IP Library Granted Patent US 12,241,063
Granted Patent B2
US 12,241,063 · App. 17/933,500 · Granted Mar 4, 2025

Modified messenger RNA comprising functional RNA elements

Inventors: Melissa J. Moore (Cambridge, MA); Caroline Köhrer (Cambridge, MA); Ruchi Jain (Cambridge, MA); Vladimir Presnyak (Cambridge, MA)
Assignee: ModernaTX, Inc.
C12N15/11A61K47/6929C12N15/85C12N15/88C12N2310/321C12N2310/322C12N2310/335
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,241,063
App. No.
17/933,500
Granted
Mar 4, 2025
Kind
B2
Abstract

The present disclosure provides messenger RNAs (mRNAs) having chemical and/or structural modifications, including RNA elements and/or modified nucleotides, which provide a desired translational regulatory activity to the mRNA.

Claims (34)

1. A method of expressing a messenger RNA (mRNA) in a cell, comprising contacting the cell with the mRNA, wherein the mRNA comprises

(i) a 5′ untranslated region (UTR) comprising an RNA element as set forth in SEQ ID NO: 2; and

(ii) an open reading frame comprising an initiation codon and encoding a polypeptide;

wherein the RNA element has a 3′end located 10-20 nucleotides or 6-10 nucleotides upstream of the initiation codon in the 5′UTR, and

wherein the mRNA comprises one or more chemically modified nucleotides,

thereby expressing the mRNA in the cell.

2. The method of claim 1 , wherein the RNA element has a 3′ end located 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides upstream of the initiation codon.

3. The method of claim 1 , wherein the mRNA comprises a 5′ cap, a 3′ UTR, and a poly A tail.

4. The method of claim 1 , wherein the mRNA comprises one or more pseudouridines or pseudouridine analogs.

5. The method of claim 1 , wherein the mRNA is fully modified with N1-methylpseudouridine.

6. The method of claim 1 , wherein the mRNA is formulated in a lipid nanoparticle.

7. A method of expressing a mRNA in a cell, comprising contacting the cell with the mRNA, wherein the mRNA comprises

(i) a 5′UTR comprising an RNA element inserted into the nucleotide sequence set forth in SEQ ID NO: 33, and

(ii) an open reading frame comprising an initiation codon and encoding a polypeptide;

wherein the RNA element is CCCCGGCGCC (SEQ ID NO: 2),

wherein the RNA element has a 3′end located 10-20 nucleotides or 6-10 nucleotides upstream of the initiation codon in the 5′UTR, and

wherein the mRNA comprises one or more chemically modified nucleotides,

thereby expressing the mRNA in the cell.

8. The method of claim 7 , wherein the RNA element has a 3′end located 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides upstream of the initiation codon.

9. The mRNA of claim 7 , wherein the mRNA comprises a 5′ cap, a 3′ UTR, and a poly A tail.

10. The mRNA of claim 7 , wherein the mRNA comprises one or more pseudouridines or pseudouridine analogs.

11. The mRNA of claim 7 , wherein the mRNA is fully modified with N1-methylpseudouridine.

12. The method of claim 7 , wherein the mRNA is formulated in a lipid nanoparticle.

13. A method of expressing a mRNA in a cell, comprising contacting the cell with the mRNA, wherein the mRNA comprises

(i) a 5′UTR comprising a nucleotide sequence as set forth in SEQ ID NO: 34;

(ii) an open reading frame comprising an initiation codon and encoding a polypeptide; and

wherein the mRNA comprises one or more chemically modified nucleotides,

thereby expressing the mRNA in the cell.

14. The method of claim 13 , wherein the mRNA comprises a 5′ cap, a 3′ UTR, and a poly A tail.

15. The method of claim 13 , wherein the mRNA comprises one or more pseudouridines or pseudouridine analogs.

16. The method of claim 13 , wherein the mRNA is fully modified with N1-methylpseudouridine.

17. The method of claim 13 , wherein the mRNA is formulated in a lipid nanoparticle.

18. The method of claim 2 , wherein the RNA element has a 3 ′ end located 7 nucleotides upstream of the initiation codon.

19. The method of claim 8 , wherein the RNA element has a 3 ′ end located 7 nucleotides upstream of the initiation codon.

