siRNA脱靶效应研究进展

RNA干扰过程中,siRNA和mRNA特异结合能够使得靶基因沉默。但研究证实,siRNA可能与非靶基因结合而导致非靶基因沉默,这种现象称为siRNA脱靶效应。多种真核生物中的RNA干扰实验证实了脱靶效应的存在。对脱靶机制的研究发现脱靶可能与模体匹配、结构和长dsRNA等有关,很多新方法被提出来预测脱靶概率和检测脱靶基因。通过利用siRNApool、化学修饰和生物信息学方法能够尽可能地降低脱靶效应,提高RNAi实验的质量。对脱靶效应方面的研究进行了总结论述。     

Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity

Small interfering RNAs (siRNAs) and microRNAs (miRNAs) guide catalytic sequence-specific cleavage of fully or nearly fully complementary target mRNAs or control translation and/or stability of many mRNAs that share 6-8 nucleotides (nt) of complementarity to the siRNA and miRNA 5' end. siRNA- and miRNA-containing ribonucleoprotein silencing complexes are assembled from double-stranded 21- to 23-nt RNase III processing intermediates that carry 5' phosphates and 2-nt overhangs with free 3' hydroxyl groups. Despite the structural symmetry of a duplex siRNA, the nucleotide sequence asymmetry can generate a bias for preferred loading of one of the two duplex-forming strands into the RNA-induced silencing complex (RISC). Here we show that the 5'-phosphorylation status of the siRNA strands also acts as an important determinant for strand selection. 5'-O-methylated siRNA duplexes refractory to 5' phosphorylation were examined for their biases in siRNA strand selection. Asymmetric, single methylation of siRNA duplexes reduced the occupancy of the silencing complex by the methylated strand with concomitant elimination of its off-targeting signature and enhanced off-targeting signature of the phosphorylated strand. Methylation of both siRNA strands reduced but did not completely abolish RNA silencing, without affecting strand selection relative to that of the unmodified siRNA. We conclude that asymmetric 5' modification of siRNA duplexes can be useful for controlling targeting specificity.     

A comparison of siRNA efficacy predictors

Short interfering RNA (siRNA) efficacy prediction algorithms aim to increase the probability of selecting target sites that are applicable for gene silencing by RNA interference. Many algorithms have been published recently, and they base their predictions on such different features as duplex stability, sequence characteristics, mRNA secondary structure, and target site uniqueness. We compare the performance of the algorithms on a collection of publicly available siRNAs. First, we show that our regularized genetic programming algorithm GPboost appears to have a higher and more stable performance than other algorithms on the collected datasets. Second, several algorithms gave close to random classification on unseen data, and only GPboost and three other algorithms have a reasonably high and stable performance on all parts of the dataset. Third, the results indicate that the siRNAs' sequence is sufficient input to siRNA efficacy algorithms, and that other features that have been suggested to be important may be indirectly captured by the sequence.     

Clinical advances of siRNA therapeutics

Small interfering RNA (siRNA) enables efficient target gene silencing by employing a RNA interference (RNAi) mechanism, which can compromise gene expression and regulate gene activity by cleaving mRNA or repressing its translation. Twenty years after the discovery of RNAi in 1998, ONPATTRO? (patisiran) (Alnylam Pharmaceuticals, Inc.), a lipid formulated siRNA modality, was approved for the first time by United States Food and Drug Administration and the European Commission in 2018. With this milestone achievement, siRNA therapeutics will soar in the coming years. Here, we review the discovery and the mechanisms of RNAi, briefly describe the delivery technologies of siRNA, and summarize recent clinical advances of siRNA therapeutics.     

