Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs

Jiaxin Hu, Jing Liu, K. Jayaprakash Narayanannair, Jeremy G. Lackey, Satya Kuchimanchi, Kallanthottathil G. Rajeev, Muthiah Manoharan, Eric E. Swayze, Walt F. Lima, Thazha P. Prakash, Qin Xiang, Carlos Martinez, David R. Corey

Research output: Contribution to journalArticle

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Abstract

Dentatorubral-pallidoluysian atrophy (DRPLA) is a progressive neurodegenerative disorder that currently has no curative treatments. DRPLA is caused by an expansion of a CAG trinucleotide repeat region within the protein-encoding sequence of the atrophin-1 (ATN-1) gene. Inhibition of mutant ATN-1 protein expression is one strategy for treating DRPLA, and allele-selective gene silencing agents that block mutant expression over wild-type expression would be lead compounds for therapeutic development. Here we develop an assay for distinguishing mutant from wild-type ATN-1 protein by gel electrophoresis. We use this assay to evaluate duplex RNAs and single-stranded silencing RNAs (ss-siRNAs) for allele-selective inhibition of ATN-1 protein expression. We observed potent and allele-selective inhibition by RNA duplexes that contain mismatched bases relative to the CAG target and have the potential to form miRNA-like complexes. ss-siRNAs that contained mismatches were as selective as mismatch-containing duplexes. We also report allele-selective inhibition by duplex RNAs containing unlocked nucleic acids or abasic substitutions, although selectivities are not as high. Five compounds that showed >8-fold allele selectivity for mutant ATN-1 were also selective for inhibiting the expression of two other trinucleotide repeat disease genes, ataxin-3 (ATXN-3) and huntingtin (HTT). These data demonstrate that the expanded trinucleotide repeat within ATN-1 mRNA is a potential target for compounds designed to achieve allele-selective inhibition of ATN-1 protein, and one agent may allow the targeting of multiple disease genes.

Original languageEnglish (US)
Pages (from-to)4510-4518
Number of pages9
JournalBiochemistry
Volume53
Issue number28
DOIs
StatePublished - Jul 22 2014

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Alleles
Progressive Myoclonic Epilepsy
Trinucleotide Repeats
Genes
Proteins
Assays
Trinucleotide Repeat Expansion
Lead compounds
Gene Silencing
RNA Interference
atrophin-1
Electrophoresis
MicroRNAs
Neurodegenerative Diseases
Nucleic Acids
Substitution reactions
Gels
RNA
Messenger RNA
Therapeutics

ASJC Scopus subject areas

  • Biochemistry

Cite this

Hu, J., Liu, J., Narayanannair, K. J., Lackey, J. G., Kuchimanchi, S., Rajeev, K. G., ... Corey, D. R. (2014). Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs. Biochemistry, 53(28), 4510-4518. https://doi.org/10.1021/bi500610r

Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs. / Hu, Jiaxin; Liu, Jing; Narayanannair, K. Jayaprakash; Lackey, Jeremy G.; Kuchimanchi, Satya; Rajeev, Kallanthottathil G.; Manoharan, Muthiah; Swayze, Eric E.; Lima, Walt F.; Prakash, Thazha P.; Xiang, Qin; Martinez, Carlos; Corey, David R.

In: Biochemistry, Vol. 53, No. 28, 22.07.2014, p. 4510-4518.

Research output: Contribution to journalArticle

Hu, J, Liu, J, Narayanannair, KJ, Lackey, JG, Kuchimanchi, S, Rajeev, KG, Manoharan, M, Swayze, EE, Lima, WF, Prakash, TP, Xiang, Q, Martinez, C & Corey, DR 2014, 'Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs', Biochemistry, vol. 53, no. 28, pp. 4510-4518. https://doi.org/10.1021/bi500610r
Hu J, Liu J, Narayanannair KJ, Lackey JG, Kuchimanchi S, Rajeev KG et al. Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs. Biochemistry. 2014 Jul 22;53(28):4510-4518. https://doi.org/10.1021/bi500610r
Hu, Jiaxin ; Liu, Jing ; Narayanannair, K. Jayaprakash ; Lackey, Jeremy G. ; Kuchimanchi, Satya ; Rajeev, Kallanthottathil G. ; Manoharan, Muthiah ; Swayze, Eric E. ; Lima, Walt F. ; Prakash, Thazha P. ; Xiang, Qin ; Martinez, Carlos ; Corey, David R. / Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs. In: Biochemistry. 2014 ; Vol. 53, No. 28. pp. 4510-4518.
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AU - Hu, Jiaxin

