Combining serial analysis of gene expression and array technologies to identify genes differentially expressed in breast cancer

Cancer Research

Volumn 59, Issue 21, 1999, Pages 5464-5470

  Nacht, Mariana ^c   Ferguson, Anne T ^b   Zhang, Wen ^c   Petroziello, Joseph M ^c   Cook, Brian P ^c   Gao, Yu Hong ^c   Maguire, Sharon ^d   Riley, Deborah ^e   Coppola, George ^c   Landes, Gregory M ^c   Madden, Stephen L ^c   Sukumar, Saraswati ^a,b  

^a Calydon Inc   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c Genzyme Molecular Oncology   (United States)

^d NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^e Lion Bioscience   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CANCER; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; HUMAN CELL; MARKER GENE; PRIORITY JOURNAL;

BREAST NEOPLASMS; DNA MUTATIONAL ANALYSIS; DNA, COMPLEMENTARY; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE LIBRARY; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; TRANSCRIPTION, GENETIC; TUMOR CELLS, CULTURED; TUMOR MARKERS, BIOLOGICAL;

EID: 0033229892     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (49)

1. Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. Serial analysis of gene expression. Science (Washington DC), 270; 484-487, 1995.
2. Prashar, Y., and Weissman, S. M. READS: a method for display of 3′-end fragments of restriction enzyme-digested cDNAs for analysis of differential gene expression. Methods Enzymol., 303: 258-272, 1999.
3. Bachem, C. W., van der Hoeven, R. S., de Bruijn, S. M., Vreugdenhil, D., Zabeau, M., and Visser, R. G. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J., 9: 745-753, 1996.
4. Drmanac, S., Stavropoulos, N. A., Labat, J., Vonau, J., Hauser, B., Soares, M. B., and Drmanac, R. Gene-representing cDNA clusters defined by hybridization of 57,419 clones from infant brain libraries with short oligonucleotide probes. Genomics, 37: 29-40, 1996.
5. Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., and Brown, E. L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14: 1675-1680, 1996.
6. Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D., Jr., Hieter, P., Vogelstein, B., and Kinzler, K. W. Characterization of the yeast transcriptome. Cell, 88: 243-251, 1997.
7. Polyak, K., Xia, Y., Zweier, J. L., Kinzler, K. W., and Vogelstein, B. A model for p53-induced apoptosis. Nature (Lond.), 389: 300-305, 1997.
8. Hibi, K., Robinson, C. R., Booker, S., Wu, L., Hamilton, S. R., Sidransky, D., and Jen, J. Serial analysis of gene expression in non-small cell lung cancer. Cancer Res., 58: 5690-5694, 1998.
9. Zhang, L., Zhou, W., Velculescu, V. E., Kern, S. E., Hruban, R. H., Hamilton, S. R., Vogelstein, B., and Kinzler, K. W. Gene expression profiles in normal and cancer cells. Science (Washington DC), 276: 1268-1272, 1997.
10. Band, V., Zajchowski, D., Swisshelm, K., Trask, D., Kulesa, V., Cohen, C., Connolly, J., and Sager, R. Tumor progression in four mammary epithelial cell lines derived from the same patient. Cancer Res., 50: 7351-7357, 1990.
11. Chomczynski, P., and Sacchi, N. Single-step method of RNA isolation by acid guanidinium thiocyanate- phenol-chloroform extraction. Anal. Biochem., 162: 156-159, 1987.
12. Welch, D. R., and Wei, L. L. Genetic and epigenetic regulation of human breast cancer progression and metastasis. Endocrine-Related Cancer, 5: 155-197, 1998.
13. Aoki, R., Tanaka, S., Haruma, K., Yoshihara, M., Sumii, K., Kajiyama, G., Shimamoto, F., and Kohno, N. MUC-1 expression as a predictor of the curative endoscopie treatment of submucosally invasive colorectal carcinoma. Dis. Colon Rectum, 41: 1262-1272, 1998.
14. Segal Eiras, A., and Croce, M. V. Breast cancer associated mucin: a review. Allergol. Immunopathol., 25: 176-181, 1997.
15. Diez Itza, I., Sanchez, L. M., Allende, M. T., Vizoso, F., Ruibal, A., and Lopez-Otin, C. Zn-α2-glycoprotein levels in breast cancer cytosols and correlation with clinical, histological and biochemical parameters. Eur. J Cancer, 9: 1256-1260, 1993.
