RNA targeting by small molecules: Binding of protoberberine, benzophenanthridine and aristolochia alkaloids to various RNA structures

Studies on RNA targeting by small molecules to specifically control certain cellular functions is an area of remarkable current interest. For this purpose, a basic understanding of the molecular aspects of the interaction of small molecules with various RNA structures is essential. Alkaloids are a group of natural products with potential therapeutic utility, and very recently, their interaction with many RNA structures have been reported. Especially noteworthy are the protoberberines and aristolochia alkaloids distributed widely in many botanical families. Many of the alkaloids of these group exhibit excellent binding affinity to many RNA structures that may be exploited to develop RNA targeted therapeutics. This review attempts to present the current status on the understanding of the interaction of these alkaloids with various RNA structures, mainly highlighting the biophysical aspects.     

长链非编码RNA在白血病发生发展中的调控机制研究进展

长链非编码RNA (Long noncoding RNA,lncRNA) 是一类长度大于200 nt且不具备蛋白编码能力或仅编码微肽的RNA分子。LncRNA参与调控细胞增殖、分化和凋亡等生物学过程,与多种恶性血液病的发生、复发及转移密切相关。文章结合最新研究报道,对lncRNA在白血病发生过程中异常表达的功能、调控机制和潜在临床应用方面进行综述。概括了lncRNA可以通过表观遗传修饰、核糖体RNA转录、竞争性结合miRNA,以及参与糖代谢途径、活化肿瘤相关信号通路等多种方式调控白血病的发生发展及化疗中产生的多药耐药性。这些机制研究为深入了解白血病的发病机理、发现新的预后标志物和潜在的治疗靶标,为解决临床上治疗白血病所面临的患者耐药性的产生和治疗后复发等难题提供了新的参考依据。     

Inducible RNAi system and its application in novel therapeutics

RNA interference (RNAi) was discovered as a cellular defense mechanism more than decade ago. It has been exploited as a powerful tool for genetic manipulation. Characterized with specifically silencing target gene expression, it has great potential application for disease treatment. Currently, there are human clinical trials in progress or planned. Despite the excitement regarding this prominent technology, there are many obstacles and concerns that prevent RNAi from being widely used in the therapeutic field. Among them, the non-spatial and non-temporal control is the most difficult challenge, as well as off-target effects and triggering type I immune responses. Inducible RNAi technology can effectively regulate target genes by inducer-mediated small hairpin RNA expression. Combination with inducible regulation systems this makes RNAi technology more sophisticated and may provide a wider application field. This review discusses approaches of inducible RNAi systems, the potential problem areas and solutions and their therapeutic applications. Given the limitations discussed herein being resolved, we believe that inducible RNAi will be a major therapeutic modality within the next several years.     

HIV envelope: challenges and opportunities for development of entry inhibitors

The HIV envelope proteins glycoprotein 120 (gp120) and glycoprotein 41 (gp41) play crucial roles in HIV entry, therefore they are of extreme interest in the development of novel therapeutics. Studies using diverse methods, including structural biology and mutagenesis, have resulted in a detailed model for envelope-mediated entry, which consists of multiple conformations, each a potential target for therapeutic intervention. In this review, the challenges, strategies and progress to date for developing novel entry inhibitors directed at disrupting HIV gp120 and gp41 function are discussed.     

Polymers in small-interfering RNA delivery

This review will cover the current strategies that are being adopted to efficiently deliver small interfering RNA using nonviral vectors, including the use of polymers such as polyethylenimine, poly(lactic-co-glycolic acid), polypeptides, chitosan, cyclodextrin, dendrimers, and polymers-containing different nanoparticles. The article will provide a brief and concise account of underlying principle of these polymeric vectors and their structural and functional modifications which were intended to serve different purposes to affect efficient therapeutic outcome of small-interfering RNA delivery. The modifications of these polymeric vectors will be discussed with reference to stimuli-responsiveness, target specific delivery, and incorporation of nanoconstructs such as carbon nanotubes, gold nanoparticles, and silica nanoparticles. The emergence of small-interfering RNA as the potential therapeutic agent and its mode of action will also be mentioned in a nutshell.     

