Tissue-Wide Expression Profiling Using cDNA Subtraction and Microarrays to Identify Tumor-Specific Genes

Cancer Research

Volumn 64, Issue 3, 2004, Pages 844-856

  Amatschek, Stefan ^a   Koenig, Ulrich ^a   Auer, Herbert ^b   Steinlein, Peter ^c   Pacher, Margit ^a   Gruenfelder, Agnes ^a   Dekan, Gerhard ^a   Vogl, Sonja ^a   Kubista, Ernst ^a   Heider, Karl Heinz ^d   Stratowa, Christian ^d   Schreiber, Martin ^a   Sommergruber, Wolfgang ^d  

^a UNIVERSITY OF VIENNA   (Austria)

^b OHIO STATE UNIVERSITY   (United States)

^c RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

^d BOEHRINGER INGELHEIM RCV GMBH AND CO KG   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

HYPOXIA INDUCIBLE FACTOR 1;

ARTICLE; B MYB GENE; BONE MINERALIZATION; BREAST CANCER; CAK GENE; CALCA GENE; CALCIUM HOMEOSTASIS; CANCER SURVIVAL; CD44 GENE; CELL HYBRIDIZATION; CELL INFILTRATION; CELL TYPE; CLUSTER ANALYSIS; CONTROLLED STUDY; CYCLIN B1 GENE; DNA LIBRARY; DNA MICROARRAY; EGLN3 GENE; ERG2 GENE; ESP15 GENE; EXPRESSED SEQUENCE TAG; GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ANALYSIS; HUMAN; HUMAN TISSUE; IMMUNE SYSTEM; KIDNEY CANCER; LUNG ADENOCARCINOMA; LUNG SQUAMOUS CELL CARCINOMA; MIG 6 GENE; NUCLEOTIDE SEQUENCE; ONCOGENE; OPN GENE; OSF 2 GENE; OSN GENE; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RCN1 GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; S100 PROTEIN GENE; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; SURVIVAL TIME; TGF B3 GENE; TISSUE WIDE EXPRESSION PROFILING; UNINDEXED SEQUENCE; UPREGULATION; VCAM 1 GENE;

ADENOCARCINOMA; BREAST NEOPLASMS; CARCINOMA, RENAL CELL; CARCINOMA, SQUAMOUS CELL; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; HUMANS; KIDNEY NEOPLASMS; LUNG NEOPLASMS; NEOPLASM STAGING; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, NEOPLASM; SURVIVAL RATE;

EID: 10744219705     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-03-2361     Document Type: Article

References (54)

