Differences between the HT29 and HT29- MTX epithelial cell lines - An analysis of gene expression data

Introduction: Epithelial cancerous cell lines are used in a wide variety of research because of the unique possibility to study isolated cellular mechanisms in detail. This can be used for wider understanding of pathological processes of disease but also physiological traits. When treating the epithelial cell line HT29 with methotrexate, the remaining population of cancer cells constitute the HT29-MTX cells, a proposed goblet cell model. In this thesis, we study the mRNA level in HT29 and HT29-MTX to investigate differences in regulation of gene expression and thereby how these cell lines differ in cellular network activity. Material and methods: The gene expression levels in the HT29 and HT29-MTX cells after four days of cultivation were measured by microarray. Statistical analysis in Bioconductor gave 6788 differentially expressed genes. Through data analysis in Metacore, differentially regulated cellular processes between the cell lines were characterized. Results: We show significant upregulation of goblet cell differentiation genes in HT29-MTX when compared to HT29, but a lack of increase in expression of the main mucus component MUC2. Also, we find that several processes related to immune function and cancerous traits in cells are altered. Conclusion: This study reveals that differentiation into goblet cells is indeed a possibility in the HT29- MTX cell, but that important traits such as MUC2 production is more uncertain. Several additional changes in gene expression are seen compared to the HT29 cell, and this must be kept in mind when utilizing the HT29-MTX for mechanistic studies