Evaluation and control of miRNA-like off-target repression for RNA interference

RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes. Despite early recognition of the severity of miRNA-like off-target repression, this effect has often been overlooked because of difficulties in recognizing and avoiding off-targets. However, recent advances in genome-wide methods and knowledge of Ago–miRNA target interactions have set the stage for properly evaluating and controlling miRNA-like off-target repression. Here, we describe the intrinsic problems of miRNA-like off-target effects caused by canonical and noncanonical interactions. We particularly focus on various genome-wide approaches and chemical modifications for the evaluation and prevention of off-target repression to facilitate the use of RNAi with secured specificity.     

Multispecies-compatible antitumor effects of a cross-species small-interfering RNA against mammalian target of rapamycin

Successful development of sequence-specific siRNA (small interfering RNA)-based drugs requires an siRNA design that functions consistently in different organisms. Utilizing the CAPSID program previously developed by our group, we here designed siRNAs against mammalian target of rapamycin (mTOR) that are entirely complementary among various species and investigated their multispecies-compatible gene-silencing properties. The mTOR siRNAs markedly reduced mTOR expression at both the mRNA and protein levels in human, mouse, and monkey cell lines. The reduction in mTOR expression resulted in inactivation of both mTOR complex I and II signaling pathways, as confirmed by reduced phosphorylation of p70S6K (70-kDa ribosomal protein S6 kinase), 4EBP1 (eIF4E-binding protein 1), and AKT, and nuclear accumulation of FOXO1 (forkhead box O1), with consequent cell-cycle arrest, proliferation inhibition, and autophagy activation. Moreover, interfering with mTOR activity in vivo using mTOR small-hairpin RNA-expressing recombinant adeno-associated virus led to significant antitumor effects in xenograft and allograft models. Thus, the present study demonstrates that cross-species siRNA successfully silences its target and readily produces multispecies-compatible phenotypic alterations-antitumor effects in the case of mTOR siRNA. Application of cross-species siRNA should greatly facilitate the development of siRNA-based therapeutic agents.     

Regulation of microRNA biogenesis and turnover by animals and their viruses

MicroRNAs (miRNAs) are a ubiquitous component of gene regulatory networks that modulate the precise amounts of proteins expressed in a cell. Despite their small size, miRNA genes contain various recognition elements that enable specificity in when, where and to what extent they are expressed. The importance of precise control of miRNA expression is underscored by functional studies in model organisms and by the association between miRNA mis-expression and disease. In the last decade, identification of the pathways by which miRNAs are produced, matured and turned-over has revealed many aspects of their biogenesis that are subject to regulation. Studies in viral systems have revealed a range of mechanisms by which viruses target these pathways through viral proteins or non-coding RNAs in order to regulate cellular gene expression. In parallel, a field of study has evolved around the activation and suppression of antiviral RNA interference (RNAi) by viruses. Virus encoded suppressors of RNAi can impact miRNA biogenesis in cases where miRNA and small interfering RNA pathways converge. Here we review the literature on the mechanisms by which miRNA biogenesis and turnover are regulated in animals and the diverse strategies that viruses use to subvert or inhibit these processes.     

Targeted inhibition of Livin resensitizes renal cancer cells towards apoptosis

Cancer cells are typically characterized by apoptosis deficiency. In order to investigate a possible role for the anti-apoptotic livin gene in renal cell cancer (RCC), we analyzed its expression in tumor tissue samples and in RCC-derived cell lines. In addition, we studied the contribution of livin to the apoptotic resistance of RCC cells by RNA interference (RNAi). Livin gene expression was detected in a significant portion of RCC tumor tissue specimens (13/14, 92.9%) and tumor-derived cell lines (12/15, 80.0%). Moreover, targeted inhibition of livin by RNAi markedly sensitized RCC cells towards proapoptotic stimuli, such as UV irradiation or the chemotherapeutic drugs etoposide, 5-fluorouracil, and vinblastine. These effects were specific for livin expressing tumor cells. We conclude that livin can contribute significantly to the apoptosis resistance of RCC cells. Targeted inhibition of livin could represent a novel therapeutic strategy to increase the sensitivity of renal cancers towards pro-apoptotic agents. Received 30 November 2006; received after revision 22 February 2007; accepted 20 March 2007     

