[show abstract][hide abstract] ABSTRACT: Oligonucleotides as short as 6 nt in length have been shown to bind specifically and tightly to proteins and affect their biological function. Yet, sparse structural data are available for corresponding complexes. Employing a recently developed hexanucleotide array, we identified hexadeoxyribonucleotides that bind specifically to the 3C protease of hepatitis A virus (HAV 3C(pro)). Inhibition assays in vitro identified the hexanucleotide 5'-GGGGGT-3' (G(5)T) as a 3C(pro) protease inhibitor. Using (1)H NMR spectroscopy, G(5)T was found to form a G-quadruplex, which might be considered as a minimal aptamer. With the help of (1)H, (15)N-HSQC experiments the binding site for G(5)T was located to the C-terminal β-barrel of HAV 3C(pro). Importantly, the highly conserved KFRDI motif, which has previously been identified as putative viral RNA binding site, is not part of the G(5)T-binding site, nor does G(5)T interfere with the binding of viral RNA. Our findings demonstrate that sequence-specific nucleic acid-protein interactions occur with oligonucleotides as small as hexanucleotides and suggest that these compounds may be of pharmaceutical relevance.
Nucleic Acids Research 12/2011; 40(7):3042-55. · 8.28 Impact Factor
[show abstract][hide abstract] ABSTRACT: Various kinds of stress on human cells induce the formation of endogenous stress granules (SGs). Human Argonaute 2 (hAgo2), the catalytic core component of the RNA-induced silencing complex (RISC), can be recruited to SGs as well as P-bodies (PBs) indicating that the dynamic intracellular distribution of hAgo2 in SGs, in PBs or at other sub-cellular sites could be related to the efficiency of the RNA interference (RNAi) machinery. Here, we studied the influence of heat shock, sodium arsenite (NaAsO2), cycloheximide (CHX) and Lipofectamine 2000-mediated transfection of phosphorothioate (PS)-modified oligonucleotides (ON) on the intracellular localization of hAgo2 and the efficiency of RNAi. Fluorescence microscopy and sedimentation analysis of cell fractions indicate stress-induced accumulation of hAgo2 in SGs and the loss of distinctly composed complexes containing hAgo2 or their sub-cellular context. Transfection of cells with PS-ON induces cell stress that is phenotypically similar to the established inducers heat shock and NaAsO2. The intracellular re-distribution of hAgo2 is related to its increased metabolic stability and to decreased RNAi directed by microRNA or by short interfering RNA. Here, we propose a functional model of the relationship between cell stress, translocation of hAgo2 to SGs providing a depot function, and loss of RNAi activity.
Nucleic Acids Research 12/2010; 39(7):2727-41. · 8.28 Impact Factor
[show abstract][hide abstract] ABSTRACT: The Argonaute proteins play essential roles in development and cellular metabolism in many organisms, including plants, flies, worms, and mammals. Whereas in organisms such as Caenorhabditis elegans and Arabidopsis thaliana, creation of Argonaute mutant strains allowed the study of their biological functions, in mammals the application of this approach is limited by its difficulty and in the specific case of Ago2 gene, by the lethality of such mutation. Hence, in human cells, functional studies of Ago proteins relied on phenotypic suppression using small interfering RNA (siRNA) which involves Ago proteins and the RNA interference mechanism. This bears the danger of undesired or unknown interference effects which may lead to misleading results. Thus, alternative methods acting by different regulatory mechanisms would be advantageous in order to exclude unspecific effects. The knockdown may be achieved by using specific antisense oligonucleotides (asONs) which act via an RNase H-dependent mechanism, not thought to interfere with processes in which Agos are involved. Different functional observations in the use of siRNA versus asONs indicate the relevance of this assumption. We developed asONs specific for the four human Agos (hAgos) and compared their activities with those obtained by siRNA. We confirm that hAgo2 is involved in microRNA (miRNA)- and in siRNA-mediated silencing pathways, while the other hAgos play a role only in miRNA-based gene regulation. Using combinations of asONs we found that the simultaneous down-regulation of hAgo1, hAgo2, and hAgo4 led to the strongest decrease in miRNA activity, indicating a main role of these proteins.
[show abstract][hide abstract] ABSTRACT: RNA-based therapeutic strategies are considered as a highly promising alternative to conventional drug development. Among
the different classes of oligonucleotide-derived prospective drugs, small interfering RNAs (siRNAs) are of particular interest.
