# Patent

## Title
Multi-armed polyrotaxane platform for protected nucleic acid delivery

## Abstract

In various embodiments a polyrotaxane carrier for in vivo delivery of a nucleic acid is provided. In certain embodiments the carrier comprises: a multi-arm polyethylene glycol (PEG) backbone comprising at least three arms; at least one cyclic compound having a cavity, where an arm of said multi-arm PEG backbone is threaded into the cavity of said cyclic compound forming an inclusion complex; a bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound where said moiety inhibits dethreading of the cyclodextrin from the arm(s) of said backbone; and where at least one arm of said PEG backbone is free of cyclic compounds; and where said carrier has a net positive charge.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a U.S. 371 National Phase of PCT International Application No. PCT/US2018/053221, filed on Sep. 27, 2018, which claims benefit of and priority to U.S. Ser. No. 62/566,100, filed on Sep. 29, 2017, and to U.S. Ser. No. 62/687,713, filed on Jun. 20, 2018, all of which are incorporated herein by reference in their entirety for all purposes.


STATEMENT OF GOVERNMENTAL SUPPORT
This invention was made with government support under Grant Number CA198846, awarded by the National Institutes of Health. The Government has certain rights in the invention.


INCORPORATION BY REFERENCE OF SEQUENCE LISTING PROVIDED AS A TEXT FILE
This application contains references to nucleic acid sequences that have been submitted concurrently herewith as the sequence listing text file “UCLA-P193US_ST25.txt”, file size 370 kb, created on 08/07/2020, which is incorporated by reference in its entirety pursuant to 37 C.F.R. § 1.52(e)(5).
BACKGROUND
The ability to deliver DNA to target cells plays a key role in the development of new approaches, such as gene therapy and DNA vaccination, for treating and controlling diseases. DNA delivery systems have been classified as viral and non-viral vector systems. Although viral vectors are highly efficient at delivering DNA into cells, their routine uses in the clinic has been limited because of, inter alia, their high toxicity, restricted targeting of cells, limited DNA carrying capacity, production and packaging problems, recombination, and high cost.
Non-viral vectors, the majority of which are synthetic gene carrier systems, have advantages in terms of simplicity of use, ease of large-scale production, and lack of specific immune response.
The use of polymers carrying/complexing DNA is a non-viral delivery approach. Most polymers used for DNA delivery consist of or comprise cationic polymer segments that form a condensed complex with DNA to protect the DNA digestion by enzymes. The condensed polymer-DNA complex also packs into compact and small nanoparticles, that can be internalized by cells through endocytosis.
Cationic polymers of linear, branched, star and dendritic structures have been studied as DNA condensation agents in the context of non-viral gene delivery. Controlled chemical synthesis of cationic polymers ensures that the size and shape of the polymers are consistent and defined, thereby improving the reproducibility of DNA delivery. Polyethyleneimine (PEI) is one of the most frequently studied polycations for use in DNA delivery. The size and the structure of PEI has strongly influenced the efficiency of nucleic acid delivery with regard to transfection activity and cytotoxicity. Generally, low molecular weight branched PEI (e.g., ≤2000 Da) has proven to be nontoxic, but has often displayed very poor transfection activity. By contrast, high molecular weight branched PEI (≥25 kDa) has showed high transgene expression, but also significant cytotoxicity. In the intermediate molecular weight range (2000 kDa-25 kDa), the PEI is of medium to low cytotoxicity and also medium transfection activity.
SUMMARY
In various embodiments polyrotaxane carriers are provided for the delivery of nucleic acids. The carriers self-assemble with nucleic acids to form complexes that are effective to deliver the nucleic acids to cells in vivo (e.g., in a mammal). The carriers described herein show reduced opsonization, improved serum half-life, improved cellular uptake and the like as compared to other polyrotaxane carriers.
Various embodiments contemplated herein may include, but need not be limited to, one or more of the following:
Embodiment 1
A polyrotaxane carrier for in vivo delivery of a nucleic acid, said carrier comprising:

    
    
        a multi-arm polyethylene glycol (PEG) backbone comprising at least three arms;
        at least one cyclic compound having a cavity, where an arm of said multi-arm PEG backbone is threaded into the cavity of said cyclic compound forming an inclusion complex;
        a bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound where said moiety inhibits dethreading of the cyclodextrin from the arm(s) of said backbone;
        where at least one arm of said PEG backbone is free of cyclic compounds; and where said carrier has a net positive charge.
    
    


Embodiment 2
The carrier of embodiment 1, wherein said carrier complexes with a nucleic acid when contacted to said nucleic acid.
Embodiment 3
The carrier according to any one of embodiments 1-2, wherein said multi-arm polyethylene glycol backbone comprises a star polymer.
Embodiment 4
The carrier according to any one of embodiments 1-3, wherein said multi-arm PEG comprises at least 2 arms free of cyclic compounds.
Embodiment 5
The carrier according to any one of embodiments 1-4, wherein said multi-arm PEG comprises from 3 up to about 12, or up to about 10, or up to about 8 arms.
Embodiment 6
The carrier according to any one of embodiments 1-5, wherein said PEG comprises 4 arms, or 5 arms, or 6 arms, or seven arms, or 8 arms.
Embodiment 7
The carrier according to any one of embodiments 1-4, wherein said PEG comprises 4 arms.
Embodiment 8
The carrier according to any one of embodiments 1-4, wherein said PEG comprise 4 arms where two of said arms are free of cyclic compounds.
Embodiment 9
The carrier according to any one of embodiments 1-8, wherein said PEG backbone has a molecular weight ranging from about 1.0 to about 10 kDA per arm.
Embodiment 10
The carrier according to any one of embodiments 1-9, wherein said PEG backbone comprise about 22 to about 227 ethylene oxides per arm.
Embodiment 11
The carrier according to any one of embodiments 1-8, wherein said PEG backbone has a molecular weight of about 2.5 kDa per arm.
Embodiment 12
The carrier according to any one of embodiments 1-11, wherein the arm(s) threaded into said cyclic compound(s) each bear on average from about 5 to about 110 cyclic compounds.
Embodiment 13
The carrier according to any one of embodiments 1-11, wherein the arm(s) threaded into said cyclic compound(s) each bear, on average, about 20 cyclic compounds per arm.
Embodiment 14
The carrier according to any one of embodiments 1-13, wherein said cyclic compound comprise a compound selected from the group consisting of a cyclodextrin, a crown ether, a cucurbituril and a cyclofructan.
Embodiment 15
The carrier of embodiment 14, wherein said cyclic compound comprises a cyclodextrin.
Embodiment 16
The carrier of embodiment 15, wherein said cyclic compound comprises a cyclodextrin selected from the group consisting of an α-cyclodextrin, a β-cyclodextrin, a γ-cyclodextrin, a hydroxypropylated α-cyclodextrin, a hydroxypropylated β-cyclodextrin, a hydroxypropoylated γ-cyclodextrin, a dimethylcyclodextrin, a chemically modified cyclodextrin (e.g., carboxyl modified cyclodextrin).
Embodiment 17
The carrier of embodiment 14, wherein said cyclic compound comprises a cucurbituril.
Embodiment 18
The carrier of embodiment 17, wherein said cyclic compound comprises a cucurbituril selected from the group consisting of cucurbit[5]uril, cucurbit[6]uril, cucurbit[7]uril, cucurbit[8]uril, cucurbit[9]uril, cucurbit[10]uril, and a chemically modified cucubituril.
Embodiment 19
The carrier of embodiment 18, wherein said cyclic compound comprises a cucurbit[6]uril (CB[6]).
Embodiment 20
The carrier according to any one of embodiments 1-19, wherein said cyclic compound(s) are substituted with one or more nucleophilic groups.
Embodiment 21
The carrier of embodiment 20, wherein said cyclic compound(s) are substituted with one or more amine groups or groups derived from an amine group.
Embodiment 22
The carrier of embodiment 21, wherein said cyclic compound(s) are substituted with one or more groups selected from the group consisting of a primary amine, a secondary amine, a tertiary amine, and an imine group.
Embodiment 23
The carrier of embodiment 22, wherein said cyclic compound(s) are substituted with one or more primary amines.
Embodiment 24
The carrier according to any one of embodiments 20-23, where the number of nucleophilic group substituted on the cyclic compound(s) ranges from 1 up to about 20 substitutions per cyclic compound.
Embodiment 25
The carrier according to any one of embodiments 20-24, wherein the cyclic compounds are substituted with nucleophilic groups to provide a positive zeta potential for said carrier ranging from about +1V or from about +5 mV up to about +50 mV, or up to about +25 mV.
Embodiment 26
The carrier according to any one of embodiments 1-25, wherein said carrier has a zeta potential of about +15 mV.
Embodiment 27
The carrier according to any one of embodiments 1-26, wherein the bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound(s) comprises a compound having a 3 dimensional size greater than the internal diameter of the cyclic compound(s).
Embodiment 28
The carrier of embodiment 27, wherein the bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound(s) comprises a moiety selected from the group consisting of Z-tyrosine, phenylalanine, a group having at least one benzene ring, and a group having at least one tertiary butyl.
Embodiment 29
The carrier of embodiment 28, wherein the bulky moiety comprises a moiety selected from the group consisting of a Z-tyrosine, phenylaline, a benzyloxycarbonyl (Z) group, a 9-fluorenylmethyloxycarbonyl (Fmoc) group, a benzyl ester (OBz) group, a tertiary butylcarbonyl (Boc) group, and an amino acid-tertiary butyl ester (OBu) group.
Embodiment 30
The carrier of embodiment 28, wherein the bulky moiety comprises Z-tyrosine.
Embodiment 31
The carrier according to any one of embodiments 1-30, wherein at least one arm not threaded into said cyclic compound is terminated with a protecting group, and/or a fluorophore, and/or a targeting moiety.
Embodiment 32
The carrier of embodiment 31, wherein all the arms not threaded into said cyclic compound are terminated with a protecting group, and/or a fluorophore, and/or a targeting moiety.
Embodiment 33
The carrier according to any one of embodiments 31-32, wherein at least one arm not threaded into said cyclic compound are terminated with a protecting group selected from the group consisting of dansyl, acetyl, amide, and 3 to 20 carbon alkyl groups, Fmoc, Tboc, 9-fluoreneacetyl group, 1-fluorenecarboxylic group, 9-florenecarboxylic group, 9-fluorenone-1-carboxylic group, benzyloxycarbonyl, Xanthyl (Xan), Trityl (Trt), 4-methyltrityl (Mtt), 4-methoxytrityl (Mmt), 4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr), Mesitylene-2-sulphonyl (Mts), 4,4-dimethoxybenzhydryl (Mbh), Tosyl (Tos), 2,2,5,7,8-pentamethyl chroman-6-sulphonyl (Pme), 4-methylbenzyl (MeBzl), 4-methoxybenzyl (MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl), Benzoyl (Bz), 3-nitro-2-pyridinesulphenyl (Npys), 1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl (2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl—Z), 2-bromobenzyloxycarbonyl (2-Br—Z), Benzyloxymethyl (Bom), t-butoxycarbonyl (Boc), cyclohexyloxy (cHxO), t-butoxymethyl (Bum), t-butoxy (tBuO), t-Butyl (tBu), Acetyl (Ac), and Trifluoroacetyl (TFA).
Embodiment 34
The carrier of embodiment 31, wherein at least one arm not threaded into said cyclic compound is attached to a fluorophore.
Embodiment 35
The carrier of embodiment 34, wherein said fluorophore is selected from the group consisting of a rhodamine, a cyanine, an oxazine, a thiazine, a porphyrin, a phthalocyanine, and a fluorescent protein.
Embodiment 36
The carrier of embodiment 34, wherein said fluorophore is selected from the group consisting of fluorescein isothiocyanate (especially fluorescein-5-isothiocyanate), 5-FAM (5-carboxyfluorescein), 6-FAM (6-carboxyfluorescein), 5,6-FAM, 7-hydroxycoumarin-3-carboxamide, 6-chloro-7-hydroxycoumarin-3-carboxamide-, dichlorotriazinylaminofluorescein, tetramethylrhodamine-5 (and-6)-isothiocyanate, 1,3-bis-(2-dialkylamino-5-thienyl)-substituted squarines, succinimidyl esters of 5 (and 6) carboxyfluoroscein, 5 (and 6)-carboxytetramethylrhodamine, 7-amino-4-methylcoumarin-3-acetic acid, DyLight 350, DyLight 405, DyLight 488, DyLight 550, DyLight 594, DyLight 633, DyLight 650, DyLight 680, DyLight 755, DyLight 800, Alexa fluor 350, Alexa fluor 405, Alexa fluor 488, Alexa fluor 546, Alexa fluor 555, Alexa fluor 568, Alexa fluor 594, Alexa fluor 633, Alexa fluor 647, and Alexa fluor 750.
Embodiment 37
The carrier of embodiment 31, wherein at least one arm not threaded into said cyclic compound is attached to a targeting moiety that specifically or preferentially binds to a cell.
Embodiment 38
The carrier of embodiment 37, wherein said targeting moiety is selected from the group consisting of an antibody, a receptor ligand, a nucleic acid aptamer, a peptide aptamer, neural cell adhesion molecule (NCAM), a cell penetrating peptide (CPP), a peptide aptamer, and a lectin.
Embodiment 39
The carrier of embodiment 38, wherein said targeting moiety comprises an antibody.
Embodiment 40
The carrier of embodiment 38, wherein said targeting moiety comprises an antibody selected from the group consisting of full-length immunoglobulins, Fab, Fab′, Fab′-SH, F(ab′)2, Fv, Fv′, Fd, Fd′, scFv, hsFv fragments, single-chain antibodies, cameloid antibodies.
Embodiment 41
The carrier according to any one of embodiments 38-40, wherein said targeting moiety binds to a stem cell.
Embodiment 42
The carrier according to any one of embodiments 38-40, wherein said targeting moiety binds to a hematopoietic cell.
Embodiment 43
The carrier according to any one of embodiments 38-40, wherein said targeting moiety binds to a T-cell.
Embodiment 44
The carrier according to any one of embodiments 38-40, wherein said targeting moiety binds to a muscle cell.
Embodiment 45
The carrier according to any one of embodiments 38-40, wherein said targeting moiety binds a target selected from the group consisting of CD45, CD3, erbB2, Her2, CD22, CD74, CD19, CD20, CD33, CD40, MUC1, IL-15R, HLA-DR, EGP-1, EGP-2, G250, prostate specific membrane antigen (PSMA), prostate specific antigen (PSA), prostatic acid phosphatase (PAP), and placental alkaline phosphatase.
Embodiment 46
The carrier according to any one of embodiments 38-40, wherein said targeting moiety binds to a cancer cell marker.
Embodiment 47
The carrier of embodiment 46, wherein said targeting moiety binds to a cancer cell marker selected from the group consisting of 5 alpha reductase, α-fetoprotein, AM-1, APC, APRIL, BAGE, β-catenin, Bc12, bcr-abl (b3a2), CA-125, CASP-8/FLICE, Cathepsins, CD19, CD20, CD21, CD23, CD22, CD38, CD33, CD35, CD44, CD45, CD46, CD5, CD52, CD55, CD59 (791Tgp72), CDCl27, CDK4, CEA, c-myc, Cox-2, DCC, DcR3, E6/E7, EGFR, EMBP, Ena78, FGF8b and FGF8a, FLK-1/KDR, Folic Acid Receptor, G250, GAGE-Family, gastrin 17, Gastrin-releasing hormone (bombesin), GD2/GD3/GM2, GnRH, GnTV, gp100/Pmel17, gp-100-in4, gp15, gp75/TRP-1, hCG, Heparanase, Her2/neu, Her3, HMTV, Hsp70, hTERT, (telomerase), IGFR1, IL-13R, iNOS, Ki 67, KIAA0205, K-ras, H-ras, N-ras, KSA, (CO17-1A), LDLR-FUT, MAGE Family (MAGE1, MAGE3, etc.), Mammaglobin, MAP17, Melan-A/, MART-1, mesothelin, MIC A/B, MT-MMP's, such as MMP2, MMP3, MMP7, MMP9, Mox, Mucin, such as MUC-1, MUC-2, MUC-3, and MUC-4, MUM-1, NY-ESO-1, Osteonectin, p15, P170/MDR, p53, p97/melanotransferrin, PAI-1, PDGF, Plasminogen (uPA), PRAME, Probasin, Progenipoietin, PSA, PSM, RAGE-1, Rb, RCAS1, SART-1, SSX gene, family, STAT3, STn, (mucin assoc.), TAG-72, TGF-α, TGF-β, Thymosin β 15, TPA, TPI, TRP-2, Tyrosinase, VEGF, ZAG, p16INK4, and Glutathione S-transferase.
Embodiment 48
The carrier of embodiment 38, wherein said targeting moiety comprises a ligand that binds a receptor where said ligand is selected from the group consisting of transferrin, mannose, glucose, and folic acid.
Embodiment 49
The carrier of embodiment 38, wherein said targeting moiety comprises a ligand that binds a receptor where said ligand comprises transferrin.
Embodiment 50
The carrier according to any one of embodiments 1-49, wherein said bulky moiety is attached to an arm of said backbone by a cleavable linkage.
Embodiment 51
The carrier according to any one of embodiments 20-49, wherein said one or more nucleophilic groups are attached to said cyclic compounds by a cleavable linkage.
Embodiment 52
The carrier according to any one of embodiments 50-51, wherein said cleavable linkage is selected from the group consisting of a redox-responsive linker, a pH responsive linker, a photo-responsive linker, a thermal responsive linker and an enzymatically cleavable linker.
Embodiment 53
The carrier of embodiment 52, wherein said cleavable linkage comprises a redox-responsive disulfide linker.
Embodiment 54
The carrier of embodiment 52, wherein said cleavable linkage comprises a pH responsive hydrazine linker.
Embodiment 55
The carrier of embodiment 52, wherein said cleavable linkage comprises an enzymatically cleavable linker.
Embodiment 56
The carrier of embodiment 55, wherein said linkage comprises a linker cleavable by a protease.
Embodiment 57
The carrier of embodiment 56, wherein said linkage comprises a linker cleavable by a matrix metalloprotease or a cathepsin.
Embodiment 58
The carrier according to any one of embodiments 56-57, wherein said peptide linker comprises a linker comprises a moiety selected from the group consisting of dipeptide valine-citrulline (Val-Cit), dipeptide Phe-Lys, Mc-vc-PAB-MMAE, Mc-vc-PAB-MMAF, Mc-va-PBD dimer, Mc-vc-PAB-CM-seco-DUBA, Gly-Phe-Leu-Gly (GFLG), GPLGV, and GPLGVRG.
Embodiment 59
The carrier according to any one of embodiments 1-58, wherein said carrier is complexed with a nucleic acid.
Embodiment 60
The carrier of embodiment 59, wherein said carrier is complexed with an RNA.
Embodiment 61
The carrier according to any one of embodiments 59-60, wherein said carrier is complexed with a DNA.
Embodiment 62
The carrier of embodiment 61, wherein said carrier is complexed with a plasmid.
Embodiment 63
The carrier of embodiment 62, wherein said carrier is complexed with a plasmid that encodes a heterologous gene or cDNA.
Embodiment 64
The carrier of embodiment 62, wherein said carrier is complexed with a plasmid that encodes a class 2 CRISPR/Cas endonuclease and a guide RNA.
Embodiment 65
The carrier of embodiment 64, wherein said class 2 CRISPR/Cas endonuclease is a type II CRISPR/Cas endonuclease.
Embodiment 66
The carrier according to any one of embodiments 64-65, wherein the class 2 CRISPR/Cas endonuclease is a Cas9 polypeptide and the corresponding CRISPR/Cas guide RNA is a Cas9 guide RNA.
Embodiment 67
The carrier of embodiment 66, wherein said Cas9 protein is selected from the group consisting of a Streptococcus pyogenes Cas9 protein (spCas9) or a functional portion thereof, a Staphylococcus aureus Cas9 protein (saCas9) or a functional portion thereof, a Streptococcus thermophilus Cas9 protein (stCas9) or a functional portion thereof, a Neisseria meningitides Cas9 protein (nmCas9) or a functional portion thereof, and a Treponema denticola Cas9 protein (tdCas9) or a functional portion thereof.
Embodiment 68
The carrier of embodiment 67, wherein said Cas9 protein comprises a Streptococcus pyogenes Cas9 protein (spCas9).
Embodiment 69
The carrier of embodiment 67, wherein said Cas9 protein comprises a Staphylococcus aureus Cas9 protein (saCas9).
Embodiment 70
The carrier of embodiment 67, wherein said Cas9 protein comprises a Streptococcus thermophilus Cas9 protein.
Embodiment 71
The carrier of embodiment 67, wherein said Cas9 protein comprises a Neisseria meningitides Cas9 protein (nmCas9).
Embodiment 72
The carrier of embodiment 67, wherein said Cas9 protein comprises a Treponema denticola Cas9 protein (tdCas9).
Embodiment 73
The carrier of embodiment 64, wherein the class 2 CRISPR/Cas endonuclease is a type V or type VI CRISPR/Cas endonuclease.
Embodiment 74
The carrier of embodiment 73, wherein the class 2 CRISPR/Cas endonuclease is selected from the group consisting of a Cpf1 polypeptide or a functional portion thereof, a C2c1 polypeptide or a functional portion thereof, a C2c3 polypeptide or a functional portion thereof, and a C2c2 polypeptide or a functional portion thereof.
Embodiment 75
The carrier of embodiment 74, wherein the class 2 CRISPR/Cas endonuclease comprises a Cpf1 polypeptide.
Embodiment 76
The carrier according to any one of embodiments 59-75, wherein the N/P ratio of said carrier complexed to a nucleic acid ranges from about 0.01:1 up to about 100:1, or from about 2:1 up to about 50:1, or up to about 40:1, or up to about 30:1, or up to about 25:1, or ranges from about 2:1 up to about 25:1.
Embodiment 77
The carrier of embodiment 70, wherein the N/P ratio of said carrier complexed to a nucleic acid is about 10:1.
Embodiment 78
A pharmaceutical formulation comprising: a polyrotaxane carrier according to any one of embodiments 1-58; and a pharmaceutically acceptable carrier.
Embodiment 79
The formulation of embodiment 78, wherein said polyrotaxane carrier is complexed with a nucleic acid.
Embodiment 80
The formulation according to any one of embodiments 78-79, wherein said formulation is formulated for administration via a route selected from the group consisting of isophoretic delivery, transdermal delivery, aerosol administration, administration via inhalation, oral administration, intravenous administration, intraarterial administration, intramuscular administration, topical delivery to the eye, intraocular injection, vaginal administration, and rectal administration.
Embodiment 81
The formulation according to any one of embodiments 78-80, wherein said formulation is a unit dosage formulation.
Embodiment 82
A construct for the treatment of Duchenne Muscular Dystrophy, said construct comprising:

    
    
        a polyrotaxane carrier according to any one of embodiments 1-58, wherein said carrier is complexed with a plasmid encoding a class 2 CRISPR/Cas endonuclease, and a guide RNA that hybridizes to a target sequence within intron 44 of a mutant dystrophin gene, and/or a second CRISPR/Cas guide RNA guide sequence that hybridizes to a target sequence within intron 55 of the mutant dystrophin gene.
    
    


