1. G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects.
- Author
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Wang F, Calvo-Roitberg E, Rembetsy-Brown JM, Fang M, Sousa J, Kartje ZJ, Krishnamurthy PM, Lee J, Green MR, Pai AA, and Watts JK
- Subjects
- Humans, Iron-Binding Proteins genetics, Iron-Binding Proteins metabolism, RNA, Messenger metabolism, Cells, Cultured, DNA-Binding Proteins genetics, DNA-Binding Proteins metabolism, Frataxin, Friedreich Ataxia genetics, Oligonucleotides, Antisense genetics, Oligonucleotides, Antisense pharmacology, Oligonucleotides, Antisense metabolism, Gene Expression Regulation
- Abstract
Friedreich's ataxia is an incurable disease caused by frataxin (FXN) protein deficiency, which is mostly induced by GAA repeat expansion in intron 1 of the FXN gene. Here, we identified antisense oligonucleotides (ASOs), complementary to two regions within the first intron of FXN pre-mRNA, which could increase FXN mRNA by ∼2-fold in patient fibroblasts. The increase in FXN mRNA was confirmed by the identification of multiple overlapping FXN-activating ASOs at each region, two independent RNA quantification assays, and normalization by multiple housekeeping genes. Experiments on cells with the ASO-binding sites deleted indicate that the ASO-induced FXN activation was driven by indirect effects. RNA sequencing analyses showed that the two ASOs induced similar transcriptome-wide changes, which did not resemble the transcriptome of wild-type cells. This RNA-seq analysis did not identify directly base-paired off-target genes shared across ASOs. Mismatch studies identified two guanosine-rich motifs (CCGG and G4) within the ASOs that were required for FXN activation. The phosphorodiamidate morpholino oligomer analogs of our ASOs did not activate FXN, pointing to a PS-backbone-mediated effect. Our study demonstrates the importance of multiple, detailed control experiments and target validation in oligonucleotide studies employing novel mechanisms such as gene activation., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2022
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