However, cellular uptake and subsequent intracellular trafficking to the effector complex (RNA-induced silencing complex;
RISC) represent major technical hurdles for the efficacy of these macromolecular drugs. Thus, the development of appropriate
delivery systems is an essential requirement to turn these molecules into medicine. In this review, we will focus on two particular
auspicious aspects in this context, the phosphorothioate-stimulated uptake of naked siRNA and the use of cell-penetrating
peptides as shuttles for a controlled cellular uptake. Moreover, we will present some of the most promising recent approaches
for siRNA delivery in vivo, which may help to pave the road to drugs of the future.
KeywordsArgonaute 2-Caveosomal endocytosis pathway-Cell-penetrating peptides-Cellular uptake-Clinical trials-Delivery-Endocytosis-Endoplasmic reticulum-Endosomal escape-Extracellular RNA-Golgi apparatus-Ilimaquinone-Microinjection-Nanoparticles-Non-covalent-Nonviral delivery systems-Oligonucleotide-based drugs-Phosphorothioate-stimulated uptake-Polycations-Protein transduction domains-RNAi-Signal peptides-siRNAs-siRNA-peptide conjugate
[show abstract][hide abstract] ABSTRACT: Objectives
MicroRNAs have been shown to be related to specific types of malignant cell growth. In case of urothelial bladder cancer (BCa), novel noninvasive diagnosis is particularly required and it is attractive to consider, as urine is an easily available source for molecular markers including RNA. In this context, we aimed to develop a clinically applicable and sensitive protocol for the preparation and molecular analysis of low molecular weight RNA from urine samples obtained from bladder cancer patients or healthy volunteers.
Urologic Oncology-seminars and Original Investigations. 01/2010; 28(6):655-661.
[show abstract][hide abstract] ABSTRACT: MicroRNAs have been shown to be related to specific types of malignant cell growth. In case of urothelial bladder cancer (BCa), novel noninvasive diagnosis is particularly required and it is attractive to consider, as urine is an easily available source for molecular markers including RNA. In this context, we aimed to develop a clinically applicable and sensitive protocol for the preparation and molecular analysis of low molecular weight RNA from urine samples obtained from bladder cancer patients or healthy volunteers.
First, a method was developed for the preparation of low molecular weight RNA from a set of urine samples from different donor groups: (1) patients with low-grade BCa, (2) patients with high-grade BCa, (3) patients with urinary tract infections, (4) healthy donors; each n = 9. The RNA extracts were then used to monitor a number of 157 microRNA species by quantitative reverse transcriptase-polymerase chain reaction. Subsequently, those microRNAs that showed a higher abundance in urine samples from BCa patients were detected in an independent set of urine samples (n = 47).
The significance and diagnostic usefulness of this methodology is reflected by the finding that the RNA ratio of microRNA-126:microRNA-152 enabled the detection of BCa from urine at a specificity of 82% and a sensitivity of 72%, with an area under the curve of 0.768 (95% confidence interval, 0.605-0.931).
This study describes a novel, robust, and useful technology platform that is suitable to analyze small RNAs, including novel RNA-based tumor markers, in urine samples. A detailed technical analysis of this methodology provides new insights into the characteristics of urine microRNA such as composition and the donor-dependent variability.
[show abstract][hide abstract] ABSTRACT: In the last decade short interfering RNA (siRNA) became an important means for functional genomics and the development of gene-specific drugs. However, major technical hurdles in the application of siRNA include its cellular delivery followed by its intracellular trafficking and its release in order to enter the RNA interference (RNAi) machinery. The novel phosphorothioate-stimulated cellular uptake of siRNA contrasts other known delivery systems because it involves a caveosomal pathway in which large amounts of siRNA are delivered to the perinuclear environment, leading to measurable though moderate target suppression. Limited efficacy seems to be related to intracellular trapping of siRNA. To study the role of intracellular trafficking of siRNA for biological effectiveness we studied whether a signal peptide for trans-membrane transport of bacterial protein toxins, which is covalently attached to siRNA, can promote its release from the perinuclear space into the cytoplasm and thereby enhance its biological effectiveness. We show that attachment of the peptide TQIENLKEKG to lamin A/C-directed siRNA improves target inhibition after its PS-stimulated delivery. This is related to increased efflux of the siRNA-peptide conjugate from the ER-specific perinuclear sites. In summary, this study strongly suggests that intracellular release of siRNA leads to increased biological effectiveness. Thus covalent peptide-siRNA conjugates are proposed as new tools to study the relationship between intracellular transport and efficacy of siRNA.
