Identification of genes that exhibit changes in expression on the 8p chromosomal arm by the Systematic Multiplex RT-PCR (SM RT-PCR) and DNA microarray hybridization methods

Gene Expression

Volumn 14, Issue 4, 2008, Pages 217-227

  Yamamoto, Fumiichiro ^a   Yamamoto, Miyako ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

Breast cancer; Chromosomal scanning; Chromosome 8p; DNA microarray hybridization; Gene expression; Real time qRT PCR; Systematic multiplex RT PCR (SM RT PCR)

Indexed keywords

TRANSCRIPTION FACTOR SOX7;

ARTICLE; BREAST CANCER; CANCER CELL CULTURE; CELL STRAIN LNCAP; CELL STRAIN MCF 7; CHROMOSOME 8P; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; DOWN REGULATION; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE LOCATION; HUMAN; HUMAN CELL; MULTIPLEX POLYMERASE CHAIN REACTION; NUCLEOTIDE SEQUENCE; PROSTATE CANCER; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

BREAST; BREAST NEOPLASMS; CELL LINE, TUMOR; CHROMOSOMES, HUMAN, PAIR 8; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, NEOPLASM; FEMALE; GENE EXPRESSION; GENES, TUMOR SUPPRESSOR; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ONCOGENES; PROSTATIC NEOPLASMS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 58149483588     PISSN: 10522166     EISSN: None     Source Type: Journal    
DOI: 10.3727/105221608786883816     Document Type: Article

References (40)

