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Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [bulk RNA-seq]

ABSTRACT: We evaluated transcriptional changes elicited by targeting AAVS1 and IL2RG genes and we found that the impact of one or few nuclease-induced DNA DSBs is minor and mainly limited to genes belonging to the p53 pathway. The same pathway was elicited by gene editing at two distinct genomic loci and was more pronounced in primitive vs. progenitor cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE119584 | GEO | 2019/03/01

REPOSITORIES: GEO

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Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [Amplicon-seq]

Project description:We evaluated transcriptional changes elicited by targeting AAVS1 and IL2RG genes and we found that the impact of one or few nuclease-induced DNA DSBs is minor and mainly limited to genes belonging to the p53 pathway. The same pathway was elicited by gene editing at two distinct genomic loci and was more pronounced in primitive vs. progenitor cells.

2019-03-01 | GSE126120 | GEO

Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [Clear-seq]

Project description:We analysed AAVS1 edited cells in presence and absence of GSE56 (p53 inhibitor) 14 days upon electroporation to evaluate whether p53 transient inhibition by GSE56 could aggravate the genotoxicity risk of the procedure

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Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [scRNA-seq]

Project description:We performed single-cell (sc)RNA-Seq on male donors FACS-sorted “primitive” (CD34+ CD133+ CD90+) and “progenitor” (CD34+ CD133+ CD90-) HSPC cells treated with IL2RG ZFN, High Specificity (HS), (Low Specificity (LS) or control RNP in a ratio 1 to 1. We also included HS RNP and the cognate repair template containing a GFP expression cassette delivered by AAV6 and sorted for targeted integration (HS/AAV6 GFP+ vs. HS/AAV6 GFP-)

2019-03-01 | GSE119594 | GEO

Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-03-01 | GSE119597 | GEO

Precise Gene Editing Preserves Hematopoietic Stem Cell Function following Transient p53-Mediated DNA Damage Response.

Project description:Precise gene editing in hematopoietic stem and progenitor cells (HSPCs) holds promise for treating genetic diseases. However, responses triggered by programmable nucleases in HSPCs are poorly characterized and may negatively impact HSPC engraftment and long-term repopulation capacity. Here, we induced either one or several DNA double-stranded breaks (DSBs) with optimized zinc-finger and CRISPR/Cas9 nucleases and monitored DNA damage response (DDR) foci induction, cell-cycle progression, and transcriptional responses in HSPC subpopulations, with up to single-cell resolution. p53-mediated DDR pathway activation was the predominant response to even single-nuclease-induced DSBs across all HSPC subtypes analyzed. Excess DSB load and/or adeno-associated virus (AAV)-mediated delivery of DNA repair templates induced cumulative p53 pathway activation, constraining proliferation, yield, and engraftment of edited HSPCs. However, functional impairment was reversible when DDR burden was low and could be overcome by transient p53 inhibition. These findings provide molecular and functional evidence for feasible and seamless gene editing in HSPCs.

| S-EPMC6458988 | biostudies-literature

Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response

Project description:Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response

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Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

Project description:We describe a robust linear amplification-mediated high-throughput genome-wide translocation sequencing (HTGTS) method that identifies endogenous or ectopic "prey" DNA double-stranded breaks (DSBs) across the human genome based on their translocation to "bait" DSBs generated by engineered nucleases. HTGTS with different Cas9:gRNA or TALEN-nuclease on-target baits revealed off-target hotspots for given nucleases that ranged from few or none to dozens or more, and greatly extended known off-target numbers for certain previously characterized engineered nucleases by more than 10-fold. Beyond various types of nuclease off-target collateral damage, we also identified collateral damage in the form of translocations between bona fide nuclease targets on homologous chromosomes. Based on frequent non-specific DSBs making any given human chromosome an HTGTS hotspot region for bait DSBs within it, we found that HTGTS also reveals wide-spread, low-level DSB-generating activities of engineered nucleases. Finally, HTGTS confirmed that the Cas9D10A paired nickase approach suppresses off-targets genome-wide and suggested other strategies to enhance desired nuclease activities.

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Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [Amplicon-seq]

Project description:Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [Amplicon-seq]

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Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [Clear-seq]

Project description:Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [Clear-seq]

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Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [scRNA-seq]

Project description:Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [scRNA-seq]

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