Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stereo-random Oligonucleotides Enable Efficient Recruitment of ADAR in vitro and in vivo

ABSTRACT: We used our previously published isASO-ID protocol to identify binders for two different adenosine deaminases acting on RNA- (ADAR-) recruiting antisense oligonucleotides (ONs). The ONs differed in their phosphorothioate content and their RNA editing potency and efficiency through the recruitment of endogenous ADAR. We aimed to get a first insight into the protein interactions of this new ON class since ON toxicity is largely defined by the protein interactions. The results will help to understand class-specific mechanisms for ON toxicity and thus to design safer ON drugs.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Mirita Franz-Wachtel

LAB HEAD: Thorsten Stafforst

PROVIDER: PXD066763 | Pride | 2025-07-31

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20221215_CO_1128ThSt_R01_A.raw	Raw
	20221215_CO_1128ThSt_R01_B.raw	Raw
	20221215_CO_1128ThSt_R02_A.raw	Raw
	20221215_CO_1128ThSt_R02_B.raw	Raw
	checksum.txt	Txt

Items per page:

1 - 5 of 6

Similar Datasets

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

Discovery of diverse DNA cytosine deaminases enables a single-enzyme method for base resolution methylation detection

Project description:Cytosine deaminases have important uses in the detection of epigenetic modifications and in genome editing. However, the range of applications of deaminases is limited by their substrate preference. To expand the toolkit of deaminases, we developed an in-vitro approach that bypasses a major hurdle with their severe toxicity in expression hosts. We screened 175 putative cytosine deaminases, primarily from bacteria, and found enzymes with strong activity on double- and single-stranded DNA in various sequence contexts, including some without any sequence constraints. We also found enzymes that do not deaminate modified cytosines. The remarkable diversity of cytosine deaminases opens new avenues for biotechnological and medical applications. As a demonstration, we developed a single-enzyme methylation sequencing (SEM-seq) method for 5-methylcytosine detection using a novel non-specific, modification-sensitive double-stranded DNA deaminase, MsddA. SEM-seq generated accurate base-resolution maps of 5-methylcytosine in human genome samples including cell free DNA and samples of 10 pg DNA, equivalent to single cell input. This simple and efficient protocol has the potential to allow high-throughput epigenome profiling of scarce biological material.

2023-10-05 | GSE233932 | GEO

Chemical proteomics reveal human off-targets of fluoroquinolone induced mitochondrial toxicity

Project description:Fluoroquinolones (FQs) are an important class of potent broad-spectrum antibiotics. However, their general use is more and more limited by adverse side effects. While general mechanisms for the Fluoroquinolone-associated disability (FQAD) have been identified, the underlying molecular origins of toxicity remain elusive. In this study, focusing on the most commonly prescribed FQs Ciprofloxacin and Levofloxacin, whole proteome analyses revealed prominent mitochondrial dysfunction in human cells, specifically of the complexes I and IV of the electron transport chain. Furthermore, global untargeted chemo-proteomic methodologies such as photo-affinity profiling with FQ-derived probes, as well as derivatization-free thermal proteome profiling, were applied to elucidate human protein off-targets of FQs in living cells. Accordingly, the interactions of FQs with mitochondrial AIFM1 and IDH2 have been identified and biochemically validated for their contribution to mitochondrial dysfunction and adverse downstream effects, including impaired redox-homeostasis, elevated matrix metalloprotease activity and epigenetic modifications. This off-target discovery study provides unique insights into FQ toxicity enabling to utilize the identified molecular principles for the design of a safer FQ generation.

2025-05-07 | PXD056813 | Pride

Chemical proteomics reveal human off-targets of fluoroquinolone induced mitochondrial toxicity

2025-05-06 | PXD047056 | Pride

Pea early-browning virus

Project description:SAFER SEEDS PULSEBIO4

| PRJNA607790 | ENA

Analyses of a deactivation genetic variation in Ha-Ras proto oncogene identified in a patient wit premature aging and insulin resistance

Project description:Inherited genetic variants of insulin receptor induced cellular signaling have long been suspected to contribute to the development of type-2- diabetes mellitus. In this report we discuss a heterozygous mutation in the first coding exon of the proto-oncogene Ha-Ras (Ha-RasA11P) that we have identified in a patient with familial premature aging syndrome. The patient has atopic sklerodermic skin alterations, insulin resistance as well as disturbances in lipid metabolism. In vitro analyzes have shown that this mutation disrupted not only the signal transduction of the insulin receptor but also other receptor tyrosine kinases, such as IGF-1, EGF, PDGF. These results demonstrate that HA-Ras has a significant role in insulin sensitivity in humans. We used microarrays to determine differences in gene expression due to a deactivating Ha-Ras mutation reducing c-fos expression in a patient with lipodystrophy and a Werner-like syndrome. Cultued fibroblasts of non diabetic controls and a patient with deactivating Ha-Ras mutation were analyzed at identical passage number and growth conditions without further additional treatment.

2013-08-07 | E-GEOD-49566 | biostudies-arrayexpress

Project description:Pulse Bio4 safer seed

| PRJNA542720 | ENA

Stereo-random Oligonucleotides Enable Efficient Recruitment of ADAR in vitro and in vivo

Project description:Site-directed RNA editing is a promising and potentially safer alternative to genome editing. Previous methods have been developed that recruit the endogenously and ubiquitously expressed ADAR enzymes to initiate site-specific A-to-I edits, but often suffer from low efficacy or dependency on viral delivery. Chemically modified oligonucleotides may be a promising alternative, but the approach still lacks systematic in-depth studies. Furthermore, the best characterized platform uses stereo-pure backbone chemistry, which is not widely used, commercially unavailable and challenging to manufacture. Here, we report on single-stranded oligonucleotides of 30-60 nt length, which are fully chemically stabilized by applying commercially available, classical RNA drug modifications, like 2´-O-methyl, 2´-fluoro, and DNA on a stereo-random phosphate/phosphorothioate backbone. We demonstrate our so-called RESTORE 2.0 oligonucleotides to induce the correction of pathogenic point mutations, efficacy after GalNAc-mediated uptake into human primary hepatocytes, and proof of in-vivo efficacy in mice upon lipid nanoparticle-mediated delivery. The discovered design principles may increase the accessibility of site-directed RNA base editing to expand and support further research in this field. Here, the transcriptome-wide precision of our RNA editing ONs is tested by RNA Seq of treated NHA cells.

2025-07-28 | GSE303437 | GEO

RNA-seq of the diatom Skeletonema marinoi grown in the presence or absence of the copepod Calanus finmarchicus

Project description:The experiment was designed to study the transcriptomic response of the centric diatom Skeletonema marinoi to the presence of cues from the grazer Calanus finmarchicus. Samples were collected in triplicate after 65 and 89 hours of exposure of diatom cells to the copepods. Control samples with no copepods were collected at the same time points.

2018-03-29 | E-MTAB-6076 | biostudies-arrayexpress

EGAS00001000233-sc-20120920 - samples

Project description:Pulldown cytosine deaminases

| EGAD00001000245 | EGA