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Open Access Research article

Distinctions in gastric cancer gene expression signatures derived from laser capture microdissection versus histologic macrodissection

Hark Kyun Kim12, Joseph Kim1, Susie Korolevich3, Il Ju Choi2, Chang Hee Kim3, David J Munroe3 and Jeffrey E Green1*

  • * Corresponding author: Jeffrey E Green jegreen@nih.gov

  • † Equal contributors

Author Affiliations

1 National Cancer Institute, Bethesda, MD, 20892, USA

2 National Cancer Center, Goyang, Gyeonggi, 410-769, Republic of Korea

3 SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD, 21701, USA

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BMC Medical Genomics 2011, 4:48  doi:10.1186/1755-8794-4-48

Published: 2 June 2011

Abstract

Background

Gastric cancer samples obtained by histologic macrodissection contain a relatively high stromal content that may significantly influence gene expression profiles. Differences between the gene expression signature derived from macrodissected gastric cancer samples and the signature obtained from isolated gastric cancer epithelial cells from the same biopsies using laser-capture microdissection (LCM) were evaluated for their potential experimental biases.

Methods

RNA was isolated from frozen tissue samples of gastric cancer biopsies from 20 patients using both histologic macrodissection and LCM techniques. RNA from LCM was subject to an additional round of T7 RNA amplification. Expression profiling was performed using Affymetrix HG-U133A arrays. Genes identified in the expression signatures from each tissue processing method were compared to the set of genes contained within chromosomal regions found to harbor copy number aberrations in the tumor samples by array CGH and to proteins previously identified as being overexpressed in gastric cancer.

Results

Genes shown to have increased copy number in gastric cancer were also found to be overexpressed in samples obtained by macrodissection (LS P value < 10-5), but not in array data generated using microdissection. A set of 58 previously identified genes overexpressed in gastric cancer was also enriched in the gene signature identified by macrodissection (LS P < 10-5), but not in the signature identified by microdissection (LS P = 0.013). In contrast, 66 genes previously reported to be underexpressed in gastric cancer were enriched in the gene signature identified by microdissection (LS P < 10-5), but not in the signature identified by macrodissection (LS P = 0.89).

Conclusions

The tumor sampling technique biases the microarray results. LCM may be a more sensitive collection and processing method for the identification of potential tumor suppressor gene candidates in gastric cancer using expression profiling.