N1-methylpseudouridine-incorporated mRNA enhances exogenous protein expression and suppresses immunogenicity in primary human fibroblast-like synoviocytes

Cytotechnology - Studies conducted using murine arthritis models have indicated that the use of in vitro-transcribed messenger RNA (IVT mRNA) is an effective therapeutic approach for joint...     

miRNA in Parkinson's disease: From pathogenesis to theranostic approaches

Parkinson's disease (PD) is an age associated neurological disorder which is specified by cardinal motor symptoms such as tremor, stiffness, bradykinesia, postural instability, and non-motor symptoms. Dopaminergic neurons degradation in substantia nigra region and aggregation of αSyn are the classic signs of molecular defects noticed in PD pathogenesis. The discovery of microRNAs (miRNA) predicted to have a pivotal part in various processes regarding regularizing the cellular functions. Studies on dysregulation of miRNA in PD pathogenesis has recently gained the concern where our review unravels the role of miRNA expression in PD and its necessity in clinical validation for therapeutic development in PD. Here, we discussed how miRNA associated with ageing process in PD through molecular mechanistic approach of miRNAs on sirtuins, tumor necrosis factor-alpha and interleukin-6, dopamine loss, oxidative stress and autophagic dysregulation. Further we have also conferred the expression of miRNAs affected by SNCA gene expression, neuronal differentiation and its therapeutic potential with PD. In conclusion, we suggest more rigorous studies should be conducted on understanding the mechanisms and functions of miRNA in PD which will eventually lead to discovery of novel and promising therapeutics for PD.     

siRNA在治疗学中的应用

小干扰RNA（small interfering RNA,siRNA）是外源性双链RNA（double strand RNA,dsRNA）的加工产物,在细胞内能介导RNA干扰（RNA interference,RNAi）效应,识别特异性mRNA,沉默同源基因表达。其特异性和高效性显示出很高的实用价值,siRNA已成为许多疾病潜在的治疗手段。对于siRNA的应用,尽管还需要在减少非特异反应,发掘高效递药载体,应对新的基因变异等方面进行深入研究,但其可望在抗病毒、神经系统疾病和肿瘤治疗等许多领域发挥治疗作用。     

Recognition of the unique structure of DNA:RNA hybrids

Targeting nucleic acids using small molecules routinely uses the end products in the conversion pathway of "DNA to RNA, RNA to protein". However, the intermediate processes in this path have not always been targeted. The DNA-RNA interaction, specifically DNA:RNA hybrid formation, provides a unique target for controlling the transfer of genetic information through binding by small molecules. Not only do DNA:RNA hybrids differ in conformation from widely targeted DNA and RNA, the low occurrence within biological systems further validates their therapeutic potential. Surprisingly, a survey of the literature reveals only a handful of ligands that bind DNA:RNA hybrids; in comparison, the number of ligands designed to target DNA is in the thousands. DNA:RNA hybrids, from their scientific inception to current applications in ligand targeting, are discussed.     

高通量RNA甲基化测序数据处理与分析研究进展

随着高通量测序技术快速发展,Me RIP-seq(methylated RNA immunoprecipitation sequencing)测序技术开启了RNA表观遗传学研究新局面,能够在全基因组范围内描述RNA甲基化.从Me RIP-seq高通量数据中挖掘RNA甲基化模式,有助于揭示m RNA甲基化在调控基因表达、剪切等方面所发挥的潜在功能,有效指导癌症的干预治疗.本文从Me RIP-seq测序原理出发,较全面地综述Me RIP-seq数据处理和分析方法研究现状,并对其所面临的计算问题进行讨论和展望.     