1. Sporn, M. B. The war on cancer. Lancet, 347: 1377-1381, 1996.
2. Fedi, P., Tronick, S. R., and Aaronson, S. A. Growth Factors. In: J. F. Holland (ed.), Cancer Medicine, pp. 41-64. Baltimore: Williams and Wilkins, 1997.
3. Hanahan, D., and Weinberg, R. A. The hallmarks of carcer. Cell. 100: 57-70, 2000.
4. Kaelin, W. G., Jr. Choosing anticancer drug targets in the postgenomic era. J. Clin. Investig., 104: 1503-1506, 1999.
5. Perou, C. M., Sorlie, T., Eisen, M. B., van de, R. M., Jeffrey, S. S., Rees, C. A., Pollack, J. R., Ross, D. T., Johnsen, H., Akslen, L. A., Fluge, O., Pergamenschikov, A., Williams, C., Zhu, S. X., Lonning, P. E., Borresen-Dale, A. L., Brown, P. O., and Botstein, D. Molecular portraits of human breast tumours. Nature (Lond.), 406: 747-752, 2000.
6. Takahashi, M., Rhodes, D. R., Fruge, K. A., Kanayama, H., Kagawa, S., Haab, B. B., and Teh, B. T. Gene expression profiling of clear cell renal cell carcinoma: gene identification and prognostic classification. Proc. Natl. Acad. Sci. USA, 98: 9754-9759, 2001.
7. 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.
8. Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. C., Saber, H., Tran, T., Yu, X., Powell, J. I., Yang, L., Marti, G. E., Moore, T., Hudson, J., Jr., Lu, L., Lewis, D. B., Tibshirani, R., Sherlock, G., Chan, W. C., Greiner, T. C., Weisenburger, D. D., Armitage, J. O., Warnke, R., Levy, R., Wilson, W., Grever, M. R., Byrd, J. C., Botstein, D., Brown, P. O., and Staudt, L. M. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature (Lond.), 403: 503-511, 2000.
9. Bittner, M., Meltzer, P., Chen, Y., Jiang, Y., Seftor, E., Hendrix, M., Radmacher, M., Simon, R., Yakhini, Z., Ben Dor, A., Sampas, N., Dougherty, E., Wang, E., Marincola, F., Gooden, C., Lueders, J., Glatfelter, A., Pollock, P., Carpten, J., Gillanders, E., Leja, D., Dietrich, K., Beaudry, C., Berens, M., Alberts, D., and Sondak, V. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature (Lond.), 406: 536-540, 2000.
10. Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O. P., Willfond, B., Borg, A., and Trent, J. Gene-expression profiles in hereditary breast cancer. N. Engl. J. Med., 344: 539-548, 2001.
11. Bangur, C. S., Switzer, A., Fan, L., Marton, M. J., Meyer, M. R., and Wang, T. Identification of genes over-expressed in small cell lung carcinoma using suppression subtractive hybridization and cDNA microarray expression analysis. Oncogene, 21: 3814-3825, 2002.
12. Bouras, T., Southey, M. C., Chang, A. C., Reddel, R. R., Willhite, D., Glynne, R., Henderson, M. A., Armes, J. E., and Venter, D. J. Stanniocalcin 2 is an estrogen-responsive gene coexpressed with the estrogen receptor in human breast cancer. Cancer Res., 62: 1289-1295, 2002.
13. Buckley, C. D., Pilling, D., Henriquez, N. V., Parsonage, G., Threlfall, K., Scheel-Toellner, D., Simmons, D. L., Akbar, A. N., Lord, J. M., and Salmon, M. RGD peptides induce apoptosis by direct caspase-3 activation. Nature (Lond.), 397: 534-539, 1999.
14. Diatchenko, L., Lau, Y. F., Campbell, A. P., Chenchik, A., Moqadam, F., Huang, B., Lukyanov, S., Lukyanov, K., Gurskaya, N., Sverdlov, E. D., and Siebert, P. D. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA, 93: 6025-6030, 1996.
15. Sambrook, J., and Russell, D. W. Molecular Cloning, Ed. 3. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2001.
16. Eisen, M. B., and Brown, P. O. DNA arrays for analysis of gene expression. Methods Enzymol., 303: 179-205, 1999.
17. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (Wash. DC), 270: 467-470, 1995.
18. Dudoit, S., Yang, Y. H., Speed, T. P., and Callow, M. J. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica. 12: 111-139, 2002. 19
19. Takahashi, K., Paladini, R. D., and Coulombe, P. A. Cloning and characterization of multiple human genes and cDNAs encoding highly related type II keratin 6 isoforms. J. Biol. Chem., 270: 18581-18592, 1995.
