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


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
22 03 2022
Historique:
received: 08 04 2021
accepted: 07 02 2022
entrez: 23 3 2022
pubmed: 24 3 2022
medline: 5 4 2022
Statut: epublish

Résumé

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.

Identifiants

pubmed: 35318324
doi: 10.1038/s41467-022-28776-w
pii: 10.1038/s41467-022-28776-w
pmc: PMC8940940
doi:

Substances chimiques

RNA, Messenger 0
Pseudouridine 1445-07-4
RNA 63231-63-0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

1536

Subventions

Organisme : NICHD NIH HHS
ID : F30 HD100123
Pays : United States
Organisme : NICHD NIH HHS
ID : R01 HD086634
Pays : United States
Organisme : NCI NIH HHS
ID : R21 CA219847
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM122579
Pays : United States

Commentaires et corrections

Type : UpdateOf

Informations de copyright

© 2022. The Author(s).

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Auteurs

Kathrin Leppek (K)

Department of Genetics, Stanford University, Stanford, CA, 94305, USA.

Gun Woo Byeon (GW)

Department of Genetics, Stanford University, Stanford, CA, 94305, USA.

Wipapat Kladwang (W)

Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.

Hannah K Wayment-Steele (HK)

Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.

Craig H Kerr (CH)

Department of Genetics, Stanford University, Stanford, CA, 94305, USA.

Adele F Xu (AF)

Department of Genetics, Stanford University, Stanford, CA, 94305, USA.

Do Soon Kim (DS)

Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.

Ved V Topkar (VV)

Program in Biophysics, Stanford University, Stanford, CA, 94305, USA.

Christian Choe (C)

Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.

Daphna Rothschild (D)

Department of Genetics, Stanford University, Stanford, CA, 94305, USA.

Gerald C Tiu (GC)

Department of Genetics, Stanford University, Stanford, CA, 94305, USA.

Roger Wellington-Oguri (R)

Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA.

Kotaro Fujii (K)

Department of Genetics, Stanford University, Stanford, CA, 94305, USA.

Eesha Sharma (E)

Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.

Andrew M Watkins (AM)

Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.

John J Nicol (JJ)

Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA.

Jonathan Romano (J)

Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA.
Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, New York, 14260, USA.

Bojan Tunguz (B)

Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
NVIDIA Corporation, 2788 San Tomas Expy, Santa Clara, CA, 95051, USA.

Fernando Diaz (F)

Pfizer Vaccine Research and Development, Pearl River, NY, USA.

Hui Cai (H)

Pfizer Vaccine Research and Development, Pearl River, NY, USA.

Pengbo Guo (P)

Pfizer Vaccine Research and Development, Pearl River, NY, USA.

Jiewei Wu (J)

Pfizer Vaccine Research and Development, Pearl River, NY, USA.

Fanyu Meng (F)

Pfizer Vaccine Research and Development, Pearl River, NY, USA.

Shuai Shi (S)

Pfizer Vaccine Research and Development, Pearl River, NY, USA.

Eterna Participants (E)

Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA.

Philip R Dormitzer (PR)

Pfizer Vaccine Research and Development, Pearl River, NY, USA.
GlaxoSmithKline, 1000 Winter St., Waltham, MA, 02453, USA.

Alicia Solórzano (A)

Pfizer Vaccine Research and Development, Pearl River, NY, USA.

Maria Barna (M)

Department of Genetics, Stanford University, Stanford, CA, 94305, USA. mbarna@stanford.edu.

Rhiju Das (R)

Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA. rhiju@stanford.edu.
Program in Biophysics, Stanford University, Stanford, CA, 94305, USA. rhiju@stanford.edu.
Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA. rhiju@stanford.edu.

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