Embodiment 83
The construct of embodiment 82, wherein: the first CRISPR/Cas guide RNA comprises a guide sequence having 100% complementarity over 17 or more contiguous nucleotides with a first target sequence corresponding to intron 44 of the human dystrophin gene, and/or the second CRISPR/Cas guide RNA comprises a guide sequence having 100% complementarity over 17 or more contiguous nucleotides with a second target sequence corresponding to intron 55 of the human dystrophin gene.
Embodiment 84
The construct of embodiment 82, wherein the class 2 CRISPR/Cas endonuclease is a type II CRISPR/Cas endonuclease.
Embodiment 85
The construct of embodiment 84, wherein the class 2 CRISPR/Cas endonuclease is a Cas9 protein and the corresponding CRISPR/Cas guide RNA is a Cas9 guide RNA.
Embodiment 86
The construct of embodiment 82, wherein the class 2 CRISPR/Cas endonuclease is a type V or type VI CRISPR/Cas endonuclease.
Embodiment 87
The construct of embodiment 86, wherein the class 2 CRISPR/Cas endonuclease is a Cpf1 protein, a C2c1 protein, a C2c3 protein, or a C2c2 protein.
Embodiment 88
The construct of any of embodiments 82-85, wherein the guide sequence of the first CRISPR/Cas guide RNA comprises a sequence selected from the group consisting of guguccuuug aauaugc (SEQ ID NO:225), uuguccagga uauaauu (SEQ ID NO:226), gcaaccaaau uauaucc (SEQ ID NO:227), gaaauuaaac uacacac (SEQ ID NO:228), and uuuaccugca uauucaa (SEQ ID NO:229) (the 17 nucleotide sequence set forth in any of SEQ ID NOs: 1155-1159 of PCT/US2017/017255).
Embodiment 89
The construct of embodiment 88, wherein the guide sequence of the first CRISPR/Cas guide RNA comprises a sequence selected from the group consisting of gugguguccu uugaauaugc (SEQ ID NO:78), agauugucca ggauauaauu (SEQ ID NO:80), uuagcaacca aauuauaucc (SEQ ID NO:82), guugaaauua aacuacacac (SEQ ID NO:84), aucuuuaccu gcauauucaa (SEQ ID NO:86), cucugcauug uuuuggccuc (SEQ ID NO:88), uccuccaaag aguagaaugg (SEQ ID NO:90), gcccuaaacu uacacuguuc (SEQ ID NO:92), aaagauagau uagauugucc (SEQ ID NO:94), guugcuaaau uacauaguuu (SEQ ID NO:96), uguugcaaua gucaaucaag (SEQ ID NO:98), auacugauua agacagauga (SEQ ID NO:100), aauacugauu aagacagaug (SEQ ID NO:102), cucuauacaa augccaacgc (SEQ ID NO:104), acuugcaugc acaccagcgu (SEQ ID NO:106), uugggcuaau guagcauaau (SEQ ID NO:108), gcguuggcau uuguauagag (SEQ ID NO:110), ugggcuaagu agcauaaug (SEQ ID NO:112), uuugggcuaa uguagcauaa (SEQ ID NO:114), gcuuaacucc uuaauauuaa (SEQ ID NO:116), ucuucuauau uaaagcagau (SEQ ID NO:118), cuucuauauu aaagcagauu (SEQ ID NO:120), aauauauaac uaccuugggu (SEQ ID NO:122), accuccauuc uacucuuugg (SEQ ID NO:124), uuucaaugau auccaaccca (SEQ ID NO:126), aguaccucca uucuacucuu (SEQ ID NO:128), cuauccucca aagaguagaa (SEQ ID NO:130), uuuugcuaca uauuucaggc (SEQ ID NO:132), uuugcuacau auuucaggcu (SEQ ID NO:134), ggguuggaua ucauugaaaa (SEQ ID NO:136), auauuucagg cuggguucu (SEQ ID NO:138), uugaaauaua uaacuaccuu (SEQ ID NO:140), auugaaauau auaacuaccu (SEQ ID NO:142), gugaguagug gggcacuuua (SEQ ID NO:144), uguauguaga agguuaacua (SEQ ID NO:146), gagccuaaua aauguacaau (SEQ ID NO:148), uuguauguag aagguuaacu (SEQ ID NO:150), caauuuguuu ugaguaacu (SEQ ID NO:152), ugccuucuga aauaguccag (SEQ ID NO:154), guuaauaggg aaacagcaua (SEQ ID NO:156), aacaaugcag aguuaauugu (SEQ ID NO:158), gaacauguug aguagacaca (SEQ ID NO:160), uuuaucaucu gugucuauuc (SEQ ID NO:162), ucuuuacuuu cuugacuaua (SEQ ID NO:164), aauauucuca aaccucguuc (SEQ ID NO:166), auuaacugug uuccagaacg (SEQ ID NO:168), uaacugcuuc uuuggaugac (SEQ ID NO:170), gaccagaaca guguaaguuu (SEQ ID NO:172), accagaacag uguaaguuua (SEQ ID NO:174), cuacuuuuuc cccacuacug (SEQ ID NO:176), uggaacacag uuaauucacu (SEQ ID NO:178), and guguuguuua acugcuucuu (SEQ ID NO:180), (the 20 nucleotide sequence set forth in any of SEQ ID NOs: 1150-1154 and SEQ ID NOs: 1223-1269 of PCT/US2017/017255).
Embodiment 90
The construct of any of embodiments 82-85, 88, or 89, wherein the guide sequence of the second CRISPR/Cas guide RNA comprises a sequence selected from the group consisting of acauuuuuag gcuugac (SEQ ID NO:339), uccugggagu cugucau (SEQ ID NO:340), augaugcuau aauacca (SEQ ID NO:341), gaaaguacau aggaccu (SEQ ID NO:342), and uaucauaacu cuuacca (SEQ ID NO:343) (the 17 nucleotide sequence set forth in any of SEQ ID NOs: 1175-1179 of PCT/US2017/017255).
Embodiment 91
The construct of embodiment 82-85, 88, or 89, wherein the guide sequence of the second CRISPR/Cas guide RNA comprises a sequence selected from the group consisting of uacacauuuu uaggcuugac (SEQ ID NO:182), cauuccuggg agucugucau (SEQ ID NO:184), uguaugaugc uauaauacca (SEQ ID NO:186), guggaaagua cauaggaccu (SEQ ID NO:188), and ucuuaucaua acucuuacca (SEQ ID NO:190), aacugucagu ugcauauucc (SEQ ID NO:192), cagaaaggaa ugcugguacc (SEQ ID NO:194), ucugccuaca caaugaaugg (SEQ ID NO:196), cacagaucaa uccaauuguu (SEQ ID NO:198), uugacaggug gaaaguacau (SEQ ID NO:200), acauuuuuag gcuugacagg (SEQ ID NO:202), cucucccaug acagacuccc (SEQ ID NO:204), uugguaagag uuaugauaag (SEQ ID NO:206), aacacaaauu aaguucaccu (SEQ ID NO:208), aggaucagug cuguagugcc (SEQ ID NO:210), ggccguuuau uauuauugac (SEQ ID NO:212), ucucaggauu gcuaugcaac (SEQ ID NO:214), caggaagaca uaccauguaa (SEQ ID NO:216), agcagggcuc uuucaguuuc (SEQ ID NO:218), uaacauuuuc agcuugaacc (SEQ ID NO:230), ucaagcugaa aauguuacac (SEQ ID NO:223), guaacauuuu cagcuugaac (SEQ ID NO:224), cagaaugaau uuuggagcac (SEQ ID NO:226), uuuauuauua uugacuggug (SEQ ID NO:228), agaagaaucu gaccuuuaca (SEQ ID NO:230), gcagggcucu uucaguuucu (SEQ ID NO:232), cuaaacagua gecaggegug (SEQ ID NO:234), cgccuggcua cuguuuagug (SEQ ID NO:236), cuccgcacua aacaguagcc (SEQ ID NO:238), guagccagge guguggaugu (SEQ ID NO:240), cuuggcuuug acuauucugc (SEQ ID NO:242), aguagccagg cguguggaug (SEQ ID NO:244), uccucccaca uccacacgcc (SEQ ID NO:246), uuggcuuuga cuauucugcu (SEQ ID NO:248), auaaugucuc uggcuuguaa (SEQ ID NO:250), ugguacccgg cagcucucug (SEQ ID NO:252), gugggaggaa ccucaaagag (SEQ ID NO:254), ugacuauucu gcugggaaca (SEQ ID NO:256), cucucugagg aauguucccu (SEQ ID NO:258), aacauuccuc agagageuge (SEQ ID NO:260), auucugaagc uccaaacaau (SEQ ID NO:262), uaaauuacuc ugcuaaagua (SEQ ID NO:264), aguacaaacc agguuuguac (SEQ ID NO:266), auauccuucc aguacaaacc (SEQ ID NO:268), caaaccaggu uuguacugga (SEQ ID NO:270), ggcagcuaaa gcaucacuga (SEQ ID NO:272), aucucugagu aguacaaacc (SEQ ID NO:274), gugucccauu cucuuugacu (SEQ ID NO:276), ugugucccau ucucuuugac (SEQ ID NO:278), uucugaaugu ugaacaagua (SEQ ID NO:280), gucucccagu caaagagaau (SEQ ID NO:282), auucucuuug acugggagac (SEQ ID NO:284), and ucuuugacug ggagacaggc (SEQ ID NO:286), (the 20 nucleotide sequence set forth in any of SEQ ID NOs: 1170-1174 and SEQ ID NOs: 1318-1365 of PCT/US2017/017255).
Embodiment 92
The construct of any of embodiments 82-85, wherein the guide sequence of the first CRISPR/Cas guide RNA comprises the 17 nucleotide sequence GAAAUUAAACUACACAC (SEQ ID NO:305) (SEQ ID NO:1158 in PCT/US2017/017255), and the guide sequence of the second CRISPR/Cas guide RNA comprises the 17 nucleotide sequence AUGAUGCUAUAAUACCA (SEQ ID NO:306) (SEQ ID NO:1177 in PCT/US2017/017255).
Embodiment 93
The construct of any of embodiments 82-85, wherein the guide sequence of the first CRISPR/Cas guide RNA comprises the 20 nucleotide sequence GUUGAAAUUAAACUACACAC (SEQ ID NO:307) (SEQ ID NO:1153 in PCT/US2017/017255) and the guide sequence of the second CRISPR/Cas guide RNA comprises the 20 nucleotide sequence UGUAUGAUGCUAUAAUACCA (SEQ ID NO:308) (SEQ ID NO:1172 in PCT/US2017/017255).
Embodiment 94
The construct of any of embodiments 82-87, wherein the target sequence within intron 44 and the target sequence within intron 55 are separated from each other by 500 kb or more.
Embodiment 95
The construct of embodiment 94, wherein the target sequence within intron 44 and the target sequence within intron 55 are separated from each other by 700 kb or more.
Embodiment 96
A method of modifying a mutant dystrophin gene in a cell's genome of a mammal in vivo, said method comprising: administering to said mammal an effective amount of a construct according to any one of embodiments 82-95.
Embodiment 97
The method of embodiment 96, wherein said cell comprises a muscle cell or a pericyte.
Embodiment 98
The method of embodiment 97, wherein said cell comprises a skeletal muscle cell.
Embodiment 99
The method of embodiment 97, wherein said cell comprises a cardiomyocyte.
Embodiment 100
The method of embodiment 96, wherein said cell comprises a stem cell.
Embodiment 101
The method according to any one of embodiments 96-100, wherein said administering comprises administration via a route selected from the group consisting of epidural, intracerebral, intracerebroventricular, epicutaneous, intraarterial, intracardiac intracavernous injection, an injection into the base of the penis, intradermal, intralesional, intramuscular, intraocular administration, intraocular, intraosseous infusion, intraperitoneal, intrathecal, intrauterine, intravaginal administration, intravenous, intravesical infusion, intravitreal, subcutaneous, transdermal, perivascular administration, and transmucosal administration.
Embodiment 102
The method according to any one of embodiments 96-100, wherein said administering comprises systemic administration.
Embodiment 103
The method of embodiment 101, wherein said administration comprises nasal administration, intramuscular administration, or intravenous administration.
Embodiment 104
The method according to any one of embodiments 96-103, wherein said mammal is a human.
Embodiment 105
The method of embodiment 104, wherein said mammal is a human diagnosed with DMD or BMD.
Embodiment 106
The method of embodiment 105, wherein CRISPR acts to restore the shifted DMA reading frame and switch said DMD to the milder Becker's muscular dystrophy (BMD) phenotype.
Embodiment 107
The method according to any one of embodiments 96-103, wherein said mammal is a non-human mammal.
Embodiment 108
The method according to any one of embodiments 96-107, wherein said method is performed in combination with another treatment for DMD.
Embodiment 109
The method of embodiment 108, wherein said another treatment comprises administration of one or more drugs selected from the group consisting of Eteplirsen (Exondys 51), a steroid, and a blood pressure medication.
Embodiment 110
The method of embodiment 109, wherein said another treatment comprises administration of the oral corticosteroid deflazacort (Emflaza), and/or prednisone.
Embodiment 111
A method of delivering a nucleic acid to a cell in vivo in a mammal, said method comprising:

    
    
        providing a carrier according to any one of embodiments 1-58 where said carrier forms a complex with the nucleic acid to be delivered, and
        administering said complex to said mammal in an amount effective to deliver said nucleic acid to said cell.
    
    


Embodiment 112
The method of embodiment 111, wherein said cell comprises a muscle cell, a neural cell, a hematopoietic cell, a stem cell, or a T-cell.
Embodiment 113
The method of embodiment 112, wherein said cell comprises a cancer cell.
Embodiment 114
The method of embodiment 113, wherein said cancer cell comprises a cell selected from the group consisting of a solid tumor cell, a metastatic cell, and a cancer stem cell.
Embodiment 115
The method according to any one of embodiments 111-114, wherein said administering comprises systemic administration.
Embodiment 116
The method of embodiment 115, wherein said administration comprises nasal or intravenous administration.
Embodiment 117
The method according to any one of embodiments 111-116, wherein said mammal is a human.
Embodiment 118
The method according to any one of embodiments 111-116, wherein said mammal is a non-human mammal.
Embodiment 119
The method according to any one of embodiments 111-118, wherein said nucleic acid comprises RNA.
Embodiment 120
The method according to any one of embodiments 111-118, wherein said nucleic acid comprises DNA.
Embodiment 121
The method of embodiment 120, wherein said nucleic acid comprises a plasmid.
Embodiment 122
The method of embodiment 121, wherein said nucleic acid comprises a plasmid that encodes a heterologous gene or cDNA.
Embodiment 123
The method of embodiment 121, wherein said nucleic acid comprises a plasmid that encodes a class 2 CRISPR/Cas endonuclease and a guide RNA.
Embodiment 124
The method of embodiment 123, wherein said class 2 CRISPR/Cas endonuclease is a type II CRISPR/Cas endonuclease.
Embodiment 125
The method according to any one of embodiments 123-124, wherein the class 2 CRISPR/Cas endonuclease is a Cas9 polypeptide and the corresponding CRISPR/Cas guide RNA is a Cas9 guide RNA.
Embodiment 126
The method of embodiment 125, wherein said Cas9 protein is selected from the group consisting of a Streptococcus pyogenes Cas9 protein (spCas9) or a functional portion thereof, a Staphylococcus aureus Cas9 protein (saCas9) or a functional portion thereof, a Streptococcus thermophilus Cas9 protein (stCas9) or a functional portion thereof, a Neisseria meningitides Cas9 protein (nmCas9) or a functional portion thereof, and a Treponema denticola Cas9 protein (tdCas9) or a functional portion thereof.
Embodiment 127
The method of embodiment 126, wherein said Cas9 protein comprises a Streptococcus pyogenes Cas9 protein (spCas9).
Embodiment 128
The method of embodiment 126, wherein said Cas9 protein comprises a Staphylococcus aureus Cas9 protein (saCas9).
Embodiment 129
The method of embodiment 126, wherein said Cas9 protein comprises a Streptococcus thermophilus Cas9 protein.
Embodiment 130
The method of embodiment 126, wherein said Cas9 protein comprises a Neisseria meningitides Cas9 protein (nmCas9).
Embodiment 131
The method of embodiment 126, wherein said Cas9 protein comprises a Treponema denticola Cas9 protein (tdCas9).
Embodiment 132
The method of embodiment 123, wherein the class 2 CRISPR/Cas endonuclease is a type V or type VI CRISPR/Cas endonuclease.
Embodiment 133
The method of embodiment 132, wherein the class 2 CRISPR/Cas endonuclease is selected from the group consisting of a Cpf1 polypeptide or a functional portion thereof, a C2c1 polypeptide or a functional portion thereof, a C2c3 polypeptide or a functional portion thereof, and a C2c2 polypeptide or a functional portion thereof.
Embodiment 134
The method of embodiment 132, wherein the class 2 CRISPR/Cas endonuclease comprises a Cpf1 polypeptide.
Embodiment 135
The method according to any one of embodiments 111-134, wherein the N/P ratio of said carrier complexed to a nucleic acid ranges from about 0.01:1 up to about 100:1, or from about 2:1 up to about 25:1.
Embodiment 136
The method of embodiment 135, wherein the N/P ratio of said carrier complexed to a nucleic acid is about 10:1.
Embodiment 137
A method of making a polyrotaxane carrier for in vivo delivery of a nucleic acid, said method comprising:

    
    
        providing a multi-arm PEG backbone comprising m arms where m ranges from 3 to 8;
        coupling first protecting groups to x arms of said backbone where x ranges from 1 to m−1;
        forming cyclic compound inclusion bodies on the arms of said PEG backbone that are not coupled to said first protecting groups; and
        adding blocking groups to the arms of said PEG backbone that bear cyclic compound inclusion bodies.
    
    


