Widespread 8-oxoguanine modifications of miRNA seeds differentially regulate redox-dependent cancer development.

Oxidative stress contributes to tumourigenesis by altering gene expression. One accompanying modification, 8-oxoguanine (o8G) can change RNA-RNA interactions via o8G•A base pairing, but its regulatory roles remain elusive. Here, on the basis of o8G-induced guanine-to-thymine (o8G > T) variations featured in sequencing, we discovered widespread position-specific o8Gs in tumour microRNAs, preferentially oxidized towards 5' end seed regions (positions 2-8) with clustered sequence patterns and clinically associated with patients in lower-grade gliomas and liver hepatocellular carcinoma. We validated that o8G at position 4 of miR-124 (4o8G-miR-124) and 4o8G-let-7 suppress lower-grade gliomas, whereas 3o8G-miR-122 and 4o8G-let-7 promote malignancy of liver hepatocellular carcinoma by redirecting the target transcriptome to oncogenic regulatory pathways. Stepwise oxidation from tumour-promoting 3o8G-miR-122 to tumour-suppressing 2,3o8G-miR-122 occurs and its specific modulation in mouse liver effectively attenuates diethylnitrosamine-induced hepatocarcinogenesis. These findings provide resources and insights into epitranscriptional o8G regulation of microRNA functions, reprogrammed by redox changes, implicating its control for cancer treatment.

8-Oxoguanine: from oxidative damage to epigenetic and epitranscriptional modification.

In pathophysiology, reactive oxygen species control diverse cellular phenotypes by oxidizing biomolecules. Among these, the guanine base in nucleic acids is the most vulnerable to producing 8-oxoguanine, which can pair with adenine. Because of this feature, 8-oxoguanine in DNA (8-oxo-dG) induces a G > T (C > A) mutation in cancers, which can be deleterious and thus actively repaired by DNA repair pathways. 8-Oxoguanine in RNA (o8G) causes problems in aberrant quality and translational fidelity, thereby it is subjected to the RNA decay pathway. In addition to oxidative damage, 8-oxo-dG serves as an epigenetic modification that affects transcriptional regulatory elements and other epigenetic modifications. With the ability of o8G•A in base pairing, o8G alters structural and functional RNA-RNA interactions, enabling redirection of posttranscriptional regulation. Here, we address the production, regulation, and function of 8-oxo-dG and o8G under oxidative stress. Primarily, we focus on the epigenetic and epitranscriptional roles of 8-oxoguanine, which highlights the significance of oxidative modification in redox-mediated control of gene expression.

Position-specific oxidation of miR-1 encodes cardiac hypertrophy.

In pathophysiology, reactive oxygen species oxidize biomolecules that contribute to disease phenotypes1. One such modification, 8-oxoguanine2 (o8G), is abundant in RNA3 but its epitranscriptional role has not been investigated for microRNAs (miRNAs). Here we specifically sequence oxidized miRNAs in a rat model of the redox-associated condition cardiac hypertrophy4. We find that position-specific o8G modifications are generated in seed regions (positions 2-8) of selective miRNAs, and function to regulate other mRNAs through o8G•A base pairing. o8G is induced predominantly at position 7 of miR-1 (7o8G-miR-1) by treatment with an adrenergic agonist. Introducing 7o8G-miR-1 or 7U-miR-1 (in which G at position 7 is substituted with U) alone is sufficient to cause cardiac hypertrophy in mice, and the mRNA targets of o8G-miR-1 function in affected phenotypes; the specific inhibition of 7o8G-miR-1 in mouse cardiomyocytes was found to attenuate cardiac hypertrophy. o8G-miR-1 is also implicated in patients with cardiomyopathy. Our findings show that the position-specific oxidation of miRNAs could serve as an epitranscriptional mechanism to coordinate pathophysiological redox-mediated gene expression.

siAbasic: a comprehensive database for potent siRNA-6Ø sequences without off-target effects.

