IP Library › Granted Patent US 12,697,350
Granted Patent B2
US 12,697,350 · App. 17/773,112 · Granted Aug 4, 2026

Methods and compositions for treating a premature termination codon-mediated disorder

Inventors: Sean McFarland (Dorchester Center, MA); Ying-Hsin Chen (Ashland, MA); Peter M. Eimon (Brighton, MA)
Assignee: Tevard Biosciences, Inc.
A61K31/7115C12N15/86C12N2750/14143
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 12,697,350
App. No.
17/773,112
Filed
Apr 29, 2022
Granted
Aug 4, 2026
Kind
B2
Art Unit
1631
USPC
514/44R
Abstract

The invention relates generally to modified tRNAs and the use of modified tRNAs to express in a mammalian cell a functional gene product encoded by a gene containing a premature termination codon and/or to treat a disease mediated by a premature termination codon, e.g., Dravet syndrome.

Claims (27)

1 . A tRNA comprising the nucleotide sequence of SEQ ID NO: 20, 19, 21, or 2, wherein each thymine in SEQ ID NO: 20, 19, 21, or 2 is replaced by uracil.

2 . An expression vector comprising a nucleotide sequence encoding the tRNA of claim 1 .

3 . The expression vector of claim 2 , wherein the expression vector comprises:

(a) 1, 2, 3, 4, or more than 4 copy numbers of the nucleotide sequence encoding the tRNA; and/or

(b) the nucleotide sequence set forth in any one of SEQ ID NOs: 869-888 that is immediately 5′ to the nucleotide sequence encoding the tRNA.

4 . The expression vector of claim 2 , wherein the expression vector is a viral vector.

5 . The expression vector of claim 4 , wherein the viral vector:

(a) is a DNA virus vector; and/or

(b) is an adeno-associated virus (AAV) vector.

6 . A pharmaceutical composition comprising a nucleic acid encoding the tRNA of claim 1 and a pharmaceutically acceptable excipient.

7 . The pharmaceutical composition of claim 6 , wherein the composition does not comprise an aminolipid particle, an aminolipid delivery compound, or a nanoparticle.

8 . A method of expressing in a mammalian cell a functional gene product encoded by a gene containing a premature termination codon, the method comprising introducing into the cell an effective amount of a nucleic acid encoding the tRNA of claim 1 , wherein expression of the tRNA permits an arginine amino acid to be incorporated into the gene product at a position that would otherwise result in a truncated gene product caused by the premature termination codon, and wherein the premature termination codon is TGA.

9 . The method of claim 8 , wherein the cell contains:

(a) less truncated gene product than a cell without the tRNA; and/or

(b) a greater amount of functional gene product than a cell without the tRNA.

10 . The method of claim 8 , wherein the gene is a dystrophin gene or an SCN1A gene.

11 . A method of increasing in a cell voltage-gated sodium channel activity encoded by a SCN1A gene containing a premature termination codon, the method comprising introducing into the cell an effective amount of a nucleic acid encoding the tRNA of claim 1 , wherein expression of the tRNA permits an arginine amino acid to be incorporated into the SCN1A gene product at a position that would otherwise result in a truncated SCN1A gene product caused by the premature termination codon, and wherein the premature termination codon is TGA.

12 . The method of claim 8 , wherein:

(a) the cell is a human cell; and/or

(b) the tRNA becomes aminoacylated in the cell.

13 . A method of treating a premature termination codon-mediated disorder in a subject in need thereof, wherein the subject has a gene with a premature termination codon and the premature termination codon is TGA, the method comprising administering to the subject an effective amount of a nucleic acid encoding the tRNA of claim 1 , thereby to treat the disorder in the subject.

14 . The method of claim 13 , wherein the disorder is Duchenne Muscular Dystrophy or Dravet syndrome.

15 . The method of claim 13 , wherein the subject is a human.

16 . The tRNA of claim 1 , comprising the nucleotide sequence of SEQ ID NO: 20.

17 . The tRNA of claim 1 , comprising the nucleotide sequence of SEQ ID NO: 19.

18 . The tRNA of claim 1 , comprising the nucleotide sequence of SEQ ID NO: 21.

