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Leppek K, Byeon GW, Kladwang W, Wayment-Steele HK, Kerr CH, Xu AF, Kim DS, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Participants E, Barna M, Das R. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. bioRxiv 2021:2021.03.29.437587. [PMID: 33821271 PMCID: PMC8020971 DOI: 10.1101/2021.03.29.437587] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein expression. Here, we describe design principles that overcome these barriers. We develop a new RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. We find that, surprisingly, in-cell stability is a greater driver of protein output than high ribosome load. We further introduce a method called In-line-seq, applied to thousands of diverse RNAs, that reveals sequence and structure-based rules for mitigating hydrolytic degradation. Our findings show that "superfolder" mRNAs can be designed to improve both stability and expression that are further enhanced through pseudouridine nucleoside modification. Together, our study demonstrates simultaneous improvement of mRNA stability and protein expression and provides a computational-experimental platform for the enhancement of mRNA medicines.
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Affiliation(s)
- Kathrin Leppek
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Adele F Xu
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Do Soon Kim
- Department of Biochemistry, Stanford University, California 94305, USA
| | - Ved V Topkar
- Program in Biophysics, Stanford University, Stanford, California 94305, USA
| | - Christian Choe
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Daphna Rothschild
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Gerald C Tiu
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | | | - Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Eesha Sharma
- Department of Biochemistry, Stanford University, California 94305, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Jonathan Romano
- Eterna Massive Open Laboratory
- Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, New York, 14260, USA
| | - Bojan Tunguz
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Maria Barna
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, California 94305, USA
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