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SNP array for ABE- and Cas9-treated human zygotes as well as ABE treated embryos at fertilization

ABSTRACT: Donated human MII oocytes and zygotes were injected with ABE mRNA or RNP, or Cas9 RNP targeting indicated genes. The purpose of the experiment is to study DNA repair after base editing in preimplantation human embryos. Key findings are a lack of chromosomal aneuploidies in base editing samples, contrasting with the outcomes after Cas9 cleavage at the same sites. Off target base editing is highly gRNA dependent. Base editing is efficient, and lacks the genotoxicity of Cas9.

ORGANISM(S): Homo sapiens

PROVIDER: GSE290961 | GEO | 2026/06/19

REPOSITORIES: GEO

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SNP array for ABE- and Cas9-treated human zygotes

Project description:Donated human MII oocytes and zygotes were injected with ABE mRNA or RNP, or Cas9 RNP targeting indicated genes. The purpose of the experiment is to study DNA repair after base editing in preimplantation human embryos.

2026-09-18 | GSE315671 | GEO

SNP array for Cas9 treated human zygotes

Project description:Donated 2PN human zygotes were injected with a Cas9 RNP targeting pericentromeric and mid-arm sites on chromosomes 16 and X. The purpose of this experiments was to determine if CRISPR induced genetic changes (e.g. indels or chromosomal changes) differ based on the targeted chromosome and position in the chromosome (pericentromeric vs chromosome mid-arm targets). We found whole and segmental chromosome loss in over one third of chromosomes targeted by CRISPR/Cas9. Chromosome loss was seen after targeting different chromosomes, and different positions in the chromosome. These results highlight additional limitations of CRISPR/Cas9 genome editing, as well as potential mechanisms of origin of aneuploidies in the human embryo.

2026-05-14 | GSE186407 | GEO

SNP array for ABE- and Cas9-treated human zygotes

Project description:SNP array for ABE- and Cas9-treated human zygotes

| PRJNA1398654 | ENA

SNP array for ABE- and Cas9-treated human zygotes as well as ABE treated embryos at fertilization

Project description:SNP array for ABE- and Cas9-treated human zygotes as well as ABE treated embryos at fertilization

| PRJNA1231089 | ENA

CRISPR adenine and cytosine base editors with reduced RNA off-target activities [ABE]

Project description:CRISPR-guided DNA base editors enable the efficient installation of targeted single-nucleotide changes. Cytosine or adenine base editors (CBEs or ABEs), which are fusions of cytidine or adenosine deaminases to CRISPR-Cas nickases, can efficiently induce DNA C-to-T or A-to-G alterations in DNA, respectively. We recently demonstrated that both the widely used CBE BE3 (harboring a rat APOBEC1 cytidine deaminase) and the optimized ABEmax editor can induce tens of thousands of guide RNA-independent, transcriptome-wide RNA base edits in human cells with high efficiencies. In addition, we showed the feasibility of creating SElective Curbing of Unwanted RNA Editing (SECURE)-BE3 variants that exhibit substantially reduced unwanted RNA editing activities while retaining robust and more precise on-target DNA editing. Here we describe structure-guided engineering of SECURE-ABE variants that not only possess reduced off-target RNA editing with comparable on-target DNA activities but are also the smallest Streptococcus pyogenes Cas9 (SpCas9) base editors described to date. In addition, we tested CBEs composed of cytidine deaminases other than APOBEC1 and found that human APOBEC3A (hA3A) cytidine deaminase CBE induces substantial transcriptome-wide RNA base edits with high efficiencies. By contrast, a previously described “enhanced” A3A (eA3A) cytidine deaminase CBE or a human activation-induced cytidine deaminase (hAID) CBE induce substantially reduced or near background levels of RNA edits. In sum, our work describes broadly useful SECURE-ABE and -CBE base editors and reinforces the importance of minimizing RNA editing activities of DNA base editors for research and therapeutic applications.

