Jørgen Kjems

A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3′-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.

Improved silencing properties using small internally segmented interfering RNAs

RNA interference is mediated by small interfering RNAs (siRNAs) that upon incorporation into the RNA-induced silencing complex (RISC) can target complementary mRNA for degradation. Standard siRNA design usually feature a 19–27 base pair contiguous double-stranded region that is believed to be important for RISC incorporation. Here, we describe a novel siRNA design composed of an intact antisense strand complemented with two shorter 10–12 nt sense strands. This three-stranded construct, termed small internally segmented interfering RNA (sisiRNA), is highly functional demonstrating that an intact sense strand is not a prerequisite for RNA interference. Moreover, when using the sisiRNA design only the antisense strand is functional in activated RISC thereby completely eliminating unintended mRNA targeting by the sense strand. Interestingly, the sisiRNA design supports the function of chemically modified antisense strands, which are non-functional within the context of standard siRNA designs. This suggests that the sisiRNA design has a clear potential of improving the pharmacokinetic properties of siRNA in vivo.

A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects.

Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low.

The miR-143/-145 cluster regulates plasminogen activator inhibitor-1 in bladder cancer

Background:Upregulation of the proto-oncogene plasminogen activator inhibitor-1 (PAI-1) is a common hallmark of various solid tumours, but the mechanisms controlling its expression are not fully understood.Methods:We investigate microRNAs (miRNAs) regulating PAI-1 in a panel of normal bladder urothelial biopsies, superficial Ta bladder tumours and invasive T1–T4 tumours using expression microarrays and qRT–PCR. The prognostic implications of PAI-1 deregulation are established by tissue microarray staining of non-muscle-invasive bladder tumours. MicroRNA repression of PAI-1 is assayed by ectopic miRNA expression, argonaute immunoprecipitation and luciferase assays.Results:We found that the miR-143/-145 cluster is downregulated in all stages of bladder cancer and inversely correlated with PAI-1 expression. Mature miR-143 and miR-145 are coordinately expressed, and both directly target the PAI-1 3′UTR, leading to reduced PAI-1 mRNA and protein levels. Furthermore, we show that PAI-1 and miR-145 levels may serve as useful prognostic markers for non-muscle-invasive bladder tumours for which accurate progressive outcome is currently difficult to predict.Conclusion:This report provides the first evidence for direct miRNA regulation of PAI-1 in bladder cancer. We also demonstrate mRNA co-targeting by a cluster of non-family miRNAs, and suggest miR-145 and PAI-1 as clinically relevant biomarkers in bladder cancer.

High‐Resolution Inelastic Neutron Scattering from Some Aromatic Molecular Polycrystals for Study of Crystal Excitations and Anharmonic Effects

Inelastic neutron scattering spectra have been obtained at high resolution from a number of aromatic polycrystals, mainly halogenated benzenes, in the range 4 cm−1‐1600 cm−1, at room temperature and below. Since the spectra observed reflect only nuclear motion (in contrast to optical spectroscopy), analysis reveals direct information on the harmonicity. In para‐dichlorobenzene the angular dependence of the intensity of incoherent scattering, both elastic and inelastic, the relation between the total inelastic and total elastic intensities, and the temperature dependence of these spectra (and those for other substances) are all consistent with a weakly anharmonic model of the dynamics (phonons which interact with one another to give a temperature dependent lifetime and frequency). Assuming that multiphonon effects are negligible, this weakly anharmonic model is valid in p–C6H4Cl2 up to room temperature, 30°K below the melting point. At low temperatures (100°K) the phonon lifetimes are long enough to allow ...

Lattice vibrations in chlorobenzenes: Experimental dispersion curves for β‐paradichlorobenzene by neutron scattering

Lattice vibrational dispersion curves for the ``intermolecular modes in the triclinic, one molecule per unit cell β phase of p‐C6D4Cl2 and p‐C6H4Cl2 have been obtained by inelastic neutron scattering. The deuterated sample was investigated at 295 and at 90°K and a linear extrapolation to 0°K was applied in order to correct for anharmonic effects. Calculations based on the atom‐atom model for van der Waals interaction and on general potential parameters for the aromatic compounds agree reasonably well with the experimental observations. There is no substantial improvement in fit obtained either by consideration of electrostatic forces or by further anisotropy in the dispersion forces not described in the atom‐atom model. Anharmonic effects are shown to be large, but the dominant features in the temperature variation of frequencies are describable by a quasiharmonic model.

