Preparation
阅读说明：本技术 制剂 (Preparation ) 是由 K·M·伍德 N·P·加德纳 R·R·沙 S·S·斯库利 R·马伊祖布 于 2018-09-28 设计创作，主要内容包括：本发明提供具有改善的递送生物活性剂的特性的基于脂质纳米粒子的组合物、工程化的细胞和递送所述剂的方法。(The present invention provides lipid nanoparticle-based compositions, engineered cells, and methods of delivering bioactive agents with improved properties for delivery of the agents.)
1. a lipid nanoparticle ("L NP") composition, the lipid nanoparticle composition comprising:
an RNA component; and
a lipid component, wherein the lipid component comprises:
about 50-60 mol% amine lipid;
about 8-10 mol% neutral lipid; and
about 2.5-4 mol% PEG lipid,
wherein the remainder of the lipid component is a helper lipid, and
wherein the N/P ratio of the L NP composition is about 6.
2. An L NP composition, the L NP composition comprising:
an RNA component;
about 50-60 mol% amine lipid;
about 27-39.5 mol% helper lipid;
about 8-10 mol% neutral lipid; and
about 2.5-4 mol% PEG lipid,
wherein the L NP composition has an N/P ratio of about 5 to 7.
3. The L NP composition of claim 2 wherein the N/P ratio is about 6.
4. An L NP composition, the L NP composition comprising:
an RNA component; and
a lipid component, wherein the lipid component comprises
About 50-60 mol% amine lipid;
about 5-15 mol% neutral lipid; and
about 2.5-4 mol% PEG lipid,
wherein the remainder of the lipid component is a helper lipid, and
wherein the L NP composition has an N/P ratio of about 3 to 10.
5. An L NP composition, the L NP composition comprising:
an RNA component; and
a lipid component, wherein the lipid component comprises
About 40-60 mol% amine lipid;
about 5-15 mol% neutral lipid; and
about 2.5-4 mol% PEG lipid,
wherein the remainder of the lipid component is a helper lipid, and
wherein the N/P ratio of the L NP composition is about 6.
6. An L NP composition, the L NP composition comprising:
an RNA component; and
a lipid component, wherein the lipid component comprises:
about 50-60 mol% amine lipid;
about 5-15 mol% neutral lipid; and
about 1.5-10 mol% PEG lipid,
wherein the remainder of the lipid component is a helper lipid, and
wherein the N/P ratio of the L NP composition is about 6.
7. An L NP composition, the L NP composition comprising:
an RNA component; and
a lipid component, wherein the lipid component comprises
About 40-60 mol% amine lipid;
about 0-10 mol% neutral lipid; and
about 1.5-10 mol% PEG lipid,
wherein the remainder of the lipid component is a helper lipid, and
wherein the L NP composition has an N/P ratio of about 3 to 10.
8. An L NP composition, the L NP composition comprising:
an RNA component; and
a lipid component, wherein the lipid component comprises:
about 40-60 mol% amine lipid;
less than about 1 mol% neutral lipids; and
about 1.5-10 mol% PEG lipid,
wherein the remainder of the lipid component is a helper lipid, and
wherein the L NP composition has an N/P ratio of about 3 to 10.
9. An L NP composition, the L NP composition comprising:
an RNA component; and
a lipid component, wherein the lipid component comprises:
about 40-60 mol% amine lipid; and
about 1.5-10 mol% PEG lipid,
wherein the remainder of the lipid component is a helper lipid,
wherein the L NP composition has an N/P ratio of about 3 to 10, and
wherein the L NP composition is substantially free or free of neutral phospholipids.
10. An L NP composition, the L NP composition comprising:
an RNA component; and
a lipid component, wherein the lipid component comprises:
about 50-60 mol% amine lipid;
about 8-10 mol% neutral lipid; and
about 2.5-4 mol% PEG lipid,
wherein the remainder of the lipid component is a helper lipid, and
wherein the L NP composition has an N/P ratio of about 3 to 7.
11. The composition of any one of the preceding claims, wherein the RNA component comprises mRNA.
12. The composition of any one of the preceding claims, wherein the RNA component comprises an RNA-guided DNA binding agent, such as Cas nuclease mRNA.
13. The composition of any one of the preceding claims, wherein the RNA component comprises class 2 Cas nuclease mRNA.
14. The composition of any one of the preceding claims, wherein the RNA component comprises Cas9 nuclease mRNA.
15. The composition of any one of claims 11-14, wherein the mRNA is a modified mRNA.
16. The composition of any one of the preceding claims, wherein said RNA component comprises RNA comprising an open reading frame encoding an RNA-guided DNA binding agent, wherein said open reading frame has a uridine content in the range of from its minimum uridine content to 150% of said minimum uridine content.
17. The composition of any one of the preceding claims, wherein said RNA component comprises an mRNA comprising an open reading frame encoding an RNA-guided DNA binding agent, wherein said open reading frame has a uridine dinucleotide content in the range of its minimum uridine dinucleotide content to 150% of said minimum uridine dinucleotide content.
18. The composition of any one of the preceding claims, wherein the RNA component comprises an mRNA comprising a sequence at least 90% identical to any one of SEQ ID NOs 1, 4, 7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66, wherein the mRNA comprises an open reading frame encoding an RNA-guided DNA binding agent.
19. The composition of any one of the preceding claims, wherein the RNA component comprises a gRNA nucleic acid.
20. The composition of claim 19, wherein the gRNA nucleic acid is a gRNA.
21. The composition of any one of the preceding claims, wherein the RNA component comprises a class 2 Cas nuclease mRNA and a gRNA.
22. The composition of any one of claims 19-21, wherein the gRNA nucleic acid is or encodes a dual guide rna (dgrna).
23. The composition of any one of claims 19-21, wherein the gRNA nucleic acid is or encodes a sgRNA.
24. The composition of any one of claims 19-23, wherein the gRNA is modified.
25. The composition of claim 24, wherein the gRNA comprises a modification selected from: 2 '-O-methyl (2' -O-Me) -modified nucleotides, Phosphorothioate (PS) linkages between nucleotides; and 2 '-fluoro (2' -F) -modified nucleotides.
26. The composition of any one of claims 24-25, wherein the gRNA comprises a modification at one or more of the first five nucleotides of the 5' end.
27. The composition of any one of claims 24-26, wherein the gRNA comprises a modification at one or more of the last five nucleotides of the 3' end.
28. The composition of any one of claims 24-27, wherein the gRNA comprises a PS bond between the first four nucleotides.
29. The composition of any one of claims 24-28, wherein the gRNA comprises a PS bond between the last four nucleotides.
30. The composition of any one of claims 24-29, further comprising a 2'-O-Me modified nucleotide at the first three nucleotides of the 5' end.
31. The composition of any one of claims 24-30, further comprising a 2'-O-Me modified nucleotide at the last three nucleotides of the 3' end.
32. The composition of any one of claims 19-31, wherein the gRNA and the class 2 Cas nuclease mRNA are present in a ratio ranging from about 10:1 to about 1:10 by weight.
33. The composition of any one of claims 19-31, wherein the gRNA and the class 2 Cas nuclease mRNA are present in a ratio ranging from about 5:1 to about 1:5 by weight.
34. The composition of any one of claims 19-33, wherein the gRNA and the class 2 Cas nuclease mRNA are present in a ratio ranging from about 3:1 to about 1:1 by weight.
35. The composition of any one of claims 19-34, wherein the gRNA and the class 2 Cas nuclease mRNA are present in a ratio ranging from about 2:1 to about 1:1 by weight.
36. The composition of any one of claims 19-35, wherein the gRNA and the class 2 Cas nuclease mRNA are present in a ratio of about 2:1 by weight.
37. The composition of any one of claims 19-35, wherein the gRNA and the class 2 Cas nuclease mRNA are present in a ratio of about 1:1 by weight.
38. The composition of any one of the preceding claims, further comprising at least one template.
39. The composition of any one of the preceding claims, wherein the PEG lipid mol% is about 3.
40. The composition of any one of the preceding claims, wherein the amine lipid mol% is about 50.
41. The composition of any one of the preceding claims, wherein the amine lipid mol% is about 55.
42. The composition of any one of the preceding claims, wherein the amine lipid mol% is ± 3 mol%.
43. The composition of any one of the preceding claims, wherein the amine lipid mol% is ± 2 mol%.
44. A composition according to any preceding claim, wherein the amine lipid mol% is 47-53 mol%.
45. The composition of any one of the preceding claims, wherein the amine lipid mol% is 48-53 mol%.
46. A composition according to any preceding claim, wherein the amine lipid mol% is 53-57 mol%.
47. The composition of any one of the preceding claims, wherein the N/P ratio is 6 ± 1.
48. The composition of any one of the preceding claims, wherein the N/P ratio is 6 ± 0.5.
49. The composition of any one of the preceding claims, wherein the amine lipid is lipid a.
50. The composition of any one of the preceding claims, wherein the amine lipid is an analog of lipid a.
51. The composition of claim 50, wherein the analog is an acetal analog.
52. The composition of claim 51, wherein the acetal analog is a C4-C12 acetal analog.
53. The composition of claim 50, wherein the acetal analog is a C5-C12 acetal analog.
54. The composition of claim 50, wherein the acetal analog is a C5-C10 acetal analog.
55. The composition of claim 50, wherein the acetal analog is selected from the group consisting of C4, C5, C6, C7, C9, C10, C11, and C12 analogs.
56. The composition of any one of the preceding claims, wherein the helper lipid is cholesterol.
57. The composition of any one of the preceding claims, wherein the neutral lipid is DSPC.
58. The composition of any one of the preceding claims, wherein the neutral lipid is DPPC.
59. The composition of any one of the preceding claims, wherein the PEG lipid comprises dimyristoyl glycerol (DMG).
60. The composition of any one of the preceding claims, wherein the PEG lipid comprises PEG-2 k.
61. The composition of any one of the preceding claims, wherein the PEG lipid is PEG-DMG.
62. The composition of claim 61, wherein the PEG-DMG is PEG2 k-DMG.
63. The composition of claim 9 wherein the L NP composition is substantially free of neutral lipids.
64. The composition of claim 63, wherein the neutral lipid is a phospholipid.
65. A method of gene editing comprising contacting a cell with the L NP composition of any of claims 12-64.
66. A gene editing method comprising delivering a class 2 Cas nuclease mRNA and a guide RNA nucleic acid to a cell, wherein the class 2 Cas mRNA and the guide RNA nucleic acid are formulated as at least one L NP composition of any one of claims 13-64.
67. A method of producing a genetically engineered cell, the method comprising contacting a cell with at least one L NP composition of any one of claims 12-64.
68. The method of any one of claims 65-67, wherein the L NP composition is administered at least twice.
69. The method of claim 68, wherein the L NP composition is administered 2-5 times.
70. The method of claim 68 or 69, wherein editing is improved upon reapplication.
71. The method of any one of claims 65-70, further comprising introducing at least one template nucleic acid into the cell.
72. The method of any one of claims 65-71, wherein the mRNA is formulated in a first L NP composition and the guide RNA nucleic acid is formulated in a second L NP composition.
73. The method of claim 72, wherein the first L NP composition and the second L NP composition are administered simultaneously.
74. The method of claim 72, wherein the first L NP composition and the second L NP composition are administered sequentially.
75. The method of any one of claims 65-73, wherein the mRNA and the guide RNA nucleic acid are formulated in a single L NP composition.
Drawings
Figure 1 shows the percentage of TTR gene editing achieved in mouse liver following delivery of CRISPR/Cas gene editing components Cas9mRNA and gRNA in L NP compositions, as indicated in single doses of 1mpk (figure 1A)) or 0.5mpk (figure 1B).
Figure 2 shows particle distribution data for L NP compositions comprising Cas9mRNA and grnas.
Figure 3 depicts the physicochemical characteristics of L NP compositions comparing the log-differential molar mass (figure 3A) and average molecular weight measurements (figure 3B) of the compositions.
FIG. 4 shows the polydispersity calculations in FIG. 4A and the Burchard-Stockmeyer analysis of the L NP composition of FIG. 3 analyzed in FIG. 4B.
Figure 5 provides the results of experiments evaluating the effect of L NP compositions with increased PEG lipid concentrations on serum TTR knockdown, gene editing in the liver, and cytokine MCP-1 levels after a single dose administration to rats figure 5A illustrates serum TTR levels, figure 5B illustrates the percentage of editing in liver samples, and figure 5C provides MCP-1 levels in pg/m L.
Figure 6 shows that L NP compositions maintained gene editing potency at various PEG lipids (as measured by serum TTR levels (figure 6A and figure 6B) and percent editing (figure 6C).
Figure 7 shows that lipid a analogs efficiently deliver gene-edited cargo in L NP compositions as measured by% liver editing after a single dose administration to mice.
Fig. 8 shows dose response curves for compiled percentages in the case of various L NP compositions in primary cynomolgus monkey hepatocytes.
Fig. 9A and 9B show serum TTR and percent edit results when the ratio of gRNA to mRNA was varied, and fig. 9C and 9D show serum TTR and percent edit results in the liver when the amount of Cas9mRNA remained constant and the amount of gRNA was varied after a single dose was administered to mice.
Fig. 10A and 10B show serum TTR and liver editing results after administration of L NP compositions with and without neutral lipids.
Detailed Description
The present disclosure provides lipid nanoparticle (L NP) compositions and methods of use of the compositions for delivery of RNA, including CRISPR/Cas component RNA ("cargo"), to cells L NP compositions can exhibit improved properties over previous delivery techniques L NP compositions can contain an RNA component and a lipid component as defined herein.
CRISPR/Cas cargo
For example, comprising mRNA for expressing a protein such as Green Fluorescent Protein (GFP), and an RNA-guided DNA binding agent, or Cas nuclease, L NP compositions are provided that include Cas nuclease mRNA, e.g., class 2 Cas nuclease mRNA that allows expression of Cas9 protein in a cell.
"mRNA" refers to a polynucleotide comprising an open reading frame that can be translated into a polypeptide (i.e., can serve as a substrate for translation by ribosomes and aminoacylated tRNA's). The mRNA may comprise a phosphate-sugar backbone comprising ribose residues or analogs thereof, such as 2' -methoxy ribose residues. In some embodiments, the sugar of the mRNA phosphate-sugar backbone consists essentially of ribose residues, 2' -methoxy ribose residues, or a combination thereof. Generally, the mRNA does not contain significant thymidine residues (e.g., 0 residues or less than 30, 20, 10, 5, 4, 3, or 2 thymidine residues; or less than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.2%, or 0.1% thymidine content). The mRNA may contain modified uridines at some or all of its uridine positions.
CRISPR/Cas nuclease system
One component of the disclosed formulations is mRNA encoding an RNA-guided DNA binding agent (such as a Cas nuclease).
As used herein, "RNA-guided DNA binding agent" means a polypeptide or polypeptide complex having RNA and DNA binding activity, or a DNA-binding subunit of such a complex, wherein the DNA binding activity is sequence-specific and depends on the sequence of the RNA. Exemplary RNA-guided DNA binding agents include Cas lyase/nickase and their unactivated forms ("dCasDNA binding agents"). As used herein, "Cas nuclease" encompasses Cas lyase, Cas nickase, and dCas DNA-binding agents. Cas lyase/nickase and dCasDNA binding agents include the Csm or Cmr complex of a type III CRISPR system, Cas10, Csm1, or Cmr2 subunits thereof; a cascade complex of a type I CRISPR system, Cas3 subunit thereof; and a class 2 Cas nuclease. As used herein, a "class 2 Cas nuclease" is a single-stranded polypeptide having RNA-guided DNA binding activity. Class 2 Cas nucleases include class 2 Cas lyases/nickases (e.g., H840A, D10A, or N863A variants) that also have RNA-guided DNA lyase or nickase activity; and class 2 dCas DNA binding agents, wherein the lyase/nickase activity is not activated. Class 2 Cas nucleases include, for example, Cas9, Cpf1, C2C1, C2C2, C2C3, HF Cas9 (e.g., N497A, R661A, Q695A, Q926A variants), HypaCas9 (e.g., N692A, M694A, Q695A, H698A variants), eSPCas9(1.0) (e.g., K810A, K1003A, R1060A variants) and eSPCas9(1.1) (e.g., K848A, K1003A, R1060A variants) proteins and modified forms thereof. Cpf1 protein (Zetsche et al, Cell,163:1-13(2015)) is homologous to Cas9 and contains a RuvC-like nuclease domain. The Cpf1 sequence from Zetsche is incorporated by reference in its entirety. See, e.g., Zetsche, table S1, and table S3. See, e.g., Makarova et al, Nat Rev Microbiol,13(11):722-36 (2015); shmakov et al, Molecular Cell,60: 385-.