16. Bussemakers, M. J., van de Ven, W. J., Debruyne, F. M., and Schalken, J. A. Identification of high mobility group protein I(Y) as potential progression marker for prostate cancer by differential hybridization analysis. Cancer Res., 51: 606-611, 1991.
17. Giancotti, V., Buratti, E., Perissin, L., Zorzet, S., Balmain, A., Portella, G., Fusco, A., and Goodwin, G. H. Analysis of the HMGI nuclear proteins in mouse neoplastic cells induced by different procedures. Exp. Cell Res., 184: 538-545, 1989.
18. Chiappetta, G., et al. The expression of the high mobility group HMG1 (Y) proteins correlates with the malignant phenotype of human thyroid neoplasias. Oncogene. 1995, 10(7): p. 1307-14.
19. Ram, T. G., Reeves, R., and Hosick, H. L. Elevated high mobility group-I(Y) gene expression is associated with progressive transformation of mouse mammary epithelial cells. Cancer Res., 53: 2655-2660, 1993.
20. 6-alkylguanine and N-alkylpurines to the formation of sister chromatid exchanges, chromosomal aberrations, and gene mutations: new insights gained from studies of genetically engineered mammalian cell lines. Environ. Mol. Mutagen., 22: 283-292, 1993.
21. Brotherick, I., Robson, C. N., Bronell, D. A., Shentine, J., While, M. D., Cunliffe, W. J., Shenton, B. K., Egan, M., Webb, L. A., Lunt, L. J., Young, J. R., and Higgs, M. Cytokeratin expression in breast cancer: phenotypic changes associated with disease progression. Cytometry, 32: 301-308, 1998.
22. Stetler Stevenson, W. G., Aznavoorian, S., and Liotta, L. A. Tumor cell interactions with the extracellular matrix during invasion and metastasis. Annu. Rev. Cell Biol., 9: 541-573, 1993.
23. Sager, R., Sheng, S., Pemberton, P., and Hendrix, M. J. Maspin: a tumor suppressing serpin. Adv. Exp. Med. Biol., 425: 77-88, 1997.
24. Manni, A., Badger, B., Wei, L., Zaenglein, A., Grove, R., Khin, S., Heitjan, D., Shimasaki, S., and Ling, N. Hormonal regulation of insulin-like growth factor II and insulin-like growth factor binding protein expression by breast cancer cells in vivo: evidence for stromal epithelial interactions. Cancer Res., 54: 2934-2942, 1994.
25. Nickerson, T., Zhang, J., and Pollak, M. Regression of DMBA-induced breast carcinoma following ovariectomy is associated with increased expression of genes encoding insulin-like growth factor binding proteins. Int. J. Oncol., 14: 987-990, 1999.
26. Lee, S. W., Tomasetto, C., Swisshelm, K., Keyomarsi, K., and Sager, R. Down-regulation of a member of the S100 gene family in mammary carcinoma cells and reexpression by azadeoxycytidine treatment. Proc. Natl. Acad. Sci. USA, 89: 2504-2508, 1992.
27. Franzen, B., Linder, S., Alaiya, A. A., Eriksson, E., Uruy, K., Hirano, T., Okuzawa, K., and Auer, G. Analysis of polypeptide expression in benign and malignant human breast lesions: down-regulation of cytokeratins. Br. J. Cancer, 74: 1632-1638, 1996.
28. Lee, W. H., Morton, R. A., Epstein, J. I., Brooks, J. D., Campbell, P. A., Bova, G. S., Hsieh, W. S., Isaacs, W. B., and Nelson, W. G. Cytidine methylation of regulatory sequences near the pi-class glutathione 5-transferase gene accompanies human prostatic carcinogenesis. Proc. Natl. Acad. Sci. USA, 91: 11733-11737, 1994.
29. Esteller, M., Corn, P. G., Urena, J. M., Gabrielson, E., Baylin, S. B., and Herman, J. G. Inactivation of glutathione S-transferase P1 gene by promoter hypermethylation in human neoplasia. Cancer Res., 58: 4515-4518, 1998.
30. Magnaldo, T., Fowlis, D., and Darmon, M. Galectin-7, a marker of all types of stratified epithelia. Differentiation, 63: 159-168, 1998.
31. Franzen, B., Linder, S., Uryu, K., Alaiya, A. A., Hirano, T., Kato H., and Auer, G. Expression of tropomyosin isoforms in benign and malignant human breast lesions. Br. J. Cancer, 73: 909-913, 1996.
