Oral Oncology
Volume 39, Issue 3 , Pages 259-268 , April 2003

Genomic dissection for characterization of cancerous oral epithelium tissues using transcription profiling

  • Daehee Hwang

      Affiliations

    • Department of Chemical Engineering, Room 56-469, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
  • ,
  • Ilias Alevizos

      Affiliations

    • Department of Chemical Engineering, Room 56-469, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
  • ,
  • William A Schmitt

      Affiliations

    • Department of Chemical Engineering, Room 56-469, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
  • ,
  • Jatin Misra

      Affiliations

    • Department of Chemical Engineering, Room 56-469, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
  • ,
  • Hiroe Ohyama

      Affiliations

    • Laboratory of Molecular Pathology, Department of Oral Medicine and Diagnostic Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA
  • ,
  • Randy Todd

      Affiliations

    • Laboratory of Molecular Pathology, Department of Oral Medicine and Diagnostic Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA
  • ,
  • Mamatha Mahadevappa

      Affiliations

    • Affymetrix, Inc., Santa Clara, CA 95051, USA
  • ,
  • Janet A Warrington

      Affiliations

    • Affymetrix, Inc., Santa Clara, CA 95051, USA
  • ,
  • George Stephanopoulos

      Affiliations

    • Department of Chemical Engineering, Room 56-469, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
  • ,
  • David T Wong

      Affiliations

    • Laboratory of Molecular Pathology, Department of Oral Medicine and Diagnostic Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA
  • ,
  • Gregory Stephanopoulos

      Affiliations

    • Department of Chemical Engineering, Room 56-469, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    • Corresponding Author InformationCorresponding author. Fax: +1-617-253-9695

Received 11 July 2002 ,Accepted 7 August 2002.

