Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany; Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany.
J Biotechnol. 2017 Sep 10;257:150-161. doi: 10.1016/j.jbiotec.2016.11.020. Epub 2016 Nov 24.
The cellular mechanisms responsible for the versatile properties of CHO cells as the major production cell line for biopharmaceutical molecules are not entirely understood yet, although several 'omics' data facilitate the understanding of CHO cells and their reactions to environmental conditions. However, genome-wide studies of epigenetic processes such as DNA methylation are still limited. To prove the applicability and usefulness of integrating DNA methylation and gene expression data in a biotechnological context, we exemplarily analyzed the time course of cellular reactions upon butyrate addition in antibody-producing CHO cells by whole-genome bisulfite sequencing and CHO-specific cDNA microarrays. Gene expression and DNA methylation analyses showed that pathways known to be affected by butyrate, including cell cycle and apoptosis, as well as pathways potentially involved in butyrate-induced hyperproductivity such as central energy metabolism and protein biosynthesis were affected. Differentially methylated regions were furthermore found to contain binding-site motifs of specific transcription factors and were hypothesized to represent regulatory regions closely connected to the cellular response to butyrate. Generally, our experiment underlines the benefit of integrating DNA methylation and gene expression data, as it provided potential novel candidate genes for rational cell line development and allowed for new insights into the butyrate effect on CHO cells.
虽然几种“组学”数据有助于理解 CHO 细胞及其对环境条件的反应，但负责 CHO 细胞多功能特性的细胞机制尚未完全了解，CHO 细胞是生物制药分子的主要生产细胞系。然而，全基因组范围内对 DNA 甲基化等表观遗传过程的研究仍然有限。为了证明将 DNA 甲基化和基因表达数据整合到生物技术背景中的适用性和有用性，我们通过全基因组亚硫酸氢盐测序和 CHO 特异性 cDNA 微阵列，以产生抗体的 CHO 细胞中添加丁酸盐时的细胞反应时间过程为例进行了分析。基因表达和 DNA 甲基化分析表明，受丁酸盐影响的途径（包括细胞周期和细胞凋亡）以及可能与丁酸盐诱导的高生产力相关的途径（如中心能量代谢和蛋白质生物合成）受到了影响。此外，还发现差异甲基化区域包含特定转录因子的结合位点基序，并且假设它们代表与细胞对丁酸盐的反应密切相关的调节区域。总的来说，我们的实验强调了整合 DNA 甲基化和基因表达数据的好处，因为它为合理的细胞系开发提供了潜在的新候选基因，并深入了解了丁酸盐对 CHO 细胞的影响。
