Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma
Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma
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DOI：
10.1073/pnas.1011098108
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发表时间：
2011-01-11
影响因子：
11.1
通讯作者：
Patel, Tushar
中科院分区：
文献类型：
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作者：
Braconi, Chiara;Valeri, Nicola;Patel, Tushar
尽管非蛋白编码 RNA (ncRNA) 的表达在人类癌症中可以发生改变，但其功能相关性尚不清楚。超级保守区域是非编码基因组片段，在人类、小鼠和大鼠中 100% 保守。跨物种基因序列的保守性可能表明其重要的功能作用，因此我们评估了肝细胞癌 (HCC) 中超保守 RNA (ucRNA) 的表达。使用定制微阵列分析 ucRNA 的整体表达。通过实时 PCR 在细胞系中验证表达，或通过使用组织微阵列的原位杂交在组织中验证表达。用 siRNA 调节细胞 ucRNA 表达，并评估其对人和鼠 HCC 细胞整体基因表达和生长的影响。与非恶性肝细胞相比，HepG2 细胞中有 56 个 ucRNA 异常表达。在这些 ucRNA 中，最大的变化是超保守元件 338 (uc.338)，与非癌性邻近组织相比，该元件在人类 HCC 中显着增加。尽管 uc.338 部分位于聚 (rC) 结合蛋白 2 (PCBP2) 基因内，但编码 uc.338 的转录 ncRNA 独立于 PCBP2 表达，并被克隆为 590 bp RNA 基因，称为 TUC338。功能基因注释分析表明对细胞生长相关基因的主要影响。这些效应已在人类和小鼠细胞中得到实验证明。 TUC338 的 siRNA 降低了 HCC 细胞的贴壁依赖性和贴壁非依赖性生长。这些研究确定了 TUC338 在调节转化细胞生长和转录超保守 ncRNA 中的关键作用，作为参与 HCC 病理学的一类独特基因。
Although expression of non-protein-coding RNA (ncRNA) can be altered in human cancers, their functional relevance is unknown. Ultraconserved regions are noncoding genomic segments that are 100% conserved across humans, mice, and rats. Conservation of gene sequences across species may indicate an essential functional role, and therefore we evaluated the expression of ultraconserved RNAs (ucRNA) in hepatocellular cancer (HCC). The global expression of ucRNAs was analyzed with a custom microarray. Expression was verified in cell lines by real-time PCR or in tissues by in situ hybridization using tissue microarrays. Cellular ucRNA expression was modulated with siRNAs, and the effects on global gene expression and growth of human and murine HCC cells were evaluated. Fifty-six ucRNAs were aberrantly expressed in HepG2 cells compared with nonmalignant hepatocytes. Among these ucRNAs, the greatest change was noted for ultraconserved element 338 (uc.338), which was dramatically increased in human HCC compared with noncancerous adjacent tissues. Although uc.338 is partially located within the poly(rC) binding protein 2 (PCBP2) gene, the transcribed ncRNA encoding uc.338 is expressed independently of PCBP2 and was cloned as a 590-bp RNA gene, termed TUC338. Functional gene annotation analysis indicated predominant effects on genes involved in cell growth. These effects were experimentally demonstrated in both human and murine cells. siRNA to TUC338 decreased both anchorage-dependent and anchorage-independent growth of HCC cells. These studies identify a critical role for TUC338 in regulation of transformed cell growth and of transcribed ultraconserved ncRNA as a unique class of genes involved in the pathobiology of HCC.