In some embodiments, the RNA-guided DNA-binding agent is a class 2 Cas nuclease. In some embodiments, the RNA-guided DNA-binding agent has a lyase activity, which may also be referred to as a double-stranded endonuclease activity. In some embodiments, the RNA-guided DNA-binding agent comprises a Cas nuclease, such as a class 2 Cas nuclease (which may be, for example, a type II, V, or VI Cas nuclease). Class 2 Cas nucleases include, for example, Cas9, Cpf1, C2C1, C2C2 and C2C3 proteins and modified forms thereof. Examples of Cas9 nucleases include those of the type II CRISPR system of streptococcus pyogenes, staphylococcus aureus and other prokaryotes (see, e.g., the list in the next paragraph), and modified (e.g., engineered or mutated) versions thereof. See, e.g., U.S.2016/0312198a 1; U.S.2016/0312199A 1. Other examples of Cas nickases include the Csm or Cmr complex of a type III CRISPR system, or Cas10, Csm1, or Cmr2 subunits thereof; and the cascade complex of the type I CRISPR system, or Cas3 subunit thereof. In some embodiments, the Cas nuclease may be from a type IIA, type IIB, or type IIC system. See, e.g., Makarova et al, nat. rev. microbiol.9: 467-; makarova et al, nat. Rev. Microbiol,13:722-36 (2015); shmakov et al, Molecular Cell,60: 385-.
Non-limiting examples of species from which Cas nucleases can be derived include Streptococcus pyogenes (Streptococcus coccus species), Streptococcus thermophilus (Streptococcus thermophilus), Streptococcus species (Streptococcus sp), Staphylococcus aureus (Staphylococcus aureus), Lactobacillus innominate (L innocus), Lactobacillus gasseri (L Lactobacillus gasseri), Francisella neoformans (Francisella novaculeatus), Lactobacillus succinogenes (Wolinella suis), Lactobacillus plantarum (Candida albicans), Clostridium butyricum (Corynebacterium thermoacidophilus), Streptococcus faecalis (Lactobacillus plantarum), Streptococcus faecalis (Streptococcus faecalis), Streptococcus faecalis strain (Streptococcus sp), Streptococcus faecalis strain (Streptococcus), Streptococcus faecalis strain (Streptococcus faecalis), Streptococcus sp), Streptococcus faecalis strain (Corynebacterium sp), Streptococcus faecalis strain (Corynebacterium parvularis), Streptococcus faecalis strain (Corynebacterium sp), Streptococcus faecalis), Streptococcus strain (Corynebacterium parvus strain (Corynebacterium sp), Streptococcus faecalis strain (Corynebacterium sp), Streptococcus faecalis strain (Corynebacterium parvus), Streptococcus faecalis strain (Corynebacterium sp), Streptococcus faecalis strain (Corynebacterium parvus strain (Corynebacterium sp), Streptococcus faecalis strain (Corynebacterium sp), Streptococcus faecalis strain (Corynebacterium sp), Streptococcus faecalis), Streptococcus sp), Streptococcus strain (Corynebacterium sp), Streptococcus faecalis), Streptococcus sp), Streptococcus strain (Corynebacterium parvus strain (Corynebacterium sp), Streptococcus sp), Clostridium sp), Streptococcus faecalis strain (Corynebacterium parvulus), Streptococcus faecalis strain (Corynebacterium parvus), Streptococcus sp), Streptococcus strain (Corynebacterium parvularis (Corynebacterium sp), Streptococcus faecalis strain (Corynebacterium parvulus), Streptococcus faecalis strain (Corynebacterium parvus), Clostridium sp), Streptococcus faecalis strain (Corynebacterium parvus), Clostridium sp), Clostridium (Corynebacterium parvus), Clostridium (Corynebacterium parvus strain (Corynebacterium parvus), Clostridium sp), Clostridium (Corynebacterium parvus), Clostridium sp), Clostridium (Corynebacterium parvus strain (Corynebacterium parvus strain (Corynebacterium parvus), Clostridium sp), Clostridium (Corynebacterium parvus strain (Corynebacterium parvus strain (Corynebacterium parvus), Clostridium sp), Bacillus sp), Clostridium sp), Lactobacillus strain (Corynebacterium parvus), Lactobacillus strain (Corynebacterium parvus), Clostridium sp), Lactobacillus strain (Corynebacterium parvus strain (Corynebacterium parvus), Clostridium sp), Lactobacillus strain (Corynebacterium parvus), Clostridium sp), Bacillus sp), Clostridium sp), Lactobacillus strain (Corynebacterium parvus (.
In some embodiments, the Cas nuclease is Cas9 nuclease from streptococcus pyogenes, in some embodiments Cas9 nuclease from streptococcus thermophilus, in some embodiments Cas9 nuclease from neisseria meningitidis, in some embodiments Cas9 nuclease from staphylococcus aureus, in some embodiments Cas nuclease is Cpf1 nuclease from francisco franciscensis, in some embodiments Cas nuclease is Cpf1 nuclease from the species aminoacid bacillus, in some embodiments Cas nuclease is Cpf1 nuclease from rhodospiraceae ND2006, in other embodiments Cas nuclease is Cpf1 nuclease from the genera.
Wild-type Cas9 has two nuclease domains: RuvC and HNH. The RuvC domain cleaves non-target DNA strands and the HNH domain cleaves target DNA strands. In some embodiments, the Cas9 nuclease comprises more than one RuvC domain and/or more than one HNH domain. In some embodiments, the Cas9 nuclease is wild-type Cas 9. In some embodiments, Cas9 is capable of inducing double strand breaks in the target DNA. In certain embodiments, the Cas nuclease can cleave dsDNA, it can cleave one strand of dsDNA, or it can have no DNA cleaving enzyme or nickase activity. An exemplary Cas9 amino acid sequence is provided in the form of SEQ ID NO: 3. An exemplary Cas9mRNA ORF sequence including a start codon and a stop codon is provided in the form of SEQ ID No. 4. An exemplary Cas9mRNA coding sequence suitable for inclusion in the fusion protein is provided in SEQ ID NO: 10.
In some embodiments, a chimeric Cas nuclease is used in which one domain or region of a protein is replaced with a portion of a different protein. In some embodiments, the Cas nuclease domain may be replaced with a domain from a different nuclease such as Fok 1. In some embodiments, the Cas nuclease may be a modified nuclease.
In other embodiments, the Cas nuclease may be from a type I CRISPR/Cas system. In some embodiments, the Cas nuclease may be a component of a cascade complex of a type I CRISPR/Cas system. In some embodiments, the Cas nuclease may be a Cas3 protein. In some embodiments, the Cas nuclease may be from a type III CRISPR/Cas system. In some embodiments, the Cas nuclease may have RNA cleavage activity.
In some embodiments, the RNA-guided DNA binding agent has single-strand nickase activity, i.e., can cleave one DNA strand to produce a single-strand break, also referred to as a "nick. In some embodiments, the RNA-guided DNA-binding agent comprises a Cas nickase. Nicking enzymes are enzymes that make nicks in dsDNA, i.e., that cleave one strand but not the other strand of the DNA duplex. In some embodiments, the Cas nickase is a version of a Cas nuclease (e.g., the Cas nucleases discussed above) in which the endonuclease active site is inactivated, e.g., by one or more alterations (e.g., point mutations) of the catalytic domain. See, e.g., U.S. patent No. 8,889,356 for a discussion of Cas nickases and exemplary catalytic domain changes. In some embodiments, a Cas nickase, such as a Cas9 nickase, has an unactivated RuvC or HNH domain. An exemplary Cas9 nickase amino acid sequence is provided in the form of SEQ ID No. 6. An exemplary Cas9 nickase mRNA ORF sequence including a start codon and a stop codon is provided in SEQ ID No. 7. An exemplary Cas9 nickase mRNA coding sequence suitable for inclusion in the fusion protein is provided in the form of SEQ ID NO: 11.
In some embodiments, the RNA-guided DNA binding agent is modified to contain only one functional nuclease domain. For example, the agent protein may be modified such that one of the nuclease domains is mutated or deleted in whole or in part to reduce its nucleolytic activity. In some embodiments, a nickase having a RuvC domain with reduced activity is used. In some embodiments, a nickase having an inactive RuvC domain is used. In some embodiments, a nickase having an HNH domain with reduced activity is used. In some embodiments, a nickase having an inactive HNH domain is used.
In some embodiments, a conserved amino acid in a Cas protein nuclease domain is substituted to reduce or alter nuclease activity. In some embodiments, the Cas nuclease may comprise an amino acid substitution in a RuvC or RuvC-like nuclease domain. Exemplary amino acid substitutions in the RuvC or RuvC-like nuclease domain include D10A (based on the streptococcus pyogenes Cas9 protein). See, e.g., Zetsche et al (2015) Cell Oct 22:163(3): 759-. In some embodiments, the Cas nuclease may comprise an amino acid substitution in an HNH or HNH-like nuclease domain. Exemplary amino acid substitutions in HNH or HNH-like nuclease domains include E762A, H840A, N863A, H983A, and D986A (based on streptococcus pyogenes Cas9 protein). See, e.g., Zetsche et al (2015). Other exemplary amino acid substitutions include D917A, E1006A, and D1255A (based on the franccpf 1(FnCpf1) sequence of franciscella foeniculis U112 Cpf1 (UniProtKB-A0Q7Q2(Cpf1_ FRATN)).
In some embodiments, a pair of guide RNAs complementary to the sense and antisense strands, respectively, of the target sequence are combined to provide an mRNA encoding a nicking enzyme. In this embodiment, the guide RNA directs the nicking enzyme to the target sequence and introduces the DSB by making a nick on the opposite strand of the target sequence (i.e., double nicking). In some embodiments, the use of double nicks can improve specificity and reduce off-target effects. In some embodiments, a nickase is used in conjunction with two independent guide RNAs that target opposite strands of DNA to create a double nick in the target DNA. In some embodiments, a nicking enzyme is used in conjunction with two independent guide RNAs that are selected to be in close proximity to create a double nick in the target DNA.
In some embodiments, the RNA-guided DNA binding agent lacks lyase and nickase activity. In some embodiments, the RNA-guided DNA binding agent comprises a dCas DNA binding polypeptide. dCas polypeptides have DNA binding activity and essentially lack catalytic (lyase/nickase) activity. In some embodiments, the dCas polypeptide is a dCas9 polypeptide. In some embodiments, an RNA-guided DNA-binding agent or dCas DNA-binding polypeptide lacking lyase and nickase activity is a version of a Cas nuclease (e.g., the Cas nucleases discussed above) in which the endonuclease active site is inactivated, e.g., by one or more alterations (e.g., point mutations) of the catalytic domain. See, e.g., U.S.2014/0186958a 1; U.S.2015/0166980A 1. An exemplary dCas9 amino acid sequence is provided in the form of SEQ ID NO: 8. An exemplary Cas9mRNA ORF sequence including a start codon and a stop codon is provided in the form of SEQ ID No. 9. An exemplary Cas9mRNA coding sequence suitable for inclusion in the fusion protein is provided in SEQ ID No. 12.
In some embodiments, the RNA-guided DNA binding agent comprises one or more heterologous functional domains (e.g., is or comprises a fusion polypeptide).
In some embodiments, the heterologous functional domain may facilitate the delivery of an RNA-directed DNA binding agent into the nucleus, for example, the heterologous functional domain may be a nuclear localization signal (N L S), in some embodiments, the RNA-directed DNA binding agent may be fused to 1-10N L S, in some embodiments, the RNA-directed DNA binding agent may be fused to 1-5N L S, in some embodiments, the RNA-directed DNA binding agent may be fused to one N L S, in the case of using one N L2S, N L S may be linked at the N-terminus or C-terminus of the RNA-directed DNA binding agent sequence N L S may also be inserted within the RNA-directed DNA binding agent sequence, in other embodiments, the RNA-directed DNA binding agent may be fused to more than one N L S, in some embodiments, the RNA-directed DNA binding agent may be fused to 2, 3,4 or 5N L S at two N465S, in some embodiments, the RNA-directed DNA binding agent may be fused to two N849, N595S, such as a single RNA-directed DNA binding agent, in some embodiments, such as a single RNA-directed RNA-targeting protein, a single RNA-targeting sequence, a RNA-targeting protein, a single RNA-targeting protein, such as a RNA-targeting protein, a targeting protein, such as a targeting protein.
In some embodiments, the heterologous functional domain may be capable of modifying the intracellular half-life of an RNA-guided DNA binding agent in some embodiments, the half-life of the RNA-guided DNA binding agent may be increased in some embodiments, the half-life of the RNA-guided DNA binding agent may be decreased in some embodiments, the heterologous functional domain may be capable of increasing the stability of the RNA-guided DNA binding agent in some embodiments, the heterologous functional domain may be capable of decreasing the stability of the RNA-guided DNA binding agent in some embodiments, the heterologous functional domain may act as a signal peptide for protein degradation in some embodiments, protein degradation may be mediated by proteolytic enzymes such as proteasomes, lysosomal proteases or calpain proteases in some embodiments, the heterologous functional domain may comprise a PEST 865st sequence in some embodiments, the RNA-guided DNA binding agent may be modified by adding ubiquitin or multiple ubiquitin strands in some embodiments, ubiquitin-like protein (UB L), non-limiting examples of ubiquitin-like proteins include small ubiquitin-like modification factor (mo), cross-reactive protein modification (sug) also known as sump-binding protein 15), ubiquitin-related ubiquitin-like ubiquitin-binding protein antigen expressed in human ubiquitin-binding cell, such as ubiquitin-binding protein laid down (atubg-3635), ubiquitin-like ubiquitin-binding protein, ubiquitin-binding protein laid down (atyup-3635), ubiquitin-like ubiquitin-binding protein-3635, atyup-related protein, atyup-369-9, and similar to stimulate human ubiquitin-9-12, similar to stimulate cell-12.
In some embodiments, the heterologous functional domain may be a marker domain non-limiting examples of marker domains include fluorescent proteins, purification tags, epitope tags, and reporter gene sequences in some embodiments, the marker domain may be a fluorescent protein non-limiting examples of suitable fluorescent proteins include Green fluorescent proteins (e.g., GFP-2, tagGFP, turboGFP, sfGFP, EGFP, Emerald (Emerald), Azami Green (Azami Green), single Azami Green (monocami Green), CopGFP, AceGFP, ZsGreen1), yellow fluorescent proteins (e.g., YFP, EYFP, Citrine, nuves, YPet, PhiYFP, ZsYellonel 1), blue fluorescent proteins (e.g., sSRsSREBFP, EBFTFP, Aftite, mlamamal, Puv, Sapphire-blue protein, Sapphire-yellow fluorescent protein, Sapphire-peroxidase, Orange protein, luciferase-11, peroxidase-11-7-8, GFP, luciferase.
