REWRITE Enables Locus-Scale Engineering of Synthetic HLA Haplotypes in Human Pluripotent Stem Cells

Abstract

Human leukocyte antigen (HLA) polymorphism underlies antigen presentation, immune recognition, and central tolerance, yet the complex, multigenic structure of native HLA loci has precluded systematic engineering in human pluripotent stem cells (hPSCs). Existing genome engineering demonstrations in hPSCs focus on smaller integrations or at ectopic sites, leaving scar-minimized rewriting of native human loci at >100 kb scale a major technical challenge. Here, we present REWRITE, a modular platform for scar-minimized genome writing that enables engineering of large human genomic loci exceeding 100 kb at their native chromosomal sites. Using REWRITE, we deleted 105 kb spanning the dispersed HLA class-I locus and installed either compact or full-length refactored synthetic HLA haplotypes. Both refactored architectures exhibited transient activity before re-acquiring the native inactive state; upon extended culture, engineered lines yielded global transcriptomes nearly indistinguishable from parental cells. The engineered loci were genomically stable, retained interferon-responsive HLA expression, and remained compatible with differentiation into endothelial-like and thymic epithelial-like cells. Together, these results establish REWRITE as a platform for locus-scale genome engineering in hPSCs and provides a system for studying HLA haplotype structure and function in an isogenic pluripotent cell background. One sentenceA practical platform for scar-minimized rewriting of native human loci exceeding 100 kb in hPSCs, demonstrated through synthetic refactoring of the class-I HLA region.