Circular RNAs in cancer: opportunities and challenges in the field

Circular RNA (circRNA) is a novel member of the noncoding cancer genome with distinct properties and diverse cellular functions, which is being explored at a steadily increasing pace. The list of endogenous circRNAs involved in cancer continues to grow; however, the functional relevance of the vast majority is yet to be discovered. In general, circRNAs are exceptionally stable molecules and some have been shown to function as efficient microRNA sponges with gene-regulatory potential. Many circRNAs are highly conserved and have tissue-specific expression patterns, which often do not correlate well with host gene expression. Here we review the current knowledge on circRNAs in relation to their implications in tumorigenesis as well as their potential as diagnostic and prognostic biomarkers and as possible therapeutic targets in future personalized medicine. Finally, we discuss future directions for circRNA cancer research and current caveats, which must be addressed to facilitate the translation of basic circRNA research into clinical use.

In vivo screening of modified siRNAs for non-specific antiviral effect in a small fish model: number and localization in the strands are important

Small interfering RNAs (siRNAs) are promising new active compounds in gene medicine but the induction of non-specific immune responses following their delivery continues to be a serious problem. With the purpose of avoiding such effects chemically modified siRNAs are tested in screening assay but often only examining the expression of specific immunologically relevant genes in selected cell populations typically blood cells from treated animals or humans. Assays using a relevant physiological state in biological models as read-out are not common. Here we use a fish model where the innate antiviral effect of siRNAs is functionally monitored as reduced mortality in challenge studies involving an interferon sensitive virus. Modifications with locked nucleic acid (LNA), altritol nucleic acid (ANA) and hexitol nucleic acid (HNA) reduced the antiviral protection in this model indicative of altered immunogenicity. For LNA modified siRNAs, the number and localization of modifications in the single strands was found to be important and a correlation between antiviral protection and the thermal stability of siRNAs was found. The previously published sisiRNA will in some sequences, but not all, increase the antiviral effect of siRNAs. The applied fish model represents a potent tool for conducting fast but statistically and scientifically relevant evaluations of chemically optimized siRNAs with respect to non-specific antiviral effects in vivo.

Neutron scattering study of the human complement proteins C3, C4 and C5 and the methylamine derivative of C4

Abstract The complement proteins C3, C4, and C5, which shows close similarities in size and shape, differ with regard to their internal structures. This is shown by small-angle neutron scattering using the contrast variation method. The Stuhrmann plot yields a positive parameter α for C5 with a numerical value of 5.5 × 10−4, while these parameters are markedly negative for C4, −10 × 10−4, and slightly negative for C3, −2 × 10 −4 ; thus, the scattering density distribution within these molecules is noticeably different. These data are discussed in relation to surface hydrophobicity, where increasing negative α-values are supposed to correlate, on the average, with an increase of hydrophobic residues close to the surface of the molecule. The radii of gyration at infinite contrast, RC, were virtually identical for C3 and C4 with RC = 4.5 and 4.6 nm, and somewhat larger for C5 with RC = 5.0 nm. When C4 reacts with methylamine there is an increase in RC from 4.6 to 5.3 nm simultaneously as the parameter α increases from −10 × 10−4 to −3 × 10−4. This is in agreement with a conformational change resulting in a redistribution of the scattering density within the molecule so that the surface hydrophobicity decreases.

A neutron scattering study of the ternary complex EF-Tu.GTP-valyl-tRNAVal1A

The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNAVal1A has been investigated in a hepes buffer of pH 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D2O where EF-Tu (42% D2O) and tRNA (71% D2O) are successively matched by the solvents. The results indicate that EF-Tu undergoes a conformational change and contracts as a result of the complex formation, since the radius of gyration decreases by 15% from 2.82 to 2.39 nm. tRNAVal1A, on the other hand, seems to mainly retain its conformation within the complex, since the radii of gyration for the free (after correction for interparticular scattering) and complexed form are essentially the same, 2.38 and 2.47 nm, respectively.