Human Genome REWRITE for Off-the-Shelf Stem Cells Reveals an "Epigenetic Ghost".

bioRxiv : the preprint server for biology Pub Date : 2025-10-02 DOI:10.1101/2025.09.16.676382

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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Abstract

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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免疫界面的基因组重写揭示了人类干细胞中可遗传的表观遗传记忆。

人类白细胞抗原（HLA）多态性阻碍同种异体治疗。我们开发了REWRITE，这是一个模块化平台，用于在人类多能干细胞（hPSCs）中迭代，最小化疤痕的合成构建体基因组编写。通过重写，我们删除了105-209 kb的HLA位点，并在原生和异位位点安装了24 kb或100 kb的合成HLA单倍型，以及62 kb的抗原处理位点。这揭示了活性状态的可遗传表观遗传记忆，其向沉默状态的解决是由原生基因间DNA驱动的。这些基因座恢复了关键谱系的诱导表达，使细胞免于nk介导的杀伤，并建立了hla匹配的t细胞耐受性。REWRITE为编程人类细胞中的多基因行为提供了一个可扩展的平台——从免疫界面设计到人类基因组结构原理的发现。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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bioRxiv : the preprint server for biology

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