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Allele-specific silencing of mutant huntingtin and ataxin-3 genes by targeting expanded CAG repeats in mRNAs

Nature Biotechnology volume 27, pages 478–484 (2009)Cite this article

Abstract

Expanded trinucleotide repeats1 cause many neurological diseases. These include Machado-Joseph disease (MJD)2 and Huntington's disease (HD)3, which are caused by expanded CAG repeats within an allele of the ataxin-3 (ATXN3) and huntingtin (HTT) genes, respectively. Silencing expression of these genes is a promising therapeutic strategy, but indiscriminate inhibition of both the mutant and wild-type alleles may lead to toxicity, and allele-specific approaches have required polymorphisms that differ among individuals. We report that peptide nucleic acid and locked nucleic acid antisense oligomers that target CAG repeats can preferentially inhibit mutant ataxin-3 and HTT protein expression in cultured cells. Duplex RNAs were less selective than single-stranded oligomers. The activity of the peptide nucleic acids does not involve inhibition of transcription, and differences in mRNA secondary structure or the number of oligomer binding sites may be important. Antisense oligomers that discriminate between wild-type and mutant genes on the basis of repeat length may offer new options for developing treatments for MJD, HD and related hereditary diseases.

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Figure 1: PNAs, LNAs and inhibition of HTT expression by PNA-peptide conjugates.
Figure 2: Effect of PNA modification, LNAs and siRNAs on selectivity.
Figure 3: Selectivity is affected by the number of repeats in mutant HTT.
Figure 4: Potent and selective inhibition of mutant ataxin-3 in GM06151 fibroblasts.

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Acknowledgements

This work was supported by the High-Q Foundation, the US National Institutes of Health (NIGMS 60642 and 73042 to D.R.C.; NINDS RO1NS056224 to I.B.; NIBIB EB 05556 to J.C.S.), and the Robert A. Welch Foundation (I-1244 and I-1336) and Ataxia MJD research project. We thank B. Janowski for helpful comments and Y. Li for help maintaining the YAC128 mouse colony.

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Author notes

  1. Jiaxin Hu and Masayuki Matsui: These authors contributed equally to this work.

Authors and Affiliations

  1. Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA

    Jiaxin Hu, Masayuki Matsui, Keith T Gagnon, Jacob C Schwartz & David R Corey

  2. Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA

    Jun Wu & Ilya Bezprozvanny

  3. SIGMA-Aldrich Genopole Campus, Evry, Cedex, France

    Sylvie Gabillet & Khalil Arar

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Contributions

J.H. and M.M. designed and performed experiments in patient-derived fibroblast cells. J.W. and J.H. designed and performed experiments in MSN cells. K.T.G. and J.C.S assisted with experiments. K.A. and S.G. supplied LNAs. D.R.C. and I.B. supervised experiments.

Corresponding author

Correspondence to David R Corey.

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Competing interests

D.R.C and J.H. have filed a patent application related to this research. S.G. and K.A. are employed by Sigma-Aldrich.

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Supplementary Figures 1–13 Supplementary Tables 1,2 and Supplementary Methods (PDF 6266 kb)

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Hu, J., Matsui, M., Gagnon, K. et al. Allele-specific silencing of mutant huntingtin and ataxin-3 genes by targeting expanded CAG repeats in mRNAs. Nat Biotechnol 27, 478–484 (2009). https://doi.org/10.1038/nbt.1539

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