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RNA-seq approach to study the specific effects of SREBF1-depleting antisense oligonucleotide (ASO) reagent in human melanoma cells.

ABSTRACT: RNA-seq approach to study the specific effects of SREBF1-depleting antisense oligonucleotide (ASO) reagent in human melanoma cells.

PROVIDER: PRJNA506045 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8207680_1.fastq.gz	Fastqsanger.gz
	SRR8207680_2.fastq.gz	Fastqsanger.gz
	SRR8207690_1.fastq.gz	Fastqsanger.gz
	SRR8207690_2.fastq.gz	Fastqsanger.gz
	SRR8207681_1.fastq.gz	Fastqsanger.gz

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RNA-seq approach to study the specific effects of SREBF1-depleting antisense oligonucleotide (ASO) reagent in human melanoma cells.

Project description:Purpose: Detailed exploration of de novo Fatty Acid Synthesis (DNFA) transcription regulation and clinical relevance in melanomas. This study was designed to achieve the following goals: 1) determine the impact of SREBP1 depletion on gene expression in metastatic melanoma cells; 2) determine the specificity of ASO and other reagents inhibiting SREBF1 mRNA. Method: RNA-Seq was performed after culture with control and various SREBF1-depleting agents, including pooled siRNAs and individual ASOs, in HT-144 cells. Results: using STAR, we mapped about 2 X 4 million pair-end sequence reads per sample to the human genome (build GRCh38.94) and identified around 2 million annotated transcripts per sample.

2018-11-20 | GSE122707 | GEO

Antisense oligonucleotide therapy for calmodulinopathy

Project description:Calmodulinopathies are rare inherited arrhythmia syndromes caused by dominant gain of function variants in one of three genes, CALM1, CALM2, and CALM3, which each encode the identical calmodulin (CaM) protein. We hypothesized that antisense oligonucleotide (ASO)-mediated depletion of an affected calmodulin gene would ameliorate disease manifestations, while the other two calmodulin genes would preserve CaM level and function. Here we tested this hypothesis using human induced pluripotent stem cell-derived cardiomyocyte (iPSC-CM) and mouse models of CALM1 pathogenic variants. Human CALM1F142L/+ iPSC-CMs exhibited prolonged action potentials, modeling congenital long QT syndrome. CALM1-depleting ASOs did not alter CaM protein level and normalized repolarization of CALM1F142L/+ iPSC-CMs. Similarly, an ASO targeting murine Calm1 depleted Calm1 transcript without affecting CaM protein level. This ASO alleviated drug-induced arrhythmia in CalmN98S/+ mice without causing observable toxicity. These results provide proof-of-concept that ASOs targeting individual calmodulin genes are potentially effective and safe therapies for calmodulinopathies.

2024-06-13 | GSE245945 | GEO

Small RNAseq of human breast cancer cell line MDA-MB-231 transfected with antisense oligonucleotide 1537S (ASO-1537S), compared to control oligonucleotide (ASO-C) and untreated cells

Project description:Small RNAseq of human breast cancer cell line MDA-MB-231 transfected with antisense oligonucleotide 1537S (ASO-1537S), compared to control oligonucleotide (ASO-C) and untreated cells

| PRJEB26666 | ENA

Heart RNA-seq of therapeutic RBM20 antisense oligonucleotide (ASO) treatment in a mouse model of heart failure with preserved ejection fraction (HFpEF)

Project description:We report the heart RNA-sequencing of control animals and animals of a mouse model of heart failure treated or not with RBM20 antisense oligonucleotide. This study aims to investigate the therapeutic effect of antisense oligonucleotide (ASO)-mediated downregulation of the cardiac splice factor RBM20 in a mouse model of heart failure with preserved ejection fraction. 8-week old wild type and titin N2B KO mice with increased wall stiffness were subcutaneously injected with 50 mg/kg/week RBM20 ASO for 8 weeks. RNA from 4 left ventricles per group were isolated using TRIzol followed by a clean-up with the QIAGEN RNA micro kit. The cDNA libraries were generated using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit and 2x150 paired end sequenced on HiSeq4000. The RNA-Sequencing analysis confirms that RBM20 ASO treatment increased the expression of compliant titin isoforms and improved impaired ventricular filling and cardiac function. RNA-seq confirmed RBM20 dependent isoform changes of known targets such as Titin, Ldb3, Camk2d, and Ank3, and served as a sensitive indicator of potential side effects, largely limited to genes related to the immune response.