References 

  1. Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays. Nature. 2000;405:827–836
  2. Vokes EE, Weichselbaum RR, Lippman SM, Hong WK. Head and neck cancer. N Engl J Med. 1993;328:184–194
  3. Schantz SP. Biologic markers, cellular differentiation, and metastatic head and neck cancer. Eur Arch Otorhinolaryngol. 1993;250:424–428
  4. Alevizos I, Mahadevappa M, Zhang X, Ohyama H, Kohno Y, Posner M, et al.  Oral cancer in vivo gene expression profiling assisted by laser capture microdissection and microarray analysis. Oncogene. 2001;20:6196–6204
  5. Ponder BA. Cancer genetics. Nature. 2001;411:336–341
  6. Evan GI, Vousden KH. Proliferation, cell cycle and apoptosis in cancer. Nature. 2001;411:342–348
  7. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeck M, Mesirov JP, et al.  Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science. 1999;286:531–537
  8. Thomas JG, Olson JM, Tapscott SJ, Zhao LP. An efficient and robust statistical modeling approach to discover diffentially expressed genes using genomic expression profiles. Genome Research. 2001;11:1227–1236
  9. Johnson RA, Wichern DW. Applied multivariate statistical analysis. New Jersey: Prentice Hall; 1992;
  10. Dillon WR, Goldstein M. Multivariate analysis. New York: Wiley; 1984;
  11. Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica. 2002;12:111–139
  12. Blume-Jensen P, Hunter T. Oncogenic kinase signaling. Nature. 2001;411:355–365
  13. Lachenbruch PA, Mickey MR. Estimation of error rates in discriminant analysis. Technometrics. 1968;10:1–11
  14. Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci. 2000;97:10101–10106
  15. Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV. Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci. 2000;97:8409–8414
  16. Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, Barker JL, et al.  Large-scale temporal gene expression mapping of central nervous system development. Proc Natl Acad Sci. 1998;95:334–339
  17. Stephanopoulos G, Hwang D, Schmitt WA, Misra J, Stephanopoulos G. Mapping Physiological States from Microarray Expression Measurements. Bioinformatics 2002;18:1054–63.
  18. Kawamata H, Nakashiro K, Uchida D, Harada K, Yoshida H, Sato M. Possible contribution of active MMP2 to lymph-node metastasis and secreted cathepsin L to bone invasion of newly established human oral- squamous-cancer cell lines. Int J Cancer. 1997;70:120–127
  19. Nozaki S, Endo Y, Kawashiri S, Nagagawa K, Yamamoto E, Yonemura Y, et al.  Immunohistochemical localization of a urokinase-type plasminogen activator system in squamous cell carcinoma of the oral cavity: association with mode of invasion and lymph node metastasis. Oral Oncol. 1998;34:58–62
  20. Shillitoe EJ, May M, Patel V, Lethanakul C, Ensley JF, Strausberg RL, et al.  Genome-wide analysis of oral cancer—early results from the Cancer Genome Anatomy Project. Oral Oncol. 2000;36:8–16
  21. Strojan P, Budihna M, Smid L, Svetic B, Vrhovec I, Kos J, et al.  Prognostic significance of cysteine proteinases cathepsins B and L and their endogenous inhibitors stefins A and B in patients with squamous cell carcinoma of the head and neck. Clin Cancer Res. 2000;6:1052–1062
  22. Murray GI, Shaw D, Weaver RJ, McKay JA, Ewen SW, Melvin WT, et al.  Cytochrome P450 expression in oesophageal cancer. Gut. 1994;35:599–603
  23. Leethanakul C, Patel V, Gillespie J, Shillitoe E, Kellman RM, Ensley JF, et al.  Gene expression profiles in squamous cell carcinomas of the oral cavity: use of laser capture microdissection for the construction and analysis of stage-specific cDNA libraries. Oral Oncol. 2000;36:474–483
  24. Richards BL, Eisma RJ, Spiro JD, Lindquist RL, Kreutzer DL. Coexpression of interleukin-8 receptors in head and neck squamous cell carcinoma. Am J Surg. 1997;174:507–512
  25. Bauer S, Groh V, Wu J, Steinle A, Phillips JH, Lanier LL, et al.  Activation of NK cells and T cells by NKG2D, a receptor for stress-inducible MICA. Science. 1999;285:727–729
  26. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci. 2001;98:5116–5121
  27. Thall PF. Recent advances in clinical trial design and analysis. Boston: Kluwer Academic Publishers; 1995;
  28. Hwang D, Schmitt WA, Stephanopoulos G, Stephanopoulos G. Determination of minimum sample size and discriminatory expression patterns in microarray data. Bioinformatics. 2002;18:1184–1193
  29. Szekeres PG, Muir AI, Spinage LD, Miller JE, Butler SI, Smith A, et al.  Neuromedin U is a potent agonist at the orphan G protein-coupled receptor FM3. J Biol Chem. 2000;275:20247–20250
  30. Scheufler C, Brinker A, Bourenkov G, Pegoraro S, Moroder L, Bartunik H, et al.  Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine. Cell. 2000;101:199–210
  31. Nathan DF, Lindquist S. Mutational analysis of Hsp90 function (interactions with a steroid receptor and a protein kinase). Mol Cell Biol. 1995;15:3917–3925
  32. van der Straten A, Rommel C, Dickson B, Hafen E. The heat shock protein 83 (Hsp83) is required for Raf-mediated signalling in Drosophila. Embo J. 1997;16:1961–1969
  33. Madsen P, Rasmussen HH, Flint T, Gromov P, Kruse TA, Honore B, et al.  Cloning, expression, and chromosome mapping of human galectin-7. J Biol Chem. 1995;270:5823–5829
  34. Carnemolla B, Leprini A, Borsi L, Querze G, Urbini S, Zardi L, et al.  Human tenascin-R. Complete primary structure, pre-mRNA alternative splicing and gene localization on chromosome 1q23-q24. J Biol Chem. 1996;271:8157–8160
  35. Watanabe H, Iwase M, Ohashi M, Nagumo M. Role of interleukin-8 secreted from human oral squamous cell carcinoma cell lines. Oral Oncol. 2002;Oct;38(7):670–679
  36. Vaidya MM, Sawant SS, Borges AM, Ogale SB, Bhisey AN. Cytokeratin expression in precancerous lesions of the human oral cavity. Oral Oncol. 1998;Jul;34(4):261–264

PII: S1368-8375(02)00108-2

doi: 10.1016/S1368-8375(02)00108-2

Oral Oncology
Volume 39, Issue 3 , Pages 259-268 , April 2003