Trems for use in correction of missense mutations
AssigneeFlagship Pioneering Innovations VI, LLC
InventorsTheonie Anastassiadis, Siddharth Shukla, Stephen William Eichhorn, Amanda Marie Papakyrikos
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Abstract
The invention relates generally to tRNA-based effector molecules for use in inserting a missense mutation into an open reading frame (ORF) of a gene, e.g., for treatment of a repeat expansion disease.
Claims71
A method for inserting a missense mutation into an open reading frame (ORF) of a gene, wherein the missense mutation results in replacing a repeat expansion disease (RED) codon with a replacement codon,
- the method comprising contacting the ORF with a tRNA effector molecule (TREM) comprising a sequence of Formula (A):
- wherein:
- independently, [L1] and [VL Domain], are optional and x=0 or 1,
- thereby inserting the missense mutation into the ORF of the gene.
The method of any one of the preceding claims, wherein the RED codon is CAG.
The method of any one of the preceding claims, wherein the ORF comprises at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, or more copies (e.g., consecutive copies) of the RED codon.
The method of any one of the preceding claims, wherein the ORF comprises at least 10 copies (e.g., consecutive copies) of the RED codon.
The method of any one of the preceding claims, wherein the gene is selected from HTT, ATXN1, ATXN3, DMPK, GIPC1, ARX, ATN1, AR, ATXN7, TBP, COMP, RUNX2, HOXD13, ATXN2, GLS, CBL2, AFF3, FMR1, ATXN8OS, ATXN8b, LOC642361, NUTM2b-AS1, JPH3, FOXL2, PHOX2B, ZIC2, SOX3, and C9orf72.
The method of any one of the preceding claims, wherein the gene is selected from HTT, ATXN1, ATXN3, ATN1, AR, ATXN7, TBP, ATXN2, and GLS.
The method of any one of the preceding claims, wherein the gene is HTT.
The method of any one of the preceding claims, wherein the replacement codon is a codon that encodes for leucine, alanine, or serine.
The method of any one of the preceding claims, wherein the replacement codon is selected from TTA, TTG, TCT, TCC, TCA, TCG, CTT, CTC, CTA, CTG, AGT, AGC, GCT, GCC, GCA, and GCG.
The method of any one of the preceding claims, wherein the TREM comprises a TREM having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity with the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by 10, 15, 20, 25, 30, 35 or 40 nucleotides from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by more than 5 nucleotides from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by more than 10 nucleotides from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by no more than 10, 15, 20, 25, 30, 35 or 40 nucleotides from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by no more than 1 nucleotide from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by no more than 5 nucleotides from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a nucleotide sequence that differs by no more than 10 nucleotides from the nucleotide sequence of a TREM provided in FIG. 1.
The method of any one of the preceding claims, wherein the replacement of a RED codon with a replacement codon results in a reduction of a symptom of a disease, disorder, or condition.
The method of any one of the preceding claims, wherein the TREM is capable of inserting a RED codon into the ORF of a gene, e.g., with at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, 99.9% efficiency, e.g., compared to a reference TREM.
The method of any one of the preceding claims, wherein the TREM is capable of modulating a functional parameter.
The method of any one of the preceding claims, wherein the TREM comprises a non-naturally occurring modification.
The method of any one of the preceding claims, wherein the TREM has a sequence selected from a sequence provided in FIG. 1.
The method of any one of the preceding claims, wherein the TREM comprises a sequence selected from:
- TREM NO. 3 (SEQ ID NO:
- 627), TREM NO. 4 (SEQ ID NO:
- 628), TREM NO. 5 (SEQ ID NO:
- 629), TREM NO. 6 (SEQ ID NO:
- 630), TREM NO. 7 (SEQ ID NO:
- 631, TREM NO. 9 (SEQ ID NO:
- 633), and TREM NO. 11 (SEQ ID NO:
- 635).
The method of any one of the preceding claims, wherein the non-naturally occurring modification is present at a nucleotide position which corresponds to one or more of nucleotides 1-76, according to the CtNS.
A TREM having the nucleotide sequence of a TREM provided in FIG. 1 (e.g., a TREM having any one of SEQ ID NOs.:
- 625-693).
Dependencies are inferred from the claim text.