HOXD10 甲基化水平与表达水平的关联及其对肺腺癌预后的影响
| 作者: |
1吴稚晖,
2袁悉奥,
2李慧源,
2龚强,
2彭千,
2吴秋,
1李文灿
1 株洲市中心医院心胸外科，湖南 株洲 412000 2 长沙金域医学检验所，长沙 410000 |
| 通讯: |
李文灿
Email: lwccom@sina.com |
| DOI: | 10.3978/j.issn.2095-6959.2020.11.008 |
| 基金: | 湖南省自然科学基金(2017JJ4072)。 |
摘要
目的：分析HOXD10基因启动子区甲基化水平与基因表达水平的关联并探索HOXD10与肺腺癌临床病理特征和预后的关系。方法：采用R语言拓展包TCGAbiolinks进行基因差异表达分析和差异甲基化分析，利用肿瘤基因组计划(The Cancer Genome Atlas，TCGA)项目肺腺癌(lung adenocarcinoma，LUAD)数据集中521例癌症组织和58例癌旁组织的RNA-seq数据分析HOXD10基因差异表达，利用同一数据集中461例癌症组织和32例癌旁组织的甲基化芯片数据分析HOXD10启动子区差异甲基化，并计算启动子区差异甲基化与基因表达水平的相关性，最后分析HOXD10表达与LUAD临床病理特征和预后的关系。结果：在TCGA项目LUAD数据集中，521例癌症组织HOXD10基因的平均表达量为30.4(normalized read counts)，低于58例癌旁组织的平均表达量170.8，差异具有统计学意义(P<0.05)；在癌症和癌旁组织配对(即来源于同一患者的癌症和癌旁组织组成配对，n=56)时HOXD10基因表达水平的平均差异值为−141.2，差异具有统计学意义(P<0.05)。通过比较461例癌症组织和32例癌旁组织的甲基化芯片数据，鉴定出一个位于HOXD10基因启动子区内的差异甲基化区域，甲基化水平癌症组织高于癌旁组织(Δβ=0.3656，fwer=0)。该区域位于以hg19作为参考基因组的2号染色体176980837~176982342坐标位置，共包含12个甲基化探针，其中cg03918304，cg10364040，cg13217260，cg20649017，cg21591742和cg25371634等6个探针的β值与HOXD10基因的表达情况呈负相关(r<−0. 1，P<0.05)。250例肺腺癌患者的完整临床信息显示：HOXD10表达水平与每天抽烟根数和肿瘤大小两个临床病理指标有关(P<0.05)，HOXD10低表达组的5年中位生存时间为37.2个月，低于高表达组的59.9个月(P<0.05)。结论：HOXD10基因在TCGA肺腺癌癌症组织中的表达水平明显高于癌旁组织，而甲基化水平明显低于癌旁组织；HOXD10的表达与肺腺癌的临床病理特征有关，是肺腺癌预后的可能影响因素。
关键词：
肺腺癌；HOXD10；甲基化；预后
Association of DNA methylation and HOXD10 expression and its effect on the prognosis of lung adenocarcinoma
CorrespondingAuthor: LI Wencan Email: lwccom@sina.com
DOI: 10.3978/j.issn.2095-6959.2020.11.008
Foundation: This work was supported by the Natural Science Foundation of Hunan Province, China (2017JJ4072).
Abstract
Objective: To analyze the association of DNA methylation and gene expression of HOXD10 and explore the relations between HOXD10 and clinicopathological features and prognosis of lung adenocarcinoma (LUAD). Methods: R-language expansion package TCGAbiolinks was used to analyze retrospectively the expression of HOXD10 in LUAD datasets of The Cancer Genome Atlas (TCGA) project. The RNA-seq data of 521 tumor tissues and 58 adjacent tissues were collected for differentially expressed gene (DEG) analysis, and the methylation microarray data of 461 tumor tissues and 32 adjacent tissues were collected for differentially methylated region (DMR) analysis. The correlations between methylations of the promoter regions and gene expressions were calculated. The relations of HOXD10 and clinicopathological features and prognosis were analyzed. Results: The average expression value of HOXD10 in 521 tumor tissues was 30.4 (normalized read counts), lower than the value of 58 adjacent tissues (170.8), and the difference was statistically significant (P<0.05). The different value was −141.2 (P<0.05) when tumor tissue and adjacent tissue from the same patient were compared (n=56). A DMR (chr2: 176980837–176982342) containing 12 probes was identified via differentially methylated region analysis (461 tumor tissues vs 32 adjacent tissues, Δβ=0.3656, fwer=0). The β values of six probes (cg03918304, cg10364040, cg13217260, cg20649017, cg21591742 and cg25371634) were negatively correlated with the expressions of HOXD10 (r<−0. 1, P<0.05). From clinical information of 250 LUAD patients, the expression of HOXD10 was associated with number of cigarettes per day and tumor volume (P<0.05). The 5-year median survival time of HOXD10 low-expression group was 37.2 months, lower than 59.9 months of HOXD10 high-expression group (P<0.05). Conclusion: The HOXD10 expressions of tumor tissues in TCGA LUAD datasets are significantly higher than adjacent tissues while the methylation β values are significantly lower than adjacent tissues. The expression of HOXD10 is related to clinicopathological features of LUAD and could be a potential prognostic factor.
Keywords：
lung adenocarcinoma; HOXD10; methylation; prognosis