Genome-wide differentially methylated genes in prostate cancer tissues from African-American and Caucasian men
Genome-wide differentially methylated genes in prostate cancer tissues from African-American and Caucasian men
复制标题
DOI：
10.1080/15592294.2015.1022019
复制
发表时间：
2015-04-01
期刊：
影响因子：
3.7
通讯作者：
Kwabi-Addo, B.
中科院分区：
文献类型：
--
作者：
Devaney, J. M.;Wang, S.;Kwabi-Addo, B.
越来越多的证据表明，异常的DNA甲基化变化可能导致前列腺癌（PCa）的种族差异。为了全面鉴定PCa差异中的DNA甲基化改变，我们使用Illumina 450 K甲基化平台来询问485，577个CpG位点的甲基化状态，重点关注人类基因组的基因相关区域。在分析中使用来自非裔美国人（AA; 7例正常和3例癌症）和高加索人（Cau; 8例正常和3例癌症）的基因组DNA。层次聚类分析确定探针集AA和Cau样品，以及共同的。我们选择了25个启动子相关的新CpG位点，这些位点在人种之间甲基化差异最大（倍数变化> 1.5倍;调整后的P < 0.05），并比较了由Illumina，Inc.在7个前列腺细胞系中通过焦磷酸测序获得的具有定量甲基化的阵列。我们发现β值和焦磷酸测序之间的甲基化水平非常一致。在用5-氮杂-2 '-脱氧胞苷和/或阿司他汀处理后，在8个基因的子集中使用qRT-PCR的基因表达分析显示PCa细胞中基因表达的上调。在来自AA和Cau PCa患者的匹配的正常和PCa组织中对SNRPN、SHANK 2、MST 1 R和ABCG 5 4个基因的定量分析表明，AA与Cau的前列腺组织中存在差异启动子甲基化和伴随的mRNA表达差异。在正常和PCa组织中作为种族函数的回归分析显示，AA与Cau样本相比，SNRPN（P = 0.012）、MST 1 R（P = 0.038）和ABCG 5（P < 0.0002）的甲基化流行率显著更高。我们选择ABCG 5和SNRPN基因，并通过Western blot分析和siRNA基因敲除对4个PCa细胞系（2个AA和2个Cau患者来源的细胞系）的细胞增殖和侵袭的影响来验证它们的生物学功能。敲低ABCG 5或SNRPN导致Cau PCa细胞系的侵袭和增殖显著降低，但我们在AA PCa细胞系中没有观察到这些显著的功能丧失效应。我们的研究表明，差异全基因组DNA甲基化水平如何影响AA和Cau PCa的基因表达和生物学功能。
Increasing evidence suggests that aberrant DNA methylation changes may contribute to prostate cancer (PCa) ethnic disparity. To comprehensively identify DNA methylation alterations in PCa disparity, we used the Illumina 450K methylation platform to interrogate the methylation status of 485,577 CpG sites focusing on gene-associated regions of the human genome. Genomic DNA from African-American (AA; 7 normal and 3 cancers) and Caucasian (Cau; 8 normal and 3 cancers) was used in the analysis. Hierarchical clustering analysis identified probe-sets unique to AA and Cau samples, as well as common to both. We selected 25 promoter-associated novel CpG sites most differentially methylated by race (fold change > 1.5-fold; adjusted P < 0.05) and compared the beta-value of these sites provided by the Illumina, Inc. array with quantitative methylation obtained by pyrosequencing in 7 prostate cell lines. We found very good concordance of the methylation levels between beta-value and pyrosequencing. Gene expression analysis using qRT-PCR in a subset of 8 genes after treatment with 5-aza-2'-deoxycytidine and/or trichostatin showed up-regulation of gene expression in PCa cells. Quantitative analysis of 4 genes, SNRPN, SHANK2, MST1R, and ABCG5, in matched normal and PCa tissues derived from AA and Cau PCa patients demonstrated differential promoter methylation and concomitant differences in mRNA expression in prostate tissues from AA vs. Cau. Regression analysis in normal and PCa tissues as a function of race showed significantly higher methylation prevalence for SNRPN (P = 0.012), MST1R (P = 0.038), and ABCG5 (P < 0.0002) for AA vs. Cau samples. We selected the ABCG5 and SNRPN genes and verified their biological functions by Western blot analysis and siRNA gene knockout effects on cell proliferation and invasion in 4 PCa cell lines (2 AA and 2 Cau patients-derived lines). Knockdown of either ABCG5 or SNRPN resulted in a significant decrease in both invasion and proliferation in Cau PCa cell lines but we did not observe these remarkable loss-of-function effects in AA PCa cell lines. Our study demonstrates how differential genome-wide DNA methylation levels influence gene expression and biological functions in AA and Cau PCa.