Embodiment 138
The method of embodiment 137, wherein said cyclic compound comprise a compound selected from the group consisting of a cyclodextrin, a crown ether, a cucurbituril and a cyclofructan.
Embodiment 139
The method of embodiment 138, wherein said cyclic compound comprises a cyclodextrin.
Embodiment 140
The method of embodiment 139, wherein said cyclic compound comprises a cyclodextrin selected from the group consisting of an α-cyclodextrin, a β-cyclodextrin, a γ-cyclodextrin, a hydroxypropylated α-cyclodextrin, a hydroxypropylated β-cyclodextrin, a hydroxypropoylated γ-cyclodextrin, and a dimethylcyclodextrin.
Embodiment 141
The method of embodiment 138, wherein said cyclic compound comprises a cucurbituril.
Embodiment 142
The method of embodiment 141, wherein said cyclic compound comprises a cucurbituril selected from the group consisting of cucurbit[5]uril, cucurbit[6]uril, cucurbit[7]uril, cucurbit[8]uril, cucurbit[9]uril, and cucurbit[10]uril.
Embodiment 143
The method of embodiment 142, wherein said cyclic compound comprises a cucurbit[6]uril (CB[6]).
Embodiment 144
The method according to any one of embodiments 137-143, wherein said method comprises introducing one or more nucleophilic groups on cyclic compound(s).
Embodiment 145
The method of embodiment 144, wherein said cyclic compound(s) are substituted with one or more amine groups or groups derived from an amine group.
Embodiment 146
The method of embodiment 145, wherein said cyclic compound(s) are substituted with one or more groups selected from the group consisting of a primary amine, a secondary amine, a tertiary amine, and an imine group.
Embodiment 147
The method of embodiment 146, wherein said cyclic compound(s) are substituted with one or more primary amines.
Embodiment 148
The method according to any one of embodiments 144-147, where the number of nucleophilic group substituted on the cyclic compound(s) ranges from 1 up to about 20 substitutions per cyclic compound.
Embodiment 149
The method according to any one of embodiments 144-148, wherein the cyclic compounds are substituted with nucleophilic groups to provide a positive zeta potential for said carrier ranging from about +5 My up to about +50 mV.
Embodiment 150
The method according to any one of embodiments 144-149, wherein the cyclic compounds are substituted with nucleophilic groups to provide a zeta potential of about 15 mV.
Embodiment 151
The method according to any one of embodiments 137-150, wherein said multi-arm PEG comprises at least 2 arms free of cyclic compounds.
Embodiment 152
The method according to any one of embodiments 137-151, wherein said multi-arm PEG comprises from 3 up to about 12, or up to about 10, or up to about 8 arms.
Embodiment 153
The method according to any one of embodiments 137-152, wherein said PEG comprises 4 arms, or 5 arms, or 6 arms, or seven arms, or 8 arms.
Embodiment 154
The method according to any one of embodiments 137-151, wherein said PEG comprises 4 arms.
Embodiment 155
The method according to any one of embodiments 137-151, wherein said PEG comprise 4 arms where two of said arms are free of cyclic compounds.
Embodiment 156
The method according to any one of embodiments 137-155, wherein said PEG backbone has a molecular weight ranging from about 2.5 to about 10 kDA per arm.
Embodiment 157
The method according to any one of embodiments 137-156, wherein said PEG backbone comprise about 56 to about 227 ethylene oxides per arm.
Embodiment 158
The method according to any one of embodiments 137-155, wherein said PEG backbone has a molecular weight of about 1.0 kDa up to about 10 kDa per arm.
Embodiment 159
The method according to any one of embodiments 137-158, wherein the arm(s) threaded into said cyclic compound(s) each bear on average from about 5 up to about 110 cyclic compounds.
Embodiment 160
The method according to any one of embodiments 137-158, wherein the arm(s) threaded into said cyclic compound(s) each bear, on average, about 20 cyclic compounds per arm.
Embodiment 161
The method according to any one of embodiments 137-160, wherein the blocking group(s) comprise a moiety selected from the group consisting of Z-tyrosine, phenylalanine, a group having at least one benzene ring, and a group having at least one tertiary butyl.
Embodiment 162
The method of embodiment 161, wherein the blocking group(s) comprise a moiety selected from the group consisting of a Z-tyrosine, phenylaline, a benzyloxycarbonyl (Z) group, a 9-fluorenylmethyloxycarbonyl (Fmoc) group, a benzyl ester (OBz) group, a tertiary butylcarbonyl (Boc) group, and an amino acid-tertiary butyl ester (OBu) group.
Embodiment 163
The method of embodiment 161, wherein the blocking groups comprises Z-tyrosine.
Embodiment 164
The method according to any one of embodiments 137-163, wherein said first protecting group(s) comprise a protecting group, and/or a fluorophore, and/or a targeting moiety.
Embodiment 165
The method of embodiment 164, wherein said first protecting group(s) comprise a protecting group selected from the group consisting of dansyl, acetyl, amide, and 3 to 20 carbon alkyl groups, Fmoc, Tboc, 9-fluoreneacetyl group, 1-fluorenecarboxylic group, 9-florenecarboxylic group, 9-fluorenone-1-carboxylic group, benzyloxycarbonyl, Xanthyl (Xan), Trityl (Trt), 4-methyltrityl (Mtt), 4-methoxytrityl (Mmt), 4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr), Mesitylene-2-sulphonyl (Mts), 4,4-dimethoxybenzhydryl (Mbh), Tosyl (Tos), 2,2,5,7,8-pentamethyl chroman-6-sulphonyl (Pmc), 4-methylbenzyl (MeBzl), 4-methoxybenzyl (MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl), Benzoyl (Bz), 3-nitro-2-pyridinesulphenyl (Npys), 1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl (2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl—Z), 2-bromobenzyloxycarbonyl (2-Br—Z), Benzyloxymethyl (Bom), t-butoxycarbonyl (Boc), cyclohexyloxy (cHxO), t-butoxymethyl (Bum), t-butoxy (tBuO), t-Butyl (tBu), Acetyl (Ac), and Trifluoroacetyl (TFA).
Embodiment 166
The method of embodiment 164, wherein said first protecting group(s) comprise a fluorophore.
Embodiment 167
The method of embodiment 166, wherein said fluorophore is selected from the group consisting of a rhodamine, a cyanine, an oxazine, a thiazine, a porphyrin, a phthalocyanine, a fluorescent protein, and a quantum dot.
Embodiment 168
The method of embodiment 166, wherein said fluorophore is selected from the group consisting of fluorescein isothiocyanate (especially fluorescein-5-isothiocyanate), 5-FAM (5-carboxyfluorescein), 6-FAM (6-carboxyfluorescein), 5,6-FAM, 7-hydroxycoumarin-3-carboxamide, 6-chloro-7-hydroxycoumarin-3-carboxamide-, dichlorotriazinylaminofluorescein, tetramethylrhodamine-5 (and-6)-isothiocyanate, 1,3-bis-(2-dialkylamino-5-thienyl)-substituted squarines, succinimidyl esters of 5 (and 6) carboxyfluoroscein, 5 (and 6)-carboxytetramethylrhodamine, 7-amino-4-methylcoumarin-3-acetic acid, DyLight 350, DyLight 405, DyLight 488, DyLight 550, DyLight 594, DyLight 633, DyLight 650, DyLight 680, DyLight 755, DyLight 800, Alexa fluor 350, Alexa fluor 405, Alexa fluor 488, Alexa fluor 546, Alexa fluor 555, Alexa fluor 568, Alexa fluor 594, Alexa fluor 633, Alexa fluor 647, and Alexa fluor 750.
Embodiment 169
The method of embodiment 164, wherein said first protecting group(s) comprise a targeting moiety that specifically or preferentially binds to a cell.
Embodiment 170
The method of embodiment 169, wherein said targeting moiety is selected from the group consisting of an antibody, a receptor ligand, neural cell adhesion molecule (NCAM), a cell penetrating peptide (CPP), a nucleic acid aptamer, a peptide aptamer, and a lectin.
Embodiment 171
The method of embodiment 170, wherein said targeting moiety comprises an antibody.
Embodiment 172
The method according to any one of embodiments 170-171, wherein said targeting moiety comprises a moiety that binds to a stem cell.
Embodiment 173
The method according to any one of embodiments 170-171, wherein said targeting moiety comprises a moiety that binds to a hematopoietic cell.
Embodiment 174
The method according to any one of embodiments 170-171, wherein said targeting moiety comprises a moiety that binds to a T-cell.
Embodiment 175
The method according to any one of embodiments 170-171, wherein said targeting moiety comprises a moiety that binds to a muscle cell.
Embodiment 176
The method according to any one of embodiments 170-171, wherein said targeting moiety binds a target selected from the group consisting of CD45, CD3, erbB2, Her2, CD22, CD74, CD19, CD20, CD33, CD40, MUC1, IL-15R, HLA-DR, EGP-1, EGP-2, G250, prostate specific membrane antigen (PSMA), prostate specific antigen (PSA), prostatic acid phosphatase (PAP), and placental alkaline phosphatase.
Embodiment 177
The method according to any one of embodiments 170-171, wherein said targeting moiety comprises a moiety that binds to a cancer cell marker.
Embodiment 178
The method of embodiment 177, wherein said targeting moiety comprises a moiety that binds to a cancer cell marker selected from the group consisting of 5 alpha reductase, α-fetoprotein, AM-1, APC, APRIL, BAGE, β-catenin, Bc12, bcr-abl (b3a2), CA-125, CASP-8/FLICE, Cathepsins, CD19, CD20, CD21, CD23, CD22, CD38, CD33, CD35, CD44, CD45, CD46, CD5, CD52, CD55, CD59 (791Tgp72), CDCl27, CDK4, CEA, c-myc, Cox-2, DCC, DcR3, E6/E7, EGFR, EMBP, Ena78, FGF8b and FGF8a, FLK-1/KDR, Folic Acid Receptor, G250, GAGE-Family, gastrin 17, Gastrin-releasing hormone (bombesin), GD2/GD3/GM2, GnRH, GnTV, gp100/Pmel17, gp-100-in4, gp15, gp75/TRP-1, hCG, Heparanase, Her2/neu, Her3, HMTV, Hsp70, hTERT, (telomerase), IGFR1, IL-13R, iNOS, Ki 67, KIAA0205, K-ras, H-ras, N-ras, KSA, (CO17-1A), LDLR-FUT, MAGE Family (MAGE1, MAGE3, etc.), Mammaglobin, MAP17, Melan-A/, MART-1, mesothelin, MIC A/B, MT-MMP's, such as MMP2, MMP3, MMP7, MMP9, Mox1, Mucin, such as MUC-1, MUC-2, MUC-3, and MUC-4, MUM-1, NY-ESO-1, Osteonectin, p15, P170/MDR1, p53, p97/melanotransferrin, PAI-1, PDGF, Plasminogen (uPA), PRAME, Probasin, Progenipoietin, PSA, PSM, RAGE-1, Rb, RCAS1, SART-1, SSX gene, family, STAT3, STn, (mucin assoc.), TAG-72, TGF-□, TGF-β, Thymosin β 15, IFN-□, TPA, TPI, TRP-2, Tyrosinase, VEGF, ZAG, p16INK4, and Glutathione S-transferase.
Embodiment 179
The method of embodiment 170, wherein said targeting moiety comprises a transferrin.
Embodiment 180
The method according to any one of embodiments 137-179, wherein said blocking group(s) are attached arm(s) of said backbone by a cleavable linkage.
Embodiment 181
The method according to any one of embodiments 144-179, wherein said a or more nucleophilic groups are attached to said cyclic compounds by a cleavable linkage.
Embodiment 182
The method according to any one of embodiments 180-181, wherein said cleavable linkage comprises a redox-responsive linker, a pH responsive linker, and an enzymatically cleavable linker.
Embodiment 183
The method of embodiment 182, wherein said cleavable linkage comprises a redox-responsive disulfide linker.
Embodiment 184
The method of embodiment 182, wherein said cleavable linkage comprises a pH responsive hydrazine linker.
Embodiment 185
The method of embodiment 182, wherein said cleavable linkage comprises an enzymatically cleavable linker.
Embodiment 186
The method of embodiment 185, wherein said linkage comprises a linker cleavable by a protease.
Embodiment 187
The method of embodiment 186, wherein said linkage comprises a linker cleavable by a matrix metalloprotease or a cathepsin.
Embodiment 188
The construct according to any one of embodiments 186-187, wherein said peptide linker comprises a linker comprises a moiety selected from the group consisting of dipeptide valine-citrulline (Val-Cit), dipeptide Phe-Lys, Mc-vc-PAB-MMAE, Mc-vc-PAB-MMAF, Mc-va-PBD dimer, Mc-vc-PAB-CM-seco-DUBA, Gly-Phe-Leu-Gly (GFLG), GPLGV, and GPLGVRG.
Embodiment 189
A kit for delivering a nucleic acid in vivo to a mammal, said kit comprising: a container containing a polyrotaxane carrier according to any one of embodiments 1-58.
Embodiment 190
The kit of embodiment 189, wherein said kit further comprises a container containing a nucleic acid that is to be delivered to said mammal.
Embodiment 191
The kit of embodiment 190, wherein said nucleic acid is in a container separate from the container containing said carrier.
Embodiment 192
The kit of embodiment 191, wherein said nucleic acid comprises a nucleic acid as recited in any one of embodiments 59-93.
Embodiment 193
The kit of embodiment 190, wherein said nucleic acid is provided as a complex with said carrier.
Embodiment 194
The kit of embodiment 193, wherein said carrier complexed with said nucleic acid comprises a complex according to any one of embodiments 59-77.
Embodiment 195
The kit of embodiment 193, wherein said carrier complexed with said nucleic acid comprises a construct according to any one of embodiments 82-95.
Embodiment 196
The kit according to any one of embodiments 189-195, wherein said kit comprise instructional materials teaching the use of said carrier to deliver a nucleic acid to a cell in vivo.
Embodiment 197
A construct for the treatment of a cancer, said construct comprising: a polyrotaxane carrier according to any one of embodiments 1-58, wherein said carrier is complexed with a plasmid encoding a cytokine.
Embodiment 198
The construct of embodiment 197, wherein said cytokine comprises one or more cytokines selected from the group consisting of interleukin 12 (IL-12), interferon alpha (IFN-α), interferon beta (IFN-β), interferon gamma (IFN-γ), interleukin 1 (IL-1), interleukin (IL-2), interleukin 4 (IL-4), interleukin 6 (IL-6), interleukin 7 (IL-7), interleukin 11 (IL-11), interleukin 15 (IL-15), and interleukin 18 (IL-18).
Embodiment 199
The construct of embodiment 197, wherein said cytokine comprises IL-12.
Embodiment 200
The construct of embodiment 199, wherein said cytokine comprises a combination of IL2 and IL-12.
Embodiment 201
The construct of embodiment 199, wherein said cytokine comprises a combination of IL-15 and IL-12.
Embodiment 202
The construct of embodiment 199, wherein said cytokine comprises a combination of IL-7 and IL-12.
Embodiment 203
The construct of embodiment 199, wherein said cytokine comprises a combination of IL-21 and IL-12.
Embodiment 204
The construct of embodiment 199, wherein said cytokine comprises a combination of IL-18 and IL-12.
Embodiment 205
The construct of embodiment 199, wherein said cytokine comprises a combination of GM-CSF and IL-12.
Embodiment 206
The construct of embodiment 199, wherein said cytokine comprises a combination of interferon alpha and IL-12.
Embodiment 207
The construct of embodiment 199, wherein said cytokine comprises a combination of a chemokine and/or an antiogenic cytokine and IL-12.
Embodiment 208
The construct of embodiment 197, wherein said cytokine comprises an interferon.
Embodiment 209
The construct of embodiment 208, wherein said cytokine comprises an interferon alpha.
Embodiment 210
The construct of embodiment 209, wherein said cytokine comprises an interferon beta.
Embodiment 211
The construct of embodiment 209, wherein said cytokine comprises an interferon gamma.
Embodiment 212
The construct according to any one of embodiments 197-211, wherein said plasmid comprises a nucleic acid encoding said cytokine under the control of a constitutive promoter.
Embodiment 213
The construct according to any one of embodiments 197-211, wherein said plasmid comprises a nucleic acid encoding said cytokine under the control of an inducible promoter.
Embodiment 214
The construct according to any one of embodiments 197-211, wherein said plasmid comprises a nucleic acid encoding said cytokine under the control of a tissue-specific promoter.
Embodiment 215
A pharmaceutical formulation comprising: a polyrotaxane construct according to any one of embodiments 197-214; and a pharmaceutically acceptable carrier.
Embodiment 216
The formulation of embodiment 215, wherein said polyrotaxane carrier is complexed with a nucleic acid.
Embodiment 217
The formulation according to any one of embodiments 215-216, wherein said formulation is formulated for administration via a route selected from the group consisting of isophoretic delivery, transdermal delivery, aerosol administration, administration via inhalation, oral administration, intravenous administration, intraarterial administration, intramuscular administration, topical delivery to the eye, intraocular injection, vaginal administration, and rectal administration.
Embodiment 218
The formulation according to any one of embodiments 215-217, wherein said formulation is a unit dosage formulation.
Embodiment 219
A method of treating a cancer in a mammal, said method comprising: administering to said mammal an effective amount of a construct according to any one of embodiments 197-214.
Embodiment 220
The method of embodiment 219, wherein said cancer comprises a colon cancer.
Embodiment 221
The method of embodiment 219, wherein said cancer comprises pancreatic ductal adenocarcinoma (PDAC).
Embodiment 222
The method of embodiment 219, wherein said cancer comprises a cancer selected from the group consisting of acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), Adrenocortical carcinoma, AIDS-related cancers (e.g., Kaposi sarcoma, lymphoma), anal cancer, appendix cancer, astrocytomas, atypical teratoid/rhabdoid tumor, bile duct cancer, extrahepatic cancer, bladder cancer, bone cancer (e.g., Ewing sarcoma, osteosarcoma, malignant fibrous histiocytoma), brain stem glioma, brain tumors (e.g., astrocytomas, brain and spinal cord tumors, brain stem glioma, central nervous system atypical teratoid/rhabdoid tumor, central nervous system embryonal tumors, central nervous system germ cell tumors, craniopharyngioma, ependymoma, breast cancer, bronchial tumors, burkitt lymphoma, carcinoid tumors (e.g., childhood, gastrointestinal), cardiac tumors, cervical cancer, chordoma, chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), chronic myeloproliferative disorders, colon cancer, colorectal cancer, craniopharyngioma, cutaneous t-cell lymphoma, duct cancers e.g. (bile, extrahepatic), ductal carcinoma in situ (DCIS), embryonal tumors, endometrial cancer, ependymoma, esophageal cancer, esthesioneuroblastoma, extracranial germ cell tumor, extragonadal germ cell tumor, extrahepatic bile duct cancer, eye cancer (e.g., intraocular melanoma, retinoblastoma), fibrous histiocytoma of bone, malignant, and osteosarcoma, gallbladder cancer, gastric (stomach) cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumors (GIST), germ cell tumors (e.g., ovarian cancer, testicular cancer, extracranial cancers, extragonadal cancers, central nervous system), gestational trophoblastic tumor, brain stem cancer, hairy cell leukemia, head and neck cancer, heart cancer, hepatocellular (liver) cancer, histiocytosis, langerhans cell cancer, Hodgkin lymphoma, hypopharyngeal cancer, intraocular melanoma, islet cell tumors, pancreatic neuroendocrine tumors, kaposi sarcoma, kidney cancer (e.g., renal cell, Wilm's tumor, and other kidney tumors), langerhans cell histiocytosis, laryngeal cancer, leukemia, acute lymphoblastic (ALL), acute myeloid (AML), chronic lymphocytic (CLL), chronic myelogenous (CML), hairy cell, lip and oral cavity cancer, liver cancer (primary), lobular carcinoma in situ (LCIS), lung cancer (e.g., childhood, non-small cell, small cell), lymphoma (e.g., AIDS-related, Burkitt (e.g., non-Hodgkin lymphoma), cutaneous T-Cell (e.g., mycosis fungoides, Sezary syndrome), Hodgkin, non-Hodgkin, primary central nervous system (CNS)), macroglobulinemia, Waldenström, male breast cancer, malignant fibrous histiocytoma of bone and osteosarcoma, melanoma (e.g., childhood, intraocular (eye)), merkel cell carcinoma, mesothelioma, metastatic squamous neck cancer, midline tract carcinoma, mouth cancer, multiple endocrine neoplasia syndromes, multiple myeloma/plasma cell neoplasm, mycosis fungoides, myelodysplastic syndromes, Myelogenous Leukemia, Chronic (CML), multiple myeloma, nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, neuroblastoma, oral cavity cancer, lip and oropharyngeal cancer, osteosarcoma, ovarian cancer, pancreatic cancer, pancreatic neuroendocrine tumors (islet cell tumors), papillomatosis, paraganglioma, paranasal sinus and nasal cavity cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pheochromocytoma, pituitary tumor, plasma cell neoplasm, pleuropulmonary blastoma, primary central nervous system (CNS) lymphoma, prostate cancer, rectal cancer, renal cell (kidney) cancer, renal pelvis and ureter, transitional cell cancer, rhabdomyosarcoma, salivary gland cancer, sarcoma (e.g., Ewing, Kaposi, osteosarcoma, rhadomyosarcoma, soft tissue, uterine), Sezary syndrome, skin cancer (e.g., melanoma, merkel cell carcinoma, basal cell carcinoma, nonmelanoma), small intestine cancer, squamous cell carcinoma, squamous neck cancer with occult primary, stomach (gastric) cancer, testicular cancer, throat cancer, thymoma and thymic carcinoma, thyroid cancer, trophoblastic tumor, ureter and renal pelvis cancer, urethral cancer, uterine cancer, endometrial cancer, uterine sarcoma, vaginal cancer, vulvar cancer, Waldenstrom macroglobulinemia, and Wilm's tumor.
Embodiment 223
The method according to any one of embodiments 219-222, wherein said method comprises a primary therapy in a chemotherapeutic regimen.
Embodiment 224
The method according to any one of embodiments 219-222, wherein said method comprises an adjunct therapy in a chemotherapeutic regimen.
Embodiment 225
The method according to any one of embodiments 219-224, wherein said polyrotaxane construct is a component in a multi-drug chemotherapeutic regimen.
Embodiment 226
The method according to any one of embodiments 219-225, wherein said administering comprises administration via a route selected from the group consisting of isophoretic delivery, transdermal delivery, aerosol administration, administration via inhalation, oral administration, intravenous administration, intraarterial administration, intramuscular administration, topical delivery to the eye, intraocular injection, vaginal administration, and rectal administration.
Embodiment 227
The method according to any one of embodiments 219-225, wherein said administering comprises systemic administration.
Embodiment 228
The method according to any one of embodiments 219-227, wherein said mammal is a human.
Embodiment 229
The method according to any one of embodiments 219-227, wherein said mammal is a non-human mammal.
Embodiment 230
The method according to any one of embodiments 219-229, wherein said polyrotaxane carrier comprises a targeting moiety that specifically or preferentially binds to a cell.
Embodiment 231
The method of embodiment 228, wherein said targeting moiety is selected from the group consisting of an antibody, a receptor ligand, neural cell adhesion molecule (NCAM), a cell penetrating peptide (CPP), a nucleic acid aptamer, a peptide aptamer, and a lectin.
Embodiment 232
The method of embodiment 228, wherein said targeting moiety comprises an antibody.
Embodiment 233
The method according to any one of embodiments 228-232, wherein said targeting moiety comprises a moiety that binds to cancer cell marker.
Embodiment 234
The method of embodiment 233, wherein said targeting moiety binds a target selected from the group consisting of 5 alpha reductase, α-fetoprotein, AM-1, APC, APRIL, BAGE, β-catenin, Bc12, bcr-abl (b3a2), CA-125, CASP-8/FLICE, Cathepsins, CD19, CD20, CD21, CD23, CD22, CD38, CD33, CD35, CD44, CD45, CD46, CD5, CD52, CD55, CD59 (791Tgp72), CDCl27, CDK4, CEA, c-myc, Cox-2, DCC, DcR3, E6/E7, EGFR, EMBP, Ena78, FGF8b and FGF8a, FLK-1/KDR, Folic Acid Receptor, G250, GAGE-Family, gastrin 17, Gastrin-releasing hormone (bombesin), GD2/GD3/GM2, GnRH, GnTV, gp100/Pmel17, gp-100-in4, gp15, gp75/TRP-1, hCG, Heparanase, Her2/neu, Her3, HMTV, Hsp70, hTERT, (telomerase), IGFR1, IL-13R, iNOS, Ki 67, KIAA0205, K-ras, H-ras, N-ras, KSA, (CO17-1A), LDLR-FUT, MAGE Family (MAGE1, MAGE3, etc.), Mammaglobin, MAP17, Melan-A/, MART-1, mesothelin, MIC A/B, MT-MMP's, such as MMP2, MMP3, MMP7, MMP9, Mox, Mucin, such as MUC-1, MUC-2, MUC-3, and MUC-4, MUM-1, NY-ESO-1, Osteonectin, p15, P170/MDR1, p53, p97/melanotransferrin, PAI-1, PDGF, Plasminogen (uPA), PRAME, Probasin, Progenipoietin, PSA, PSM, RAGE-1, Rb, RCAS1, SART-1, SSX gene, family, STAT3, STn, (mucin assoc.), TAG-72, TGF-α, TGF-β, Thymosin β 15, TPA, TPI, TRP-2, Tyrosinase, VEGF, ZAG, p16INK4, and Glutathione S-transferase.
Embodiment 235
The method of embodiment 228, wherein said targeting moiety comprises a transferrin.
While the polyrotaxane nucleic acid delivery vehicles are described herein with respect to polyethylene glycol (PEG) backbones, in certain embodiments, other polymer backbones are contemplated. Accordingly, in certain embodiments, the polymer backbone comprise one or more polymers selected from the group consisting of polyethylene glycol, polypropylene glycol, polybutylene glycol, polypentylene glycol, polyhexylene glycol, polymethyl vinyl ether, polyethyl vinyl ether, polyisoprene, polyisobutylene, polybutadiene, and copolymers thereof. In one embodiment, the polymer is a poly(ethylene glycol), a derivative thereof, or a copolymer that reacts with the poly(ethylene glycol) segment. In certain embodiments, the polymer can also be poly(propylene glycol) or other poly(alkylene glycols). In certain embodiments, the copolymer may be any one of a variety of biodegradable and biocompatible copolymers that contain ethylene glycol units such as polyesters, polyurethanes, polyamides, polyethers, polysaccharides, poly(amino acids), polypeptides, or a protein. Modified poly(ethylene glycol) may be also be used, such as pegylated polysaccharides, pegylated polyaminoacids, and pegylated proteins. In certain embodiments, the poly(ethylene glycol) derivatives or copolymers may have poly(ethylene glyol) or polypropylene oxide) segment(s) at the end(s), in which the middle segment carries positive charge.
In various embodiments, the carriers described and/or claimed herein exclude backbones that are dendrimers.
Definitions
The terms “subject,” “individual,” and “patient” and “mammal” may be used interchangeably and refer to a mammal, preferably a human or a non-human primate, but also domesticated mammals (e.g., canine or feline), laboratory mammals (e.g., mouse, rat, rabbit, hamster, guinea pig), and agricultural mammals (e.g., equine, bovine, porcine, ovine). In various embodiments, the subject can be a human (e.g., adult male, adult female, adolescent male, adolescent female, male child, female child) under the care of a physician or other health worker in a hospital, psychiatric care facility, as an outpatient, or other clinical context. In certain embodiments, the subject may not be under the care or prescription of a physician or other health worker.
