Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma.
Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma.
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DOI：
10.1186/1752-0509-4-51
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发表时间：
2010-04-27
影响因子：
--
通讯作者：
Bhanot GV
中科院分区：
文献类型：
--
作者：
Liu H;Brannon AR;Reddy AR;Alexe G;Seiler MW;Arreola A;Oza JH;Yao M;Juan D;Liou LS;Ganesan S;Levine AJ;Rathmell WK;Bhanot GV
microRNA以组织特异性方式调节mRNA水平，通过诱导转录物降解或通过抑制翻译或转录。从种子序列匹配中鉴定的microRNA的推定mRNA靶标可在许多数据库中获得。然而，这样的匹配具有高的假阳性率，并且不能识别调节的组织特异性。我们描述了一种简单的方法来确定直接mRNA靶的microRNA失调的癌症患者匹配的肿瘤/正常样品中的表达水平测量。这里使用的“直接”一词是严格意义上的：a）代表在其3 'UTR中与微小RNA具有精确种子序列匹配的mRNA，B）种子序列匹配在小鼠、人、大鼠和狗基因组中严格保守，c）mRNA和microRNA表达水平可以以高度显著性区分肿瘤与正常，以及在肿瘤和/或正常样品中相关。我们使用透明细胞肾细胞癌（ccRCC）和匹配的正常肾脏样本应用并验证了该方法，将我们的分析限制在由于完美的种子序列匹配而经历mRNA转录物降解的mRNA靶点。首先通过比较它们在肿瘤与正常样品中的表达水平来鉴定失调的microRNA和mRNA。使用种子序列匹配从这些中鉴定推定的失调的microRNA/mRNA对，要求种子序列在人/狗/大鼠/小鼠基因组中保守。通过要求肿瘤和/或正常样品中的强反相关特征来进一步修剪这些。该方法揭示了ccRCC中的许多新规则。例如，miR-149、miR-200 c和mir-141的缺失分别导致癌基因（KCNMA 1、LOX）、VEGFA和SEMA 6A的功能获得，并且miR-142- 3 p、miR-185、mir-34 a、miR-224、miR-21的水平增加分别导致肿瘤抑制因子LRRC 2、PTPN 13、SFRP 1、ERBB 4和（SLC 12 A1、TCF 21）的功能缺失。我们还发现VEGFA与miR-200家族的microRNA：miR-200 a *、200 b、200 c和miR-141之间存在强烈的反相关性。在一组独立的匹配ccRCC/正常样品上验证了几种鉴定的微小RNA/mRNA对。通过转染测定验证miR-141对SEMA 6A的调节。我们描述了一种简单可靠的方法来识别任何癌症中microRNA的直接基因靶点。我们施加的限制（肿瘤/正常样品之间microRNA和mRNA水平的强失调特征，种子序列的进化保守性和表达水平的强反相关性）消除了虚假匹配，并确定了失调microRNA的稳健的，组织特异性的，功能性mRNA靶点的子集。
MicroRNA regulate mRNA levels in a tissue specific way, either by inducing degradation of the transcript or by inhibiting translation or transcription. Putative mRNA targets of microRNA identified from seed sequence matches are available in many databases. However, such matches have a high false positive rate and cannot identify tissue specificity of regulation. We describe a simple method to identify direct mRNA targets of microRNA dysregulated in cancers from expression level measurements in patient matched tumor/normal samples. The word "direct" is used here in a strict sense to: a) represent mRNA which have an exact seed sequence match to the microRNA in their 3'UTR, b) the seed sequence match is strictly conserved across mouse, human, rat and dog genomes, c) the mRNA and microRNA expression levels can distinguish tumor from normal with high significance and d) the microRNA/mRNA expression levels are strongly and significantly anti-correlated in tumor and/or normal samples. We apply and validate the method using clear cell Renal Cell Carcinoma (ccRCC) and matched normal kidney samples, limiting our analysis to mRNA targets which undergo degradation of the mRNA transcript because of a perfect seed sequence match. Dysregulated microRNA and mRNA are first identified by comparing their expression levels in tumor vs normal samples. Putative dysregulated microRNA/mRNA pairs are identified from these using seed sequence matches, requiring that the seed sequence be conserved in human/dog/rat/mouse genomes. These are further pruned by requiring a strong anti-correlation signature in tumor and/or normal samples. The method revealed many new regulations in ccRCC. For instance, loss of miR-149, miR-200c and mir-141 causes gain of function of oncogenes (KCNMA1, LOX), VEGFA and SEMA6A respectively and increased levels of miR-142-3p, miR-185, mir-34a, miR-224, miR-21 cause loss of function of tumor suppressors LRRC2, PTPN13, SFRP1, ERBB4, and (SLC12A1, TCF21) respectively. We also found strong anti-correlation between VEGFA and the miR-200 family of microRNA: miR-200a*, 200b, 200c and miR-141. Several identified microRNA/mRNA pairs were validated on an independent set of matched ccRCC/normal samples. The regulation of SEMA6A by miR-141 was verified by a transfection assay. We describe a simple and reliable method to identify direct gene targets of microRNA in any cancer. The constraints we impose (strong dysregulation signature for microRNA and mRNA levels between tumor/normal samples, evolutionary conservation of seed sequence and strong anti-correlation of expression levels) remove spurious matches and identify a subset of robust, tissue specific, functional mRNA targets of dysregulated microRNA.
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影响因子：
7
作者：
Boer, JM;Huber, WK;Poustka, A
通讯作者：
Poustka, A
影响因子：
2
作者：
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作者：
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影响因子：
3.2
作者：
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通讯作者：
Bloomston, Mark
影响因子：
3.8
作者：
Baudis M
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