Liu Xiangzhen, Zhao Xinyuan, Gou Chenyu
First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
Stomatological Hospital, Southern Medical University, Guangzhou, China.
J Cancer. 2019 May 21;10(10):2250-2260. doi: 10.7150/jca.31156. eCollection 2019.
Aberrant DNA methylation pattern plays an indispensable role in the initiation and development of head and neck squamous cell carcinoma (HNSCC). It is well recognized that lymph node metastasis is closely with unfavorable prognosis of HNSCC. Therefore, exploring the methylation events accounting for the lymph node metastasis of HNSCC is very important for improving the clinical outcome of HNSCC. Methylation data, RNA-seq data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler. MethylMix was use for data analysis by integrating both methylation and gene expression data on HNSCC patients with lymph node metastasis and without lymph node metastasis. Pathway analysis was performed on significantly altered genes using ConsensusPathDB. The role of our interested gene zinc figure protein 569 (ZNF569) in HNSCC was further evaluated. Our results identified many novel hypermethylated/hypomethylated genes that might be closely associated with the lymph node metastasis of HNSCC. Pathway analysis revealed that increase in methylation of genes involved in generic transcription pathway including zinc figure proteins. ZNF569 was hypermethylated in HNSCC tissues especially those with lymph node metastasis. In addition, the expression levels of ZNF569 mRNA and protein were significantly lower in HNSCC tissues and cell lines compared to their respective controls. Moreover, overexpression of ZNF569 inhibited the proliferation, migration and invasion of HNSCC cells. HNSCC patients with lower ZNF569 expression suffered a significantly shorter overall survival than those with higher ZNF569 expression. In conclusion, we have identified many novel differentially methylated genes that might be important for the lymph node metastasis of HNSCC. In addition, ZNF569 might play a tumor suppressive role in carcinogenesis of HNSCC.
异常的DNA甲基化模式在头颈部鳞状细胞癌（HNSCC）的发生和发展中起着不可或缺的作用。众所周知，淋巴结转移与HNSCC的不良预后密切相关。因此，探索导致HNSCC淋巴结转移的甲基化事件对于改善HNSCC的临床结局非常重要。甲基化数据、RNA测序数据和临床数据从癌症基因组图谱（TCGA）下载，并使用R包TCGA-Assembler进行处理。通过整合有淋巴结转移和无淋巴结转移的HNSCC患者的甲基化和基因表达数据，使用MethylMix进行数据分析。使用ConsensusPathDB对显著改变的基因进行通路分析。进一步评估了我们感兴趣的基因锌指蛋白569（ZNF569）在HNSCC中的作用。我们的结果鉴定出许多可能与HNSCC淋巴结转移密切相关的新的高甲基化/低甲基化基因。通路分析显示，包括锌指蛋白在内的参与一般转录通路的基因甲基化增加。ZNF569在HNSCC组织中尤其是有淋巴结转移的组织中高度甲基化。此外，与各自的对照相比，HNSCC组织和细胞系中ZNF569 mRNA和蛋白的表达水平显著降低。此外，ZNF569的过表达抑制了HNSCC细胞的增殖、迁移和侵袭。ZNF569表达较低的HNSCC患者的总生存期明显短于ZNF569表达较高的患者。总之，我们鉴定出许多可能对HNSCC淋巴结转移很重要的新的差异甲基化基因。此外，ZNF569可能在HNSCC的致癌过程中发挥肿瘤抑制作用。
