Structure Variations and 3D Genome Disruption: Implications in Safety of hPSC-Based Cell Therapy

Human pluripotent stem cells (hPSCs) are a promising source for regenerative medicine due to their self-renewal and differentiation capacities. However, genetic instability acquired during reprogramming and in vitro culture presents major safety challenges for clinical translation. Recurrent mutations, especially structural variants (SVs), are of particular concern as they can impair differentiation and increase tumorigenic risk. In this review, we establish and systematically explore a central causal axis: SVs-three dimensional (3D) genome disruption-safety of hPSC-based therapy. We propose that SVs critically compromise therapeutic safety by perturbing the 3D architecture of the genome, leading to pathogenic rewiring of enhancer-promoter interactions. This rewiring, exemplified by "enhancer hijacking" and "enhancer loss," can aberrantly activate oncogenes or silence tumor suppressors even in the absence of copy number variations. Thus, 3D genome disruption provides a key mechanistic explanation for SV-driven tumorigenic potential and impaired differentiation fidelity in hPSCs. By highlighting this causal axis, our review not only advances the mechanistic understanding of SV-associated risks but also provides actionable insights for the development of more rigorous quality standards for hPSC-based cell therapy products.