The potential therapeutic of siRNA eye drops in ocular diseases

In recent years, researchers have expressed an ongoing interest in developing RNA interference (RNAi) technology for therapeutic gene suppression in various diseases. Preclinical studies in animal models and cultured cell studies indicated that RNAi technology was an effective experimental tool against a variety of ocular diseases, and some small interference RNA (siRNA) drugs have been entered into clinical trials in Stage I and Stage II. However, in these studies siRNAs were delivered into ocular tissues via either systemic or subconjunctival/intravitreous injection, which is invasive and harmful if repeated. Based on this evidence, we hypothesize that topical application of siRNA eye drops may be a safe and effective therapeutic option in ocular surface diseases with temporary changes of gene expression. Furthermore, siRNA eye drops targeting different genes may simultaneously treat several ocular surface diseases.     

Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions

Contradictory reports in the literature have emphasised either the sequence of small interfering RNAs (siRNA) or the structure of their target molecules to be the major determinant of the efficiency of RNA interference (RNAi) approaches. In the present study, we analyse systematically the contributions of these parameters to siRNA activity by using deliberately designed mRNA constructs. The siRNA target sites were included in well-defined structural elements rendering them either highly accessible or completely involved in stable base-pairing. Furthermore, complementary sequence elements and various hairpins with different stem lengths and designs were used as target sites. Only one of the strands of the siRNA duplex was found to be capable of silencing via its respective target site, indicating that thermodynamic characteristics intrinsic to the siRNA strands are a basic determinant of siRNA activity. A significant obstruction of gene silencing by the same siRNA, however, was observed to be caused by structural features of the substrate RNA. Bioinformatic analysis of the mRNA structures suggests a direct correlation between the extent of gene-knockdown and the local free energy in the target region. Our findings indicate that, although a favourable siRNA sequence is a necessary prerequisite for efficient RNAi, complex target structures may limit the applicability even of carefully chosen siRNAs.     

Targeting siRNA in colorectal cancer therapy: Nanotechnology comes into view

Colorectal cancer (CRC) is known as one of the most important causes of death and mortality worldwide. Although several efforts have been made for finding new therapies, no achievements have been made in this area. Multidrug resistance (MDR) mechanisms are one of the key factors that could lead to the failure of chemotherapy. Moreover, it has been shown that various chemotherapy drugs are associated with several side effects. Hence, it seems that finding new drugs or new therapeutic platforms is required. Among different therapeutic approaches, utilization of nanoparticles (NPs) for targeting a variety of molecules such as siRNAs are associated with good results for the treatment of CRC. Targeting siRNA-mediated NPs could turn off the effects of oncogenes and MDR-related genes. In the current study, we summarized various siRNAs targeted by NPs which could be used for the treatment of CRC. Moreover, we highlighted other routes such as liposome for targeting siRNAs in CRC therapy.     

siRNAs targeting mouse myostatin

Eight different mouse myostatin small interfering RNA (siRNAs) were synthesized and tested. Five siRNAs showed a pronounced biological effect reducing myostatin mRNA content. For two of them, the myostatin mRNA level was reduced 3- and 4-fold, respectively. The obtained siRNAs can be used for study of biological effects of myostatin, both in vitro and in vivo.     

Competition potency of siRNA is specified by the 5'-half sequence of the guide strand

Small-interfering RNAs (siRNAs) execute specific cellular gene silencing by exploiting the endogenous RNA interference (RNAi) pathway. Therefore, excess amounts of siRNAs can saturate cellular RNAi machineries. Indeed, some siRNAs saturate the RNA-induced silencing complex (RISC) and competitively inhibit silencing by other siRNAs. However, the molecular feature of siRNAs that specifies competition potency has been undetermined. While previous reports suggested a correlation between the competition potency and silencing efficiency of siRNAs, we found that the silencing efficiency was insufficient to explain the competition potency. Instead, we show that the nucleotide sequence of the 5′-half of the guide strand determines the competition potency of an siRNA. Our finding provides important information for understanding the mechanistic basis of competition in combinatorial RNAi treatment.     

