Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas.
Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas.
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DOI：
10.1053/j.gastro.2019.09.056
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发表时间：
2020-05-16
期刊：
影响因子：
29.4
通讯作者：
Wong, Nathalie
中科院分区：
文献类型：
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作者：
Ding, Xiaofan;He, Mian;Wong, Nathalie
背景与目的：肿瘤内的异质性以及原发和复发的肝细胞癌之间不同的克隆谱系给患者的治疗带来了挑战。我们调查了肝脏肿瘤内部、肝脏病变之间以及原发和复发肿瘤之间的遗传和表观遗传差异。方法：收集了113例在香港两家医院接受部分肝切除术的原发性或复发性肝癌患者的肿瘤和配对的非肿瘤肝脏标本。我们对来自多个肿瘤区域和匹配的初发和复发肿瘤的356例肝癌标本进行了全基因组、全外显子组或靶向捕获测序分析。我们对95个样本进行了平行DNA甲基化图谱分析。对含有肝硬变或纤维化区域的非肿瘤组织的基因组和表观基因组进行分析。我们建立了内源性表达突变形式的TP53(R249S)或过表达突变形式的STAT3(D170Y、K348E和Y640F)或JAK1(S703I和L910P)的肝癌细胞系，并测试了药物降低活性的能力。用免疫印迹和染色质免疫沉淀结合定量聚合酶链式反应对细胞进行分析。结果：我们使用单一样本收集方法确定了单个肿瘤的单克隆性起源，该方法捕获了在肿瘤所有区域检测到的90%以上的突变。系统发育和系统表观遗传学分析表明，HCCs的基因组特征和表观基因组特征之间存在相互作用和相互依赖。甲基化分析显示，在肝硬变组织中存在场效应，使其易于发生肿瘤发展。遗传学特征的比较表明，52%的复发肝癌来自最初肿瘤的克隆性谱系。复发性肝癌的克隆起源使得构建与肿瘤复发相关的基因改变的时间图谱成为可能。JAK信号对STAT的激活是肝细胞癌进展的一个特征，它通过与药物敏感性相关的突变来实现。增加TP53功能的突变和17p染色体缺失的组合可能为肝癌细胞提供复制优势。带有R249S替换的TP53的染色质免疫沉淀分析表明，它与编码染色质调节基因(MLL1和ML12)的相互作用。我们验证了MLL1和MLL2作为TP53R249S的直接靶标，并在癌症基因组图谱数据集中确认了它们的相关性。MLL复合体拮抗剂MI-2-2(蛋白相互作用抑制物)和OICR-9492(活性抑制物)在纳摩尔浓度下特异性地抑制表达TP53R249S的肝癌细胞的增殖。结论：我们对肝癌样本中肿瘤内和肿瘤间的遗传异质性进行了系统的评估，并确定了与肿瘤进展和复发相关的遗传和表观遗传变化。我们确定了肝癌细胞中由突变型TP53上调的染色质调节因子和抑制这些细胞增殖的抑制剂。肝硬变或肝纤维化组织中的DNA甲基化模式可能被用来识别那些有发展为肝细胞癌风险的人。
BACKGROUND & AIMS: Intratumor heterogeneity and divergent clonal lineages within and among primary and recurrent hepatocellular carcinomas (HCCs) produce challenges to patient management. We investigated genetic and epigenetic variations within liver tumors, among hepatic lesions, and between primary and relapsing tumors.METHODS: Tumor and matched nontumor liver specimens were collected from 113 patients who underwent partial hepatectomy for primary or recurrent HCC at 2 hospitals in Hong Kong. We performed whole-genome, whole-exome, or targeted capture sequencing analyses of 356 HCC specimens collected from multiple tumor regions and matched initial and recurrent tumors. We performed parallel DNA methylation profiling analyses of 95 specimens. Genomes and epigenomes of nontumor tissues that contained areas of cirrhosis or fibrosis were analyzed. We developed liver cancer cell lines that endogenously expressed a mutant form of TP53 (R249S) or overexpressed mutant forms of STAT3 (D170Y, K348E, and Y640F) or JAK1 (S703I and L910P) and tested the abilities of pharmacologic agents to reduce activity. Cells were analyzed by immunoblotting and chromatin immunoprecipitation with quantitative polymerase chain reaction.RESULTS: We determined the monoclonal origins of individual tumors using a single-sample collection approach that captured more than 90% of mutations that are detected in all regions of tumors. Phylogenetic and phyloepigenetic analyses showed interactions and codependence between the genomic and epigenomic features of HCCs. Methylation analysis showed a field effect in cirrhotic liver tissues that predisposes them to tumor development. Comparisons of genetic features showed that 52% of recurrent HCCs derive from the clonal lineage of the initial tumor. The clonal origin of recurrent HCCs allowed construction of a temporal map of genetic alterations that were associated with tumor recurrence. Activation of JAK signaling to STAT was a characteristic of HCC progression via mutations that are associated with response to drug sensitivity. The combination of a mutation that increases the function of TP53 and the 17p chromosome deletion might provide liver cancer cells with a replicative advantage. Chromatin immunoprecipitation analysis of TP53 with the R249S substitution showed its interaction with genes that encode chromatin regulators (MLL1 and MLL2). We validated MLL1 and MLL2 as direct targets of TP53R249S and affirmed their association in the cancer genome atlas data set. The MLL-complex antagonists MI-2-2 (inhibitor of protein interaction) and OICR-9492 (inhibitor of activity) specifically inhibited proliferation of HCC cells that express TP53R249S at nanomolar concentrations.CONCLUSIONS: We performed a systematic evaluation of intra- and intertumor genetic heterogeneity in HCC samples and identified genetic and epigenetic changes that are associated with tumor progression and recurrence. We identified chromatin regulators that are up-regulated by mutant TP53 in HCC cells and inhibitors that reduce proliferation of these cells. DNA methylation patterns in cirrhotic or fibrotic liver tissues might be used to identify those at risk of HCC development.