巫丽娟, 辛兆丹, 黄燕春, 等.结核感染相关差异基因的甲基化芯片筛选及验证.四川大学学报(医学版),2019,50(2):234-240
结核感染相关差异基因的甲基化芯片筛选及验证
Methylation Chip Screening and Verification of Differential Genes Related to Tuberculosis Infection
  
中文关键词:  结核分枝杆菌DNA甲基化甲基化芯片焦磷酸测序技术活动性结核病
英文关键词:Mycobacterium tuberculosis (MTB)DNA methylationMicroarrayPyrosequencing Aactive tuberculosis
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中文摘要:
      目的应用甲基化芯片筛选活动性结核患者DNA甲基化水平显著变化的基因。方法①甲基化芯片筛选:纳入9例活动性结核患者、3例潜伏性结核患者和3例健康对照(年龄与性别均匹配),分别提取人全血单个核细胞DNA并进行亚硫酸盐转化,与Illumina HD 450K Infinium MehtylationBeadChip芯片杂交,比较3组间甲基化差异基因,进行聚类分析,检测甲基化差异片段(DMRs),对差异基因进行GO和KEGG pathway功能富集分析并与表达芯片进行联合分析,筛选结核感染相关差异基因,用于大样本验证。②大样本验证:收集活动性结核患者与健康对照各60例(年龄与性别均匹配),分别提取人全血DNA并进行亚硫酸盐转化,使用焦磷酸测序方法对甲基化芯片预测出的结核病相关基因(IFNGR2、PTPN6、CRK1、ATP6V0B、WIF1、DKK1和SFRP1)进行甲基化程度检测;RT-PCR方法进行上述基因mRNA表达检测。结果活动性结核患者与健康对照相比,呈现低甲基化改变的片段占绝大部分,大部分的DMRs位于基因主体区域,其次为转录起始位点上游区域,DMRs分布最少的区域为3′UTR区。GO与Pathway功能富集结果显示,甲基化差异基因的功能主要富集在白细胞分化、凋亡、细胞因子调节及炎症反应等与结核病密切相关的生物过程中。待后续验证的7个结核病相关甲基化差异基因IFNGR2、PTPN6、CRK-1、ATP6V0B、WIF1、DKK1和SFRP1包含32个CpG位点,其中,16个CpG位点显示出统计学差异(P<0.05),分布于6个基因:PTPN6、WIF1、CRK1、SFRP1、DKK1、IFNGR2。发生高甲基化的基因为PTPN6,发生低甲基化的基因为WIF1、CRK1、SFRP1、DKK1、IFNGR2。SFRP1和CRK-1基因mRNA表达在活动性结核患者中显著升高。结论在结核感染过程中存在基因组DNA的甲基化状态改变,且以低甲基化变化为主。SFRP1基因和CRK-1基因mRNA在结核组中表达上调。SFRP1和CRK-1在结核病发病过程中的作用不可忽视。
英文摘要:
      ObjectiveTo screen the genes with significant changes in DNA methylation level in active tuberculosis patients, we used the methylation chips and expanded the sample size to verify candidate genes. Methods① This study enrolled 9 cases of active tuberculosis patients, 3 cases of latent tuberculosis patients and 3 cases of healthy controls whose age and gender were all matched. Genome DNA was extracted from peripheral blood mononuclear cell in blood samples collected from these candidates, and bisulfite conversion treatment was then conducted. After hybridization with the Illumina HD 450K Infinium Mehtylation BeadChip, the results were compared between patients group and control group, and GO and KEGG pathway analyses were performed to evaluate the function of differentially expressed genes. ② We further enrolled 60 cases of active tuberculosis patients and 60 cases of health controls (age-and gender-matched), DNA was extracted from their peripheral blood and also followed bisulfite conversion treatment. Pyrosequencing method was used to detect the methylation levels of candidate genes (IFNGR2, PTPN6, CRK1, ATP6V0B, WIF1, DKK1 and SFRP1) screened by gene chip. ResultsCompared with healthy controls, the fragments in the patients that showed low methylation change accounted for the vast majority. Most of the methylation differential fragments (DMRs) were located in the main body region, followed by the upstream region of transcription initiation site, and the lowest DMRs distribution area was 3′UTR area. GO and Pathway analysis showed that the functions of the differentially methylated regions related genes are mainly enriched in the biological processes of the regulation of leukocyte differentiation, apoptosis,cytokine regulation and inflammatory response which are closely related to tuberculosis. There were 32 CpG sites involved in the verified 7 tuberculosis related genes, and 16 CpG locus showed significant difference (P<0.05), they were distributed in 6 genes: PTPN6, WIF1, CRK1, SFRP1, DKK1 and IFNGR2.Of these genes with significant difference, PTPN6 genes showed hypermethylation status and WIF1, CRK1, SFRP1, DKK1 and IFNGR2 genes exhibited demethylation status in the patients group compared to the health controls. SFRP1 and CRK-1 mRNA up-regulated in the patients group compared with health controls. ConclusionsIn the course of MTB infection, the methylation status of genomic DNA is altered, and most of the differentially methylated regions (DMRs) are showed status of demethylation. The expressions of SFRP1 and CRK-1 gene up-regulate in tuberculosis infection.
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