siRNA纳米递送系统研究进展

小干扰RNA (small interfering RNA,siRNA)是RNA干扰的引发物,激发与之互补的目标mRNA沉默,对基因调控及疾病治疗有重要意义。siRNA作为药物需要克服血管屏障、实现细胞内吞及溶酶体逃逸,同时还需要避免核酸酶作用下发生降解。因此,设计合适的纳米载体以帮助siRNA成功递送进细胞并发挥作用是目前siRNA药物发展的重要目标。纳米载体的材料种类、尺寸、结构、表面修饰等精确设计是实现siRNA药物成功递送的重要因素。随着研究的深入和应用的发展,siRNA药物纳米载体的精确控制制备、精准靶向递送及多功能化取得了较好的成果。本文围绕siRNA药物纳米载体,对siRNA药物应用及其递送困难、siRNA药物纳米载体主要设计策略、目前siRNA药物上市情况进行介绍,同时对其未来发展方向进行展望。     

Dual-target gene silencing by using long,synthetic siRNA duplexes without triggering antiviral responses

Chemically synthesized small interfering RNAs (siRNAs) can specifically knock-down expression of target genes via RNA interference (RNAi) pathway. To date, the length of synthetic siRNA duplex has been strictly maintained less than 30 bp, because an early study suggested that double-stranded RNAs (dsRNAs) longer than 30 bp could not trigger specific gene silencing due to the induction of nonspecific antiviral interferon responses. Contrary to the current belief, here we show that synthetic dsRNA as long as 38 bp can result in specific target gene silencing without nonspecific antiviral responses. Using this longer duplex structure, we have generated dsRNAs, which can simultaneously knock-down expression of two target genes (termed as dual-target siRNAs or dsiRNAs). Our results thus demonstrate the structural flexibility of gene silencing siRNAs, and provide a starting point to construct multifunctional RNA structures. The dsiRNAs could be utilized to develop a novel therapeutic gene silencing strategy against diseases with multiple gene alternations such as viral infection and cancer.     

RNA interference: a mammalian SID-1 homologue enhances siRNA uptake and gene silencing efficacy in human cells

SID-1 is a transmembrane protein that mediates systemic RNA interference in Caenorhabditis elegans. Here we show that the mammalian SID-1 homologue FLJ20174 localizes to the cell membrane of human cells and enhances their uptake of small interfering RNA (siRNA), resulting in increased siRNA-mediated gene silencing efficacy. This is the first demonstration to show that overexpression of a membrane protein enhances siRNA internalization in mammalian cells. This observation raises the possibility of enhancing the efficacy of RNA interference.     

基因表达调控多面手——microRNA和siRNA的作用机制

miRNA(microRNA)是一类广泛存在于高等真核细胞中的长度约为21个碱基的小分子非编码RNA,参与调控三分之一以上基因的表达,并与多种人类疾病存在重要关联。而siRNA(small interfering RNA)是RNA干扰(RNA interference,RNAi)中的效应分子,其结构和作用机制与miRNA存在许多类似之处。由于miRNA和siRNA具有重要的生物学功能。因此,对它们作用机制的理解具有非常重要的理论意义和应用指导价值。该综述将对它们作用机制的研究进展做一总结和回顾。     

siRNA降低肿瘤细胞端粒酶活性的研究

利用T7RNA聚合酶在体外转录合成针对端粒酶模板RNA(hTR)的两条互补单链RNA,经退火形成siRNA.采用TRAP法检测端粒酶活性,分析siRNA在肿瘤细胞裂解液的干扰作用.结果表明:T7RNA聚合酶可以高效地转录出短的单链RNA,制备的siRNA可明显地降低肿瘤端粒酶的活性,其降低肿瘤端粒酶活性的作用强于等量的反义链RNA.该法廉价、高效、简易,有可能为肿瘤的基因治疗提供一种新的探索途径.     

siRNA targeting midkine inhibits gastric cancer cells growth and induces apoptosis involved caspase-3,8,9 activation and mitochondrial depolarization

