DNA methylation and gene expression profiling of ewing sarcoma primary tumors reveal genes that are potential targets of epigenetic inactivation.
DNA methylation and gene expression profiling of ewing sarcoma primary tumors reveal genes that are potential targets of epigenetic inactivation.
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作者：
Patel N;Black J;Chen X;Marcondes AM;Grady WM;Lawlor ER;Borinstein SC
DNA甲基化异常在尤文肉瘤中的作用尚不完全清楚。使用珠芯片甲基化分析，将52个福尔马林固定石蜡包埋的EWS肿瘤和3个EWS细胞系中的503个基因的甲基化状态与人间充质干细胞原代培养物（hMSCs）进行比较。通过基因表达和定量RT-PCR评估了5-Aza-2-脱氧胞苷-（5-AZA）处理的EWS细胞系和一组原代EWS样品和hMSC中甲基化基因的相对表达。与hMSC相比，EWS肿瘤中有129个基因表现出统计学显着的高甲基化。36个基因在EWS中高度甲基化，在hMSCs中未甲基化。5-AZA处理EWS细胞系导致包括162个基因在内的数百个基因的表达上调，其增加至少2倍。在36个候选的高甲基化基因中，有19个在5-AZA后表达增加。对来自一个独立肿瘤队列的基因表达的分析证实了19个高甲基化基因中的6个（AXL、COL 1A 1、CYP 1B 1、林恩、SERPINE 1）和VCAN的表达降低。比较基因表达和DNA甲基化分析被证明是一种有效的方法，以确定在EWS表观遗传调控的基因。进一步的研究正在进行中，以阐明这些表观遗传改变在EWS发病机制中的作用。
The role of aberrant DNA methylation in Ewing sarcoma is not completely understood. The methylation status of 503 genes in 52 formalin-fixed paraffin-embedded EWS tumors and 3 EWS cell lines was compared to human mesenchymal stem cell primary cultures (hMSCs) using bead chip methylation analysis. Relative expression of methylated genes was assessed in 5-Aza-2-deoxycytidine-(5-AZA)-treated EWS cell lines and in a cohort of primary EWS samples and hMSCs by gene expression and quantitative RT-PCR. 129 genes demonstrated statistically significant hypermethylation in EWS tumors compared to hMSCs. Thirty-six genes were profoundly methylated in EWS and unmethylated in hMSCs. 5-AZA treatment of EWS cell lines resulted in upregulation of expression of hundreds of genes including 162 that were increased by at least 2-fold. The expression of 19 of 36 candidate hypermethylated genes was increased following 5-AZA. Analysis of gene expression from an independent cohort of tumors confirmed decreased expression of six of nineteen hypermethylated genes (AXL, COL1A1, CYP1B1, LYN, SERPINE1,) and VCAN. Comparing gene expression and DNA methylation analyses proved to be an effective way to identify genes epigenetically regulated in EWS. Further investigation is ongoing to elucidate the role of these epigenetic alterations in EWS pathogenesis.