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Off-target analysis of intein, AAVLINK, and StitchR delivery ABE8e systems in HEK293T cells

ABSTRACT: In this study, off-target analysis of intein, AAVLINK, and StitchR based ABE8e systems by flow sorting and deep sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE348336 | GEO | 2026/09/30

REPOSITORIES: GEO

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Comparative evaluation of intein, AAVLINK, and StichR ABE8e systems targeting DMD-E50 in HEK293T cells

Project description:In this study, comparative evaluation of editing efficiencies of non-targeting, full-length, intein, AAVLINK, StichR ABE8e systems targeting DMD-E50 in HEK293T cells by flow sorting and amplicon sequencing.

2026-09-30 | GSE348335 | GEO

Comparative evaluation of intein, AAVLINK, StichR, and coiled-coil ABE8e systems targeting endogenous genomic loci and at 2 engineered KCNQ2 target sites carrying different mutations.

Project description:In this study, comparative evaluation of editing efficiencies of non-targeting, full-length, intein, AAVLINK, StichR, and coiled-coil ABE8e systems targeting endogenous genomic loci and at ABE target sites carrying different mutations by flow sorting and deep sequencing.

2026-09-30 | GSE348338 | GEO

Comparison of editing efficiencies of intein, AAVLINK, and StitchR delivery ABE8e systems at the mouse TA

Project description:In this study, intein, AAVLINK, and StitchR delivery ABE8e systems were packaged into viral vectors (AAV) and intramuscular injected into mice. Genomic DNA was extracted from the mouse tibialis anterior (TA) muscle, followed by deep sequencing to analyze the editing efficiency.

2026-09-30 | GSE348337 | GEO

Homo sapiens strain:HEK293T

Project description:ABE8e

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ABE8e adenine base editor precisely and efficiently corrects a COL7A1 nonsense mutation

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

ABE8e adenine base editor precisely and efficiently corrects a COL7A1 nonsense mutation

Project description:ABE8e adenine base editor precisely and efficiently corrects a COL7A1 nonsense mutation

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Project description:Off-target analysis of ABE8e by deep sequencing

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Project description:ABE8e

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Nanoengineering facilitating the target mission: targeted extracellular vesicles delivery systems design.

Project description: Not available

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

Project description:To assess CHANGE-seq-BE performance, we used it to characterize ABE8e-NRCH base editor activity targeting sickle mutation (HBBS) in the HBB gene and identified additional 29 (53% more) bona fide off-targets than CIRCLE-seq. Furthermore, CHANGE-seq-BE applied for ABE8e targeting five therapeutically relevant loci (B2M, CBLB, CD7, CIITA, and PDCD1) in human primary T-cells and compared with Digenome-seq. CHANGE-seq-BE is highly sensitive and capable of detecting bona fide off-targets while requiring approximately 20-fold less sequencing reads.

2025-11-05 | GSE307740 | GEO

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