Elsevier

Genomics

Volume 82, Issue 1, July 2003, Pages 78-85
Genomics

Regular article
Analysis of gene expression profiles of gastric normal and cancer tissues by SAGE

https://doi.org/10.1016/S0888-7543(03)00098-3Get rights and content

Abstract

In an attempt to understand the molecular bases of gastric cancer progression, we have analyzed the differentially expressed genes in gastric cancer by SAGE. Four SAGE cDNA tag libraries were constructed from two sets of gastric cancer and normal tissues and 241,127 tags were obtained. By comparing the tags from cancer and normal tissues, 414 differentially expressed tags, representing 383 genes, were identified in cancer tissues (p ≤ 0.01). Of the 414 tags, 50 tags were previously unidentified and potentially novel genes. Although each gastric cancer tissue revealed more than 200 differentially expressed genes compared to the respective normal tissue, the number of genes with consistent regulation patterns in both cancer tissues was 51: 12 up-regulated and 39 down-regulated genes. The genes that showed consistent regulation patterns included well-known genes such as Trefoil factor 3, RegIV, gastric intrinsic factor, and lactotransferrin as well as a few novel candidates. Interestingly, the expression of several genes, such as osteoglycin, prostate stem cell antigen, and histone deacetylase 3, was variable in the two normal tissues but similar in the cancer tissues. The expression profiles of these genes in normal tissues, possibly due to genetic background, could greatly affect individual sensitivity to cancer development and/or progression. The genes identified in this study will provide useful target genes for diagnosis and molecular treatment of gastric cancer.

Section snippets

Analysis of SAGE libraries

Each SAGE library contained more than 50,000 tags and the number of unique transcripts in each library ranged from 17,724 to 23,131 (Table 1). Overall about 70% of the unique tags were matched to either known genes or EST clusters in the NCBI Unigene database. About 30% of the unique tags had no matches to any known sequence in the database (no match), representing potentially novel genes.

Overall gene expression profiles of normal and cancer gastric tissues

The gene expression profiles of the two normal tissues and two cancer tissues from two patients were not

Discussion

In an effort to provide new molecular markers and to understand the molecular mechanism of gastric cancer better, we have generated complete and comprehensive gene expression profiles for two sets of human normal and cancer gastric tissues using the SAGE technique and obtained a large number of genes differentially expressed in cancer, including previously unidentified genes. The gene profiles of the normal tissues showed that the expression of at least 10% of genes was significantly different,

Normal and cancer gastric tissues

The cancer tissues and the corresponding adjacent normal gastric tissues of two patients were obtained from surgical resections with informed consent from patients. Both patients were Korean females in their 50s and had advanced diffuse-type gastric carcinoma. Both cancer tissues invaded more than the muscularis propria and had accompanied lymph node metastasis, diagnosed intraoperatively by frozen section analysis of isolated lymph nodes. The presence of ulceration in tumorous lesions or

Acknowledgements

We greatly thank Dr. Sang-Gyu Lee (University of Chicago) for his helpful technical advice and Sun-Hee Jung for her editorial assistance. This research is supported by the Project of Functional Analysis of Human Genome, 21C Frontier (M101KB010001-02K0201-00220).

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    These authors contributed equally to this article.

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