19 . The tRNA of claim 1 , comprising the nucleotide sequence of SEQ ID NO: 2.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 27, 2023
From: EIMON, PETER M.; MCFARLAND, SEAN; CHEN, YING-HSIN
To: TEVARD BIOSCIENCES, INC.
Reel/Frame 063109/0220 →
Continuity (2)
Provisional Application 62929428 · Nov 1, 2019
Related Publication 20240148772A1 · May 9, 2024
References Cited (100)
US 4687737A · Sharp et al. · 1987 [cited by applicant]
US 5840702A · Bedwell · 1998 [cited by applicant]
US 6309830B1 · Panchal et al. · 2001 [cited by applicant]
US 6964859B2 · Rajbhandary et al. · 2005 [cited by applicant]
US 7029665B2 · Panchal et al. · 2006 [cited by applicant]
US 8338386B2 · McLean et al. · 2012 [cited by applicant]
US 10513699B2 · Short · 2019 [cited by applicant]
US 10905778B2 · Coller et al. · 2021 [cited by applicant]
US 10982209B2 · Xia et al. · 2021 [cited by applicant]
US 11661600B2 · Ahern et al. · 2023 [cited by applicant]
US 20040219516A1 · Bennett et al. · 2004 [cited by applicant]
US 20050014835A1 · Arakawa et al. · 2005 [cited by applicant]
US 20090298920A1 · Dardel et al. · 2009 [cited by applicant]
US 20120077186A1 · Skach et al. · 2012 [cited by applicant]
US 20120117673A1 · Ardell · 2012 [cited by applicant]
US 20160222379A1 · Brasch et al. · 2016 [cited by applicant]
US 20170342422A1 · Holzmann et al. · 2017 [cited by applicant]
US 20170354672A1 · Siegwart et al. · 2017 [cited by applicant]
US 20180171321A1 · Mureev et al. · 2018 [cited by applicant]
US 20180320175A1 · Lee et al. · 2018 [cited by applicant]
US 20200101174A1 · Coller et al. · 2020 [cited by applicant]
US 20200263180A1 · Mali et al. · 2020 [cited by applicant]
US 20200277607A1 · Mali et al. · 2020 [cited by applicant]
US 20200291401A1 · Ahern et al. · 2020 [cited by applicant]
US 20200407714A1 · Ignatova et al. · 2020 [cited by applicant]
US 20210023120A1 · Siegwart et al. · 2021 [cited by applicant]
US 20210163948A1 · Mali et al. · 2021 [cited by applicant]
US 20210198673A1 · Mali et al. · 2021 [cited by applicant]
US 20230203482A1 · Puchalt et al. · 2023 [cited by applicant]
US 20230407300A1 · Ahern et al. · 2023 [cited by applicant]
CN 107177592A · 2017 [cited by applicant]
WO WO1999036519A1 · 1999 [cited by applicant]
WO WO2007070659A2 · 2007 [cited by applicant]
WO WO2017049409A1 · 2017 [cited by applicant]
WO WO2017152809A1 · 2017 [cited by applicant]
WO WO2017201091A1 · 2017 [cited by applicant]
WO WO2018031531A4 · 2018 [cited by applicant]
WO WO2018161032A1 · 2018 [cited by applicant]
WO WO2019090154A1 · 2019 [cited by applicant]
WO WO2019090169A1 · 2019 [cited by applicant]
WO WO2020069194A1 · 2020 [cited by applicant]
WO WO2020069199A1 · 2020 [cited by applicant]
WO WO2020208169A1 · 2020 [cited by applicant]
WO WO2021072201A1 · 2021 [cited by applicant]
WO WO2021087401A1 · 2021 [cited by applicant]
WO WO2021092064A1 · 2021 [cited by applicant]
WO WO2021113218A1 · 2021 [cited by applicant]
WO WO2022235861A1 · 2022 [cited by applicant]
Albers, et al. (2021) “Repurposing tRNAs for nonsense suppression”, Nature Communications 12(3850): 1-10. [cited by applicant]
Andersen, et al. (2003) “Elongation factors in protein biosynthesis,” Trends in Biochemical Sci., 28(8): 434-441. [cited by applicant]
Atkinson, et al. (1994) “Mutations to nonsense codons in human genetic disease: implications for gene therapy by nonsense suppressor tRNAs”, Nucleic Acids Research 22(8): 1327-1334. [cited by applicant]
Bednarova, et al. (2017) “Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders,” Front Mol Neurosci, 10: 135. [cited by applicant]
