Ji Un (Department of Biomedical Laboratory Science, Korea Nazarene University)
  • Received : 2014.07.17
  • Accepted : 2014.09.27
  • Published : 2014.12.31
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Abstract

Cancers are based upon an array of orchestrated genetic changes and the identification of changes causally related to the carcinogenic process. To elucidate the mechanism of cancer carcinogenesis, it is necessary to reconstruct these molecular events at each level. Microarray technologies have been extensively used to evaluate genetic alterations associated with cancer onset and progression in clinical oncology. The clinical impact of the genomic alterations identified by microarray technologies are growing rapidly and array analysis has been evolving into a diagnostic tool to better identify high-risk patients and predict patient outcomes from their genomic profiles. Here, we discuss the state-of-the-art microarray technologies and their applications in clinical oncology, and describe the potential benefits of these analysis in the clinical implications and biological insights of cancer biology.

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References

  1. 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, Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000. 403: 503-511. https://doi.org/10.1038/35000501
  2. Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, Lonning PE, Tibshirani R, Borresen-Dale AL, Pollack JR. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer. 2006. 45: 1033-1040. https://doi.org/10.1002/gcc.20366
  3. Carrasco DR, Tonon G, Huang Y, Zhang Y, Sinha R, Feng B, Stewart JP, Zhan F, Khatry D, Protopopova M, Protopopov A, Sukhdeo K, Hanamura I, Stephens O, Barlogie B, Anderson KC, Chin L, Shaughnessy JD Jr, Brennan C, Depinho RA. Highresolution genomic profiles define distinct clinicopathogenetic subgroups of multiple myeloma patients. Cancer Cell. 2006. 9: 313-325. https://doi.org/10.1016/j.ccr.2006.03.019
  4. Cavallaro S, Paratore S, de Snoo F, Salomone E, Villari L, Buscarino C, Ferrau F, Banna G, Furci M, Strazzanti A, Cunsolo R, Pezzino S, Gangi S, Basile F. Genomic analysis: toward a new approach in breast cancer management. Crit Rev Oncol Hematol. 2012. 81: 207-223. https://doi.org/10.1016/j.critrevonc.2011.03.006
  5. Chin K, DeVries S, Fridlyand J. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006. 10: 529-541. https://doi.org/10.1016/j.ccr.2006.10.009
  6. De Braekeleer E, Douet-Guilbert N, Basinko A, Morel F, Le Bris MJ, Ferec C, De Braekeleer M. Using bacterial artificial chromosomes in leukemia research: the experience at the university cytogenetics laboratory in Brest, France. J Biomed Biotechnol. 2011. doi:10.1155/2011/329471.
  7. de Leon J, Susce MT, Murray-Carmichael E. The AmpliChip CYP450 genotyping test: Integrating a new clinical tool. Mol Diagn Ther. 2006. 10: 135-151. https://doi.org/10.1007/BF03256453
  8. Gorringe KL, Jacobs S, Thompson ER, Sridhar A, Qiu W, Choong DY, Campbell IG. High-resolution single nucleotide polymorphism array analysis of epithelial ovarian cancer reveals numerous microdeletions and amplifications. Clin Cancer Res. 2007. 13: 4731-4739. https://doi.org/10.1158/1078-0432.CCR-07-0502
  9. Jong K, Marchiori E, van der Vaart A, Chin SF, Carvalho B, Tijssen M, Eijk PP, van den Ijssel P, Grabsch H, Quirke P, Oudejans JJ, Meijer GA, Caldas C, Ylstra B. Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene. 2007. 26: 1499-1506. https://doi.org/10.1038/sj.onc.1209919
  10. Kallioniemi A. CGH microarrays and cancer. Curr Opin Biotechnol. 2008. 19: 36-40. https://doi.org/10.1016/j.copbio.2007.11.004
  11. Kang JU, Koo SH, Kwon KC, Park JW, Kim JM. Identification of novel candidate target genes, including EPHB3, MASP1 and SST at 3q26.2-q29 in squamous cell carcinoma of the lung. BMC Cancer. 2009. 9: 237. https://doi.org/10.1186/1471-2407-9-237
  12. Kang JU, Koo SH, Jeong TE, Kwon KC, Park JW, Jeon CH. Multitarget fluorescence in situ hybridization and melanoma antigen genes analysis in primary bladder carcinoma. Cancer Genet Cytogenet. 2006. 164: 32-38. https://doi.org/10.1016/j.cancergencyto.2005.06.006
  13. Lockwood WW, Chari R, Chi B, Lam WL. Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet. 2006. 14: 139-148. https://doi.org/10.1038/sj.ejhg.5201531
  14. Maciejewski JP, Mufti GJ. Whole genome scanning as a cytogenetic tool in hematologic malignancies. Blood. 2008. 112: 965-974. https://doi.org/10.1182/blood-2008-02-130435
  15. Martinez-Climent JA, Alizadeh A.A, Segraves R, Blesa D, Rubio-Moscardo F, Albertson DG, Garcia-Conde J, Dyer MJ, Levy R, Pinkel D, Lossos IS. Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations. Blood. 2003. 101: 3109-3117. https://doi.org/10.1182/blood-2002-07-2119
  16. Midorikawa Y, Tang W, Sugiyama Y. High-resolution mapping of copy number aberrations and identification of target genes in hepatocellular carcinoma. Biosci Trends. 2007. 1: 26-32.
