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Epigenetic profiling of bronchial epithelial cells : DNA methylation Taplin, Christopher David


Epigenetic regulation of gene expression is critical for normal human development and cellular differentiation. Although each somatic cell in the human body is genetically identical, epigenetic marks including the DNA methylation pattern are tissue-specific and critical for determining the vast array of cellular phenotypes. For studying respiratory disease, the airway epithelium is the ideal target tissue since it is the first point of contact for inhaled particles, viruses and airborne allergens. Cultured airway epithelial cells of asthmatic children show striking phenotypic differences compared to those from non-asthmatic individuals such as poor wound healing and enhanced expression of inflammatory cytokines. The altered state of the asthmatic epithelium could be due to underlying differences in gene expression associated with changes in their DNA methylation profile. Therefore, in this study, the purpose was to determine the extent to which DNA methylation, a reportedly stable epigenetic mark, is altered by standard cell culture conditions over passage for primary and immortalized bronchial epithelial cells. We analyzed four individual primary bronchial epithelial cell lines and a 1HBEO- immortalized bronchial epithelial cell line in triplicate. CpG DNA methylation was characterized during stages of cell propagation for 1505 CpG sites in promoter regions and/or first exons of 807 genes and compared with its gene expression. A comparison of 1HBEO- cells and primary bronchial epithelial cell lines revealed that 1HBEO- cells have significantly higher levels of overall methylation and more hyper- and heterogeneously-methylated CpG loci. In addition, there were a large number of CpG sites that had variable DNA methylation over passage in the primary cell lines but not in the immortalized cell lines. In summary, there were extensive differences in DNA methylation profiles between primary and immortalized bronchial epithelial cell lines during cell propagation, revealing the importance of this epigenetic modification in cell culture. This work is critical because, although little is known about the CpG specific changes that occur in cell culture, passaged cells are still regularly grouped together and phenotyped for major biological studies.

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