Extensive in vitro and in vivo protein translation via in situ circularized RNAs

• Published in: bioRxiv 2022-02
• Main Authors: Kumar, Aditya, Palmer, Nathan, Miyasaki, Katelyn, Finburgh, Emma, Xiang, Yichen, Portell, Andrew, Dailamy, Amir, Suhardjo, Amanda, Wei Leong Chew, Kwon, Ester J, Mali, Prashant
• Format: Article
• Language: English
• Subjects: Genomes; Immune response (humoral); Immunogenicity; Nuclease; Protein engineering; Protein purification; Proteins; Ribonucleic acid; RNA; Severe acute respiratory syndrome coronavirus 2; Spike protein; Therapeutic applications; Translation; Zinc finger proteins
• DOI: 10.1101/2022.02.11.480072

RNAs are a powerful therapeutic class. However their inherent transience impacts their activity both as an interacting moiety as well as a template. Circularization of RNA has been demonstrated as a means to improve persistence, however simple and scalable approaches to achieve this are lacking. Utilizing autocatalytic RNA circularization, here we engineer in situ circularized RNAs (icRNAs). This approach enables icRNA delivery as simple linear RNA that is circularized upon delivery into the cell, thus making them compatible with routine synthesis, purification, and delivery formulations. We confirmed extensive protein translation from icRNAs both in vitro and in vivo and explored their utility in three contexts: first, we delivered the SARS-CoV-2 Omicron spike protein in vivo as icRNAs and showed corresponding induction of humoral immune responses; second, we demonstrated robust genome targeting via zinc finger nucleases delivered as icRNAs; and third, to enable compatibility between persistence of expression and immunogenicity, we developed a novel long range multiplexed (LORAX) protein engineering methodology to screen progressively deimmunized Cas9 proteins, and demonstrated efficient genome and epigenome targeting via their delivery as icRNAs. We anticipate this highly simple and scalable icRNA methodology could have broad utility in basic science and therapeutic applications. Competing Interest Statement Authors have filed patents based on this work. P.M. is a scientific co-founder of Shape Therapeutics, Navega Therapeutics, Diagon Therapeutics, Boundless Biosciences, and Engine Biosciences. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. The remaining authors declare no competing interests.