20. Klade, C. S., Dohnal, A., Furst, W., Sommergruber, W., Heider, K. H., Gharwan, H., Ratschek, M., and Adolf, G. R. Identification and characterization of 9D7, a novel human protein overexpressed in renal cell carcinoma. Int. J. Cancer, 97: 217-224, 2002.
21. Epstein, A. C., Gleadle, J. M., McNeill, L. A., Hewitson, K. S., O'Rourke, J., Mole, D. R., Mukherji, M., Metzen, E., Wilson, M. I., Dhanda, A., Tian, Y. M., Masson, N., Hamilton, D. L., Jaakkola, P., Barstead, R., Hodgkin, J., Maxwell, P. H., Pugh, C. W., Schofield, C. J., and Ratcliffe, P. J. C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Cell. 107: 43-54, 2001.
22. Yang, G. P., Ross, D. T., Kuang, W. W., Brown, P. O., and Weigel, R. J. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucleic Acids Res., 27: 1517-1523, 1999.
23. Xu, J., Stolk, J. A., Zhang, X., Silva, S. J., Houghton, R. L., Matsumura, M., Vedvick, T. S., Leslie, K. B., Badaro, R., and Reed, S. G. Identification of differentially expressed genes in human prostate cancer using subtraction and microarray. Cancer Res., 60: 1677-1682, 2000.
24. Wang, T., Hopkins, D., Schmidt, C., Silva, S., Houghton, R., Takita, H., Repasky, E., and Reed, S. G. Identification of genes differentially over-expressed in lung squamous cell carcinoma using combination of cDNA subtraction and microarray analysis. Oncogene, 19: 1519-1528, 2000.
25. Welford, S. M., Gregg, J., Chen, E., Garrison, D., Sorensen, P. H., Denny, C. T., and Nelson, S. F. Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization. Nucleic Acids Res., 26: 3059-3065, 1998.
26. Stillman, B. A., and Tonkinson, J. L. Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate. Anal. Biochem., 295: 149-157, 2001.
27. Streilein, J. W. Unraveling immune privilege. Science (Wash. DC), 270: 1158-1159, 1995.
28. Pardoll, D. M. Inducing autoimmune disease to treat cancer. Proc. Natl. Acad. Sci. USA, 96: 5340-5342, 1999.
29. Lee, L. F., Guan, J., Qiu, Y., and Kung, H. J. Neuropeptide-induced androgen independence in prostate cancer cells: roles of nonreceptor tyrosine kinases Etk/Bmx, Src, and focal adhesion kinase. Mol. Cell Biol., 21: 8385-8397, 2001.
30. Lopez-Boado, Y. S., Puente, X. S., Alvarez, S., Tolivia, J., Binderup, L., and Lopez-Otin, C. Growth inhibition of human breast cancer cells by 1,25-dihydroxyvitamin D3 is accompanied by induction of apolipoprotein D expression. Cancer Res., 57: 4091-4097, 1997.
31. Zhang, S. X., Bentel, J. M., Ricciardelli, C., Horsfall, D. J., Haagensen, D. E., Marshall, V. R., and Tilley, W. D. Immunolocalization of apolipoprotein D, androgen receptor and prostate specific antigen in early stage prostate cancers. J. Urol., 159: 548-554, 1998.
32. Chuman, Y., Bergman, A., Ueno, T., Saito, S., Sakaguchi, K., Alaiya, A. A., Franzen, B., Bergman, T., Arnort, D., Auer, G., Appella, E., Jornvall, H., and Linder, S. Napsin A, a member of the aspartic protease family, is abundantly expressed in normal lung and kidney tissue and is expressed in lung adenocarcinomas. FEBS Lett., 462: 129-134, 1999.
33. Krajinovic, M., Ghadirian, P., Richer, C., Sinnett, H., Gandini, S., Perret, C., Lacroix, A., Labuda, D., and Sinnett, D. Genetic susceptibility to breast cancer in French-Canadians: role of carcinogen-metabolizing enzymes and gene-environment interactions. Int. J. Cancer, 92: 220-225, 2001.
34. Hibi, K., Liu, Q., Beaudry, G. A., Madden, S. L., Westra, W. H., Wehage, S. L., Yang, S. C., Heitmiller, R. F., Bertelsen, A. H., Sidransky, D., and Jen, J. Serial analysis of gene expression in non-small cell lung cancer. Cancer Res., 58: 5690-5694, 1998.
35. Davidson, L. A., Black, M., Carey, F. A., Logue, F., and McNicol, A. M. Lung tumours immunoreactive for parathyroid hormone related peptide: analysis of serum calcium levels and tumour type. J. Pathol., 178: 398-401, 1996.
36. Mueller, A., Bachi, T., Hochli, M., Schafer, B. W., and Heizmann, C. W. Subcellular distribution of S100 proteins in tumor cells and their relocation in response to calcium activation. Histochem. Cell Biol., 111: 453-459, 1999.
