Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression
- PMID: 15477757
- DOI: 10.4161/cbt.3.12.1238
Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression
Abstract
Serial analysis of gene expression (SAGE) is a powerful tool for the discovery of novel tumor markers. The publicly available online SAGE libraries of normal and neoplastic tissues (http://www.ncbi.nlm.nih.gov/SAGE/) have recently been expanded; in addition, a more complete annotation of the human genome and better biocomputational techniques have substantially improved the assignment of differentially expressed SAGE "tags" to human genes. These improvements have provided us with an opportunity to re-evaluate global gene expression in pancreatic cancer using existing SAGE libraries. SAGE libraries generated from six pancreatic cancers were compared to SAGE libraries generated from 11 non-neoplastic tissues. Compared to normal tissue libraries, we identified 453 SAGE tags as differentially expressed in pancreatic cancer, including 395 that mapped to known genes and 58 "uncharacterized" tags. Of the 395 SAGE tags assigned to known genes, 223 were overexpressed in pancreatic cancer, and 172 were underexpressed. In order to map the 58 uncharacterized differentially expressed SAGE tags to genes, we used a newly developed resource called TAGmapper (http://tagmapper.ibioinformatics.org), to identify 16 additional differentially expressed genes. The differential expression of seven genes, involved in multiple cellular processes such as signal transduction (MIC-1), differentiation (DMBT1 and Neugrin), immune response (CD74), inflammation (CXCL2), cell cycle (CEB1) and enzymatic activity (Kallikrein 6), was confirmed by either immunohistochemical labeling of tissue microarrays (Kallikrein 6, CD74 and DMBT1) or by RT-PCR (CEB1, Neugrin, MIC1 and CXCL2). Of note, Neugrin was one of the genes whose previously uncharacterized SAGE tag was correctly assigned using TAGmapper, validating the utility of this program. Novel differentially expressed genes in a cancer type can be identified by revisiting updated and expanded SAGE databases. TAGmapper should prove to be a powerful tool for the discovery of novel tumor markers through assignment of uncharacterized SAGE tags.
Similar articles
-
Highly expressed genes in pancreatic ductal adenocarcinomas: a comprehensive characterization and comparison of the transcription profiles obtained from three major technologies.Cancer Res. 2003 Dec 15;63(24):8614-22. Cancer Res. 2003. PMID: 14695172
-
Discovery of new markers of cancer through serial analysis of gene expression: prostate stem cell antigen is overexpressed in pancreatic adenocarcinoma.Cancer Res. 2001 Jun 1;61(11):4320-4. Cancer Res. 2001. PMID: 11389052
-
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 Dec;7(12):3862-8. Clin Cancer Res. 2001. PMID: 11751476
-
Technology evaluation: SAGE, Genzyme molecular oncology.Curr Opin Mol Ther. 2001 Feb;3(1):85-96. Curr Opin Mol Ther. 2001. PMID: 11249736 Review.
-
[Transcriptomes for serial analysis of gene expression].J Soc Biol. 2002;196(4):303-7. J Soc Biol. 2002. PMID: 12645300 Review. French.
Cited by
-
Laminin, gamma 2 (LAMC2): a promising new putative pancreatic cancer biomarker identified by proteomic analysis of pancreatic adenocarcinoma tissues.Mol Cell Proteomics. 2013 Oct;12(10):2820-32. doi: 10.1074/mcp.M112.023507. Epub 2013 Jun 24. Mol Cell Proteomics. 2013. PMID: 23798558 Free PMC article.
-
Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling.Neoplasia. 2023 Feb;36:100871. doi: 10.1016/j.neo.2022.100871. Epub 2023 Jan 5. Neoplasia. 2023. PMID: 36610378 Free PMC article.
-
Perineural invasion and associated pain in pancreatic cancer.Nat Rev Cancer. 2011 Sep 23;11(10):695-707. doi: 10.1038/nrc3131. Nat Rev Cancer. 2011. PMID: 21941281 Review.
-
Human Mitoribosome Biogenesis and Its Emerging Links to Disease.Int J Mol Sci. 2021 Apr 7;22(8):3827. doi: 10.3390/ijms22083827. Int J Mol Sci. 2021. PMID: 33917098 Free PMC article. Review.
-
Ocoxin Oral Solution Exerts an Antitumoral Effect in Pancreatic Cancer and Reduces the Stromal-Mediated Chemoresistance.Pancreas. 2019 Apr;48(4):555-567. doi: 10.1097/MPA.0000000000001277. Pancreas. 2019. PMID: 30946238 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Medical