Small interfering RNA (siRNA) is widely used to specifically silence target gene expression, but its microRNA (miRNA)-like function inevitably suppresses hundreds of off-targets. Recently, complete elimination of the off-target repression has been achieved by introducing an abasic nucleotide to the pivot (position 6; siRNA-6Ø), of which impaired base pairing destabilizes transitional nucleation (positions 2-6). However, siRNA-6Ø varied in its conservation of on-target activity (∼80-100%), demanding bioinformatics to discover the principles underlying its on-target efficiency. Analyses of miRNA-target interactions (Ago HITS-CLIP) showed that the stability of transitional nucleation correlated with the target affinity of RNA interference. Furthermore, interrogated analyses of siRNA screening efficiency, experimental data and broadly conserved miRNA sequences showed that the free energy of transitional nucleation (positions 2-5) in siRNA-6Ø required the range of stability for effective on-target activity (-6 ≤ ΔG[2:5] ≤ -3.5 kcal mol-1). Taking into consideration of these features together with locations, guanine-cytosine content (GC content), nucleotide stretches, single nucleotide polymorphisms and repetitive elements, we implemented a database named 'siAbasic' that provided the list of potent siRNA-6Ø sequences for most of human and mouse genes (≥ ∼95%), wherein we experimentally validated some of their therapeutic potency. siAbasic will aid to ensure potency of siRNA-6Ø sequences without concerning off-target effects for experimental and clinical purposes.

Visualization of the degradation of a disulfide polymer, linear poly(ethylenimine sulfide), for gene delivery.

Polyethylenimine (PEI) shows high transfection efficiency and cytoxicity due to its high amine density. The new disulfide cationic polymer, linear poly(ethylenimine sulfide) (l-PEIS), was synthesized for efficient and safe gene delivery. As the amine density of l-PEIS increased, the transfection efficiency also increased. l-PEIS-6 and l-PEIS-8 show transfection efficiencies that are similar to that of PEI. However, cytotoxicity of l-PEIS was not observed due to the biodegradable disulfide bond. The disulfide bonds are stable in the oxidative extracellular condition and can be degraded rapidly in the reductive intracellular condition. The degradation of l-PEIS in HeLa cells was visualized by fluorescence microscopy using the probe-probe dequenching effect of BODIPY-FL fluorescence dye. l-PEIS was degraded completely within 3 h.

Preparation and characterization of biodegradable nanoparticles entrapping immunodominant peptide conjugated with PEG for oral tolerance induction.

PEG-conjugated immunodominant peptides for collagen-induced arthritis (CIA) were prepared for oral tolerance induction instead of whole Type II collagen (CII), because a small peptide can be converted to a macromolecule soluble in methylene chloride by the coupling of poly-ethylene glycol (PEG). PEG-pep1 was synthesized from a peptide and mPEG-NH2 (Mw approximately 5000) using SPDP as a linker, whereas PEG-pep2 was prepared by the direct disulfide coupling between PEG-OD (Mw approximately 10,000) and the peptide. PEG-pep1 and PEG-pep2 were purified by gel permeation chromatography (GPC), and the peak fractions of GPC were identified by GPC and MALDI-TOF mass spectroscopy. The peptide coupling gave much earlier retention times for PEG-pep1 (11.26 min) and PEG-pep2 (10.61 min) than for mPEG-SPDP (15.63 min) and mPEG-OD (14.58 min). The Mw's of mPEG-NH2, mPEG-SPDP, PEG-pep1, mPEG-OD and PEG-pep2 were 5451, 5588, 7035, 10,360 and 11,826, respectively, suggesting that PEG-pep1 and PEG-pep2 of high purity could be obtained. The nanoparticles entrapping PEG-pep1 and PEG-pep2 (NP/PEG-pep1 and NP/PEG-pep2) were prepared by the o/w solvent evaporation method, whereas the peptide-loaded nanoparticles (NP/pep) were prepared by the w/o/w double emulsion method. Although all the nanoparticles had a similar spherical morphology under scanning electron microscopy, NP/pep showed up as having a larger mean size than the others, which was confirmed by dynamic light scattering analysis (NP/pep, 499.7+/-27.2 nm; NP/PEG-pep1, 333.0+/-16.8 nm; NP/PEG-pep2, 342.4+/-15.1 nm). The lower encapsulation efficiency of NP/pep (21.0+/-1.6%) than NP/PEG-pep1 (66.5+/-5.0%) and NP/PEG-pep2 (73.8+/-5.5%) can also be attributed to the preparation method. In in vitro release studies, NP/PEG-pep1 and NP/PEG-pep2 displayed a similar release profile, close to a linear release pattern, whereas NP/pep displayed a tri-phasic release profile. From these results, it was demonstrated that nanoparticles entrapping a PEG-conjugated peptide could be an alternative delivery method for the induction of oral tolerance rather than CII and peptide.