In other embodiments, the heterologous functional domain can target the RNA-guided DNA binding agent to a particular organelle, cell type, tissue, or organ. In some embodiments, the heterologous functional domain can target an RNA-guided DNA binding agent to the mitochondria.
In other embodiments, the heterologous functional domain may be an effector domain. When an RNA-guided DNA binding agent is directed to its target sequence, e.g., when a Cas nuclease is directed to the target sequence through a gRNA, the effector domain may modify or affect the target sequence. In some embodiments, the effector domain can be selected from a nucleic acid binding domain, a nuclease domain (e.g., a non-Cas nuclease domain), an epigenetic modification domain, a transcriptional activation domain, or a transcriptional repression domain. In some embodiments, the heterologous functional domain is a nuclease, such as fokl nuclease. See, for example, U.S. patent No. 9,023,649. In some embodiments, the heterologous functional domain is a transcriptional activator or repressor. See, e.g., Qi et al, "reproducing CRISPR as an RNA-guided platform for sequence-specific control gene expression," Cell 152:1173-83 (2013); Perez-Pinera et al, "RNA-guided genetic analysis by CRISPR-Cas9-based transformation factors," nat. methods 10:973-6 (2013); mali et al, "CAS 9transcriptional activators for target specific crystallization and targeted amino for cooperative genome engineering," nat. Biotechnol.31:833-8 (2013); gilbert et al, "CRISPR-mediated modular RNA-guided regulation of transformation in eukaryotes," Cell 154:442-51 (2013). Thus, an RNA-guided DNA binding agent essentially becomes a transcription factor that can be guided using a guide RNA to bind a desired target sequence. In certain embodiments, the DNA modification domain is a methylation domain, such as a demethylation or methyltransferase domain. In certain embodiments, the effector domain is a DNA modification domain, such as a base editing domain. In particular embodiments, a DNA modification domain is a nucleic acid editing domain, such as a deaminase domain, that introduces specific modifications into DNA. See, e.g., WO 2015/089406; U.S. 2016/0304846. The nucleic acid editing domain, deaminase domain and Cas9 variants described in WO 2015/089406 and u.s.2016/0304846 are incorporated herein by reference.
The nuclease may comprise at least one domain that interacts with a guide RNA ("gRNA"). In addition, nucleases can be directed to the target sequence through the gRNA. In class 2 Cas nuclease systems, the gRNA interacts with a nuclease and a target sequence such that it directs binding to the target sequence. In some embodiments, the grnas provide specificity for targeted cleavage, and the nucleases can be universal and paired with different grnas to cleave different target sequences. Class 2 Cas nucleases can be paired with gRNA scaffold structures of the types, orthologs, and exemplary species listed above.
Guide RNA (gRNA)
In some embodiments of the present disclosure, the cargo of the L NP preparation includes at least one gRNA that can direct a Cas nuclease or class 2 Cas nuclease to a target sequence on a target nucleic acid molecule in some embodiments, the gRNA binds to the class 2 Cas nuclease and provides cleavage specificity by the class 2 Cas nuclease in some embodiments, the gRNA and Cas nuclease can form a Ribonucleoprotein (RNP), e.g., a CRISPR/Cas complex, such as a CRISPR/Cas9 complex, which can be delivered by a L NP composition.
"guide RNA," "gRNA," and simply "guide" are used interchangeably herein to refer to crRNA (also referred to as CRISPR RNA), or a combination of crRNA and trRNA (also referred to as tracrRNA). The crRNA and trRNA may associate as a single RNA molecule (single guide RNA, sgRNA) or as two separate RNA molecules (double guide RNA, dgRNA). "guide RNA" or "gRNA" refers to each type. the trRNA may be a naturally occurring sequence or a trRNA sequence having modifications or alterations compared to the naturally occurring sequence.
As used herein, "guide sequence" refers to a sequence in a guide RNA that is complementary to a target sequence and serves to direct the guide RNA to the target sequence for binding or modification (e.g., cleavage) by an RNA-guided DNA binding agent. A "guide sequence" may also be referred to as a "target sequence" or a "spacer sequence". The guide sequence can be 20 base pairs in length, for example in the case of streptococcus pyogenes (i.e., SpyCas9) and related Cas9 homologs/orthologs. Shorter or longer sequences may also be used as guides, for example 15, 16, 17, 18, 19, 21, 22, 23, 24 or 25 nucleotides in length. In some embodiments, the target sequence is, for example, in a gene or on a chromosome, and is complementary to the guide sequence. In some embodiments, the degree of complementarity or identity between a guide sequence and its corresponding target sequence may be about 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the guide sequence may be 100% complementary or identical to the target region. In other embodiments, the guide sequence and target region may contain at least one mismatch. For example, the guide sequence and target sequence may contain 1,2, 3, or 4 mismatches, with the total length of the target sequence being at least 17, 18, 19, 20, or more base pairs. In some embodiments, the guide sequence and target region may contain 1-4 mismatches, wherein the guide sequence comprises at least 17, 18, 19, 20 or more nucleotides. In some embodiments, the guide sequence and target region may contain 1,2, 3, or 4 mismatches, wherein the guide sequence comprises 20 nucleotides.
Target sequences for Cas proteins include both the positive and negative strands of genomic DNA (i.e., the given sequence and the reverse complement of the sequence) because the nucleic acid substrate of Cas protein is a double-stranded nucleic acid. Thus, where a guide sequence is said to be "complementary to" a target sequence, it is understood that the guide sequence can direct the binding of a guide RNA to the reverse complement of the target sequence. Thus, in some embodiments, where the guide sequence binds to the reverse complement of the target sequence, the guide sequence is identical to certain nucleotides of the target sequence (e.g., a target sequence that does not include PAM) except that U replaces T in the guide sequence.
The length of the targeting sequence may depend on the CRISPR/Cas system and components used. For example, different class 2 Cas nucleases from different bacterial species have varying optimal targeting sequence lengths. Thus, the targeting sequence may comprise 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, or greater than 50 nucleotides in length. In some embodiments, the targeting sequence length is 0, 1,2, 3,4, or 5 nucleotides longer or shorter than the guide sequence of the naturally occurring CRISPR/Cas system. In certain embodiments, the Cas nuclease and gRNA scaffold will be derived from the same CRISPR/Cas system. In some embodiments, the targeting sequence may comprise or consist of 18-24 nucleotides. In some embodiments, the targeting sequence may comprise or consist of 19-21 nucleotides. In some embodiments, the targeting sequence may comprise or consist of 20 nucleotides.
In some embodiments, the sgRNA is a "Cas 9 sgRNA" capable of RNA-guided DNA cleavage mediated by a Cas9 protein. In some embodiments, the sgRNA is a "Cpf 1 sgRNA" capable of RNA-directed DNA cleavage mediated by a Cpf1 protein. In certain embodiments, the gRNA comprises crRNA and tracr RNA sufficient to form an active complex with Cas9 protein and mediate RNA-guided DNA cleavage. In certain embodiments, the gRNA comprises crRNA sufficient to form an active complex with the Cpf1 protein and mediate RNA-guided DNA cleavage. See Zetsche 2015.
Certain embodiments of the invention also provide nucleic acids, e.g., expression cassettes, encoding grnas described herein. A "guide RNA nucleic acid" is used herein to refer to a guide RNA (e.g., sgRNA or dgRNA) and a guide RNA expression cassette, which is a nucleic acid encoding one or more guide RNAs.
In some embodiments, the nucleic acid may be a DNA molecule. In some embodiments, the nucleic acid may comprise a nucleotide sequence encoding a crRNA. In some embodiments, the nucleotide sequence encoding the crRNA comprises a targeting sequence flanked by all or a portion of a repeat sequence from a naturally occurring CRISPR/Cas system. In some embodiments, the nucleic acid may comprise a nucleotide sequence encoding a tracr RNA. In some embodiments, the crRNA and tracr RNA may be encoded by two separate nucleic acids. In other embodiments, the crRNA and tracr RNA may be encoded by a single nucleic acid. In some embodiments, the crRNA and tracr RNA may be encoded by opposite strands of a single nucleic acid. In other embodiments, the crRNA and tracr RNA may be encoded by the same strand of a single nucleic acid. In some embodiments, the gRNA nucleic acid encodes an sgRNA. In some embodiments, the gRNA nucleic acid encodes a Cas9 nuclease sgRNA. In some embodiments, the gRNA nucleic acid encodes a Cpf1 nuclease sgRNA.
The nucleotide sequence encoding the guide RNA can be operably linked to at least one transcriptional or regulatory control sequence, such as a promoterA seed, a 3'UTR or a 5' UTR. In one example, the promoter can be a tRNA promoter, e.g., a tRNALys3Or a tRNA chimera. See Mefferd et al, RNA.201521: 1683-9; scherer et al, Nucleic Acids Res.200735: 2620-2628. In certain embodiments, the promoter is recognized by RNA polymerase iii (pol iii). Non-limiting examples of Pol III promoters also include the U6 and H1 promoters. In some embodiments, the nucleotide sequence encoding the guide RNA may be operably linked to a mouse or human U6 promoter. In some embodiments, a gRNA nucleic acid is a modified nucleic acid. In certain embodiments, a gRNA nucleic acid includes a modified nucleoside or nucleotide. In some embodiments, gRNA nucleic acids include 5' end modifications, such as modified nucleosides or nucleotides to stabilize and prevent nucleic acid integration. In some embodiments, a gRNA nucleic acid comprises a double-stranded DNA having a 5' end modification on each strand. In certain embodiments, a gRNA nucleic acid includes an inverted dideoxy-T or inverted abasic nucleoside or nucleotide as a 5' end modification. In some embodiments, gRNA nucleic acids include labels such as biotin, desthiobiotin-TEG (desthiobioten-TEG), digoxigenin, and fluorescent labels including, for example, FAM, ROX, TAMRA, and AlexaFluor.
In certain embodiments, more than one gRNA nucleic acid, such as a gRNA, can be used in a CRISPR/Cas nuclease system. Each gRNA nucleic acid can contain a different targeting sequence, such that the CRISPR/Cas system cleaves more than one target sequence. In some embodiments, one or more grnas can have the same or different properties, such as activity or stability, within the CRISPR/Cas complex. Where more than one gRNA is used, each gRNA may be encoded on the same or different gRNA nucleic acid. The promoters used to drive expression of more than one gRNA may be the same or different.
Modified RNA
In certain embodiments, the L NP composition comprises modified RNA.
The modified nucleoside or nucleotide can be present in an RNA, such as a gRNA or mRNA. Grnas or mrnas comprising one or more modified nucleosides or nucleotides, for example, are referred to as "modified" RNAs, and are used to describe the presence of one or more non-natural and/or naturally occurring components or configurations used in place of or in addition to the typical A, G, C and U residues. In some embodiments, the modified RNA is synthesized from atypical nucleosides or nucleotides, referred to herein as "modified.
Modified nucleosides and nucleotides can include one or more of the following: (i) changes, such as substitutions (exemplary backbone modifications), of one or both of the non-bonded phosphate oxygens and/or one or more of the bonded phosphate oxygens in the phosphodiester backbone linkage; (ii) alterations in the ribose moiety, e.g., the 2' hydroxyl group on ribose, such as substitutions (exemplary sugar modifications); (iii) bulk replacement of phosphate moieties with "dephosphorylated" linkers (exemplary backbone modifications); (iv) modifications or substitutions of naturally occurring nucleobases, including with atypical nucleobases (exemplary base modifications); (v) substitution or modification of the ribose-phosphate backbone (exemplary backbone modifications); (vi) modification of the 3 'end or 5' end of the oligonucleotide, such as removal, modification or substitution of a terminal phosphate group or conjugation of a moiety, cap or linker (such 3 'or 5' cap modifications may include sugar and/or backbone modifications); and (vii) modifications or substitutions of sugars (exemplary sugar modifications). Certain embodiments comprise 5' end modifications of mRNA, gRNA, or nucleic acids. Certain embodiments comprise a 3' end modification of the mRNA, gRNA, or nucleic acid. The modified RNA can contain 5 'and 3' end modifications. The modified RNA may contain one or more modified residues in non-terminal positions. In certain embodiments, the gRNA includes at least one modified residue. In certain embodiments, the mRNA includes at least one modified residue.
As used herein, a first sequence is considered to be "comprising a sequence that is at least X% identical to a second sequence" if an alignment of the first sequence to the second sequence shows that X% or more of the positions of all of the second sequence match the first sequence. For example, sequence AAGA comprises a sequence that is 100% identical to sequence AAG, since an alignment will result in 100% identity because there is a match for all three positions of the second sequence. Differences between RNA and DNA (generally, uridine is replaced by thymidine or vice versa) and the presence of nucleoside analogues, such as modified uridine, do not cause differences in identity or complementarity between polynucleotides, as long as the relevant nucleotides (such as thymidine, uridine or modified uridine) have the same complementary sequence (e.g. adenosine for all thymidine, uridine or modified uridine; another example is cytosine and 5-methylcytosine, both having guanosine or modified guanosine as the complementary sequence). Thus, for example, the sequence 5'-AXG (where X is any modified uridine such as pseudouridine, N1-methylpseuduridine or 5-methoxyuridine) is considered to be 100% identical to AUG, since both are fully complementary to the same sequence (5' -CAU). Exemplary contrast algorithms are the Smith-waterman algorithm (Smith-waterman algorithm) and the Needleman-Wunsch algorithm (Needleman-Wunsch algorithm), which are well known in the art. Those skilled in the art will understand which algorithm choices and parameter settings are appropriate for a given pair of sequences to be aligned; for sequences of generally similar length and > 50% expected identity for amino acids or > 75% expected identity for nucleotides, the niemann-winche algorithm with default settings of the niemann-winche algorithm interface provided by the EBI at www.ebi.ac.uk website server is generally suitable.
mRNA
In some embodiments, a composition or formulation disclosed herein comprises an mRNA comprising an Open Reading Frame (ORF) encoding an RNA-guided DNA-binding agent, such as a Cas nuclease, or a class 2 Cas nuclease as described herein. In some embodiments, an mRNA comprising an ORF encoding an RNA-guided DNA-binding agent, such as a Cas nuclease or class 2 Cas nuclease, is provided, used, or administered. In some embodiments, the ORF encoding the RNA-guided DNA-binding agent is a "modified RNA-guided DNA-binding agent ORF" or simply a "modified ORF" that is used as a shorthand to indicate that the ORF is modified in one or more of the following ways: (1) the uridine content of the modified ORF is in the range of its minimum uridine content to 150% of the minimum uridine content; (2) the uridine dinucleotide content of the modified ORF is in the range of its minimum uridine dinucleotide content to 150% of its minimum uridine dinucleotide content; (3) the modified ORF is at least 90% identical to any one of SEQ ID NOs 1, 4, 7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66; (4) the modified ORF consists of a set of codons, wherein at least 75% of the codons are the smallest uridine codons of a given amino acid, e.g. codons with the least uridine (typically 0 or 1 in addition to codons for phenylalanine (wherein the smallest uridine codon has 2 uridines)); or (5) the modified ORF comprises at least one modified uridine. In some embodiments, the modified ORF is modified in at least two, three, or four of the aforementioned ways. In some embodiments, the modified ORF comprises at least one modified uridine and is modified with at least one, two, three, or all of (1) - (4) above.
"modified uridine" is used herein to refer to nucleosides other than thymidine that have the same hydrogen bond acceptor as uridine and one or more structural differences from uridine. In some embodiments, the modified uridine is a substituted uridine, i.e., a uridine in which one or more aprotic substituents (e.g., alkoxy groups, such as methoxy groups) replace a proton. In some embodiments, the modified uridine is a pseudouridine. In some embodiments, the modified uridine is a substituted pseudouridine, i.e., a pseudouridine in which one or more aprotic substituents (e.g., alkyl groups, such as methyl groups) replace a proton. In some embodiments, the modified uridine is any one of a substituted uridine, a pseudouridine, or a substituted pseudouridine.
