Impact of DNA amplification on gene expression patterns in breast cancer

Cancer Research

Volumn 62, Issue 21, 2002, Pages 6240-6245

  Hyman, Elizabeth ^a,b   Kauraniemi, Päivikki ^b,c   Hautaniemi, Sampsa ^b,d   Wolf, Maija ^b   Mousses, Spyro ^b   Rozenblum, Ester ^b   Ringnér, Markus ^b   Sauter, Guido ^e   Monni, Outi ^f   Elkahloun, Abdel ^b   Kallioniemi, Olli P ^b   Kallioniemi, Anne ^b,c  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF TAMPERE   (Finland)

^d TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^e UNIVERSITY OF BASEL   (Switzerland)

^f HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; COMPLEMENTARY DNA; GENE PRODUCT; PROTEIN HOXB7; UNCLASSIFIED DRUG;

AMPLICON; ARTICLE; BREAST CANCER; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA MICROARRAY; GENE AMPLIFICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE MAPPING; GENE OVEREXPRESSION; GENE TARGETING; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROGNOSIS; TUMOR GROWTH;

BREAST NEOPLASMS; DNA, NEOPLASM; GENE AMPLIFICATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; TUMOR CELLS, CULTURED;

EID: 0036829790     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (32)

1. Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D., and Lander, E. S. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science (Wash. DC), 286: 531-537. 1999.
2. Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. C., Sabet, H., Tran, T., Yu, X., et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature (Lond.), 403: 503-511. 2000.
3. Bittner, M., Meltzer, P., Chen, Y., Jiang, Y., Seftor, E., Hendrix, M., Radmacher, M., Simon, R., Yakhini, Z., Ben-Dor, A., et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature (Lond.), 406: 536-540, 2000.
4. Perou, C. M., Sorlie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., Rees, C. A., Pollack, J. R., Ross, D. T., Johnsen, H., Akslen, L. A., et al. Molecular portraits of human breast tumours. Nature (Lond.), 406: 747-752, 2000.
5. Dhanasekaran, S. M., Barrette, T. R., Ghosh, D., Shah, R., Varambally, S., Kurachi, K., Pienta, K. J., Rubin, M. A., and Chinnaiyan, A. M. Delineation of prognostic biomarkers in prostate cancer. Nature (Lond.), 412: 822-826, 2001.
6. Sorlie, T., Perou, C. M., Tibshirani, R., Aas, T., Geisler, S., Johnsen, H., Hastie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., et al., Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. USA, 98: 10869-10874, 2001.
7. Ross, J. S., and Fletcher, J. A. The HER-2/neu oncogene: Prognostic factor, predictive factor and target for therapy. Semin. Cancer Biol., 9: 125-138, 1999.
8. Arteaga, C. L. The epidermal growth factor receptor: From mutant oncogene in nonhuman cancers to therapeutic target in human neoplasia. J. Clin. Oncol. 19: 32-40. 2001.
9. Knuutila, S., Bjorkqvist, A. M., Autio, K., Tarkkanen, M., Wolf, M., Monni, O., Szymanska, J., Larramendy, M. L., Tapper, J., Pere, H., El-Rifai, W., et al. DNA copy number amplifications in human neoplasms: Review of comparative genomic hybridization studies. Am. J. Pathol., 152: 1107-1123, 1998.
10. Knuutila S., Autio K., and Aalto Y. Online access to CGH data of DNA sequence copy number changes. Am. J. Pathol., 157: 689. 2000.
11. DeRisi, J., Penland, L., Brown, P. O., Bittner, M. L., Meltzer, P. S., Ray, M., Chen, Y., Su, Y. A., and Trent, J. M. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet., 14: 457-460, 1996.
12. Shalon, D., Smith, S. J., and Brown, P. O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res., 6: 639-645, 1996.
13. Mousses, S., Bittner, M. L., Chen, Y., Dougherty, E. R., Baxevanis, A., Meltzer, P. S., and Trent, J. M. Gene expression analysis by cDNA microarrays. In: F. J. Livesey and S. P. Hunt (eds.), Functional Genomics, pp. 113-137. Oxford: Oxford University Press. 2000.
14. Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D., and Brown, P. O. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23: 41-46, 1999.
15. Monni, O., Bärlund, M., Mousses, S., Kononen, J., Sauter, G., Heiskanen, M., Paavola, P., Avela, K., Chen, Y., Bitmer, M. L., and Kallioniemi, A. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc. Natl. Acad. Sci. USA, 98: 5711-5716, 2001.