The terms “cyclic compound”, “cyclic molecule” and grammatical variations thereof refer to a molecule that is cyclic in that it has a ring structure and also to a molecule which is of a substantial ring structure. That is, the term “substantial ring” means to include molecules in which the ring is not closed completely, as in the letter “C”, and molecules having a helical structure in which as in the letter “C”, one end and the other end are not connected and placed in a piled manner. Cyclic compounds include, but are not limited to, cyclodextrins, crown ethers, cucurbiturils cyclofructans, and the like.
Cucurbiturils are macrocyclic molecules made of glycoluril (═C4H2N4O2═) monomers linked by methylene bridges (—CH2—). The oxygen atoms are located along the edges of the band and are tilted inwards, forming a partly enclosed cavity. The name is derived from the resemblance of this molecule with a pumpkin of the family of Cucurbitaceae.
An “inclusion compound” or “inclusion complex” is a complex in which one chemical compound forms a cavity in which molecules of a second “guest” compound are located.
The term “nucleophile-substituted cyclic compound” refers to a cyclic compound having at least one attached nucleophilic group.
The term “amine-substituted cyclic compound” refers to a cyclic compound having at least one attached amine group. Likewise, the term “amine-substituted cyclodextrins” refers to a cyclodextrin compound having at least one attached amine group.
The term “amine group” refers to primary, secondary and tertiary amine groups as well as groups derived from amine groups, such as imine groups.
The term “nucleic acid”, and equivalent terms such as polynucleotide, refers to a polymeric form of nucleotides of any length, such as ribonucleotides, deoxyribonucleotides or peptide nucleic acids (PNAs), that comprise purine and pyrimidine bases, or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. The nucleic acid may be double stranded or single stranded. References to single stranded nucleic acids include references to the sense or antisense strands. The backbone of the polynucleotide can comprise sugars and phosphate groups, as may typically be found in RNA or DNA, or modified or substituted sugar or phosphate groups. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. The sequence of nucleotides may be interrupted by non-nucleotide components. The terms nucleoside, nucleotide, deoxynucleoside and deoxynucleotide generally include complements, fragments and variants of the nucleoside, nucleotide, deoxynucleoside and deoxynucleotide, or analogs thereof.
As used herein, the term recombinant refers to a compound or composition produced by human intervention.
As used herein, a “recombinant” nucleic acid or protein molecule is a molecule where the nucleic acid molecule which encodes the protein has been modified in vitro, so that its sequence is not naturally occurring, or corresponds to naturally occurring sequences that are not positioned as they would be positioned in a genorne which has not been modified.
The term “target cell” is used herein to mean any cell into which an exogenous nucleic acid molecule is to be introduced.
The term “branched” polymer is meant to designate a polymer having side chains or branches that are bonded to the polymer (e.g., PEG) backbone. In certain embodiments side-chains all branch from the same or approximately the same location on the backbone. In certain embodiments, different side-chains attach to different locations along the backbone. In certain embodiments, the backbone comprises a star polymer. The term “star polymer” is used to describe polymer molecule structures that have multiple arms extending generally from a central core.
The term “bulky moieties” and grammatical variations thereof refers to any substituents group that has sufficient bulk to substantially inhibit dethreading of cyclic compounds from a chain (arm) chain of a polymer backbone.
The terms “cleavable linkage”, “biocleavable linkage”, “biocleavable linker” “biodegradable linker”, “biodegradable linkages”, “bio responsive linker or linkage”, “on-demand released linker or linkage” and grammatical variations thereof are defined as types of specific chemical moieties or groups used within the polycation that couple and optionally cross-link a bulky moiety to the polymer backbone and which, in vivo, and preferably during or after transfection, cleave the bulky moieties from said polymer backbone.
The terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, this term includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.
By “hybridizable” or “complementary” or “substantially complementary” it is meant that a nucleic acid (e.g. RNA, DNA) comprises a sequence of nucleotides that enables it to non-covalently bind, i.e. form Watson-Crick base pairs and/or G/U base pairs, “anneal”, or “hybridize,” to another nucleic acid in a sequence-specific, antiparallel, manner (i.e., a nucleic acid specifically binds to a complementary nucleic acid) under the appropriate in vitro and/or in vivo conditions of temperature and solution ionic strength. Standard Watson-Crick base-pairing includes: adenine (A) pairing with thymidine (T), adenine (A) pairing with uracil (U), and guanine (G) pairing with cytosine (C) [DNA, RNA]. In addition, for hybridization between two RNA molecules (e.g., dsRNA), and for hybridization of a DNA molecule with an RNA molecule (e.g., when a DNA target nucleic acid base pairs with a guide RNA, etc.): guanine (G) can also base pair with uracil (U). For example, G/U base-pairing is partially responsible for the degeneracy (i.e., redundancy) of the genetic code in the context of tRNA anti-codon base-pairing with codons in mRNA. Thus, in the context of this disclosure, a guanine (G) (e.g., of a guide RNA molecule; of a target nucleic acid base pairing with a guide RNA, etc.) is considered complementary to both a uracil (U) and to an adenine (A). For example, when a G/U base-pair can be made at a given nucleotide position of a protein• binding segment (e.g., dsRNA duplex) of a guide RNA molecule, the position is not considered to be non-complementary, but is instead considered to be complementary.
Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1 therein; and Sambrook, J. and Russell, W., Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2001). The conditions of temperature and ionic strength determine the “stringency” of the hybridization.
Hybridization requires that the two nucleic acids contain complementary sequences, although mismatches between bases are possible. The conditions appropriate for hybridization between two nucleic acids depend on the length of the nucleic acids and the degree of complementarity, variables well known in the art. The greater the degree of complementarity between two nucleotide sequences, the greater the value of the melting temperature (Tm) for hybrids of nucleic acids having those sequences. For hybridizations between nucleic acids with short stretches of complementarity (e.g., complementarity over 35 or less, 30 or less, 25 or less, 22 or less, 20 or less, or 18 or less nucleotides) the position of mismatches can become important (see Sambrook et al., supra). Typically, the length for a hybridizable nucleic acid is 8 nucleotides or more (e.g., 10 nucleotides or more, 12 nucleotides or more, 15 nucleotides or more, 20 nucleotides or more, 22 nucleotides or more, 25 nucleotides or more, or 30 nucleotides or more). Temperature, wash solution salt concentration, and other conditions may be adjusted as necessary according to factors such as length of the region of complementation and the degree of complementation.
It is understood that the sequence of a polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable or hybridizable. Moreover, a polynucleotide may hybridize over one or more segments such that intervening or adjacent segments are not involved in the hybridization event (e.g., a bulge, a loop structure or hairpin structure, etc.). A polynucleotide can comprise 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 98% or more, 99% or more, 99.5% or more, or 100% sequence complementarity to a target region within the target nucleic acid sequence to which it will hybridize. For example, an antisense nucleic acid in which 18 of 20 nucleotides of the antisense compound are complementary to a target region, and would therefore specifically hybridize, would represent 90 percent complementarity. In this example, the remaining noncomplementary nucleotides may be clustered or interspersed with complementary nucleotides and need not be contiguous to each other or to complementary nucleotides. Percent complementarity between particular stretches of nucleic acid sequences within nucleic acids can be determined using any convenient method. Example methods include BLAST programs (basic local alignment search tools) and PowerBLAST programs (see, e.g., Altschul et al. (1990) J. Mol. Biol., 215: 403-410; Zhang and Madden (1997) Genome Res., 7: 649-656), the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), e.g., using default settings, which uses the algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2: 482-489), and the like.
“Binding” as used herein (e.g. with reference to an RNA-binding domain of a polypeptide, binding to a target nucleic acid, and the like) refers to a non-covalent interaction between macromolecules (e.g., between a protein and a nucleic acid; between a Cas9 protein/guide RNA complex and a target nucleic acid; and the like). While in a state of non• covalent interaction, the macromolecules are said to be “associated” or “interacting” or “binding” (e.g., when a molecule X is said to interact with a molecule Y, it is meant the molecule X binds to molecule Yin a non-covalent manner). Not all components of a binding interaction need be sequence-specific (e.g., contacts with phosphate residues in a DNA backbone), but some portions of a binding interaction may be sequence-specific. Binding interactions are generally characterized by a dissociation constant (KD) of less than 10−6 M, less than 10−7 M, less than 10−8M, less than 10−9 M, less than 10−10 M, less than 10−+ M, less than 10−12 M, less than 10−13 M, less than 10−4 M, or less than 10−1 M. “Affinity” refers to the strength of binding, increased binding affinity being correlated with a lower KD.
A DNA sequence that “encodes” a particular RNA is a DNA nucleic acid sequence that is transcribed into RNA. A DNA polynucleotide may encode an RNA (mRNA) that is translated into protein (and therefore the DNA and the mRNA both encode the protein), or a DNA polynucleotide may encode an RNA that is not translated into protein (e.g. tRNA, rRNA, microRNA (miRNA), a “non-coding” RNA (ncRNA), a guide RNA, etc.).
A “protein coding sequence” or a sequence that encodes a particular protein or polypeptide, is a nucleic acid sequence that is transcribed into mRNA (in the case of DNA) and is translated (in the case of mRNA) into a polypeptide in vitro or in vivo when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a start codon at the 5′ terminus (N-terminus) and a translation stop nonsense codon at the 3′ terminus (C-terminus). A coding sequence can include, but is not limited to, cDNA from prokaryotic or eukaryotic mRNA, genomic DNA sequences from prokaryotic or eukaryotic DNA, and synthetic nucleic acids. A transcription termination sequence will usually be located 3′ to the coding sequence.
The terms “DNA regulatory sequences,” “control elements,” and “regulatory elements,” used interchangeably herein, refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and/or regulate transcription of a non-coding sequence (e.g., guide RNA) or a coding sequence (e.g., a class 2 CRISPR/Cas endonuclease such as a Cas9 protein) and/or regulate translation of an encoded polypeptide.
As used herein, a “promoter sequence” is a DNA regulatory region capable of binding RNA polymerase and initiating transcription of a downstream (3′ direction) coding or non-coding sequence. For purposes of the present disclosure, the promoter sequence is bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation site, as well as protein binding domains responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain “TATA” boxes and “CAT” boxes. Various promoters, including inducible promoters, may be used to drive the various vectors of the present disclosure.
The term “naturally-occurring” or “unmodified” or “wild type” as used herein as applied to a nucleic acid, a polypeptide, a cell, or an organism, refers to a nucleic acid, polypeptide, cell, or organism that is found in nature. For example, a polypeptide or polynucleotide sequence that is present in an organism (including viruses) that can be isolated from a source in nature and which has not been intentionally modified by a human in the laboratory is wild type (and naturally occurring).
“Heterologous,” as used herein, means a nucleotide or polypeptide sequence that is not found in the native nucleic acid or protein, respectively. For example, in a chimeric Cas9 protein, the RNA-binding domain of a naturally-occurring bacterial Cas9 polypeptide (or a variant thereof) may be fused to a heterologous polypeptide sequence (i.e. a polypeptide sequence from a protein other than Cas9 or a polypeptide sequence from another organism). The heterologous polypeptide sequence may exhibit an activity (e.g., enzymatic activity) that will also be exhibited by the chimeric Cas9 protein (e.g., methyltransferase activity, acetyltransferase activity, kinase activity, ubiquitinating activity, etc.). A heterologous nucleic acid sequence may be linked to a naturally-occurring nucleic acid sequence (or a variant thereof) (e.g., by genetic engineering) to generate a chimeric nucleotide sequence encoding a chimeric polypeptide. As another example, in a fusion variant Cas9 polypeptide, a variant Cas9 polypeptide may be fused to a heterologous polypeptide (i.e. a polypeptide other than Cas9), which exhibits an activity that will also be exhibited by the fusion variant Cas9 polypeptide. A heterologous nucleic acid sequence may be linked to a variant Cas9 polypeptide (e.g., by genetic engineering) to generate a nucleotide sequence encoding a fusion protein.
A “vector” or “expression vector” is a replicon, such as plasmid, or cosmid, to which another DNA segment, i.e. an “insert”, may be attached so as to bring about the expression of the attached segment in a cell.
An “expression cassette” comprises a DNA coding sequence operably linked to a promoter. “Operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence (or the coding sequence can also be said to be operably linked to the promoter) if the promoter affects its transcription or expression.
The terms “recombinant expression vector,” or “DNA construct” are used interchangeably herein to refer to a DNA molecule comprising a vector and one insert. Recombinant expression vectors are usually generated for the purpose of expressing and/or propagating the insert(s), or for the construction of other recombinant nucleotide sequences. The insert(s) may or may not be operably linked to a promoter sequence and may or may not be operably linked to DNA regulatory sequences.
A “target nucleic acid” as used herein is a polynucleotide (e.g., DNA such as genomic DNA) that includes a site (“target site” or “target sequence”) targeted by a construct, e.g., a genome editing endonuclease. When the genome editing endonuclease is a CRISPR/Cas endonuclease, the target sequence is the sequence to which the guide sequence of a subject CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) will hybridize. For example, the target site (or target sequence) 5′-GAGCAUATC-3′ within a target nucleic acid is targeted by (or is bound by, or hybridizes with, or is complementary to) the sequence 5′-GAUAUGCUC-3′. Suitable hybridization conditions include physiological conditions normally present in a cell. For a double stranded target nucleic acid, the strand of the target nucleic acid that is complementary to and hybridizes with the guide RNA is referred to as the “complementary strand” or “target strand”; while the strand of the target nucleic acid that is complementary to the “target strand” (and is therefore not complementary to the guide RNA) is referred to as the “non-target strand” or “non• complementary strand”.
By “cleavage” it is meant the breakage of the covalent backbone of a target molecule, e.g., a nucleic acid molecule (e.g., RNA, DNA). Cleavage can be initiated by a variety of methods including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single-stranded cleavage and double-stranded cleavage are possible, and double-stranded cleavage can occur as a result of two distinct single-stranded cleavage events. In some embodiments, a complex comprising a CRISPR/Cas protein (e.g., a Cas9 protein) and a corresponding guide RNA is used for targeted cleavage of a double stranded DNA (dsDNA), e.g., induction of a double-stranded DNA break (DSB).
“Nuclease” and “endonuclease” are used interchangeably herein to mean an enzyme which possesses catalytic activity for nucleic acid cleavage (e.g., ribonuclease activity (ribonucleic acid cleavage), deoxyribonuclease activity (deoxyribonucleic acid cleavage), etc.). A “genome editing endonuclease” is an endonuclease that can be used for the editing of a cell's genome (e.g., by cleaving at a targeted location within the cell's genomic DNA). Examples of genome editing endonucleases include but are not limited to class 2 CRISPR/Cas endonucleases such as: (a) type II CRISPR/Cas proteins, e.g., a Cas9 protein; (b) type V CRISPR/Cas proteins, e.g., a Cpf1 protein, a C2c1 protein, a C2c3 protein, and the like; and (c) type VI CRISPR/Cas proteins, e.g., a C2c2 protein.
By “cleavage domain” or “active domain” or “nuclease domain” of a nuclease it is meant the polypeptide sequence or domain within the nuclease which possesses the catalytic activity for nucleic acid cleavage. A cleavage domain can be contained in a single polypeptide chain or cleavage activity can result from the association of two (or more) polypeptides. A single nuclease domain may consist of more than one isolated stretch of amino acids within a given polypeptide.
The terms “treatment”, “treating” and the like are used herein to generally mean obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease. “Treatment” as used herein covers any treatment of a disease or symptom in a mammal, and includes: (a) preventing the disease or symptom from occurring in a subject which may be predisposed to acquiring the disease or symptom but has not yet been diagnosed as having it; (b) inhibiting the disease or symptom, i.e., arresting its development; or (c) relieving the disease, i.e., causing regression of the disease. The therapeutic agent may be administered before, during or after the onset of disease or injury. The treatment of ongoing disease, where the treatment stabilizes or reduces the undesirable clinical symptoms of the patient, is of particular interest. Such treatment is desirably performed prior to complete loss of function in the affected tissues. The subject therapy will desirably be administered during the symptomatic stage of the disease, and in some cases after the symptomatic stage of the disease.
In some instances, a component (e.g., a nucleic acid component (e.g., a CRISPR/Cas guide RNA); a protein component (e.g., genome editing endonuclease such as a Cas9 protein); and the like) includes a label moiety. The terms “label”, “detectable label”, or “label moiety” as used herein refer to any moiety that provides for signal detection and may vary widely depending on the particular nature of the assay. Label moieties of interest include both directly detectable labels (direct labels)(e.g., a fluorescent label) and indirectly detectable labels (indirect labels)(e.g., a binding pair member). A fluorescent label can be any fluorescent label (e.g., a fluorescent dye (e.g., fluorescein, Texas red, rhodamine, ALEXAFLUOR® labels, and the like), a fluorescent protein (e.g., green fluorescent protein (GFP), enhanced GFP (EGFP), yellow fluorescent protein (YFP), red fluorescent protein (RFP), cyan fluorescent protein (CFP), cherry, tomato, tangerine, and any fluorescent derivative thereof), etc.). Suitable detectable (directly or indirectly) label moieties for use in the methods include any moiety that is detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical, chemical, or other means. For example, suitable indirect labels include biotin (a binding pair member), which can be bound by streptavidin (which can itself be directly or indirectly labeled). Labels can also include: a radiolabel (a direct label) (e.g., 3H, 125I, 35S 14C, 32P, and the like); an enzyme (an indirect label) (e.g., peroxidase, alkaline phosphatase, galactosidase, luciferase, glucose oxidase, and the like); a fluorescent protein (a direct label)(e.g., green fluorescent protein, red fluorescent protein, yellow fluorescent protein, and any convenient derivatives thereof); a metal label (a direct label); a colorimetric label; a binding pair member; and the like. By “partner of a binding pair” or “binding pair member” is meant one of a first and a second moiety, wherein the first and the second moiety have a specific binding affinity for each other. Suitable binding pairs include, but are not limited to: antigen/antibodies (for example, digoxigenin/anti-digoxigenin, dinitrophenyl (D NP)/anti-D NP, dansyl-X-anti-dansyl, fluorescein/anti-fluorescein, lucifer yellow/anti-lucifer yellow, and rhodamine anti-rhodamine), biotin/avidin (or biotin/streptavidin) and calmodulin binding protein (CBP)/calmodulin. Any binding pair member can be suitable for use as an indirectly detectable label moiety. Any given component, or combination of components can be unlabeled, or can be detectably labeled with a label moiety. In some cases, when two or more components are labeled, they can be labeled with label moieties that are distinguishable from one another.
As used herein, an “antibody” refers to a protein consisting of one or more polypeptides substantially encoded by immunoglobulin genes or fragments of immunoglobulin genes. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.
A typical immunoglobulin (antibody) structural unit is known to comprise a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chains, respectively.
Antibodies exist as intact immunoglobulins or as a number of well characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)′2, a dimer of Fab which itself is a light chain joined to VH-CH1 by a disulfide bond. The F(ab)′2 may be reduced under mild conditions to break the disulfide linkage in the hinge region thereby converting the (Fab′)2 dimer into a Fab′ monomer. The Fab′ monomer is essentially a Fab with part of the hinge region (see, Fundamental Immunology, W. E. Paul, ed., Raven Press, N.Y. (1993), for a more detailed description of other antibody fragments). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such Fab′ fragments may be synthesized de novo either chemically or by utilizing recombinant DNA methodology. Thus, the term antibody, as used herein also includes antibody fragments either produced by the modification of whole antibodies or synthesized de novo using recombinant DNA methodologies. Certain preferred antibodies include single chain antibodies (antibodies that exist as a single polypeptide chain), more preferably single chain Fv antibodies (sFv or scFv) in which a variable heavy and a variable light chain are joined together (directly or through a peptide linker) to form a continuous polypeptide. The single chain Fv antibody is a covalently linked VH-VL heterodimer which may be expressed from a nucleic acid including VH- and VL-encoding sequences either joined directly or joined by a peptide-encoding linker. Huston, et al. (1988) Proc. Nat. Acad. Sci. USA, 85: 5879-5883. While the VH and VL are connected to each as a single polypeptide chain, the VH and VL domains associate non-covalently. The first functional antibody molecules to be expressed on the surface of filamentous phage were single-chain Fvs (scFv), however, alternative expression strategies have also been successful. For example, Fab molecules can be displayed on phage if one of the chains (heavy or light) is fused to g3 capsid protein and the complementary chain exported to the periplasm as a soluble molecule. The two chains can be encoded on the same or on different replicons. The important point is that the two antibody chains in each Fab molecule assemble post-translationally and the dimer is incorporated into the phage particle via linkage of one of the chains to, e.g., g3p (see, e.g., U.S. Pat. No. 5,733,743). The scFv antibodies and a number of other structures converting the naturally aggregated, but chemically separated light and heavy polypeptide chains from an antibody V region into a molecule that folds into a three-dimensional structure substantially similar to the structure of an antigen-binding site are known to those of skill in the art (see e.g., U.S. Pat. Nos. 5,091,513, 5,132,405 and 4,956,778). In various embodiments antibodies include all that have been displayed on phage (e.g., scFv, Fv, Fab and disulfide linked Fv) (Reiter et al. (1995) Protein Eng. 8: 1323-1331). In certain embodiments antibodies include, but are not limited to antibodies or antibody fragments selected from the group consisting of Fab, Fab′, Fab′-SH, F(ab′)2, Fv, Fv′, Fd, Fd′, scFv, hsFv fragments, single-chain antibodies, cameloid antibodies, diabodies, and other fragments.
General methods in molecular and cellular biochemistry can be found in such standard textbooks as Molecular Cloning: A Laboratory Manual, 3rd Ed. (Sambrook et al., HaRBor Laboratory Press 2001); Short Protocols in Molecular Biology, 4th Ed. (Ausubel et al. eds., John Wiley & Sons 1999); Protein Methods (Bollag et al., John Wiley & Sons 1996); Nonviral Vectors for Gene Therapy (Wagner et al. eds., Academic Press 1999); Viral Vectors (Kaplift & Loewy eds., Academic Press 1995); Immunology Methods Manual (1. Lefkovits ed., Academic Press 1997); and Cell and Tissue Culture: Laboratory Procedures in Biotechnology (Doyle & Griffiths, John Wiley & Sons 1998).



