Integrative genomic and gene expression analysis of chromosome 7 identified novel oncogene loci in non-small cell lung cancer

Genome

Volumn 51, Issue 12, 2008, Pages 1032-1039

  Campbell, Jennifer M ^a   Lockwood, William W ^a   Buys, Timon P H ^a   Chari, Raj ^a   Coe, Bradley P ^a   Lam, Stephen ^a   Lam, Wan L ^a  

^a BRITISH COLUMBIA CANCER RESEARCH CENTRE   (Canada)

Author keywords

Array CGH; Chromosome 7; Gene amplification; Gene expression; NSCLC

Indexed keywords

ARTICLE; CHROMOSOME 7; DNA MICROARRAY; GENE AMPLIFICATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HUMAN; LUNG NON SMALL CELL CANCER; LUNG TUMOR; METHODOLOGY; ONCOGENE; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; TUMOR CELL LINE; VALIDATION STUDY;

CARCINOMA, NON-SMALL-CELL LUNG; CELL LINE, TUMOR; CHROMOSOMES, HUMAN, PAIR 7; GENE AMPLIFICATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; LUNG NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ONCOGENES; QUANTITATIVE TRAIT LOCI;

EID: 57149099426     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G08-086     Document Type: Article

References (48)

1. Albertson, D.G. 2006. Gene amplification in cancer. Trends Genet. 22: 447-455. doi:10.1016/j.tig.2006.06.007. PMID:16787682.
2. Albright, S.R., and Tjian, R. 2000. TAFs revisited: more data reveal new twists and confirm old ideas. Gene, 242: 1-13. doi:10.1016/S0378-1119(99) 00495-3. PMID:10721692.
3. Arslantas, A., Artan, S., Oner, U., Muslumanoglu, M.H., Ozdemir, M., Durmaz, R., et al. 2007. Genomic alterations in low-grade, anaplastic astrocytomas and glioblastomas. Pathol. Oncol. Res. 13: 39-46. PMID:17387387.
4. Balsara, B.R., and Testa, J.R. 2002. Chromosomal imbalances in human lung cancer. Oncogene, 21: 6877-6883. doi:10.1038/sj.onc.1205836. PMID:12362270.
5. Bell, B., and Tora, L. 1999. Regulation of gene expression by multiple forms of TFIID and other novel TAFII-containing complexes. Exp. Cell Res. 246: 11-19. doi:10.1006/excr.1998.4294. PMID:9882510.
6. Bild, A.H., Yao, G., Chang, J.T., Wang, Q., Potti, A., Chasse, D., et al. 2006. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature, 439: 353-357. doi:10.1038/nature04296. PMID:16273092.
7. Chari, R., Lockwood, W.W., Coe, B.P., Chu, A., Macey, D., Thomson, A., et al. 2006. SIGMA: a system for integrative genomic microarray analysis of cancer genomes. BMC Genomics, 7: 324. doi:10.1186/1471-2164-7-324. PMID:17192189.
8. Chi, B., deLeeuw, R.J., Coe, B.P., MacAulay, C., and Lam, W.L. 2004. SeeGH - a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformatics, 5: 13. doi:10.1186/1471-2105-5-13. PMID:15040819.
9. Chi, B., deLeeuw, R.J., Coe, B.P., Ng, R.T., MacAulay, C., and Lam, W.L. 2008. MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data. BMC Bioinformatics, 9: 243. doi:10.1186/1471-2105-9-243. PMID:18492270.
10. Ching, Y.P., Zhou, H.J., Yuan, J.G., Qiang, B.Q., Kung Hf, H.F., and Jin, D.Y. 2002. Identification and characterization of FTSJ2, a novel human nucleolar protein homologous to bacterial ribosomal RNA methyltransferase. Genomics, 79: 2-6. doi:10.1006/geno.2001.6670. PMID:11827451.