As used herein, "uridine position" refers to a position in a polynucleotide occupied by uridine or a modified uridine. Thus, for example, a polynucleotide in which "100% of the uridine positions are modified uridine" contains a modified uridine at each position of the uridine in a conventional RNA (in which all bases are the standard A, U, C or G bases) that will be the same sequence. Unless otherwise indicated, U in the polynucleotide sequences of the sequence table (sequence listing) in or accompanying the present disclosure may be uridine or modified uridine.
TABLE 1 minimum uridine codon
In any of the preceding embodiments, the modified ORF may consist of a set of codons, wherein at least 75%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% of the codons are those listed in the table of smallest uridine codons. In any of the preceding embodiments, the modified ORF may comprise a sequence at least 90%, 95%, 98%, 99% or 100% identical to any of SEQ ID NOs 1, 4, 7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65 or 66.
In any of the preceding embodiments, the modified ORF may comprise a sequence at least 90%, 95%, 98%, 99% or 100% identical to any of SEQ ID NOs 1, 4, 7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65 or 66.
In any of the foregoing embodiments, the uridine content of the modified ORF may range from its minimum uridine content to 150%, 145%, 140%, 135%, 130%, 125%, 120%, 115%, 110%, 105%, 104%, 103%, 102%, or 101% of the minimum uridine content.
In any of the foregoing embodiments, the uridine dinucleotide content of the modified ORF may range from its minimum uridine dinucleotide content to 150%, 145%, 140%, 135%, 130%, 125%, 120%, 115%, 110%, 105%, 104%, 103%, 102%, or 101% of its minimum uridine dinucleotide content.
In any of the preceding embodiments, the modified ORF may comprise a modified uridine at least at one, more or all uridine positions. In some embodiments, the modified uridine is a uridine modified at position 5, for example with halogen, methyl or ethyl. In some embodiments, the modified uridine is a pseudouridine modified at position 1, for example with halogen, methyl or ethyl. The modified uridine may be, for example, pseudouridine, N1-methylpseudouridine, 5-methoxyuridine, 5-iodouridine or a combination thereof. In some embodiments, the modified uridine is 5-methoxyuridine. In some embodiments, the modified uridine is 5-iodouridine. In some embodiments, the modified uridine is a pseudouridine. In some embodiments, the modified uridine is N1-methylpseuduridine. In some embodiments, the modified uridine is a combination of pseudouridine and N1-methylpseuduridine. In some embodiments, the modified uridine is a combination of pseudouridine and 5-methoxyuridine. In some embodiments, the modified uridine is a combination of N1-methylpseudouridine and 5-methoxyuridine. In some embodiments, the modified uridine is a combination of 5-iodouridine and N1-methylpseuduridine. In some embodiments, the modified uridine is a combination of pseudouridine and 5-iodouridine. In some embodiments, the modified uridine is a combination of 5-iodouridine and 5-methoxyuridine.
In some embodiments, at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or 100% of the uridine positions in an mRNA according to the present disclosure are modified uridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in an mRNA according to the present disclosure are modified uridine, such as 5-methoxyuridine, 5-iodouridine, N1-methylpseudouridine, pseudouridine, or a combination thereof. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in mRNA according to the present disclosure are 5-methoxyuridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in mRNA according to the present disclosure are pseudouridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in mRNA according to the present disclosure are N1-methylpseudouridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in mRNA according to the present disclosure are 5-iodouridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in mRNA according to the present disclosure are 5-methoxyuridine, and the remainder are N1-methylpseudouridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in mRNA according to the present disclosure are 5-iodouridine, and the remainder are N1-methylpseudouridine.
In any of the preceding embodiments, the modified ORF may comprise a reduced uridine dinucleotide content, such as the lowest possible uridine dinucleotide (UU) content, e.g., (a) using the smallest uridine codon at each position (as discussed above) and (b) an ORF encoding the same amino acid sequence as the given ORF. The uridine dinucleotide (UU) content can be expressed in absolute terms as a count of UU dinucleotides in the ORF or, based on ratios, as a percentage of the positions occupied by the uridine of the uridine dinucleotide (e.g., the uridine dinucleotide content of AUUAU will be 40%, since the uridine of the uridine dinucleotide occupies 2 of the 5 positions). For the purpose of assessing the minimum uridine dinucleotide content, modified uridine residues are considered to be equivalent to uridine.
In some embodiments, the mRNA comprises at least one UTR from an expressed mammalian mRNA, such as a constitutively expressed mRNA. An mRNA is considered to be constitutively expressed in a mammal if it is transcribed continuously in at least one tissue of a healthy adult mammal. In some embodiments, the mRNA comprises a 5'UTR, a 3' UTR, or 5 'and 3' UTRs from an expressed mammalian RNA, such as a constitutively expressed mammalian mRNA. Actin mRNA is an example of a constitutively expressed mRNA.
In some embodiments, the mRNA comprises at least one UTR from hydroxysteroid 17- β dehydrogenase 4(HSD17B4 or HSD), e.g., 5'UTR from HSD in some embodiments, the mRNA comprises at least one UTR from globin mRNA, e.g., human α globin (HBA) mRNA, human β globin (HBB) mRNA or non Xenopus laevis (Xenopus laevis) β globin (xg) mRNA in some embodiments, the mRNA comprises 5' UTR, 3'UTR or 5' and 3'UTR from globin mRNA, e.g., HBA, HBB or xgg in some embodiments, the mRNA comprises 5' UTR from bovine growth hormone, Cytomegalovirus (CMV), mouse HBA-a1, HSD albumin, a gene, HBA, HBB or xgg in some embodiments, the mRNA comprises 5'UTR from bovine growth hormone, murine Cytomegalovirus (CMV), murine HBA-a1, HSD albumin, bovine cytomegalovirus (HBA-1), murine HBA-a, bovine serum albumin (Hsp-c-5' Hsp-c, bovine serum albumin, bovine serum.
In some embodiments, the mRNA comprises 5 'and 3' UTRs from the same source, e.g., a constitutively expressed mRNA, such as actin, albumin, or globulin (such as HBA, HBB, or xgg).
In some embodiments, the mRNA does not comprise a 5'UTR, e.g., there are no additional nucleotides between the 5' cap and the start codon. In some embodiments, the mRNA comprises a Kozak sequence (described below) between the 5 'cap and the start codon, but without any additional 5' UTR. In some embodiments, the mRNA does not comprise a 3' UTR, e.g., no additional nucleotides are present between the stop codon and the poly a (poly-a) tail.
In some embodiments, the mRNA comprises a Kozak sequence. The Kozak sequence can affect translation initiation and overall production of the polypeptide translated from the mRNA. The Kozak sequence includes a methionine codon that can serve as a start codon. The minimum Kozak sequence is NNNRUGN, where at least one of the following is true: the first N is A or G and the second N is G. In the case of the nucleotide sequence, R means purine (A or G). In some embodiments, the Kozak sequence is RNNRUGN, NNNRUGG, RNNRUGG, RNNAUGN, NNNAUGG, or RNNAUGG. In some embodiments, the Kozak sequence is rcrugg with zero mismatches or at most one or two mismatches at positions in lower case form. In some embodiments, the Kozak sequence is rccAUGg with zero mismatches or at most one or two mismatches at positions in lower case form. In some embodiments, the Kozak sequence is gccRccAUGG with zero mismatches or at most one, two, or three mismatches at positions in lowercase form. In some embodiments, the Kozak sequence is gcccaccaug with zero mismatches or at most one, two, three, or four mismatches at positions in lower case form. In some embodiments, the Kozak sequence is GCCACCAUG. In some embodiments, the Kozak sequence is gccgccrcccaugg with zero mismatches or at most one, two, three, or four mismatches at positions in lowercase.
In some embodiments, the mRNA comprising an ORF encoding an RNA-guided DNA binding agent comprises a sequence having at least 90% identity to SEQ ID NO:43, optionally wherein the ORF of SEQ ID NO:43 (i.e., SEQ ID NO:4) is replaced with an alternative ORF to any one of SEQ ID NO:7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the mRNA comprising an ORF encoding an RNA-guided DNA binding agent comprises a sequence having at least 90% identity to SEQ ID NO:44, optionally wherein the ORF of SEQ ID NO:44 (i.e., SEQ ID NO:4) is replaced with an alternative ORF to any one of SEQ ID NO:7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the mRNA comprising an ORF encoding an RNA-directed DNA binding agent comprises a sequence having at least 90% identity to SEQ ID NO:56, optionally wherein the ORF of SEQ ID NO:56 (i.e., SEQ ID NO:4) is replaced with an alternative ORF to any one of SEQ ID NO:7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the mRNA comprising an ORF encoding an RNA-guided DNA binding agent comprises a sequence having at least 90% identity to SEQ ID NO:57, optionally wherein the ORF of SEQ ID NO:57 (i.e., SEQ ID NO:4) is replaced with an alternative ORF to any one of SEQ ID NO:7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the mRNA comprising an ORF encoding an RNA-directed DNA binding agent comprises a sequence having at least 90% identity to SEQ ID NO:58, optionally wherein the ORF of SEQ ID NO:58 (i.e., SEQ ID NO:4) is replaced with an alternative ORF to any one of SEQ ID NO:7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the mRNA comprising an ORF encoding an RNA-guided DNA binding agent comprises a sequence having at least 90% identity to SEQ ID NO:59, optionally wherein the ORF of SEQ ID NO:59 (i.e., SEQ ID NO:4) is replaced with an alternative ORF to any one of SEQ ID NO:7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the mRNA comprising an ORF encoding an RNA-directed DNA binding agent comprises a sequence having at least 90% identity to SEQ ID NO:60, optionally wherein the ORF of SEQ ID NO:60 (i.e., SEQ ID NO:4) is replaced with an alternative ORF to any one of SEQ ID NO:7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the mRNA comprising an ORF encoding an RNA-guided DNA binding agent comprises a sequence having at least 90% identity to SEQ ID NO:61, optionally wherein the ORF of SEQ ID NO:61 (i.e., SEQ ID NO:4) is replaced with an alternative ORF to any one of SEQ ID NO:7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the mRNA comprises an alternative ORF for any one of SEQ ID NOs 7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 50, 52, 54, 65, or 66.
In some embodiments, the degree of identity to the optionally substituted sequence of SEQ ID NOs 43, 44 or 56-61 is 95%. In some embodiments, the degree of identity to the optionally substituted sequence of SEQ ID NOs 43, 44, or 56-61 is 98%. In some embodiments, the degree of identity to the optionally substituted sequence of SEQ ID NOs 43, 44 or 56-61 is 99%. In some embodiments, the degree of identity to the optionally substituted sequence of SEQ ID NOs 43, 44 or 56-61 is 100%.
In some embodiments, an mRNA disclosed herein comprises a 5' Cap, such as Cap0, Cap1, or Cap 2. The 5' cap is typically a 7-methylguanosine nucleotide (which may be further modified, as discussed below, e.g., with regard to ARCA) linked to the first nucleotide of the 5' to 3' strand of the mRNA by a 5' -triphosphate, i.e., the 5' position of the proximal nucleotide of the first cap. In Cap0, the ribose sugars of the proximal nucleotides of both the first and second caps of the mRNA contain a 2' -hydroxyl group. In Cap1, the ribose sugars of the first and second transcribed nucleotides of mRNA contain a 2 '-methoxy group and a 2' -hydroxy group, respectively. In Cap2, the ribose sugars of the proximal nucleotides of both the first and second caps of the mRNA contain a 2' -methoxy group. See, e.g., Katibah et al (2014) Proc Natl Acad Sci USA111(33): 12025-30; abbas et al (2017) Proc Natl Acad Sci USA114(11): E2106-E2115. Most endogenous higher eukaryote mrnas, including mammalian mrnas (such as human mrnas), comprise Cap1 or Cap 2. Due to recognition as "non-self" by components of the innate immune system, such as IFIT-1 and IFIT-5, Cap0, as well as other Cap structures other than Cap1 and Cap2, may be immunogenic in mammals, such as humans, which may result in elevated levels of cytokines, including type I interferons. Components of the innate immune system, such as IFIT-1 and IFIT-5, can also compete with eIF4E for binding to mrnas with caps other than Cap1 or Cap2, potentially inhibiting mRNA translation.
The cap may be included in a co-transcribed form. For example, ARCA (anti-inversion cap analog; Thermo Fisher scientific Catalogue No. AM8045) is a cap analog comprising 7-methylguanine 3' -methoxy-5 ' -triphosphate linked to the 5' position of a guanine ribonucleotide, which can be initially incorporated into a transcript in vitro. ARCA produces a Cap of Cap0 in which the 2' position of the proximal nucleotide of the first Cap is a hydroxyl group. See, for example, Stepinski et al, (2001) "Synthesis and properties of mRNAs modifying the novel 'anti-reverse' cap analogs7-methyl (3'-O-methyl) GpppG and 7-methyl (3' deoxy) GpppG," RNA 7: 1486-. The ARCA structure is shown below.
CleanCapTMAG (m7G (5') ppp (5') (2' OMeA) pG; Tri L ink Biotechnologies Cat No. N-7113) or CleanCapTMGG (m7G (5') ppp (5') (2' OMeG) p G; Tri L ink Biotechnologies catalog number N-7133) can be used to provide Cap1 structures in a co-transcriptional fashion CleanCapTMAG and CleanCapTMGG 3' -O-methylated versions are also available from Tri L ink Biotechnologies, Cl eanCap under catalog numbers N-7413 and N-7433, respectivelyTMThe AG structure is shown below.
Alternatively, caps can be added to RNA post-transcriptionally. For example, vaccinia capping enzyme is commercially available (NewEngland Biolabs catalog number M2080S) and has RNA triphosphatase and guanosine acyltransferase activities provided by its D1 subunit, and guanine methyltransferase provided by its D12 subunit. Thus, 7-methylguanine can be added to RNA in the presence of S-adenosylmethionine and GTP to produce Cap 0. See, e.g., Guo, P. and Moss, B. (1990) Proc.Natl.Acad.Sci.USA 87, 4023-; mao, X, and Shuman, S. (1994) J.biol.chem.269, 24472-24479.
In some embodiments, the mRNA further comprises a poly-adenylated (poly-a) tail. In some embodiments, the poly-a tail comprises at least 20, 30, 40, 50, 60, 70, 80, 90, or 100 adenines, optionally up to 300 adenines. In some embodiments, the poly-A tail comprises 95, 96, 97, 98, 99, or 100 adenine nucleotides. In some cases, the poly-A tail is "interrupted" by one or more non-adenine nucleotide "anchors" at one or more positions in the poly-A tail. The poly-A tail may comprise at least 8 consecutive adenine nucleotides, but also one or more non-adenine nucleotides. As used herein, "non-adenine nucleotide" refers to any natural or non-natural nucleotide that does not contain adenine. Guanine, thymine, and cytosine nucleotides are exemplary non-adenine nucleotides. Thus, a poly-a tail on an mRNA described herein can comprise consecutive adenine nucleotides located 3' to the nucleotides encoding the RNA-guided DNA binding agent or target sequence. In some cases, the poly-a tail on the mRNA comprises non-contiguous adenine nucleotides located 3' to the nucleotides encoding the RNA-guided DNA binding agent or target sequence, wherein the non-adenine nucleotides interrupt the adenine nucleotides at regular or irregular intervals.
