Chromosomal aberrations and gene expression profiles in non-small cell lung cancer

Lung Cancer

Volumn 56, Issue 2, 2007, Pages 175-184

  Dehan, E ^a   Ben Dor, A ^b   Liao, W ^c   Lipson, D ^d   Frimer, H ^e   Rienstein, S ^e   Simansky, D ^e   Krupsky, M ^e   Yaron, P ^e   Friedman, E ^e   Rechavi, G ^e   Perlman, M ^e   Aviram Goldring, A ^e   Izraeli, S ^e   Bittner, M ^c   Yakhini, Z ^b,d   Kaminski, N ^e,f  

^a TEL AVIV UNIVERSITY   (Israel)

^b AGILENT LABORATORIES   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^d TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^e SHEBA MEDICAL CENTER   (Israel)

^f UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

Author keywords

Array CGH; Chromosomal aberrations; Expression microarrays; Expression profiling; Non small cell lung cancer

Indexed keywords

BETA CATENIN; COLLAGENASE 3; INTERSTITIAL COLLAGENASE; MACROPHAGE ELASTASE; MATRIX METALLOPROTEINASE; WNT PROTEIN;

ARTICLE; CHROMOSOME 11Q; CHROMOSOME 12P; CHROMOSOME 3P; CHROMOSOME 3Q; CHROMOSOME 7Q; CHROMOSOME 8Q; CHROMOSOME ABERRATION; CHROMOSOME DELETION; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA REPLICATION; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE LOCATION; GENE OVEREXPRESSION; HUMAN; HUMAN TISSUE; LUNG CARCINOGENESIS; LUNG NON SMALL CELL CANCER; PRIORITY JOURNAL;

CARCINOMA, NON-SMALL-CELL LUNG; CHROMOSOME ABERRATIONS; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; LUNG NEOPLASMS; NUCLEIC ACID HYBRIDIZATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 34247274716     PISSN: 01695002     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.lungcan.2006.12.010     Document Type: Article

References (50)

