Exploring the Effect of Sequence Length and Composition on Allele-Selective Inhibition of Human Huntingtin Expression by Single-Stranded Silencing RNAs

Hu, Jiaxin; Liu, Jing; Yu, Dongbo; Aiba, Yuichiro; Lee, Suheung; Pendergraff, Hannah M.; Boubaker, Jihane; Artates, Jonathan W.; Lagier‐Tourenne, Clotilde; Lima, Walt F.; Swayze, Eric E.; Prakash, Thazha P.; Corey, David R.

doi:10.1089/nat.2013.0476

Cited by 20 publications

(24 citation statements)

References 31 publications

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“…The reason for the development of this alternative is the fact that cellular uptake for single-stranded oligonucleotides is much more facile in vivo than that of the double stranded. This strategy has found particular application in allele-selective inhibition of genes with an expanded CAG repeat such as in Huntington and Machado-Joseph diseases [85][86][87]. In these single-stranded siRNA oligonucleotides, the backbone also contains phosphorothioates.…”

Section: Ecksteinmentioning

confidence: 99%

Phosphorothioates, Essential Components of Therapeutic Oligonucleotides

Eckstein

2014

Nucleic Acid Therapeutics

475

385

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Phosphorothioates have found their usefulness in the general area of oligonucleotide therapeutic applications. Initially this modification was introduced into the antisense methodology because of the nuclease resistance of the phosphorothioate linkage in comparison with that of the phosphate linkage. However, as experimental data accumulated, it was detected that this chemical modification also facilitates cellular uptake and bioavailibity in vivo. Thus, today the majority of therapeutic oligonucleotides contain this modification. This review will discuss the historical development of this modification and present some of its chemical properties where they differ from those of the phosphate group. The antisense application will be discussed in the original context with cleavage of the target mRNA, but other target RNAs such as microRNAs and long noncoding RNAs will also be covered. It continues with applications where the target RNA should not be cleaved. A brief presentation of decoy oligonucleotides will be included, as well as some miscellaneous applications. Cellular uptake is a crucial step for oligonucleotides to reach their target and will be briefly reviewed. Lastly, a most surprising recent observation is the presence of phosphorothioate groups in bacterial DNA where functions still remain to be fully determined.

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Section: Ecksteinmentioning

confidence: 99%

Phosphorothioates, Essential Components of Therapeutic Oligonucleotides

Eckstein

2014

Nucleic Acid Therapeutics

475

385

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“…While modified ONs as mRNA targeting therapeutics have made major progress lately, also in relation to triplet-repeat diseases [57,58], successful DNA targeting of nucleotide repeats using ONs has not been reported. In this study we aimed to target the alternative DNA structures at FRDA (GAA) n repeats using modified ONs.…”

Section: Introductionmentioning

confidence: 99%

Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

et al. 2016

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Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)4-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)5-PNA did not. We present evidence that (GAA)4-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)5-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression.

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“…Several CAG repeat-targeting silencing reagents are under pre-clinical development and have shown great promise when tested in cells from juvenile HD patients [28], [35]–[38], whom display a more severe form of the disease with onset before the age of 20 [39]. Juvenile HD accounts for less than 5–10% of HD patients [40] and it remains to be determined if this approach will be appropriate when the difference between the upper and lower CAG tracts is smaller, as with the majority of HD patients [41].…”

Section: Introductionmentioning

confidence: 99%

Allele-Specific Suppression of Mutant Huntingtin Using Antisense Oligonucleotides: Providing a Therapeutic Option for All Huntington Disease Patients

et al. 2014

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Huntington disease (HD) is an inherited, fatal neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene. The mutant protein causes neuronal dysfunction and degeneration resulting in motor dysfunction, cognitive decline, and psychiatric disturbances. Currently, there is no disease altering treatment, and symptomatic therapy has limited benefit. The pathogenesis of HD is complicated and multiple pathways are compromised. Addressing the problem at its genetic root by suppressing mutant huntingtin expression is a promising therapeutic strategy for HD. We have developed and evaluated antisense oligonucleotides (ASOs) targeting single nucleotide polymorphisms that are significantly enriched on HD alleles (HD-SNPs). We describe our structure-activity relationship studies for ASO design and find that adjusting the SNP position within the gap, chemical modifications of the wings, and shortening the unmodified gap are critical for potent, specific, and well tolerated silencing of mutant huntingtin. Finally, we show that using two distinct ASO drugs targeting the two allelic variants of an HD-SNP could provide a therapeutic option for all persons with HD; allele-specifically for roughly half, and non-specifically for the remainder.

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Exploring the Effect of Sequence Length and Composition on Allele-Selective Inhibition of Human Huntingtin Expression by Single-Stranded Silencing RNAs

Cited by 20 publications

References 31 publications

Phosphorothioates, Essential Components of Therapeutic Oligonucleotides

Phosphorothioates, Essential Components of Therapeutic Oligonucleotides

Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

Allele-Specific Suppression of Mutant Huntingtin Using Antisense Oligonucleotides: Providing a Therapeutic Option for All Huntington Disease Patients

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