Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1026949 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26351400.fastq.gz | Fastqsanger.gz | |||
| SRR26368100_1.fastq.gz | Fastqsanger.gz | |||
| SRR26368100_2.fastq.gz | Fastqsanger.gz | |||
| SRR26368200_1.fastq.gz | Fastqsanger.gz | |||
| SRR26368200_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 823 |
Similar Datasets
Project description:Lipid nanoparticles (LNPs) play a critical role in the delivery of therapeutic mRNA. Despite extensive efforts to optimize lipid formulations for in vivo delivery, efficacy of mRNA by LNPs remains suboptimal in many organs. Here, we demonstrate that LNP delivery efficacy is influenced by cellular metabolism, with the physiologic metabolome imposing constraints on mRNA expression from LNPs. Using an in vitro system, we found that simulated physiologic metabolic conditions led to the downregulation of certain amino acid metabolic programs. Supplementation of an optimized formulation of methionine, arginine, and serine as an amino acid supplement (AAS) which enhanced the uptake of LNPs and the expression of delivered mRNA cargo in epithelial cells in vitro. Co-administration of AAS with LNPs led to a 5- to 20-fold improvement in mRNA expression across various cell types and lipid formulations in vitro . In vivo delivery of mRNA by LNPs co-administered with AAS by multiple routes enhanced in vivo mRNA expression. Delivery of growth hormone encoding mRNA by LNPs with co-administration of AAS improved the liver GH expression and the therapeutic outcomes in a model of inflammatory liver damage. Delivery of gene editing materials by LNP and AAS through intratracheal route increased lung-targeted in vivo gene editing efficiency compared with LNP alone. The addition of an optimized amino acid supplement as a co-delivered agent with LNPs may provide a simple strategy to broadly improve the efficacy of mRNA-based cell and gene therapies.
2026-03-11 | GSE314463 | GEO
Project description:Prime editing is a highly versatile CRISPR-based genome editing technology with the potential to correct the vast majority of genetic defects1. However, correction of a disease phenotype in vivo in somatic tissues has not been achieved yet. Here, we establish proof-of-concept for in vivo prime editing, that resulted in rescue of a metabolic liver disease. We first develop a size-reduced prime editor (PE) lacking the RNaseH domain of the reverse transcriptase (SpCas9-PERnH), and a linker- and NLS-optimized intein-split PE construct (SpCas9-PE p.1153) for delivery by adeno-associated viruses (AAV). Systemic dual AAV-mediated delivery of this variant in neonatal mice enables installation of a transversion mutation at the Dnmt1 locus with 15% efficiency on average. Next, we targeted the disease-causing mutation in the phenylalanine hydroxylase (Pah)enu2 mouse model for phenylketonuria (PKU). Correction rates of 1.5% using the dual AAV approach could be increased to up to 14% by delivery of full-length SpCas9-PE via adenoviral vector 5 (AdV5), leading to full restoration of physiological blood phenylalanine (L-Phe) levels below 120 µmol/L. Our study demonstrates in vivo prime editing in the liver at two independent loci, emphasizing the potential of PEs for future therapeutic applications.
2021-12-29 | GSE174757 | GEO
Project description:RNA-programmable deaminases, known as base editors (BEs), enable precise single base conversions on genomic DNA and hold great promise for therapeutic application in patients. Recent studies, however, have raised serious concern with regard to off-target effects, questioning translatability of BEs to the clinic. Here we analyze transcriptome- and genome-wide off-target effects following AAV-mediated delivery of cytosine base editors (CBEs) in vivo in an unbiased manner. We show that low expression of CBEs allows sufficient on-target editing to cure a disease phenotype with no increase in off-target effects compared to untreated controls. To further improve safety of in vivo base editing, we developed a lipid nanoparticle (LNP)-mediated delivery system to transiently express BEs. We reach up to 21% on-target editing with no detectable transcriptome- or genome-wide off-target effects, and are able to reverse the disease phenotype of a phenylketonuria mouse model. These results have important implications, underlining the feasibility of transient in vivo base editing for therapeutic use in patients.
2020-08-24 | GSE148349 | GEO
Project description:Ex-vivo gene editing in T cells and hematopoietic stem/progenitor cells (HSPCs) holds promise for treating diseases by non-homologous end joining (NHEJ) gene disruption or homology-driven repair (HDR) gene correction. Gene editing encompasses delivery of nucleases by electroporation and, when aiming to HDR, of a DNA template often provided by viral vectors. Whereas HSPCs activate robust p53-dependent DNA damage response (DDR) upon editing, the responses triggered in T cells remain poorly characterized. Here, we performed comprehensive multi-omics analyses and found that electroporation is the culprit of cytotoxicity in T cells, causing death and cell cycle delay, perturbing metabolism and inducing inflammatory response. Nuclease delivery by lipid nanoparticles (LNPs) nearly abolished cell death and ameliorated cell growth, improving tolerance to the procedure and yielding higher number of edited cells compared to electroporation. Transient transcriptomic changes upon LNP treatment were mostly caused by cellular loading with exogenous cholesterol, whose potentially detrimental impact could be overcome by limiting exposure. Notably, LNP-based HSPC editing dampened p53 pathway induction and supported higher reconstitution by long-term repopulating HSPCs compared to electroporation, reaching similar editing efficiencies. Overall, LNPs may allow efficient and stealthier ex-vivo gene editing in hematopoietic cells for treatment of human diseases.