AU - Liu, Jing

AU - Narayanannair, K. Jayaprakash

AU - Lackey, Jeremy G.

AU - Kuchimanchi, Satya

AU - Rajeev, Kallanthottathil G.

AU - Manoharan, Muthiah

AU - Swayze, Eric E.

AU - Lima, Walt F.

AU - Prakash, Thazha P.

AU - Xiang, Qin

AU - Martinez, Carlos

AU - Corey, David R.

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N2 - Dentatorubral-pallidoluysian atrophy (DRPLA) is a progressive neurodegenerative disorder that currently has no curative treatments. DRPLA is caused by an expansion of a CAG trinucleotide repeat region within the protein-encoding sequence of the atrophin-1 (ATN-1) gene. Inhibition of mutant ATN-1 protein expression is one strategy for treating DRPLA, and allele-selective gene silencing agents that block mutant expression over wild-type expression would be lead compounds for therapeutic development. Here we develop an assay for distinguishing mutant from wild-type ATN-1 protein by gel electrophoresis. We use this assay to evaluate duplex RNAs and single-stranded silencing RNAs (ss-siRNAs) for allele-selective inhibition of ATN-1 protein expression. We observed potent and allele-selective inhibition by RNA duplexes that contain mismatched bases relative to the CAG target and have the potential to form miRNA-like complexes. ss-siRNAs that contained mismatches were as selective as mismatch-containing duplexes. We also report allele-selective inhibition by duplex RNAs containing unlocked nucleic acids or abasic substitutions, although selectivities are not as high. Five compounds that showed >8-fold allele selectivity for mutant ATN-1 were also selective for inhibiting the expression of two other trinucleotide repeat disease genes, ataxin-3 (ATXN-3) and huntingtin (HTT). These data demonstrate that the expanded trinucleotide repeat within ATN-1 mRNA is a potential target for compounds designed to achieve allele-selective inhibition of ATN-1 protein, and one agent may allow the targeting of multiple disease genes.

AB - Dentatorubral-pallidoluysian atrophy (DRPLA) is a progressive neurodegenerative disorder that currently has no curative treatments. DRPLA is caused by an expansion of a CAG trinucleotide repeat region within the protein-encoding sequence of the atrophin-1 (ATN-1) gene. Inhibition of mutant ATN-1 protein expression is one strategy for treating DRPLA, and allele-selective gene silencing agents that block mutant expression over wild-type expression would be lead compounds for therapeutic development. Here we develop an assay for distinguishing mutant from wild-type ATN-1 protein by gel electrophoresis. We use this assay to evaluate duplex RNAs and single-stranded silencing RNAs (ss-siRNAs) for allele-selective inhibition of ATN-1 protein expression. We observed potent and allele-selective inhibition by RNA duplexes that contain mismatched bases relative to the CAG target and have the potential to form miRNA-like complexes. ss-siRNAs that contained mismatches were as selective as mismatch-containing duplexes. We also report allele-selective inhibition by duplex RNAs containing unlocked nucleic acids or abasic substitutions, although selectivities are not as high. Five compounds that showed >8-fold allele selectivity for mutant ATN-1 were also selective for inhibiting the expression of two other trinucleotide repeat disease genes, ataxin-3 (ATXN-3) and huntingtin (HTT). These data demonstrate that the expanded trinucleotide repeat within ATN-1 mRNA is a potential target for compounds designed to achieve allele-selective inhibition of ATN-1 protein, and one agent may allow the targeting of multiple disease genes.

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