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A schematically illustrates various design features of a multi-arm polyrotaxane (PRX) carrier. The illustrated embodiment shows a 4-arm PEG backbone. Various design features include, but are not limited to the formation of inclusion complexes using cyclic compounds (e.g., cyclodextrin) threaded on at least one arm, but not on all arms of the backbone. The inclusion complexes are retained on the arms by bulky groups R1 and R1′ which can be the same or different. One or more of the inclusion-complex free arms can be attached to (e.g., terminated with) a protecting group, and/or a fluorophore and/or a targeting moiety (R2 and R2′ which can be the same or different). The cyclic compound(s) can optionally be functionalized with a nucleophile (e.g., an amine) to regulate the charge of the carrier. In certain embodiments, the nucleophile and/or the bulky groups are attached to the backbone and/or to the cyclic compound by a cleavable linkage. The backbone need not be a 4-arm backbone. FIG. 1B illustrates a multi-arm polyrotaxane (PRX) with a total of m arms. In certain embodiments the number of arms in the multi-arm PEG backbone m ranges from 3 to 12, or from 3 to 10, or from 3 to 8. In certain embodiments, the number of cyclic molecule threaded PEG arms (x) ranges from 1 to m−1. In certain embodiments, the backbone comprises 3 arms, or 4 arms, or 5 arms, or 6 arms, or 7 arms, or 8 arms.
FIG. 2 shows a comparison of the multi-arm PRX compared to the linear PRX.
FIGS. 3A and 3B, illustrate various design features of a fourth generation (G4) polyrotaxane carrier (PRX). As shown in FIG. 3A, the G4 PRX combines the use of a multi-arm PEG backbone to improve biodistribution and bio-cleavable linkages to enhance intracellular plasmid release. R1 and R1′ are independently selected bulky end groups (e.g., with aromatic rings and/or fused rings) (e.g., Z-tyrosine, phenylalanine). R2 and R2′ are independently selected protecting groups and/or fluorophores, and/or targeting moieties (e.g., FITC, folic acid, targeting peptide, antibody, etc.). The cleavable linkers are cleavable in response to biological conditions at the target site (e.g., target cell). Such linkages include, but are not limited to redox-responsive disulfide linkers, pH-responsive hydrazine linkers, enzyme responsive linkers, etc.). and include. FIG. 3B illustrates a G4 PRX with cleavable linkages (e.g., a disulfide linkage) between the PEG backbone and bulky stopper (top), or between the cyclic compound (e.g., CD ring) and its conjugated cationic tertiary amine groups, which upon cleavage and removal of amines, can lead to the PRX and plasmid dissociation via a charge reduction mechanism.
FIGS. 4, panels A and B, shows results of a study of intracellular uptake and in vitro transfection using G3 PRX as a carrier. Panel A) Cellular uptake of the plasmid loaded by G3 PRX. Myotube cells received Cy3 labeled plasmid loaded G3 PRX for 3 days. Panel B) Demonstration of in vitro transfection effectiveness of mCherry plasmid delivered by G3 PRX in myotube cells. The commercial transfection reagents, such as Lipofectamine, are very inefficient in myotube cells.
FIGS. 5, panels A-D, shows that PRXs demonstrate successful uptake and plasmid delivery to muscle cells in vitro. Panel A: Cartoon of the DMD gene targeted for CRISPR-mediated deletion of exons 45-55. Guide RNAs (lightening bolts) targeting introns 44 and 55 cause cutting and NHEJ of the region restoring the reading frame for out-of-frame mutations (black arrow head). Purple arrows represent deletion PCR primers. Panel B: Imaging of G1 PRX nanoparticles labeled with FITC (green) and plasmid cargo (labeled with Cy3, red) in hDMD myotubes at day 3 after administration. There is a high colocalization of the particle and cargo signal in the cells demonstrating a lack of plasmid release. Panel C: Imaging of G1 and G2 PRX particles carrying a GFP plasmid in hDMD myotubes at day 7 after administration. G2, which contains the disulfide linker, results in more GFP positive cells. Panel D: Genomic DNA PCR for an exon 45-55 deletion (using primers that flank the deletion, shown in panel A 7 or 14 days after administration of G1 or G2 carrying the CRISPR/Cas9 plasmid to hDMD myotubes. G2 PRX-CRISPR results in deletion at day 7. Untreated (untreat) negative and positive (pos) controls are shown.
FIG. 6, panels A-C, shows a comparison between classic linear PRX vs 4-arm PRX. Panel A: The cartoon shows the two main designs of PRX. The linear structure has a PEG backbone (black line) and cationic CD rings (pink) that bind nucleic acid (blue) via an electrostatic mediated self-assembly process. Since 2 out of 4 arms were pre-protected by a bulky group (green ball in the left panel) in the 4-arm PRX design, this leads to CD ring-free PEG chains during the complex process. This design differs from the classic linear design in which the PEG backbone is already occupied during the introduction of positive CD, leading to a non- or low PEG nanoparticle. Panel B: Typical AFM pictures of free plasmid and self-assembled PRX/plasmid. Panel C) IVIS imaging of mdx muscles from mice injected with either the linear or the 4-arm PRX. More abundant plasmid was observed in muscles of mice injected with the 4-arm PRX. Plasmid was labeled by Cy3 for IVIS.
FIG. 7 shows sections of quadriceps muscle tissues were collected 24 hours post Cy3 plasmid laden G3 PRX injection and embedded in OCT for frozen section. Slides were visualized under a fluorescence microscope. The particle and plasmid biodistribution in the muscle section was visualized. Laminin was labelled using IHC (white).
FIG. 8 illustrates determination of the N/P ratio of a multi-arm PRX.
FIG. 9, panels A-B, shows that multi-arm PRXs demonstrate successful uptake and plasmid delivery to muscle cells in vitro. Panel A) Imaging of G3 and G4 PRX nanoparticles labeled with FITC (green) and labeled plasmid cargo (red) in hDMD del45 myoblasts 24 hrs after administration. There is less particle/plasmid colocalization in the cells seen with G4, which contains a disulfide linker. Panel B) Genomic DNA PCR for an exon 45-55 deletion at day 7 after administration of G3 or G4 carrying the CRISPR/Cas9 plasmid to hDMD del45 myoblasts. G4 PRX-CRISPR results in successful deletion. Untreated (untreat), water only (ddH2O), and positive (pos) controls are shown.
FIG. 10 illustrates DTT induced reductive cleavage of cationic charge on G4 PRX. The cleavage further resulted in size change of G4/plasmid complex.
FIG. 11 shows the general synthesis steps of multiarm PRX.
FIG. 12 shows illustrative synthesis steps of a representative G4 PRX.
FIG. 13 shows NMR data of the intermediary product for G4 PRX, namely, pyridyldithiol-polyrotaxane.
FIG. 14. In cancer cells, GFP (M.W.=3.4 kpb, 2,210 kD) and CRISPR/Cas9 knockout plasmid (M.W.=9.3 kpb, 6,045 kD) were encapsulated by G3 PRX. The pmaxGFP plasmid is constructed with CMV promoter to facilitate the expression of GFP, the plasmid is also with kanamycin resistance for amplification. CRISPR/Cas9 knockout plasmid is constructed with U6 promoter to facilitate the expression of gRNA (sequence: CTGAATTAGCTGTATCGTCA (SEQ ID NO:1) and GAATATAAACTTGTGGTAGT (SEQ ID NO:2)) to target KRAS gene, as well as Cas9 protein functionalized with nuclear-localization sequence (NLS).
FIG. 15 shows a comparative analysis of GFP plasmid delivered by G3 PRX versus Lipofectamine 2000 in B16 melanoma cells. B16 cells were seeded into 12-well plate and received plasmid laden G3 PRX at a plasmid dose of 1 μg plasmid per well. The cells were used for imaging by a fluorescent microscope. The images were taken at day 4.
FIG. 16 shows CRISPR/Cas9 knockout plasmid delivered by G3 PRX in Kras-mutated human pancreatic and colon cells. Panc-1 and HCT116 cells were seeded into 12-well plate and received plasmid laden G3 PRX at a plasmid dose of 1 μg plasmid per well. The cells were used for imaging by a fluorescent microscope. The images were taken at day 4. The commercial transfection reagent, i.e. lipofectamine 2000, exhibited inefficient transfection effect (not shown).
FIG. 17. Use of confocal microscope to study the lysosomal escape and G3 PRX/CRISPR plasmid disassociation in cells.
FIG. 18. Panel A: Schematic of 4-arm PRX delivery platform for systemic plasmid delivery. Cationic α-CDs were threaded onto 4-arm PEG backbone in a spatially selective fashion, resulting in available PEG moieties for enhanced delivery performances in vivo. Panel B: The detailed synthesis routes of 4-arm PRX. Detailed synthetic procedures were described in the result and method sections in Example 3. Panel C: The number of amines per α-CDs can be calculated via the 1H-NMR spectra in deuterated water (D2O), which demonstrated the tuning of charge density on 4-arm PRX. Panel D) In vitro transfection of tdTomato reporter plasmid by 4-arm PRX with different cationic charge densities. 4-arm PRXs with  ̃1,  ̃3 or  ̃6 amines per α-CD were complexed with tdTomato plasmid at multiple N/P ratios and incubated with MC38 colon cancer cells for 72 h (1 μg plasmid/mL). The percentages of tdTomato+ MC38 cells were quantitatively displayed at various N/P ratios in the heat map. In vitro transfection efficiency at the optimum N/P ratio was compared between 4-arm PRX with different charge densities (n=6). Representative fluorescence image of tdTomato+ MC38 cells (red) confirmed that 4-arm PRX with 6 amines per α-CD resulted in the most efficient reporter transfection in vitro. Nuclei were counterstained with DAPI. The results are expressed as mean±SD. *p<0.05.
FIG. 19, panels A-E, illustrates use of abiotic and in vitro assays to determine the optimal multi-arm design and polymer backbone size. Panel A: The chemical structure of 4-arm PRX with different level of available PEG moieties. Panel B: The structural scheme of 4-arm PEG precursors occupied with different number of end-caps, which provided the steric hindrance for the selective threading of α-CD. MALDI-TOF molecular weight detection demonstrated the synthesis success of the 4-arm PEG precursors. Panel C: The number of total α-CDs per PRX was calculated via the 1H-NMR spectra of 1/4CD, 2/4CD, and 3/4CD 4-arm polypseudototaxane in DMSO-d6, which demonstrated the tuning of the level of available PEG moieties. Panel D: In vitro reporter gene transfection by 1/4CD, 2/4CD, and 3/4CD 4-arm PRX analogues was performed on MC38 cells for 72 h (1 μg plasmid/mL). The tdTomato expression at various N/P ratios was quantitatively expressed in the heat map. The reporter gene transfection efficiency at the optimum N/P ratio was compared between 4-arm PRX with different level of available PEG moieties (n=6). The results are expressed as mean±SD. *p<0.05. (E) The tuning of the molecular weight of the backbone was demonstrated by 1H-NMR spectra of 2/4CD 4-arm polypseudototaxane with 5 kDa, 10 kDa or 20 kDa 4-arm PEG backbone size in DMSO-d6.
FIG. 20, panels A-D, show that optimized 4-arm PRX enhanced the PK and tumor biodistribution of Cy3-labeled plasmid after IV injection in mice. Panel A: The summary of physicochemical properties of the optimized 4-arm PRX. Representative AFM images of free plasmid (upper left) and plasmid after complexation with optimized 4-arm PRX (upper right). Scale bar represents 200 nm. Panel B: Evaluating the PK profile of Cy3-plasmid in C57BL/6 mice (n=3). Normal mice received single IV injection of Cy3-plasmid laden 4-arm PRX or linear PRX (5 mg plasmid/kg). Plasma was collected after 0.083, 1, 2, 4, 8 and 24 h, the Cy3-plasmid content were quantified by fluorescence spectroscopy and expressed as % total injected dose (% ID) per mL. The PK parameters were calculated by PKSolver software. Panel C: In a separate study, MC38 subcutaneous tumor bearing mice received single IV injection of Cy3-plasmid laden optimized 4-arm PRX or linear PRX (5 mg plasmid/kg). 24 h post IV injection, tumors and organs were collected for ex vivo IVIS imaging. The fluorescence intensity of Cy3-plasmid in different organs were quantitatively expressed by normalizing to saline-treated control (n=3). Panel D: In the same experiment, confocal microscopy confirmed higher intratumoral abundance of Cy-3 plasmid (red) delivered by 4-arm PRX, compared to linear PRX. The blood vessels (green) and nuclei (blue) at the tumor site were stained with CD31 and DAPI, respectively. Scale bar represents 100 μm. The results are expressed as mean±SD. *p<0.05.
FIG. 21, panels A-E, shows that systemic delivery of a placmid encoding interleukin (pIL-12) by 4-arm PRX nanocarrier induced effective anti-colon cancer immunity in the MC38 tumor model. Panel A: MC38 tumor bearing mice received single IV injection of pIL-12 laden 4-arm PRX (5 mg plasmid/kg). ELISA detection of IL-12 protein in tumor extracts were performed 3 and 7 day post IV injection. Mice injected with pC laden 4-arm PRX (as non-functional control) were also tested as non-functional control (n=3). Panel B) MC38-luc bearing mice received repetitive IV injection of pIL-12 laden 4-arm PRX (5 mg plasmid/kg/injection). Interval IVIS imaging was used for monitoring tumor growth, which was quantitatively expressed according to the tumor signal at the operator-defined ROI (n=4). Representative bioluminescence images demonstrated the anti-tumor efficacy of pIL-12 laden 4-arm PRX. Panel C: The scheme for IL-12 mediated anti-tumor immunity, by activation of NK cells, CD8 T cells and anti-angiogenesis machinery in the tumor microenvironment. Panel D: MC38-luc bearing mice from the same experiment in panel B were sacrificed at day 21. The tumor cells were analyzed by multi-parameter flow cytometry to identify CD45+NK1.1+ and CD45+CD3+CD8+ tumor infiltrating lymphocytes TILs. IFN-γ secreting TIL population (IFN-γ+CD45+NK1.1+ and IFN-γ+CD45+CD8+) were also determined (n=4). Representative IHC staining of IL-12, NK1.1, CD8 and IFN-γ in tumor section further demonstrated the concurrent innate and adaptive immuno-activation effect of pIL-12 4-arm PRX at the tumor site. Panel E: Immunofluorescence staining of CD31 (red) and quantitative display of CD31+ blood vessel in tumor section confirmed the anti-angiogenesis effect of pIL-12 4-arm PRX. Scale bar represents 100 μm. The results are expressed as mean±SD. *p<0.05.
FIG. 22, panels A and B, shows that multi-arm PRX nanocarrier improved the safety of pIL-12 immunogene therapy in the MC38 mouse model. In a separate experiment, C57BL/6 mice received IV injection of pIL-12 laden 4-arm PRX, following the same treatment regimen as the tumor inhibition study shown in FIG. 4. Saline and pC laden 4-arm PRX were used as controls. For comparison purpose, we also included IV administration of mouse rIL-12 as an additional control. The dose rIL-12 (100 μg/kg/injection) was designed based on literature (see, e.g., Brunda et al. (1993) J. Exp. Med. 178(4): 1223-1230). Panel A: Blood chemistry test and complete blood count test were performed on day 7 and day 21. The results are expressed as mean±SD. *p<0.05. Panel B: Representative lung and kidney histology obtained from C57BL/6 mice sacrificed on day 21. The arrows in the H&E staining of rIL-12 treated lung sections point to interstitial thickening and macrophage infiltrates, and the sites marked with asterisks denote pulmonary edema. The arrows in rIL-12 treated kidneys sections marked the zoomed-in morphology of glomerulus, where glomerular swelling and edema of Bowman's space were observed. Scale bar represents 200 μm.
FIG. 23 shows Scheme 1 illustrating various polyrotaxane structural design features and their possible impacts.
FIG. 24 shows a schematic of the structure of linear PRX, with CD rings distributed non-selectively along the linear PEG backbone. Self-assembled nanoparticles were formed from linear PRX and plasmid DNA. This leads to cationic nanoparticles with low or no PEG modification, which is unfavorable for in vivo application because of poor PK, short circulatory t1/2, non-specific binding and off-target distribution.
FIG. 25, panel A shows a scheme for the synthesis of modified 4-arm PEG backbone selectively end-capped with bulky groups (fluorescein). The number of bulky end-caps was manipulated via different feed ratio between 4-arm PEG-tetra-amine and NHS-fluorescein. FIG. 25, panel B, shows 1H-NMR characterization of 2-occupied 4-arm PEG backbone in deuterated water (D2O).
FIG. 26, panel A: 1H-NMR characterization of 2/4CD 4-arm PEG backbone with different cationic charge densities in deuterated water (D2O). FIG. 26, panel B: 1H-NMR spectra of 1/4CD, 2/4CD, and 3/4CD 4-arm polypseudototaxane in DMSO-d6. FIG. 26, panel C: 1H-NMR spectra of 2/4CD4-arm polypseudototaxane with 5 kDa, 10 kDa or 20 kDa 4-arm PEG backbone in DMSO-d6. The calculation for cationic charge density and total CD per PRX were shown in FIG. 18, panel C, 19, panels C and E, respectively. Collectively, the comprehensive characterization confirms successful synthesis of 4-arm PRX analogues and manipulation over different design parameters.
FIG. 27, panel A: In vitro transfection of MC38 cells by tdTomato plasmid. The reporter gene was delivered by 4-arm PRX analogues with different molecular weights (MW) of the PEG backbone and incubated with MC38 cells for 72 h (1 μg plasmid/mL). Percentage of red positive MC38 cells treated by reporter gene laden 4-arm PRX with 5 kDa, 10 kDa or 20 kDa backbone at the optimum N/P ratio, and representative fluorescence images of reporter gene expression by each treatment (scale bar represents 50 μm). Values represent the mean±SD (n=3). FIG. 27, panel B: Heat map display of in vitro transfection by 4-arm PRX at various N/P ratios. The optimum N/P ratio was defined by the threshold N/P ratio that provided the most efficient reporter expression. FIG. 27, panel C: We also tested the tdTomato plasmid transfection efficiency in another cancer cell line. B16 melanoma cells incubated with tdTomato plasmid laden optimized 4-arm PRX (1 μg plasmid/mL) for 72 h and the representative fluorescence image of Td+ cells were shown (scale bar represents 100 μm). This allowed us to demonstrate abundant Td+ cells (19% of total cell population) in tissue culture, similar to what we found in MC38 cells.
FIG. 28 shows the viability of MC38 cells after 72 h incubation with tdTomato plasmid laden 4-arm at various N/P ratios, the concentration of plasmid was fixed at 1 μg/mL. Values represent the mean±SD (n=6).
FIG. 29, panel A: DNA gel retardation assay of optimized 4-arm PRX (2/4CD 4-arm PRX with 10 kDa backbone, 6 cationic charge per CD) at various N/P ratios. Classic linear PRX was included for comparison. FIG. 29, panel B: Size and ζ-potential characterization of plasmid laden optimized 4-arm PRX or linear PRX at various N/P ratios. Values represent the mean±SD (n=3). While the optimized 4-arm PRX showed similar plasmid packaging capability, hydrodynamic size and ζ-potential (zeta potential) compared to the linear PRX, we found distinct features between these two PRX types in terms of PK and biodistribution in vivo (see FIG. 20).
FIG. 30, panel A: MC 38 cells were incubated with pIL-12 laden optimized 4-arm PRX or linear PRX (1 μg plasmid/mL) for 72 h. pIL-12 complexed with Lipofectamine 2000 reagents were tested as positive control, and tdTomato plasmid (control plasmid, pC) laden 4-arm PRX was tested as non-functional negative control. Panel A: ELISA detection of IL-12 protein release in the cell culture supernatant. FIG. 30, panel B: RT-qPCR detection of the fold change of IL-12 gene expression normalized to untreated control cells. Values represent the mean±SD (n=3). Statistical significance: *, p<0.05.
FIG. 31. Use of native gel electrophoresis to demonstrate 4-arm design is capable of interfering with nanoparticle opsonization. Mouse IgG (10 μg/μL) was incubated with pIL-12 laden 4-arm PRX or linear PRX for 30 min at 37° C., the concentration of plasmid was 1 μg/μL. After incubation, the samples were loaded into the gel at 40 μg IgG per lane. The electrophoresis condition was 150 V for 30 min. Only the non-bound IgG can migrate and be detected by silver staining in the gel. Image J was used to semi-quantify the free IgG in each group. While 76% free IgG was found in 4-arm PRX group, only 28% free IgG was detected in linear PRX. This suggested a prevention of nanoparticle opsonization due to the availability of PEG in the multi-arm PRX. Lane 1: Free IgG without nanoparticle; Lane 2: IgG incubated with 4-arm PRX (that led to 24% IgG binding and 76% free non-bound IgG); and Lane 3: IgG incubated with linear PRX (that led to 72% IgG attachment and 28% non-bound IgG).
FIG. 32. Mice bearing MC38 subcutaneous tumors received single IV injection of tdTomato plasmid laden 4-arm PRX or linear PRX (5 mg plasmid/kg). 7 day post IV injection, the tumors were harvested for the detection of tdTomato reporter protein. Western blot detection of tdTomato protein from tumor tissue extracts treated by tdTomato plasmid laden 4-arm PRX or linear PRX. Saline treated tumor extract was tested as negative control. Lysate from MC38 cells transfected with tdTomato plasmid 4-arm PRX in vitro was tested as positive control. tdTomato plasmid delivered by 4-arm PRX IV, but not the linear PRX, led to tdTomato expression at tumor site.
FIG. 33. Mice bearing MC38 subcutaneous tumors received single IV injection of pIL-12 laden 4-arm PRX or tdTomato plasmid (pC) laden 4-arm PRX (5 mg plasmid/kg). 3 or 7 day post IV injection, the tumors and major organs were harvested for the ELISA detection of IL-12 protein. The fold increase values of IL-12 protein in different organs were obtained by normalizing to saline treated control. Values represent the mean SD (n=3). Multiple injections of therapeutic dose of pIL-12 PRX led to minimal increase of IL-12 levels in serum as well as most organs. Interestingly, while a slight increase of IL-12 was found in the liver at day 7, we did not found abnormality in the liver panel of our blood chemistry analysis (FIG. 22, panel A). We surmise that the relatively low rate of IL-12 production in the liver may explain why low liver toxicity was seen in animals injected with pIL-12 laden PRX. This contrasts with the use of rIL12 protein in which the rapid buildup of the cytokine may overwhelm the hepatic metabolism capacity.
FIG. 34, panels A and B: Mice bearing MC38-luc subcutaneous tumors were IV injected with pIL-12 laden 4-arm PRX, as shown in FIG. 21, panel B. Panel A: After first injection, the tumor size were determined by caliper and plotted vs. time. Values represent the mean±SD (n=4). Panel B: Image of tumor tissues harvested on day 21.
FIG. 35 shows representative raw flow cytometry data of single cell suspensions prepared from MC38 tumors on day 21 in the study of anti-tumor efficacy, as shown in FIG. 21, panel D. Representative images from cell populations were gated with: IFN-γ+CD45+NK1.1+, IFN-γ+CD45+CD8+, CD45+NK1.1+, and CD45+CD3+CD8+.
FIG. 36 shows representative H&E staining of heart and spleen tissue harvested from C57BL/6 mice on day 21. The mice received IV injection of pIL-12 or pC laden 4-arm PRX, 5 mg plasmid/kg/injection, 5 injections in total, as shown in FIG. 22, panel B. Organs from mice receiving IV injection of recombinant IL-12 (rIL-12) (100 μg/kg/injection, the same injection frequency as 4-arm PRX) were also studied as control. Scale bar represents 200 μm.
FIG. 37, panels A-C, shows that peptide conjugated PRXs demonstrate improved delivery of a reporter plasmid in muscle cells in vitro. Panel A: Imaging of an NCAM peptide labeled with FITC added to C2C12 myotubes or B16 skin cancer cells for 6 hrs. There is increased binding of the peptide on the C2C12 cells compared to the controls, demonstrating successful peptide binding to NCAM. Panel B: Imaging of G3, G4 and peptide conjugated G3 PRXs carrying a TdTomato (TdT, red) reporter plasmid in hDMD del45 myoblasts 48 hrs after administration. Both peptide conjugated versions demonstrate a higher percentage of TdTomato+ cells ( ̃70 fold higher than unconjugated). Panel C: Imaging of peptide conjugated G3 PRXs carrying a TdTomato reporter plasmid in hDMD del45 myotubes 24 hrs after administration, demonstrating successful delivery.
FIG. 38, panels A and B, show that PRX nanoparticles appear trapped in the basal lamina or ECM after in vivo delivery. Panel A: Imaging of quadriceps muscle 24 hrs after i.v. administration of G4 PRX where the nanoparticle is labeled with FITC (green), the cargo with Cy3 (red) and the fibers stained with laminin (grey). No particles are found within fibers and many appear to be trapped in the basement membrane marked by laminin near nuclei, that could be myonuclei, satellite cells or other interstitial cells (insets 1 and 3). Inset 2 highlights PRXs found within a blood vessel. Scale bar 20 μm. Panel B: Imaging of interosseous muscle 24 hrs after footpad injection of G3 PRX where the nanoparticle is labeled with FITC (green), the cargo with Cy3 (red) and the fibers stained with laminin (grey). No particles are found within fibers and they appear to be trapped in the interstitial space. Scale bar 20 μm.
FIG. 39, illustrates detection of dystrophin positive fibers after systemic administration of nano-CRISPR. Shown are micrographs taken of hDMD del45 mdx quadriceps muscle cross sections stained with laminin (white), human dystrophin (red) or mouse/human dystrophin targeting exons 55/56. The latter antibody is used to identify revertant fibers (“R”). Animals were treated with 4 injections of G3-PRX carrying the pX333 CRISPR platform targeting exons 45-55 and harvested 5 weeks later.



