BAP1 Loss Is Associated with DNA Methylomic Repatterning in Highly Aggressive Class 2 Uveal Melanomas
BAP1 Loss Is Associated with DNA Methylomic Repatterning in Highly Aggressive Class 2 Uveal Melanomas
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DOI：
10.1158/1078-0432.ccr-19-0366
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发表时间：
2019-09-01
影响因子：
11.5
通讯作者：
Harbour, J. William
中科院分区：
文献类型：
--
作者：
Field, Matthew G.;Kuznetsov, Jeffim N.;Harbour, J. William
目的：BAP 1突变和转移性2类葡萄膜黑色素瘤（UM）之间的强相关性表明，表观遗传学改变可能在肿瘤进展中起重要作用。因此，我们的特点是在UM.Experimental Design的DNA甲基化组的影响BAP 1损失：全球DNA甲基化进行了分析，在47类1和45类2主要UM和UM细胞工程诱导消耗BAP 1。RNA-Seq分析了80 UM样品和工程UM cells.Results：3号染色体上的超甲基化与包括BAP 1所在的3 p21在内的几个位点的基因表达下调相关。高甲基化和下调基因的基因集分析确定轴突导向和黑素生成为失调途径，其中几个基因位于3号染色体上。在所有2类肿瘤中发现了BAP 1基因座内的一个新的高甲基化位点，这表明BAP 1本身是表观遗传调节的。使用亚硫酸氢盐测序对高度差异甲基化的探针进行正交验证，它们在100%的病例中成功区分了1类和2类肿瘤。在功能验证实验中，UM细胞中的BAP 1敲低诱导了类似于UM肿瘤的甲基化组学再形成，富集了参与轴突导向、黑素生成和发育的基因。这项研究，加上以前的工作，表明在分歧的初始事件2类UM从1类UM是一个拷贝的染色体3的损失，随后在3号染色体的剩余拷贝上发生BAP 1突变，导致2类UM的甲基化组学再图案化特征。
Purpose: The strong association between BAP1 mutations and metastasizing Class 2 uveal melanoma (UM) suggests that epigenetic alterations may play a significant role in tumor progression. Thus, we characterized the impact of BAP1 loss on the DNA methylome in UM.Experimental Design: Global DNA methylation was analyzed in 47 Class 1 and 45 Class 2 primary UMs and in UM cells engineered to inducibly deplete BAP1. RNA-Seq was analyzed in 80 UM samples and engineered UM cells.Results: Hypermethylation on chromosome 3 correlated with downregulated gene expression at several loci, including 3p21, where BAP1 is located. Gene set analysis of hypermethylated and downregulated genes identified axon guidance and melanogenesis as deregulated pathways, with several of these genes located on chromosome 3. A novel hypermethylated site within the BAP1 locus was found in all Class 2 tumors, suggesting that BAP1 itself is epigenetically regulated. Highly differentially methylated probes were orthogonally validated using bisulfite sequencing, and they successfully distinguished Class 1 and Class 2 tumors in 100% of cases. In functional validation experiments, BAP1 knockdown in UM cells induced methylomic repatterning similar to UM tumors, enriched for genes involved in axon guidance, melanogenesis, and development.Conclusions: This study, coupled with previous work, suggests that the initial event in the divergence of Class 2 UM from Class 1 UM is loss of one copy of chromosome 3, followed by mutation of BAP1 on the remaining copy of chromosome 3, leading to the methylomic repatterning profile characteristic of Class 2 UMs.