不同培养方法对乳腺癌MDA-MB-231细胞DNA甲基化状态的影响

摘要

Objective:To explore the influence of different cell culture methods in the genome-wide DNA methylation status of breast cancer MDA-MB-231 cells,and to clarify the relationship between genome-wide DNA methylation status and cell growth environment and the role of genome-wide DNA methylation status in the occurrence and development of tumor.Methods:The MDA-MB-231 cells were cultured with 2D and 3D cell culture models and mouse orthotopic transplantation model (Ti model)and collected, then DNA was extracted by DNA extraction kit and the genome-wide DNA methylation status of MDA-MB-231 cells after cultured with three different culture methods was detected by DNA methylation chip,then the value of beta,DiffScore and Delta_Beta of the CpG loci of each gene were calculated by applying Genomestudio software, and the differential methylation genes were screened by Genomestudio software and GO and Pathway analysis of these genes were performed in DAVID on-line analysis tool.Results:All 480 genes of the MDA-MB-231 cells showed significant differences in the degree of methylation in 3D and 2D models (P<0.05);86 448 genes in 3D and Ti models (P<0.05);90 005 genes in Ti and 2D models (P<0.05).The differential methylation genes in 3D and 2D,3D and Ti,and Ti and 2D models were enriched on the multicellular organismal development term and cell differentiation term (P<0.05);also on MAPK signaling pathway,cell adhesion molecules (CAMs),and regulation of actin cytoskeleton (P<0.05). Conclusion:There are differences in genome-wide DNA methylation status of MDA-MB-231 cells cultured in 2D, 3D cell culture and Ti models.%目的：探讨不同细胞培养方法对乳腺癌 MDA-MB-231细胞全基因组DNA甲基化状态的影响，阐明基因组甲基化状态与细胞生长环境的关系及其在肿瘤发生发展中的作用。方法：采用二维（2 D）、三维（3 D）细胞培养模型及小鼠肿瘤细胞原位移植（Ti）模型培养 MDA-MB-231细胞并收集，分别用 DNA提取试剂盒对收集的细胞进行DNA提取，DNA甲基化芯片检测3种模型培养后乳腺癌 MDA-MB-231细胞全基因组 DNA甲基化状态，应用 Genomestudio软件计算每1个基因CpG位点的β值、DiffScore和Delta＿Beta，并在2种模型之间比较，筛选出差异甲基化基因；采用 DAVID在线分析工具对筛选的基因进行 GO和 Pathway分析。结果：3D与2D模型培养的 MDA-MB-231细胞共发现480个差异甲基化基因（P＜0.05），3D与 Ti模型有86448个差异甲基化基因（P＜0.05），Ti与2D模型有90005个差异甲基化基因（P＜0.05）；3D与2D、3D与Ti和Ti与2D模型的差异甲基化基因在多细胞生物体发育和细胞分化条目上有富集（P＜0.05）；亦在 MAPK信号通路、细胞黏附分子和肌动蛋白骨架调节通路上有富集（P＜0.05）。结论：采用2D、3D和 Ti 模型3种方法培养 MDA-MB-231细胞其全基因组DNA甲基化状态存在差异。