DETAILED DESCRIPTION
In certain embodiments carriers are provided for the effective in vivo delivery of nucleic acids including small or large nucleic acids (such as plasmids). The nanocarriers described herein are polyrotaxane (PRX) structures comprised of a multi-arm polymer backbone with cyclic compounds threaded on the arms of the backbone thereby forming inclusion complexes. The complexes are designed to readily complex via self-assembly with nucleic acids to form a carrier/nucleic acid complex that can readily be administered to an organism.
Advantages of the multi-arm polyrotaxane carriers described herein include, but are not limited to, large packaging space, nucleic acid (e.g., plasmid) encapsulation via self-assembly, potential for modification to increase targeting, high stability, multi-functionality, bio-degradability and intrinsic safety.
One of the applications of the multi-arm polyrotaxane carriers described herein is the in vivo delivery nucleic acids to cell. In certain embodiments, the delivery can be systemic, while in other embodiments, the delivery can be targeted (e.g., to particular cell or tissue type) by the incorporation of targeting moieties. In either approach, however the carriers are well suited to systemic administration and show a long serum half-life and effective delivery of the nucleic acid to cells.
In certain embodiments the nucleic acids to be delivered include, but are not limited to antisense molecules, ribozymes, and plasmids encoding one or more heterologous gene(s), RNAs, and the like. In certain embodiments, the carriers described herein are particularly well suited for the delivery of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 plasmid for various biological applications.
One example is the CRISPR/Cas9 based gene editing to reframe the mutated gene in Duchenne Muscular Dystrophy (DMD). Our data demonstrated that CRISPR/Cas9 plasmid delivery by PRX nanocarriers showed improved biodistribution at muscle sites over various controls in a stringent DMD mouse model. We have also achieved progress in plasmid delivery to cancer cells. In this regard, the polyrotaxane carriers have been used for comparison against commercial transfection reagents in a range of cancer cell types to provide proof-of-principle demonstration of the wider utility of this platform, including for example, treatment of melanoma, pancreatic cancer, colon cancer, and the like.
In various embodiments the carriers described herein are polyrotaxane (PRX) structures comprised of a multi-arm polymer (e.g., polyethylene glycol) backbone with cyclic compounds (e.g., cationic cyclodextrins (CDs)) threaded on the arms of the backbone thereby forming inclusion complexes. The cyclic molecules are retained on the backbones by the presence of bulky moieties capping the terminals of the arms bearing cyclic compounds. Notably at least one of the arms of the polymer, and in certain embodiments two or more of the arms of the polymer backbone do not bear any cyclic compounds. Thus, the polyrotaxane (PRX) carrier comprises cyclic molecules selectively threaded on the backbone (e.g., threaded on some arms, but not other arms, and not on all arms of the backbone). In certain embodiments, the bulky capping groups can be attached to the arms of the backbone (the arm(s) bearing cyclic compounds) with or without a cleavable linkage. The cleavable linkage, when present, can facilitate unloading of a complexed nucleic acid in response to local (e.g., intracellular) conditions such as low pH, redox-potential, the presence of various proteases, and the like.
In certain embodiments the arms of the backbone that are free of cyclic compounds can be attached to protecting groups, and/or to a fluorophore (or quantum dot), and/or to one or more targeting moieties.
In certain embodiments the charge of the polyrotaxane carrier can be controlled by the functionalization of the cyclic compounds with one or more nucleophiles (e.g., amines).
One of a number of key innovations in the design of the polyrotaxane carriers described herein is the use of a multi-arm PRX polymer that was constructed from a multi-arm polyethylene glycol (PEG) backbone for spatially selective inclusion complexation, leading to an appropriately tuned PEGylation density and positive charge density, that are suitable for in vivo applications including systemic nucleic acid delivery. Through an electrostatic mediated self-assembly progress, the mixing of PRX carrier and a nucleic acid (e.g., plasmid) leads to the spontaneous formation of nanosized particles that are resistant to enzyme-mediated nucleic acid degradation. In a DMD mouse model (e.g. mdx mice) receiving intravenous injected (IV) plasmid laden PRXs, a long particle circulation half-life and abundant skeletal muscle distribution via passive targeting mechanism were demonstrated.
Without being bound to a particular theory, it is believed that the spatially selective complexation (inclusion of cyclic molecules on some, but not all polymer arms) in the polyrotaxane carriers described herein result in reduced particle opsonization and unwanted uptake by reticuloendothelial system.
Certain design features of this multi-arm PRX carrier platform are shown in FIG. 1A. As illustrated in this figure, the multi-arm part of the polymer backbone was blocked by bulky groups (R2 and R2′ groups in FIG. 1A) before inclusion complexation. This was followed by introducing cyclic compounds (e.g., CD rings) to the unblocked PEG arms via inclusion complexation process. The polyseudorotaxane was blocked to prevent the cyclic molecules from falling off the arm(s) by the attachment of a bulky capping group (R1 and R1′ group in FIG. 1A), such as an aromatic molecule. In certain embodiments R2 and R2′ can be the same or different and can comprise a protecting group and/or an imaging probe (e.g. FITC or NIR dye), and/or a targeting moiety (e.g., an antibody or targeting peptide). Using similar strategy, it is possible to extrapolate the design principle to build additional multi-arm PRXs with spatially selective inclusion complexes.
The general characteristics of these novel PRXs include the following chemical properties (see, e.g., FIG. 1B): (i) A multi-arm polymer (e.g., PEG) backbone that contains m arms (where 3≤m≤12, or 3≤m≤10, 3≤m≤8); (ii) Where the backbone comprises PEG, the PEG MW ranges from about 2.5 kDa per arm up to about 10 kDa per arm, which means about 56-227 ethylene oxide repeat units per arm; (iii) Prior to the inclusion complex process, pre-introduction of bulky molecules (R2 group(s) in FIG. 1B), such as fluorophore (e.g. FITC and NIR dye) or targeting modalities (e.g., antibody, targeting peptide, folic acid, etc.) in at least 1 PEG arm, up to m−1 arms; (iv) Spatially selective formation of inclusion complex using cyclic compounds (e.g., alpha, beta cyclodextrin, or cyclodextrin derivatives (e.g. 2-Hydroxypropyl-α-cyclodextrin)) with appropriate ring number per PEG arm; (v) polyseudorotaxane is stabilized by ending group with appropriate steric hindrance molecules (e.g., aromatic rings and fused rings; R1 group(s) in FIG. 1B); (vi) Cationic cyclic molecules (e.g., cyclodextrin) can be achieved by positive functional group(s), such as primary, secondary and tertiary amine; (vii) bio-cleavable linker(s) can be introduced at pendant sides or chain ends if necessary (see, e.g., FIG. 3B). It is believed the resulting multi-arm PRXs with spatially selective inclusion complexes are a group of new chemical entities.
The availability of the free (inclusion complex-free) backbone arms helps prevent nanocomplex opsonization in blood circulation, which is important to facilitate long plasma half-life and high accumulation in targeted sites in vivo.
The polyrotaxane delivery vehicle (carrier) is believed to be particularly effective in the complexation/encapsulation and delivery of large nucleic acids such as plasmids and other therapeutic nucleic acids or a mixture of therapeutic nucleic acids. In certain embodiments, the nucleic acid can comprise a plasmid (e.g., a plasmid ranging in size up to 20 kb, or up to about 15 kb, or up to about 12 kb, or up to about 10 kb. In certain embodiments the nucleic acid comprises a linear nucleic acid (e.g., a linear nucleic acid up to about 15 kb, or up to about 12 kb, or up to about 10 kb). In certain embodiments, the complexed nucleic acid can comprise an RNA (e.g., an RNA up to about 10 kb, or up to about 8 kb, or up to about 6 kb, or up to about 5 kb, or multiple pieces of RNA). Accordingly, in various embodiments, the PRX carrier is an excellent supramolecular carrier for delivery of gene therapeutics, such as expression vectors for expressing heterologous genes and/or for delivering CRISPR enzymes and guide RNAs.
Compared to other carriers in the field, the unique advantages of polyrotaxane (PRX) carriers described herein for nucleic acid delivery involves the formation of a stable polyplex complex against a counter polyanion. The design also includes controllable intracellular release mechanisms via supramolecular dissociation in response to specific intracellular stimuli, i.e. lysosomal low pH and high intracellular GSH. The PRX features additionally include tunable particle sizes, controllable charge type and density, tailorable backbone rigidity, colloidal stability in biological medium, and the ability to functionalize the ends of the PEG chain and surface of the cyclic compounds (e.g., CDs) (for targeting and/or imaging). Moreover, these materials are highly bio-compatible, due to the intrinsic safety of PEG and CD.
The presently described polyrotaxane carriers are the product of multiple iterations of rotaxane carrier development involving systematic tuning of physicochemical properties of the, such as PEG molecular weight and structure, type and density of amine group(s), CD ring number, the presence or absence of cleavable linkers, etc., in order to overcome a list of challenges for the delivery of large nucleic acids (e.g., plasmids) in vivo.
For example, therapeutic plasmids (e.g., CRISPR/Cas9 plasmids) are rapidly degraded macromolecules in the presence of DNases in vivo. In order to overcome this challenge, we synthesized a first generation (G1) of polyrotaxane nucleic acid carrier using a linear PEG backbone (see, e.g., FIG. 2, left illustration). Through an electrostatic mediated self-assembly progress, the plasmid was fully protected by the complexation with the rotaxane, leading to a  ̃100 nm nanoparticulate.
Based on the first generation polyrotaxane carrier a list of key characteristics (e.g. PEG molecular weight, number of CD rings, type and density of amines, etc.) was determined which served as the basis for the next iteration (generation 2 (G2)). Although the first generation PRX exhibited effective cellular uptake, we showed a slow rate of release of the plasmid inside the cells (e.g. cultured primary myotubes). This informed design of a second generation polyrotaxane carrier (G2 PRX), which contained a disulfide linker that responds to an intracellular reducing environment. Compared to G1, delivery of a plasmid containing the CRISPR platform (px333 with gRNAs 44C4 and 55C36) using G2 PRXs showed successful exon 45-55 deletion in myotube cells at an early time point. In order to utilize the polyrotaxane carrier in vivo, the multi-arm polyrotaxane carriers described herein (generation 3 (G3), see, e.g., FIG. TA). The selective inclusion complex design of these carriers has been discussed above. The rest of characteristics, such as CD ring density and type of amines were determined. The multi-arm design is important for systemic delivery because, inter alia, of the introduction of free PEG chain and higher PEGylation that prevent opsonization and unwanted uptake by reticuloendothelial system in vivo.
As illustrated in FIG. 2, the G3 (and G4) multi-arm PRX design where cyclic compounds (e.g., cyclodextrins) form inclusion complexes on a subset of the polymer arms offers numerous advantages over the classical linear (and certain other polyrotaxane deliver vehicles). As illustrated the linker PRX structures are not effectively pegylated. The particles can form a protein corona in vivo. Additionally, particle opsonization can occur and the particles have a short serum half-life. In contrast introduction of the cyclic molecules in a spatially selective fashion provides available (inclusion complex-free) polymer backbone arms that afford effective pegylation. Particle opsonization is prevented in vivo and the PRX/nucleic acid complex shows a long serum half-life.
Experiments shows that the multi-arm carriers show improved biodistribution, post intravenous injection (IV) and are capable of CRISPR-mediated gene cutting. In particular, FIG. 4, panels A shows the results of a study of intracellular uptake and in vitro transfection using G3 PRX as a carrier. Myotube cells received Cy3 labeled plasmid loaded G3 PRX for 3 days and showed effective uptake. Panel B shows a demonstration of in vitro transfection effectiveness of mCherry plasmid delivered by G3 PRX in myotube cells. The commercial transfection reagents, such as Lipofectamine, are very inefficient in myotube cells.
FIG. 5 illustrates the delivery of plasmid by G1 and G2 PRX. Panel A schematically illustrates targeting of exons 44-55 of the DMD gene. Panel B demonstrates high colocalization of cargo and PRX in G1. Panel C demonstrates improved GFP reporter plasmid delivery in G2 compared to G1 PRX. Panel D demonstrates successful application of CRISPR and an exon 45-55 deletion in myotubes using G2 PRX 7 days post treatment compared to G1.
FIG. 6 shows the comparative biodistribution and PK profiles of linear vs multi-arm PRX in DMD mice. Panel A: The cartoon shows the two main designs of PRX. The linear structure has a PEG backbone (black line) and cationic CD rings (pink) that bind nucleic acid (blue) via an electrostatic mediated self-assembly process. Since 2 out of 4 arms were pre-protected by a bulky group (green ball in the left panel) in the 4-arm PRX design, this leads to CD ring-free PEG chains during the complex process. This design differs from the classic linear design in which the PEG backbone is already occupied during the introduction of positive CD, leading to a non- or low PEG nanoparticle. Panel B: Typical AFM pictures of free plasmid and self-assembled PRX/plasmid. Panel C) IVIS imaging of mdx muscles from mice injected with either the linear or the 4-arm PRX. More abundant plasmid was observed in muscles of mice injected with the 4-arm PRX. Plasmid was labeled by Cy3 for IVIS.
FIG. 7 shows the carrier (G3 PRX loaded with Cy3 plasmid) particle and plasmid biodistribution in quadriceps muscle section.
Based on the third generation multi-arm polyrotaxane carrier, fourth generation (G4) polyrotaxane carrier was developed that combined the use of a multi-arm PEG backbone (with selectively distributed inclusion complexes to provide at least one inclusion complex-free arm) to improve biodistribution and one or more cleavable linkages (e.g., bio-cleavable linkers) to enhance intracellular plasmid release (see, e.g., FIGS. 3A and 3B). Through medicinal chemistry, we have identified functional groups in the PRX where cleavable linkages can be placed to enhance intracellular release of a complexed nucleic acid (e.g., a plasmid). In one illustrated embodiment, the cleavable linkage is placed between the backbone (e.g., the PEG backbone) and one or more of the bulky moieties (bulky stopper(s) that prevent cyclic compounds from falling off the backbone arm(s). In another illustrative, but non-limiting embodiment, a cleavable linkage (e.g., a disulfide linker) is placed between the cyclic compound(s) (e.g., cyclodextrin) and their conjugated nucleophile(s) (e.g., conjugated cationic tertiary amine groups), which upon cleavage and removal of the nucleophile(s), can lead to the PRX and plasmid dissociation via a charge reduction mechanism. Two representative examples were shown to demonstrate the site of an illustrative disulfide linker in multi-arm PRX (see, e.g., FIG. 3B).
FIG. 8 illustrates determination of the N/P ratio of a multi-arm (G3) PRX. As shown, in certain embodiments, an optimal N/P ratio is about 10:1. However, in various embodiments, the N:P ratio ranges from about 0.01:1 up to about 100:1, or from about 0.1:1 up to about 50:1, or from about 1:1 up to about 30:1, or up to about 20:1, or up to about 10:1.
FIG. 6, panel B, illustrates formation (self-assembly) of the G3 plasmid-PRX complex.
FIG. 9 demonstrates G3 and G4 PRX are taken up efficiently in vitro. This figure also shows that a CRISPR/Cas9 plasmid laden G4 multi-arm PRX exhibited CRISPR-mediated cutting effect at day 7 in cultured myotube cells. Without being bound by a particular theory, it is believed that the fourth generation (G4) multi-PRX carriers described herein incorporating cleavable linkages can increase intracellular release of a complexed nucleic acid (e.g., a plasmid). In this regard, FIG. 10 illustrates data obtained from a G4 multi-arm PRX using option 1 (reducing steric hindrance).
In view of the foregoing (and the Examples presented herein) it will be recognized that the polyrotaxane (PRX) nanocarriers described herein can deliver large nucleic acids (e.g., large plasmids, and other constructs) in vivo. While the use of cationic nanoparticles for nucleic acid delivery has been reported in the literature, the delivery of 1) This nanoparticle is designed to deliver large plasmids in vivo. While the use of cationic nanoparticle for gene product delivery is reported in the literature, the delivery of large constructs (e.g., an intact plasmid) has heretofore proven to be particularly challenging due to the large molecular weight, steric hindrance, loading capacity of the carrier, etc.
Moreover, the carries described herein offer a non-viral method of in vivo nucleic acid deliver which is advantageous over competing technologies such viral vectors (e.g., AAV-CRISPR). AAV is not able to efficiently target muscle stem cells in vivo, which is a requirement for a long term sustained effect, as the corrected myofibers may be lost over time during muscle degeneration/regeneration.
On the other hand, the PRX nanoparticle carriers described herein can be easily modified and targeted and can be adapted and optimized to target muscle stem cells or any other cell or tissue type of interest.
In addition, viral vectors can typically only be delivered a single time, due to the immune response that often develops against the viral serotype. So, unless the nucleic acid construct (e.g., CRISPR) works at very high efficiency, the potential to lose the corrected cells after treatment is high. Conversely, the nanoparticle PRX carriers described herein can be repeatedly administered. Also, importantly, with viral mediated delivery, the active agent (e.g., CRISPR/Cas9) can be present for an extended period of time, which increases the potential for off target effects and for development of an immune response. In contrast, the PRX carriers and complexes thereof are believed to be non-immunogenic and biodegradable to surpass these downfalls.
Multi-Arm Polyrotaxane (PRX) Nucleic Acid Carriers.
In view of the foregoing, in various embodiments, a polyrotaxane carrier for in vivo delivery of a nucleic acid is provided. In certain embodiments the carrier comprises a multi-arm polyethylene glycol (PEG) backbone comprising at least three arms; at least one cyclic compound having a cavity, where an arm of said multi-arm PEG backbone is threaded into the cavity of said cyclic compound forming an inclusion complex; a bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound where said moiety inhibits dethreading of the cyclodextrin from the arm(s) of said backbone; and where at least one arm of said PEG backbone is free of cyclic compounds; and where said carrier has a net positive charge. Typically, the carrier complexes with (self-assembles with) a nucleic acid when contacted to the nucleic acid. In certain embodiments, the multi-arm polyethylene glycol backbone comprises a star polymer. In certain embodiments, the multi-arm backbone comprises multiple branches along a main chain. In certain embodiments, the multi-arm PEG comprises at least 2 arms free of cyclic compounds. In certain embodiments, the multi-arm PEG comprises from 3 up to about 12, or up to about 10, or up to about 8 arms. In certain embodiments, the PEG comprises 4 arms, or 5 arms, or 6 arms, or seven arms, or 8 arms. In certain embodiments, the PEG comprises 4 arms. In certain embodiments, the PEG comprise 4 arms where two of said arms are free of cyclic compounds.
In various embodiments, the PEG backbone has a molecular weight ranging from about 1.0 to about 10 kDa per arm. In certain embodiments, the PEG backbone comprises about 22 to about 227 ethylene oxides per arm. In certain embodiments, the PEG backbone has a molecular weight of about 2.5 kDa per arm. In certain embodiments, the arm(s) threaded into said cyclic compound(s) each bear on average from about 5, or from about 10, or from about 15 up to about 110, or up to about 80, or up to about 50, or up to about 40, or up to about 30 cyclic compounds. In certain embodiments, the arm(s) threaded into said cyclic compound(s) each bear, on average, about 10 to about 20 cyclic compounds per arm.
Any of a number of cyclic compounds are known to those of skill in the art. Illustrative cyclic molecules include, but are not limited to a cyclodextrin, a crown ether, a cucurbituril, or a cyclofructan. Other cyclic compounds that may be used include, but are not limited to various heterocyclic compounds, inorganic cyclic compounds, carbocycles, and chelating macrocyclic compounds. Typically, all of the cyclic molecules in a PRX carrier are the same type of cyclic molecule. However, in certain embodiments, the PRX can comprise multiple species of cyclic compound. In certain embodiments the cyclic compound comprises a cyclodextrin. Illustrative, but non-limiting, cyclodextrins include a cyclodextrin selected from the group consisting of α-cyclodextrins, β-cyclodextrins, and γ-cyclodextrins. In certain embodiments, the cyclodextrin comprises about 5 to about 8, or about 6 to about 7, aminated D-glucose units. In certain embodiments, the α-cyclodextrins may comprise from 1 to 6 aminated D-glucose units. In certain embodiments the β-cyclodextrins may comprise from 1 to 7 aminated D-glucose units. In certain embodiments the γ-cyclodextrins may comprise from 1 to 8 aminated D-glucose units. In certain embodiments the aminated D-glucose units may be represented by the general Formula:




Where p is an integer from 0 to about 8, or 0 to 1 to 4, and where T is optional, and when present is an alkyl selected from the group consisting of methyl (—CH3), ethyl (—CH2CH3) and propyl (—CH2CH2CH3). In one illustrative embodiment, p=5. In one illustrative embodiment, T is ethyl.

In certain embodiments the cyclic compound comprises a cyclodextrin selected from the group consisting of an α-cyclodextrin, a β-cyclodextrin, a γ-cyclodextrin, a hydroxypropylated α-cyclodextrin, a hydroxypropylated β-cyclodextrin, a hydroxypropoylated γ-cyclodextrin, and a dimethylcyclodextrin. In certain embodiments, the cyclic compound comprises a cucurbituril (e.g., cucurbit[5]uril, cucurbit[6]uril, cucurbit[7]uril, cucurbit[8]uril, cucurbit[9]uril, and cucurbit[10]uril, etc.). In certain embodiments, the cyclic compound comprises a cucurbit[6]uril (CB[6]).
In certain embodiments, the cyclic compound(s) are substituted with one or more nucleophilic groups. In certain embodiments, the cyclic compound(s) are substituted with one or more amine groups or groups derived from an amine group. In certain embodiments, the cyclic compound(s) are substituted with one or more groups selected from the group consisting of a primary amine, a secondary amine, a tertiary amine, and an imine group. In certain embodiments, the cyclic compound(s) are substituted with one or more primary amines. In certain embodiments, the number of nucleophilic group substituted on the cyclic compound(s) ranges from 1 up to about 20 substitutions per cyclic compound. In certain embodiments, the cyclic compounds are substituted with nucleophilic groups to provide a positive zeta potential for said carrier ranging from about 5 mV up to about 50 mV, or from about 5 mV, or from about 10 mV up to about 40 mV, or up to about 30 mV, or up to about 20 mV. In certain embodiments, the carrier has a zeta potential of about 15 mV.
In certain embodiments, the moiety capping the terminal of the arm(s) threaded into said cyclic compound(s) comprises a moiety selected from the group consisting of Z-tyrosine, phenylalanine, a group having at least one benzene ring, and a group having at least one tertiary butyl. In certain embodiments, the bulky moiety comprises moiety selected from the group consisting of a Z-tyrosine, phenylaline, a benzyloxycarbonyl (Z) group, a 9-fluorenylmethyloxycarbonyl (Fmoc) group, a benzyl ester (OBz) group, a tertiary butylcarbonyl (Boc) group, and an amino acid-tertiary butyl ester (OBu) group. In certain embodiments, the bulky moiety comprises Z-tyrosine.
In various embodiments, at least one arms not threaded into the cyclic compound is terminated with a protecting group, and/or a fluorophore, and/or a targeting moiety. In certain embodiments, all the arms not threaded into the cyclic compound are terminated with a protecting group, and/or a fluorophore, and/or a targeting moiety. In certain embodiments, least one arm not threaded into said cyclic compound is terminated with a protecting group selected from the group consisting of dansyl, acetyl, amide, and 3 to 20 carbon alkyl groups, Fmoc, Tboc, 9-fluoreneacetyl group, 1-fluorenecarboxylic group, 9-florenecarboxylic group, 9-fluorenone-1-carboxylic group, benzyloxycarbonyl, Xanthyl (Xan), Trityl (Trt), 4-methyltrityl (Mtt), 4-methoxytrityl (Mmt), 4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr), Mesitylene-2-sulphonyl (Mts), 4,4-dimethoxybenzhydryl (Mbh), Tosyl (Tos), 2,2,5,7,8-pentamethyl chroman-6-sulphonyl (Pme), 4-methylbenzyl (MeBzl), 4-methoxybenzyl (MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl), Benzoyl (Bz), 3-nitro-2-pyridinesulphenyl (Npys), 1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl (2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl—Z), 2-bromobenzyloxycarbonyl (2-Br—Z), Benzyloxymethyl (Bom), t-butoxycarbonyl (Boc), cyclohexyloxy (cHxO), t-butoxymethyl (Bum), t-butoxy (tBuO), t-Butyl (tBu), Acetyl (Ac), and Trifluoroacetyl (TFA).
In certain embodiments, at least one arm not threaded into said cyclic compound is attached to a fluorophore (e.g., a rhodamine, a cyanine, an oxazine, a thiazine, a porphyrin, a phthalocyanine, a fluorescent protein, a quantum dot, etc.). In certain embodiments, the fluorophore is selected from the group consisting of fluorescein isothiocyanate (especially fluorescein-5-isothiocyanate), 5-FAM (5-carboxyfluorescein), 6-FAM (6-carboxyfluorescein), 5,6-FAM, 7-hydroxycoumarin-3-carboxamide, 6-chloro-7-hydroxycoumarin-3-carboxamide-, dichlorotriazinylaminofluorescein, tetramethylrhodamine-5 (and-6)-isothiocyanate, 1,3-bis-(2-dialkylamino-5-thienyl)-substituted squarines, succinimidyl esters of 5 (and 6) carboxyfluoroscein, 5 (and 6)-carboxytetramethylrhodamine, and 7-amino-4-methylcoumarin-3-acetic acid, DyLight 350, DyLight 405, DyLight 488, DyLight 550, DyLight 594, DyLight 633, DyLight 650, DyLight 680, DyLight 755, DyLight 800. Alexa fluor 350, Alexa fluor 405, Alexa fluor 488, Alexa fluor 546, Alexa fluor 555, Alexa fluor 568, Alexa fluor 594, Alexa fluor 633, Alexa fluor 647, Alexa fluor 750.
In certain embodiments, at least one backbone arm not threaded into said cyclic compound is attached to a targeting moiety that specifically or preferentially binds to a cell. In certain embodiments, the targeting moiety is selected from the group consisting of an antibody, a receptor ligand, a nucleic acid aptamer, a peptide aptamer, and a lectin. In certain embodiments targeting moiety comprises an antibody (e.g., a full-length antibody, an scFV, an affibody, an antibody fragment, etc.). In certain embodiments, the targeting moiety binds to a stem cell. In certain embodiments, the targeting moiety binds to a hematopoietic cell. In certain embodiments, the targeting moiety binds to a T-cell. In certain embodiments, the targeting moiety binds a target selected from the group consisting of CD45, CD3, erbB2, Her2, CD22, CD74, CD19, CD20, CD33, CD40, MUC1, IL-15R, HLA-DR, EGP-1, EGP-2, G250, prostate specific membrane antigen (PSMA), prostate specific antigen (PSA), prostatic acid phosphatase (PAP), and placental alkaline phosphatase. In certain embodiments, the targeting moiety binds to a cancer cell marker. In certain embodiments, the targeting moiety binds to a cancer cell marker selected from the group consisting of 5 alpha reductase, α-fetoprotein, AM-1, APC, APRIL, BAGE, 0-catenin, Bc12, bcr-abl (b3a2), CA-125, CASP-8/FLICE, Cathepsins, CD19, CD20, CD21, CD23, CD22, CD38, CD33, CD35, CD44, CD45, CD46, CD5, CD52, CD55, CD59 (791Tgp72), CDCl27, CDK4, CEA, c-myc, Cox-2, DCC, DcR3, E6/E7, EGFR, EMBP, Ena78, FGF8b and FGF8a, FLK-1/KDR, Folic Acid Receptor, G250, GAGE-Family, gastrin 17, Gastrin-releasing hormone (bombesin), GD2/GD3/GM2, GnRH, GnTV, gp100/Pmel17, gp-100-in4, gp15, gp75/TRP-1, hCG, Heparanase, Her2/neu, Her3, HMTV, Hsp70, hTERT, (telomerase), IGFR1, IL-13R, iNOS, Ki 67, KIAA0205, K-ras, H-ras, N-ras, KSA, (CO17-1A), LDLR-FUT, MAGE Family (MAGE1, MAGE3, etc.), Mammaglobin, MAP17, Melan-A/, MART-1, mesothelin, MIC A/B, MT-MMP's, such as MMP2, MMP3, MMP7, MMP9, Mox, Mucin, such as MUC-1, MUC-2, MUC-3, and MUC-4, MUM-1, NY-ESO-1, Osteonectin, p15, P170/MDR1, p53, p97/melanotransferrin, PAI-1, PDGF, Plasminogen (uPA), PRAME, Probasin, Progenipoietin, PSA, PSM, RAGE-1, Rb, RCAS1, SART-1, SSX gene, family, STAT3, STn, (mucin assoc.), TAG-72, TGF-α, TGF-β, Thymosin β 15, IFN-α, TPA, TPI, TRP-2, Tyrosinase, VEGF, ZAG, p16INK4, and Glutathione S-transferase.
Any of the foregoing markers can be used as targets for the targeting moieties comprising the multi-arm PRX carriers described herein. In certain embodiments the target markers include, but are not limited to members of the epidermal growth factor family (e.g., HER2, HER3, EGF, HER4), CD1, CD2, CD3, CD5, CD7, CD13, CD14, CD15, CD19, CD20, CD21, CD23, CD25, CD33, CD34, CD38, 5E10, CEA, HLA-DR, HM 1.24, HMB 45, 1a, Leu-M1, MUC1, PMSA, TAG-72, phosphatidyl serine antigen, and the like.
In certain embodiments the one or more targeting moieties on the PRX carrier can comprise a cell penetrating peptide (CPP). Cell Penetrating Peptides (CPPs, also known as Cell Permeable Peptides or as Protein Transduction Domains, PTDs), are carriers with small peptide domains (generally less than 40 amino acids) that can easily cross cell membranes. Multiple cell permeable peptides have been identified that facilitate cellular uptake of various molecular cargo, ranging from nanosize particles to small chemical molecules.
The most commonly used CPP is the HIV-TAT sequence. There are multiple other cell penetrating sequences, a small selection of which is shown below in Table 1. For a comprehensive review of currently available CPPs see, e.g., Reissman (2014) J. Pept. Sci. 20: 760-784).







