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Transporter and ion channel gene expression after Caco-2 cell differentiation using 2 different microarray
Christopher P Landowski1, Pascale Anderle, Duxin Sun
1Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
Abstract:
mRNA expression profiles had previously been measured in Caco-2 cells (human colonic carcinoma cells) using either custom-designed spotted oligonucleotide arrays or Affymetrix GeneChip oligonucleotide arrays. The Caco-2 cells used were from different clones and were examined under slightly different culture conditions commonly encountered when Caco-2 cells are used as a model tissue for studying intestinal transport and metabolism in different laboratories. In this study, we compared gene expression profiles of Caco-2 cells generated with different arrays to assess the validity of conclusions derived from the 2 independent studies, with a focus on changes in transporter and ion channel mRNA expression levels on Caco-2 cell differentiation. Significant changes in expression levels upon differentiation were observed with 78 genes, with probes common to both arrays. Of these, 18 genes were upregulated and 36 genes were downregulated. The 2 arrays yielded discrepant results for 24 genes, showing significant changes upon differentiation. The results from the 2 arrays correlated well for genes expressed above average levels (r = 0.75, P < 0.01, n = 25) and poorly for genes expressed at low levels (r = 0.08, P > 0.05, n = 25). Overall correlation across the 2 platforms was r = 0.45 (P < 0.01) for the 78 genes, with similar results from both arrays. Despite differences in experimental conditions and array technology, similar results were obtained for most genes.
Insights
Comparing gene expression arrays in Caco-2 cells revealed that despite different conditions, both custom spotted oligonucleotide arrays and Affymetrix GeneChip arrays provided similar results for most transporter and ion channel mRNA levels.
Area of Science:
- Cell Biology
- Genomics
- Molecular Biology
Background:
- Caco-2 cells are a widely used model for intestinal studies.
- Previous mRNA expression profiling used different array technologies and conditions.
- Variability in experimental setups can impact study conclusions.
Purpose of the Study:
- To compare gene expression profiles from two distinct array platforms in Caco-2 cells.
- To assess the reliability of conclusions drawn from independent studies using these arrays.
- To focus on changes in transporter and ion channel mRNA during Caco-2 cell differentiation.
Main Methods:
- Utilized custom-designed spotted oligonucleotide arrays and Affymetrix GeneChip arrays.
- Analyzed mRNA expression profiles of Caco-2 cells under differentiation.
- Focused on genes with common probes across both array platforms.
Main Results:
- Significant expression changes were observed for 78 genes common to both arrays upon differentiation.
- 18 genes were upregulated and 36 were downregulated.
- Correlation was high for highly expressed genes (r=0.75) and low for lowly expressed genes (r=0.08).
- Overall correlation across platforms was moderate (r=0.45).
Conclusions:
- Despite differences in array technology and experimental conditions, both platforms yielded largely similar results for Caco-2 cell mRNA expression.
- Conclusions regarding transporter and ion channel mRNA changes during differentiation are generally valid across platforms.
- Lowly expressed genes may show greater variability between array platforms.
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