Interplays between gene therapy vector and host cell genome [ATAC-Seq]

Lentiviral vectors are commonly used to deliver ectopic genetic material into host cells, but our knowledge of how integrated DNA sequences—such as cis-regulatory elements (CREs)—interact with the host genome remains limited. In this study, we analyzed chromatin accessibility, three-dimensional chromatin organization, and transcriptome profiles at 254 precisely mapped integration sites of a clinically used lentiviral vector. We found that the expression of integrated transgenes is influenced by the chromatin environment of the host cell. Moreover, integrated lentiviral vectors can form chromatin loops with the host genome, increase chromatin accessibility in adjacent regions, and alter splicing patterns of host gene transcripts. Notably, adding insulator elements reduced fluctuations in transgene expression levels and minimized changes in chromatin accessibility near integration sites. While insulator elements decreased local chromatin interactions, they did not affect the structure of topologically associating domains (TADs) or global chromatin organization. By assessing various genomic factors influencing the risk of integrated lentiviral vectors, we found that insulators consistently reduced genotoxicity.