Generating the optimal mRNA for therapy: HPLC purification eliminates immune activation and improves translation of nucleoside-modified, protein-encoding mRNA

In vitro-transcribed mRNA has great therapeutic potential to transiently express the encoded protein without the adverse effects of viral and DNA-based constructs. Mammalian cells, however, contain RNA sensors of the innate immune system that must be considered in the generation of therapeutic RNA. Incorporation of modified nucleosides both reduces innate immune activation and increases translation of mRNA, but residual induction of type I interferons (IFNs) and proinflammatory cytokines remains. We identify that contaminants, including double-stranded RNA, in nucleoside-modified in vitro-transcribed RNA are responsible for innate immune activation and their removal by high performance liquid chromatography (HPLC) results in mRNA that does not induce IFNs and inflammatory cytokines and is translated at 10- to 1000-fold greater levels in primary cells. Although unmodified mRNAs were translated significantly better following purification, they still induced high levels of cytokine secretion. HPLC purified nucleoside-modified mRNA is a powerful vector for applications ranging from ex vivo stem cell generation to in vivo gene therapy.     

RNA interference of metastasis-associated gene 1 inhibits metastasis of B16F10 melanoma cells in a C57BL/6 mouse model.

BACKGROUND INFORMATION: MTA1 (metastasis-associated gene 1) has been reported to be overexpressed in cancers with high potential to metastasize. Studies of the molecular mechanisms revealed that MTA1 plays an important role in the process of metastasis of many types of cancer. However, the role of MTA1 in melanoma development is unclear. RESULTS: We have investigated the therapeutic value of MTA1 in the B16F10 melanoma cell line with the C57BL/6 mouse model. Studies in vitro showed that MTA1 promoted the metastatic ability of B16F10 cancer cells. MTA1 down-regulation by RNA interference greatly reversed the malignant phenotypes of cancer cells. Immunohistochemical staining of MTA1 in human melanoma samples confirmed the up-regulation of MTA1 in the process of carcinogenesis. Studies in vivo confirmed down-regulation of MTA1 suppressed the growth and experimental metastasis of B16F10 melanoma cells. CONCLUSIONS: MTA1 plays an important role in melanoma development and metastasis. It has a promising potential as a target for in cancer gene therapy or chemotherapy.     

Spermine supports catalysis of hairpin ribozyme variants to differing extents

Because of the ability to cleave RNA substrates in trans, the hairpin ribozyme has great potential for therapeutic application. Activity of a three-stranded version of the minimal truncated form is enhanced by the presence of the polyamine spermine. Since spermine is the most abundant polyamine in eucariots, improved prospects for the hairpin ribozyme as therapeutic agent were predicted. We have found that not all hairpin ribozyme variants accept spermine equally well as counter-ion. Particularly the two-stranded versions commonly used for therapeutic studies show rather decreased activity when spermine is present. We have investigated a number of hairpin ribozyme derivatives regarding their ability to carry out spermine supported catalysis. Among the studied structures a two-stranded reverse-joined hairpin ribozyme displayed the highest cleavage rates in a synergistic mixture of magnesium ions and spermine. The specific features of this ribozyme along with its potential for in vivo application are discussed.     

RNA干扰抑制乙型肝炎病毒复制及基因表达研究进展

RNA干扰(RNAinterference,RNAi)是指由21～23个核苷酸组成的双链RNA(dsRNA)所引发的生物细胞内同源基因转录后沉默的现象,是生物体在进化过程中普遍存在的一种基因调控机制。目前对由乙型肝炎病毒(HBV)引起的病毒性肝炎尚无令人满意的治疗效果,而RNA干扰技术的出现为各类慢性HBV感染的治疗开辟了新的途径。本文对RNA干扰抑制HBV复制及基因表达的研究现状、存在问题及应用前景进行了综述。     

The effect of secondary structure on cleavage of the phosphodiester bonds of RNA

This review discusses the effects the secondary structure of an RNA molecule has on the inherent reactivity of its phosphodiester bonds, and on the catalytic activity of metal ion-based cleaving agents. The basic principles of the intramolecular transesterification of RNA phosphodiester bonds, particularly cleavage, are first briefly described. Studies of the structural effects on the cleavage, in the absence and in the presence of metal ion catalysts, are then reviewed, and the sources of the reactivity differences observed in different structures are discussed.