37. Hough, C. D., Cho, K. R., Zonderman, A. B., Schwartz, D. R., and Morin, P. J. Coordinately up-regulated genes in ovarian cancer. Cancer Res., 61: 3869-3876, 2001.
38. Bronckart, Y., Decaestecker, C., Nagy, N., Harper, L., Schafer, B. W., Salmon, I., Pochet, R., Kiss, R., and Heizman, C. W. Development and progression of malignancy in human colon tissues are correlated with expression of specific Ca(2+)-binding S100 proteins. Histol. Histopathol., 16: 707-712, 2001.
39. Bellahcene, A., and Castronovo, V. Expression of bone matrix proteins in human breast cancer: potential roles in microcalcification formation and in the genesis of bone metastases. Bull. Cancer, 84: 17-24, 1997.
40. Fata, J. M., Kong, Y-Y., Li, J., Sassaki, T., Irie-Sasaki, J., Moorehead R. A., Elliott, R., Scully, S., Voura, E. B., Lacey, D. L., Boyle, W. J., Khokha, R., and Penninger, J. M. The osteoclast differentiation factor osteoprotegerin-ligand is essential for mammary gland development. Cell, 103: 41-50, 2000.
41. van 't Veer, L. J., Dai, H., van de Vijver, M. J., He, Y. D., Hart, A. A.; Mao, M., Peterse, H. L., van der, K. K., Marton, M. J., Witteveen, A. T., Schreiber, G. J., Kerkhoven, R. M., Roberts, C., Linsley, P. S., Bernards, R., and Friend, S. H. Gene expression profiling predicts clinical outcome of breast cancer. Nature (Lond.), 415: 530-536, 2002.
42. van de Vijver, M. J., He, Y. D., van't Veer, L. J., Dai, H., Hart, A. A., Voskuil, D. W., Schreiber, G. J., Peterse, J. L., Roberts, C., Marton, M. J., Parrish, M., Atsma, D., Witteveen, A., Glas, A., Delahaye, L., van der Velde, T., Bartelink, H., Rodenhuis, S., Rutgers, E. T., Friend, S. H., and Bernards, R. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med., 347: 1999-2009, 2002.
43. Bernards, R., and Weinberg, R. A. A progression puzzle. Nature (Lond.), 418: 823, 2002.
44. Kallioniemi, A. Molecular signatures of breast cancer: predicting the future. N. Engl. J. Med., 347: 2067-2068, 2002.
45. Ghellal, A., Li, C., Hayes, M., Byrne, G., Bundred, N., and Kumar, S. Prognostic significance of TGF β1 and TGF β3 in human breast carcinoma. Anticancer Res., 20: 4413-4418, 2000.
46. Byrne, G. J., and Bundred, N. J. Surrogate markers of tumoral angiogenesis. Int. J. Biol. Markers, 15: 334-339, 2000.
47. Herrera-Gayol, A., and Jothy, S. Adhesion proteins in the biology of breast cancer: contribution of CD44. Exp. Mol. Pathol., 66: 149-156, 1999.
48. Shao, Z. M., Sheikh, M. S., Rishi, A. K., Dawson, M. I., Li, X. S., Wilber, J. F., Feng, P., and Fontana, J. A. Thyroid hormone enhancement of estradiol stimulation of breast carcinoma proliferation. Exp. Cell Res., 218: 1-8, 1995.
49. 1 phase of human breast cancer cells. Cell Biol. Int., 26: 19-28, 2002.
50. 2-M checkpoint regulators cyclin B1 and P34CDC2 in breast cancer: a correlation with cellular kinetics. Anticancer Res., 19: 163-169, 1999.
51. Tang, C. K., Gong, X. Q., Moscatello, D. K., Wong, A. J., and Lippman, M. E., Epidermal growth factor receptor vIII enhances tumorigenicity in human breast cancer. Cancer Res., 60: 3081-3087, 2000.
52. Kim, H., and Muller, W. J. The role of the epidermal growth factor receptor family in mammary tumorigenesis and metastasis. Exp. Cell Res., 253: 78-87, 1999. R. E., Nairn, A. C., Greengard, P., Gandy, S. E., and Kirino, Y. Phosphorylationn of Alzheimer β-amyloid precursor-like proteins. Biochemistry, 36: 4643-4649, 1997.
53. Kim, H., and Muller, W. J. The role of the epidermal growth factor receptor family in mammary tumorigenesis and metastasis. Exp. Cell Res., 253: 78-87, 1999. R. E., Nairn, A. C., Greengard, P., Gandy, S. E., and Kirino, Y. Phosphorylationn of Alzheimer β-amyloid precursor-like proteins. Biochemistry, 36: 4643-4649, 1997.
54. Sobin L. H., and Wittekind, W. Ch. International Union Against Cancer. TNM Classification of Malignant Tumors, Ed. 5th. New York: John Wiley & Sons, 1997.