16. Chen, Y., Dougherty, E. R., and Bitmer, M. L. Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Optics, 2: 364-374, 1997.
17. Bärlund, M., Forozan, F., Kononen, J., Bubendorf, L., Chen, Y., Bittner, M. L., Torhorst, J., Haas, P., Bucher, C., Sauter, G., et al. Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis. J. Natl. Cancer Inst., 92: 1252-1259, 2000.
18. Andersen, C. L., Hostetter, G., Grigoryan, A., Sauter, G., and Kallioniemi, A. Improved procedure for fluorescence in situ hybridization on tissue microarrays. Cytometry. 45: 83-86, 2001.
19. Kauraniemi, P., Bärlund, M., Monni, O., and Kallioniemi, A. New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Res., 61: 8235-8240, 2001.
20. Clark, J., Edwards, S., John, M., Flohr, P., Gordon, T., Maillard, K., Giddings, I., Brown, C., Bagherzadeh, A., Campbell, C., Shipley, J., Wooster, R., and Cooper, C. S. Identification of amplified and expressed genes in breast cancer by comparative hybridization onto microarrays of randomly selected cDNA clones. Genes Chromosomes Cancer, 34: 104-114, 2002.
21. Varis, A., Wolf, M., Monni, O., Vakkari, M. L., Kokkola, A., Moskaluk, C., Frierson, H., Powell, S. M., Knuutila, S., Kallioniemi, A., and El-Rifai, W. Targets of gene amplification and overexpression at 17q in gastric cancer. Cancer Res., 62: 2625-2629, 2002.
22. Hughes, T. R., Roberts, C. J., Dai, H., Jones, A. R., Meyer, M. R., Slade, D., Burchard, J., Dow, S., Ward, T. R., Kidd, M. J., Friend, S. H., and Marton, M. J. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat. Genet., 25: 333-337, 2000.
23. Virtaneva, K., Wright, F. A., Tanner, S. M., Yuan, B., Lemon, W. J., Caligiuri, M. A., Bloomfield, C. D., de La Chapelle, A., and Krahe, R. Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. Proc. Natl. Acad. Sci. USA. 98: 1124-1129, 2001.
24. Phillips, J, L., Hayward, S, W., Wang, Y., Vasselli, J., Pavlovich, C., Padilla-Nash, H., Pezullo, J. R., Ghadimi, B. M., Grossfeld, G. D., Rivera, A., Linehan, W. M., Cunha, G. R., and Ried, T. The consequences of chromosomal aneuploidy on gene expression profiles in a cell line model for prostate carcinogenesis. Cancer Res., 61: 8143-8149, 2001.
25. Bärlund, M., Tirkkonen, M., Forozan, F., Tanner, M. M., KallioniemL O. P., and Kallioniemi, A. Increased copy number at 17q22-q24 by CGH in breast cancer is due to high-level amplification of two separate regions, Genes Chromosomes Cancer, 20: 372-376, 1997.
26. Tanner, M. M., Tirkkonen, M., Kallioniemi, A., Isola, J., Kuukasjärvi, T., Collins, C., Kowbel, D., Guan, X. Y., Trent, J., Gray, J. W., Meltzer, P., and Kallioniemi O. P. Independent amplification and frequent co-amplification of three nonsyntenic regions on the long arm of chromosome 20 in human breast cancer. Cancer Res., 56: 3441-3445, 1996.
27. Cillo, C., Faiella, A., Cantile, M., and Boncinelli, E. Homeobox genes and cancer. Exp. Cell Res., 248: 1-9, 1999.
28. Cillo, C., Cantile, M., Faiella, A., and Boncinelli, E. Homeobox genes in normal and malignant cells. J. Cell. Physiol., 188: 161-169. 2001.
29. Care, A., Silvani, A., Meccia, E., Mattia, G., Stoppacciaro, A., Parmiani, G., Peschle, C., and Colombo, M. P. HOXB7 constitutively activates basic fibroblast growth factor in melanomas. Mol. Cell. Biol., 16: 4842-4851, 1996.
30. Care, A., Silvani, A., Meccia, E., Mattia, G., Peschle, C., and Colombo, M. P. Transduction of the SkBr3 breast carcinoma cell line with the HOXB7 gene induces bFGF expression, increases cell proliferation and reduces growth factor dependence. Oncogene., 16: 3285-3289, 1998.
31. Care, A., Felicetti, F., Meccia, E., Bottero, L., Parenza, M., Stoppacciaro, A., Peschle, C., and Colombo, M. P. HOXB7: A key factor for tumor-associated angiogenic switch. Cancer Res., 61: 6532-6539, 2001.
32. Naora, H., Yang, Y. Q., Montz, F. J., Seidman, J. D., Kurman, R. J., and Roden, R. B. A serologically identified tumor antigen encoded by a homeobox gene promotes growth of ovarian epithelial cells. Proc. Natl. Acad. Sci. USA, 98: 4060-4065, 2001.