In some embodiments, the mRNA further comprises a poly-adenylated (poly-a) tail. In some embodiments, the poly-a tail comprises at least 20, 30, 40, 50, 60, 70, 80, 90, or 100 adenines, optionally up to 300 adenines. In some embodiments, the poly-A tail comprises 95, 96, 97, 98, 99, or 100 adenine nucleotides. In some cases, the poly-A tail is "interrupted" by one or more non-adenine nucleotide "anchors" at one or more positions in the poly-A tail. The poly-A tail may comprise at least 8 consecutive adenine nucleotides, but also one or more non-adenine nucleotides. As used herein, "non-adenine nucleotide" refers to any natural or non-natural nucleotide that does not contain adenine. Guanine, thymine, and cytosine nucleotides are exemplary non-adenine nucleotides. Thus, a poly-a tail on an mRNA described herein can comprise consecutive adenine nucleotides located 3' to the nucleotides encoding the RNA-guided DNA binding agent or target sequence. In some cases, the poly-a tail on the mRNA comprises non-contiguous adenine nucleotides located 3' to the nucleotides encoding the RNA-guided DNA binding agent or target sequence, wherein the non-adenine nucleotides interrupt the adenine nucleotides at regular or irregular intervals.
In some embodiments, one or more non-adenine nucleotides are positioned to interrupt a continuous adenine nucleotide such that a poly (a) binding protein can bind to a stretch of continuous adenine nucleotides. In some embodiments, the one or more non-adenine nucleotides are located after at least 8, 9, 10, 11, or 12 consecutive adenine nucleotides. In some embodiments, one or more non-adenine nucleotides are located after at least 8-50 consecutive adenine nucleotides. In some embodiments, one or more non-adenine nucleotides are located after at least 8-100 consecutive adenine nucleotides. In some embodiments, the non-adenine nucleotide is one, two, three, four, five, six, or seven adenine nucleotides later and then at least 8 consecutive adenine nucleotides later.
The poly-A tail may comprise a sequence of consecutive adenine nucleotides followed by one or more non-adenine nucleotides, optionally followed by additional adenine nucleotides.
In some embodiments, the poly-A tail comprises or contains one non-adenine nucleotide or one contiguous stretch of 2-10 non-adenine nucleotides. In some embodiments, the one or more non-adenine nucleotides are located after at least 8, 9, 10, 11, or 12 consecutive adenine nucleotides. In some cases, one or more non-adenine nucleotides are located after at least 8-50 consecutive adenine nucleotides. In some embodiments, one or more non-adenine nucleotides are located after at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 consecutive adenine nucleotides.
In some embodiments, the non-adenine nucleotide is guanine, cytosine, or thymine. In some cases, the non-adenine nucleotide is a guanine nucleotide. In some embodiments, the non-adenine nucleotide is a cytosine nucleotide. In some embodiments, the non-adenine nucleotide is a thymine nucleotide. In some cases where more than one non-adenine nucleotide is present, the non-adenine nucleotide may be selected from: a) guanine and thymine nucleotides; b) guanine and cytosine nucleotides; c) thymine and cytosine nucleotides; or d) guanine, thymine and cytosine nucleotides. An exemplary poly-A tail comprising a non-adenine nucleotide is provided in SEQ ID NO: 62.
In some embodiments, mRNA is purified using a precipitation method (e.g., L iCl precipitation, alcohol precipitation, or equivalent methods, e.g., as described herein). in some embodiments, mRNA is purified using a chromatography-based method, such as an HP L C-based method or equivalent methods (e.g., as described herein). in some embodiments, mRNA is purified using both a precipitation method (e.g., L iCl precipitation) and an HP L C-based method.
In some embodiments, at least one gRNA is provided in combination with an mRNA disclosed herein. In some embodiments, the gRNA is provided in the form of a molecule that is isolated from mRNA. In some embodiments, the gRNA is provided as a portion of an mRNA disclosed herein, such as a portion of a UTR.
Chemically modified gRNA
In some embodiments, the gRNA is chemically modified. Grnas comprising one or more modified nucleosides or nucleotides are referred to as "modified" grnas or "chemically modified" grnas to describe the presence of one or more non-natural and/or naturally occurring components or configurations used in place of or in addition to the typical A, G, C and U residues. In some embodiments, a modified gRNA is synthesized from atypical nucleosides or nucleotides, referred to herein as "modified. Modified nucleosides and nucleotides can include one or more of the following: (i) changes, such as substitutions (exemplary backbone modifications), of one or both of the non-bonded phosphate oxygens and/or one or more of the bonded phosphate oxygens in the phosphodiester backbone linkage; (ii) alterations in the ribose moiety, e.g., the 2' hydroxyl group on ribose, such as substitutions (exemplary sugar modifications); (iii) bulk replacement of phosphate moieties with "dephosphorylated" linkers (exemplary backbone modifications); (iv) modifications or substitutions of naturally occurring nucleobases, including with atypical nucleobases (exemplary base modifications); (v) substitution or modification of the ribose-phosphate backbone (exemplary backbone modifications); (vi) modification of the 3 'end or 5' end of the oligonucleotide, such as removal, modification or substitution of a terminal phosphate group or conjugation of a moiety, cap or linker (such 3 'or 5' cap modifications may include sugar and/or backbone modifications); and (vii) modifications or substitutions of sugars (exemplary sugar modifications).
In some embodiments, the gRNA comprises a modified uridine at some or all of the uridine positions. In some embodiments, the modified uridine is a uridine modified at position 5, for example with halogen or C1-C6 alkoxy. In some embodiments, the modified uridine is a pseudouridine modified at position 1, for example with a C1-C6 alkyl group. The modified uridine may be, for example, pseudouridine, N1-methylpseudouridine, 5-methoxyuridine, 5-iodouridine or a combination thereof. In some embodiments, the modified uridine is 5-methoxyuridine. In some embodiments, the modified uridine is 5-iodouridine. In some embodiments, the modified uridine is a pseudouridine. In some embodiments, the modified uridine is N1-methylpseuduridine. In some embodiments, the modified uridine is a combination of pseudouridine and N1-methylpseuduridine. In some embodiments, the modified uridine is a combination of pseudouridine and 5-methoxyuridine. In some embodiments, the modified uridine is a combination of N1-methylpseudouridine and 5-methoxyuridine. In some embodiments, the modified uridine is a combination of 5-iodouridine and N1-methylpseuduridine. In some embodiments, the modified uridine is a combination of pseudouridine and 5-iodouridine. In some embodiments, the modified uridine is a combination of 5-iodouridine and 5-methoxyuridine.
In some embodiments, at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% of the uridine positions in a gRNA according to the present disclosure are modified uridines. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in a gRNA according to the present disclosure are modified uridine, such as 5-methoxyuridine, 5-iodouridine, N1-methylpseuduridine, pseudouridine, or a combination thereof. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in a gRNA according to the present disclosure are 5-methoxyuridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in a gRNA according to the present disclosure are pseudouridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in a gRNA according to the present disclosure are N1-methylpseudouridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in a gRNA according to the present disclosure are 5-iodouridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in a gRNA according to the present disclosure are 5-methoxyuridine, and the remainder is N1-methylpseudouridine. In some embodiments, 10% -25%, 15% -25%, 25% -35%, 35% -45%, 45% -55%, 55% -65%, 65% -75%, 75% -85%, 85% -95%, or 90% -100% of the uridine positions in a gRNA according to the present disclosure are 5-iodouridine, and the remainder is N1-methylpseudouridine.
Chemical modifications, such as those listed above, can be combined to yield modified grnas comprising nucleosides and nucleotides (collectively, "residues") that can have two, three, four, or more modifications. For example, a modified residue can have a modified sugar and a modified nucleobase. In some embodiments, each base of the gRNA is modified, e.g., all bases have a modified phosphate group, such as a phosphorothioate group. In certain embodiments, all or substantially all of the phosphate groups of the gRNA molecule are replaced with phosphorothioate groups. In some embodiments, the modified gRNA comprises at least one modified residue at or near the 5' end of the RNA. In some embodiments, the modified gRNA comprises at least one modified residue at or near the 3' end of the RNA.
In some embodiments, the gRNA comprises one, two, three, or more modified residues. In some embodiments, at least 5% (e.g., at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100%) of the positions in the modified gRNA are modified nucleosides or nucleotides.
Unmodified nucleic acids can be readily degraded by nucleases such as those found in intracellular nucleases or in serum. For example, nucleases can hydrolyze nucleic acid phosphodiester bonds. Thus, in one aspect, a gRNA described herein can contain one or more modified nucleosides or nucleotides, e.g., to introduce stability towards intracellular nucleases or serum-based nucleases. In some embodiments, the modified gRNA molecules described herein can exhibit a reduced innate immune response when introduced into a population of cells in vivo and ex vivo. The term "innate immune response" encompasses cellular responses to exogenous nucleic acids (including single-stranded nucleic acids), involving the induction of cytokine (especially interferon) expression and release, and cell death.
In some embodiments of backbone modifications, the phosphate group of the modified residue may be modified by replacing one or more oxygens with different substituents. In addition, a modified residue, e.g., a modified residue present in a modified nucleic acid, can comprise a bulk replacement of an unmodified phosphate moiety with a modified phosphate group as described herein. In some embodiments, backbone modifications of the phosphate backbone may include alterations that result in charged linkers with no electrical linkers or with asymmetric charge distributions.
Examples of modified phosphate groups include phosphorothioates, phosphoroselenoates, boranophosphates, hydrogenphosphonates, phosphoramidates, alkyl or aryl phosphonates, and phosphotriesters. The phosphorus atom in the unmodified phosphate group is achiral. However, replacement of one of the non-bridging oxygens with one of the above atom or group of atoms may render the phosphorus atom chiral. The stereosymmetric phosphorus atom may have an "R" configuration (herein Rp) or an "S" configuration (herein Sp). The backbone may also be modified by replacing the bridging oxygen (i.e., the oxygen linking the phosphate to the nucleoside) with nitrogen (bridging phosphoramidate), sulfur (bridging phosphorothioate), and carbon (bridging methylenephosphonate). The displacement may occur at either or both of the connecting oxygens.
The phosphate group may be replaced in certain backbone modifications by a phosphorus-free linking group. In some embodiments, the charged phosphate groups may be replaced by neutral moieties. Examples of moieties that can replace a phosphate group can include, but are not limited to, methyl phosphonates, hydroxyamines, siloxanes, carbonates, carboxymethyl, carbamates, amides, thioethers, ethylene oxide linkers, sulfonates, sulfonamides, thiometals, formals, oximes, methyleneimino, methylenemethylimino, methylenehydrazine, methylenedimethylhydrazine, and methyleneoxymethylimino, for example.
Template nucleic acid
The compositions and methods disclosed herein can include a template nucleic acid. The template can be used to alter or insert a nucleic acid sequence at or near a target site of a Cas nuclease. In some embodiments, the method comprises introducing the template into the cell. In some embodiments, a single template may be provided. In other embodiments, two or more templates may be provided such that editing may occur at two or more target sites. For example, different templates may be provided to edit a single gene in a cell, or two different genes in a cell.
In some embodiments, the template may be used in homologous recombination. In some embodiments, homologous recombination can result in the integration of a template sequence or a portion of a template sequence into a target nucleic acid molecule. In other embodiments, the template may be used for homology directed repair involving DNA strand invasion at a cleavage site in a nucleic acid. In some embodiments, homology directed repair can result in the inclusion of a template sequence in the edited target nucleic acid molecule. In other embodiments, the template may be used for gene editing mediated by non-homologous end joining. In some embodiments, the template sequence does not have similarity to a nucleic acid sequence near the cleavage site. In some embodiments, a template or a portion of a sequence of templates is incorporated. In some embodiments, the template comprises a flanking Inverted Terminal Repeat (ITR) sequence.
In some embodiments, the template may comprise a first homology arm and a second homology arm (also referred to as a first nucleotide sequence and a second nucleotide sequence) that are complementary to sequences located upstream and downstream of the cleavage site, respectively. When the template contains two homology arms, each arm may be the same length or a different length, and the sequence between the homology arms may be substantially similar or identical to the target sequence between the homology arms, or the sequences may be completely unrelated. In some embodiments, the degree of complementarity or percent identity between the first nucleotide sequence on the template and the sequence upstream of the cleavage site, and between the second nucleotide sequence on the template and the sequence downstream of the cleavage site, can permit homologous recombination, such as high fidelity homologous recombination, between the template and the target nucleic acid molecule. In some embodiments, the degree of complementarity may be about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%. In some embodiments, the degree of complementarity may be about 95%, 97%, 98%, 99%, or 100%. In some embodiments, the degree of complementarity may be at least 98%, 99%, or 100%. In some embodiments, the degree of complementarity may be 100%. In some embodiments, the percent identity may be about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%. In some embodiments, the percent identity may be about 95%, 97%, 98%, 99%, or 100%. In some embodiments, the percent identity may be at least 98%, 99%, or 100%. In some embodiments, the percent identity may be 100%.
In some embodiments, the template sequence may correspond to, comprise, or consist of an endogenous sequence of the target cell. The template sequence may additionally or alternatively correspond to, comprise or consist of a sequence foreign to the target cell. As used herein, the term "endogenous sequence" refers to a sequence that is native to a cell. The term "exogenous sequence" refers to a sequence that is not native to a cell, or a sequence that is at a different location in the genome of a cell from the native location. In some embodiments, the endogenous sequence can be a genomic sequence of the cell. In some embodiments, the endogenous sequence can be a chromosomal or extra-chromosomal sequence. In some embodiments, the endogenous sequence can be a plasmid sequence of the cell. In some embodiments, the template sequence may be substantially identical to a portion of the endogenous sequence at or near the site of cleavage in the cell, but comprise at least one nucleotide change. In some embodiments, cleavage of a target nucleic acid molecule with template editing can result in a mutation comprising an insertion, deletion, or substitution of one or more nucleotides of the target nucleic acid molecule. In some embodiments, the mutation may result in one or more amino acid changes in a protein expressed by a gene comprising the target sequence. In some embodiments, the mutation may result in one or more nucleotide changes in the RNA expressed by the target gene. In some embodiments, the mutation can alter the expression level of the target gene. In some embodiments, the mutation may result in increased or decreased expression of the target gene. In some embodiments, the mutation can result in gene knockdown. In some embodiments, the mutation can result in a gene knockout. In some embodiments, the mutation may result in restoring gene function. In some embodiments, cleavage of a target nucleic acid molecule with template editing can result in changes in the exonic sequences, intronic sequences, regulatory sequences, transcriptional control sequences, translational control sequences, splice sites, or non-coding sequences of the target nucleic acid molecule (such as DNA).
In other embodiments, the template sequence may comprise an exogenous sequence. In some embodiments, the exogenous sequence can comprise a protein or RNA coding sequence operably linked to an exogenous promoter sequence such that when the exogenous sequence is integrated into the target nucleic acid molecule, the cell is capable of expressing the protein or RNA encoded by the integrated sequence. In other embodiments, when the exogenous sequence is integrated into the target nucleic acid molecule, expression of the integrated sequence can be regulated by an endogenous promoter sequence. In some embodiments, the exogenous sequence can provide a cDNA sequence encoding a protein or a portion of a protein. In other embodiments, the exogenous sequence may comprise or consist of an exonic sequence, an intronic sequence, a regulatory sequence, a transcriptional control sequence, a translational control sequence, a splice site, or a non-coding sequence. In some embodiments, integration of the exogenous sequence can result in restoring gene function. In some embodiments, integration of the exogenous sequence can result in a gene knock-in. In some embodiments, integration of the exogenous sequence can result in gene knock-out.
The template may have any suitable length. In some embodiments, the length of the template may comprise 10, 15, 20, 25, 50, 75, 100, 150, 200, 500, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000 or more nucleotides. The template may be a single stranded nucleic acid. The template may be a double-stranded or partially double-stranded nucleic acid. In certain embodiments, the single stranded template is 20, 30, 40, 50, 75, 100, 125, 150, 175, or 200 nucleotides in length. In some embodiments, a template can comprise a nucleotide sequence that is complementary to a portion of a target nucleic acid molecule comprising a target sequence (i.e., a "homology arm"). In some embodiments, the template may comprise a homology arm that is complementary to a sequence located upstream or downstream of the cleavage site on the target nucleic acid molecule.
