Serial analysis of gene expression and cancer

Current Opinion in Oncology

Volumn 15, Issue 1, 2003, Pages 44-49

  Hermeking, Heiko ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; FLUOROURACIL;

CANCER; CANCER DIAGNOSIS; CANCER GENETICS; CELL SPECIFICITY; DISEASE MARKER; DNA MICROARRAY; FUTUROLOGY; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC COMPLEMENTATION; HUMAN; HUMAN CELL; HUMAN TISSUE; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE DIAGNOSIS; REVIEW; TRANSCRIPTION REGULATION;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, TUMOR SUPPRESSOR; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION, GENETIC; TUMOR MARKERS, BIOLOGICAL;

EID: 0037246597     PISSN: 10408746     EISSN: None     Source Type: Journal    
DOI: 10.1097/00001622-200301000-00006     Document Type: Review

References (44)

1. Velculescu VE, Zhang L, Vogelstein B, et al.: Serial analysis of gene expression. Science 1995, 270:484-487.
2. Griffin TJ, Gygi SP, Ideker T, et al.: Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 2002, 1:323-333. • A pilot study combining transcriptome and proteome analysis.
3. Polyak K, Xia Y, Zweier JL, et al.: A model for p53-induced apoptosis. Nature 1997, 389:300-305.
4. van den Berg A, van der Leij J, Poppema S: Serial analysis of gene expression: rapid RT-PCR analysis of unknown SAGE tags. Nucleic Acids Res 1999, 1;27:e17.
5. Chen J, Lee S, Zhou G, et al.: High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3′ complementary DNAs. Genes Chromosomes Cancer 2002, 33:252-261.
6. Saha S, Sparks AB, Rago C, et al.: Using the transcriptome to annotate the genome. Nat Biotechnol 2002, 20:508-512. •• Use of Mme I instead of BsmF I allows the researcher to obtain 21-bp SAGE tags sufficient for genome annotation.
7. Buetow KH, Klausner RD, Fine H, et al.: Cancer Molecular Analysis Project: weaving a rich cancer research tapestry. Cancer Cell 2002, 1:315-318. •• Detailed description of the search features on the CGAP-SAGE Web site.
8. Strausberg RL, Camargo AA, Riggins GJ, et al.: An international database and integrated analysis tools for the study of cancer gene expression. Pharmacogenomics J 2002, 2:156-164.
9. Boon K, Osorio EC, Greenhut SF, et al.: An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A 2002, 99:11287-11292. •• Official publication of the SAGE Genie software used for the CGAP-Web site.
10. Zhang L, Zhou W, Velculescu VE, et al.: Gene expression profiles in normal and cancer cells. Science 1997, 276:1268-1272.
11. Riggins GJ: Using serial analysis of gene expression to identify tumor markers and antigens. Dis Markers 2001, 17:41-48.
12. Sawiris GP, Sherman-Baust CA, Becker KG, et al.: Development of a highly specialized cDNA array for the study and diagnosis of epithelial ovarian cancer. Cancer Res 2002, 62:2923-2928. •• A combination of SAGE and microarray analysis that promises to be useful for other types of cancer.
13. Buckhaults P, Rago C, St Croix B, et al.: Secreted and cell surface genes expressed in benign and malignant colorectal tumors. Cancer Res 2001, 61:6996-7001.
14. Porter DA, Krop IE, Nasser S, et al.: A SAGE (serial analysis of gene expression) view of breast tumor progression. Cancer Res 2001, 61:5697-5702. •• Extensive analysis of expression profiles during breast cancer progression.
15. Nacht M, Dracheva T, Gao Y, et al.: Molecular characteristics of non-small cell lung cancer. Proc Natl Acad Sci U S A 2001, 98:15203-15208.
16. Mitas M, Mikhitarian K, Hoover L, et al.: Prostate-specific Ets (PSE) factor: a novel marker for detection of metastatic breast cancer in axillary lymph nodes. Br J Cancer 2002, 86:899-904.
17. Miksicek RJ, Myal Y, Watson PH, et al.: Identification of a novel breast- and salivary gland-specific, mucin-like gene strongly expressed in normal and tumor human mammary epithelium. Cancer Res 2002, 62:2736-2740.
18. Argani P, Iacobuzio-Donahue C, Ryu B, et al.: Mesothelin is overexpressed in the vast majority of ductal adenocarcinomas of the pancreas: identification of a new pancreatic cancer marker by serial analysis of gene expression (SAGE). Clin Cancer Res 2001, 7:3862-3868.
19. Argani P, Rosty C, Reiter RE, et al.: Discovery of new markers of cancer through serial analysis of gene expression: prostate stem cell antigen is overexpressed in pancreatic adenocarcinoma. Cancer Res 2001, 61:4320-4324.
