Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Neoplasia. 2021 Feb;23(2):257-269. doi: 10.1016/j.neo.2020.12.010. Epub 2021 Jan 7.
Canonical Wnt signaling is crucial for intestinal homeostasis as TCF4, the major Wnt signaling effector in the intestines, is required for stem cell maintenance. The capability of TCF4 to maintain the stem cell phenotype is contingent upon β-catenin, a potent transcriptional activator, which interacts with histone acetyltransferases and chromatin remodeling complexes. We used RNAi to explore the influence of TCF4 on chromatin structure (Hi-C) and gene expression (RNA sequencing) across a 72-hour time series in colon cancer. We found that TCF4 reduction results in a disproportionate up-regulation of gene expression, including a powerful induction of SOX2. Integration of RNA sequencing and Hi-C data revealed a TAD boundary loss, which occurred concomitantly with the over-expression of a cluster of CEACAM genes on chromosome 19. We identified EMT and E2F as the 2 most deregulated pathways upon TCF4 depletion and LUM, TMPO, and AURKA as highly influential genes in these networks using measures of centrality. Results from gene expression, chromatin structure, and centrality analyses were integrated to generate a list of candidate transcription factors crucial for colon cancer cell homeostasis. The top ranked factor was c-JUN, an oncoprotein known to interact with TCF4 and β-catenin, confirming the usefulness of this approach.
经典 Wnt 信号通路对于肠道稳态至关重要，因为 TCF4 是肠道中主要的 Wnt 信号效应物，对于干细胞的维持是必需的。TCF4 维持干细胞表型的能力依赖于β-连环蛋白，β-连环蛋白是一种有效的转录激活物，它与组蛋白乙酰转移酶和染色质重塑复合物相互作用。我们使用 RNAi 技术在结肠癌中研究了 TCF4 对染色质结构（Hi-C）和基因表达（RNA 测序）的影响，这一研究跨越了 72 小时的时间序列。我们发现 TCF4 的减少导致基因表达的不成比例上调，包括 SOX2 的强烈诱导。RNA 测序和 Hi-C 数据的整合揭示了 TAD 边界的丧失，这与 19 号染色体上一组 CEACAM 基因的过度表达同时发生。我们发现，在 TCF4 耗竭后，EMT 和 E2F 是最失调的两条通路，而在这些网络中，LUM、TMPO 和 AURKA 是具有高度影响力的基因，使用中心性测度来确定。基因表达、染色质结构和中心性分析的结果被整合在一起，生成了一组候选转录因子，这些转录因子对于结肠癌细胞稳态至关重要。排名最高的因子是 c-JUN，这是一种已知与 TCF4 和 β-连环蛋白相互作用的癌蛋白，证实了这种方法的有用性。