In some embodiments, the template contains ssDNA or dsDNA having flanking Inverted Terminal Repeat (ITR) sequences. In some embodiments, the template is provided in the form of a vector, plasmid, minicircle, nanoring, or PCR product.
Purification of nucleic acids
In some embodiments, nucleic acids are purified using a precipitation method (e.g., L iCl precipitation, alcohol precipitation, or equivalent methods, e.g., as described herein). in some embodiments, nucleic acids are purified using a chromatography-based method, such as an HP L C-based method or equivalent methods (e.g., as described herein). in some embodiments, nucleic acids are purified using both a precipitation method (e.g., L iCl precipitation) and an HP L C-based method.
Target sequence
In some embodiments, the CRISPR/Cas system of the present disclosure can target and cleave a target sequence on a target nucleic acid molecule. For example, the target sequence may be recognized and cleaved by a Cas nuclease. In certain embodiments, the target sequence of the Cas nuclease is located near the homologous PAM sequence of the nuclease. In some embodiments, a class 2 Cas nuclease can be guided to a target sequence of a target nucleic acid molecule by a gRNA, wherein the gRNA hybridizes to the target sequence and the class 2 Cas protein cleaves the target sequence. In some embodiments, the guide RNA hybridizes to a target sequence adjacent to or comprising its cognate PAM and the class 2 Cas nuclease cleaves the target sequence. In some embodiments, the target sequence may be complementary to the targeting sequence of the guide RNA. In some embodiments, the degree of complementarity between the targeting sequence of the guide RNA and the portion of the corresponding target sequence that hybridizes to the guide RNA may be about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%. In some embodiments, the percentage of identity between the targeting sequence of the guide RNA and the portion of the corresponding target sequence that hybridizes to the guide RNA can be about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%. In some embodiments, the homologous regions of the target are adjacent to homologous PAM sequences. In some embodiments, the target sequence may comprise a sequence that is 100% complementary to the targeting sequence of the guide RNA. In other embodiments, the target sequence may comprise at least one mismatch, deletion, or insertion as compared to the targeting sequence of the guide RNA.
The length of the target sequence may depend on the nuclease system used. For example, the length of the targeting sequence of the guide RNA of the CRISPR/Cas system can comprise 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, or more than 50 nucleotides and the target sequence is the corresponding length, optionally adjacent to a PAM sequence. In some embodiments, the length of the target sequence may comprise 15-24 nucleotides. In some embodiments, the length of the target sequence may comprise 17-21 nucleotides. In some embodiments, the target sequence may comprise 20 nucleotides in length. When a nicking enzyme is used, the target sequence may comprise a pair of target sequences recognized by a pair of nicking enzymes that cleave opposite strands of the DNA molecule. In some embodiments, the target sequence may comprise a pair of target sequences recognized by a pair of nicking enzymes that cleave the same strand of a DNA molecule. In some embodiments, the target sequence may comprise a portion of the target sequence recognized by one or more Cas nucleases.
The target nucleic acid molecule can be any DNA or RNA molecule that is endogenous or exogenous to the cell. In some embodiments, the target nucleic acid molecule can be episomal DNA, plasmid, genomic DNA, viral genome, mitochondrial DNA, or chromosomal DNA from or in the cell. In some embodiments, the target sequence of a target nucleic acid molecule can be a genomic sequence from or in a cell (including a human cell).
In other embodiments, the target sequence may be a viral sequence. In other embodiments, the target sequence may be a pathogen sequence. In other embodiments, the target sequence may be a synthetic sequence. In other embodiments, the target sequence may be a chromosomal sequence. In certain embodiments, the target sequence may comprise a translocation junction, such as a translocation associated with cancer. In some embodiments, the target sequence may be on a eukaryotic chromosome, such as a human chromosome. In certain embodiments, the target sequence is a liver-specific sequence in that it is expressed in liver cells.
In some embodiments, the target sequence may be located in a coding sequence of a gene, an intron sequence of a gene, a regulatory sequence, a transcriptional control sequence of a gene, a translational control sequence of a gene, a splice site, or a non-coding sequence between genes. In some embodiments, the gene may be a protein-encoding gene. In other embodiments, the gene may be a non-coding RNA gene. In some embodiments, the target sequence may comprise all or a portion of a disease-associated gene. In some embodiments, the target sequence may be located in a non-gene functional site in the genome, for example, a site that controls aspects of chromatin organization, such as a scaffold site or a locus control region.
In embodiments involving Cas nucleases, such as class 2 Cas nucleases, the target sequence may be adjacent to a protospacer adjacent motif ("PAM"). In some embodiments, the PAM may be adjacent to or within 1,2, 3 or 4 nucleotides of the 3' end of the target sequence. The length and sequence of the PAM may depend on the Cas protein used. For example, PAM can be selected from a common sequence of a particular Cas9 protein or Cas9 ortholog or a particular PAM sequence, including those disclosed in FIG. 1 of Ran et al, Nature,520: 186-containing 191(2015), and in FIG. S5 of Zetsche 2015, the relevant disclosures of which are each incorporated herein by reference. In some embodiments, the PAM can be 2, 3,4, 5, 6, 7, 8, 9, or 10 nucleotides in length. Non-limiting exemplary PAM sequences include NGG, NGGNG, NG, NAAAAN, nnaaw, NNNNACA, GNNNCNNA, TTN, and NNNNGATT (where N is defined as any nucleotide and W is defined as a or T). In some embodiments, the PAM sequence may be NGG. In some embodiments, the PAM sequence may be NGGNG. In some embodiments, the PAM sequence may be TTN. In some embodiments, the PAM sequence can be nnaaaw.
Lipid formulations
Disclosed herein are various embodiments of L NP formulations of RNA (including CRISPR/Cas cargo.) such L NP formulations include "amine lipids" along with helper lipids, neutral lipids, and PEG lipids in some embodiments such L NP formulations include "amine lipids" along with helper lipids and PEG lipids in some embodiments L NP formulations include less than 1% neutral phospholipids in some embodiments L NP formulations include less than 0.5% neutral phospholipids.
Amine lipids
L NP compositions for delivery of bioactive agents comprise "amine lipids," which are defined as lipid A or its equivalent, including acetal analogs of lipid A.
In some embodiments, the amine lipid is lipid a, which is octadeca-9, 12-dienoic acid (9Z,12Z) -3- ((4, 4-bis (octyloxy) butyryl) oxy) -2- ((((3- (diethylamino) propoxy) carbonyl) oxy) methyl) propyl ester, also known as (9Z,12Z) -octadeca-9, 12-dienoic acid 3- ((4, 4-bis (octyloxy) butyryl) oxy) -2- ((((3- (diethylamino) propoxy) carbonyl) oxy) methyl) propyl ester. Lipid a can be depicted as:
lipid a can be synthesized according to WO2015/095340 (e.g. pages 84-86). In certain embodiments, the amine lipid is the equivalent of lipid a.
In certain embodiments, the amine lipid is an analog of lipid a in certain embodiments, the lipid a analog is an acetal analog of lipid a in certain L NP compositions, the acetal analog is a C4-C12 acetal analog, in some embodiments, the acetal analog is a C5-C12 acetal analog, in other embodiments, the acetal analog is a C5-C10 acetal analog, in other embodiments, the acetal analog is selected from the group consisting of C4, C5, C6, C7, C9, C10, C11, and C12 acetal analogs.
Amine lipids suitable for L NPs described herein are biodegradable in vivo and suitable for delivery of biologically active agents, such as RNA, to cells the amine lipids have low toxicity (e.g., tolerated in animal models without adverse effects in amounts greater than or equal to 10mg/kg of RNA cargo) in certain embodiments, L NPs comprising amine lipids include L NPs wherein at least 75% of the amine lipids are cleared from plasma within 8, 10, 12, 24, or 48 hours or 3,4, 5, 6, 7, or 10 days, in certain embodiments, L NPs comprising amine lipids include L NPs wherein at least 50% of the mRNA or grna is cleared from plasma within 8, 10, 12, 24, or 48 hours or 3,4, 5, 6, 7, or 10 days.
Lipid clearance can be measured as described in the literature. See Maier, m.a. et alBiodegradable Lipids Enabling Rapidly Eliminated Lipid Nanoparticles for Systemic Delivery of RNAi Therapeutics.Mol.Ther.2013,21(8),
1570-78 ("Maier"). for example, in Maier, a L NP-siRNA system containing sirnas targeting luciferase is administered by intravenous bolus injection via lateral tail vein to six to eight week old male C57Bl/6 mice at 0.3 mg/kg. blood, liver and spleen samples are collected at 0.083, 0.25, 0.5, 1,2, 4, 8, 24, 48, 96 and 168 hours after administration.blood, liver and spleen samples are perfused and blood samples are treated to obtain plasma prior to tissue collection.furthermore, Maier describes a procedure for assessing toxic sirnas after administration of L NP-siRNA formulation. for example, 0, 1,3, 5 and 10mg/kg (5 animals/group) are administered via single intravenous bolus injection at a dose volume of 5m L/kg to Sprague-dole rats (Sprague-body weight luciferase) at 24 hours, and serum free for assessing clinical signs of toxicity of animals although the serum is applicable to post mortem methods for assessing clinical clearance of animals, clinical clearance of serum samples, clinical studies, clinical clearance of serum samples, clinical procedures for assessing clinical grade of NPs, clinical grade, and grade, and grade.
In some embodiments, the clearance rate is an RNA clearance rate, such as the rate of clearance of mRNA or gRNA from blood, serum, or plasma, in some embodiments, the clearance rate is the rate of clearance of L NP from blood, serum, or plasma.
The amine lipids of the present disclosure are ionizable (e.g., can form salts) depending on the pH of the medium in which they are located. For example, in a weakly acidic medium, amine lipids may be protonated and thus positively charged. Conversely, in weakly basic media, such as blood at a pH of about 7.35, amine lipids may not be protonated and therefore uncharged. In some embodiments, the amine lipids of the present disclosure can be protonated at a pH of at least about 9. In some embodiments, the amine lipids of the present disclosure can be protonated at a pH of at least about 9. In some embodiments, the amine lipids of the present disclosure can be protonated at a pH of at least about 10.
In some embodiments, the amine lipids of the present disclosure may each independently have a pKa in the range of about 5.1 to about 7.4. in some embodiments, the amine lipids of the present disclosure may each independently have a pKa in the range of about 5.5 to about 6.6. in some embodiments, the amine lipids of the present disclosure may each independently have a pKa in the range of about 5.6 to about 6.4. in some embodiments, the amine lipids of the present disclosure may each independently have a pKa in the range of about 5.8 to about 6.2. for example, the amine lipids of the present disclosure may each independently have a pKa in the range of about 5.8 to about 6.5. the amine lipids of the present disclosure may be an important consideration for formulating L NPs since cationic lipids having a pKa in the range of about 5.1 to about 7.4 are found to be effective for in vivo delivery of a cargo (e.g., delivery to the liver; further, the cationic lipid of about 5.3 to about 2014/136086. see, for example, the in vivo delivery of a tumor.
Additional lipids
Examples of neutral phospholipids suitable for use in the present disclosure include, but are not limited to, 5-heptadecylbenzene-1, 3-diol (resorcinol), Dipalmitoylphosphatidylcholine (DPPC), Distearoylphosphatidylcholine (DSPC), phosphatidylcholine (DOPC), Dimyristoylphosphatidylcholine (DMPC), phosphatidylcholine (P L PC), 1, 2-distearoylphosphatidylcholine-sn-glycero-3-phosphatidylcholine (DAPC), Phosphatidylethanolamine (PE), phosphatidylcholine (EPC), dilauroylphosphatidylcholine (D L PC), Dimyristoylphosphatidylcholine (DMPC), 1-myristoylphosphatidylcholine-2-palmitoylphosphatidylcholine (MPPC), 1-palmitoyl-2-myristoylphosphatidylcholine (PMPC), 1-palmitoyl-2-stearoylphosphatidylcholine (PSPC), 1, 2-diacylphosphatidylcholine-sn-glycero-3-phosphate (DBPC), 1-palmitoylethanolamine (dpc), phosphatidylethanolamine, dipalmitoylphosphatidylcholine (dpe), phosphatidylethanolamine), and, as in one embodiment, the neutral phospholipids may be in the group consisting of neutral phosphatidylcholine (DPPC), Dipalmitoylphosphatidylphosphatidylcholine (DPPC), phosphatidylethanolamine, Dipalmitoylphosphatidylcholine (DMPC), dipalmitoylphosphatidylcholine (dpe), phosphatidylethanolamine, Dipalmitoylphosphatidylcholine (DMPC), phosphatidylethanolamine, dipalmitoyl phosphatidylethanolamine, a neutral phosphatidylcholine (DMPC), and another embodiment of which may be in one embodiment in the following, neutral phosphatidylcholine (DPPC).
"helper lipids" include steroids, sterols, and alkylresorcinols. Helper lipids suitable for use in the present disclosure include, but are not limited to, cholesterol, 5-heptadecylresorcinol, and cholesterol hemisuccinate. In one embodiment, the helper lipid may be cholesterol. In one embodiment, the helper lipid may be cholesterol hemisuccinate.
PEG lipids can assist in the formulation process by, for example, reducing particle aggregation and controlling particle size.
In some embodiments, the lipid moiety may be derived from diacylglycerols or diacyloleamides (diacylglycylamides), including those comprising a dialkylglycerol or dialkylglyceramide group having an alkyl chain length independently comprising from about C4 to about C40 saturated or unsaturated carbon atoms, wherein the chain may comprise one or more functional groups, such as an amide or an ester. In some embodiments, the alkyl chain length comprises from about C10 to C20. The dialkylglycerol or dialkylglyceroamide group may further comprise one or more substituted alkyl groups. The chain length may be symmetrical or asymmetrical.
As used herein, unless otherwise indicated, the term "PEG" means any polyethylene glycol or other polyalkylene ether polymer. In one embodiment, the PEG moiety is an optionally substituted linear or branched polymer of ethylene glycol or ethylene oxide. In certain embodiments, the PEG moiety is, or the PEG moiety may be substituted with, for example, one or more alkyl, alkoxy, acyl, hydroxy, or aryl groups. In one embodiment, the PEG moiety comprises a PEG copolymer, such as PEG-polyurethane or PEG-polypropylene (see, e.g., J.Milton Harris, Poly (ethylene glycol) chemistry: biotechnical and biological applications (1992)); alternatively, the PEG moiety does not include a PEG copolymer, e.g., it can be a PEG homopolymer. In one embodiment, the molecular weight of the PEG is from about 130 to about 50,000, in sub-embodiments from about 150 to about 30,000, in sub-embodiments from about 150 to about 20,000, in sub-embodiments from about 150 to about 15,000, in sub-embodiments from about 150 to about 10,000, in sub-embodiments from about 150 to about 6,000, in sub-embodiments from about 150 to about 5,000, in sub-embodiments from about 150 to about 4,000, in sub-embodiments from about 150 to about 3,000, in sub-embodiments from about 300 to about 3,000, in sub-embodiments from about 1,000 to about 3,000, and in sub-embodiments from about 1,500 to about 2,500.