Assignments (2)
SECURITY INTEREST Recorded Nov 19, 2025
From: MODERNATX, INC.
To: ARES CAPITAL CORPORATION, AS AGENT
Reel/Frame 073634/0354 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 21, 2022
From: MOORE, MELISSA J.; KÖHRER, CAROLINE; JAIN, RUCHI; PRESNYAK, VLADIMIR
To: MODERNATX, INC.
Reel/Frame 061839/0252 →
Continuity (5)
Continuation 16614245
Provisional Application 62667824 · May 7, 2018
Provisional Application 62519800 · Jun 14, 2017
Provisional Application 62508318 · May 18, 2017
Related Publication 20230257738A1 · Aug 17, 2023
References Cited (65)
US 7842467B1 · Heidbrink et al. · 2010 [cited by applicant]
US 11485972B2 · Moore et al. · 2022 [cited by applicant]
US 20120283317A1 · Teitell et al. · 2012 [cited by applicant]
US 20160237134A1 · Hoge et al. · 2016 [cited by applicant]
US 20200208145A1 · Moore et al. · 2020 [cited by applicant]
US 20210163928A1 · Reid et al. · 2021 [cited by applicant]
US 20220251577A1 · Bicknell et al. · 2022 [cited by applicant]
US 20220387628A1 · Jain et al. · 2022 [cited by applicant]
WO WO2007044894A2 · 2007 [cited by examiner]
WO WO2014111858A1 · 2014 [cited by applicant]
WO WO2017049275A2 · 2017 [cited by applicant]
WO WO2018081459A1 · 2018 [cited by applicant]
WO WO2018213789A1 · 2018 [cited by applicant]
WO WO2019104160A2 · 2019 [cited by applicant]
WO WO2019200171A1 · 2019 [cited by applicant]
WO WO2020263883A1 · 2020 [cited by applicant]
WO WO2020263985A1 · 2020 [cited by applicant]
Barendt et al., “Broad-Specificity mRNA-rRNA Complementarity in Efficient Protein Translation,” PLoS Genetics, 2012, 8(3): e1002598, 13 pages. [cited by applicant]
Bicknell and Ricci, “When mRNA translation meets decay,” Biochemical Society Transactions (2017) 45, 339-351. [cited by applicant]
Boehm et al., “Interrogating The Degradation Pathways Of Unstable mRNAs With XRN1-resistant Sequences,” Nature Communications, Dec. 5, 2016, 7:13691, 15 pages. [cited by applicant]
Braun and Young, “Coupling mRNA Synthesis and Decay,” Molecular and Cellular Biology, Nov. 2014, vol. 34, No. 22, pp. 4078-4087. [cited by applicant]
Chin et al., “Optimized Mitochondrial Targeting of Proteins Encoded by Modified mRNAs Rescues Cells Harboring Mutations in mtATP6,” Cell Reports, Mar. 13, 2018, 22, 2818-2826. [cited by applicant]
Chung et al., “The 3′ Untranslated Region of Manganese Superoxide Dismutase RNA Contains a Translational Enhancer Element,” Biochemistry 1998, 37, 16298-16306. [cited by applicant]
Database EMBL, “Sequence 163 from Patent WO2017201346,” EBI Accession No. LP886038, Apr. 29, 2018, 1 page. [cited by applicant]
Ei-Brolosy et al., “Genetic compensation triggered by mutant mRNA degradation,” Nature, Apr. 2019, vol. 568, pp. 193-197. [cited by applicant]
Firth and Brierley, “Non-canonical translation in RNA viruses,” Journal of General Virology (2012), 93, 1385-1409. [cited by applicant]
Gold et al., “Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo-tomography,” EMBO Reports, 2017, vol. 18, No. 10, 1786-1800. [cited by applicant]
International Preliminary Report on Patentability for International Application No. PCT/US2020/039228 mailed Jan. 6, 2022, 7 pages. [cited by applicant]
International Search Report and Written Opinion for Application No. PCT/US2020/039365, mailed Oct. 8, 2020, 11 pages. [cited by applicant]
International Search Report and Written Opinion for International Application No. PCT/US2020/039228, dated Sep. 22, 2020, 10 pages. [cited by applicant]
Kalef-Ezra et al., “Import of a major mitochondrial enzyme depends on synergy between two distinct helices of its presequence,” Biochemical Journal (2016) 473: 2813-2829. [cited by applicant]
Knirsch and Clerch, “A Region in the 39 UTR of MnSOD RNA Enhances Translation of a Heterologous RNA,” Biochemical and Biophysical Research Communications (2000) 272, 164-168. [cited by applicant]
Lesnik et al., “Localized translation near the mitochondrial outer membrane: An update,” RNA Biology, Aug. 2015, 12:8, 801-809. [cited by applicant]
Margeot et al., “In [cited by applicant]
Medina et al., “Cytoplasmic 5′-3′ Exonuclease Xrn1pis Also A Genome-wide Transcription Factor In Yeast,” Frontiers In Genetics, Feb. 2014, vol. 5, Article 1, 10 pages. [cited by applicant]
Stacey et al., “Leaky Scanning Is the Predominant Mechanism for Translation of Human Papillomavirus Type 16 E7 Oncoprotein from E6/E7 Bicistronic mRNA,” Journal of Virology, Aug. 2000, vol. 74, No. 16, pp. 7284-7297. [cited by applicant]
Sylvestre et al., “The Role of the 3′ Untranslated Region in mRNA Sorting to the Vicinity of Mitochondria Is Conserved from Yeast to Human Cells,” Molecular Biology of the Cell, Sep. 2003, vol. 14, pp. 3848-3856. [cited by applicant]