1. Parkin D.M., Bray F.I., and Devesa S.S. Cancer burden in the year 2000. The global picture. Eur J Cancer 37 Suppl. 8 (2001) S4-S66
2. Balsara B.R., and Testa J.R. Chromosomal imbalances in human lung cancer. Oncogene 21 45 (2002) 6877-6883
3. Pinkel D., Segraves R., Sudar D., Clark S., Poole I., Kowbel D., et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20 2 (1998) 207-211
4. Pollack J.R., Chou F.L., Rees C.A., Christian A.T., Bedford J.S., Brown P.O., et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Genome Biol 3 6 (2002) [RESEARCH0026]
5. Pinkel D., and Albertson D.G. Array comparative genomic hybridization and its applications in cancer. Nat Genet 37 Suppl. (2005) S11-S17
6. Pollack J.R., Sorlie T., Perou C.M., Rees C.A., Jeffrey S.S., Lonning P.E., et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 99 20 (2002) 12963-12968
7. Wilhelm M., Veltman J.A., Olshen A.B., Jain A.N., Moore D.H., Presti Jr. J.C., et al. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res 62 4 (2002) 957-960
8. Nakao K., Mehta K.R., Fridlyand J., Moore D.H., Jain A.N., Lafuente A., et al. High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis 25 8 (2004) 1345-1357
9. DeLeeuw R.J., Davies J.J., Rosenwald A., Bebb G., Gascoyne R.D., Dyer M.J., et al. Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes. Hum Mol Genet (2004)
10. Massion P.P., Kuo W.L., Stokoe D., Olshen A.B., Treseler P.A., Chin K., et al. Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway. Cancer Res 62 13 (2002) 3636-3640
11. Minna J.D., Roth J.A., and Gazdar A.F. Focus on lung cancer. Cancer Cell 1 1 (2002) 49-52
12. Kaminski N., and Krupsky M. Gene expression patterns, prognostic and diagnostic markers, and lung cancer biology. Chest 125 5 Suppl. (2004) 111S-115S
13. Potti A., Mukherjee S., Petersen R., Dressman H.K., Bild A., Koontz J., et al. A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med 355 6 (2006) 570-580
14. Daniely M., Aviram A., Adams E.F., Buchfelder M., Barkai G., Fahlbusch R., et al. Comparative genomic hybridization analysis of nonfunctioning pituitary tumors. J Clin Endocrinol Metab 83 5 (1998) 1801-1805
15. Khan J., Simon R., Bittner M., Chen Y., Leighton S.B., Pohida T., et al. Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res 58 22 (1998) 5009-5013
16. Erez A., Perelman M., Hewitt S.M., Cojacaru G., Goldberg I., Shahar I., et al. Sil overexpression in lung cancer characterizes tumors with increased mitotic activity. Oncogene 23 31 (2004) 5371-5377
17. Ortiz L.A., Gambelli F., McBride C., Gaupp D., Baddoo M., Kaminski N., et al. Mesenchymal stem cell engraftment in lung is enhanced in response to bleomycin exposure and ameliorates its fibrotic effects. Proc Natl Acad Sci USA 100 14 (2003) 8407-8411
18. Kaminski N., and Friedman N. Practical approaches to analyzing results of microarray experiments. Am J Respir Cell Mol Biol 27 2 (2002) 125-132
19. Ben-Dor A., Bruhn L., Friedman N., Nachman I., Schummer M., and Yakhini Z. Tissue classification with gene expression profiles. J Comput Biol 7 3-4 (2000) 559-583
20. Kaminski N., Allard J.D., Pittet J.F., Zuo F., Griffiths M.J., Morris D., et al. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proc Natl Acad Sci USA 97 4 (2000) 1778-1783
21. Bittner M., Meltzer P., Chen Y., Jiang Y., Seftor E., Hendrix M., et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406 6795 (2000) 536-540
22. Bhattacharjee A., Richards W.G., Staunton J., Li C., Monti S., Vasa P., et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 98 24 (2001) 13790-13795
23. Sekido Y., Ahmadian M., Wistuba I.I., Latif F., Bader S., Wei M.H., et al. Cloning of a breast cancer homozygous deletion junction narrows the region of search for a 3p21.3 tumor suppressor gene. Oncogene 16 24 (1998) 3151-3157
24. Lerman M.I., and Minna J.D. The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium. Cancer Res 60 21 (2000) 6116-6133
25. Garnis C., Lockwood W.W., Vucic E., Ge Y., Girard L., Minna J.D., et al. High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. Int J Cancer 118 6 (2006) 1556-1564
26. Jiang F., Yin Z., Caraway N.P., Li R., and Katz R.L. Genomic profiles in stage I primary non small cell lung cancer using comparative genomic hybridization analysis of cDNA microarrays. Neoplasia 6 5 (2004) 623-635
27. Wistuba I.I., Behrens C., Virmani A.K., Mele G., Milchgrub S., Girard L., et al. High resolution chromosome 3p allelotyping of human lung cancer and preneoplastic/preinvasive bronchial epithelium reveals multiple, discontinuous sites of 3p allele loss and three regions of frequent breakpoints. Cancer Res 60 7 (2000) 1949-1960
28. Hung J., Kishimoto Y., Sugio K., Virmani A., McIntire D.D., Minna J.D., et al. Allele-specific chromosome 3p deletions occur at an early stage in the pathogenesis of lung carcinoma. JAMA 273 7 (1995) 558-563
