Orthogonal and multiplexable genetic perturbations with an engineered prime editor and a diverse RNA array

Qichen Yuan, Hongzhi Zeng, Tyler C. Daniel, Qingzhuo Liu, Yongjie Yang, Emmanuel C. Osikpa, Qiaochu Yang, Advaith Peddi, Liliana M. Abramson, Boyang Zhang, Yong Xu and Xue Gao ()
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Qichen Yuan: Rice University
Hongzhi Zeng: Rice University
Tyler C. Daniel: Rice University
Qingzhuo Liu: Baylor College of Medicine
Yongjie Yang: Baylor College of Medicine
Emmanuel C. Osikpa: Rice University
Qiaochu Yang: Rice University
Advaith Peddi: Rice University
Liliana M. Abramson: Rice University
Boyang Zhang: Rice University
Yong Xu: Baylor College of Medicine
Xue Gao: Rice University

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Programmable and modular systems capable of orthogonal genomic and transcriptomic perturbations are crucial for biological research and treating human genetic diseases. Here, we present the minimal versatile genetic perturbation technology (mvGPT), a flexible toolkit designed for simultaneous and orthogonal gene editing, activation, and repression in human cells. The mvGPT combines an engineered compact prime editor (PE), a fusion activator MS2–p65–HSF1 (MPH), and a drive-and-process multiplex array that produces RNAs tailored to different types of genetic perturbation. mvGPT can precisely edit human genome via PE coupled with a prime editing guide RNA and a nicking guide RNA, activate endogenous gene expression using PE with a truncated single guide RNA containing MPH-recruiting MS2 aptamers, and silence endogenous gene expression via RNA interference with a short-hairpin RNA. We showcase the versatility of mvGPT by simultaneously correcting a c.3207C>A mutation in the ATP7B gene linked to Wilson’s disease, upregulating the PDX1 gene expression to potentially treat Type I diabetes, and suppressing the TTR gene to manage transthyretin amyloidosis. In addition to plasmid delivery, we successfully utilize various methods to deliver the mvGPT payload, demonstrating its potential for future in vivo applications.

Date: 2024
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DOI: 10.1038/s41467-024-55134-9

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