si—DNMT1对肝门部胆管癌细胞抑癌基因甲基化的作用

目的研究RNA干扰对肝门部胆管癌细胞株QRC939抑癌基因甲基化的影响,初步探谤其在胆管癌治疗中的价值。方法构建靶向hDNMT1的发夹式siRNA表达载体;运用脂质体介导法将其转染人胆管癌细胞QBC939;RT-PCR法检测不同时间点hDNMT1、CDH1、p15的表达水平;MSP方法检测转染前后抑癌基因CDH1、p15的甲基纯状态;MTT检测各组细胞的增殖能力。结果1）hDNMT1的基因沉默恢复了抑癌基因CDH1、p15的表达水平;2）CDH1、p15的表达沉默是由启动子高甲基亿导致的;3）转染靶向hDNMT1的发夹式siRNA表达载体能有效地抑制QBC939的增殖能力。结论靶向hDNMT1的发夹式siRNA表达载体能有效、持续、稳定发挥对hDNMT1的基因沉默作用,恢复抑癌基因CDH1、p15的表达水平,从而抑制QBC939肿瘤细胞增殖。     

Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus

In the hepatitis delta virus, ribozymes are encoded in both the genomic strand RNA and its complement, the antigenomic strand. The two ribozymes are similar in sequence and structure, are most active in the presence of divalent cation and catalyze RNA cleavage reactions which generate a 5′-hydroxyl group and a 2′,3′-cyclic phosphate group. Recent progress has been made in understanding the catalytic mechanism. One key was a crystal structure of the genomic ribozyme that revealed a specific cytosine positioned to act as a general acid-base catalyst. The folding of the ribozyme in the context of the longer viral RNA is another area of interest. The biology requires that each ribozyme act only once, and mechanisms proposed for regulation of ribozyme activity sometimes invoke alternative RNA structures. Likewise, interference of ribozyme function by polyadenylation of the antigenomic RNA strand could be controlled through alternative structures, and a model for such control is proposed. Received 21 June 2001; received after revision 18 July 2001; accepted 20 July 2001     

Understanding paternal genome demethylation through live-cell imaging and siRNA

Identification of a DNA demethylase responsible for zygotic paternal DNA demethylation has been one of the most challenging goals in the field of epigenetics. Several candidate molecules have been proposed, but their involvement in the demethylation remains controversial, partly due to the difficulty of preparing a sufficient quantity of materials for biochemical analysis. In this review, we utilize a recently developed method for live-cell imaging of mouse zygotes combined with RNA interference (RNAi) to search for factors that affect zygotic paternal DNA demethylation. The combined use of various fluorescent probes and RNAi is a useful approach for the study of not only DNA demethylation but also the spatiotemporal dynamics of histone depositions in zygotes, although it is not appropriate for large-scale screening or knockdown of genes that are abundantly expressed before fertilization. This new technique enables us to understand the epigenetic hierarchy during cellular response and differentiation in preimplantation embryos.     

Interaction and cross-talk between non-coding RNAs

Non-coding RNA (ncRNA) has been shown to regulate diverse cellular processes and functions through controlling gene expression. Long non-coding RNAs (lncRNAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites. Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation. These interactions form complicated and intertwined networks. Certain lncRNAs encode miRNAs and small nucleolar RNAs (snoRNAs), and may regulate expression of these small RNAs as precursors. SnoRNAs have also been reported to be precursors for PIWI-interacting RNAs (piRNAs) and thus may regulate the piRNAs as a precursor. These miRNAs and piRNAs target messenger RNAs (mRNAs) and regulate gene expression. In this review, we will present and discuss these interactions, cross-talk, and co-regulation of ncRNAs and gene regulation due to these interactions.     