  17. Nakaya K, Yamagata HD, Arita N, Nakashiro KI, Nose M, Miki T, Hamakawa H. Identification of homozygous deletions of tumor suppressor gene FAT in oral cancer using CGH-array. Oncogene. 2007. 26: 5300-5308. https://doi.org/10.1038/sj.onc.1210330
  18. Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, Febbo PG, Chinnaiyan AM, Pienta KJ, Carroll PR, Rubin MA, Collins C, van Dekken H. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet. 2004. 13: 1303-1313. https://doi.org/10.1093/hmg/ddh155
  19. 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. https://doi.org/10.1038/35021093
  20. Pfeifer D, Pantic M, Skatulla I, Rawluk J, Kreutz C, Martens UM, Fisch P, Timmer J, Veelken H. Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood. 2007. 109: 1202-1210.
  21. Ramaswamy S, Ross KN, Lander ES, Golub TR. A molecular signature of metastasis in primary solid tumors. Nat Genet. 2003. 33: 49-54.
  22. Ray ME, Yang ZQ, Albertson D, Kleer CG, Washburn JG, Macoska JA, Ethier SP. Genomic and expression analysis of the 8p11-12 amplicon in human breast cancer cell lines. Cancer Res. 2004. 64: 40-47. https://doi.org/10.1158/0008-5472.CAN-03-1022
  23. Rubio-Moscardo F, Climent J, Siebert R, Piris MA, Martin-Subero JI, Nielander I, Garcia-Conde J, Dyer MJ, Terol MJ, Pinkel D, Martinez-Climent JA. Mantle-cell lymphoma genotypes identified with CGH to BAC microarrays define a leukemic subgroup of disease and predict patient outcome. Blood. 2005. 105: 4445-4454. https://doi.org/10.1182/blood-2004-10-3907
  24. Ruiz C, Tolnay M, Bubendorf L. Application of personalized medicine to solid tumors: opportunities and challenges. Swiss Med Wkly. 2012. 142: 150.
  25. Sandberg AA, Meloni-Ehrig AM. Cytogenetics and genetics of human cancer: methods and accomplishments. Cancer Genet Cytogenet . 2010. 203: 102-126. https://doi.org/10.1016/j.cancergencyto.2010.10.004
  26. Sato-Otsubo A, Sanada M, Ogawa S. Single-nucleotide polymorphism array karyotyping in clinical practice: where, when, and how? Semin Oncol. 2012. 39: 13-25. https://doi.org/10.1053/j.seminoncol.2011.11.010
  27. Simons A, Sikkema-Raddatz B, de Leeuw N, Konrad NC, Hastings RJ, Schoumans J. Genome-wide arrays in routine diagnostics of hematological malignancies. Hum Mutat. 2012. 33: 941-948. https://doi.org/10.1002/humu.22057
  28. Smeets SJ, Braakhuis BJM, Abbas S. Genome-wide DNA copy number alterations in head and neck squamous cell carcinomas with or without oncogene-expressing human papillomavirus. Oncogene. 2006. 25: 2558-2564. https://doi.org/10.1038/sj.onc.1209275
  29. Tagawa H, Karnan S, Suzuki R, Matsuo K, Zhang X, Ota A, Morishima Y, Nakamura S, Seto M. Genome-wide array-based CGH for mantle cell lymphoma: identification of homozygous deletions of the proapoptotic gene BIM. Oncogene. 2005. 24: 1348-1358. https://doi.org/10.1038/sj.onc.1208300
  30. van Beers EH, Nederlof PM. Array-CGH and breast cancer. Breast Cancer Res. 2006. 8: 210. https://doi.org/10.1186/bcr1510
  31. Varella-Garcia M. Molecular cytogenetics in solid tumors: laboratorial tool for diagnosis, prognosis, and therapy. Oncologist. 2003. 8: 45-58. https://doi.org/10.1634/theoncologist.8-1-45
  32. Vincent-Salomon A, Lucchesi C, Gruel N, Raynal V, Pierron G, Goudefroye R, Reyal F, Radvanyi F, Salmon R, Thiery JP, Sastre-Garau X, Sigal-Zafrani B, Fourquet A, Delattre O. Integrated genomic and transcriptomic analysis of ductal carcinoma in situ of the breast. Clin Cancer Res. 2008. 14: 1956-1965. https://doi.org/10.1158/1078-0432.CCR-07-1465
  33. Waddell N, Arnold J, Cocciardi S, da Silva L, Marsh A, Riley J, Johnstone CN, Orloff M, Assie G, Eng C, Reid L, Keith P, Yan M, Fox S, Devilee P, Godwin AK, Hogervorst FB, Couch F; kConFab Investigators, Grimmond S, Flanagan JM, Khanna K, Simpson PT, Lakhani SR, Chenevix-Trench G. Subtypes of familial breast tumours revealed by expression and copy number profiling. Breast Cancer Res Treat. 2010. 123: 661-677. https://doi.org/10.1007/s10549-009-0653-1
  34. Weiss MM, Kuipers EJ, Postma C. Genomic profiling of gastric cancer predicts lymph node status and survival. Oncogene. 2003. 22: 1872-1879. https://doi.org/10.1038/sj.onc.1206350
  35. Weiss MM, Kuipers EJ, Postma C, Snijders AM, Pinkel D, Meuwissen SG, Albertson D, Meijer GA. Genomic alterations in primary gastric adenocarcinomas correlate with clinicopathological characteristics and survival. Cell Oncol. 2004. 26: 307-317.
  36. Wessels LF, van Welsem T, Hart AA, van't Veer LJ, Reinders MJ, Nederlof PM. Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors. Cancer Res. 2002. 62: 7110-7117.
  37. Wilting S, Snijders P, Meijer G. Increased gene copy numbers at chromosome 20q are frequent in both squamous cell carcinomas and adenocarcinomas of the cervix. J Pathol. 2006. 209: 220-230. https://doi.org/10.1002/path.1966