TET2突变是如何引起超甲基化

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TET2突变是如何引起超甲基化

癌症病人体内会检测到不正常的甲基化现象。
TET2可以氧化5mC成为5hmC，进而通过其它机制形成5fC和5caC。
很多血液肿瘤病人的TET2基因突变了，同时会显示出全局的5hmC水平下降。
有趣的是，全局的5hmC水平下降同样发生在很多实体肿瘤病人身上，但是那些病人很少有TET2突变发生。
那么，TET2突变，或者全局的5hmC水平下降，是如何导致启动子区域的CG岛的甲基化水平上升的呢？
有其它文献报道 hypermethylation和oxidative stress (OS)有关系
作者认为 oxidative stress (OS) 在其中起了关键的作用。

关键结论

  • We now demonstrate TET2 forms ‘‘Yin-Yang’’ complexes with DNMTs and is targeted to chromatin during OS.
  • TET2 actively removes abnormal DNAm induced by OS in promoter CGIs as well as enhancers by converting unwanted 5mC to 5hmC.
  • Long-term reduction of TET2 caused even more DNA hypermethylation on these gene promoters and enhancers.

    数据

    作者用了 Agilent-026652 Whole Human Genome Microarray 4x44K v2 和 Illumina HumanMethylation450 BeadChip 来联合表达量和甲基化进行分析。

  • GSE81426
    Genome wide DNA methylation profiling of A2780 cells

  • untreated (mock)

    • treated with H2O2 for 30 min (H2O2 30 min)
    • treated with H2O2 for 30 min with additional 2.5 hour resting ( H2O2 3h) .

  • GSE81427
    Genome wide DNA methylation profiling of A2780 cells

  • 1) infected with control virus, no H2O2 (Scr_mock),
    • 2) infected with control virus with H2O2 treatment (30 min plus 2.5 h resting) (Scr_H2O2),
    • 3) infected with shTET2 virus, no H2O2 (shTET2_mock)
    • _4) infected with shTET2 virus, with H2O2 treatment (30 min plus 2.5 h resting) (shTET2_H2O2, two biological replicates).
  • GSE79808
  • GSE83750
  • GSE83751

    数据分析要点及结论

    主要是集中在 Figure 7. TET2 Protects against Abnormal DNAm

    图1

    把TET2基因使用LentiCRISPR病毒KO掉前后的A2780细胞系，选取那些表达量下调非常显著的基因集。然后再根据它们这些基因的甲基化芯片的promoter CGI 探针的 β值来分成3类：DNAm of unmethylated (b < 0.25) and intermediately methylated (0.25 < b < 0.75) ，分析发现它们的甲基化程度显著上升。
    图1

    图2

    还是针对那些TET2基因敲除后表达下降的基因，热图展现它们的甲基化芯片的promoter CGI 探针的 β值，共2947个探针。
    图2

    图3

    把TET2基因敲除后那些超甲基化的1406个基因跟以前发表的bivalent genes in hESCs, and cancer specific hypermethylated genes.基因集用韦恩图展现交叉情况。
    图3

    图4

    把TET2基因敲除后那些超甲基化的1406个基因进行GO富集分析
    图4

    图5

    把TET2基因敲除前后细胞表达量的变化以及它们对应的promoter CGI 探针的 β值变化的散点图
    图5
    同时也分析了增强子区域：
    2,107 hypermethylated enhancer regions identified by Rasmussen et al. (2015) to similar subgroups based on their basal methylation levels and found a very similar pattern for gains of DNAm in their TET2 KO scenario

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