2019-07-11 | GSE129889 | GEO

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for CBE and ABE]

Project description:To assess genome-wide off-target activity of base editors and Cas9 nucleases identified by CHANGE-seq-BE, Digenome-seq, and CHANGE-seq, we performed hybrid capture sequencing for five therupatic loci (B2M, CBLB, CD7, CIITA, PDCD1) in human primary T-cells and PCSK9 in human hepatocytes. We observed high on-target editing for ABE, CBE, Cas9 mRNA edited cells and potential off-targets confirmed by hybrid capture sequencing. Our results demonstrate that CHANGE-seq-BE is highly sensitive than Digenome-seq to detect more bona fide off-targets with cellular activity ranging from 0.5% to 92.2%. Moreover, ABE exhibit more off-targets than Cas9 under same delivery conditions.

2025-11-05 | GSE308237 | GEO

Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [RNA-seq]

Project description:Genome editing technologies have enabled the clinical development of allogeneic cellular therapies, yet the optimal gene editing modality for multiplex editing of therapeutic T cell product manufacturing remains elusive. In this study, we conducted a comprehensive comparison of CRISPR/Cas9 nuclease and adenine base editor (ABE) technologies in generating allogeneic chimeric antigen receptor (CAR) T cells, utilizing extensive in vitro and in vivo analyses. Both methods achieved high editing efficiencies across four target genes, critical for mitigating graft-versus-host disease and allograft rejection: TRAC or CD3E, B2M, CIITA, and PVR. Notably, ABE demonstrated higher manufacturing yields and distinct off-target profiles compared to Cas9, with translocations observed exclusively in Cas9-edited products. Functionally, ABE-edited CAR T cells exhibited superior in vitro effector functions under continuous antigen stimulation, including enhanced proliferative capacity and increased surface CAR expression. Transcriptomic analysis revealed that ABE editing resulted in reduced activation of p53 and DNA damage response pathways at baseline, along with sustained activation of metabolic pathways during antigen stress. Consistently, ATAC-seq data indicated that Cas9-edited, but not ABE-edited, CAR T cells showed enrichment of chromatin accessibility peaks associated with double-strand break repair and DNA damage response pathways. In a preclinical leukemia model, ABE-edited CAR T cells demonstrated improved tumor control and extended overall survival compared to their Cas9-edited counterparts. Collectively, these findings position ABE as a superior choice of Cas9 nucleases for multiplex gene editing in therapeutic T cells.

2025-04-09 | GSE290621 | GEO

Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [ATAC-seq]

2025-04-09 | GSE290620 | GEO

Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells

Project description:Background The safety of CRISPR-based gene editing methods is of the utmost priority in clinical applications. Previous studies have reported that Cas9 cleavage induced frequent aneuploidy in primary human T cells, but whether cleavage-mediated editing of base editors would generate off-target structure variations remains unknown. Here, we investigated the potential off-target structural variations associated with CRISPR/Cas9, ABE and CBE editing in mouse embryos and primary human T cells by whole-genome sequencing and single-cell RNA-seq analyses. Results The results showed that both Cas9 and ABE generated off-target structural variations (SVs) in mouse embryos, while CBE induced rare SVs. In addition, off-target large deletions were detected in 32.74% of primary human T cells transfected with Cas9 and 9.17% of cells transfected with ABE. Moreover, Cas9-induced aneuploid cells activated the P53 and apoptosis pathways, whereas ABE-associated aneuploid cells significantly upregulated cell cycle-related genes and arrested in G0 phase. A percentage of 16.59% and 4.29% aneuploid cells were still observable at 3 weeks post transfection of Cas9 or ABE. These off-target phenomena in ABE were universal as observed in other cell types such as B cells and Huh7. Furthermore, the off-target SVs were significantly reduced in cells treated with high-fidelity ABE (ABE-V106W). Conclusions This study raises urgent need for minimizing the off-target SVs of CRISPR/Cas9 and ABE.

2024-11-01 | GSE280767 | GEO

A-T to G-C base editing efficiency at targeted gene sites in HEK293T cell line

Project description:A-T to G-C base editing efficiency at targeted gene sites in HEK293T cells using the dCas12f-ABE design or the Cas12f-ABE design. Found that the total A-T to G-C conversion efficiency of Circular gRNAs exhibited about two-fold increase compared with U6 gRNAs. We further analyzed the pattern for A-T to G-C conversion on the target site, and observed that the most efficient base editing occurred in a narrow window A3 (3bp downstream of the PAM) similar to U6 gRNAs. In summary, Circular gRNAs with dCas12f-ABE design could enhance A-T to G-C base editing efficiency in a narrow window.

2024-03-11 | GSE260967 | GEO

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