Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression analysis of mice hepatic NMuLi cells treated LNA gapmer ASO containing nucleobase modification

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE197166 | GEO | 2022/07/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression analysis of Huh-7 cells treated with LNA gapmer targeting glucocorticoid receptor (GR) RNA

Project description:Antisense oligonucleotide (ASO) has the potential to induce off-target effects due by inadvertent binding of ASOs to unintended RNAs that have a sequence similar to the target RNA. In the present study, we focused on the effects of oligonucleotide extension of gapmer ASOs on off-target effects. We performed microarray analysis using Huh-7 cells (human liver-derived cells) treated with a 14-mer LNA gapmer ASO and the extended 18-mer derivatives with the same core 14-mer region.

2021-12-15 | GSE188684 | GEO

Expression analysis of mice hepatic NMuLi cells treated LNA gapmer ASO containing nucleobase modification

Project description:Expression analysis of mice hepatic NMuLi cells treated LNA gapmer ASO containing nucleobase modification

| PRJNA809303 | ENA

Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells

Project description:Antisense oligonucleotide (ASO) has the potential to induce off-target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. In this study, we evaluated off-target effects of gapmer ASOs, which cleave the target RNA in an RNase H-dependent manner, by introducing the ASO into human cells and performing microarray analysis. Our data indicate that gapmer ASOs induce off-target effects depending on the degree of complementarity between the ASO and off-target candidate genes. Based on our results, we also propose a scheme for assessment of off-target effects of gapmer ASOs.

2021-12-08 | GSE190473 | GEO

Knockdown of circular RNAs using LNA-modified antisense oligonucleotides

Project description:Circular RNAs (circRNAs) constitute an abundant class of covalently closed non-coding RNA molecules that are formed by backsplicing from eukaryotic protein-coding genes. Recent studies have shown that circRNAs can act as microRNA or protein decoys as well as transcriptional regulators. However, the functions of most circRNAs are still poorly understood. Because circRNA sequences overlap with their linear parent transcripts, depleting specific circRNAs without affecting host gene expression remains a challenge. Here, we assessed the utility of LNA-modified antisense oligonucleotides (ASOs) to knock down circRNAs for loss-of-function studies. We identified 5807 circRNAs in total RNA sequencing data from 4 liver cancer cell lines and used the back splice junction (BSJ) sequences of 7 validated circRNAs as target sites for designing different LNA-modified ASOs for circRNA knockdown. We found that while most RNase H-dependent gapmer ASOs mediate effective knockdown of their target circRNAs, some gapmers reduce the levels of the linear parent transcript and may also cause degradation of unintended off-targets. The circRNA targeting specificity can be enhanced using design-optimized gapmer ASOs or LNA/DNA mixmer ASOs, which display potent and specific circRNA knockdown with a minimal effect on the host genes or predicted off-targets. In summary, our results demonstrate that LNA-modified ASOs complementary to BSJ sequences mediate robust knockdown of circRNAs in vitro and, thus, represent a useful tool to explore the biological roles of circRNAs in loss-of-function studies in cultured cells and animal models.

2022-11-01 | GSE145592 | GEO

Drugging the lncRNA MALAT1 via LNA gapmeR ASO inhibits gene expression of proteasome subunits and triggers anti-multiple myeloma activity

Project description:Drugging the lncRNA MALAT1 via LNA gapmeR ASO inhibits gene expression of proteasome subunits and triggers anti-multiple myeloma activity

| PRJNA428744 | ENA

Drugging the lncRNA MALAT1 via LNA gapmeR ASO inhibits gene expression of proteasome subunits and triggers anti-multiple myeloma activity

Project description:The biological role and therapeutic potential of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) are still to be investigated. Here, we studied the functional significance and the druggability of the oncogenic lncRNA MALAT1 in MM. Targeting MALAT1 by novel LNA-gapmeR anti-sense oligonucleotide antagonized MM cell proliferation and triggered apoptosis both in vitro and in vivo in a murine xenograft model of human MM. Of note, antagonism of MALAT1 dowmodulated the two major transcriptional activators of proteasome subunit genes, namely NRF1 and NRF2, and resulted in reduced trypsin, chymotrypsin and caspase-like proteasome activities and in accumulation of polyubiquitinated proteins. NRF1 and NRF2 decrease upon MALAT1-targeting was due to transcriptional activation of their negative regulator KEAP1, and resulted in reduced expression of anti-oxidant genes and increased ROS levels. In turn, NRF1 promoted MALAT1 expression thus establishing a positive feedback loop. Our findings demonstrate a crucial role of MALAT1 in the regulation of the proteasome machinery, and provide proof-of-concept that its targeting is a novel powerful option for the treatment of MM.

2018-12-31 | GSE108824 | GEO

Transcriptomic analysis of the effect of ASO-mediated CD33 knock-down on the microglial gene network in an APP/PS1 mouse model of Alzheimer’s disease. [LNA-006]

Project description:Microglia, the resident innate immune cells of the central nervous system (CNS), are increasingly recognized as critical for normal CNS function as well as for the pathophysiology of CNS disorders, including Alzheimer's disease (AD). Advances in transcriptomic analyses, such as weighted gene co-expression network analysis, reveal that the most perturbed gene networks identified in AD brains fall squarely within microglial pathways and these findings are consistent with genetic and epigenetic genome-wide association studies linking specific microglial genes to AD risk. Increased expression of full-length CD33 increases AD risk and CD33 is a component of the microglial gene network, yet relatively little is known about the significance of CD33 in this gene network or in microglial biology. To gain further insight into these questions, we first identified and characterized locked nucleic acid (LNA) antisense oligonucleotides (ASOs) as tools to knock down CD33 in APP/PS1 mice in vivo. We report here that CD33 LNA ASO results in robust knockdown of CD33 mRNA the frontal cortex and hippocampus of APP/PS1 mice and that this knockdown causes changes to the AD-associated microglial gene network. This work suggests that CD33 may be a viable therapeutic target in AD.

2016-09-30 | GSE74437 | GEO

Transcriptomic analysis of the effect of ASO-mediated (40ug/day) CD33 knock-down on the microglial gene network in an APP/PS1 mouse model of Alzheimer’s disease. [LNA-013]

2016-09-30 | GSE74440 | GEO

Transcriptomic analysis of the effect of ASO-mediated (50ug/day) CD33 knock-down on the microglial gene network in an APP/PS1 mouse model of Alzheimer’s disease. [LNA-012]

2016-09-30 | GSE74438 | GEO

An inhaled therapeutic targeting a conserved RNA structure in SARS-CoV-2

Project description:The Covid-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and which may partially evade vaccine and antibody immunity. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the Covid-19 pandemic. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identified an LNA ASO binding to the 5’ leader sequence of SARS-CoV-2 ORF1a/b and which disrupts a highly conserved stem-loop structure, with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the K18-hACE2 humanized Covid-19 mouse model potently (98-99%) suppressed viral replication in the lungs of infected mice, revealing strong prophylactic and treatment effects. We found that the LNA ASO is highly efficacious in countering all SARS-CoV-2 variants of concern (VOC) tested in vitro and in vivo, including B.1.427 (CA), B.1.1.7 (UK), and B.1.351 (SA) variants. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences. Hence, virus-targeting LNA ASOs represent a promising therapeutic approach to reduce the transmission of SARS-CoV-2, especially in areas where vaccine distribution is a challenge, and it may be stockpiled for future coronavirus pandemics.

2022-06-30 | GSE174382 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data