COMPOSITIONS AND METHODS FOR GENOME EDITING

• US 20180258411A1
• Filed: 09/23/2016
• Published: 09/13/2018
• Est. Priority Date: 09/25/2015
• Status: Abandoned Application

• Current Assignee: TVA LLC
• Original Assignee: Tarveda Therapeutics, Inc.
• Inventors: Kadiyala, Sudhakar, Bilodeau, Mark T., Ward, Donna T.
• Application Number:
  US15/762,627
• Publication Number:
  US 20180258411A1
• Time in Patent Office: Days
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C12N 15/102 Mutagenizing nucleic acids
• CPC Class Codes: C12N 15/11 DNA or RNA fragments; Modified forms thereof DNA or RNA not used in recombinant technology, C07H21/00; Non-coding nucleic acids having a biological activity
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 15/87 Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
• CPC Class Codes: C12N 15/907 in mammalian cells
• CPC Class Codes: C12N 2310/20 involving clustered regularly interspaced short palindromic repeats [CRISPRs]
• CPC Class Codes: C12N 2310/3515 Lipophilic moiety, e.g. cholesterol
• CPC Class Codes: C12N 2320/32 Special delivery means, e.g. tissue-specific
• CPC Class Codes: C12N 9/22 Ribonucleases RNAses, DNAses catalytic nucleic acids C12N15/113

Abstract

The present invention provides conjugates, nanoparticles and compositions comprising components of a CRISPR-Cas system; these compositions can be used for genetic editing in a cell or an organism.

Claims

1. A conjugate for editing a polynucleotide sequence in a cell or an organism comprising the structure of the formula X—

Y—

Z, wherein X is a targeting moiety;

Y is an optional linker; and

Z is a guide RNA.

2. The conjugate of claim 1, wherein the active agent, Z, is a single guide RNA (sgRNA).

3. The conjugate of claim 2, wherein the sgRNA is about 10 nucleotides to about 250 nucleotides in length.

4. The conjugate of claim 3, wherein the sgRNA is about 20 nucleotides to about 100 nucleotides in length.

5. The conjugate of claim 3, wherein the sgRNA comprises a polynucleotide sequence that consists of three regions:

a target recognition sequence, a trans-activating crRNA (tracr) sequence and a sequence that is complementary to the tracr sequence.

6. The conjugate of claim 5, wherein the target recognition sequence of the sgRNA comprises about 12 to about 25 nucleotides that are complementary to and hybridize to the 12-25 consecutive nucleotides of a selected target polynucleotide in the genome of said cell or organism.

7. The conjugate of claim 6, wherein the target recognition sequence of the sgRNA comprises 15-20 nucleotides that are complementary to and hybridize to the 15-20 consecutive nucleotides of the selected target polynucleotide in the genome of said cell or organism.

8. The conjugate of claim 5, wherein the tracr sequence of the sgRNA comprises a wild type tracrRNA sequence identified from a bacteria strain in which a CRISPR-Cas system is identified, wherein the tracr sequence hybridizes to the sequence complementary to the tracr sequence that is linked to the target recognition sequence of the sgRNA, and forms part of a CRISPR-Cas complex.

9. The conjugate of claim 8, wherein the tracr sequence comprises about 20 to about 100 nucleotides.

10. The conjugates of claim 8, wherein the complementarity between the tracr sequence and the sequence that is complementary to the tracr sequence is between at least about 70% and at least 100%.

11. The conjugate of claim 6, wherein the selected target polynucleotide in the genome locates immediately at the 5′

end of a postspacer adjacent motif (PAM), wherein the PAM sequence is not included in the target recognition sequence of the sgRNA molecule.

12. The conjugate of claim 11, wherein the PAM comprising the sequence selected from the group consisting of NGG, NNGRRT, NNNGATT, NNNAGAAW and NNAAAC, wherein N represents any one of A, T, G, C. and W represents A or T.

13. The conjugate of claim 5, wherein the sgRNA molecule further comprises one or more additional nucleotides at the 5′

end of the RNA molecule that is not complementary to the selected target polynucleotide in the genome.

14. The conjugate of claim 13, wherein the sgRNA comprises one, or two, or three additional nucleotides at the 5′

end of the RNA molecule.

