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CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE298535 | GEO | 2025/10/20

REPOSITORIES: GEO

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CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity IV

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 | GSE307892 | GEO

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity V

2025-11-05 | GSE308237 | GEO

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity II

Project description:To adapt and apply for cytosone base editors (CBEs), we perfomed CHANGE-seq-BE using eA3A-BE3 to target B2M, CBLB, CD7, CIITA and PDCD1 regions at different loci. CHANGE-seq-BE identified low frequency off-target editing rates ranging from 1.7% to 7.5% that are not identified by Digenome-seq further implies CHANGE-seq-BE is highly sensitive and can identify true off-targets while requiring 20-fold fewer sequencing reads.

2025-11-05 | GSE298534 | GEO

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity I

Project description:By CHANGE-seq-BE, we identified a total of 81 potential off-targets and confirmed 95.4% frequencies of on-target editing with no evident off-targets above the detection threshold compared to controls (rhAmp-seq, IDT).

2025-11-05 | GSE298465 | GEO

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity III

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

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity

Project description:CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity

| PRJNA1269627 | ENA

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity I

Project description:CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity I

| PRJNA1269500 | ENA

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity II

Project description:CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity II

| PRJNA1269623 | ENA

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity V

Project description:CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity V

| PRJNA1329275 | ENA

Cytosine base editor 4 but not adenine base editor generates off-target mutations in mouse embryos.

Project description:Deaminase base editing has emerged as a tool to install or correct point mutations in the genomes of living cells in a wide range of organisms. However, the genome-wide off-target effects introduced by base editors in the mammalian genome have been examined in only one study. Here, we have investigated the fidelity of cytosine base editor 4 (BE4) and adenine base editors (ABE) in mouse embryos using unbiased whole-genome sequencing of a family-based trio cohort. The same sgRNA was used for BE4 and ABE. We demonstrate that BE4-edited mice carry an excess of single-nucleotide variants and deletions compared to ABE-edited mice and controls. Therefore, an optimization of cytosine base editors is required to improve its fidelity. While the remarkable fidelity of ABE has implications for a wide range of applications, the occurrence of rare aberrant C-to-T conversions at specific target sites needs to be addressed.

| S-EPMC6952419 | biostudies-literature

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