1. Albertson, D. G.; Ylstra, B.; Segraves, R.; Collins, C.; Dairkee, S. H.; Kowbel, D.; Kuo, W. L.; Gray, J. W.; Pinkel, D. Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat. Genet. 25:144-146; 2000.
2. Capon, D. J.; Seeburg, P. H.: McGrath, J. P.; Hayflick, J. S.; Edman, U.; Levinson, A. D.; Goeddel, D. V. Activation of Ki-ras2 gene in human colon and lung carcinomas by two different point mutations. Nature 304: 507-513; 1983.
3. Cher, M. L.; MacGrogan, D.; Bookstein, R.; Brown, J. A.; Jenkins, R. B.; Jensen, R. H. Comparative genomic hybridization, allelic imbalance, and fluorescence in situ hybridization on chromosome 8 in prostate cancer. Genes Chromosomes Cancer 11:153-162; 1994.
4. Clark, J.; Edwards, S.; Feber, A.; Flohr, P.; John, M.; Giddings, I.; Crossland, S.; Stratton, M. R.; Wooster, R.; Campbell, C.; Cooper, C. S. Genome-wide screening for complete genetic loss in prostate cancer by comparative hybridization onto cDNA microarrays. Oncogene 22:1247-1252; 2003.
5. Courjal, F.; Theillet, C. Comparative genomic hybridization analysis of breast tumors with predetermined profiles of DNA amplification. Cancer Res. 57:4368-4377; 1997.
6. Dong, J. T. Chromosomal deletions and tumor suppressor genes in prostate cancer. Cancer Metastasis Rev. 20:173-193; 2001.
7. Finch, P. W.; He, X.; Kelley, M. J.; Uren, A.; Schaudies, R. P.; Popescu, N. C.; Rudikoff, S.; Aaronson, S. A.; Varmus, H. E.; Rubin, J. S. Purification and molecular cloning of a secreted, Frizzled-related antagonist of Wnt action. Proc. Natl. Acad. Sci. USA 94: 6770-6775; 1997.
8. Forozan, F.; Mahlamaki, E. H.; Monni, O.; Chen, Y.; Veldman, R.; Jiang, Y.; Gooden, G. C.; Ethier, S. P.; Kallioniemi, A.; Kallioniemi, O. P. Comparative genomic hybridization analysis of 38 breast cancer cell lines: A basis for interpreting complementary DNA microarray data. Cancer Res. 60:4519-4525; 2000.
9. Gaudet, S.; Branton, D.; Lue, R. A. Characterization of PDZ-binding kinase, a mitotic kinase. Proc. Natl. Acad. Sci. USA 97:5167-5172; 2000.
10. Grasso, A. W.; Wen, D.; Miller, C. M.; Rhim, J. S.; Pretlow, T. G.; Kung, H. J. ErbB kinases and NDF signaling in human prostate cancer cells. Oncogene 15: 2705-2716; 1997.
11. Holmes, W. E.; Sliwkowski, M. X.; Akita, R. W.; Henzel, W. J.; Lee, J.; Park, J. W.; Yansura, D.; Abadi, N.; Raab, H.; Lewis, G. D.; Shepard, H. M.; Kuang, W-J.; Wood, W.; Goeddel, D. V.; Vandlen, R. L. Identification of heregulin, a specific activator of p185erbB2. Science 256:1205-1210; 1992.
12. Hou, F.; Zou, H. Two human orthologues of Eco1/Ctf7 acetyltransferases are both required for proper sister-chromatid cohesion. Mol. Biol. Cell 16:3908-3918; 2005.
13. Kallioniemi, A.; Kallioniemi, O. P.; Sudar, D.; Rutovitz, D.; Gray, J. W.; Waldman, F.; Pinkel, D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818-821; 1992.
14. Katoh, M.; Katoh, M. Comparative genomics on FGF20 orthologs. Oncol. Rep. 14:287-290; 2005.
15. Koch, J.; Gartner, S.; Li, C. M.; Quintern, L. E.; Bernardo, K.; Levran, O.; Schnabel, D.; Desnick, R. J.; Schuchman, E. H.; Sandhoff, K. Molecular cloning and characterization of a full-length complementary DNA encoding human acid ceramidase. Identification of the first molecular lesion causing Farber disease. J. Biol. Chem. 271:33110-33115; 1996.
16. Kohl, N. E.; Kanda, N.; Schreck, R. R.; Bruns, G.; Latt, S. A.; Gilbert, F.; Alt, F. W. Transposition and amplification of oncogene-related sequences in human neuroblastomas. Cell 35:359-367; 1983.
17. Lee, Z. H.; Kim, H.; Ahn, K. Y.; Seo, K. H.; Kim, J. K.; Bae, C. S.; Kim, K. K. Identification of a brain specific protein that associates with a refsum disease gene product, phytanoyl-CoA alpha-hydroxylase. Brain Res. Mol. Brain Res. 75:237-247; 2000.
18. Li, J.; Yen, C.; Liaw, D.; Podsypanina, K.; Bose, S.; Wang, S. I.; Puc, J.; Miliaresis, C.; Rodgers, L.; McCombie, R.; Bigner, S. H.; Giovanella, B. C.; Ittmann, M.; Tycko, B.; Hibshoosh, H.; Wigler, M. H.; Parsons, R. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 275:1943-1947; 1997.
19. Lodygin, D.; Epanchintsev, A.; Menssen, A.; Diebold, J.; Hermeking, H. Functional epigenomics identifies genes frequently silenced in prostate cancer. Cancer Res. 65:4218-4227; 2005.
20. Melkonyan, H. S.; Chang, W. C.; Shapiro, J. P.; Mahadevappa, M.; Fitzpatrick, P. A.; Kiefer, M. C.; Tomei, L. D.; Umansky, S. R. SARPs: A family of secreted apoptosis-related proteins. Proc. Natl. Acad. Sci. USA 94:13636-13641; 1997.
21. Nakano, H.; Yamamoto, F.; Neville, C.; Evans, D.; Mizuno, T.; Perucho, M. Isolation of transforming sequences of two human lung carcinomas: structural and functional analysis of the activated c-K-ras oncogenes. Proc. Natl. Acad. Sci. USA 81:71-75; 1984.