11. Choi, J.S., Zheng, L.T., Ha, E., Lim, Y.J., Kim, Y.H., Wang, Y.P., et al. 2006. Comparative genomic hybridization array analysis and real-time PCR reveals genomic copy number alteration for lung adenocarcinomas. Lung, 184: 355-362. doi:10.1007/s00408-006-0009-0. PMID:17086460.
12. Choi, Y.W., Choi, J.S., Zheng, L.T., Lim, Y.J., Yoon, H.K., Kim, Y.H., et al. 2007. Comparative genomic hybridization array analysis and real time PCR reveals genomic alterations in squamous cell carcinomas of the lung. Lung Cancer, 55: 43-51. doi:10.1016/j.lungcan.2006.09.018. PMID:17109992.
13. Chong, I.W., Chang, M.Y., Chang, H.C., Yu, Y.P., Sheu, C.C., Tsai, J.R., et al. 2006. Great potential of a panel of multiple hMTH1, SPD, ITGA11 and COL11A1 markers for diagnosis of patients with non-small cell lung cancer. Oncol. Rep. 16: 981-988. PMID:17016581.
14. Coe, B.P., Lockwood, W.W., Girard, L., Chari, R., Macaulay, C., Lam, S., et al. 2006. Differential disruption of cell cycle pathways in small cell and non-small cell lung cancer. Br. J. Cancer, 94: 1927-1935. doi:10.1038/sj.bjc.6603167. PMID:16705311.
15. Engelman, J.A., Zejnullahu, K., Mitsudomi, T., Song, Y., Hyland, C., Park, J.O., et al. 2007. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science, 316: 1039-1043. doi:10.1126/science.1141478. PMID:17463250.
16. Fanciulli, M., Bruno, T., Di Padova, M., De Angelis, R., Iezzi, S., Iacobini, C., et al. 2000. Identification of a novel partner of RNA polymerase II subunit 11, Che-1, which interacts with and affects the growth suppression function of Rb. FASEB J. 14: 904-912. PMID:10783144.
17. Frye, M., and Watt, F.M. 2006. The RNA methyltransferase Misu (NSun2) mediates Myc-induced proliferation and is upregulated in tumors. Curr. Biol. 16: 971-981. doi:10.1016/j.cub.2006.04.027. PMID:16713953.
18. Garcia, J.L., Hernandez, J.M., Gutierrez, N.C., Flores, T., Gonzalez, D., Calasanz, M.J., et al. 2003. Abnormalities on 1q and 7q are associated with poor outcome in sporadic Burkitt's lymphoma. A cytogenetic and comparative genomic hybridization study. Leukemia, 17: 2016-2024. doi:10.1038/sj.leu.2403080. PMID:14513052.
19. Garnis, C., Lockwood, W.W., Vucic, E., Ge, Y., Girard, L., Minna, J.D., et al. 2006. High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. Int. J. Cancer, 118: 1556-1564. doi:10.1002/ijc.21491. PMID:16187286.
20. Green, M.R. 2000. TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes. Trends Biochem. Sci. 25: 59-63. doi:10.1016/S0968-0004(99)01527-3. PMID:10664584.
21. Hibi, K., Liu, Q., Beaudry, G.A., Madden, S.L., Westra, W.H., Wehage, S.L., et al. 1998. Serial analysis of gene expression in non-small cell lung cancer. Cancer Res. 58: 5690-5694. PMID:9865724.
22. Ishkanian, A.S., Malloff, C.A., Watson, S.K., DeLeeuw, R.J., Chi, B., Coe, B.P., et al. 2004. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet. 36: 299-303. doi:10.1038/ng1307. PMID:14981516.