20. Iacobuzio-Donahue CA, Maitra A, Shen-Ong GL, et al.: Discovery of novel tumor markers of pancreatic cancer using global gene expression technology. Am J Pathol 2002, 160:1239-1249.
21. Shawver LK, Slamon D, Ullrich A: Smart drugs: tyrosine kinase inhibitors in cancer therapy. Cancer Cell 2002, 1:117-123.
22. Saha S, Bardelli A, Buckhaults P, et al.: A phosphatase associated with metastasis of colorectal cancer. Science 2001, 294:1343-1346. •• Identification of a tyrosine phosphatase with potential therapeutic relevance.
23. Folkman J: Angiogenesis-dependent diseases. Semin Oncol 2001, 28:536-542.
24. St Croix B, Rago C, Velculescu V, et al.: Genes expressed in human tumor endothelium. Science 2000, 289:1197-1202.
25. Carson-Walter EB, Watkins DN, Nanda A, et al.: Cell surface tumor endothelial markers are conserved in mice and humans. Cancer Res 2001, 61:6649-6655. •• Excellent example of tumor-specific gene expression with relevance for cancer therapy.
26. Hwang PM, Bunz F, Yu J, et al.: Ferredoxin reductase affects p53-dependent, 5-fluorouracil-induced apoptosis in colorectal cancer cells. Nat Med 2001, 7:1111-1117.
27. Hermeking H, Lengauer C, Polyak K, et al.: 14-3-3 sigma is a p53-regulated inhibitor of G2/M progression. Mol Cell 1997, 1:3-11.
28. He TC, Sparks AB, Rago C, et al.: Identification of c-MYC as a target of the APC pathway. Science 1998, 281:1509-1512.
29. He TC, Chan TA, Vogelstein B, et al.: PPARdelta is an APC-regulated target of nonsteroidal anti-inflammatory drugs. Cell 1999, 99:335-345.
30. Hermeking H, Rago C, Schuhmacher M, et al.: Identification of CDK4 as a target of c-MYC. Proc Natl Acad Sci U S A 2000, 97:2229-2234.
31. Polyak K, Riggins GJ: Gene discovery using the serial analysis of gene expression technique: implications for cancer research. J Clin Oncol 2001, 19:2948-2958.
32. Trumpp A, Refaeli Y, Oskarsson T, et al.: c-Myc regulates mammalian body size by controlling cell number but not cell size. Nature 2001, 414:768-773.
33. Jain M, Arvanitis C, Chu K, et al.: Sustained loss of a neoplastic phenotype by brief inactivation of MYC. Science 2002, 297:102-104.
34. Menssen A, Hermeking H: Characterization of the c-MYC-regulated transcriptome by SAGE: Identification and analysis of c-MYC target genes. Proc Natl Acad Sci U S A 2002, 99:6274-6279. •• Confirmation of SAGE results by microarray analysis, quantitative polymerase chain reaction, and chromatin immunoprecipitation.
35. Sin N, Meng L, Wang MQW, et al.: The anti-angiogenic agent fumagillin covalently binds and inhibits the methionine aminopeptidase, MetAP-2. Proc Nat Acad Sci U S A 1997, 94:6099-6103.
36. Caldwell MC, Hough C, Furer S, et al.: Serial analysis of gene expression in renal carcinoma cells reveals VHL-dependent sensitivity to TNFalpha cytotoxicity. Oncogene 2002, 21:929-936.
37. Zawel L, Yu J, Torrance CJ, et al.: DEC1 is a downstream target of TGF-beta with sequence-specific transcriptional repressor activities. Proc Natl Acad Sci U S A 2002, 99:2848-2853.
38. Elbashir SM, Harborth J, Lendeckel W, et al.: Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001, 411:494-498.
39. Brummelkamp TR, Bernards R, Agami R: A system for stable expression of short interfering RNAs in mammalian cells. Science 2002, 296:550-553.
40. Jiang C, Lu H, Vincent KA, et al.: Gene expression profiles in human cardiac cells subjected to hypoxia or expressing a hybrid form of HIF-1 alpha. Physiol Genomics 2002, 8:23-32.
41. Lal A, Peters H, St Croix B, et al.: Transcriptional response to hypoxia in human tumors. J Natl Cancer Inst 2001, 93:1337-1343. •• A step toward understanding therapy resistance and angiogenesis induced by hypoxia in tumors.
42. Seth P, Krop I, Porter D, et al.: Novel estrogen and tamoxifen induced genes identified by SAGE (serial analysis of gene expression). Oncogene 2002, 21:836-843.
43. Waghray A, Feroze F, Schober MS, et al.: Identification of androgen-regulated genes in the prostate cancer cell line LNCaP by serial analysis of gene expression and proteomic analysis. Proteomics 2001, 1:1327-1338.
44. Untergasser G, Koch HB, Menssen A, et al.: Characterization of Epithelial Senescence by Serial Analysis of Gene Expression: Identification of Genes Potentially Involved in Prostate Cancer. Cancer Research 2002, 62:6255-6262. •• The first SAGE analysis of senescence in epithelial cells.