15. The conjugate of claim 5, wherein the sgRNA molecule comprises one or more modified nucleotides.

16. The conjugate of claim 5, wherein the complementarity between the target recognition sequence of the sgRNA molecule and the selected target polynucleotide is from about 70% to about 100%.

17. The conjugate of claim 1, wherein the linker is a cleavable linker.

18. The conjugate of claim 17, wherein the linker is enzymatic-cleavable.

19. The conjugate of claim 17, wherein the linker is non-enzymatic cleavable.

20. The conjugate of claim 17, wherein the linker is selected from the group consisting of an alkyl chain, a peptide, a beta-glucuronide, a self-stabilizing group, a hydrophilic group and a disulfate group.

21. The conjugate of claim 1, wherein the targeting moiety and the active agent of the conjugate are directly connected.

22. A nanoparticle for editing a polynucleotide in a genome of a cell or an organism comprising

(i) at least one conjugate comprising the structure of the formula X—

Y—

Z, wherein X is a targeting moiety;

Y is an optional linker; and

Z is a guide RNA; and

(ii) at least one Cas protein.

23. The nanoparticle of claim 22, wherein the nanoparticle comprises a polymeric matrix.

24. The nanoparticle of claim 23, wherein the polymeric matrix comprises one or more polymers selected from the group consisting of hydrophobic polymers, hydrophilic polymers, and copolymers thereof.

25-26. -26. (canceled)

27. The nanoparticle of claim 23, wherein the polymeric matrix comprises one or more polymers selected from the group consisting of poly(lactic acid), poly(glycolic acid), poly(lactic-co-glycolic acid), poly(ethylene oxide), poly(ethylene glycol), poly(propylene glycol), and copolymers thereof.

28. The nanoparticle of claim 23, wherein the size of the nanoparticle is between 10 nm and 5000 nm.

29. (canceled)

30. The nanoparticle of claim 23, wherein the weight percentage of the conjugate is between 0.1% and 35%.

31. The nanoparticle of claim 22, wherein the Cas protein is selected from Cas9 or Cpf1.

32. A composition for editing a polynucleotide in a cell or an organism comprising the conjugate of claim 1 and a Cas protein.

33. The composition of claim 32, wherein the Cas protein is selected from Cas9 or Cpf1.

34. A method for editing a selected polynucleotide in a cell or in a subject, the method comprising

(i) introducing into the cell, or the subject, of at least one conjugate as defined in claim 1, and

(ii) at least one Cas protein,

wherein the CAS protein is introduced into the cell or the subject as a polypeptide, or its variants, a RNA molecule that encodes the Cas protein or its variants, a construct including a nucleic acid molecule that encodes the Cas protein or its variants, or an expression vector that is used to express the Cas protein or its variants.

35. The method of claim 34, wherein the Cas protein is a Type II CRISPR Cas9 endonuclease or a variant thereof.

36. The method of claim 34, wherein the Cas protein is Cpf1 or a variant thereof.

37. A method for editing a selected polynucleotide in a cell, or in a subject, the method comprising introducing into the cell, or the subject, of a nanoparticle of claim 22, or a composition of claim 31.

38. The method of claim 35, wherein the variants of the Cas9 endonuclease include Cas9 proteins isolated from other bacterial strains, a Cas9 nickase having one inactive nuclease domain, a nuclease-null dead Cas9 protein (dCas9), and a fusion protein comprising a dCas9 protein is fused with one or more heterogeneous effector domains.

39. The method of claim 34, wherein the selected polynucleotide in the cell or the subject locates immediately at the 5′

end of a postspacer adjacent motif (PAM) that is specifically recognized by a Cas9 nuclease.

40. The method of claim 36, wherein said one or more heterogeneous effector domains fused with the dCas9 protein comprise domains having activities of transcriptional activation;

transcription suppression, methylase activity, demethylase activity, histone modification activity, RNA cleavage activity and nucleic acid binding activity, and chromatin modification activity.

41. The method of claim 36, wherein said one or more heterogeneous effector domains fused with the dCas9 protein comprises epitope tags and reporter gene sequences.