TABLE 1







Illustrative, but non-limiting list


of cell penetrating peptides.













SEQ ID



Name
Sequence
NO.















HIV-TAT
GRKKRRQRRRPQ
3



 



Oligo-
RRRRRRRR
4



Arginine





 



MPG
Ac-GALFLGFLGAAGSTMG
5




AWSQPKKKRKV-cya




 



PEP-1
Ac-KETWWETWWTEWSQPK
6




KKRKC-cya




 



EB1
LIKLWSHLIHIWFQNRRLK
7




WKKK




 



Transportan
GWTLNSAGYLLGKINLKAL
8




AALAKKIL




 



p-Antp
RQIKIWFQNRRMKWKK
9



 



hCT(18-32)
KFHTFPQTAIGVGAP-NH2
10



 



KLAseq
KLALKLALKALKAALKLA
11










In certain embodiments, the targeting moiety comprises a moiety that binds surface markers of skeletal muscle cells. Illustrative muscle cell markers include, but are not limited to N-CAM (see, e.g., Walsh (1990) N-CAM is a Target Cell Surface Antigen for the Purification of Muscle Cells for Myoblast Transfer Therapy. In: Griggs R. C., Karpati G. (eds) Myoblast Transfer Therapy. Advances in Experimental Medicine and Biology, vol 280. Springer, Boston, Mass.), and 16.3A5 (see, e.g., Woodroofe et al. (1984) Som. Cell Mol. Genet. 10(5): 535-540).
The foregoing markers (targets) are intended to be illustrative and not limiting. Other tumor associated antigens will be known to those of skill in the art.
Where the tumor marker is a cell surface receptor, ligand to that receptor can function as targeting moieties. Similarly, mimetics of such ligands can also be used as targeting moieties.
In certain embodiments, the targeting moiety comprises a folic acid or a transferrin.
In certain embodiments the multi-arm polyrotaxane carrier is a fourth generation carrier (G4-PRX). Accordingly, in certain embodiments the bulky moiety is attached to an arm of the backbone by a cleavable linkage and/or the one or more nucleophilic groups are attached to the cyclic compounds by a cleavable linkage. A linkage or linking agent as used herein, refers to a molecule or functional group that is used to join two or more molecules. In certain embodiments, the linker is typically capable of forming covalent bonds to both molecule(s). Suitable linkages/linkers are well known to those of skill in the art and include, but are not limited to, straight or branched-chain carbon linkers, heterocyclic carbon linkers, or peptide linkers.
In certain embodiments, the cleavable linkage comprises a redox-responsive linker, a pH responsive linker, an enzymatically cleavable linker, a photo-responsive linker, or a thermal-responsive linker. In certain embodiments, the cleavable linkage comprises a redox-responsive disulfide linker. In certain embodiments, the cleavable linkage comprises a pH responsive hydrazine linker. In certain embodiments, the cleavable linkage comprises an enzymatically cleavable linker. In certain embodiments, the linkage comprises a linker cleavable by a protease. In certain embodiments, the linkage comprises a linker cleavable by a matrix metalloprotease or a cathepsin. In certain embodiments, the peptide linker comprises a dipeptide valine-citrulline (Val-Cit), or Phe-Lys. Additional linker can include, but are not limited to, Mc-vc-PAB-MMAE, Mc-vc-PAB-MMAF, Mc-va-PBD dimer, Mc-vc-PAB-CM-seco-DUBA, and the like.
As noted above, the multi-polyrotaxane carries can be complexed with the nucleic acid simply by combining the two moieties where they self-assemble to form a deliverable nanocarrier.
In various embodiments the multi-arm polyrotaxane carriers are made by:

    
    
        providing a multi-arm PEG backbone comprising m arms where m ranges from 3 to 8;
        coupling first protecting groups to x arms of said backbone where x ranges from 1 to m−1;
        forming cyclic compound inclusion bodies on the arms of said PEG backbone that are not coupled to said first protecting groups; and
        adding blocking groups to the arms of said PEG backbone that bear cyclic compound inclusion bodies.
    
    


A synthesis scheme for making a third generation (G3) multi-arm polyrotaxane carrier described herein is shown in FIG. 11, and protocols are also provided in the Examples. An illustrative synthesis scheme for making a fourth generation (G4) multi-arm polyrotaxane carrier incorporating cleavable linkages described herein is shown in FIG. 12, and NMR data of the intermediary product (pyridyldithiol-polyrotaxane) for this G4 PRX is shown in FIG. 13 and described in the Examples. These synthesis schemes are illustrative and non-limiting. Using the teachings provided herein, numerous variants of the multi-arm polyrotaxanes shown herein will be available to one of skill in the art and readily synthesized.
Uses.
One of skill in the art will recognize that the PRX carriers described herein can be used to deliver any of a number of nucleic acid constructs to cells and/or tissues in vivo. Moreover, particularly when the nanocarriers bear one or more targeting moieties, specific cell and tissue types can be directly targeted while reducing systemwide exposure to the nanocarrier.
The nanocarriers described herein find a number of uses. As proof of principle, the a nanocarrier targeted to skeletal muscle that delivers a CRISPR/Cas9 platform for the correction of the dystrophin gene and treatment of Duchenne's Muscular Dystrophy by restoration on of the DMD reading frame.
The nanocarriers, however are not limited to the use of a CRISPR/Cas9 platform for this purpose. For example, in certain embodiments, the polyrotaxane carriers (e.g., G3 or G4 carriers) complexed with a plasmid that encodes a CRISPR/Cas9 construct that targets (e.g., knocks out) particular genes (e.g., genes that are mutated in various cancers) can be used in the treatment of a number of cancers or other diseases. Illustrative, but non-limiting, list of conditions and associated targets is shown in Table 2.







TABLE 2







Illustrative diseases that can be targeted/treated using CRISPR/Cas9 


constructs delivered using the polyrotaxane constructs described herein.








Disease
Target





Breast cancer
Her2/Neu, BRCA


Lung cancer
EGFR


Pancreatic cancer
KRAS


Colon cancer
KRAS


Melanoma
BRAF


Thyroid cancer
TERT promoter


Lymphoma
cMyc, TRP53


Multiple cancers
PD-1, PD-L1


Alzheimer's disease
Presenilin 1


Beta-thalassemia
HBB


Huntington
RNF216









As indicated in Table 2, in certain embodiments, the constructs delivered by the multi-arm polyrotaxane carriers can encode a gene or cDNA encoding a protein that shows efficacy against various cancers. In certain embodiments the protein comprises a cytokine. A number of cytokines have been used for the treatment of cancer. These include, but are not hinted to interferon alpha (IFN-α), interferon beta (IFN-β), interferon gamma (IFN-γ), interleukin 1 (IL-1), interleukin (IL-2), and interleukin 12 (IL-12). These cytokines demonstrate their efficacy by inducing apoptosis and other anticancer functions in tumor microenvironment. For example, IFN-α exerts its anticancer efficacy by inducing NK cells and DCs against tumor cells by inhibiting cell proliferation and killing cancer cells, thus showing anticancer effects in, inter alia, melanoma and Kaposi sarcoma (see, e.g., Sutlu & Alici (2009) J. Intern. Med. 266: 154-181; Joshi et al. (2009) Proc. Natl. Acad. Sci. USA, 106: 12097-12102; Jonasch & Haluska (2001) Oncologist, 6: 34-55). IL-1α shows cytotoxic-cytostatic activity against refractory malignancies and solid tumor cells (see, e.g., Rosenthal et al. 91998) J. Immunother. 21: 371-378; Furman et al. (1997) Med. Pediatr. Oncol. 28: 444-450).
Th1 cytokine IL-2 shows anticancer efficacy against several types of cancer including hematologic malignancies in in vitro, in vivo, and clinical studies (see, e.g., Sznol & Parkinson (1994) Blood, 83: 2020-2022). Cytokine IL-2 exerts it anticancer efficacy by enhancing anticancer immunity that is evident by the use of recombinant antibody-IL-2 fusion protein (huKS1/4-IL-2) in colorectal carcinoma (see, e.g., Xiang et al. (1998) Cancer Res. 58: 3918-3925). IL-4 has been reported to facilitate its anticancer efficacy by inhibiting growth of human lung tumor cells (see, e.g., Topp et al. (1993) Blood, 82: 2837-2844). In MCF-7 breast cancer cells, IL-4 showed growth inhibition and induction of apoptosis via insulin receptor substrates and STAT-6 phosphorylation (see, e.g., Gooch et al. (2002) Neoplasia, 4: 324-331).
While IL-6 expression has often been viewed as undesirable in regulation/treatment of cancers, a lesser known role for IL-6 signaling has emerged in which it plays a beneficial role that opposes tumor growth by mobilizing anti-tumor T cell immune responses to attain tumor control. Accumulating evidence establishes IL-6 as a key player in the activation, proliferation and survival of lymphocytes during active immune responses. IL-6 signaling can also resculpt the T cell immune response, shifting it from a suppressive to a responsive state that can effectively act against tumors. Additionally IL-6 plays a role in boosting T cell trafficking to lymph nodes and to tumor sites, where they have the opportunity to become activated and execute their cytotoxic effector functions, respectively (see, e.g., Fisher et al. (2014) Semin. Immunol., 26(1): 38-47).
IL-7 in combination with human T cells has been shown to exert significant anticancer activity in human colon carcinoma (see, e.g., Murphy et al. (1993) J. Clin. Invest. 92: 1918-1924). It is believed the protective function of IL-7 is mediated via activation of the PI3K/AKT pathway (see, e.g., Zhang et al. (2011) Clin. Cancer Res. 17: 4975-4986). IL-11 is used in myelosuppressive chemotherapy to minimize the chance of thrombocytopenia in patients with malignancies (see, e.g., Bhatia et al. (2007) Leuk. Lymphoma, 48: 9-15).
Being a key player in cellular immunity against tumor, IL-12 has been an attractive option for immunotherapy, but prior to the development of the polyrotaxane delivery system described herein (see, e.g., Example 3) the presence of severe toxicity has minimized its use in cancer therapy.
IL-15 plays important role in the induction of NK cells, T-cells, and B cells that demonstrate therapeutic potential of this key cytokine in malignancy (see, e.g., Mishra et al. (2014) Clin. Cancer Res. 20: 2044-2050).
Accordingly, in certain embodiments the constructs delivered by the multi-arm polyrotaxane carriers described herein comprise plasmids that encode and express a cytokine. In certain embodiments the plasmids encode a cytokine selected from the group consisting of interleukin 12 (IL-12), interferon alpha (IFN-α), interferon beta (IFN-β), interferon gamma (IFN-γ), interleukin 1 (IL-1), interleukin (IL-2), interleukin 4 (IL-4), interleukin 6 (IL-6), interleukin 7 (IL-7), interleukin 11 (IL-11), interleukin 15 (IL-15), interleukin 18 (IL-18), and the like.
In certain embodiments the constructs delivered by the multi-arm polyrotaxane carriers described herein comprise a plasmid that encodes multiple cytokines and/or multiple plasmids where each plasmid encodes a different cytokines. Accordingly the the multi-arm polyrotaxane carriers described herein can effectively used to deliver any of a number of combinations of cytokines. Illustrative combinations of cytokines include, but are not limited to IL-2/IL-12, IL-15/IL-12, IL-7/IL-12, IL-21/IL-12, IL-18/IL-12, GM-CSF/IL-12, IFN alpha/IL-12, chemokines and anti-angiogenic cytokines plus IL-12 and the like. These various combinations of cytokines have found utility in the treatment of various cancers (see, e.g., Weiss et al. (2007) Exp. Opin. Biol. Ther. 7(11):1705-1721).
Plasmids expressing any of these cytokines are readily created by one of skill in the art and a number are commercially available. The creation of a plasmid expressing IL-12 and incorporating that plasmid in a polyrotaxane carrier is illustrated in Example 3. Using the teachings provided there polyrotaxane carriers incorporating plasmids encoding any of the above-described cytokines or any other cytokine or other protein can readilby be produced by one of skill in the art.
The constructs delivered by the multi-arm polyrotaxane carriers described herein are not limited to plasmids encoding CRISPR/Cas9 components or cytokines. For example, in certain embodiments, the complexed plasmid can encode a heterologous gene whose expression corrects a genetic deficiency or improves the health of a subject. In certain embodiments, the complexed plasmid can encode one or a pluralityh of inhibitory nucleic acids (e.g., antisense nucleic acids, ribozymes, and the like) that inhibit or downregulate the expression of particular genes.
By way of illustration, angiotensin-converting enzyme (ACE) inhibitors are used in medicine to treat hypertension and life extension by ACE inhibition has been shown in nematode worms. Similarly, knockout of Adenylyl Cyclase Type 5 (AC5) extends life in mice, with the most plausible mechanism being increased resilience of the cardiovascular system. Accordingly, in certain embodiments, the plasmid complexed with the multi-arm polyrotaxane carriers described herein can encode a CRISPR/Cas9 construct, or other construct, that inhibits (or knocks out) ACE or AC5.
A recent study suggests that a rare variant in the Angiopoietin-like 4 (ANGPTL4) gene, present in less than 1% of the European population, reduces the risk of heart attack by half. In certain embodiments, the polyrotaxane constructs described herein can deliver a complexed plasmid that encodes this genetic variant.
Other gene therapies that can be delivered using the multi-polyrotaxane carriers described herein include, but are not limited to: Lowering angiotensin II receptor type 1 (Agtr1a) which protects mitochondrial function and has been observed to modestly extends life in mice. Increasing Apolipoprotein A-1, can alter cholesterol metabolism in a beneficial way, slowing progression of atherosclerosis by transporting away some of the damaged lipids where they are build up in blood vessel walls. APOE is one of the only human genes with variants that are robustly associated with greater longevity. Gene knockout of ARID1A has been observed to produce regenerative capacity in mice, particularly in the liver. Increased levels of Activating transcription factor 4 (ATF4) in the liver are found in many of the methods of slowing aging in laboratory species. Increased amounts of atoh1 have been used to spur growth of hair cells in guinea pigs, making it one of a number of possible approaches to address the proximate cause of forms of age-related deafness that result from loss of these cells, rather than from other causes. The azot gene in fruit flies is a part of a mechanism by which cells collaborate to identify damaged or dysfunctional neighbors, flagging them for destruction and replacement. Adding an extra copy of the azot gene to increase levels of the azot protein results in more effective destruction of less fit cells, and an increase in life span—in fruit flies at least. The gene and associated mechanism of quality control appears to be conserved in mammals. Inhibition of bcat-1 is shown to extend life in nematode worms, possibly via a form of hormesis or calorie restriction effect by blocking the processing of some dietary molecules. β2 microglobulin (B2M) levels rise with age, and in mice and reducing the amount of B2M in older individuals restores some of the loss of cognitive decline that occurs in aging. Mice engineered to express higher levels of BubR1 have lower levels of cancer, greater exercise capacity, and live modestly longer. The cancer effect makes sense in the context of what is known of BubR1, that it is involved in an important checkpoint mechanism of cellular replication. Researchers have shown that lowered levels of c-myc can modestly slow aging and extend life in mice, with some evidence that this is due to effects on insulin metabolism. The C1Q gene plays a role in the immune system. Removing it from mice spurs greater regeneration via Wnt signaling. C1Q levels rise in the brain with aging, and again, removing it improves the state of cognitive function in later life in mice. Gene therapy to increase levels of the antioxidant catalase in the mitochondria in mice have produced mixed results, but some studies show improved health and extended life. Other approaches to mitochondrially targeted antioxidants have produced similar benefits. The prevailing theory is that this reduces damage to mitochondria occurring as a result of the reactive oxygen species generated within these organelles, with localized antioxidants soaking up reactive molecules before they can cause harm. Reduced CLK1 activity can extend life in mice due to altered mitochondrial function and consequently lowered generation of reactive oxygen species. A reduced amount of CRTC1 can extend life in nematode worms, and is probably involved in the calorie restriction response. This protein is closely related to AMPK, and manipulations of both CRTC1 and AMPK are likely achieving much the same alterations in the operation of metabolism. Increased levels of cyclin A2 have been shown to increase the regenerative capacity of heart tissue, one of an array of proteins that might for the basis for regenerative gene therapies for heart disease, and thus also might be beneficial to undergo far in advance of old age so as to slow or postpone degeneration of the heart. Overexpression of FGF21 occurs in the calorie restriction response, and when induced artificially using gene therapy it can extend life in mice. Gene therapy to boost levels of FKBP1b to youthful levels can reverse age-related dysfunction of calcium metabolism in the brains of rats. Cognitive function improved as a result, as assessed with tests of spatial memory. Increased follistatin produces increased muscle growth, a potentially useful compensation for the loss of muscle mass and strength that occurs with aging. It is the flip-side of myostatin, as increased follistatin blocks the activity of myostatin: either increased follistatin or reduced myostatin produce similar outcomes in animal studies, with treated individuals demonstrating increased muscle mass. A variant of FOXO3 is associated with a modest reduction in cardiovascular disease and mortality in human data. Higher levels of GDF11 have been shown to improve numerous measures of aging in mice, such as heart function, exercise capacity, and sense of smell. This is most likely occurring due to increased stem cell activity, though there continues to be some debate as to what exactly the researchers are observing in these studies. The level of GHK in blood and tissues declines with aging, and is implicated in some of the detrimental changes in wound healing that occur in later life. Since delivering GHK on its own appears to be beneficial, using gene therapy to reset GHK levels may restore some of this loss of regenerative capacity. In flies, higher levels of Glycine N-methyltransferase (Gnmt) act to inhibit the use of methionine in protein synthesis, which mimics some of the efforts of calorie restriction on health and longevity. Reaction to lower methionine levels—or the appearance of lower methionine levels—is a key trigger for the calorie restriction response. The longest lived genetically altered mice are those without a functional growth hormone receptor gene (growth hormone/growth hormone receptor/insulin-like growth factor/insulin receptor). They are small and vulnerable to cold, but otherwise healthy. Many similar approaches to disrupting the well-studied operations of growth hormone and insulin metabolism also extend life in mice to various degrees, some of which are whole-body, while others are tissue-specific. Mice engineered to have low levels of—or entirely absent histone deacetylase 2 (HDAC2) have improved memory function and neural plasticity. Heat shock proteins are molecular chaperones involved in cellular housekeeping processes that clear out damaged or misfolded proteins. Their activity increases in response to heat, toxins, and various other forms of cellular stress, and dialing up the activity of heat shock proteins is involved in a number of methods demonstrated to slow aging in laboratory animals. Many of these invoke altering the level of other proteins that interact with or regulate heat shock proteins. A range of hepatic transcription factors are associated with development and regeneration in the liver. Researchers have demonstrated that some of these can be upregulated to reduce liver fibrosis by steering cell lineages away from the production of scar tissue and towards the production of useful liver cells. Hepatocyte growth factor (HGF) is a potential compensatory therapy to spur remodeling and regrowth of blood vessels in ischemic disease. The INDY gene, I'm Not Dead Yet, was one of the first longevity-associated genes discovered in flies. Reduced levels of the INDY protein extend life, with the evidence pointing to increased intestinal stem cell function as the cause. Delivering higher levels of IL-21 has been demonstrated to improve the state of the immune system by increasing the pace at which new immune cells are generated. Loss of immune function with age is an important component of age-related frailty, and even partially compensating for this decline might be very beneficial. Selectively lowering levels of klf4 in smooth muscle cells in blood vessel walls causes beneficial changes in the behavior of these cells. Their overreaction to damaged lipids arriving in the bloodstream is muted, which slows the progression of damage and reaction to that damage that leads towards atherosclerosis. Overexpression of klotho has been shown to increase life span in mice, possibly through some of the same mechanisms as calorie restriction. There are three lamin isoforms, A, B, and C. The cause of progeria, a rare condition with the appearance of accelerated aging, is a mutation in Lamin A. Much smaller amounts of malformed lamin A are found in old tissues, though it is uncertain as to whether or not this contributes in any meaningful way to the progression of aging. Intriguingly, mice engineered to produce only lamin C live modestly longer. The A variant of lysosome-associated membrane protein 2 (LAMP2a) is a receptor involved in the cellular maintenance processes of autophagy, but levels decrease with age, and in at least some species this appears to be one of the factors involved in the age-related decline of autophagy. Nearly a decade ago now, researchers demonstrated restoration of more youthful levels of liver function in old mice by adding a duplicate gene to increase amounts of this protein. Increased efficiency of autophagy shows up as a feature of many of the interventions shown to slow aging in animals, but this is one of the few examples in which some rejuvenation of function in old animals was observed. Altered Leukemia inhibitory factor (LIF) levels have been used to spur neural cells into greater activity that can better restore lost myelin sheathing on nerves. Since we all lose some of this sheathing with age, this is of general interest, applicable to more than just conditions such as multiple sclerosis in which a great deal of myelin is lost. Increased Lin28a expression enhances regenerative capacity in mice. This is another gene that has been used in reprogramming ordinary cells to become stem cells. LOS1 may be involved in a variety of fundamental cellular processes, ranging from protein synthesis to DNA repair. The effects of LOS1 knockout on longevity have only been explored in yeas. The microRNA miR-195 interacts with telomerase, and inhibiting it has much the same beneficial effect on stem activity as increasing levels of telomerase. More stem cell activity means more regeneration, though possibly also a higher risk of cancer in later life. Since stem cell activity declines with age, there are many research groups working on potential ways to restore that activity to youthful levels. Partial disruption of the function of mitochondrial complex I has been shown to modestly extend life in a number of species, with the dominant theory being that this is a hormetic effect—an increase in the creation of reactive oxygen species prompts cells to react with greater repair and maintenance efforts. Alterations to the Mechanistic target of rapamycin (mTOR) gene and levels of protein produced have been shown to modestly extend life span in several species. There are also a few synergistic genetic alterations involving mTOR and other genes discovered in lower animals that produce much larger effects. The mTOR protein is involved in many fundamental cellular processes, like many of the longevity-associated genes in laboratory species, and produces fairly sweeping alterations in cellular metabolism. Reduced myostatin produces increased muscle growth, which may be a useful compensation for the loss of muscle mass and strength that occurs with aging. As a result of a number of natural animal lineages with this mutation, myostatin knockout is by far the most examined and tested of all potential gene therapies. There have been human trials of myostatin blockade via antibodies, for example, and there are even a few well-muscled natural human myostatin loss of function mutants. Higher levels of NAD-dependent methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase (NMDMC) have been shown to modestly slow aging in flies, most likely through improved mitochondrial function. Inhibition of NF-κB extends life modestly in a number of lower species, though given its involvement in immunity, inflammation, apoptosis, and other fundamental processes. Increased levels of NRF2 in mice or its homolog SKN-1 in nematodes results in slower aging and modestly extended life spans—normally NRF2 levels decline with age. This can be achieved by manipulation of the levels of other, interacting proteins such as glutathione transferase (gGsta4). The mechanism of action here is thought to involve resistance to oxidative damage and increased quality control of damaged proteins. Interestingly, long-lived naked mole rats exhibit high levels of NRF2. One of the target genes used in reprogramming cells into induced pluripotent stem cells is Oct4. It was recently found that Oct4 can act to stabilize plaques in atherosclerosis to make the disease less deadly. P16 is perhaps best known as an indicator of cellular senescence, a part of the mechanisms that cause damaged cells or those at the Hayflick limit to become senescent or self-destruct. There are signs that targeted reductions in p16 levels can in some cases produce a net benefit, such as when used to make stem cell populations more active in old age. Both MRL mice and P21 knockout mice can regenerate small injuries with no scarring, something that most other mammals cannot achieve, and reduced levels of the p21 protein seems to be the common factor in these engineered mouse lineages. The protein p53 plays the role of tumor suppressor, but creating a general increase in p53 levels will, in addition to reducing cancer incidence, also accelerate aging by reducing tissue maintenance through the creation of new cells. There are, however, a number of ways in which p53 levels can be increased only when needed. One involves reduced levels of mdm2, a p53 inhibitor. Another involves an additional copy of the p53 gene, inserted without disrupting the existing regulatory process that manages p53 levels. In the latter case, engineered mice live modestly longer thanks to a lower rate of cancer. An increased level of parkin is one of the ways in which greater cell maintenance via autophagy can be induced, resulting in improved health and modestly extended life spans. There is a lot of support in the literature for more autophagy as an unalloyed good when it comes to health and aging. Many methods of extending life in laboratory species are associated with increased autophagy, and in some cases—such as calorie restriction—that autophagy has been shown to be necessary for life extension. Loss of function mutations in PCSK9 reduce the risk of cardiovascular disease, most likely through lowered blood cholesterol levels. Proof of principle studies have been carried out in mice. Deletion of the PER2 gene in mice, associated with the mechanisms of circadian rhythm, appears to improve DNA repair in stem cell populations relevant to the immune system, resulting in a healthier immune cell population, better immune function in old age, and a modestly extended life span. Increased levels of PGC-1 in the intestinal tissues of flies extend life, possibly due to improved mitochondrial and stem cell function. Intestinal function is especially important as a determinant of fly aging and mortality, and many exploratory interventions target this organ. In mice, introducing a variant of PGC-1 produces enhanced muscle growth, most likely via its interaction with myostatin. The protein PHD1 serves as an oxygen sensor. Mice lacking this protein are protected from ischemic injury in stroke, suffering less cell death and recovering to a greater degree afterwards. Increased levels of PEPCK achieved through genetic engineering produces mice that are much more energetic, eat more, but are also modestly longer lived than their unmodified counterparts. Overexpression of PIM1 in the heart produces mice that live longer by improving the ability of heart tissue to repair and maintain itself. Reducing levels of plasminogen activator inhibitor-1 appears to modestly slow aging, possibly by removing one aspect of the harmful impact of senescent cells. Knockout of pregnancy-associated plasma protein-A (PAPP-A) gene interferes with insulin metabolism, and produces a similar extension of health and life in mice when compared with other methods of achieving this end. Adding an extra copy of the tumor suppressor gene PTEN to mice produces lower rates of cancer, much as expected, but also increased life span. Levels of RbAp48 fall with age in the hippocampus. Researchers have demonstrated that targeted restoration of youthful levels of this protein in old mice reversed a large fraction of age-related decline in memory function. Lowered levels of RTN4R can increase plasticity in the adult brain in mice, improving recovery from brain injury and increasing the ability to learn new tasks. This appears to be a part of the mechanism by which plasticity is dialed down after childhood. A reduction in Rpd3 level produces improved cardiac function and modestly increased longevity in flies, though the mechanism of action remains to be explored in more detail. Increased levels of either SERCA2a/SUMO-1 can produce greater beneficial remodeling of blood vessels and heart tissue than would normally take place, and is thus a potential compensatory therapy that might slow the progression of many cardiovascular and circulatory diseases. Increased levels of telomerase have been shown to extend life in mice, as well as reducing cancer incidence in that species. TGF-β1 expression rises with age, and is implicated in loss of stem cell function. Interfering in this pathway via any of the related proteins so as to reduce TGF-β1 levels may be a viable way to increase stem cell activity in later life. Increased activation of Transcription factor EB (TFEB) spurs greater autophagy and so helps to ensure better maintenance of cells. Higher levels of autophagy seem to be an unalloyed good in near all situations, and appear as a feature of many of the ways of modestly slowing aging in laboratory species. Researchers have shown that delivering a modified version of the calcium receptor troponin C into the mammalian heart can improve heart function and the performance of the cardiovascular system. Gene knockout of the pain receptor TRPV1 is one of a number of methods of slowing aging and extending life in mice that appears to work through altered insulin signaling. Another potential mechanism is that this gene knockout blocks the interaction between pain receptors and chronic inflammation, a process that is thought to cause harm in old tissues and organs. Uncoupling proteins manipulate mitochondrial function in order to regulate body heat. As is the case for many proteins that interact with mitochondrial function, altered levels or genetic variants can improve health and longevity. The UMUPA mouse lineage has the addition of a urokinase gene and has a longer life span as a result. The uPA gene is related to PAI-1, also in this list, and is argued to achieve life extension in mice through behavioral change—these mice eat less, and thus the calorie restriction response comes into play. A number of research and development efforts have focused on delivery of VEGF to spur regeneration in the cardiovascular system, and particularly in the heart, an organ with only limited regenerative capacity in mammals. One of the more effective of these attempts in rodents used a mix of VEGF, Gata4, Mef 2c, and Tbx5 to encourage scar tissue in the heart to change itself into healthy tissue.
The foregoing therapeutic modalities are illustrative and non-limiting. These interventions and numerous others can be facilitated by using the multi-arm polyrotaxane carriers described herein for the delivery of the relevant nucleic acid construct(s).
The CRISPR/Cas System—Class 2 CRISPR/Cas Endonucleases
As noted above, the polyrotaxane (PRX) carriers described herein are particularly well suited for the in vivo delivery of large nucleic acid including, but not limited to plasmids. In certain embodiments the plasmid can encode a heterologous gene, or other nucleic acid construct (e.g., an antisense molecule, a ribozyme, etc.).
In certain embodiments, the plasmid or RNA can encode components of a CRISPR/Cas system (e.g., Class 2 CRISPR/Cas endonuclease and one or more guide RNAs) as illustrated in the proofs of principle shown herein. The plasmid(s) encoding the CRISPR/Cas system, when delivered to a cell in vivo using the polyrotaxane carriers described herein can be designed/exploited to introduce extremely specific alterations to the genomic DNA of the target cell(s).
Compelling evidence has recently emerged for the existence of an RNA-mediated genome defense pathway in archaea and many bacteria that has been hypothesized to parallel the eukaryotic RNAi pathway (for reviews, see Godde and Bickerton (2006) J. Mol. Evol. 62: 718-729; Lillestol et al. (2006) Archaea 2: 59-72; Makarova et al. (2006) Biol. Direct 1: 7.; Sorek et al. (2008) Nat. Rev. Microbiol. 6: 181-186). Known as the CRISPR-Cas system or prokaryotic RNAi (pRNAi), the pathway is believed to arise from two evolutionarily and often physically linked gene loci: the CRISPR (clustered regularly interspaced short palindromic repeats) locus, that encodes RNA components of the system, and the cas (CRISPR-associated) locus, that encodes proteins (see, e.g., Jansen et al. (2002) Mol. Microbiol. 43: 1565-1575; Makarova et al., (2002) Nucl. Acids Res. 30: 482-496; Makarova et al. (2006) Biol. Direct 1: 7; Haft et al. (2005) PLoS Comput. Biol. 1: e60). CRISPR loci in microbial hosts contain a combination of CRISPR-associated (Cas) genes as well as non-coding RNA elements capable of programming the specificity of the CRISPR-mediated nucleic acid cleavage. The individual Cas proteins do not share significant sequence similarity with protein components of the eukaryotic RNAi machinery, but have analogous predicted functions (e.g., RNA binding, nuclease, helicase, etc.) (see, e.g., Makarova et al. (2006) Biol. Direct 1: 7). The CRISPR-associated (cas) genes are often associated with CRISPR repeat-spacer arrays. More than forty different Cas protein families have been described. Of these protein families, Cas1 appears to be ubiquitous among different CRISPR/Cas systems. Particular combinations of cas genes and repeat structures have been used to define 8 CRISPR subtypes (Ecoli, Ypest, Nmeni, Dvulg, Tneap, Hmari, Apern, and Mtube), some of which are associated with an additional gene module encoding repeat-associated mysterious proteins (RAMPs). More than one CRISPR subtype may occur in a single genome. The sporadic distribution of the CRISPR/Cas subtypes suggests that the system is subject to horizontal gene transfer during microbial evolution.
In class 2 CRISPR systems, the functions of the effector complex (e.g., the cleavage of target DNA) can be carried out by a single endonuclease (see, e.g., Zetsche et al. (2015) Cell, 163(3): 759-771; Makarova et al. (2015) Nat. Rev. Microbiol. 13(11): 722-736; Shmakov et al. (2015) Mol. Cell. 60(3): 385-397; and the like). As such, the term “class 2 CRISPR/Cas protein” is used herein to encompass the endonuclease (the target nucleic acid cleaving protein) from class 2 CRISPR systems. Thus, the term “class 2 CRISPR/Cas endonuclease” as used herein encompasses type II CRISPR/Cas proteins (e.g., Cas9), type V CRISPR/Cas proteins (e.g., Cpf1, C2c1, C2C3), and type VI CRISPR/Cas proteins (e.g., C2c2). To date, class 2 CRISPR/Cas proteins encompass type II, type V, and type VI CRISPR/Cas proteins, but the term is also meant to encompass any class 2 CRISPR/Cas protein suitable for binding to a corresponding guide RNA and forming an RNP complex (e.g., and cleaving target DNA).
Type II CRISPR/Cas Endonucleases (e.g., Cas 9)
In natural Type II CRISPR/Cas systems, Cas9 functions as an RNA-guided endonuclease that uses a dual-guide RNA having a crRNA and trans-activating crRNA (tracrRNA) for target recognition and cleavage by a mechanism involving two nuclease active sites in Cas9 that together generate double-stranded DNA breaks (DSBs), or can individually generate single-stranded DNA breaks (SSBs). The Type II CRISPR endonuclease Cas9 and engineered dual-(dgRNA) or single guide RNA (sgRNA) form a ribonucleoprotein (RNP) complex that can be targeted to a desired DNA sequence. Guided by a dual-RNA complex or a chimeric single-guide RNA, Cas9 generates site-specific DSBs or SSBs within double-stranded DNA (dsDNA) target nucleic acids, that are repaired either by non-homologous end joining (NHEJ) or homology-directed recombination (HDR).
In some cases, the plasmid or other therapeutic nucleic acid including RNA, mRNA, etc. complexed with and delivered by the polyrotaxane (PRX) carriers described herein encodes a Cas9 protein. A Cas9 protein forms a complex with a Cas9 guide RNA. The guide RNA provides target specificity to a Cas9-guide RNA complex by having a nucleotide sequence (a guide sequence) that is complementary to a sequence (the target site) of a target nucleic acid (as described elsewhere herein). The Cas9 protein of the complex provides the site-specific activity. In other words, the Cas9 protein is guided to a target site (e.g., stabilized at a target site) within a target nucleic acid sequence (e.g. genomic DNA) by virtue of its association with the protein-binding segment of the Cas9 guide RNA.
In some cases, the CRISPR/Cas endonuclease (e.g., Cas9 protein) is a naturally-occurring protein (e.g., naturally occurs in bacterial and/or archaeal cells). In other cases, the CRISPR/Cas endonuclease (e.g., Cas9 protein) is not a naturally-occurring polypeptide (e.g., the CRISPR/Cas endonuclease is a variant CRISPR/Cas endonuclease, a chimeric protein, and the like, e.g., in some cases the CRISPR/Cas endonuclease includes one or more NLSs).
Examples of suitable Cas9 proteins include, but are not limited to, those set forth in SEQ ID NOs: 5-816 of PCT Application No: PCT/US2017/017255 (WO 2017/139505), which are incorporated herein by reference for the sequences described therein. Naturally occurring Cas9 proteins bind a Cas9 guide RNA, are thereby directed to a specific sequence within a target nucleic acid (a target site), and cleave the target nucleic acid (e.g., cleave dsDNA to generate a double strand break). A chimeric Cas9 protein is a fusion protein comprising a Cas9 polypeptide that is fused to a heterologous protein (referred to as a fusion partner), where the heterologous protein provides an activity (e.g., one that is not provided by the Cas9 protein). The fusion partner can provide an activity, e.g., enzymatic activity (e.g., nuclease activity, activity for DNA and/or RNA methylation, activity for DNA and/or RNA cleavage, activity for histone acetylation, activity for histone methylation, activity for RNA modification, activity for RNA-binding, activity for RNA splicing etc.). In some cases, a portion of the Cas9 protein (e.g., the RuvC domain and/or the HNH domain) exhibits reduced nuclease activity relative to the corresponding portion of a wild type Cas9 protein (e.g., in some cases the Cas9 protein is a nickase). In some cases, the Cas9 protein is enzymatically inactive, or has reduced enzymatic activity relative to a wild-type Cas9 protein (e.g., relative to Streptococcus pyogenes Cas9). In some cases, the Cas9 protein is enzymatically enhanced, e.g., or has enhanced enzymatic activity and/or specificity relative to a wild-type Cas9 protein (e.g., relative to Streptococcus pyogenes Cas9).
Assays to determine whether given protein interacts with a Cas9 guide RNA can be any convenient binding assay that tests for binding between a protein and a nucleic acid. Suitable binding assays (e.g., gel shift assays) will be known to one of ordinary skill in the art (e.g., assays that include adding a Cas9 guide RNA and a protein to a target nucleic acid).
Assays to determine whether a protein has an activity (e.g., to determine if the protein has nuclease activity that cleaves a target nucleic acid and/or some heterologous activity) can be any convenient assay (e.g., any convenient nucleic acid cleavage assay that tests for nucleic acid cleavage). Suitable assays (e.g., cleavage assays) will be known to one of ordinary skill in the art and can include adding a Cas9 guide RNA and a protein to a target nucleic acid.
In some cases, a chimeric Cas9 protein includes a heterologous polypeptide that has enzymatic activity that modifies a target nucleic acid (e.g., nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity or glycosylase activity).
In some cases, a chimeric Cas9 protein includes a heterologous polypeptide that has enzymatic activity that modifies a polypeptide (e.g., a histone) associated with target nucleic acid (e.g., methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, u biquitin ligase activity, deu biquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity or demyristoylation activity).
In some cases, a CRISPR/Cas endonuclease (e.g., a Cas9 protein) includes a heterologous polypeptide that provides for localization within the cell. For example, in some cases, a subject CRISPR/Cas endonuclease (e.g., a Cas9 protein) includes one or more (e.g., 2 or more, 3 or more, 4 or more, 5 or more, etc.) nuclear localization sequences (NLSs). The one or more (e.g., 2 or more, 3 or more, 4 or more, 5 or more, etc.) NLSs can be at any convenient position within the CRISPR/Cas endonuclease (e.g., a Cas9 protein), e.g., N-terminus, C-terminus, internal, etc. In some cases, a CRISPR/Cas endonuclease (e.g., a Cas9 protein) includes one or more (e.g., 2 or more, 3 or more, 4 or more, 5 or more, etc.) NLSs at the N-terminus and one or more (e.g., 2 or more, 3 or more, 4 or more, 5 or more, etc.) NLSs at the C-terminus.
Many Cas9 orthologs from a wide variety of species have been identified and in some cases the proteins share only a few identical amino acids. Identified Cas9 orthologs have similar domain architecture with a central HNH endonuclease domain and a split RuvC/RNaseH domain (e.g., RuvCI, RuvCII, and RuvCIII) (e.g., see Table 3). For example, a Cas9 protein can have 3 different regions (sometimes referred to as RuvC-I, RuvC-11, and RucC-III), that are not contiguous with respect to the primary amino acid sequence of the Cas9 protein, but fold together to form a RuvC domain once the protein is produced and folds. Thus, Cas9 proteins can be said to share at least 4 key motifs with a conserved architecture. Motifs 1, 2, and 4 are RuvC like motifs while motif 3 is an HNH-motif. The motifs set forth in Table 3 may not represent the entire RuvC-like and/or HNH domains as accepted in the art, but Table 3 does present motifs that can be used to help determine whether a given protein is a Cas9 protein.







