PDF(Pubmed)
Abstract：
The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular functions. Here, we report the physical, biochemical, and genomic differences between T47D breast cancer cells cultured in 2D and as 3D spheroids. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, as well as altered expression of ~2000 genes, the majority of which become repressed. Hi-C analysis reveals that cells in 3D are enriched for regions belonging to the B compartment, have decreased chromatin-bound CTCF and increased fusion of topologically associating domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, thereby likely causing the observed TAD fusions. 3D cells show higher chromatin binding of progesterone receptor (PR), leading to an increase in the number of hormone-regulated genes. This effect is in part mediated by LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal.
摘要：
已经在二维（2D）单层培养的细胞中研究了癌症表观基因组，但是最近的研究强调了细胞外基质和三维（3D）环境对多种细胞功能的影响。这里,我们报告身体，生物化学，在2D和3D球体中培养的T47D乳腺癌细胞之间的基因组差异。3D球状体内的细胞表现出更圆的细胞核，难以接近，更紧密的染色质，以及~2000基因表达的改变，其中大多数被压抑。Hi-C分析显示，3D中的细胞富集了属于B区室的区域，染色质结合的CTCF减少，拓扑关联域（TAD）的融合增加。在3D球体中Hippo途径的上调导致LATS1激酶的激活,促进CTCF从DNA的磷酸化和置换，从而可能导致观察到的TAD融合。3D细胞显示更高的孕激素受体（PR）染色质结合，导致激素调节基因的数量增加。这种效应部分是由LATS1激活介导的，这有利于YAP和CTCF去除的细胞质保留。
