Poster abstracts
Poster number 16 submitted by Gillian Browne
Effective and long lasting KD of nuclear retained lncRNA in a broad range of mouse tissues achieved with single stranded LNA enhanced antisense oligonucleotides
Gillian Browne, Barbara Gould, Henrik M. Pfundheller, Niels M. Frandsen, Ni (Exiqon, Vedbaek, Denmark), Johnathan Lai, Peter Mouritzen (Exiqon, Vedbaek, Denmark), Bodo Brunner (Sanofi-Aventis Deutschland GmbH), Mike Helms (Sanofi-Aventis Deutschland GmbH), Katharina M. Michalik (R&D Biologics / Nucleic Acid Therap., Frankfurt, Germany, FF Institute for Cardiovascular Regeneration), Reinier A. Boon (R&D Biologics / Nucleic Acid Therap., Frankfurt, Germany, FF Institute for Cardiovascular Regeneration)
Abstract:
One of the most interesting results from the ENCODE NGS project is the observation that a major part of the transcriptome is non-coding. The few lncRNAs that have been studied suggest that they have important and diverse functions involved in epigenetics and regulation of both transcription and translation. There is therefore an urgent need for the development of tools for functional analysis of lncRNAs in cell cultures and animals.
For this purpose Exiqon has focused on single strand LNA enhanced antisense technology that catalyzes RNaseH dependent degradation of target RNA. We have developed an empirically derived design algorithm that provides antisense oligonucleotides (ASOs) that achieve potent target KD with a high hit-rate. To illustrate the power of the design algorithm we show that by screening just 10 ASOs with high design scores we identified three capable of potent KD of the nuclear retained and ubiquitously expressed lncRNA Malat1 in a broad range of tissues upon systemic delivery in mice.
We selected one ASO for extended analysis. 12 different tissue samples were selected 2 days, 5 weeks and 15 weeks after the last ASO administration. We report broad range KD of Malat1 although with some differences between tissue types. Interesting variations in the duration of the KD were observed. This suggests that the long term fate of intracellular ASOs differ significantly between cell types. In conclusion we show that LNA enhanced gapmers are important and powerful tools for the analysis of lncRNA function both in cell cultures as well as animal models which make them particularly promising antisense drugs of the future.
Keywords: lncRNA, gapmers, NGS