背景:空间染色质结构与体细胞畸变错综复杂地联系在一起,以及各种癌症相关基因的体细胞突变,称为共突变(CoMuts),在癌症开始和进展期间以某些模式发生。在甲状腺癌(TC)中,这些遗传事件的潜在功能机制仍不清楚。有了不同的区分,甲状腺乳头状癌(PTC)和间变性甲状腺癌(ATC)在特征和预后上差异很大。我们旨在揭示两种TC亚型之间的空间基因变化和调控。
方法:我们系统地研究并比较了ATC(8305C)之间的空间共变,PTC(BCPAP和TPC-1),和正常甲状腺细胞(Nthy-ori-3-1)。我们构建了一个整合全基因组测序(WGS)的框架,高通量染色体构象捕获(Hi-C),和转录组测序,为了系统地检测癌症相关基因的体细胞共突变之间的关联,结构变化(SV),拷贝数变化(CNVs),和高阶染色质构象。
结果:空间共突变热点在TC的拓扑关联域(TAD)周围富集。在ATC和PTC中确定了一组共有的227个边界,它们之间有明显的重叠。两种TC类型的共突变基因对的空间接近度明显大于基因水平和整体背景,与PTC电池相比,ATC电池具有更高的TAD接触频率,CoMuts>10。与正常甲状腺细胞相比,在ATC中,创建的新型三维染色质结构域的数量增加了10%,移位的TAD数量减少了7%。我们发现了5个具有ATC特异性CoMut基因/事件的TAD区块,这些基因包括MAST-NSUN4,AM129B/TRUB2,COL5A1/PPP1R26,PPP1R26/GPSM1/CCDC183和PRAC2/DLX4。对于大多数ATC和PTC电池,TAD中靠近CoMut基因转录起始位点的HOXA10和HIF2α信号明显强于背景信号。在两种TC亚型中,CNV断点与TAD边界显著重叠。ATCs有更多与TAD边界重叠的CNV损失,和非编码SVs参与染色体内SVs,放大倒置,ATC和PTC之间的串联复制有所不同。短程TAD在ATC中比PTC中更丰富。与PTC相比,ATC电池中存在更多的A/B隔室类型开关。基因表达显著同步,并由复杂的表观遗传学和调控元件精心策划。
结论:在TC中,染色质相互作用和基因改变和调控在很大程度上是异质的。CNVs和复杂SVs可能通过与TAD相互作用而在TC基因组中起作用,ATC和PTC之间的差异很大。TC基因组的复杂性,通过介导突变和结构变异以及基因激活的3D全基因组相互作用高度组织,可能在很大程度上被低估了。我们的综合分析可能为更定制的TC诊断和治疗提供关键证据和目标。
BACKGROUND: Spatial chromatin structure is intricately linked with somatic aberrations, and somatic mutations of various cancer-related genes, termed co-mutations (CoMuts), occur in certain patterns during cancer initiation and progression. The functional mechanisms underlying these genetic events remain largely unclear in thyroid cancer (TC). With discrepant differentiation, papillary thyroid cancer (PTC) and anaplastic thyroid cancer (ATC) differ greatly in characteristics and prognosis. We aimed to reveal the spatial gene alterations and regulations between the two TC subtypes.
METHODS: We systematically investigated and compared the spatial co-mutations between ATC (8305C), PTC (BCPAP and TPC-1), and normal thyroid cells (Nthy-ori-3-1). We constructed a framework integrating whole-genome sequencing (WGS), high-throughput chromosome conformation capture (Hi-C), and transcriptome sequencing, to systematically detect the associations between the somatic co-mutations of cancer-related genes, structural variations (SVs), copy number variations (CNVs), and high-order chromatin conformation.
RESULTS: Spatial co-mutation hotspots were enriched around topologically associating domains (TADs) in TC. A common set of 227 boundaries were identified in both ATC and PTC, with significant overlaps between them. The spatial proximities of the co-mutated gene pairs in the two TC types were significantly greater than in the gene-level and overall backgrounds, and ATC cells had higher TAD contact frequency with CoMuts > 10 compared with PTC cells. Compared with normal thyroid cells, in ATC the number of the created novel three-dimensional chromatin structural domains increased by 10%, and the number of shifted TADs decreased by 7%. We found five TAD blocks with CoMut genes/events specific to ATC with certain mutations in genes including MAST-NSUN4, AM129B/TRUB2, COL5A1/PPP1R26, PPP1R26/GPSM1/CCDC183, and PRAC2/DLX4. For the majority of ATC and PTC cells, the HOXA10 and HIF2α signals close to the transcription start sites of CoMut genes within TADs were significantly stronger than those at the background. CNV breakpoints significantly overlapped with TAD boundaries in both TC subtypes. ATCs had more CNV losses overlapping with TAD boundaries, and noncoding SVs involved in intrachromosomal SVs, amplified inversions, and tandem duplication differed between ATC and PTC. TADs with short range were more abundant in ATC than PTC. More switches of A/B compartment types existed in ATC cells compared with PTC. Gene expression was significantly synchronized, and orchestrated by complex epigenetics and regulatory elements.
CONCLUSIONS: Chromatin interactions and gene alterations and regulations are largely heterogeneous in TC. CNVs and complex SVs may function in the TC genome by interplaying with TADs, and are largely different between ATC and PTC. Complexity of TC genomes, which are highly organized by 3D genome-wide interactions mediating mutational and structural variations and gene activation, may have been largely underappreciated. Our comprehensive analysis may provide key evidence and targets for more customized diagnosis and treatment of TC.