32. Bergstraesser, L. M., Srinivasan, G., Jones, J. C., Stahl, S., and Weitzman, S. A. Expression of hemidesmosomes and component proteins is lost by invasive breast cancer cells. Am. J. Pathol., 147: 1823-1839, 1995.
33. Monta, K., Furuse, M., Fujimoto, K., and Tsukita, S. Claudin multigene family encoding four-transmembrane domain protein components of tight junction strands. Proc. Natl. Acad. Sci. USA, 96: 511-516, 1999.
34. Moll, I., Kurzen, H., Langbein, L., and Franke, W. W. The distribution of the desmosomal protein, plakophilin 1, in human skin and skin tumors. J. Investig. Dermatol., 108: 139-146, 1997.
35. Shaw, L. M., Chao, C., Wewer, U. M., and Mercurio, A. M. Function of the integrin α6β1 in metastatic breast carcinoma cells assessed by expression of a dominant-negative receptor. Cancer Res., 56: 959-963, 1996.
36. Zumbrunn, J., and Trueb, B. Primary structure of a putative serine protease specific for IGF-binding proteins. FEBS Lett., 398: 187-192, 1996.
37. Chandrasekharappa, S. C., Guru, S. C., Manickam, P., Olujemi, S. E., Collins, F. S., Emmert-Buck, M. R., Debelenko, I. V., Zhuang, Z., Lubensky, I. A., Liotta, L. A., Crabtree, J. S., Wang, Y., Roe, B. A., Weisemann, J., Boguski, M. S., Agarwal, S. K., Kester, M. B., Kim, Y. S., Heppner, C., Dong, Q., Spiegel, A. M., Bums, A. L., and Marx, S. J. Positional cloning of the gene for multiple endocrine neoplasia-type 1. Science (Washington DC), 276: 404-407, 1997.
38. Zhou, Q., Stetler-Stevenson, M., and Steeg, P. S. Inhibition of cyclin D expression in human breast carcinoma cells by retinoids in vitro. Oncogene, 15: 107-115, 1997.
39. DeMuth, J. P., Weaver, D. A., Crawford, E. L., Jackson, C. M., and Willey, J. C. Loss of spr1 expression measurable by quantitative RT-PCR in human bronchogenic carcinoma cell lines. Am. J. Respir. Cell Mol. Biol., 19: 25-29, 1998.
40. Yaar, M., Gilani, A., DiBenedetto, P. J., Harkness, D. D., and Gilchrest, B. A. Gene modulation accompanying differentiation of normal versus malignant keratinocytes. Exp. Cell Res., 206: 235-243, 1993.
41. Boyd, N. F., Connelly, P., Lynch, H., Knaus, M., Michal, S., Fili, M., Martin, L. J., Lockwood, G., and Tritchler, D. Plasma lipids, lipoproteins, and familial breast cancer. Cancer Epidemiol. Biomark. Prev., 4: 117-122, 1995.
42. Lane, D. M., Boatman, K. K., and McConathy, W. J. Serum lipids and apolipoproteins in women with breast masses. Breast Cancer Res. Treat., 34: 161-169, 1995.
43. Gumbiner, B. M. Breaking through the tight junction barrier. J. Cell Biol., 123 (6 Pt. 2): 1631-1633, 1993.
44. Stoesz, S. P., Friedl, A., Haag, J. D., Lindstrom, M. J., Clark, G. M., and Gould, M. N. Heterogeneous expression of the lipocalin NGAL in primary breast cancers. Int. J. Cancer, 79: 565-572, 1998.
45. Furutani, M., Arii, S., Mizumoto, M., Kato, M., and Imamura, M. Identification of a neutrophil gelatinase-associated lipocalin mRNA in human pancreatic cancers using a modified signal sequence trap method. Cancer Lett., 122: 209-214, 1998.
46. Nielsen, B. S., Borregaard, N., Bundgaard, J. R., Timshel, S., Sehested, M., and Kjeldsen, L. Induction of NGAL synthesis in epithelial cells of human colorectal neoplasia and inflammatory bowel diseases. Gut, 38: 414-420, 1996.
47. Freije, J. P., Fueyo, A., Uria, J. A., Velasco, G., Sanchez, L. M., Lopez-Boado, Y. S., and Lopez-Otin, C. Human Zn-α2-glycoprotein. complete genomic sequence, identification of a related pseudogene and relationship to class I major histocompatibility complex genes. Genomics, 18: 575-587, 1993.
48. Hu, R., Wu, R., Deng, J., and Lau, D. A small proline-rich protein, spr1: specific marker for squamous lung carcinoma. Lung Cancer, 20: 25-30, 1998.
49. Kartasova, T., Darwiche, N., Kohno, Y., Koizumi, H., Osada, S., Huh, N., Lichti, U., Steinert, P. M., and Kuroki, T. Sequence and expression patterns of mouse SPR1: correlation of expression with epithelial function. J. Investig. Dermatol., 106: 294-304, 1996.