23. Jong, K., Marchiori, E., Meijer, G., Vaart, A.V., and Ylstra, B. 2004. Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics, 20: 3636-3637. doi:10.1093/ bioinformatics/bth355. PMID:15201182.
24. Kennedy, C.H., Cueto, R., Belinsky, S.A., Lechner, J.F., and Pryor, W.A. 1998. Overexpression of hMTH1 mRNA: a molecular marker of oxidative stress in lung cancer cells. FEBS Lett. 429: 17-20. doi:10.1016/S0014-5793(98) 00505-5. PMID:9657375.
25. Khojasteh, M., Lam, W.L., Ward, R.K., and MacAulay, C. 2005. A stepwise framework for the normalization of array CGH data. BMC Bioinformatics, 6: 274. doi:10.1186/1471-2105-6-274. PMID:16297240.
26. Lockwood, W.W., Coe, B.P., Williams, A.C., MacAulay, C., and Lam, W.L. 2007. Whole genome tiling path array CGH analysis of segmental copy number alterations in cervical cancer cell lines. Int. J. Cancer, 120: 436-443. doi:10.1002/ijc.22335. PMID:17096350.
27. Lockwood, W.W., Chari, R., Coe, B.P., Girard, L., Macaulay, C., Lam, S., et al. 2008. DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers. Oncogene, 27: 4615-4624. doi:10.1038/onc.2008. 98. PMID:18391978.
28. Lu, H., and Levine, A.J. 1995. Human TAFII31 protein is a transcriptional coactivator of the p53 protein. Proc. Natl. Acad. Sci. U.S.A. 92: 5154-5158. doi:10.1073/pnas.92.11.5154. PMID:7761466.
29. Martinez-Climent, J.A., Alizadeh, A.A., Segraves, R., Blesa, D., Rubio-Moscardo, F., Albertson, D.G., et al. 2003. Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations. Blood, 101: 3109-3117. doi:10.1182/blood-2002-07-2119. PMID:12406872.
30. Okamoto, K., Toyokuni, S., Kim, W.J., Ogawa, O., Kakehi, Y., Arao, S., et al. 1996. Overexpression of human mutT homologue gene messenger RNA in renal-cell carcinoma: evidence of persistent oxidative stress in cancer. Int. J. Cancer, 65: 437-441. doi:10.1002/(SICI)1097-0215(19960208)65:4〈437: :AID-IJC7〉3.0.CO;2-Y. PMID:8621223.
31. Panani, A.D., and Roussos, C. 2006. Cytogenetic and molecular aspects of lung cancer. Cancer Lett. 239: 1-9. doi:10.1016/j.canlet.2005.06.030. PMID:16112428.
32. Pei, J., Balsara, B.R., Li, W., Litwin, S., Gabrielson, E., Feder, M., et al. 2001. Genomic imbalances in human lung adenocarcinomas and squamous cell carcinomas. Genes Chromosomes Cancer, 31: 282-287. doi:10.1002/gcc.1145. PMID:11391799.
33. Reis-Filho, J.S., Pinheiro, C., Lambros, M.B., Milanezi, F., Carvalho, S., Savage, K., et al. 2006. EGFR amplification and lack of activating mutations in metaplastic breast carcinomas. J. Pathol. 209: 445-453. doi:10.1002/path.2004. PMID:16739104.
34. Reissmann, P.T., Koga, H., Figlin, R.A., Holmes, E.C., Slamon, D.J., and The Lung Cancer Study Group. 1999. Amplification and overexpression of the cyclin D1 and epidermal growth factor receptor genes in non-small-cell lung cancer. J. Cancer Res. Clin. Oncol. 125: 61-70. doi:10.1007/ s004320050243. PMID:10190311.
35. Rossi, M.R., La Duca, J., Matsui, S., Nowak, N.J., Hawthorn, L., and Cowell, J.K. 2005. Novel amplicons on the short arm of chromosome 7 identified using high resolution array CGH contain over expressed genes in addition to EGFR in glioblastoma multiforme. Genes Chromosomes Cancer, 44: 392-404. doi:10.1002/gcc.20256. PMID:16110500.
