Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

• Published in: Nature communications Vol. 13; no. 1; p. 1536
• Main Authors: Leppek, Kathrin, Byeon, Gun Woo, Kladwang, Wipapat, Wayment-Steele, Hannah K., Kerr, Craig H., Xu, Adele F., Kim, Do Soon, Topkar, Ved V., Choe, Christian, Rothschild, Daphna, Tiu, Gerald C., Wellington-Oguri, Roger, Fujii, Kotaro, Sharma, Eesha, Watkins, Andrew M., Nicol, John J., Romano, Jonathan, Tunguz, Bojan, Diaz, Fernando, Cai, Hui, Guo, Pengbo, Wu, Jiewei, Meng, Fanyu, Shi, Shuai, Participants, Eterna, Dormitzer, Philip R., Solórzano, Alicia, Barna, Maria, Das, Rhiju
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22-03-2022; Nature Publishing Group; Nature Portfolio
• Subjects: 119/118; 13/109; 38/109; 38/43; 38/47; 38/77; 38/88; 38/90; 38/91; 49/22; 49/23; 631/337/1645/2020; 631/337/1645/501; 631/337/574; 631/45/500; 692/4017; Combinatorial analysis; Computer applications; COVID-19; COVID-19 - therapy; Gene expression; Gene sequencing; Humanities and Social Sciences; Humans; Libraries; mRNA stability; multidisciplinary; Optimization; Principles; Protein expression; Proteins; Pseudouridine - metabolism; RNA; RNA Stability - genetics; RNA, Messenger - metabolism; Science; Science (multidisciplinary); Structural stability; Vaccines
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-28776-w

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 an 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 highly structured “superfolder” mRNAs can be designed to improve both stability and expression with further enhancement 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.
The authors develop an RNA sequencing-based platform, PERSIST-seq, to simultaneously delineate in-cell mRNA stability, ribosome load, and in-solution stability of a diverse mRNA library to derive design principles for improved mRNA therapeutics.