2021-12-06 | E-MTAB-9361 | biostudies-arrayexpress

Preliminary small RNAseq of human breast cancer cell line MDA-MB-231 transfected with antisense oligonucleotide 1537S (ASO-1537S), compared to control oligonucleotide (ASO-C) and untreated cells

Project description:Preliminary small RNAseq of human breast cancer cell line MDA-MB-231 transfected with antisense oligonucleotide 1537S (ASO-1537S), compared to control oligonucleotide (ASO-C) and untreated cells

| PRJEB26664 | ENA

Preliminary small RNAseq of human breast cancer cell line MDA-MB-231 transfected with antisense oligonucleotide 1537S (ASO-1537S), compared to control oligonucleotide (ASO-C) and untreated cells

Project description:Proliferation of tumor cells transfected with ASO-1537S is inhibited compared to controls. The aim of the experiment is to determine changes in microRNA expression profiles with treatment, compared to controls.

2023-06-02 | E-MTAB-6762 | biostudies-arrayexpress

Small RNAseq of human breast cancer cell line MDA-MB-231 transfected with antisense oligonucleotide 1537S (ASO-1537S), compared to control oligonucleotide (ASO-C) and untreated cells

2023-06-02 | E-MTAB-6768 | biostudies-arrayexpress

Profiling the interactome of oligonucleotide drugs by proximity biotinylation

Project description:Drug-ID applies proximity biotinylation to identify drug-protein interactions inside living cells. The covalent conjugation of a drug molecule with a biotin ligase enables targeted biotinylation of the drug-bound proteome and its identification by SILAC-MS/MS. We investigate the interactome of two well-known small molecule drugs, JQ1 and SAHA, and applied it for the identification of the interactome of RNaseH-recruiting antisense oligonucleotides (ASO). Drug-ID allows to de novo profile the drug-protein interactome under native conditions, directly inside living cells and at the pharmacologically effective concentration of the drug using minimal amount of input material. We apply the technology to study the dose-dependent aggregation of ASOs and the effect of different wing chemistries (LNA, Fluoro, MOE) and ASO lengths on the ASO-protein interactome. Finally, we demonstrate the detection of stress-induced interactome changes (Actinomycin D treatment) in living cells. Particularly broadly applicable in the field of oligonucleotide therapeutics is the in situ variant of the approach, which uses a recombinant biotin ligase and does not require genetic manipulation of the target cell.

2024-01-09 | PXD045992 | Pride

CREB regulated transcriptional coactivator 2 proteome landscape is plausibly modulated by SREBF1

Project description:CRTC2 is a critical transcription cofactor that induces the glucose homeostatic genes by activating CREB. However, energy homeostasis is maintained by multiple pathways, therefore, it is possible that CRTC2 may interact with other transcription factors, especially under metabolic stress. Thereby, CRTC2 liver-specific knockout mice were created and the global proteome, phosphoproteome and acetylome from liver tissue under the high fat diet conditions were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis. As expected, differentially expressed proteins (DEPs) are enriched in metabolic pathways that were subsequently corroborated by animal experiments. The consensus DEPs from these datasets were used as seed proteins to generate a protein-protein interaction (PPI) network using STRING and GeneMANIA identified fatty acid synthase (FASN) as the mutually relevant protein. Additional local-PPI (LPPI) analysis of CRTC2 and FASN with DEPs, SREBF1 was found to be a common mediator. CRTC2/CREB and SREBF1 are transcription factors, DNA-binding motif analysis showed multiple CRTC2/CREB regulated genes also possess SREBF1 binding motifs that unveil the possible induction by CRTC2/SREBF1 complex, which is reinforced by structural analysis. Thus, CRTC2/SREBF1 complex plausibly modulate the transcription of multiple proteins that fine-tune the cellular metabolism under metabolic stress.

2023-10-24 | PXD039817 | Pride

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

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.

2022-07-12 | GSE197166 | GEO

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