Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Adenine Base Editing of Hematopoietic Stem Cells Rescues T-Cell Development for CD3δ Severe Combined Immune Deficiency

ABSTRACT: CD3δ SCID is a devastating inborn error of immunity caused by mutations in CD3D, encoding the invariant CD3δ chain of the CD3/TCR complex necessary for normal thymopoiesis. We demonstrate an adenine base editing (ABE) strategy to restore CD3δ in autologous hematopoietic stem and progenitor cells (HSPC). Delivery of mRNA encoding a laboratory-evolved ABE and guide RNA into CD3δ SCID patient’s HSPCs resulted in 71.2±7.85% (n=3) correction of the pathogenic mutation. Edited HSPCs differentiated in artificial thymic organoids produced mature T cells exhibiting diverse TCR repertoires and TCR-dependent functions. Edited human HSPCs transplanted into immunodeficient mice showed 88% reversion of the CD3D defect in human CD34+ cells isolated from mouse bone marrow after 16 weeks, indicating correction of long-term repopulating HSCs. These findings demonstrate preclinical efficacy of ABE in HSPC for the treatment of CD3δ SCID, providing a foundation for the development of a one-time treatment for CD3δ SCID patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE220611 | GEO | 2023/03/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Generation of mature T cells from human hematopoietic stem/progenitor cells in artificial thymic organoids

Project description:Mechanistic studies of human T cell development require robust model systems that recapitulate the full span of thymopoiesis, from hematopoietic stem and progenitor cells (HSPC) through to mature naïve T cells. We developed a serum free, artificial thymic organoid (ATO) system that supports highly efficient and reproducible in vitro differentiation and positive selection to generate conventional human T cells from all sources of HSPCs. Deep-sequencing of the TCR variable genes was performed to compare the diversity of the TCR repertoire between ATO-derived CD8SP T cells and naive CD8SP T cells from thymus and blood.

2017-02-17 | GSE94968 | GEO

Lipid nanoparticles improves ex vivo gene editing of human hematopoietic cells

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

RNA-seq expression data from EB-HSPCs after HOXA7 overexpression

Project description:HOXA7 regulates FL-HSPC self-renewal in vitro and in vivo. We profiled EB-HSPCs after HOXA7 overexpression (EB-HOXA7), or with a control vector (EB-CTR), to assess the gene expression programs regulated by HOXA7. CD34+CD38-CD43+CD90+ HSPCs were infected with lentiviral FUGW vector either empty (FUGW-GFP) or encoding HOXA7(FUGW-GFP-HOXA7) protein. Cells were expanded on op9 for 15 days and than sorted for GFP HSPC immunophenotype.

2016-05-16 | E-GEOD-76684 | biostudies-arrayexpress

A p38 MAPK-ROS axis fuels proliferation stress and DNA damage during CRISPR/Cas9 gene editing in Hematopoietic Stem and Progenitor Cells

Project description:Ex vivo activation is a prerequisite to reaching adequate levels of gene editing by homology-driven repair (HDR) for hematopoietic stem and progenitor cell (HSPC)-based clinical applications. Here, we show that shortening culture time mitigates the p53-mediated DNA damage response to CRISPR/Cas9-induced DNA double-strand breaks, enhancing the reconstitution capacity of edited HSPCs. However, this results in lower HDR efficiency, rendering ex vivo culture necessary yet detrimental. Mechanistically, ex vivo activation triggers a multi-step process initiated by p38 MAPK phosphorylation, which generates mitogenic ROS, promoting fast cell cycle progression and subsequent proliferation-induced DNA damage. Thus, p38 inhibition before gene editing delays G1/S transition and expands transcriptionally-defined HSCs, ultimately endowing edited cells with superior multi-lineage differentiation, persistence throughout serial transplantation, enhanced polyclonal repertoire, and better-preserved genome integrity. Our data identify proliferative stress as a driver of HSPC dysfunction with fundamental implications for designing more effective and safer gene correction strategies for clinical applications.

2024-10-14 | GSE238189 | GEO

Exonic knock-out/in gene editing in hematopoietic stem and progenitor cells fully rescues RAG1 immunodeficiency [RNA-Seq]

Project description:Recombination Activating Genes (RAG) are tightly regulated during lymphoid differentiation and their mutations cause a spectrum of severe immunological disorders. Haematopoietic stem/progenitor cell (HSPC) transplantation is the treatment of choice but limited by donor availability and toxicity. To overcome these issues, we developed and validated gene editing (GE) strategies targeting a corrective sequence into the human RAG1 gene by homology-directed repair (HDR). Off-target and RNA-Seq analyses were performed on edited human and patient-derived HSPCs to assesse the genome integrity and the trascriptomic profile. Whereas integration into intron 1 achieved suboptimal levels of correction, in-frame insertion into exon 2 drove faithful recapitulation of physiologic hRAG1 expression and activity.

2023-12-31 | GSE244672 | GEO

Exonic knock-out/in gene editing in hematopoietic stem and progenitor cells fully rescues RAG1 immunodeficiency [GUIDE2]

2023-12-31 | GSE244671 | GEO

Exonic knock-out/in gene editing in hematopoietic stem and progenitor cells fully rescues RAG1 immunodeficiency [GUIDE1]

2023-12-31 | GSE244669 | GEO

Exonic knock-out/in gene editing in hematopoietic stem and progenitor cells fully rescues RAG1 immunodeficiency [OFFTARGET]

2023-12-31 | GSE244752 | GEO

Single Stem Cell Lineage Analysis of the Leukemic Clones Responsible for Acute Myeloid Leukemia Relapse Based on the Functional and Genomic Properties at Diagnosis

Project description:Single cell lineage analysis was used to assess clonal genetic heterogeneity and functional aspects of AML HSPCs derived at diagnosis and relapse. To address inherent limitations of single cell analysis, we developed a unique high-resolution technique capable of following single cell-derived subclones of different HSPC subpopulations during the AML course. Each of these subclones was evaluated for chemo-resistance, in-vivo leukemogenic potential in Nod Scid Gamma (NSG) mice, mutational profile, and the subclone cell of origin identified using retrospective cell lineage reconstruction.

2022-08-12 | E-MTAB-11884 | biostudies-arrayexpress

Identification of osteolineage cell-derived extracellular vesicle cargo implicated in hematopoietic support

Project description:Osteolineage cell-derived extracellular vesicles (EVs) play a regulatory role in hematopoiesis and have been shown to promote the ex vivo expansion of human hematopoietic stem and progenitor cells (HSPCs). Here, we demonstrate that EVs from different human osteolineage sources do not have the same HSPC expansion promoting potential. Comparison of stimulatory and non-stimulatory osteolineage EVs by next-generation sequencing and mass spectrometry analyses revealed distinct microRNA and protein signatures identifying EV-derived candidate regulators of ex vivo HSPC expansion. Accordingly, the treatment of umbilical cord blood-derived CD34+ HSPCs with stimulatory EVs altered HSPC transcriptome, including genes with known roles in cell proliferation. An integrative bioinformatics approach, which connects the HSPC gene expression data with the candidate cargo in stimulatory EVs, delineated the potentially targeted biological functions and pathways during hematopoietic cell expansion and development. In conclusion, our study gives novel insights into the complex biological role of EVs in osteolineage cell-HSPC crosstalk and promotes the utility of EVs and their cargo as therapeutic agents in regenerative medicine.

2020-02-28 | PXD017172 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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