背景:三维(3D)基因组结构在调节基因表达中起着关键作用。然而,在生长激素肿瘤中这种结构的具体改变及其对基因表达的影响在很大程度上仍未被探索。
方法:我们使用Hi-C和RNA-seq分析来比较生长型肿瘤与正常垂体组织的3D基因组结构。这种全面的方法实现了A/B隔室的表征,拓扑关联域(TAD),和染色质循环,将这些与基因表达模式整合在一起。
结果:我们观察到,与正常组织相比,肿瘤组织中染色体相互作用的频率和TAD的大小均降低。相反,发现肿瘤中TAD和染色质环的数量增加.对Hi-C和RNA-seq数据的综合分析表明,结构中高阶色度的变化与基因表达的改变有关。具体来说,A区室中的基因相对于B区室中的基因显示出更高的密度和增加的表达。此外,确定了弱和增强的绝缘边界,并在Wnt/β-Catenin信号通路中富集相关基因。我们确定了肿瘤中的增益和丢失的环,并将这些差异与转录变化整合在一起,以检查已确定环的功能相关性。值得注意的是,我们观察到肿瘤内TCF7L2基因区域的绝缘边界增强和更多数量的环,伴随着TCF7L2表达的上调。随后,通过qRT-PCR确认TCF7L2表达,并上调TCF7L2促进体外细胞增殖和生长激素(GH)分泌。
结论:我们的研究结果提供了生长型肿瘤的全面3D染色质结构图,并为进一步理解基因表达调控的潜在生物学和机制提供了宝贵的资源。
BACKGROUND: The three-dimensional (3D) genome architecture plays a critical role inregulating gene expression. However, the specific alterations in thisarchitecture within somatotroph tumors and their implications for gene expression remain largely unexplored.
METHODS: We employed Hi-C and RNA-seq analyses to compare the 3D genomic structures of somatotroph tumors with normal pituitary tissue. This comprehensive approachenabled the characterization of A/B compartments, topologically associateddomains (TADs), and chromatin loops, integrating these with gene expression patterns.
RESULTS: We observed a decrease in both the frequency of chromosomal interactions andthe size of TADs in tumor tissue compared to normal tissue. Conversely, the number of TADs and chromatin loops was found to be increased in tumors. Integrated analysis of Hi-C and RNA-seq data demonstrated that changes inhigher-order chromat in structure were associated with alterations in gene expression. Specifically, genes in A compartments showed higher density and increased expression relative to those in B compartments. Moreover, the weakand enhanced insulation boundaries were identified, and the associated genes were enriched in the Wnt/β-Catenin signaling pathway. We identified the gainedand lost loops in tumor and integrated these differences with transcriptional changes to examine the functional relevance of the identified loops. Notably, we observed an enhanced insulation boundary and a greater number of loops in the TCF7L2 gene region within tumors, which was accompanied by an upregulation of TCF7L2 expression. Subsequently, TCF7L2 expression was confirmed through qRT-PCR, and upregulated TCF7L2 prompted cell proliferation and growth hormone (GH) secretion in vitro.
CONCLUSIONS: Our results provide comprehensive 3D chromatin architecture maps of somatotroph tumors and offer a valuable resource for furthering the understanding of the underlying biology and mechanisms of gene expression regulation.