Stability and heterogeneity of expression profiles in lung cancer specimens harvested following surgical resection

Neoplasia

Volumn 6, Issue 6, 2004, Pages 761-767

  Blackhall, Fiona H ^a   Pintilie, Melania ^a   Wigle, Dennis A ^a   Jurisica, Igor ^a   Liu, Ni ^a   Radulovich, Nikolina ^a   Johnston, Michael R ^a   Keshavjee, Shaf ^a   Tsao, Ming Sound ^a,b  

^a TORONTO GENERAL HOSPITAL   (Canada)

^b PRINCESS MARGARET HOSPITAL   (Canada)

Author keywords

Lung cancer; Microarray; Real time RT PCR; Surgical specimen; Tumor heterogeneity

Indexed keywords

RNA;

ARTICLE; DNA MICROARRAY; FREEZING; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; HYPOXIA; LUNG CANCER; LUNG RESECTION; NUCLEOTIDE SEQUENCE; PATHOLOGY; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; SAMPLING; STRESS;

EID: 11144263678     PISSN: 15228002     EISSN: None     Source Type: Journal    
DOI: 10.1593/neo.04301     Document Type: Article

References (24)

1. Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, and Hanash S (2002). Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 8, 816-824.
2. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, and Meyerson M (2001). Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 98, 13790-13795.
3. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, and Petersen I (2001). Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA 98, 13784-13789.
4. Wigle DA, Jurisica I, Radulovich N, Pintilie M, Rossant J, Liu N, Lu C, Woodgett J, Seiden I, Johnston M, Keshavjee S, Darling G, Winton T, Breitkreutz BJ, Jorgenson P, Tyers M, Shepherd FA, and Tsao MS (2002). Molecular profiling of non-small cell lung cancer and correlation with disease-free survival. Cancer Res 62, 3005-3008.
5. Mizuno T, Nagamura H, Iwamoto KS, Ito T, Fukuhara T, Tokunaga M, Tokuoka S, Mabuchi K, and Seyama T (1998). RNA from decades-old archival tissue blocks for retrospective studies. Diagn Mol Pathol 7, 202-208.
6. Chomczynski P and Sacchi N (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
7. Tsao MS, Zhu H, and Viallet J (1996). Autocrine growth loop of the epidermal growth factor receptor in normal and immortalized human bronchial epithelial cells. Exp Cell Res 223, 268-273.
8. Wang KK, Liu N, Radulovich N, Wigle DA, Johnston MR, Shepherd FA, Minden MD, and Tsao MS (2002). Novel candidate tumor marker genes for lung adenocarcinoma. Oncogens 21, 7598-7604.
9. Tusher VG, Tibshirani R, and Chu G (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98, 5116-5121.
10. Sultan M, Wigle DA, Cumbaa CA, Maziarz M, Glasgow J, Tsao MS, and Jurisica I (2002). Binary tree-structured vector quantization approach to clustering and visualizing microarray data. Bioinformatics 18, S111-S119.
11. D'Orazio D, Stumm M, and Sieber C (2002). Accurate gene expression measurement in formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 160, 383-384.
12. Dash A, Maine IP, Varambally S, Shen R, Chinnaiyan AM, and Rubin MA (2002). Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens. Am J Pathol 161, 1743-1748.
13. Koken MH, Reynolds P, Jaspers-Dekker I, Prakash L, Prakash S, Bootsma D, and Hoeijmakers JH (1991). Structural and functional conservation of two human homologs of the yeast DNA repair gene RAD6. Proc Natl Acad Sci USA 88, 8865-8869.
14. Premkumar DR, Adhikary G, Overholt JL, Simonson MS, Cherniack NS, and Prabhakar NR (2000). Intracellular pathways linking hypoxia to activation of c-fos and AP-1. Adv Exp Med Biol 475, 101-109.
15. Potter C and Harris AL (2004). Hypoxia inducible carbonic IX anhydrase, marker of tumour hypoxia, survival pathway and therapy target. Cell Cycle 3, 164-167.
16. Hu MC, Qiu WR, and Wang YP (1997). JNK1, JNK2 and JNK3 are p53 N-terminal serine 34 kinases. Oncogene 15, 2277-2287.
17. Hara T, Mies G, Hata R, and Hossmann KA (2001). Gene expressions after thrombolytic treatment of middle cerebral artery clot embolism in mice. Stroke 32, 1912-1919.
18. Jones JM, Datta P, Srinivasula SM, Ji W, Gupta S, Zhang Z, Davies E, Hajnoczky G, Saunders TL, VanKeuren ML, Fernandes-Alnemri T, Meisler MH, and Alnemri ES (2003). Loss of Omi mitochondrial protease activity causes the neuromuscular disorder of mnd2 mutant mice. Nature 425, 721-727.
19. Vasselli JR, Shih JH, Iyengar SR, Maranchie J, Riss J, Worrell R, Torres-Cabala C, Tabios R, Mariotti A, Stearman R, Merino M, Walther MM, Simon R, Klausner RD, and Linehan WM (2003). Predicting survival in patients with metastatic kidney cancer by gene-expression profiling in the primary tumor. Proc Natl Acad Sci USA 100, 6958-6963.
20. Loncaster JA, Harris AL, Davidson SE, Logue JP, Hunter RD, Wykoff CC, Pastorek J, Ratcliffe PJ, Stratford IJ, and West CM (2001). Carbonic anhydrase (CA IX) expression, a potential new intrinsic marker of hypoxia: correlations with tumor oxygen measurements and prognosis in locally advanced carcinoma of the cervix. Cancer Res 61, 6394-6399.
21. Hedley D, Pintilie M, Woo J, Morrison A, Birle D, Fyles A, Milosevic M, and Hill R (2003). Carbonic anhydrase IX expression, hypoxia, and prognosis in patients with uterine cervical carcinomas. Clin Cancer Res 9, 5666-5674.
22. Sugiyama Y, Sugiyama K, Hirai Y, Akiyama F, and Hasumi K (2002). Microdissection is essential for gene expression profiling of clinically resected cancer tissues. Am J Clin Pathol 117, 109-116.
23. Kamme F, Salunga R, Yu J, Tran DT, Zhu J, Luo L, Bittner A, Quo HQ, Miller N, Wan J, and Erlander M (2003). Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity. J Neurosci 23, 3607-3615.
24. Giatromanolaki A, Koukourakis MI, Sivridis E, Pastorek J, Wykoff CC, Gatter KC, and Harris AL (2001). Expression of hypoxia-inducible carbonic anhydrase-9 relates to angiogenic pathways and independently to poor outcome in non-small cell lung cancer. Cancer Res 1, 7992-7998.