Midkine (MK), a heparin-binding growth factor, is expressed highly in various malignant tumors, so it acts as attractive therapeutic target. In the present study, we used siRNA targeting MK to downregulate human MK expression in human gastric cancer cell line BGC823 and SGC7901 so as to determine the advantages of this anticancer therapeutic. The cell proliferation was evaluated by a WST-8 (4-[3-(2-methoxy-4-nitrophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio]-1, 3-benzene disulfonate sodium salt) assay and colony formation assay. Apoptosis was determined by flow cytometer analysis and colorimetric assay. Our results showed that the BGC823 and SGC7901 cell growth were significantly inhibited by knockdown of MK gene. The loss of mitochondrial membrane potential, release of cytochrome c from the mitochondria into cytosol and increased activity of caspase-3, 8 and 9 occurred concomitantly with inhibition of MK gene. These results indicated that siRNA targeting MK gene can inhibit gastric cancer cells growth and induce apoptosis via mitochondrial depolarization and caspase-3 activation. MK siRNA may be a promising novel and potential therapeutic strategy for the treatment of gastric cancers.     

Initial evidence of functional siRNA machinery in dinoflagellates

Dinoflagellates are a major group of protists widely distributed in the aquatic environments. Many species in this lineage are able to form harmful algal blooms (HAB), some even producing toxins, making this phylum the most important contributors of HAB in the marine ecosystem. Despite the ecological importance, the molecular mechanisms underpinning the basic biology and HAB formation of dinoflagellates are poorly understood. While the high-throughput sequencing studies have documented a large and growing number of genes in dinoflagellates, their functions remained to be experimentally proven using a functional genetic tool. Unfortunately, no such tool is yet available. This study was aimed to adopt the RNA interference (RNAi) gene-silencing tool for dinoflagellate research, and to investigate the potential effects of RNAi-based silencing of proton-pump rhodopsin and CO₂-fixing enzyme Rubisco encoding genes in dinoflagellates. It was found that RNAi treatment caused a significant decrease in growth rate in both species. Compared with the non- endogenous target (GFP-siRNA) and the blank control, RNAi treatments also suppressed the expression of the target genes. These results constitute the first experimental evidence of the existence and operation of siRNA in two species of dinoflagellates, present initial evidence that dinoflagellate rhodopsins are functional as a supplemental energy acquisition mechanism, and provide technical information for future functional genetic research on dinoflagellates.     

Identification of the suppressive factors for human immunodeficiency virus type-1 replication using the siRNA mini-library directed against host cellular genes

We performed the screening to find the novel host factors affecting human immunodeficiency virus type-1 (HIV-1) replication using the siRNA mini-library consisted with 257 siRNAs directed against cellular genes. J111 cells, a human acute monocytic leukemia cell line, were transfected with individual siRNA, followed by either infected or transfected with the HIV-1 molecular clone with luciferase reporter gene in 96-well plate format. The results showed that six siRNAs significantly enhanced the HIV-1 replication in J111 cells, indicating that the target cellular genes of those siRNAs may negatively regulate HIV-1 replication in normal cell culture condition. We also discuss the possible mechanisms by which those cellular proteins regulate viral replication.     

.限制性siRNA干涉文库的构建以及影响HeLa细胞增殖新功能基因的扫描

利用RNA干涉文库进行大规模高通量的功能基因扫描,已成为发现新功能基因的重要方式和手段．为了寻找在细胞增殖和分化过程中的新功能基因,根据斯坦福大学公布的与人类胚胎干细胞和造血干细胞增殖和分化过程中有关基因的基因芯片的分析结果,组建了与细胞增殖和分化有关的RNA限制性干涉文库．该文库包括靶向各类基因的载体,如包括转录因子、各类蛋白激酶、细胞周期调控蛋白以及一些未知功能基因在内的225个基因．利用这个限制性RNA干涉文库对控制HeLa细胞增殖的基因进行筛选．并通过WST-1高通量检测,发现了2个同HeLa细胞增殖相关的基因：CNKSR3(Homo sapiens CNKSR family member 3)和Fosl2 Homo sapiens FOS like antigen 2),并初步证实：沉默CNKSR3会促进HeLa细胞的增殖,而沉默Fosl2则抑制HeLa细胞的增殖功能．