[show abstract][hide abstract] ABSTRACT: The efficient delivery of biologically functional short interfering RNA (siRNA) in vivo remains a widely unresolved technical problem in therapeutic drug development. The repertoire of concepts for the cellular uptake of oligonucleotide-based tools and drugs has been extended by the mechanistically novel finding that phosphorothioate (PS)-modified single-stranded oligodeoxyribonucleotides (ON) promote the intracellular accumulation of naked extra-cellular siRNA in a variety of cell types. This mode of delivery gives rise to substantial intracellular amounts of siRNA, up to 10(4) siRNA molecules per cell. Conversely, the moderate biological effectiveness strongly indicates that intracellular release of siRNA from sub-cellular compartments where it seems to be trapped is a necessary step towards efficient target suppression. Here, we summarize key characteristics of the PS-stimulated cellular uptake of siRNA and describe concepts for the increase of intracellular delivery of biologically functional siRNA.
Current topics in medicinal chemistry 01/2009; 9(12):1109-16. · 4.47 Impact Factor
[show abstract][hide abstract] ABSTRACT: Oligonucleotide-based therapeutic drugs of current interest include tools related to RNA interference (RNAi) such as short interfering RNA (siRNA), short hairping RNA (shRNA), or micro RNA (miRNA) as well as catalytic RNA and antisense oligonucleotides (asON). Based on resolved molecular patho-mechanisms of diseases and the causative involvement of genes in the development of diseases, their advantages include the mechanistic level of action, i.e. their ability to interfere with gene expression. On the technical level, challenges of the use of therapeutic oligonucleotide-based drugs include their delivery into target organs or tissues, their cellular uptake, the mode of their intracellular transport and their sub-cellular localization. All of those issues need to be successfully solved before their therapeutic application can be considered as sufficiently effective, i.e. before target suppression can be achieved at appropriate expense and realistic doses of the drug. Meanwhile it is obvious that the cellular delivery and the intracellular trafficking of oligomeric nucleic acid-based tools represent major technical hurdles for their successful therapeutic application. We feel that major new mechanistic insights are necessary before those steps of intracellular translocation of siRNA and/or components of RISC can be identified that are limiting in case of insufficient siRNA-induced target suppression. The cellular uptake and intracellular transport pathways as well as their underlying mechanisms need to be revealed before the technical hurdle of limited delivery and intracellular release can be conceivably addressed on a more rational basis. While the mode of action of various classes of transfectants and non-viral vector systems for oligonucleotide-based drugs seems to be largely enlightened, there is not much known on their intracellular fate. As a consequence, more quantitative methodology needs to be established in order to monitor trans-membrane transport as well as intracellular localization and mobility of siRNA as a function of their mode of delivery. Most promising approaches seem to be related to the intersection of molecular medicine, cell biology, biochemistry, biophysics, and chemistry. This view is exemplified by the collection of articles in this special issue which presents some of those interdisciplinary approaches. It provides a summary of major technologies related to the efficient cellular delivery of nucleic acid-based therapeutics. It also summarizes new methodology and new biological insights underlying the cellular and sub-cellular transport of oligonucleotides aiming their therapeutic application in vivo. Successful pre-clinical and clinical studies in the use of oligonucleotide-based therapeutics including asON and siRNA crucially rely on efficient delivery into target cells and target tissues. A comprehensive introduction into the various options for the cellular delivery of chemically synthesized siRNA by non-viral vector systems which include encapsulation, complex formation and conjugation of the cargo/siRNA is provided by Aigner in the first article of this special issue  who further includes an up-to-date list of in vivo studies in the use of formulated siRNA. Modes of administration of siRNA range from systemic and intravenous delivery to intra-tumoral, intra-thecal, nasal, and other local and applications. While systemic administration is commonly believed to deliver siRNA to a few sites and organs in vivo, local administration is thought to provide greater chances for a successful therapeutic delivery. One such example is the lung to which oligonucleotide-based drugs can be locally and topically delivery by nasal administration. Further, the lung as a target organ provides a very large and easily accessible surface for topical delivery of asON and siRNA and it is noteworthy that in a number of cases the use of transfectants could be omitted. Biological and technical characteristics of this target organ are summarized by Moschos et al.  who also provide a summary of past and ongoing in vivo studies in the use of asON and siRNA.