22. Oka, H.; Shiozaki, H.; Kobayashi, K.; Inoue, M.; Tahara, H.; Kobayashi, T.; Takatsuka, Y.; Matsuyoshi, N.; Hirano, S.; Takeichi, M. Expression of E-cadherin cell adhesion molecules in human breast cancer tissues and its relationship to metastasis. Cancer Res. 53: 1696-1701; 1993.
23. Peles, E.; Bacus, S. S.; Koski, R. A.; Lu, H. S.; Wen, D.; Ogden, S. G.; Levy, R. B.; Yarden, Y. Isolation of the neu/HER-2 stimulatory ligand: A 44 kd glycoprotein that induces differentiation of mammary tumor cells. Cell 69:205-216; 1992.
24. Pinkel, D.; Segraves, R.; Sudar, D.; Clark, S.; Poole, I.; Kowbel, D.; Collins, C.; Kuo, W. L.; Chen, C.; Zhai, Y.; Dairkee, S. H.; Ljung, B. M.; Gray, J. W.; Albertson, D. G. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20:207-211; 1998.
25. Pollack, J. R.; Perou, C. M.; Alizadeh, A. A.; Eisen, M. B.; Pergamenschikov, A.; Williams, C. F.; Jeffrey, S. S.; Botstein, D.; Brown, P. O. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23:41-46; 1999.
26. Pollack, J. R.; Sorlie, T.; Perou, C. M.; Rees, C. A.; Jeffrey, S. S.; Lonning, P. E.; Tibshirani, R.; Botstein, D.; Borresen-Dale, A. L.; Brown, P. O. 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 99:12963-12968; 2002.
27. Schena, M. Genome analysis with gene expression microarrays. Bioessays 18:427-431; 1996.
28. Schena, M.; Shalon, D.; Davis, R. W.; Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470; 1995.
29. Shimizu, K.; Birnbaum, D.; Ruley, M. A.; Fasano, O.; Suard, Y.; Edlund, L.; Taparowsky, E.; Goldfarb, M.; Wigler, M. Structure of the Ki-ras gene of the human lung carcinoma cell line Calu-1. Nature 304:497-500; 1983.
30. Sjoblom, T.; Jones, S.; Wood, L. D.; Parsons, D. W.; Lin, J.; Barber, T. D.; Mandelker, D.; Leary, R. J.; Ptak, J.; Silliman, N.; Szabo, S.; Buckhaults, P.; Farrell, C.; Meeh, P.; Markowitz, S. D.; Willis, J.; Dawson, D.; Willson, J. K.; Gazdar, A. F.; Hartigan, J.; Wu, L.; Liu, C.; Parmigiani, G.; Park, B. H.; Bachman, K. E.; Papadopoulos, N.; Vogelstein, B.; Kinzler, K. W.; Velculescu, V. E. The consensus coding sequences of human breast and colorectal cancers. Science 314:268-274; 2006.
31. Takash, W.; Canizares, J.; Bonneaud, N.; Poulat, F.; Mattei, M. G.; Jay, P.; Berta, P. SOX7 transcription factor: sequence, chromosomal localisation, expression, transactivation and interference with Wnt signalling. Nucleic Acids Res. 29:4274-4283; 2001.
32. Takayama, Y.; Kamimura, Y.; Okawa, M.; Muramatsu, S.; Sugino, A.; Araki, H. GINS, a novel multiprotein complex required for chromosomal DNA replication in budding yeast. Genes Dev. 17:1153-1165; 2003.
33. Tsujimoto, Y.; Finger, L. R.; Yunis, J.; Nowell, P. C.; Croce, C. M. Cloning of the chromosome breakpoint of neoplastic B cells with the t(14;18) chromosome translocation. Science 226:1097-1099; 1984.
34. Ugolini, F.; Charafe-Jauffret, E.; Bardou, V. J.; Geneix, J.; Adelaide, J.; Labat-Moleur, F.; Penault-Llorca, F.; Longy, M.; Jacquemier, J.; Birnbaum, D.; Pebusque, M. J. WNT pathway and mammary carcinogenesis: loss of expression of candidate tumor suppressor gene SFRP1 in most invasive carcinomas except of the medullary type. Oncogene 20:5810-5817; 2001.
35. van der Ven, P. F.; Speel, E. J.; Albrechts, J. C.; Ramaekers, F. C.; Hopman,i A. H.; Furst, D. O. Assignment of the human gene for endosarcomeric cytoskeletal M-protein (MYOM2) to 8p23.3. Genomics 55:253-255; 1999.
36. Yamamoto, F.; Yamamoto, M. Scanning copy number and gene expression on the 18q21-qter chromosomal region by the systematic multiplex PCR and reverse transcription-PCR methods. Electrophoresis 28:1882-1895; 2007.
37. Yamamoto, M.; Ahn, R. H.: Yamamoto, F. Scanning copy number and gene expression on the 16p13.3-13.2 chromosomal region by the systematic multiplex polymerase chain reaction and reverse transcription-polymerase chain reaction methods. Electrophoresis 27: 2529-2540; 2006.
38. Yamamoto, M.; Takai, D.; Yamamoto, F.; Yamamoto, F. Comprehensive expression profiling of highly homologous 39 Hox genes in 26 different human adult tissues by the Modified Systematic Multiplex RT-PCR method reveals tissue-specific expression pattern that suggests an important role of chromosomal structure in the regulation of Hox gene expression in adult tissues. Gene Expr. 11:199-210; 2003.
39. Yamamoto, M.; Yamamoto, A.; Leung, P. C.; Yamamoto, F. Gene expression analysis of an integrin family of genes by Systematic Multiplex RT-PCR. Electrophoresis 25:2201-2211; 2004.
40. Yamamoto, M.; Yamamoto, F.; Luong, T. T.; Williams, T.; Kominato, Y.; Yamamoto, F. Expression profiling of 68 glycosyltransferase genes in 27 different human tissues by the systematic multiplex reverse transcription-polymerase chain reaction method revealed clustering of sexually related tissues in hierarchical clustering algorithm analysis. Electrophoresis 24:2295-2307; 2003.