Webinar of the Month

Uncovering Mechanisms of Hepatotoxicity for High Affinity Antisense Oligonucleotides – 3’ end RNA-Seq Profilling Using GeneSpring GX

High affinity antisense oligonucleotides (ASOs) containing bicylic modifications (BNA) such as locked nucleic acid (LNA) or constrained ethyl (cEt) designed to induce target RNA cleavage have been shown to have enhanced potency along with a higher propensity to cause hepatotoxicity. In order to unravel the mechanism of this hepatotoxicity, we leveraged GeneSpring GX Analysis Software to analyze transcriptional profiles from the livers of mice treated with a panel of highly efficacious hepatotoxic or non-hepatotoxic LNA ASOs. With hierarchical clustering in GX, we demonstrated that the liver of mice treated with non-hepatotoxic LNA ASOs displayed highly selective on-target transcript knockdown, while the levels of many unintended transcripts were reduced in mice treated with hepatotoxic LNA ASOs. Using the correlation analysis option in GX, we showed that plasma ALT, a biomarker for liver toxicity, was correlated to the transcriptional signature, which was concurrent with on-target RNA reduction and preceded transaminitis. Surprisingly, mRNA transcripts commonly reduced by toxic LNA ASOs were not strongly associated with any particular biological process, cellular component or functional group, rather they tended to have much longer pre-mRNA transcripts. We also demonstrate that the off-target RNA knockdown and hepatotoxicity was dependent on RNase H1. This suggests that for a certain set of BNA ASOs, hepatotoxicity can occur as a result of unintended off-target RNase H1 dependent RNA degradation.

Sebastien A. Burel, PhD
Director, Nonclinical Development, Ionis Pharmaceuticals, California

14 June 2017, 8 AM PST