Current Pharmaceutical Design 11/2008; 14(34):3601-3602. · 3.31 Impact Factor
[show abstract][hide abstract] ABSTRACT: The cellular uptake of oligomeric nucleic acid-based tools and drugs including small-interfering RNA (siRNA) represents a major technical hurdle for the biologic effectiveness and therapeutic success in vivo. Subsequent to cellular delivery it is crucial to direct siRNA to the cellular location where it enters the RNA interference pathway. Here the authors summarise evidence that functionally active siRNA represents a minor fraction in the order of 1% of total siRNA inside a given target cell. Exploiting possibilities of steering intracellular release or trafficking of siRNA bears the potential of substantially increasing the biological activity of siRNA. The recently described phosphorothioate stimulated cellular delivery of siRNA makes use of the caveolar system ending in the Golgi apparatus, which contrasts all other known delivery systems. Therefore, it represents an attractive alternative to study whether promoted intracellular release is related to increased target suppression and, thus, increased phenotypic biologic effectiveness.
[show abstract][hide abstract] ABSTRACT: The relationship between immunostimulation of human B cells by cytosine-phosphate-guanosine (CpG) -containing oligonucleotides and their physical cellular uptake is of mechanistic interest and a prerequisite for rational improvements of the therapeutic potential of CpG-harbouring oligonucleotides. Here, a combinatorial approach was used to identify nucleotide sequence motifs that facilitate increased cellular uptake in mammalian cells. Oligonucleotides harbouring the selected hexanucleotide TCGTGT in cis show increased cellular uptake. This motif contains a CpG dinucleotide within a sequence context that shows a very strong CpG-specific stimulatory activity on human B cells. Here we describe the influence of concentration, length and sequence position of the unmethylated CpG dinucleotide on immunostimulation. A comparison between phosphorothioate-derivatives and unmodified TCGTGT-containing oligonucleotides strongly indicates a great CpG-specificity for the unmodified CpG-harbouring oligonucleotides but not for the phosphorothioate versions. This work describes a link between the physical cellular uptake of naked oligonucleotides harbouring the selected cellular uptake motif TCGTGT, its strong CpG-specific stimulation of human B cells and its relationship with the sequence context of CpG and its cellular uptake.
[show abstract][hide abstract] ABSTRACT: Short oligonucleotides below 8-10 nt in length adopt relatively simple structures. Accordingly, they represent interesting and so far unexplored lead compounds as molecular tools and, potentially, for drug development as a rational improvement of efficacy seem to be less complex than for other classes of longer oligomeric nucleic acid. As a 'proof of concept', we describe the highly specific binding of the hexanucleotide UCGUGU (Hex-S3) to human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) as a model target. Ultraviolet (UV) cross-linking studies and competition experiments with primer/template substrates and a RT-directed aptamer suggest site-specific binding of Hex-S3 to the large subunit (p66) of the viral enzyme. The affinity of 5.3 muM is related to hexanucleotide-specific suppression of HIV-1 replication in human cells by up to three orders of magnitude indicating that Hex-S3 exerts specific and biologically relevant activity. Experimental evidence described here further suggests a systematic hexamer array-based search for new tools for molecular biology and novel lead compounds in nucleic acid-based drug development.
Nucleic Acids Research 02/2006; 34(19):5631-7. · 8.28 Impact Factor
[show abstract][hide abstract] ABSTRACT: The cellular delivery of short interfering RNA (siRNA) is a main hurdle in therapeutic drug development. Here, we describe that phosphorothioate (PTO)-derived oligonucleotides stimulate the physical cellular uptake of siRNA in trans in human cells. This is reflected by an apparent dose-dependent siRNA-mediated suppression of lamin A/C in primary human umbilical vein endothelial cells. The PTO-stimulated cellular uptake in trans is concentration dependent, length dependent, related to the phosphorothioate chemistry but not sequence specific. We provide experimental evidence to support a caveolin-mediated uptake mechanism. In sum, this work strongly suggests the exploration of PTOs as facilitators in the delivery of biologically active siRNA to mammalian cells.
