Alterations of Genome Network Regulations and Chromatin Configurations related to Carcinogenesis

人类细胞中的全局基因表达网络被认为是由染色质构型调控的。几种组蛋白和DNA修饰酶以及可能的小的非编码RNA是染色质构型的主要调节因子。为了阐明癌细胞染色质构型的改变，我研究了肺癌中的（1）组蛋白去乙酰化酶基因的表达，（2）TGFβRII启动子的染色质构型，和（3）小的非编码RNA通路。每个II类HDAC基因表达的减少与不良预后显著相关，并且是不良预后的独立预测因子。分层聚类分析显示II类HDACs表达降低的组预后也较差。我们还研究了TGFβRII启动子在6个肺癌细胞系中的染色质构型。ChIP试验证明了该基因沉默的三种染色质模式（模式I：组蛋白H3乙酰化（H3-Ac）（±）/组蛋白H3赖氨酸4甲基化（H3 K4-Me）（+）/DNA-Me（-），模式II：H3-Ac（-）/H3 K4-Me（±）/DNA-Me（-），和模式III：H3-Ac（-）/H3 K4-Me（-）/DNA-Me（+））。双链RNA特异性核酸内切酶家族的两个成员Dicer和Drosha使用逐步过程将microRNA的前体形式转化为它们的成熟形式。我们首次发现，Dicer表达水平在一部分肺癌中降低，对手术治疗病例的生存具有显著的预后影响。应该注意的是，多变量考克斯回归分析显示Dicer的预后影响似乎与疾病分期无关。

Global gene expression networks in human cells are thought to be regulated by the chromatin configurations. Several histone and DNA modifying enzymes and possibly small noncoding RNAs are major regulators of the chromatin configurations. To clarify the alterations of the chromatin configurations in cancer cells, I studied (1) expressions of histone deacetylase genes, (2) chromatin configurations of TGFβRII promoter, and (3) small noncoding RNAs pathways in lung cancers. Reduced expression of each class II HDAC gene was significantly associated with poor prognosis and an independent predictor of poor prognosis. The group with reduced expression of class II HDACs indicated by the hierarchical clustering analysis showed also poor prognosis. We also studied chromatin configurations of TGFβRII promoter in six lung cancer cell lines. ChIP assays demonstrated three chromatin patterns for this gene silencing (Pattern I : histone H3 acetylation (H3-Ac)(±)/histone H3 lysine 4 methylation (H3K4-Me)(+)/DNA-Me(-), Pattern II; H3-Ac(-)/H3K4-Me(±)/DNA-Me(-), and Pattern III ; H3-Ac(-)/H3K4-Me(-)/DNA-Me(+)). Two members of the double-stranded RNA-specific endonuclease family, Dicer and Drosha, convert precursor forms of microRNA into their mature forms using a stepwise process. We found for the first time that Dicer expression levels were reduced in a fraction of lung cancers with a significant prognostic impact on the survival of surgically treated cases. It should be noted that multivariate COX regression analysis showed that the prognostic impact of Dicer appears to be independent of disease stage.