Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression.

Authors

• Steven R Hustinx
• Dengfeng Cao
• Anirban Maitra
• Norihiro Sato
• Sean T Martin
• D Sudhir
• Christine Iacobuzio-Donahue
• John L Cameron
• Charles J Yeo
• Scott E Kern
• Michael Goggins
• Jan Mollenhauer
• Akhilesh Pandey
• Ralph H Hruban

Publication/Presentation Date

12-1-2004

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.

Volume

3

Issue

12

First Page

1254

Last Page

1261

ISSN

1538-4047

Published In/Presented At

Hustinx, S. R., Cao, D., Maitra, A., Sato, N., Martin, S. T., Sudhir, D., Iacobuzio-Donahue, C., Cameron, J. L., Yeo, C. J., Kern, S. E., Goggins, M., Mollenhauer, J., Pandey, A., & Hruban, R. H. (2004). Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression. Cancer biology & therapy, 3(12), 1254–1261. https://doi.org/10.4161/cbt.3.12.1238

Disciplines

Business Administration, Management, and Operations | Health and Medical Administration | Management Sciences and Quantitative Methods

PubMedID

15477757

Department(s)

Administration and Leadership

Document Type

Article