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Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway
Prashanna Balaji Venkatasubramanian1, Gamze Toydemir2, Nicole de Wit1
1Wageningen University & Research, Food & Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands.
Abstract:
Intestinal epithelial cells, like Caco-2, are commonly used to study the interaction between food, other luminal factors and the host, often supported by microarray analysis to study the changes in gene expression as a result of the exposure. However, no compiled dataset for Caco-2 has ever been initiated and Caco-2-dedicated gene expression networks are barely available. Here, 341 Caco-2-specific microarray samples were collected from public databases and from in-house experiments pertaining to Caco-2 cells exposed to pathogens, probiotics and several food compounds. Using these datasets, a gene functional association network specific for Caco-2 was generated containing 8937 nodes 129711 edges. Two in silico methods, a modified version of biclustering and the new Differential Expression Correlation Analysis, were developed to identify Caco-2-specific gene targets within a pathway of interest. These methods were subsequently applied to the AhR and Nrf2 signalling pathways and altered expression of the predicted target genes was validated by qPCR in Caco-2 cells exposed to coffee extracts, known to activate both AhR and Nrf2 pathways. The datasets and in silico method(s) to identify and predict responsive target genes can be used to more efficiently design experiments to study Caco-2/intestinal epithelial-relevant biological processes.
Insights
This study compiles Caco-2 gene expression data, creating a dedicated network and novel analysis tools. These resources aid in efficiently studying intestinal epithelial cell responses to various exposures.
Area of Science:
- * Cell biology
- * Bioinformatics
- * Molecular biology
Background:
- * Caco-2 intestinal epithelial cells are vital models for studying host interactions with luminal factors.
- * Existing gene expression data for Caco-2 cells is fragmented, limiting network analysis.
- * There is a need for Caco-2-specific gene expression networks and analytical tools.
Purpose of the Study:
- * To create a comprehensive gene functional association network for Caco-2 cells.
- * To develop novel in silico methods for identifying Caco-2-specific gene targets.
- * To validate these methods using known signaling pathways and experimental exposures.
Main Methods:
- * Compilation of 341 Caco-2 microarray samples from public and in-house sources.
- * Generation of a Caco-2-specific gene functional association network (8937 nodes, 129711 edges).
- * Development and application of biclustering and Differential Expression Correlation Analysis (DECA) for target gene identification.
- * Validation of predicted gene targets using quantitative PCR (qPCR).
Main Results:
- * A robust Caco-2 gene functional association network was successfully constructed.
- * Novel in silico methods (biclustering, DECA) were developed to identify pathway-specific gene targets.
- * Predicted target genes in AhR and Nrf2 pathways were validated by qPCR in response to coffee extracts.
Conclusions:
- * The developed Caco-2 gene network and in silico tools enhance the study of intestinal epithelial biology.
- * These resources facilitate more efficient experimental design for investigating Caco-2 cell responses.
- * The findings provide a foundation for deeper understanding of food-host interactions at the cellular level.
