Induction of TRPV5 expression by small activating RNA targeting gene promoter as a novel approach to regulate cellular calcium transportation

Aim

Promoter-targeted small activating RNAs (saRNAs) have been shown to be able to induce target gene expression, a mechanism known as RNA activation (RNAa). The present study tested whether saRNA can induce the overexpression of TRPV5 in human cells derived from the kidney and subsequently manipulate cell calcium uptake.

Main methods

Three saRNAs complementary to the TRPV5 promoter were synthesized and transfected into cells. TRPV5 expression at the RNA and protein levels was analyzed by quantitative real-time PCR and Western blotting respectively. For functional study, transcellular Ca^2 + transportation was tested by fura-2 analysis. Dihydrotestosterone (DHT), a suppressor of cellular calcium transportation, was administered to challenge the activating effect of selected saRNA.

Key findings

One of these synthesized saRNAs, ds-2939, significantly induced the expression of TRPV5 at both mRNA and protein levels. Fura-2 analysis revealed that the intracellular Ca^2 + concentration was elevated by ds-2939. DHT treatment reduced transmembrane Ca^2 + transport, which was partially antagonized by ds-2939.

Significance

Our results suggest that a saRNA targeting TRPV5 promoter can be utilized to manipulate the transmembrane Ca^2 + transport by upregulating the expression of TRPV5 and may serve as an alternative for the treatment of Ca^2 + balance-related diseases.     

RNAi and RNAa--the yin and yang of RNAome

RNA interference (RNAi) is a powerful technology with huge applications for functional genomics, target identification in drug discovery and elucidation of molecular signaling pathways. Current RNAi studies have demonstrated the clinical potential of small interfering RNAs (siRNAs) in metabolic diseases, cancer, AIDS, malaria, neurodegenerative disorders, dental diseases and other illnesses. Interestingly, recent studies have shown that the small RNA molecules, either indigenously produced as microRNAs (miRNAs) or exogenously administered synthetic dsRNAs could effectively activate a particular gene in a sequence specific manner instead of silencing it. This novel, but still uncharacterized, phenomenon has been termed as RNA activation (RNAa). The paradoxical concept of Yin and Yang, which describe two primal opposing but complementary principles, can potentially be applied to elucidate the complex phenomenon of RNAa/RNAi in the RNAome. This warrants a proper understanding of the RNAi/RNAa molecular pathways in living organisms before any of the small dsRNAs can potentially be exploited for therapeutics in human beings.     

RNAa Is Conserved in Mammalian Cells

Background

RNA activation (RNAa) is a newly discovered mechanism of gene activation triggered by small double-stranded RNAs termed ‘small activating RNAs’ (saRNAs). Thus far, RNAa has only been demonstrated in human cells and is unclear whether it is conserved in other mammals.

Methodology/Principal Findings

In the present study, we evaluated RNAa in cells derived from four mammalian species including nonhuman primates (African green monkey and chimpanzee), mouse, and rat. Previously, we identified saRNAs leading to the activation of E-cadherin, p21, and VEGF in human cells. As the targeted sequences are highly conserved in primates, transfection of each human saRNA into African green monkey (COS1) and chimpanzee (WES) cells also resulted in induction of the intended gene. Additional saRNAs targeting clinically relevant genes including p53, PAR4, WT1, RB1, p27, NKX3-1, VDR, IL2, and pS2 were also designed and transfected into COS1 and WES cells. Of the nine genes, p53, PAR4, WT1, and NKX3-1 were induced by their corresponding saRNAs. We further extended our analysis of RNAa into rodent cell types. We identified two saRNAs that induced the expression of mouse Cyclin B1 in NIH/3T3 and TRAMP C1 cells, which led to increased phosphorylation of histone H3, a downstream marker for chromosome condensation and entry into mitosis. We also identified two saRNAs that activated the expression of CXCR4 in primary rat adipose–derived stem cells.

Conclusions/Significance

This study demonstrates that RNAa exists in mammalian species other than human. Our findings also suggest that nonhuman primate disease models may have clinical applicability for validating RNAa-based drugs.     

小激活RNA(saRNA)——肿瘤治疗新途径

在基因的表达调控过程中,一系列非编码RNA(non-coding RNA, ncRNA)发挥着广泛作用.然而,作为其重要成员的小激活RNA(small activating RNA, saRNA)却没有得到足够的认识和关注.本篇综述旨在介绍saRNA的机制与功能,并评估它的应用前景.文中归纳该领域的最新进展,特别是有关肿瘤治疗的研究. saRNA能识别基因启动子上特定序列、诱导相应基因的转录,从而实现基因激活.这不仅与siRNA(small interfering RNA)的抑制作用相反,而且有其独特的动力学特征.目前,saRNA研究主要集中于肿瘤领域,并发现它对某些肿瘤的生长和转移具有抑制作用,因而有望开辟肿瘤治疗的新途径.本文结尾简要探讨了saRNA在开发新抗癌药物等方面的应用潜力.     