Wang et al., “PNPASE Regulates RNA Import into Mitochondria,” Cell, 2010, 142(3): 456-467 (20 pages). [cited by applicant]
Williams et al., “Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling,” Science, 2014, 346(6210): 748-751 (10 pages). [cited by applicant]
Warren et al., “Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA,” Cell Stem Cell, Nov. 5, 2010, 7, 618-630. [cited by applicant]
Warren et al., Supplemental Information, Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA, Cell Stem Cell, Nov. 5, 2010, 7, 13 pages. [cited by applicant]
Andries et al., “N(1)-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice,” Journal of C… [cited by applicant]
Araujo et al., “Before It Gets Started: Regulating Translation at the 5′ UTR,” Comparative and Functional Genomics, 2012, vol. 2012, Article ID 475731, 8 pages. [cited by applicant]
Bab, I. et al., “Biosynthesis of Osteogenic Growth Peptide via Alternative Translational Initiation at AUG85 of Histone H4 mRNA,” The Journal of Biological Chemistry, vol. 274(20)(Issue of May):14474-14481 (1999). [cited by applicant]
Babendure, J.R. et al., “Control of mammalian translation by mRNA structure near caps,” RNA, vol. 12(5):851-861 (2006). [cited by applicant]
Hann, S. et al., “The alternatively initiated c-Myc proteins differentially regulate transcription through a noncanonical DNA-binding site,” Genes & Development, vol. 8:2441-2452 (1994). [cited by applicant]
Hinnebusch et al. “Translational control by5′-untranslated regions of eukaryotic mRNAs,” Science, 2016, 352, 6292, 1413-1416. [cited by applicant]
International Preliminary Report on Patentability for International Application No. PCT/US2020/039365 mailed Dec. 28, 2021, 7 pages. [cited by applicant]
International Preliminary Report on Patentability, PCT/US2018/033519, dated Nov. 19, 2019, 8 pages. [cited by applicant]
International Preliminary Report on Patentability, PCT/US2019/027089, dated Oct. 13, 2020, 12 pages. [cited by applicant]
International Search Report and Written Opinion, PCT/US2018/033519, dated Sep. 11, 2018, 13 pages. [cited by applicant]
International Search Report and Written Opinion, PCT/US2019/027089, dated Oct. 2, 2019, 20 pages. [cited by applicant]
Katayama S et al, “Antisense Transcription in the Mammalian Transcriptome” Science, American Association for the Advancement of Science. vol. 309.(5740), Sep. 2005, pp. 1564-1566. [cited by applicant]
Kozak, M., “Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes,” Proc. Nail. Acad. Sci., vol. 87:8301-8305 (1990). [cited by applicant]
Kozak, M. et al., “At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells,” Journal of Molecular Biology, vol. 196(4):947-950 (1987). [cited by applicant]
Kozak, M., “Influences of mRNA secondary structure on initiation by eukaryotic ribosomes,” Proc. Nat. Acad. Sci., vol. 83: 2850-2854 (1986). [cited by applicant]
Kozak, M., “Recognition of AUG and alternative initiator codons is augmented by G in position +4 but is not generally affected by the nucleotides in positions +5 and +6,” The EMBO Journal, vol. 16(9):2482-2492 (1997). [cited by applicant]
Kulendra, K. et al., “Elucidating the Role of Alternative RNA Export Promoting Signal Sequence Coding Regions in Potentiating Translation,” A thesis submitted in conformity with the requirements for the degree of Doctor… [cited by applicant]
Pardi et al., “Expression kinetics of nucleoside-modified mRNA delivered in lipid nanoparticles to mice by various routes,” Journal of Controlled Release, 217, 2015, 345-351. [cited by applicant]
Robbins-Pianka, A. et al., “The mRNA landscape at yeast translation initiation sites,” Bioinformatics, vol. 26(21):2651-2655 (2010). [cited by applicant]
Sakai et al., “Human galactocerebrosidase gene: promoter analysis of the 5′-flanking, region and structural organization,” Biochimica et Biophysica Acta 1395 (1998) 62-67. [cited by applicant]
Somers, J. et al., “A perspective on mammalian upstream open reading frame function,” International Journal of Biochemistry and Cell Biology, vol. 45(8):1690-1700 (2013). [cited by applicant]
Toribio, R. et al., “New insights into the topology of the scanning ribosome during translation initiation: Lessons from viruses,” RNA Biology, vol. 13(12) 1223-1227 (2016). [cited by applicant]
Tyurin A. et al., “Efficient expression of a heterologous gene in plants depends on the nucleotide composition of mRNA's 5′-region,” Russian Journal of Plant Physiology, vol. 63(4):511-522(2016). [cited by applicant]
Yabe-Wada , T. et al., “TLR signals posttranscriptionally regulate the cytokine trafficking mediator sortilin,” Scientific Report, vol. 6(1): 14 pages (2016). [cited by applicant]