In certain embodiments, PEG (e.g., conjugated to a lipid moiety or lipid, such as a stealth lipid)) Is "PEG-2K", also known as "PEG 2000", and has an average molecular weight of about 2,000 daltons. PEG-2K is represented herein by the following formula (I), wherein n is 45, meaning that the number average degree of polymerization comprises about 45 subunitsHowever, other PEG embodiments known in the art may be used, including, for example, those in which the number average degree of polymerization comprises about 23 subunits (n ═ 23) and/or 68 subunits (n ═ 68). In some embodiments, n may range from about 30 to about 60. In some embodiments, n may range from about 35 to about 55. In some embodiments, n may range from about 40 to about 50. In some embodiments, n may range from about 42 to about 48. In some embodiments, n may be 45. In some embodiments, R may be selected from H, substituted alkyl, and unsubstituted alkyl. In some embodiments, R may be unsubstituted alkyl. In some embodiments, R may be methyl.
In any of the embodiments described herein, the PEG lipid may be selected from PEG-dilauroyl glycerol, PEG-dimyristoyl glycerol (PEG-DMG) (Cat No. GM-020, available from NOF, Tokyo, Japan), PEG-dipalmitoyl glycerol, PEG-distearoyl glycerol (PEG-DSPE) (Cat No. DSPE-020CN, NOF, Tokyo, Japan), PEG-dilauryl glycerol amide, PEG-dimyristoyl glycerol amide, PEG-dipalmitoyl glycerol amide and PEG-distearoyl glycerol amide, PEG-cholesterol (1- [8' - (cholest-5-ene-3 [ β ] -oxy) carboxamido-3 ',6' -dioxaoctyl ] carbamoyl- [ omega ] -methyl-poly (ethylene glycol), PEG-DMB (3, 4-ditetradecyloxy benzyl- [ omega ] -methyl-poly (ethylene glycol) ether), 1, 2-dimyristoyl-glycerol-3-phosphoethanolamine-N- [ 2 ] (polyethylene glycol) ether) (Cat No. PEG-27, PEG-2000, PEG-bis-PEG-5-PEG-35, PEG-2000, PEG-bis-35, PEG-35-PEG-2000, PEG-2000, PEG-bis-5-PEG-35-PEG-2000, PEG-bis-35-PEG-2000, PEG-35-PEG-2000, PEG-bis-2000, PEG-2000, PEG-18-27, PEG-18-PEG-27, PEG-bis-PEG-bis-PEG-18, PEG-27, PEG-18, PEG-27, PEG-27, PEG-27, PEG-bis-PEG-bis-PEG-bis-27, PEG-.
L NP formulations
Embodiments of the present disclosure provide lipid compositions described according to respective molar ratios of lipid components in a formulation in one embodiment, the mol% of amine lipids may be from about 30 mol% to about 60 mol%, in one embodiment, the mol% of amine lipids may be from about 40 mol% to about 60 mol%, in one embodiment, the mol% of amine lipids may be from about 45 mol% to about 60 mol%, in one embodiment, the mol% of amine lipids may be from about 50 mol% to about 60 mol%, in one embodiment, the mol% of amine lipids may be from about 55 mol% to about 60 mol%, in one embodiment, the mol% of amine lipids may be from about 50 mol% to about 55 mol%, in one embodiment, the mol% of amine lipids may be about 50 mol%, in one embodiment, the mol% of amine lipids may be about 55 mol%, in one embodiment, the fraction L mol% of the target lipid component may be 30 mol%, 30 mol% of amine components, in one embodiment, the mol% of NP may be less than 5 mol%, in some embodiments, the target lipid component may be less than 5 mol% of NP 5%, in the batch, or less than 5 mol% of NP 5% NP 5, 3.5 mol% of the target lipid component may be less than 5 mol% of the target lipid component in some embodiments, 3 mol% of the batch 365 mol% of the amino lipid component ± 5.
In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be from about 5 mol% to about 15 mol%. In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be from about 7 mol% to about 12 mol%. In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be from about 0 mol% to about 5 mol%. In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be from about 0 mol% to about 10 mol%. In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be from about 5 mol% to about 10 mol%. In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be from about 8 mol% to about 10 mol%.
In one embodiment, the mol% of neutral lipid, e.g., neutral phospholipid, can be about 5 mol%, about 6 mol%, about 7 mol%, about 8 mol%, about 9 mol%, about 10 mol%, about 11 mol%, about 12 mol%, about 13 mol%, about 14 mol%, or about 15 mol%. In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be about 9 mol%.
In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be from about 1 mol% to about 5 mol%. In one embodiment, the mol% of neutral lipids may be from about 0.1 mol% to about 1 mol%. In one embodiment, the mol% of neutral lipid, such as neutral phospholipid, may be about 0.1 mol%, about 0.2 mol%, about 0.5 mol%, 1 mol%, about 1.5 mol%, about 2 mol%, about 2.5 mol%, about 3 mol%, about 3.5 mol%, about 4 mol%, about 4.5 mol%, or about 5 mol%.
In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be less than about 1 mol%. In one embodiment, the mol% of neutral lipids, e.g., neutral phospholipids, can be less than about 0.5 mol%. In one embodiment, the mol% of neutral lipid, e.g., neutral phospholipid, can be about 0 mol%, about 0.1 mol%, about 0.2 mol%, about 0.3 mol%, about 0.4 mol%, about 0.5 mol%, about 0.6 mol%, about 0.7 mol%, about 0.8 mol%, about 0.9 mol%, or about 1 mol%. In some embodiments, the formulations disclosed herein are free of neutral lipids (i.e., 0 mol% neutral lipids). In some embodiments, the formulations disclosed herein are substantially free of neutral lipids (i.e., about 0 mol% neutral lipids). In some embodiments, the formulations disclosed herein are free of neutral phospholipids (i.e., 0 mol% neutral phospholipids). In some embodiments, the formulations disclosed herein are substantially free of neutral phospholipids (i.e., about 0 mol% neutral phospholipids).
In some embodiments, the mole% of neutral lipids of the L NP batches will be ± 30%, ± 25%, ± 20%, ± 15%, ± 10%, ± 5% or ± 2.5% of the mole% of the target neutral lipids in certain embodiments, the L NP batch-to-batch rate of change will be less than 15%, less than 10% or less than 5%.
In one embodiment, the mol% of the helper lipid may be from about 20 mol% to about 60 mol%, in one embodiment, the mol% of the helper lipid may be from about 25 mol% to about 55 mol%, in one embodiment, the mol% of the helper lipid may be from about 25 mol% to about 50 mol%, in one embodiment, the mol% of the helper lipid may be from about 25 mol% to about 40 mol%, in one embodiment, the mol% of the helper lipid may be from about 30 mol% to about 50 mol%, in one embodiment, the mol% of the helper lipid may be from about 30 mol% to about 40 mol%, in one embodiment, the mol% of the helper lipid is adjusted based on the amine lipid, neutral lipid, and PEG lipid concentrations to achieve 100 mol% of the lipid component, in one embodiment, the mol% of the helper lipid is adjusted based on the amine lipid and PEG lipid concentrations to achieve 100 mol%, in one embodiment, the mol% of the helper lipid component is adjusted to achieve less than 20 mol% in one embodiment, the mole% of the helper lipid component is adjusted to achieve less than 5 mol% of the target NP 5, or less than 15 mol% in one embodiment, the other embodiments, the amino lipid component is adjusted to achieve a less than 15 mol% of 355 mol% of the target lipid component, or 15 mol% of the target NP.
In one embodiment, the mol% of PEG lipid may be from about 1 mol% to about 10 mol%, in one embodiment, the mol% of PEG lipid may be from about 2 mol% to about 8 mol%, in one embodiment, the mol% of PEG lipid may be from about 2 mol% to about 4 mol%, in one embodiment, the mol% of PEG lipid may be from about 2.5 mol% to about 4 mol%, in one embodiment, the mol% of PEG lipid may be about 3 mol%, in one embodiment, the mol% of PEG lipid may be about 2.5 mol%, in some embodiments, the mol% of PEG lipid of the L NP batch will be ± 30%, ± 25% ± 20%, ± 15%, ± 10%, ± 5%, or ± 2.5%, in some embodiments, the NP batch L%, the NP batch NP will vary less than 15%, less than 10% or less than 15% NP.
In certain embodiments, the cargo comprises mRNA encoding an RNA-guided DNA binding agent (e.g., Cas nuclease, class 2 Cas nuclease, or Cas9), and gRNA or nucleic acid encoding a gRNA, or a combination of mRNA and gRNA in one embodiment, a L NP composition may comprise lipid a or an equivalent thereof in some aspects, an amine lipid is lipid a in some aspects, an amine lipid is a lipid a equivalent, e.g., an analog of lipid a in some aspects, an amine lipid is an acetal analog of lipid a in various embodiments, a L NP composition may comprise an amine lipid, a neutral lipid, a helper lipid, and a PEG lipid in some embodiments, a helper lipid is cholesterol in some embodiments, a neutral lipid is DSPC in particular embodiments, a PEG lipid is PEG2k-DMG in some embodiments, a L NP composition may comprise a, a helper lipid, a neutral lipid, and a PEG lipid in some embodiments, a L NP composition comprises a amine, a cholesterol, and a lipid in some embodiments, a dmpc lipid-a dma composition comprises a lipid a dmpc, a lipid-acetal in some embodiments, a dmpc-dsa lipid composition comprises a lipid a dmpc, a dmpc-dsa lipid equivalent in embodiments, a dmpc, a DMG, a dmpc, a lipid-DSPC, a dmpc, a lipid-DSPC-dsa, in embodiments, a.
In various embodiments, the L NP composition comprises an amine lipid, a helper lipid, a neutral lipid, and a PEG lipid in various embodiments, the L NP composition comprises a lipid component consisting of an amine lipid, a helper lipid, a neutral lipid, and a PEG lipid in various embodiments, the L NP composition comprises an amine lipid, a helper lipid, and a PEG lipid in various embodiments, the L NP composition does not comprise a neutral lipid, such as a neutral phospholipid in various embodiments, the L composition comprises a lipid component consisting of an amine lipid, a helper lipid, and a PEG lipid in various embodiments, the neutral lipid is selected from one or more of DSPC, DPPC, DAPC, DMPC, DOPC, DOPE, and DSPE in certain embodiments, the neutral lipid is selected from the group consisting of DPPC, DMPC, DOPC, DOPE, and DMPC, the neutral lipid is selected from the group consisting of a cholesterol, DMPC-9618 NP, the neutral lipid is selected from the group consisting of a cholesterol, DMPC, DOPC, DOPE, DMPC, DOPC, DMPC, dipc, DMPC, cholesterol, DMPC.
Embodiments of the present invention also provide lipid compositions described in terms of the molar ratio between the positively charged amine groups (N) of amine lipids and the negatively charged phosphate groups (P) of the nucleic acid to be encapsulated, which may be mathematically represented by equation N/P in some embodiments, a L NP composition may comprise a lipid component comprising amine lipids, helper lipids, neutral lipids, and PEG lipids, and a nucleic acid component, wherein the N/P ratio is about 3 to 10 in some embodiments, a L NP composition may comprise a lipid component comprising amine lipids, helper lipids, and PEG lipids, and a nucleic acid component, wherein the N/P ratio is about 3 to 10 in some embodiments, a L NP composition may comprise a lipid component comprising amine lipids, helper lipids, neutral lipids, and helper lipids, and an RNA component, wherein the N/P ratio is about 3 to 10 in some embodiments, wherein the N/P ratio may be about 3 to 10 in some embodiments, a L NP composition lipid component comprising amine lipids, helper lipids, and RNA components, wherein the N/P ratio may be about 3 to 10 in embodiments, or may be less than about 2.5 to 10% in embodiments, a variation of the N/P ratio may be about 2 to 10.5 to 10, in embodiments, a variation of about 2 to 10 to 5 to 10% P ratio of about 3 to 10.
In some embodiments, the nucleic acid component, e.g., RNA component, can comprise mRNA, such as Cas nuclease-encoding mRNA, the RNA component comprises RNA, optionally accompanied by additional nucleic acids and/or proteins, e.g., RNP cargo in one embodiment, the RNA comprises Cas9mRNA in some compositions comprising Cas nuclease-encoding mRNA, L NP further comprises gRNA nucleic acid, such as gRNA.
In certain embodiments, the L NP composition can comprise mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease), an amine lipid, a helper lipid, a neutral lipid, and a PEG lipid in certain embodiments, the L NP composition can comprise mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease), an amine lipid, a helper lipid, and a PEG lipid in certain L NP compositions comprising mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease), the helper lipid is cholesterol in other compositions comprising mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease), the neutral lipid is dspc in other embodiments comprising mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease), the PEG lipid is PEG2k-DMG or PEG2k-c11 in certain compositions comprising mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease), the amine lipid is selected from lipid a and equivalents thereof, such as an acetal lipid analog lipid a.
In some embodiments, L NP compositions may comprise grnas in certain embodiments, L NP compositions may comprise amine lipids, grnas, helper lipids, neutral lipids, and PEG lipids in certain embodiments, L NP compositions may comprise amine lipids, grnas, helper lipids, and PEG lipids in certain L NP compositions comprising grnas, helper lipids are cholesterol in some compositions comprising grnas, neutral lipids are dspcs in other embodiments comprising grnas, PEG lipids are PEG2k-DMG or PEG2k-c11 in certain embodiments, amine lipids are selected from lipid a and equivalents thereof, such as acetal analogs of lipid a.
In one embodiment, an L NP composition may comprise a sgRNA in one embodiment, a L NP composition may comprise a Cas9sgRNA in one embodiment, a L NP composition may comprise a Cpf1sgRNA in some compositions comprising sgrnas, L NP comprises an amine lipid, a helper lipid, a neutral lipid, and a PEG lipid in some compositions comprising sgrnas, L NP comprises an amine lipid, a helper lipid, and a PEG lipid in some compositions comprising sgrnas, the helper lipid is cholesterol in other compositions comprising sgrnas, the neutral lipid is dspc in other embodiments comprising sgrnas, the PEG lipid is PEG2k-DMG or PEG2k-c11 in certain embodiments, the amine lipid is selected from lipid a and equivalents thereof, such as an acetal analog of lipid a.
In certain embodiments, a L NP composition comprises Cas nuclease-encoding mRNA and gRNA, which may be sgrna in one embodiment, a L NP composition may comprise an amine lipid, a Cas nuclease-encoding mRNA, gRNA, helper lipid, neutral lipid, and PEG lipid in one embodiment, a L NP composition may comprise a lipid component consisting of an amine lipid, helper lipid, neutral lipid, and PEG lipid, and a nucleic acid component consisting of Cas nuclease-encoding mRNA and gRNA in one embodiment, L NP composition may comprise a lipid component consisting of an amine lipid, helper lipid, and PEG lipid, and a nucleic acid component consisting of Cas nuclease-encoding mRNA and gRNA in certain compositions comprising Cas nuclease-encoding mRNA and gRNA, helper lipid is cholesterol in certain compositions comprising Cas nuclease-encoding mRNA and gRNA, neutral is dspc in certain compositions comprising Cas nuclease-encoding mRNA and gRNA, neutral is less than about 1 mol% neutral lipid, e.g. phospholipid in certain embodiments, a neutral lipid-encoding mRNA and gRNA composition comprises less than about 5 mol% of a phospholipid, and a lipid-encoding lipid-phospholipid in certain embodiments, such as dmpc-5 NP-5, and PEG-5-neutral lipid-encoding lipid-phospholipid, and lipid-neutral lipid-phospholipid, such as dmcas nuclease-encoding mRNA and lipid-neutral.