36. Sequist, L.V., Bell, D.W., Lynch, T.J., and Haber, D.A. 2007. Molecular predictors of response to epidermal growth factor receptor antagonists in non-small-cell lung cancer. J. Clin. Oncol. 25: 587-595. doi:10.1200/JCO.2006.07.3585. PMID:17290067.
37. Shadeo, A., and Lam, W.L. 2006. Comprehensive copy number profiles of breast cancer cell model genomes. Breast Cancer Res. 8: R9. doi:10.1186/bcr1370. PMID:16417655.
38. Speina, E., Arczewska, K.D., Gackowski, D., Zielinska, M., Siomek, A., Kowalewski, J., et al. 2005. Contribution of hMTH1 to the maintenance of 8-oxoguanine levels in lung DNA of non-small-cell lung cancer patients. J. Natl. Cancer Inst. 97: 384-395. doi:10.1093/jnci/dji058. PMID:15741575.
39. Thut, C.J., Chen, J.L., Klemm, R., and Tjian, R. 1995. p53 transcriptional activation mediated by coactivators TAFII40 and TAFII60. Science, 267: 100-104. doi:10.1126/science.7809597. PMID:7809597.
40. Tonon, G., Wong, K.K., Maulik, G., Brennan, C., Feng, B., Zhang, Y., et al. 2005. High-resolution genomic profiles of human lung cancer. Proc. Natl. Acad. Sci. U.S.A. 102: 9625-9630. doi:10.1073/pnas.0504126102. PMID:15983384.
41. Travis, W.D., Colby, T.V., Corrin, B., Shimosato, Y., and Brambilla, E., in collaboration with L.H. Sobin and pathologists from 14 countries. 1999. Histological typing of lung and pleural tumours. 3rd ed. Springer-Verlag, Berlin.
42. Waldman, F.M., Carroll, P.R., Kerschmann, R., Cohen, M.B., Field, F.G., and Mayall, B.H. 1991. Centromeric copy number of chromosome 7 is strongly correlated with tumor grade and labeling index in human bladder cancer. Cancer Res. 51: 3807-3813. PMID:1676611.
43. Wani, G., Milo, G.E., and D'Ambrosio, S.M. 1998. Enhanced expression of the 8-oxo-7,8-dihydrodeoxyguanosine triphosphatase gene in human breast tumor cells. Cancer Lett. 125: 123-130. doi:10.1016/S0304-3835(97)00507-7. PMID:9566706.
44. Watson, S.K., deLeeuw, R.J., Horsman, D.E., Squire, J.A., and Lam, W.L. 2007. Cytogenetically balanced translocations are associated with focal copy number alterations. Hum. Genet. 120: 795-805. doi:10.1007/s00439-006- 0251-9. PMID:17051368.
45. Wilson, I.M., Davies, J.J., Weber, M., Brown, C.J., Alvarez, C.E., MacAulay, C., et al. 2006. Epigenomics: mapping the methylome. Cell Cycle, 5: 155-158. PMID:16397413.
46. Yang, S. 2007. Gene amplifications at chromosome 7 of the human gastric cancer genome. Int. J. Mol. Med. 20: 225-231. PMID:17611641.
47. Zhou, B.B., Peyton, M., He, B., Liu, C., Girard, L., Caudler, E., et al. 2006. Targeting ADAM-mediated ligand cleavage to inhibit HER3 and EGFR pathways in non-small cell lung cancer. Cancer Cell, 10: 39-50. doi:10.1016/j.ccr.2006.05.024. PMID:16843264.
48. Zojer, N., Dekan, G., Ackermann, J., Fiegl, M., Kaufmann, H., Drach, J., et al. 2000. Aneuploidy of chromosome 7 can be detected in invasive lung cancer and associated premalignant lesions of the lung by fluorescence in situ hybridisation. Lung Cancer, 28: 225-235. doi:10.1016/S0169-5002(00)00097- 0. PMID:10812191.