Human Genome Safe Harbor Sites: A Comprehensive Review of Criteria, Discovery, Features, and Applications

Abstract

The stable and safe integration of exogenous DNA into the genome is crucial to both genetic engineering and gene therapy. Traditional transgenesis approaches, such as those using retroviral vectors, result in random genomic integration, posing the risk of insertional mutagenesis and transcriptional dysregulation. Safe harbor sites (SHSs), genomic loci that support reliable transgene expression without compromising endogenous gene function, genomic integrity, or cellular physiology, have been identified and characterized across various model organisms. Well-established SHSs such as AAVS1, ROSA26, and CLYBL are routinely utilized for targeted transgene integration in human cells. Recent advances in genome architecture, gene regulation, and genome editing technologies are driving the discovery of novel SHSs for precise and safe genetic modification. This review aims to provide a comprehensive overview of SHSs and their applications that will guide investigators in the choice of SHS, especially when complementary sites are needed for more than one transgene integration. First, it outlines safety and functional criteria that qualify a genomic site as a safe harbor site. It then discusses the two primary strategies for identifying SHSs: i) traditional lentiviral-based random transgenesis, and ii) modern genome-wide in silico screening followed by CRISPR-based validation. This review also provides an updated catalogue of currently known SHSs in the human genome, detailing their characteristics, uses, and limitations. Additionally, it discusses the diverse applications of SHSs in basic research, gene therapy, CAR T cell-based therapy, and biotechnological production systems. Finally, it concludes by highlighting challenges in identifying universally applicable SHSs and outlines future directions for their refinement and validation across biological systems.