In certain embodiments, the L NP composition comprises Cas nuclease mRNA, such as class 2 Cas mRNA and at least one gRNA in certain embodiments, the L NP composition comprises a ratio of about 25:1 to about 1:25 gRNA to Cas nuclease mRNA, such as class 2 Cas nuclease mRNA in certain embodiments, the L NP formulation comprises a ratio of about 10:1 to about 1:10 gRNA to Cas nuclease mRNA, such as class 2 Cas nuclease mRNA in certain embodiments, the L NP formulation comprises a ratio of about 8:1 to about 1:8 gRNA to Cas nuclease mRNA, such as class 2 Cas nuclease mRNA, as measured herein, in a ratio by weight in some embodiments, the L NP formulation comprises a ratio of about 5:1 to about 1:5 gRNA to nuclease mRNA, such as class 2 mRNA in some embodiments, in a ratio of about 3:1 to 1:3, about 2:1 to 1:2, about 5:1 to about 1:5, such as class 2 mRNA in some embodiments, in a range of about 3:1 to 1:3, about 2:1 to 1:2, about 5:1 to 5, about 1:3, about 3, or about 3 to about 1:1, such as3, 3 to about 1:1 to 10.
The L NP compositions disclosed herein can include a template nucleic acid that can be co-formulated with an mRNA encoding a Cas nuclease, such as a class 2 Cas nuclease mRNA.
In some embodiments, L NP is formed by mixing an aqueous RNA solution with an organic solvent-based lipid solution, such as 100% ethanol suitable solutions or solvents include or may contain water, PBS, Tris buffer, NaCl, citrate buffer, ethanol, chloroform, diethyl ether, cyclohexane, tetrahydrofuran, methanol, isopropanol pharmaceutically acceptable buffers may be used for in vivo administration of, for example, L NP, in some embodiments, buffers are used to maintain the pH of a composition comprising L NP at or above pH 6.5. in some embodiments, buffers are used to maintain the pH of a composition comprising L NP at or above pH 7.0. in some embodiments, the pH of a composition is in the range of about 7.2 to about 7.7. in other embodiments, the pH of a composition is in the range of about 7.3 to about 7.7, or about 7.4 to about 7.6. in some embodiments, the pH of an osmotic buffer, the buffer may include a sucrose, a sucrose, a sucrose, a sucrose, a.
In some embodiments, microfluidic mixing, T-type mixing, or cross-mixing is used in some aspects, flow rates, linker sizes, linker geometries, linker shapes, tube diameters, solutions, and/or RNA and lipid concentrations may vary L NP or L NP compositions may be concentrated or purified, for example, via dialysis, tangential flow filtration, or chromatography L NP may be stored, for example, in suspension, emulsion, or lyophilized powder form in some embodiments, L NP compositions are stored at 2 ℃ to 8 ℃, in some aspects L NP compositions are stored at room temperature in further embodiments, frozen storage, for example, at L NP compositions at-20 ℃ or-80 ℃.
L NPs may be, for example, microspheres (including unilamellar and multilamellar vesicles, such as "liposomes" -lamellar phase lipid bilayers that are generally spherical in some embodiments-and may comprise an aqueous core, e.g., comprising a majority of the RNA molecule in more particular embodiments), dispersed phases in an emulsion, micelles, or internal phases in suspension.
In addition, L NP compositions are biodegradable in that they do not accumulate to cytotoxic levels in vivo at therapeutically effective doses in some embodiments L NP compositions do not cause an innate immune response at therapeutic dose levels that results in significant adverse effects in some embodiments L NP compositions provided herein do not cause toxicity at therapeutic dose levels.
In some embodiments, the pdi may range from about 0.005 to about 0.75. In some embodiments, the pdi may be in the range of about 0.01 to about 0.5. In some embodiments, the pdi may range from about zero to about 0.4. In some embodiments, the pdi may range from about zero to about 0.35. In some embodiments, the pdi may range from about zero to about 0.35. In some embodiments, the pdi may range from about zero to about 0.3. In some embodiments, the pdi may range from about zero to about 0.25. In some embodiments, the pdi may range from about zero to about 0.2. In some embodiments, the pdi may be less than about 0.08, 0.1, 0.15, 0.2, or 0.4.
L NPs disclosed herein have a size (e.g., Z-average diameter) of about 1 to about 250nm, in some embodiments, L NPs have a size of about 10 to about 200nm, in other embodiments, L NPs have a size of about 20 to about 150nm, in some embodiments, L NPs have a size of about 50 to about 150nm, in some embodiments, L NPs have a size of about 50 to about 100nm, in some embodiments, L NPs have a size of about 50 to about 120nm, in some embodiments, L NPs have a size of about 60 to about 100nm, in some embodiments, L NPs have a size of about 75 to about 150nm, in some embodiments, L NPs have a size of about 75 to about 120nm, in some embodiments, L NPs have a size of about 75 to about 100nm unless otherwise specified, all of the sizes mentioned herein are the average size of fully-shaped nanoparticles (e.g., Zener diameter as measured by Zener light-weighted photon dilution on a Zener salt-photon counting scale (Zener) such that the measured by Zener light scattering intensity on a Zener particle size-weighted graph (Zener — Zener photon luminescence) measured as Zener photon luminescence spectroscopy, Zener photon luminescence, Zener, measured in Zener, measured on a sample, Zener.
In some embodiments, L NPs are formed to have an average encapsulation efficiency in the range of about 50% to about 100%. in some embodiments, L NPs are formed to have an average encapsulation efficiency in the range of about 50% to about 70%. in some embodiments, L NPs are formed to have an average encapsulation efficiency in the range of about 70% to about 90%. in some embodiments, L NPs are formed to have an average encapsulation efficiency in the range of about 90% to about 100%. in some embodiments, L NPs are formed to have an average encapsulation efficiency in the range of about 75% to about 95%.
In some embodiments, L NP is formed to have an average molecular weight in the range of about 1.00E +05g/mol to about 1.00E +10g/mol L NP is formed to have an average molecular weight in the range of about 5.00E +05g/mol to about 7.00E +07g/mol L NP is formed to have an average molecular weight in the range of about 1.00E +06g/mol to about 1.00E +10g/mol in some embodiments L NP is formed to have an average molecular weight in the range of about 1.00E +07g/mol to about 1.00E +09g/mol in some embodiments L NP is formed to have an average molecular weight in the range of about 5.00E +06g/mol to about 5.00E +09 g/mol.
In some embodiments, the polydispersity (Mw/Mn; ratio of weight average molar mass (Mw) to number average molar mass (Mn)) may range from about 1.000 to about 2.000. In some embodiments, the Mw/Mn can range from about 1.00 to about 1.500. In some embodiments, the Mw/Mn can range from about 1.020 to about 1.400. In some embodiments, the Mw/Mn can be in the range of about 1.010 to about 1.100. In some embodiments, the Mw/Mn can range from about 1.100 to about 1.350.
Methods of engineering cells; engineered cells
The L NP compositions disclosed herein can be used in methods of engineering cells by gene editing in vivo and in vitro in some embodiments, the methods involve contacting cells with the L NP compositions described herein.
In some embodiments, the method involves contacting a cell of a subject, such as a mammal, such as a human, in some embodiments the cell is in an organ, such as a liver, such as a mammal liver, such as a human liver in some embodiments the cell is a liver cell, such as a mammal liver cell, such as a human liver cell in some embodiments the liver cell is a stem cell in some embodiments the human liver cell may be a sinus hepatoendothelial cell (L SEC) in some embodiments the human liver cell may be a Kupffer cell.
In some embodiments, engineered cells are provided, e.g., derived from any one of the cell types of the preceding paragraphs. Such engineered cells are prepared according to the methods described herein. In some embodiments, the engineered cells reside within a tissue or organ, such as the liver of a subject.
In some of the methods and cells described herein, the cell comprises a modification, e.g., an insertion or deletion (') "insertion ordeleave (index ") or substitution. In some embodiments, the modification isComprising an insertion of 1,2, 3,4 or 5 or more nucleotides in the target sequence. In some embodiments, the modification comprises an insertion of 1 or 2 nucleotides in the target sequence. In other embodiments, the modification comprises a deletion of 1,2, 3,4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more nucleotides in the target sequence. In some embodiments, the modification comprises a deletion of 1 or 2 nucleotides in the target sequence. In some embodiments, the modification comprises an insertion or deletion that results in a frame shift mutation in the target sequence. In some embodiments, the modification comprises a substitution of 1,2, 3,4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more nucleotides in the target sequence. In some embodiments, the modification comprises a substitution of 1 or 2 nucleotides in the target sequence. In some embodiments, the modification comprises one or more nucleotide insertions, deletions, or substitutions resulting from incorporation into a template nucleic acid, e.g., any of the template nucleic acids described herein.
In some embodiments, a cell population comprising engineered cells is provided, e.g., a cell population comprising cells engineered according to the methods described herein. In some embodiments, the population comprises engineered cells cultured in vitro. In some embodiments, the population resides within a tissue or organ, e.g., a liver of the subject. In some embodiments, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% or more of the cells within a population are engineered. In certain embodiments, the methods disclosed herein result in an editing efficiency (or "percent editing") of at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%, as defined by detecting an insertion or deletion. In other embodiments, the methods disclosed herein result in at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% DNA modification efficiency, defined by detecting sequence changes (by insertions, deletions, substitutions, or otherwise). In certain embodiments, the methods disclosed herein result in an editing efficiency level or DNA modification efficiency level of between about 5% to about 100%, about 10% to about 50%, about 20% to about 100%, about 20% to about 80%, about 40% to about 100%, or about 40% to about 80% in a population of cells.
In some of the methods and cells described herein, the cells within the population comprise a modification, such as an insertion or deletion or substitution, at the target sequence. In some embodiments, the modification comprises an insertion of 1,2, 3,4, or 5 or more nucleotides in the target sequence. In some embodiments, the modification comprises an insertion of 1 or 2 nucleotides in the target sequence. In other embodiments, the modification comprises a deletion of 1,2, 3,4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more nucleotides in the target sequence. In some embodiments, the modification comprises a deletion of 1 or 2 nucleotides in the target sequence. In some embodiments, the modification results in a frameshift mutation in the target sequence. In some embodiments, the modification comprises an insertion or deletion that results in a frame shift mutation in the target sequence. In some embodiments, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or more of the engineered cells in the population comprise a frameshift mutation. In some embodiments, the modification comprises a substitution of 1,2, 3,4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more nucleotides in the target sequence. In some embodiments, the modification comprises a substitution of 1 or 2 nucleotides in the target sequence. In some embodiments, the modification comprises one or more nucleotide insertions, deletions, or substitutions resulting from incorporation into a template nucleic acid, e.g., any of the template nucleic acids described herein.
Gene editing method
In one embodiment, a L NP composition as disclosed herein can be used for in vivo and in vitro gene editing.
In some embodiments, the methods involve administering a L NP composition to cells associated with a liver disorder.
In one embodiment, a L NP composition comprising mRNA encoding a class 2 Cas nuclease and a gRNA can be administered to a cell, such as an ApoE-binding cell.
In certain embodiments, the subject may receive a single dose of the L NP composition, in other examples, the subject may receive multiple doses of the L NP composition, in some embodiments, the L NP composition is administered 2-5 times, when more than one dose is administered, the doses may be administered about 1,2, 3,4, 5, 6, 7, 14, 21, or 28 days apart, about 2, 3,4, 5, or 6 months apart, or about 1,2, 3,4, or 5 years apart, in certain embodiments, the editing improves upon re-administration of the L NP composition.
In one embodiment, an L NP composition comprising mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease) can be administered to a cell separate from the administration of a composition comprising a gRNA in one embodiment, a L NP composition comprising mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease) and a gRNA can be administered to a cell separate from the administration of a template nucleic acid to a cell in one embodiment, a L NP composition comprising mRNA encoding a Cas nuclease (such as a class 2 Cas nuclease) can be administered to a cell followed by sequential administration of a L NP composition comprising a gRNA and a template to a cell in one embodiment, administration can be about 4,6, 8, 12, or 24 hours apart, or 2, 3,4, 5, 6, or 7 days apart in an embodiment where a L NP composition comprising mRNA encoding a Cas nuclease is administered before a L NP composition comprising a gRNA.
In one embodiment, a L NP composition can be used to edit a gene, resulting in a gene knockout, in one embodiment, a L NP composition can be used to edit a gene, resulting in a gene knockout in a population of cells in another embodiment, a L NP composition can be used to edit a gene, resulting in a gene correction.
In one embodiment, administration of L NP composition may result in gene editing that results in a sustained response, for example, administration may result in a duration of response of one day, one month, one year, or more as used herein, "duration of response" means that the resulting modification is still present for a period of time after administration of L NP composition after cells have been edited using the L NP composition disclosed herein, the modification may be detected by measuring the level of target protein, the modification may be detected by detecting target DNA, in some embodiments, the duration of response may be at least 1 week, in other embodiments, the duration of response may be at least 2 weeks, in one embodiment, the duration of response may be at least 1 month, in some embodiments, the duration of response may be at least 2 months, in one embodiment, the duration of response may be at least 4 months, in one embodiment, the duration of response may be at least 6 months, in some embodiments, the duration of response may be about 26 weeks, in some embodiments, the duration of response may be at least 1 year, in embodiments, the duration of response may be at least 5 years, in some embodiments, the duration of response may be at least 6 months, or may be detected by measuring the level of target DNA, at least 10, 7, 10, or more, 16, 7, 10, or 16, 7, or 16, 7, or more after target protein levels of the administration of the target DNA has been detected by measuring target protein.
The L NP compositions may be administered parenterally, the L NP compositions may be administered directly into the bloodstream, tissue, muscle, or internal organs administration may be systemic, e.g., for injection or infusion.
L NP compositions will generally, but not necessarily, be administered in a formulation in combination with one or more pharmaceutically acceptable excipients the term "excipient" includes any ingredient other than the compounds of the present disclosure, other lipid components, and biologically active agents.
Parenteral formulations are typically aqueous or oily solutions or suspensions. When the formulation is aqueous, excipients such as sugars (including but not limited to glucose, mannitol, sorbitol, and the like), salts, carbohydrates, and buffering agents (preferably a pH of 3 to 9) may be used, but for some applications the formulation may be more suitably formulated as a sterile non-aqueous solution or in dry form to be used in combination with a suitable vehicle such as sterile pyrogen-free Water (WFI).
While the invention will be described in conjunction with the illustrated embodiments, it will be understood that it is not intended to limit the invention to those embodiments. On the contrary, the invention is intended to cover alternatives, modifications and equivalents, including equivalents of the specific features, which may be included within the invention as defined by the appended claims.
The foregoing general and detailed description, as well as the following examples, are exemplary and explanatory only and are not limiting of the teachings. The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described in any way. In the event that any document incorporated by reference contradicts any term defined in the specification, the specification controls. Unless otherwise stated, all ranges given in this application are inclusive of the endpoints.
It should be noted that, as used in this application, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a composition" includes a plurality of compositions and reference to "a cell" includes a plurality of cells and the like. Unless stated otherwise, the use of "or" is inclusive and means "and/or.
Numerical ranges include the numbers defining the range. The measured and measurable values are to be understood as approximate, taking into account the significant figures and the errors associated with the measurement. The term "about" or "approximately" means an acceptable error for a particular value as determined by one of ordinary skill in the art, which depends in part on how the value is measured or determined. A modifier such as "about" is used before a range or before a list of values to modify each end point of the range or each value in the list. "about" also includes values or endpoints. For example, "about 50-55" encompasses "about 50 to about 55". In addition, the use of "comprising", "comprises", "comprising", "containing", "including", and "including" is not restrictive.
Unless expressly indicated in the foregoing specification, embodiments in which "comprising" various components is recited in the specification are also considered to "consist of" or "consist essentially of" the components; the statement in this specification that "consists of" various components "is also considered to be" comprising "or" consisting essentially of "the components; embodiments in the present specification that recite "about" various components are also contemplated as "in" the component; and the statement in this specification that "consists essentially of" each component "is also to be taken as" consisting of "or" comprising "the component(s) (this interchangeability does not apply to the use of these terms in the claims).