[show abstract][hide abstract] ABSTRACT: The efficiency with which small interfering RNAs (siRNAs) down-regulate specific gene expression in living cells is variable and a number of sequence-governed, biochemical parameters of the siRNA duplex have been proposed for the design of an efficient siRNA. Some of these parameters have been clearly identified to influence the assembly of the RNA-induced silencing complex (RISC), or to favour the sequence preferences of the RISC endonuclease. For other parameters, it is difficult to ascertain whether the influence is a determinant of the siRNA per se, or a determinant of the target RNA, especially its local structural characteristics. In order to gain an insight into the effects of local target structure on the biological activity of siRNA, we have used large sets of siRNAs directed against local targets of the mRNAs of ICAM-1 and survivin. Target structures were classified as accessible or inaccessible using an original, iterative computational approach and by experimental RNase H mapping. The effectiveness of siRNA was characterized by measuring the IC50 values in cell culture and the maximal extent of target suppression. Mean IC50 values were tenfold lower for accessible local target sites, with respect to inaccessible ones. Mean maximal target suppression was improved. These data illustrate that local target structure does, indeed, influence the activity of siRNA. We suggest that local target screening can significantly improve the hit rate in the design of biologically active siRNAs.
Journal of Molecular Biology 06/2005; 348(4):871-81. · 3.91 Impact Factor
[show abstract][hide abstract] ABSTRACT: We propose 2'-C-methylnucleotides as a new class of 2'-modified RNA mimics. These analogues are expected to provide 2'-OH groups capable of reproducing the interactions observed in natural RNA and, due to the presence of the Me group, to possess increased stability towards nucleases. In this work, we investigate the catalytic activity and nuclease resistance of hammerhead ribozymes carrying 2'-C-methyluridines in positions 4 and 7 of the catalytic core. We describe the in vitro activity of these chimeric molecules and their stability in cell lysate, fetal calf serum, and cell culture medium. The data show that, when only position 4 is modified, activity decreases twofold; while, when both 4 and 7 positions are substituted, a sevenfold drop in activity is observed. Regarding biological stability, the main increase of the half-life time is observed when position 7 is modified. These results suggest that 2'-C-methylnucleotides may be useful in the design of chemically synthesized RNA mimics with biological activity.
[show abstract][hide abstract] ABSTRACT: To evaluate the effects of suppressing the expression of Ki-67 (expressed in proliferating cells) by antisense oligonucleotides (asON) directed against Ki-67 (which specifically inhibit the proliferation of tumour cells and tumour growth in cell culture and in subcutaneous murine tumour models) on the growth, cell viability and angiogenic activity of a preclinical renal cell carcinoma (RCC) severe combined immunodeficiency disease (SCID) mouse model.
Human RCC cells (SK-RC-35) were incubated with asON and control ON in the presence of a cationic lipid in monolayer cell culture. To test Ki-67 as a target for antitumour therapy in more complex models, asON were administered to three-dimensional RCC (SK-RC-35) spheroid cultures and to SCID mice bearing subcutaneous SK-RC-35 xenografts. For animal studies, 1 x 10(6) SK-RC-35 cells were implanted subcutaneously. Subsequently, asON or ON were injected intraperitoneally daily for 14 days at 10 mg/kg/day. Tumour size, weight and status of metastasis were documented daily and after death, respectively. The number of apoptotic cells, Ki-67-positive cells and the microvessel density in tumour sections was determined immunohistochemically. Quantitative reverse transcription-polymerase chain reaction of Ki-67 mRNA was also assessed for the tumours.
Treatment of RCC cells with asON resulted in a specific inhibition of cell growth in monolayer and spheroid cell culture. Systemic administration of Ki-67-directed asON significantly decreased tumour growth (P = 0.009) in SCID mice. Immunohistochemical staining of tumour specimens showed stronger inhibition of Ki-67-positive cells in asON-treated tumours (mean 27.8%) than in controls (mean 42.5-57%). Furthermore, there were about twice as many apoptotic cells after asON treatment. There was no significant difference among treatment groups for microvessel density.
These results indicate that Ki-67 represents a suitable antiproliferative target, and that asON are a potent agent inhibiting tumour growth and apoptosis, but not tumour vascularization, in human RCC.
BJU International 03/2005; 95(3):416-20. · 3.05 Impact Factor