2024-01-26 | PXD037529 | Pride
Project description:Base editing introduces precise single-nucleotide edits in genomic DNA and has the potential to treat genetic diseases such as the blistering skin disease recessive dystrophic epidermolysis bullosa (RDEB), which is characterized by mutations in the COL7A1 gene and type VII collagen (C7) deficiency. Adenine base editors (ABEs) convert A-T base pairs to G-C base pairs without requiring double-stranded DNA breaks or donor DNA templates. Here, we use ABE8e, a recently evolved ABE, to correct primary RDEB fibroblasts harboring the recurrent RDEB nonsense mutation c.5047 C>T (p.Arg1683Ter) in exon 54 of COL7A1 and use a next generation sequencing workflow to interrogate post-treatment outcomes. Electroporation of ABE8e mRNA into a bulk population of RDEB patient fibroblasts resulted in remarkably efficient (94.6%) correction of the pathogenic allele, restoring COL7A1 mRNA and expression of C7 protein in western blots and in 3D skin constructs. Unbiased off-target DNA and RNA editing analysis did not detect off-target editing in treated patient-derived fibroblasts. Taken together, we have established a highly efficient pipeline for gene correction in primary fibroblasts with a favorable safety profile. This work lays a foundation for developing therapies for RDEB patients using ex vivo or in vivo base editing strategies.
2022-08-25 | GSE211876 | GEO
Project description:Ex vivo gene editing in T cells and hematopoietic stem/progenitor cells (HSPCs) holds promise for treating diseases. Gene editing encompasses delivery of a programmable editor RNA or ribonucleoprotein, often achieved ex vivo by electroporation and, when aiming to homology-driven correction, of a DNA template often provided by viral vectors together with a nuclease editor. Whereas HSPCs activate robust p53-dependent DNA damage response (DDR) upon nuclease-based editing, the responses triggered in T cells remain poorly characterized. Here, we performed comprehensive multi-omics analyses and found that electroporation is the main culprit of cytotoxicity in T cells, causing death and cell cycle delay, perturbing metabolism and inducing inflammatory response. Nuclease RNA delivery by lipid nanoparticles (LNPs) nearly abolished cell death and ameliorated cell growth, improving tolerance to the procedure and yielding higher number of edited cells compared to electroporation. Transient transcriptomic changes upon LNP treatment were mostly caused by cellular loading with exogenous cholesterol, whose potentially detrimental impact could be overcome by limiting exposure. Notably, LNP-based HSPC editing dampened p53 pathway induction and supported higher clonogenic activity and similar or higher reconstitution by long-term repopulating HSPCs compared to electroporation, reaching comparable editing efficiencies. Overall, LNPs may allow efficient and harmless ex vivo gene editing in hematopoietic cells for treatment of human diseases.
2023-10-18 | GSE245626 | GEO
Project description:Ex vivo gene editing in T cells and hematopoietic stem/progenitor cells (HSPCs) holds promise for treating diseases. Gene editing encompasses delivery of a programmable editor RNA or ribonucleoprotein, often achieved ex vivo by electroporation and, when aiming to homology-driven correction, of a DNA template often provided by viral vectors together with a nuclease editor. Whereas HSPCs activate robust p53-dependent DNA damage response (DDR) upon nuclease-based editing, the responses triggered in T cells remain poorly characterized. Here, we performed comprehensive multi-omics analyses and found that electroporation is the main culprit of cytotoxicity in T cells, causing death and cell cycle delay, perturbing metabolism and inducing inflammatory response. Nuclease RNA delivery by lipid nanoparticles (LNPs) nearly abolished cell death and ameliorated cell growth, improving tolerance to the procedure and yielding higher number of edited cells compared to electroporation. Transient transcriptomic changes upon LNP treatment were mostly caused by cellular loading with exogenous cholesterol, whose potentially detrimental impact could be overcome by limiting exposure. Notably, LNP-based HSPC editing dampened p53 pathway induction and supported higher clonogenic activity and similar or higher reconstitution by long-term repopulating HSPCs compared to electroporation, reaching comparable editing efficiencies. Overall, LNPs may allow efficient and harmless ex vivo gene editing in hematopoietic cells for treatment of human diseases.
2023-06-30 | GSE216249 | GEO
Project description:Ex vivo gene editing in T cells and hematopoietic stem/progenitor cells (HSPCs) holds promise for treating diseases. Gene editing encompasses delivery of a programmable editor RNA or ribonucleoprotein, often achieved ex vivo by electroporation and, when aiming to homology-driven correction, of a DNA template often provided by viral vectors together with a nuclease editor. Whereas HSPCs activate robust p53-dependent DNA damage response (DDR) upon nuclease-based editing, the responses triggered in T cells remain poorly characterized. Here, we performed comprehensive multi-omics analyses and found that electroporation is the main culprit of cytotoxicity in T cells, causing death and cell cycle delay, perturbing metabolism and inducing inflammatory response. Nuclease RNA delivery by lipid nanoparticles (LNPs) nearly abolished cell death and ameliorated cell growth, improving tolerance to the procedure and yielding higher number of edited cells compared to electroporation. Transient transcriptomic changes upon LNP treatment were mostly caused by cellular loading with exogenous cholesterol, whose potentially detrimental impact could be overcome by limiting exposure. Notably, LNP-based HSPC editing dampened p53 pathway induction and supported higher clonogenic activity and similar or higher reconstitution by long-term repopulating HSPCs compared to electroporation, reaching comparable editing efficiencies. Overall, LNPs may allow efficient and harmless ex vivo gene editing in hematopoietic cells for treatment of human diseases.
2023-06-30 | GSE216248 | GEO