Project description:Development of LNA gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by non-target mediated hepatotoxicity issues. In the present study, we investigated hepatic transcription profiles of mice receiving non-toxic and toxic LNA gapmers after a single and repeat administration.
Project description:Transcriptional profiling of mouse liver comparing control, scrambled-oligonucleotides (Cont)-treated mice with Perilipin 2-antisense oligonucleotides (Plin2-ASO)-treated mice. C57BL/6 mice on a high-fat diet were treated with oligonucleotides in vivo. The goal was to determine the effects of Plin2 down-regulation in the liver on global gene expression. Two-condition experiment, control oligonucleotides vs. Plin2-antisense oligonucleotides. Biological replicates: 4 control replicates, 4 Plin2-ASO replicates.
Project description:Antisense oligonucleotides (AONs) have gained momentum as therapeutics for neuromuscular disorders with the clinical approval of nusinersen and eteplirsen. For microsatellite repeat expansion disorders, AONs have not reached the clinic yet. Oligonucleotide therapies in such disorders are based on preventing translation of expanded repeats or sequestration of RNA-binding proteins. This can be achieved both by steric hindrance and by degradation of the transcript, and it is unknown which approach is superior. Here, we directly compared blocking AONs with RNase H-recruiting gapmers in a myotonic dystrophy type 1 cell model. Two target sequences were selected: the triplet repeat, which offers many identical binding sites, and a unique sequence upstream of the repeat. We performed RNA sequencing to investigate both on- and off-target effects on a transcriptome-wide level.
Project description:Transcriptional profiling of mouse liver comparing control, scrambled-oligonucleotides (Cont)-treated mice with Perilipin 2-antisense oligonucleotides (Plin2-ASO)-treated mice. C57BL/6 mice on a high-fat diet were treated with oligonucleotides in vivo. The goal was to determine the effects of Plin2 down-regulation in the liver on global gene expression.
Project description:The developmental transcription factor SOX6 was found to regulate serum, as well as liver triglycerides in BL6 mice treated with SOX6 antisense gapmers compared to control gapmers. SOX6 was initially discovered as a gene over-expressed in mesenchymal stem cells derived from small for gestational age newborns. We characterized its metabolic function in BL6 mice using the above antisense knockdown approach. BL6 mice were treated with either SOX6 specific or control gapmer oligonucleotides for 48h. Knockdown efficiency was measured in liver and epididymal white adipose tissues and serum levels of triglycerides and cholesterol quantified.
Project description:We identified genes regulated by the DIRC3 long non-coding RNA and its neighbouring tumour suppressor gene IGFBP5 and determined common targets. DIRC3 and IGFBP5 were knocked down by transient transfection of antisense oligonucleotides (ASOs) in the human melanoma cell line Sk-Mel-28. RNA was extracted 72 hours after transfection and polyA selected 150-bp paired end RNA sequencing was performed on the Illumina HiSeq4000 .
Project description:Development of LNA gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by non-target mediated hepatotoxicity issues. In the present study, we investigated hepatic transcription profiles of mice receiving non-toxic and toxic LNA gapmers after a single and repeat administration. To understand the mechanism of LNA gapmer-induced heptotoxicity in mice, we investigated the transcription profiles of liver RNA isolated from mice receiving non-toxic sequence (NTS-1), toxic sequence (TS-2), or severely toxic sequence (HTS-3) of LNA gapmers at 25 mg/kg (dose volume of 10 mL/kg) at 8, 16, or 72 hrs after a single administration (by subcutaneous injection ) using microarray analysis. We also investigated the transcription profiles of liver RNA isolated from mice receiving non-toxic sequence (NTS-1) or toxic sequence (TS-2) of LNA gapmers at 25 mg/kg (dose volume of 10 mL/kg) at 2 weeks after repeated administration (by subcutaneous injection ) using microarray analysis.
Project description:NFYC-AS1 is an overlapping antisense RNA transcribed head-to-head to NFYC sense gene, encoding for the subunit C of NF-Y transcription factor, which is known as master regulator of cell cycle and proliferation in normal and tumor cells. Here we performed NFYC-AS1 silencing in lung squamous carcinoma H520 cells by Gapmer antisense oligonucleotides and CRISPR/Cas9 TSS deletion. Afterwards, we performed differentially expressed analysis and gene set enrichement analysis to investigate on NFYC-AS1 function and mechanism of action.
Project description:Antisense oligonucleotide (ASO) has the potential to induce hybridization-dependent effects by inadvertent binding of ASOs to RNA with sequences similar to that of the target RNA. In the present study, we examined the effects of the nucleobase derivatives introduced into the gapmer ASOs on gene expression. We performed microarray analysis using NMuLi cells (mouse liver-derived cells) treated with LNA gapmer ASO containing nucleobase modification.
Project description:We investigated the effects of transfecting Malat1 antisense oligonucleotides on the whole Neuro2 neuroblastoma transcriptome. In this work, global transcription analyses were combined with detailed analyses of some synaptic genes. Our results provide insight on Malat1 effect on the regulation of gene expression in a mouse neuroblastoma cell line. Keywords: Comparative transcriptome analysis from Mus Musculus Neuro2 neuroblastoma cells transfected by Malat1 or Scamble oligodeoxynucleotides.