Biddle, et al. (2016) “Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment,” Nucleic Acids Res, 44(21): 10042-10050. [cited by applicant]
Bordeira-Carrico, et al. (2014) “Rescue of wild-type E-cadherin expression from nonsense-mutated cancer cells by a suppressor-tRNA,” Eur J Hum Genet, 22(9): 1085-1092. [cited by applicant]
Capone, et al. (1985) “Amber, ochre and opal suppressor tRNA genes derived from a human serine tRNA gene”, The EMBO Journal 4(1): 213-221. [cited by applicant]
Chan, et al. (2023) TPA: Mus musculus tRNA-Arg-TCT-3-1 gene, GenBank: HG984234.1, Submitted May 13, 2014; downloaded from the internet <https://www.ncbi.nlm.nih.gov/nucleotide/HG984234.1?report=genbank&log$=nuclalign&bl… [cited by applicant]
Dreher, et al. (1999) “Quantitative Assessment of EF-1?GTP Binding to Aminoacyl-tRNAs, Aminoacyl-viral RNA, and tRNA Shows Close Correspondence to the RNA Binding Properties of EF-Tu,” The Journal of Biochemistry, 274(2… [cited by applicant]
Forster, et al. (1993) “Discrimination between initiation and elongation of protein biosynthesis in yeast: identity assured by a nucleotide modification in the initiator tRNA,” Nucleic Acids Research, 21(24): 5679-5683. [cited by applicant]
Gatti (2012) “SMRT compounds correct nonsense mutations in primary immunodeficiency and other genetic models”, Am N Y Acad Sci 1250: 33-40. [cited by applicant]
Geiduschek, et al. (1988) “Transcription by RNA Polymerase III”, Annu Rev Biochem 57, 873-914. [cited by applicant]
Guy, et al. (2014) “Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis”, Genes & Development 28, 1721-1732. [cited by applicant]
Huang, et al. (2012) “In vivo identification of essential nucleotides in tRNA Leu to its functions by using a constructed yeast tRNA Leu knockout strain,” Nucleic Acids Research 40(20), 10463-10477. [cited by applicant]
International Search Report for PCT/US2018/059065, mailed Apr. 15, 2019 (5 pages). [cited by applicant]
International Search Report for PCT/US2018/059085, mailed Feb. 21, 2019 (5 pages). [cited by applicant]
International Search Report for PCT/US2020/058415, mailed Apr. 9, 2021 (5 pages). [cited by applicant]
International Search Report for PCT/US2022/027765, mailed Oct. 13, 2022 (7 pages). [cited by applicant]
Katrekar, et al. (2017) “In vivo RNA targeting of point mutations via suppressor tRNAs and adenosine deaminases”, URL:https://www.biorxiv.org/content/biorxiv/early/2017/10/28/210278.full.pdf, doi:http://dx.doi.org/10.11… [cited by applicant]
Keeling, et al. (2014) “Therapeutics based on stop codon readthrough”, Annual Review of Genomics and Human Genetics 15(1), 371-394. [cited by applicant]
Klassen, et al. (2018) “Collaboration of tRNA modifications and elongation factor eEF1A in decoding and nonsense suppression,” Scientific Reports, 8(12749): 1-12. [cited by applicant]
Kleina, et al. (1990) “Construction of [cited by applicant]
Koukuntla, et al. (2013) “U6 promoter-enhanced GlnUAG suppressor tRNA has higher suppression efficacy and can be stably expressed in 293 cells,” Journal of Gene Medicine 15, 93-101. [cited by applicant]
Lueck, et al. (2016) “Engineered tRNA suppression of a CFTR nonsense mutation,” bioRxiv, Nov. 20, pp. 1-9. [cited by applicant]
Lueck, et al. (2018) “Engineered transfer RNAs for suppression of premature termination codons,” bioRxiv preprint first posted online Aug. 27, 2018. [online]. [cited by applicant]
Lueck, et al. (2019) “Engineered transfer RNAs for suppression of premature termination codons”, Nature Communications 10(822), 1-11. [cited by applicant]