Poly(ethylene oxide sulfide): new poly(ethylene glycol) derivatives degradable in reductive conditions.

Poly(ethylene oxide sulfide) (PEOS), polymers consisting of an internal ethylene oxide oligomer and disulfide linkage, were synthesized and characterized. The degree of polymerization was dependent upon temperature, dimethyl sulfoxide condition, and monomer hydrophobicity. The stability of PEOS was measured by the size exclusion chromatography method after the incubation both with and without 5 mM glutathione. The disulfide bond was stable in the extracellular condition but completely degraded in 2 h in the reductive cytosolic condition. Hydrophilic PEOS polymers showed no cytotoxicity on the HepG2 cell line. On the basis of these properties, PEOS can be applied in many drug delivery fields.

Enhanced transfection efficiency of PAMAM dendrimer by surface modification with L-arginine.

We designed a novel type of arginine-rich dendrimer, with a structure based on the well-defined dendrimer, polyamidoamine dendrimer (PAMAM). Further characterization was performed to prove that the polymer is a potent nonviral gene delivery carrier. The primary amines located on the surface of PAMAM were conjugated with L-arginine to generate an L-arginine-grafted-PAMAM dendrimer (PAMAM-Arg). For comparison, an L-lysine-grafted-PAMAM dendrimer (PAMAM-Lys) was also generated and compared as a control reagent. The polymers were found to self-assemble electrostatically with plasmid DNA, forming nanometer-scale complexes. From dynamic light scattering experiments, the mean diameter of the polyplexes was observed to be around 200 nm. We used PicoGreen reagent as an efficient probe for assaying complex formation of polymers with plasmid DNA. The complex composed of PAMAM-Arg/DNA showed increased gene delivery potency compared to native PAMAM dendrimer and PAMAM-Lys. The cytotoxicity and transfection efficiencies for 293, HepG2, and Neuro 2A cells were measured by comparison with PEI and PAMAM. In addition, transfection experiments were performed in primary rat vascular smooth muscle cells, and PAMAM-Arg showed much enhanced transfection efficiency. These findings suggest that the L-arginine-grafted-PAMAM dendrimer possesses the potential to be a novel gene delivery carrier for gene therapy.

Investigation of the factors influencing the release rates of cyclosporin A-loaded micro- and nanoparticles prepared by high-pressure homogenizer.

An oil-in-water solvent evaporation method was used to prepare cyclosporin A (CyA)-loaded particles varying in size (nanoparticles, 'small-sized' microparticles, 'large-sized' microparticles), polymer compositions [poly(D,L-lactide-co-glycolic acid) (PLGA) 50/50, PLGA 85/15, poly(D,L-lactic acid) (PLA)] and additive fatty acid ester (ethyl myristate; EM). The particles were characterized for drug loading and entrapment efficiency by high-performance liquid chromatography, particle size by dynamic light scattering and surface morphology by scanning electron microscopy (SEM). In vitro release kinetics were studied using a modified dialysis method. The results showed drug loadings ranging from 6.48 to 9.01% with high encapsulation efficiency (71.2-98.9%). SEM studies showed discrete and spherical particles with smooth surfaces, whereas rather gross surface defects resulted from the incorporation of EM as an additive. The release profiles of various formulations approximated zero-order release kinetics in the first 3 weeks with a negligible initial burst. In general, the smaller the particle size and the higher the glycolic acid content in the copolymer, the faster the release of CyA. The effect of EM on the release profile appeared to be rather complex since an increased release rate was observed from EM containing PLGA 50/50 particles, whereas the incorporation of EM into the PLGA 85/15 and PLA particles led to a decreased release rate. Further investigation needs to be performed to elucidate the reason why EM influences the CyA release differently depending on the particle size and polymer type.