Serena F Generoso, Sarah Levovitz, Susanna Jaramillo, Minjoo Kim, Sumanth Dara, Shean Fu Phen, Bryan Yi, Tomoki Yanagi, Thomas L DesMarais, Neta Agmon, Megan S Hogan, Leslie A Mitchell, David M Truong
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Human Genome REWRITE for Off-the-Shelf Stem Cells Reveals an "Epigenetic Ghost".
Human leukocyte antigen (HLA) polymorphism hinders off-the-shelf cell therapies. We developed REWRITE, a modular platform for iterative, scar-minimized genome writing of synthetic constructs >100 kb in human pluripotent stem cells (hPSCs). Using REWRITE, we deleted 105-209 kb of the HLA locus and installed synthetic 24 kb or 100 kb HLA haplotypes, and a 62 kb antigen-processing locus. This uncovered a persistent, heritable "epigenetic ghost" - an active state lingering despite genetic removal - whose resolution to a silenced default state is driven by native intergenic DNA. These loci restored inducible expression in key lineages, sparing cells from NK-mediated killing and establishing HLA-matched T-cell tolerance, enabling off-the-shelf cell therapies. REWRITE facilitates extensible programming of multigenic functions in allogeneic human cells - from immune design to genome architecture discovery.
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