Effects of Culture Condition on Epigenomic Profiles of Brain Tumor Cells
Effects of Culture Condition on Epigenomic Profiles of Brain Tumor Cells
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DOI：
10.1021/acsbiomaterials.9b00161
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发表时间：
2019-03-01
影响因子：
5.8
通讯作者：
Verbridge, Scott S.
中科院分区：
文献类型：
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作者：
Cox, Megan C.;Deng, Chengyu;Verbridge, Scott S.
个性化的癌症药物提供了更有效的治疗方法的承诺，这些治疗方法是针对个体自身的动态癌症表型而定制的。与此同时，组织工程方法建模肿瘤可以补充这些进步，提供强大的新策略，了解治疗过程中发生的适应动力学。然而，在这两个领域，将需要新的工具来获得在驱动抗性的小细胞群体中发生的表型动力学的遗传和表观遗传调节因子的全貌。在这项研究中，我们对从微工程三维肿瘤模型中收集的脑肿瘤细胞进行表观基因组分析，克服了与这些微组织小生境中包含的少量细胞相关的挑战，在这种情况下，每个样本收集1000个细胞。具体来说，我们使用一种高分辨率的表观基因组分析方法，称为基于微流体振荡洗涤的染色质免疫沉淀测序（MOWChIP-seq）来分析组蛋白修饰模式（H3 K4 me 3）。我们鉴定了与H3 K4 me 3修饰相关的基因位点，H3 K4 me 3修饰通常是活跃转录的标志。我们比较了H3 K4 me 3配置文件在标准的二维文化和三维文化的基础上，I型胶原蛋白水凝胶，在常氧和缺氧条件下。我们发现，文化的维度极大地影响了H3 k4 me 3的配置文件，并导致在响应缺氧应激的差异修改。在本研究中使用的培养条件下的差异H3 K4 me 3标记区域对先前观察到的基因表达差异具有重要意义。总之，我们的工作说明了细胞培养或组织生态位条件与组蛋白修饰的全基因组改变之间的直接联系，为分析癌细胞表型表观遗传调控的时空变化提供了第一步。据我们所知，这项研究也是首次将广谱表观基因组分析应用于从工程微组织中收集的小细胞样本。
Personalized cancer medicine offers the promise of more effective treatments that are tailored to an individual's own dynamic cancer phenotype. Meanwhile, tissue-engineering approaches to modeling tumors may complement these advances by providing powerful new strategies for understanding the adaptation dynamics occurring during treatment. However, in both of these areas, new tools will be required to gain a full picture of the genetic and epigenetic regulators of phenotype dynamics occurring in the small populations of cells that drive resistance. In this study, we perform epigenomic analysis of brain tumor cells that are collected from microengineered three-dimensional tumor models, overcoming the challenges associated with the small numbers of cells contained within these microtissue niches, in this case collecting 1000 cells per sample. Specifically, we use a high-resolution epigenomic analysis method known as microfluidic-oscillatory-washing-based chromatin immunoprecipitation with sequencing (MOWChIP-seq) to analyze histone modification patterns (H3K4me3). We identified gene loci that are associated with the H3K4me3 modification, which is generally a mark of active transcription. We compared H3K4me3 profiles in standard 2D cultures and 3D cultures based on type I collagen hydrogels, under both normoxic and hypoxic conditions. We found that culture dimensionality drastically impacted the H3k4me3 profile and resulted in differential modifications in response to hypoxic stress. Differentially H3K4me3-marked regions under the culture conditions used in this study have important implications for gene expression differences that have been previously observed. In total, our work illustrates a direct connection between cell culture or tissue niche condition and genome-wide alterations in histone modifications, providing the first steps toward analyzing the spatiotemporal variations in epigenetic regulation of cancer cell phenotypes. This study, to the best of our knowledge, also represents the first time broad-spectrum epigenomic analysis has been applied to small cell samples collected from engineered microtissues.