Cellular uptake and intracellular trafficking of oligonucleotides

Pharmacokinetic and Pharmacodynamic Investigations of ION-353382, a Model Antisense Oligonucleotide: Using Alpha-2-Macroglobulin and Murinoglobulin Double-Knockout Mice

To investigate the pharmacokinetics (PKs) and pharmacodynamics (PDs) for ION-353382, an antisense oligonucleotide (ASO) targeting scavenger receptor class B type I (SRB1) mRNA, using alpha-2-macroglobulin (A2M), murinoglobulin double-knockout (DKO), and wild-type mice. Wild-type and DKO homozygous mice were administered a single subcutaneous injection of ION-353382 at 0, 5, 15, 30, and 60 mg/kg. Mice were sacrificed at 72 h with plasma and organs harvested. Both liquid chromatography-mass spectrometry (LC-MS) and enzyme-linked immunosorbent assay (ELISA) were used to determine ASO exposure with real-time PCR for SRB1 expression. Immunohistochemistry was evaluated to explore hepatic uptake of ASOs. The total plasma protein binding and profiling was assessed. Finally, two-dimensional gel electrophoresis identified protein expression differences. PK exposures were comparable between wild-type and DKO mice in plasma, liver, and kidney, yet a near twofold reduction in EC50 was revealed for DKO mice based on an inhibitory effect liver exposure response model. Total plasma protein binding and profiling revealed no major dissimilarities between both groups. Plasma proteome fingerprinting confirmed protein expression variations related to A2M. Histological examination revealed enhanced ASO distribution into hepatocytes and less nonparenchymal uptake for DKO mice compared to wild-type mice. Knocking out A2M showed improved PD activities without an effect on total plasma and tissue exposure kinetics. Binding to A2M could mediate ASOs to nonproductive compartments, and thus, decreased binding of ASOs to A2M could potentially improve ASO pharmacology.

Assessment of configurations and chemistries of bridged nucleic acids-containing oligomers as external guide sequences: a methodology for inhibition of expression of antibiotic resistance genes

External guide sequences (EGSs) are short antisense oligoribonucleotides that elicit RNase P-mediated cleavage of a target mRNA, which results in inhibition of gene expression. EGS technology is used to inhibit expression of a wide variety of genes, a strategy that may lead to development of novel treatments of numerous diseases, including multidrug-resistant bacterial and viral infections. Successful development of EGS technology depends on finding nucleotide analogs that resist degradation by nucleases present in biological fluids and the environment but still elicit RNase P-mediated degradation when forming a duplex with a target mRNA. Previous results suggested that locked nucleic acids (LNA)/DNA chimeric oligomers have these properties. LNA are now considered the first generation of compounds collectively known as bridged nucleic acids (BNAs) – modified ribonucleotides that contain a bridge at the 2ʹ,4ʹ-position of the ribose. LNA and the second-generation BNA, known as BNA^NC, differ in the chemical nature of the bridge. Chimeric oligomers containing LNA or BNA^NC and deoxynucleotide monomers in different configurations are nuclease resistant and could be excellent EGS compounds. However, not all configurations may be equally active as EGSs. RNase P cleavage assays comparing LNA/DNA and BNA^NC/DNA chimeric oligonucleotides that share identical nucleotide sequence but with different configurations were carried out using as target the amikacin resistance aac(6ʹ)-Ib mRNA. LNA/DNA gapmers with 5 and 3/4 LNA residues at the 5ʹ- and 3ʹ-ends, respectively, were the most efficient EGSs while all BNA^NC/DNA gapmers showed very poor activity. When the most efficient LNA/DNA gapmer was covalently bound to a cell-penetrating peptide, the hybrid compound conserved the EGS activity as determined by RNase P cleavage assays and reduced the levels of resistance to amikacin when added to Acinetobacter baumannii cells in culture, an indication of cellular uptake and biological activity.

Noninvasive visualization of microRNA-155 in multiple kinds of tumors using a radiolabeled anti-miRNA oligonucleotide

PURPOSE

We investigated whether a (99m)Tc radiolabeled anti-miRNA-155 oligonucleotide (AMO-155) could visualize the expression of miR-155 in multiple kinds of tumors in vivo.

METHODS

AMO-155 was chemically synthesized and modified with 2'-O-methyl (2'-OMe) and phosphorothioate (PS). It was radiolabeled with (99m)Tc via the conjugation with NHS-MAG3 at 5' end. The characterization of radiolabeling and serum stability was evaluated using high performance liquid chromatography (HPLC) and agarose gel electrophoresis. The expression of C/EBPβ, one of the miR-155 target proteins, was assessed using Western blot. The cellular uptake and delivery of AMO-155 was further evaluated in tumor cells. (99m)Tc-AMO-155 was tested in vivo in multiple tumor models, including miR-155 over-expressed and low-expressed tumor models. Finally, biodistribution of (99m)Tc-AMO-155 was evaluated.

RESULTS

(99m)Tc-AMO-155 was prepared with high yield and radiochemical purity. It showed high stability in fresh human serum for 10h. (99m)Tc-AMO-155 displayed comparable capacity as unlabeled AMO-155 to increase the expression of C/EBPβ protein in MCF-7 cells. (99m)Tc-AMO-155 showed an increased radioactive uptake in MCF-7 cells after 8h of incubation, whereas no change of (99m)Tc-pertechnetate uptake was observed. Carboxyfluorescein (FAM) labeled AMO-155 had higher fluorescent delivery than Control in HeLa and HepG2 cells by confocal microscopy. In miR-155 over-expressed tumor models, (99m)Tc-AMO-155 showed significantly higher tumor accumulation than (99m)Tc-Control. Furthermore, (99m)Tc-AMO-155 was capable of discriminating between MCF-7 and MDA-MB-231 tumors based on their expression of miR-155.

CONCLUSIONS

Our study successfully prepared and proved (99m)Tc-AMO-155 as a prospective imaging agent for the noninvasive visualization of miR-155 expression in vivo.

A cytoplasmic pathway for gapmer antisense oligonucleotide-mediated gene silencing in mammalian cells

Antisense oligonucleotides (ASOs) are known to trigger mRNA degradation in the nucleus via an RNase H-dependent mechanism. We have now identified a putative cytoplasmic mechanism through which ASO gapmers silence their targets when transfected or delivered gymnotically (i.e. in the absence of any transfection reagent). We have shown that the ASO gapmers can interact with the Ago-2 PAZ domain and can localize into GW-182 mRNA-degradation bodies (GW-bodies). The degradation products of the targeted mRNA, however, are not generated by Ago-2-directed cleavage. The apparent identification of a cytoplasmic pathway complements the previously known nuclear activity of ASOs and concurrently suggests that nuclear localization is not an absolute requirement for gene silencing.

Oligonucleotide Therapies: The Past and the Present

In this review we address the development of oligonucleotide (ON) medicines from a historical perspective by listing the landmark discoveries in this field. The various biological processes that have been targeted and the corresponding ON interventions found in the literature are discussed together with brief updates on some of the more recent developments. Most ON therapies act through antisense mechanisms and are directed against various RNA species, as exemplified by gapmers, steric block ONs, antagomirs, small interfering RNAs (siRNAs), micro-RNA mimics, and splice switching ONs. However, ONs binding to Toll-like receptors and those forming aptamers have completely different modes of action. Similar to other novel medicines, the path to success has been lined with numerous failures, where different therapeutic ONs did not stand the test of time. Since the first ON drug was approved for clinical use in 1998, the therapeutic landscape has changed considerably, but many challenges remain until the expectations for this new form of medicine are met. However, there is room for cautious optimism.