Muller, et al. (2008) “Spliceosomal Peptide P140 for Immunotherapy of Systemic Lupus Erythematosus Results of an Early Phase II Clinical Trial,” Arthritis & Rheumatism 58 (12), 3873-3883. [cited by applicant]
Olejniczak, et al. (2005) “Idiosyncratic tuning of tRNAs to achieve uniform ribosome binding,” Nature Structural & Molecular Biology 12(9), 788-793. [cited by applicant]
Panchal, et al. (1999) “Partial functional correction of xeroderma pigmentosum group A cells by suppressor tRNA,” Hum Gene Ther, 10: 2209-2219. [cited by applicant]
Raftery, et al. (1987) “Systematic alterations in the anticodon arm make tRNA Glu-Suoc a more efficient suppressor,” EMBO Journal 6(5), 1499-1506. [cited by applicant]
Roy, et al. (2016) “Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression,” Proc Natl Acad Sci USA, 113: 12508-12513. [cited by applicant]
Russian Office Action for RU Application No. 2020117787, 6 pages, dated Nov. 1, 2022. [English Translation]. [cited by applicant]
Saks, et al. (2011) “Functional consequences of T-stem mutations in [cited by applicant]
Schmid, et al. (2014) “A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs,” J Virol, 88(4): 2333-2336. [cited by applicant]
Schrader, et al. (2009) “Understanding the Sequence Specificity of tRNA Binding to Elongation Factor Tu using tRNA Mutagenesis,” J Mol Biol 386, 1255-1264. [cited by applicant]
Schrader, et al. (2011) “Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding,” PNAS 108(13), 5215-5220. [cited by applicant]
Sharp, et al. (1985) “Structure and transcription of eukaryotic tRNA genes,” Crit Rev Biochem 19(2), 107-144. [cited by applicant]
Singer, et al. (1998) “Genes and genomes,” Moscow, “Mir” 1: 52, Table 1.5. [Non-English]. [cited by applicant]
Sissler, et al. (1996) “Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts”, The EMBO Journal 15(18), 5069-5076. [cited by applicant]
Temple, et al. (1982) “Construction of a functional human suppressor tRNA gene: an approach to gene therapy for beta-thalassaemia,” Nature, 296: 537-540. [cited by applicant]
Tuorto, et al. (2016) “Genome recoding by tRNA modifications,” Open Biol., 6(12): 160287. [cited by applicant]
Vasil'eva, et al. (2004) “Influence of Nucleotide Changes in tRNA [cited by applicant]
Written Opinion for PCT/US2018/059065, mailed Apr. 15, 2019 (6 pages). [cited by applicant]
Written Opinion for PCT/US2018/059085, mailed Feb. 21, 2019 (6 pages). [cited by applicant]
Written Opinion for PCT/US2020/058415, mailed Apr. 9, 2021 (6 pages). [cited by applicant]
Written Opinion for PCT/US2022/027765, mailed Oct. 13, 2022 (13 pages). [cited by applicant]
U.S. Appl. No. 18/558,926, Methods and Compositions for Treating a Premature Termination Codon-Mediated Disorder, filed Nov. 3, 2023. [cited by applicant]
U.S. Appl. No. 16/761,205, Methods of Rescuing Stop Codons via Genetic Reassignment With ACE-tRNA, filed May 1, 2020. [cited by applicant]
U.S. Appl. No. 18/137,931, Methods of Rescuing Stop Codons via Genetic Reassignment With ACE-tRNA, filed Apr. 21, 2023. [cited by applicant]
U.S. Appl. No. 18/137,942, Methods of Rescuing Stop Codons via Genetic Reassignment With ACE-tRNA, filed Apr. 21, 2023. [cited by applicant]
U.S. Appl. No. 16/760,932, Methods of Rescuing Stop Codons via Genetic Reassignment With ACE-tRNA, filed May 1, 2020. [cited by applicant]
U.S. Appl. No. 18/430,760, Methods of Rescuing Stop Codons via Genetic Reassignment With ACE-tRNA, filed Feb. 2, 2024. [cited by applicant]