29. Carboni G.L., Gao B., Nishizaki M., Xu K., Minna J.D., Roth J.A., et al. CACNA2D2-mediated apoptosis in NSCLC cells is associated with alterations of the intracellular calcium signaling and disruption of mitochondria membrane integrity. Oncogene 22 4 (2003) 615-626
30. Tomizawa Y., Sekido Y., Kondo M., Gao B., Yokota J., Roche J., et al. Inhibition of lung cancer cell growth and induction of apoptosis after reexpression of 3p21.3 candidate tumor suppressor gene SEMA3B. Proc Natl Acad Sci USA 98 24 (2001) 13954-13959
31. Ji L., Nishizaki M., Gao B., Burbee D., Kondo M., Kamibayashi C., et al. Expression of several genes in the human chromosome 3p21.3 homozygous deletion region by an adenovirus vector results in tumor suppressor activities in vitro and in vivo. Cancer Res 62 9 (2002) 2715-2720
32. Monni O., Barlund M., Mousses S., Kononen J., Sauter G., Heiskanen M., et al. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc Natl Acad Sci USA 98 10 (2001) 5711-5716
33. Ramnath N., Hernandez F.J., Tan D.F., Huberman J.A., Natarajan N., Beck A.F., et al. MCM2 is an independent predictor of survival in patients with non-small-cell lung cancer. J Clin Oncol 19 22 (2001) 4259-4266
34. Tan D.F., Huberman J.A., Hyland A., Loewen G.M., Brooks J.S., Beck A.F., et al. MCM2-a promising marker for premalignant lesions of the lung: a cohort study. BMC Cancer 1 1 (2001) 6
35. Tago K., Nakamura T., Nishita M., Hyodo J., Nagai S., Murata Y., et al. Inhibition of Wnt signaling by ICAT, a novel beta-catenin-interacting protein. Genes Dev 14 14 (2000) 1741-1749
36. Bauer A., Chauvet S., Huber O., Usseglio F., Rothbacher U., Aragnol D., et al. Pontin52 and reptin52 function as antagonistic regulators of beta-catenin signalling activity. EMBO J 19 22 (2000) 6121-6130
37. Feng Y., Lee N., and Fearon E.R. TIP49 regulates beta-catenin-mediated neoplastic transformation and T-cell factor target gene induction via effects on chromatin remodeling. Cancer Res 63 24 (2003) 8726-8734
38. Wissmann C., Wild P.J., Kaiser S., Roepcke S., Stoehr R., Woenckhaus M., et al. WIF1, a component of the Wnt pathway, is down-regulated in prostate, breast, lung, and bladder cancer. J Pathol 201 2 (2003) 204-212
39. Mazieres J., He B., You L., Xu Z., Lee A.Y., Mikami I., et al. Wnt inhibitory factor-1 is silenced by promoter hypermethylation in human lung cancer. Cancer Res 64 14 (2004) 4717-4720
40. Pennica D., Swanson T.A., Welsh J.W., Roy M.A., Lawrence D.A., Lee J., et al. WISP genes are members of the connective tissue growth factor family that are up-regulated in wnt-1-transformed cells and aberrantly expressed in human colon tumors. Proc Natl Acad Sci USA 95 25 (1998) 14717-14722
41. Virmani A.K., Rathi A., Sathyanarayana U.G., Padar A., Huang C.X., Cunnigham H.T., et al. Aberrant methylation of the adenomatous polyposis coli (APC) gene promoter 1A in breast and lung carcinomas. Clin Cancer Res 7 7 (2001) 1998-2004
42. Uematsu K., He B., You L., Xu Z., McCormick F., and Jablons D.M. Activation of the Wnt pathway in non small cell lung cancer: evidence of dishevelled overexpression. Oncogene 22 46 (2003) 7218-7221
43. Garnis C., Campbell J., Davies J.J., Macaulay C., Lam S., and Lam W.L. Involvement of multiple developmental genes on chromosome 1p in lung tumorigenesis. Hum Mol Genet 14 4 (2005) 475-482
44. He B., You L., Uematsu K., Xu Z., Lee A.Y., Matsangou M., et al. A monoclonal antibody against Wnt-1 induces apoptosis in human cancer cells. Neoplasia 6 1 (2004) 7-14
45. You L., He B., Xu Z., Uematsu K., Mazieres J., Mikami I., et al. Inhibition of Wnt-2-mediated signaling induces programmed cell death in non-small-cell lung cancer cells. Oncogene 23 36 (2004) 6170-6174
46. Hofmann H.S., Hansen G., Richter G., Taege C., Simm A., Silber R.E., et al. Matrix metalloproteinase-12 expression correlates with local recurrence and metastatic disease in non-small cell lung cancer patients. Clin Cancer Res 11 3 (2005) 1086-1092
47. Acuff H.B., Sinnamon M., Fingleton B., Boone B., Levy S.E., Chen X., et al. Analysis of host- and tumor-derived proteinases using a custom dual species microarray reveals a protective role for stromal matrix metalloproteinase-12 in non-small cell lung cancer. Cancer Res 66 16 (2006) 7968-7975
48. Kerkela E., Ala-aho R., Klemi P., Grenman S., Shapiro S.D., Kahari V.M., et al. Metalloelastase (MMP-12) expression by tumour cells in squamous cell carcinoma of the vulva correlates with invasiveness, while that by macrophages predicts better outcome. J Pathol 198 2 (2002) 258-269
49. Tonon G., Wong K.K., Maulik G., Brennan C., Feng B., Zhang Y., et al. High-resolution genomic profiles of human lung cancer. Proc Natl Acad Sci USA 102 27 (2005) 9625-9630
50. Zhao X., Weir B.A., LaFramboise T., Lin M., Beroukhim R., Garraway L., et al. Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res 65 13 (2005) 5561-5570