{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE255nnn/GSE255315/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Homo sapiens"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE255315"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Base editors provoke non-predictable chromosomal translocations and off-target editing - rhAmp","description":"Base editing has emerged as a promising alternative to CRISPR-Cas nuclease-based genome editing, in part because of its promise of reduced genotoxicity. Here, we performed a comprehensive genome-wide analysis of base editing-induced off-target effects. Primary human T cells were edited at three genomic loci (CCR5, EMX1, FANCF) using either CRISPR-Cas9 nuclease, an adenine base editor (ABE8e), one of three cytosine base editors (CBEs), or Cas9 nickase. We used CAST-Seq to identify gross chromosomal aberrations and off-target sites (OTs), followed by rhAmp-Seq to evaluate on-target activity (44-84% modified alleles) and mutagenic effects at >100 putative OTs. On-target CAST-Seq reads showed large (>200 bp) aberrations ranging from 45% for Cas9 to 5% for ABE, 2-7% for CBEs, and 0% for nickase-edited cells. While ABE8e editing induced few translocations, more than 10% of the alleles were modified in 17 of the 40 identified OTs. In contrast, chromosomal translocation events in some CBE-treated cells exceeded that found in Cas9-edited T cells by 3-fold. Furthermore, extensive C-to-T conversion (≤99% of alleles) and mutagenesis (≤7% of alleles) were detected in T cells edited with a hyperactive CBE, whereas recently developed CBE variants (TadCBEd or CBE-T1.52) showed only marginal OT activity. In conclusion, our study revealed the genotoxic potential of ABE8e and the hyperactive evoCDA1-BE4max. These base editors induced mutagenic OT editing at sites that were not altered by CRISPR-Cas9 nucleases complexed with the same gRNA, suggesting that the mechanism of gRNA-dependent OT activity of base editors is different from that of CRISPR-Cas nucleases.","dates":{"publication":"2026/09/28"},"accession":"GSE255315","cross_references":{"GSM":["GSM8862233","GSM8862232","GSM8862235","GSM8862234","GSM8862237","GSM8862236","GSM8862239","GSM8862238","GSM8862244","GSM8862243","GSM8862246","GSM8862245","GSM8862240","GSM8069002","GSM8068990","GSM8069003","GSM8068992","GSM8069000","GSM8862242","GSM8068991","GSM8862241","GSM8069001","GSM8069006","GSM8068994","GSM8068993","GSM8068996","GSM8069004","GSM8068995","GSM8069005","GSM8862248","GSM8068998","GSM8068997","GSM8862247","GSM8862249","GSM8068999","GSM8068979","GSM8862255","GSM8862254","GSM8862257","GSM8862256","GSM8862251","GSM8862250","GSM8862253","GSM8068981","GSM8068980","GSM8862252","GSM8068983","GSM8068982","GSM8068985","GSM8068984","GSM8068987","GSM8068986","GSM8068989","GSM8068988","GSM8068974","GSM8068976","GSM8068975","GSM8068978","GSM8068977"],"GPL":["24676"],"GSE":["255315"],"taxon":["Homo sapiens"]}}