{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE329nnn/GSE329615/"]},"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=GSE329615"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Base editors provoke non-predictable chromosomal translocations and off-target editing (rhAmp part2)","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":"GSE329615","cross_references":{"GSM":["GSM9707651","GSM9707640","GSM9707652","GSM9707641","GSM9707642","GSM9707653","GSM9707654","GSM9707643","GSM9707650","GSM9707648","GSM9707649","GSM9707644","GSM9707645","GSM9707646","GSM9707647"],"GPL":["24676"],"GSE":["329615"],"taxon":["Homo sapiens"]}}