RNA干扰靶向沉默COX 2基因对MG 63骨肉瘤细胞生物学特性的研究

目的 通过构建小干扰RNA(small interfering RNA,siRNA)降低MG 63骨肉瘤细胞环氧合酶 2(COX 2)基因的表达,并进一步研究其对MG 63骨肉瘤细胞增值、侵袭、迁移能力的影响及分子机制。方法 设计靶向干扰COX 2基因的siRNA,通过脂质体转染MG 63骨肉瘤细胞,使其抑制MG 63骨肉瘤细胞COX 2基因的表达,后采用噻唑蓝(MTT)比色法、Transwell小室实验研究其对MG 63骨肉瘤细胞增殖、侵袭、迁移能力的影响,采用RFQ PCR和Western blot分别从基因和蛋白的水平检测MG 63骨肉瘤细胞侵袭性相关因子基质金属酶(MMP 9)的表达及血管内皮生长因子(VEGF)的表达。结果 转染MG 63骨肉瘤细胞后,实验组与阴性对照组和空白对照组比较,通过RFQ PCR和Western blot检测COX 2基因表达降低约90%(P0.05),MTT检测MG 63骨肉瘤细胞增值能力明显受到抑制(P0.05),Transwell实验检测MG 63骨肉瘤细胞侵袭、迁移能力明显下降(P0.05),经RFQ PCR、Western blot检测侵袭性相关因子MMP 9和血管内皮生长因子VEGF的mRNA及蛋白表达降低(P0.05)。空白对照组和阴性对照组比较无明显变化,差异无统计学意义(P0.05)。结论 人MG 63骨肉瘤细胞COX 2基因被抑制后,MG 63骨肉瘤细胞增值、侵袭、迁移能力明显下降。     

转录因子TCF7L2在HePG2细胞IDE表达调控中的作用

目的 TCF7L2是一种重要的转录因子,与2型糖尿病(T2DM)发生发展密切相关.本研究探讨慢病毒介导的RNA干扰抑制TCF7L2基因表达对人肝癌细胞株HePG2胰岛素降解酶(IDE)基因的影响.方法 以人TCF7L2 mRNA编码序列作为干扰靶点,构建TCF7L2特异性短发卡RNA慢病毒表达载体(LV-TCF7 L2-shRNA)感染HePG2细胞.应用实时定量PCR及Western blot检测转染后TCF7L2与IDE表达的变化.结果 成功构建TCF7L2 shRNA慢病毒载体LV-TCF7L2-shRNA.qPCR及Westem blot结果显示干扰组HePG2细胞TCF7L2和IDE mRNA及蛋白的表达水平较空白组及阴性对照组显著降低(P＜0.05).结论 LV-TCF7L2-shRNA载体有效地抑制了IDE的表达,结果证明TCF7L2是IDE表达调控中重要的转录因子,为探讨TCF7L2与IDE在2型糖尿病发病机制中的作用奠定了基础.     

Molecular and Cellular Basis of Regeneration and Tissue Repair

Nymphs of hemimetabolous insects such as cockroaches and crickets exhibit a remarkable capacity for regenerating complex structures from damaged legs. Until recent years, however, approaches to elucidate the molecular mechanisms underlying the leg regeneration process have been lacking. Taking the cricket Gryllus bimaculatus as a model, we found that a phenotype related to regeneration frequently appears during leg regeneration, even though no phenotype is induced by RNA interference (RNAi) in the cricket nymph, designated as regeneration-dependent RNAi. Since then, we have investigated the functions of various genes encoding signaling factors and cellular adhesion proteins like Fat and Dachsous during leg regeneration. In this review, we summarize the classical knowledge about insect leg regeneration and introduce recent advances concerning the signaling cascades required for regenerating a leg. Our results provide clues to the mechanisms of regeneration which are relevant to vertebrate systems.