Vector systems of RNA interference

RNA interference is a mechanism of posttranslational (at the level of mRNA) gene silencing. Sequence-specific mRNA degradation is realized with the help of small interfering RNAs produced by processing of a precursor using Dicer, an enzyme from the RNAse III family. This mechanism is now widely used in vitro on cultures of mammalian cells in order to elucidate functions of individual genes by gene specific knockdown. Analogs of small interference RNAs are intensely expressed during embryogenesis. The mechanism of RNA interference plays an especially important role in embryogenesis of invertebrates. Identification of the functions of small noncoding RNAs is essential for understanding the genetic mechanisms underlying individual developmental stages. In order to integrate small interference RNAs in mammalian cells, various systems have been developed that allow both transient (for 48 h) and stable expression in vitro. These systems are considered in the present review.     

RNA激活效应研究

RNAa(RNA activation)即RNA激活效应,是指某些小分子非编码RNA(non-coding RNA,ncRNA)在转录水平上激活基因表达的现象,这种发挥激活作用的小RNA分子又叫激活小RNA(small activating RNA,saRNA)。saRNA与干扰小RNA(small interfer-ing RNA,siRNA)同属小分子双链非编码RNA家族,既有相似的分子特征,在靶序列、作用动力学和调控方式等方面又有显著差别。虽然RNAa的作用机制尚未完全明了,但其在肿瘤治疗中的应用前景吸引了人们的关注。本文就RNAa近年的研究进展进行了简要综述。     

RNA干扰在疾病治疗方面的应用研究

RNA干扰是由双链RNA引起的序列特异的基因沉默现象。由于RNA干扰能在细胞组织及动物模型中沉默疾病相关基因,因此,RNA干扰也是各种疾病治疗的有效手段。在哺乳动物细胞内诱导RNA干扰可以通过导入小干扰RNA（siRNA）,或是以质粒、病毒为载体表达短的发夹RNA（shRNA）而实现。本文介绍了RNA干扰在疾病治疗方面的应用,并就其面临的挑战进行讨论。     

碳纳米管作为siRNA转运载体的研究进展

随着人们对RNA干扰分子机理的研究愈加深入,siRNA作为一种新的基因治疗药物极有可能为人类攻克癌症等难以治愈的疾病带来希望。然而,目前在RNA干扰应用中遇到的最大挑战就是如何有效地将siRNA导入靶细胞且不致引起严重的细胞毒性。碳纳米管在药物传递和基因传递等生物医学领域的潜在应用受到广泛关注;但要实现碳纳米管在基因治疗领域的应用,碳纳米管的功能化是关键,也是近几年来研究的重点。综述近年来碳纳米管作为siRNA转运载体在基因治疗领域的研究进展。     

RNA interference induced by siRNAs modified with 4'-thioribonucleosides in cultured mammalian cells

Short interfering RNAs (siRNAs) variously modified with 4'-thioribonucleosides against the Photinus luciferase gene were tested for their induction of the RNA interference (RNAi) activity in cultured NIH/3T3 cells. Results indicated that modifications at the sense-strand were well tolerated for RNAi activity except for full modification with 4'-thioribonucleosides. However, the activity of siRNAs modified at the antisense-strand was dependent on the position and the number of modifications with 4'-thioribonucleosides. Since modifications of siRNAs with 4'-thioribonucleosides were well tolerated in RNAi activity compared with that of 2'-O-methyl nucleosides, 4'-thioribonucleosides might be potentially useful in the development of novel and effective chemically modified siRNAs.     

HPVomics: An integrated resource for the human papillomavirus epitome and therapeutics

Human papillomaviruses (HPVs) belongs to the Papillomaviridae family, which is divided into high-risk (HR), and low-risk (LR) HPVs based on their disease-causing competence. HR-HPVs 16 and 18 are known to cause distinct carcinomas like cervical and head and neck, whereas LR-HPVs are commonly associated with the genital warts. We have developed an integrative platform; HPVomics dedicated to the potential therapeutic regimens targeting all HPV genes including oncoproteins E6, E7 and E5. We primarily focused on eighteen HR-HPVs and eleven LR-HPVs. It mainly deals with therapeutically imperative elements, i.e., vaccine epitopes, siRNAs, sgRNAs, and anti-viral peptides. Simultaneously, it also comprises of genome browser, whole-genome sequences and annotation of HPVs with searching and filtering capabilities. Moreover, we have also developed an integrated support vector machine (SVM) based computational algorithm “HPVepi” for the prediction of HPV epitome. We hope that HPVomics (http://bioinfo.imtech.res.in/manojk/hpvomics/) will assist the scientific community engaged in HPV research.     

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.     

RNA干扰机制研究进展

RNAi是多种生物体内由dsRNA介导的同源mRNA降解现象。这是一个高度特异化的过程,涉及多种蛋白质的共同参与。在这一过程中,siRNA的结构影响其两条链装配到RISC中去的能力。除了与RISC结合外,siRNA还引导了RITS复合物结合到同源染色质,介导异染色质化过程。干扰效应的扩散,即系统性沉默可能依赖于跨膜蛋白的转运,并且很可能是在多因素调控下完成的。Abstract: RNA interference (RNAi) is a phenomenon that the double-stranded RNA (dsRNA) intermediates the degradation of complementary mRNA found in many organisms. This is a specifically mechanism involved in kinds of proteins to complete the interference function. Structure of siRNA affects which strand will be assembled into RISC. Another role of siRNA is directing RITS complex to bind with homologue chromosome, and then induces heterochromatinization. Although systemic silence induced by dsRNA is observed in Caenorhabditis elegans and plants, this progress is probably transmembrane protein-dependent, and mostly, the systemic silencing is controlled by multi-factors.