TABLE 3







Four 4 motifs that are present in Cas9


sequences from various species. The amino


acids listed in Table 1 are from the Cas9


from S. pyogenes (SEQ ID NO: 309, see also


SEQ ID NO: 5 in PCT/US2017/017255).










Motif

Amino acids
Highly


#
Motif
(residue #s)
conserved





1
RuvC-like I
IGLDIGTNSVGWAVI
D10, G12,




(7-21)
G17




(SEQ ID NO: 12)



 


2
RuvC-like II
IVIEMARE (757-766)
E762




(SEQ ID NO: 13)



 


3
HNH-motif
DVDHIVPQSFLKDDSIDN
H840, N854,




KVLTRSDKN (887-863)
N863




(SEQ ID NO: 14)



 


4
RuvC-like III
HHAHDAYL (982-989)
H982, H983,




(SEQ ID NO: 15)
A984, D986,





A987









In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 99% or more or 100% amino acid sequence identity to motifs 1-4 as set forth in SEQ ID NOs: 12-15, respectively (e.g., see Table 3), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 5-816 in PCT/US2017/017255).
In other words, in some cases, a suitable Cas9 polypeptide comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 99% or more or 100% amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth in SEQ ID NO:309 (see also SEQ ID NO:5 in PCT/US2017/017255) (e.g., the sequences set forth in SEQ ID NOs: 12-15, e.g., see Table 3), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs 6-816 in PCT/US2017/017255.
In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 60% or more amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 70% or more amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 75% or more amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 80% or more amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 85% or more amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 90% or more amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 95% or more amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 99% or more amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 4 motifs, each of motifs 1-4 having 100% amino acid sequence identity to motifs 1-4 of the Cas9 amino acid sequence set forth as SEQ ID NO:309 (the motifs are in Table 3, and are set forth as SEQ ID NOs: 12-15, respectively), or to the corresponding portions in any of the amino acid sequences set forth in SEQ ID NOs: 6-816 in PCT/US2017/017255. Any Cas9 protein as defined above can be used as a Cas9 polypeptide, as part of a chimeric Cas9 polypeptide (e.g., a Cas9 fusion protein), any of which can be used in an RNP of the present disclosure.
In some cases, a suitable Cas9 protein comprises an amino acid sequence having 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 99% or more or 100% amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255.
In some cases, a suitable Cas9 protein comprises an amino acid sequence having 60% or more amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 70% or more amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 75% or more amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 80% or more amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 85% or more amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 90% or more amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 95% or more amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 99% or more amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 100% amino acid sequence identity to amino acids 7-166 or 731-1003 of the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. Any Cas9 protein as defined above can be used as a Cas9 polypeptide, as part of a chimeric Cas9 polypeptide (e.g., a Cas9 fusion protein), any of which can be used in an RNP of the present disclosure.
In some cases, a suitable Cas9 protein comprises an amino acid sequence having 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 99% or more or 100% amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255.
In some cases, a suitable Cas9 protein comprises an amino acid sequence having 60% or more amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 70% or more amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 75% or more amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 80% or more amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 85% or more amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 90% or more amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 95% or more amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 99% or more amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. In some cases, a suitable Cas9 protein comprises an amino acid sequence having 100% amino acid sequence identity to the Cas9 amino acid sequence set forth in SEQ ID NO:309, or to any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255. Any Cas9 protein as defined above can be used as a Cas9 polypeptide, as part of a chimeric Cas9 polypeptide (e.g., a Cas9 fusion protein), any of which can be used in an RNP of the present disclosure.
In some cases, a Cas9 protein comprises 4 motifs (as listed in Table 1), at least one with (or each with) amino acid sequences having 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 99% or more or 100% amino acid sequence identity to each of the 4 motifs listed in Table 1 (SEQ ID NOs: 12-15), or to the corresponding portions in any of the amino acid sequences set forth as SEQ ID NOs: 6-816 in PCT/US2017/017255.
In some cases, a Cas9 protein is a high fidelity Cas9 protein (see, e.g., Kleinstiver et al. (2016) Nature, 529(7587): 490-495).
In some cases, a suitable Cas9 protein is a Cas9 protein as described in Slaymaker et al. (2016) Science 351: 84. For example, a suitable Cas9 protein can include a Streptococcus pyogenes Cas9 with substitutions of one or more of K810, K848, K855, K1003, and R1060 (where the amino acid numbering is based on the numbering set out in SEQ ID NO:309 (SEQ ID No:5 in PCT/US2017/017255)). For example, a suitable Cas9 protein includes a Streptococcus pyogenes Cas9 with K810A, K1003A, and R1060A substitutions (where the amino acid numbering is based on the numbering set out in SEQ ID NO:309 (SEQ ID No:5 in PCT/US2017/017255)). As another example, a suitable Cas9 protein includes a Streptococcus pyogenes Cas9 with K848A, K1003A, and R060A substitutions (where the amino acid numbering is based on the numbering set out in SEQ ID N0:5). As another example, a suitable Cas9 protein includes a Streptococcus pyogenes Cas9 with a K855A substitution (where the amino acid numbering is based on the numbering set out in SEQ ID NO:309 (SEQ ID No:5 in PCT/US2017/017255).
Type V and Type VI CRISPR/Cas Endonucleases
In certain embodiments the plasmid(s) complexed with the PRX carriers described herein encode a type V or type VI CRISPR/Cas endonuclease (e.g., Cpf1, C2c1, C2c2, C2c3) and associated guide RNA(s). Type V and type VI CRISPR/Cas endonucleases are a type of class 2 CRISPR/Cas endonuclease. Examples of type V CRISPR/Cas endonucleases include, but are not limited to, Cpf1, C2c1, and C2c3. An example of a type VI CRISPR/Cas endonuclease is C2c2. In some cases, the plasmid encodes a type V CRISPR/Cas endonuclease (e.g., Cpf1, C2c1, C2c3). In some cases, a Type V CRISPR/Cas endonuclease is a Cpf1 protein. In some cases, the plasmid encodes a type VI CRISPR/Cas endonuclease (e.g., C2c2).
Like type II CRISPR/Cas endonucleases, type V and VI CRISPR/Cas endonucleases form a complex with a corresponding guide RNA. The guide RNA provides target specificity to an endonuclease-guide RNA RNP complex by having a nucleotide sequence (a guide sequence) that is complementary to a sequence (the target site) of a target nucleic acid (as described elsewhere herein). The endonuclease of the complex provides the site-specific activity. In other words, the endonuclease is guided to a target site (e.g., stabilized at a target site) within a target nucleic acid sequence (e.g. genomic DNA) by virtue of its association with the protein-binding segment of the guide RNA.
Examples and guidance related to type V and type VI CRISPR/Cas proteins (e.g., cpf1, C2c1, C2c2, and C2c3 guide RNAs) can be found in the art (see, e.g., Zetsche et al. (2015) Cell, 163(3):759-771; Makarova et al. (2015) Nat. Rev. Microbiol. 13(11): 722-736; Shmakov et al. (2015) Mol. Cell, 60(3): 385-397; and the like).
In some cases, the Type V or type VI CRISPR/Cas endonuclease (e.g., Cpf1, C2c1, C2c2, C2c3) is enzymatically active, e.g., the Type V or type VI CRISPR/Cas polypeptide, when bound to a guide RNA, cleaves a target nucleic acid. In some cases, the Type V or type VI CRISPR/Cas endonuclease (e.g., Cpf1, C2c1, C2c2, C2c3) exhibits reduced enzymatic activity relative to a corresponding wild-type a Type V or type VI CRISPR/Cas endonuclease (e.g., Cpf1, C2c1, C2c2, C2c3), and retains DNA binding activity (e.g., in some cases the endonuclease is a nickase).
In some cases a type V CRISPR/Cas endonuclease is a Cpf1 protein. In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314 (SEQ ID NOs: 1088-1092 in PCT/US2017/017255). In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to a contiguous stretch of from 100 amino acids to 200 amino acids (aa), from 200 aa to 400 aa, from 400 aa to 600 aa, from 600 aa to 800 aa, from 800 aa to 1000 aa, from 1000 aa to 1100 aa, from 1100 aa to 1200 aa, or from 1200 aa to 1300 aa, of the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314.
In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvC1 domain of the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314. In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCII domain of the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314. In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCIII domain of the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314. In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCI, RuvCII, and RuvCIII domains of the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314.
In some cases, the Cpf1 protein exhibits reduced enzymatic activity relative to a wild-type Cpf1 protein (e.g., relative to a Cpf1 protein comprising the amino acid sequence set forth in any of SEQ ID NOs: 310-314), and retains DNA binding activity. In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314; and comprises an amino acid substitution (e.g., a D→A substitution) at an amino acid residue corresponding to amino acid 917 of the Cpf1 amino acid sequence set forth in SEQ ID NO:310. In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314; and comprises an amino acid substitution (e.g., an E→A substitution) at an amino acid residue corresponding to amino acid 1006 of the Cpf1 amino acid sequence set forth in SEQ ID NO:310. In some cases, a Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314; and comprises an amino acid substitution (e.g., a D→A substitution) at an amino acid residue corresponding to amino acid 1255 of the Cpf1 amino acid sequence set forth in SEQ ID NO:310.
In some cases, a suitable Cpf1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the Cpf1 amino acid sequence set forth in any of SEQ ID NOs: 310-314.
In some cases a type V CRISPR/Cas endonuclease is a C2c1 protein (examples include those set forth as SEQ ID NOs: 315-322 (SEQ ID NOs: 1112-1119 in PCT/US2017/017255). In some cases, a C2c1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the C2c1 amino acid sequence set forth in any of SEQ ID NOs: 315-322. In some cases, a C2c1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to a contiguous stretch of from 100 amino acids to 200 amino acids (aa), from 200 aa to 400 aa, from 400 aa to 600 aa, from 600 aa to 800 aa, from 800 aa to 1000 aa, from 1000 aa to 1100 aa, from 1100 aa to 1200 aa, or from 1200 aa to 1300 aa, of the C2c1 amino acid sequence set forth in any of SEQ ID NOs: 315-322.
In some cases, a C2c1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCI domain of the C2c1 amino acid sequences set forth in any of SEQ ID NOs: 315-322). In some cases, a C2c1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCII domain of the C2c1 amino acid sequence set forth in any of SEQ ID NOs: 315-322. In some cases, a C2c1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCIII domain of the C2c1 amino acid sequence set forth in any of SEQ ID NOs: 315-322. In some cases, a C2c1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCI, RuvCII, and RuvCIII domains of the C2c1 amino acid sequence set forth in any of SEQ ID NOs: 315-322.
In some cases, the C2c1 protein exhibits reduced enzymatic activity relative to a wild-type C2c1 protein (e.g., relative to a C2c1 protein comprising the amino acid sequence set forth in any of SEQ ID NOs: 315-322), and retains DNA binding activity. In some cases, a suitable C2c1 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the C2c1 amino acid sequence set forth in any of SEQ ID NOs: 315-322.
In some cases a type V CRISPR/Cas endonuclease is a C2c3 protein (examples include those set forth as SEQ ID NOs: 323-326 (SEQ ID NOs: 1120-1123 in pCT/US2017/017255). In some cases, a C2c3 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the C2c3 amino acid sequence set forth in any of SEQ ID NOs: 323-326. In some cases, a C2c3 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to a contiguous stretch of from 100 amino acids to 200 amino acids (aa), from 200 aa to 400 aa, from 400 aa to 600 aa, from 600 aa to 800 aa, from 800 aa to 1000 aa, from 1000 aa to 1100 aa, from 1100 aa to 1200 aa, or from 1200 aa to 1300 aa, of the C2c3 amino acid sequence set forth in any of SEQ ID NOs: 323-326.
In some cases, a C2c3 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCI domain of the C2c3 amino acid sequence set forth in any of SEQ ID NOs: 323-326. In some cases, a C2c3 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCII domain of the C2c3 amino acid sequence set forth in any of SEQ ID NOs: 323-326. In some cases, a C2c3 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCIII domain of the C2c3 amino acid sequence set forth in any of SEQ ID NOs: 323-326. In some cases, a C2c3 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCI, RuvCII, and RuvCIII domains of the C2c3 amino acid sequence set forth in any of SEQ ID NOs: 323-326.
In some cases, the C2c3 protein exhibits reduced enzymatic activity relative to a wild-type C2c3 protein (e.g., relative to a C2c3 protein comprising the amino acid sequence set forth in any of SEQ ID NOs: 323-326), and retains DNA binding activity. In some cases, a suitable C2c3 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the C2c3 amino acid sequence set forth in any of SEQ ID NOs: 323-326.
In some cases a type VI CRISPR/Cas endonuclease is a C2c2 protein (examples include those set forth as SEQ ID NOs: 327-338 (SEQ ID NOs: 1124-1135 in PCT/US2017/017255). In some cases, a C2c2 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the C2c2 amino acid sequence set forth in any of SEQ ID NOs: 327-338. In some cases, a C2c2 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to a contiguous stretch of from 100 amino acids to 200 amino acids (aa), from 200 aa to 400 aa, from 400 aa to 600 aa, from 600 aa to 800 aa, from 800 aa to 1000 aa, from 1000 aa to 1100 aa, from 1100 aa to 1200 aa, or from 1200 aa to 1300 aa, of the C2c2 amino acid sequence set forth in any of SEQ ID NOs: 327-338.
In some cases, a C2c2 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCI domain of the C2c2 amino acid sequence set forth in any of SEQ ID NOs: 327-338. In some cases, a C2c2 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCII domain of the C2c2 amino acid sequence set forth in any of SEQ ID NOs: 327-338. In some cases, a C2c2 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCIII domain of the C2c2 amino acid sequence set forth in any of SEQ ID NOs: 1124-1135. In some cases, a C2c2 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the RuvCI, RuvCII, and RuvCIII domains of the C2c2 amino acid sequence set forth in any of SEQ ID NOs: 327-338.
In some cases, the C2c2 protein exhibits reduced enzymatic activity relative to a wild-type C2c2 protein (e.g., relative to a C2c2 protein comprising the amino acid sequence set forth in any of SEQ ID NOs: 327-338), and retains DNA binding activity. In some cases, a suitable C2c2 protein comprises an amino acid sequence having 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%, at least 90%, or 100%, amino acid sequence identity to the C2c2 amino acid sequence set forth in any of SEQ ID NOs: 327-338.
PAM Sequence
A wild type class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) normally has nuclease activity that cleaves a target nucleic acid (e.g., a double stranded DNA (dsDNA)) at a target site defined by complementarity between the guide sequence of the CRISPR/Cas guide RNA and the target nucleic acid. In some cases, site-specific cleavage of the target nucleic acid occurs at locations determined by both (i) base-pairing complementarity between the CRISPR/Cas guide RNA and the target nucleic acid; and (ii) a short motif referred to as the protospacer adjacent motif (PAM) in the target nucleic acid. For example, when the class 2 CRISPR/Cas endonuclease is a wild type Cas9 protein, the PAM sequence that is recognized (e.g., bound) by the Cas9 protein is present on the non-complementary strand (the strand that does not hybridize with the guide sequence of the Cas9 guide RNA) of the target DNA and is adjacent to the target site.
In some cases, (e.g., in some cases where the class 2 CRISPR/Cas endonuclease is an S. pyogenes Cas9 protein) the PAM sequence of the non-complementary strand is 5′-XGG-3′, where X is any DNA nucleotide and Xis immediately 3′ of the target sequence of the non-complementary strand of the target DNA. As such, the sequence of the complementary strand that hybridizes with the PAM sequence is 5′-CCY-3′, where Y is any DNA nucleotide and Y is immediately 5′ of the target sequence of the complementary strand of the target DNA. In some such embodiments, X and Y can be complementary and the X-Y base pair can be any base pair (e.g., X═C and Y=G; X=G and Y═C; X=A and Y=T, X=T and Y=A).
In some cases, it may be advantageous to use plasmids encoding different class 2 CRISPR/Cas endonucleases (e.g., Cas9 proteins from various species, type V or type VI CRISPR/Cas endonucleases, and the like) for the subject methods in order to capitalize on various characteristics (e.g., enzymatic characteristics) of the different endonucleases (e.g., for different PAM sequence preferences; for increased or decreased enzymatic activity; for an increased or decreased level of cellular toxicity; to change the balance between NHEJ, homology-directed repair, single strand breaks, double strand breaks, etc.).
Class 2 CRISPR/Cas endonucleases (e.g., Cas9 proteins) from various species can require different PAM sequences in the target DNA, and different types of Class 2 CRISPR/Cas endonucleases (e.g., type II proteins, e.g., Cas9 proteins; type V proteins; type VI proteins; and the like) can have different requirements (e.g., 5′, 3′, complementary strand, non-complementary strand, distance from target sequence, and the like) for the location of the PAM sequence relative to the targeted sequence of the target DNA. Thus, for a particular Class 2 CRISPR/Cas endonuclease of choice, the PAM sequence requirement may be different than the 5′-XGG-3′ sequence described above for the S. pyogenes Cas9 protein.
In some embodiments (e.g., when the Cas9 protein is derived from S. pyogenes or a closely related Cas9 is used), a PAM sequence can be can be 5′-NGG-3′, where N is any nucleotide (see, e.g., Chylinski et al. (2013) RNA Biol. 10(5): 726-737; Jinek et al. (2012) Science, 337(6096): 816-821; and the like). In some embodiments (e.g., when a Cas9 protein is derived from the Cas9 protein of Neisseria meningitidis or a closely related Cas9 is used), the PAM sequence can be 5′-NNNNGANN-3′, 5′-NNNNGTTN-3′, 5′-NNNNGNNT-3′, 5′-NNNNGTNN-3′, 5′-NNNGNTN-3′, or 5′-NNNNGATT-3′, where N is any nucleotide. In some embodiments (e.g., when a Cas9 protein is derived from Streptococcus thermophilus #1 or a closely related Cas9 is used), the PAM sequence can be 5′-NNAGAA-3′, 5′-NNAGGA-3′, 5′-NNGGAA-3′, 5′-NNANAA-3′, or 5′-NNGGGA-3′ where N is any nucleotide. In some embodiments (e.g., when a Cas9 protein is derived from Treponema denticola (TD) or a closely related Cas9 is used), the PAM sequence can be 5′-NAAAAN-3′, 5′-NAAAAC-3′, 5′-NAAANC-3′, 5′-NANAAC-3′, or 5′-NNAAAC-3′, where N is any nucleotide.
The PAM requirements for any given Class 2 CRISPR/Cas endonuclease can be determined using standard, routine, conventional methods, which can include experimental methods and/or in silica analysis of naturally existing sequences from species of interest. For example, as would be known by one of ordinary skill in the art, additional PAM sequences for other Class 2 CRISPR/Cas endonucleases (e.g., Cas9 proteins of different species; type IV CRISPR/Cas endonucleases, type V CRISPR/Cas endonucleases, and the like) can readily be determined using bioinformatic analysis (e.g., analysis of genomic sequencing data) (see, e.g., Mojica et al. (2009) Microbiology, 155(Pt 3): 733-740; Esvelt et al. (2013) Nat. Meth. 10(11): 1116-11121; and the like).
In addition, as known in the art, the PAM-interacting domain of a Class 2 CRISPR/Cas endonuclease (e.g., a Cas9 protein) can be derived from an endonuclease (e.g., Cas9 protein) from a first species, and the PAM sequence can correspond to that domain. Thus, in some cases, a Class 2 CRISPR/Cas endonuclease has a PAM-interacting domain that is derived from (e.g., that is from) a Class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) of a first species, and other portions of the Class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) can be derived from (e.g., can be from) a second species.
Guide RNA (for CRISPR/Cas Endonucleases)
A nucleic acid molecule that binds to a class 2 CRISPR/Cas endonuclease (e.g., a Cas9 protein; a type V or type VI CRISPR/Cas protein; a Cpf1 protein; etc.) and targets the complex to a specific location within a target nucleic acid is referred to as a “guide RNA” or “CRISPR/Cas guide nucleic acid” or “CRISPR/Cas guide RNA.”
A guide RNA provides target specificity to the complex (the RNP complex) by including a targeting segment, which includes a guide sequence (also referred to herein as a targeting sequence), which is a nucleotide sequence that is complementary to a sequence of a target nucleic acid.
A guide RNA can be referred to by the protein to which it corresponds. For example, when the class 2 CRISPR/Cas endonuclease is a Cas9 protein, the corresponding guide RNA can be referred to as a “Cas9 guide RNA.” Likewise, as another example, when the class 2 CRISPR/Cas endonuclease is a Cpf1 protein, the corresponding guide RNA can be referred to as a “Cpf1 guide RNA.”
In some embodiments, a guide RNA includes two separate nucleic acid molecules: an “activator” and a “targeter” and is referred to as a “dual guide RNA”, a “double-molecule guide RNA”, a “two-molecule guide RNA”, or a “dgRNA.” In some embodiments, the guide RNA is one molecule (e.g., for some class 2 CRISPR/Cas proteins, the corresponding guide RNA is a single molecule; and in some cases, an activator and targeter are covalently linked to one another, e.g., via intervening nucleotides), and the guide RNA is referred to as a “single guide RNA”, a “single-molecule guide RNA,” a “one-molecule guide RNA”, or simply “sgRNA.”
Cas9 Guide RNA
A nucleic acid molecule that binds to a Cas9 protein and targets the complex to a specific location within a target nucleic acid is referred to herein as a “Cas9 guide RNA. A Cas9 guide RNA (can be said to include two segments, a first segment (referred to herein as a “targeting segment”); and a second segment (referred to herein as a “protein-binding segment”). By “segment” it is meant a segment/section/region of a molecule, e.g., a contiguous stretch of nucleotides in a nucleic acid molecule. A segment can also mean a region/section of a complex such that a segment may comprise regions of more than one molecule.
The first segment (targeting segment) of a Cas9 guide RNA includes a nucleotide sequence (a guide sequence) that is complementary to (and therefore hybridizes with) a specific sequence (a target site) within a target nucleic acid (e.g., a target genomic DNA). The protein-binding segment (or “protein-binding sequence”) interacts with (binds to) a Cas9 polypeptide. The protein-binding segment of a subject Cas9 guide RNA includes two complementary stretches of nucleotides that hybridize to one another to form a double stranded RNA duplex (dsRNA duplex). Site-specific binding and/or cleavage of a target nucleic acid (e.g., genomic DNA) can occur at locations (e.g., target sequence of a target locus, e.g., introns 44 and 55 of the human dystrophin gene) determined by base-pairing complementarity between the Cas9 guide RNA (the guide sequence of the Cas9 guide RNA) and the target nucleic acid.
A Cas9 guide RNA and a Cas9 protein form a complex (e.g., bind via non-covalent interactions). The Cas9 guide RNA provides target specificity to the complex by including a targeting segment, which includes a guide sequence (a nucleotide sequence that is complementary to a sequence of a target nucleic acid). The Cas9 protein of the complex provides the site-specific activity (e.g., cleavage activity). In other words, the Cas9 protein is guided to a target nucleic acid sequence (e.g. genomic DNA) by virtue of its association with the Cas9 guide RNA.
The “guide sequence” also referred to as the “targeting sequence” of a Cas9 guide RNA can be modified so that the Cas9 guide RNA can target a Cas9 protein to any desired sequence of any desired target nucleic acid, with the exception that the protospacer adjacent motif (PAM) sequence can be taken into account. Thus, for example, a Cas9 guide RNA can have a targeting segment with a sequence (a guide sequence) that has complementarity with (e.g., can hybridize to) a sequence in a nucleic acid in a eukaryotic cell (e.g., genomic DNA).
In some embodiments, a Cas9 guide RNA includes two separate nucleic acid molecules: an “activator” and a “targeter” and is referred to herein as a “dual Cas9 guide RNA”, a “double-molecule Cas9 guide RNA”, or a “two-molecule Cas9 guide RNA” a “dual guide RNA”, or a “dgRNA.” In some embodiments, the activator and targeter are covalently linked to one another (e.g., via intervening nucleotides) and the guide RNA is referred to as a “single guide RNA”, a “Cas9 single guide RNA”, a “single-molecule Cas9 guide RNA,” or a “one-molecule Cas9 guide RNA”, or simply “sgRNA.”
A Cas9 guide RNA comprises a crRNA-like (“CRISPR RNA” I “targeter”/“crRNA”/“crRNA repeat”) molecule and a corresponding tracrRNA-like (“trans-acting CRISPR RNA”/“activator” I “tracrRNA”) molecule. A crRNA-like molecule (targeter) comprises both the targeting segment (single stranded) of the Cas9 guide RNA and a stretch (“duplex-forming segment”) of nucleotides that forms one half of the dsRNA duplex of the protein-binding segment of the Cas9 guide RNA. A corresponding tracrRNA-like molecule (activator/tracrRNA) comprises a stretch of nucleotides (duplex-forming segment) that forms the other half of the dsRNA duplex of the protein-binding segment of the guide nucleic acid. In other words, a stretch of nucleotides of a crRNA-like molecule are complementary to and hybridize with a stretch of nucleotides of a tracrRNA-like molecule to form the dsRNA duplex of the protein-binding domain of the Cas9 guide RNA. As such, each targeter molecule can be said to have a corresponding activator molecule (which has a region that hybridizes with the targeter). The targeter molecule additionally provides the targeting segment. Thus, a targeter and an activator molecule (as a corresponding pair) hybridize to form a Cas9 guide RNA. The exact sequence of a given crRNA or tracrRNA molecule is characteristic of the species in which the RNA molecules are found. A subject dual Cas9 guide RNA can include any corresponding activator and targeter pair.
The term “activator” or “activator RNA” is used herein to mean a tracrRNA-like molecule (tracrRNA: “trans-acting CRISPR RNA”) of a Cas9 dual guide RNA (and therefore of a Cas9 single guide RNA when the “activator” and the “targeter” are linked together by, e.g., intervening nucleotides). Thus, for example, a Cas9 guide RNA (dgRNA or sgRNA) comprises an activator sequence (e.g., a tracrRNA sequence). A tracr molecule (a tracrRNA) is a naturally existing molecule that hybridizes with a CRISPR RNA molecule (a crRNA) to form a Cas9 dual guide RNA. The term “activator” is used herein to encompass naturally existing tracrRNAs, but also to encompass tracrRNAs with modifications (e.g., truncations, sequence variations, base modifications, backbone modifications, linkage modifications, etc.) where the activator retains at least one function of a tracrRNA (e.g., contributes to the dsRNA duplex to which Cas9 protein binds). In some cases the activator provides one or more stem loops that can interact with Cas9 protein. An activator can be referred to as having a tracr sequence (tracrRNA sequence) and in some cases is a tracrRNA, but the term “activator” is not limited to naturally existing tracrRNAs.
The term “targeter” or “targeter RNA” is used herein to refer to a crRNA-like molecule (crRNA: “CRISPR RNA”) of a Cas9 dual guide RNA (and therefore of a Cas9 single guide RNA when the “activator” and the “targeter” are linked together, e.g., by intervening nucleotides). Thus, for example, a Cas9 guide RNA (dgRNA or sgRNA) comprises a targeting segment (which includes nucleotides that hybridize with (are complementary to) a target nucleic acid, and a duplex-forming segment (e.g., a duplex forming segment of a crRNA, which can also be referred to as a crRNA repeat). Because the sequence of a targeting segment (the segment that hybridizes with a target sequence of a target nucleic acid) of a targeter is modified by a user to hybridize with a desired target nucleic acid, the sequence of a targeter will often be a non-naturally occurring sequence. However, the duplex-forming segment of a targeter (described in more detail below), which hybridizes with the duplex-forming segment of an activator, can include a naturally existing sequence (e.g., can include the sequence of a duplex-forming segment of a naturally existing crRNA, which can also be referred to as a crRNA repeat). Thus, the term targeter is used herein to distinguish from naturally occurring crRNAs, despite the fact that part of a targeter (e.g., the duplex-forming segment) often includes a naturally occurring sequence from a crRNA. However, the term “targeter” encompasses naturally occurring crRNAs.
A Cas9 guide RNA can also be said to include 3 parts: (i) a targeting sequence (a nucleotide sequence that hybridizes with a sequence of the target nucleic acid); (ii) an activator sequence (as described above)(in some cases, referred to as a tracr sequence); and (iii) a sequence that hybridizes to at least a portion of the activator sequence to form a double stranded duplex. A targeter has (i) and (iii); while an activator has (ii).
A Cas9 guide RNA (e.g. a dual guide RNA or a single guide RNA) can be comprised of any corresponding activator and targeter pair. In some cases, the duplex forming segments can be swapped between the activator and the targeter. In other words, in some cases, the targeter includes a sequence of nucleotides from a duplex forming segment of a tracrRNA (which sequence would normally be part of an activator) while the activator includes a sequence of nucleotides from a duplex forming segment of a crRNA (which sequence would normally be part of a targeter).
As noted above, a targeter comprises both the targeting segment (single stranded) of the Cas9 guide RNA and a stretch (“duplex-forming segment”) of nucleotides that forms one half of the dsRNA duplex of the protein-binding segment of the Cas9 guide RNA. A corresponding tracrRNA-like molecule (activator) comprises a stretch of nucleotides (a duplex-forming segment) that forms the other half of the dsRNA duplex of the protein-binding segment of the Cas9 guide RNA. In other words, a stretch of nucleotides of the targeter is complementary to and hybridizes with a stretch of nucleotides of the activator to form the dsRNA duplex of the protein-binding segment of a Cas9 guide RNA. As such, each targeter can be said to have a corresponding activator (which has a region that hybridizes with the targeter). The targeter molecule additionally provides the targeting segment. Thus, a targeter and an activator (as a corresponding pair) hybridize to form a Cas9 guide RNA. The particular sequence of a given naturally existing crRNA or tracrRNA molecule is characteristic of the species in which the RNA molecules are found. Examples of suitable activator and targeter are well known in the art.
A Cas9 guide RNA (e.g. a dual guide RNA or a single guide RNA) can be comprised of any corresponding activator and targeter pair. Non-limiting examples of nucleotide sequences that can be included in a Cas9 guide RNA (dgRNA or sgRNA) include sequences set forth in SEQ ID NOs: 827-1075 in PCT/US2017/017255, or complements thereof. For example, in some cases, sequences from SEQ ID NOs: 827-957 in PCT/US2017/017255 (which are from tracrRNAs) or complements thereof, can pair with sequences from SEQ ID NOs: 964-1075 in PCT/US2017/017255 (which are from crRNAs), or complements thereof, to form a dsRNA duplex of a protein binding segment. In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaataagg ctagtccgttatcaactt gaaaaagtggcac cgagtcggtgcTTTTTT (SEQ ID NO:16) (SEQ ID NO:1366 in PCT/US2017/017255), or guuuuagagcuaGAAAuagcaaguuaa aauaaggcuaguccguuaucaacuugaaa aaguggcaccgagucggug cUU UUUU (SEQ ID NO:17) (SEQ ID NO:1367 in PCT/US2017/017255).
Targeting Segment of a Cas9 Guide RNA
A subject guide RNA includes a guide sequence (i.e., a targeting sequence) (a nucleotide sequence that is complementary to a sequence (a target site) in a target nucleic acid). In other words, the targeting segment of a subject guide nucleic acid can interact with a target nucleic acid (e.g., double stranded DNA (dsDNA)) in a sequence-specific manner via hybridization (i.e., base pairing). As such, the nucleotide sequence of the targeting segment may vary (depending on the target) and can determine the location within the target nucleic acid that the Cas9 guide RNA and the target nucleic acid will interact. The targeting segment of a Cas9 guide RNA can be modified (e.g., by genetic engineering)/designed to hybridize to any desired sequence (target site) within a target nucleic acid (e.g., a eukaryotic target nucleic acid such as genomic DNA).
In various embodiments, the targeting segment can have a length of 7 or more nucleotides (nt) (e.g., 8 or more, 9 or more, 10 or more, 12 or more, 15 or more, 20 or more, or more, 30 or more, or 40 or more nucleotides). In some cases, the targeting segment can have a length of from 7 to 100 nucleotides (nt) (e.g., from 7 to 80 nt, from 7 to 60 nt, from 7 to 40 nt, from 7 to 30 nt, from 7 to 25 nt, from 7 to 22 nt, from 7 to 20 nt, from 7 to 18 nt, from 8 to 80 nt, from 8 to 60 nt, from 8 to 40 nt, from 8 to 30 nt, from 8 to 25 nt, from 8 to 22 nt, from 8 to 20 nt, from 8 to 18 nt, from 10 to 100 nt, from 10 to 80 nt, from 10 to 60 nt, from 10 to 40 nt, from 10 to 30 nt, from 10 to 25 nt, from 10 to 22 nt, from 10 to 20 nt, from 10 to 18 nt, from 12 to 100 nt, from 12 to 80 nt, from 12 to 60 nt, from 12 to 40 nt, from 12 to 30 nt, from 12 to 25 nt, from 12 to 22 nt, from 12 to 20 nt, from 12 to 18 nt, from 14 to 100 nt, from 14 to 80 nt, from 14 to 60 nt, from 14 to 40 nt, from 14 to 30 nt, from 14 to 25 nt, from 14 to 22 nt, from 14 to 20 nt, from 14 to 18 nt, from 16 to 100 nt, from 16 to 80 nt, from 16 to 60 nt, from 16 to 40 nt, from 16 to 30 nt, from 16 to 25 nt, from 16 to 22 nt, from 16 to 20 nt, from 16 to 18 nt, from 18 to 100 nt, from 18 to 80 nt, from 18 to 60 nt, from 18 to 40 nt, from 18 to 30 nt, from 18 to 25 nt, from 18 to 22 nt, or from 18 to 20 nt).
In various embodiments, the nucleotide sequence (the targeting sequence, the guide sequence) of the targeting segment that is complementary to a nucleotide sequence (target site) of the target nucleic acid can have a length of 10 nt or more. For example, the targeting sequence of the targeting segment that is complementary to a target site of the target nucleic acid can have a length of 12 nt or more, 15 nt or more, 17 nt or more, 18 nt or more, 19 nt or more, or 20 nt or more. In some cases, the nucleotide sequence (the targeting sequence) of the targeting segment that is complementary to a nucleotide sequence (target site) of the target nucleic acid has a length of 12 nt or more. In some cases, the nucleotide sequence (the targeting sequence) of the targeting segment that is complementary to a nucleotide sequence (target site) of the target nucleic acid has a length of 17 nt or more. In some cases, the nucleotide sequence (the targeting sequence) of the targeting segment that is complementary to a nucleotide sequence (target site) of the target nucleic acid has a length of 18 nt or more.
For example, in certain embodiments, the targeting sequence (guide sequence) of the targeting segment that is complementary to a target sequence of the target nucleic acid can have a length of from 10 to 100 nucleotides (nt) (e.g., from 10 to 90 nt, from 10 to 75 nt, from 10 to 60 nt, from 10 to 50 nt, from 10 to 35 nt, from 10 to 30 nt, from 10 to 25 nt, from 10 to 22 nt, from 10 to 20 nt, from 12 to 100 nt, from 12 to 90 nt, from 12 to 75 nt, from 12 to 60 nt, from 12 to 50 nt, from 12 to 35 nt, from 12 to 30 nt, from 12 to 25 nt, from 12 to 22 nt, from 12 to 20 nt, from 15 to 100 nt, from 15 to 90 nt, from 15 to 75 nt, from 15 to 60 nt, from 15 to 50 nt, from 15 to 35 nt, from 15 to 30 nt, from 15 to 25 nt, from 15 to 22 nt, from 15 to 20 nt, from 17 to 100 nt, from 17 to 90 nt, from 17 to 75 nt, from 17 to 60 nt, from 17 to 50 nt, from 17 to 35 nt, from 17 to 30 nt, from 17 to 25 nt, from 17 to 22 nt, from 17 to 20 nt, from 18 to 100 nt, from 18 to 90 nt, from 18 to 7 5 nt, from 18 to 60 nt, from 18 to 50 nt, from 18 to 35 nt, from 18 to 30 nt, from 18 to 25 nt, from 18 to 22 nt, or from 18 to 20 nt). In some cases, the targeting sequence of the targeting segment that is complementary to a target sequence of the target nucleic acid has a length of from 15 nt to 30 nt. In some cases, the targeting sequence of the targeting segment that is complementary to a target sequence of the target nucleic acid has a length of from 15 nt to 25 nt. In some cases, the targeting sequence of the targeting segment that is complementary to a target sequence of the target nucleic acid has a length of from 17 nt to 30 nt. In some cases, the targeting sequence of the targeting segment that is complementary to a target sequence of the target nucleic acid has a length of from 17 nt to 25 nt. In some cases, the targeting sequence of the targeting segment that is complementary to a target sequence of the target nucleic acid has a length of from 17 nt to 22 nt. In some cases, the targeting sequence of the targeting segment that is complementary to a target sequence of the target nucleic acid has a length of from 18 nt to 30 nt. In some cases, the targeting sequence of the targeting segment that is complementary to a target sequence of the target nucleic acid has a length of from 18 nt to 25 nt. In some cases, the targeting sequence of the targeting segment that is complementary to a target sequence of the target nucleic acid has a length of from 18 nt to 22 nt. In some cases, the targeting sequence of the targeting segment that is complementary to a target site of the target nucleic acid is 20 nucleotides in length. In some cases, the targeting sequence of the targeting segment that is complementary to a target site of the target nucleic acid is 19 nucleotides in length. In some cases, the targeting sequence of the targeting segment that is complementary to a target site of the target nucleic acid is 18 nucleotides in length. In some cases, the targeting sequence of the targeting segment that is complementary to a target site of the target nucleic acid is 17 nucleotides in length.
In various embodiments, the percent complementarity between the targeting sequence (guide sequence) of the targeting segment and the target site of the target nucleic acid can be 60% or more (e.g., 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the seven contiguous 5′-most nucleotides of the target site of the target nucleic acid. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 60% or more over about 20 contiguous nucleotides. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the fourteen contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 14 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the seven contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder.
In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 7 contiguous 5′-most nucleotides of the target site of the target nucleic acid (which can be complementary to the 3′-most nucleotides of the targeting sequence of the Cas9 guide RNA). In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 8 contiguous 5′-most nucleotides of the target site of the target nucleic acid (which can be complementary to the 3′-most nucleotides of the targeting sequence of the Cas9 guide RNA). In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 9 contiguous 5′-most nucleotides of the target site of the target nucleic acid (which can be complementary to the 3′-most nucleotides of the targeting sequence of the Cas9 guide RNA). In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 10 contiguous 5′-most nucleotides of the target site of the target nucleic acid (which can be complementary to the 3′-most nucleotides of the targeting sequence of the Cas9 guide RNA). In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 17 contiguous 5′-most nucleotides of the target site of the target nucleic acid (which can be complementary to the 3′-most nucleotides of the targeting sequence of the Cas9 guide RNA). In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 18 contiguous 5′-most nucleotides of the target site of the target nucleic acid (which can be complementary to the 3′-most nucleotides of the targeting sequence of the Cas9 guide RNA). In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 60% or more (e.g., e.g., 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) over 20 contiguous nucleotides. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 60% or more (e.g., e.g., 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) over 17 contiguous nucleotides.
In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 7 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 7 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 8 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 8 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 9 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 9 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 10 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 10 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 11 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 11 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 12 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 12 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 13 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 13 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 14 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 14 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 17 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 17 nucleotides in length. In some cases, the percent complementarity between the targeting sequence of the targeting segment and the target site of the target nucleic acid is 100% over the 18 contiguous 5′-most nucleotides of the target site of the target nucleic acid and as low as 0% or more over the remainder. In such a case, the targeting sequence can be considered to be 18 nucleotides in length.
Examples of various Cas9 proteins and Cas9 guide RNAs (as well as information regarding requirements related to protospacer adjacent motif (PAM) sequences present in targeted nucleic acids) can be found in the art (see, e.g., Jinek et al., (2012) Science, 337(6096):816-821; Chylinski et al. (2013) RNA Biol. 10(5): 726-737; Ma et al., (2013) Biomed Res Int. 2013:270805; Hou et al. (2013) Proc. Natl. Acad. Sci. USA, 110(39): 15644-15649; Jinek et al. (2013) Elife, 2: e00471; Pattanayak et al. (2013) Nat. Biotechnol. 31(9): 839-843; Qi et al. (2013) Cell, 152(5): 1173-1183; Wang et al. (2013) Cell, 153(4): 910-918; Chen et al. (2013) Nucleic Acids Res. 41(20): e19; Cheng et al. (2013) Cell Res. 23(10): 1163-1171; Cho et al. (2013) Genetics, 195(3): 1177-1180; DiCarlo et al. (2013) Nucleic Acids Res. 41(7): 4336-4343; Dickinson et al. (2013) Nat. Meth. 10(10): 1028-1034; Ebina et al. (2013) Sci Rep. 3: 2510; Fujii et. al. (2013) Nucleic Acids Res. 41(20): e187; Hu et al. (2013) Cell Res. 23(11): 1322-1325; Jiang et al. (2013) Nucleic Acids Res. 41(20): e188; Larson et al. (2013) Nat. Protoc. 8(11): 2180-2196; Mali et al. (2013) Nat. Meth. 10(10): 957-963; Nakayama et al. (2013) Genesis, 51(12): 835-843; Ran et al. (2013) Nat. Protoc. 8(11): 2281-308; Ran et al. (2013) Cell, 154(6): 1380-1389; Upadhyay et al. (2013) G3 (Bethesda) 3(12): 2233-2238; Walsh et al. (2013) Proc. Natl. Acad. Sci. USA, 110(39): 15514-15515; Yang et al. (2013) Cell, 154(6): 1370-1379; Briner et al. (2014)Mol. Cell, 56(2): 333-339; and U.S. Pat. Nos. 8,906,616; 8,895,308; 8,889,418; 8,889,356; 8,871,445; 8,865,406; 8,795,965; 8,771,945; 8,697,359; 20140068797; 20140170753; 20140179006; 20140179770; 20140186843; 20140186919; 20140186958; 20140189896; 20140227787; 20140234972; 20140242664; 20140242699; 20140242700; 20140242702; 20140248702; 20140256046; 20140273037; 20140273226; 20140273230; 20140273231; 20140273232; 20140273233; 20140273234; 20140273235; 20140287938; 20140295556; 20140295557; 20140298547; 20140304853; 20140309487; 20140310828; 20140310830; 20140315985; 20140335063; 20140335620; 20140342456; 20140342457; 20140342458; 20140349400; 20140349405; 20140356867; 20140356956; 20140356958; 20140356959; 20140357523; 20140357530; 20140364333; and 20140377868; all of which are hereby incorporated by reference in their entirety.
Guide RNAs Corresponding to Type V and Type VI CRISPR/Cas Endonucleases (e.g., Cpf1 Guide RNA)
A guide RNA that binds to a type V or type VI CRISPR/Cas protein (e.g., Cpf1, C2c1, C2c2, C2c3), and targets the complex to a specific location within a target nucleic acid is referred to herein generally as a “type V or type VI CRISPR/Cas guide RNA”. An example of a more specific term is a “Cpf1 guide RNA.”
A type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) can have a total length of from 30 nucleotides (nt) to 200 nt, e.g., from 30 nt to 180 nt, from 30 nt to 160 nt, from 30 nt to 150 nt, from 30 nt to 125 nt, from 30 nt to 100 nt, from 30 nt to 90 nt, from 30 nt to 80 nt, from 30 nt to 70 nt, from 30 nt to 60 nt, from 30 nt to 50 nt, from 50 nt to 200 nt, from 50 nt to 180 nt, from 50 nt to 160 nt, from 50 nt to 150 nt, from 50 nt to 125 nt, from 50 nt to 100 nt, from 50 nt to 90 nt, from 50 nt to 80 nt, from 50 nt to 70 nt, from 50 nt to 60 nt, from 70 nt to 200 nt, from 70 nt to 180 nt, from 70 nt to 160 nt, from 70 nt to 150 nt, from 70 nt to 125 nt, from 70 nt to 100 nt, from 70 nt to 90 nt, or from 70 nt to 80 nt). In some cases, a type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) has a total length of at least 30 nt (e.g., at least 40 nt, at least 50 nt, at least 60 nt, at least 70 nt, at least 80 nt, at least 90 nt, at least 100 nt, or at least 120 nt).
In some cases, a Cpf1 guide RNA has a total length of 35 nt, 36 nt, 37 nt, 38 nt, 39 nt, 40 nt, 41 nt, 42 nt, 43 nt, 44 nt, 45 nt, 46 nt, 47 nt, 48 nt, 49 nt, or 50 nt.
Like a Cas9 guide RNA, a type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) can include a target nucleic acid-binding segment and a duplex-forming region (e.g., in some cases formed from two duplex-forming segments, i.e., two stretches of nucleotides that hybridize to one another to form a duplex).
The target nucleic acid-binding segment of a type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) can have a length of from 15 nt to 30 nt, e.g., 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 21 nt, 22 nt, 23 nt, 24 nt, 25 nt, 26 nt, 27 nt, 28 nt, 29 nt, or 30 nt. In some cases, the target nucleic acid-binding segment has a length of 23 nt. In some cases, the target nucleic acid-binding segment has a length of 24 nt. In some cases, the target nucleic acid-binding segment has a length of 25 nt.
The guide sequence of a type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) can have a length of from 15 nt to 30 nt (e.g., 15 to 25 nt, 15 to 24 nt, 15 to 23 nt, 15 to 22 nt, 15 to 21 nt, 15 to 20 nt, 15 to 19 nt, 15 to 18 nt, 17 to 30 nt, 17 to 25 nt, 17 to 24 nt, 17 to 23 nt, 17 to 22 nt, 17 to 21 nt, 17 to 20 nt, 17 to 19 nt, 17 to 18 nt, 18 to 30 nt, 18 to 25 nt, 18 to 24 nt, 18 to 23 nt, 18 to 22 nt, 18 to 21 nt, 18 to 20 nt, 18 to 19 nt, 19 to 30 nt, 19 to 25 nt, 19 to 24 nt, 19 to 23 nt, 19 to 22 nt, 19 to 21 nt, 19 to 20 nt, 20 to 30 nt, 20 to 25 nt, 20 to 24 nt, 20 to 23 nt, 20 to 22 nt, 20 to 21 nt, 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 21 nt, 22 nt, 23 nt, 24 nt, 25 nt, 26 nt, 27 nt, 28 nt, 29 nt, or 30 nt). In some cases, the guide sequence has a length of 17 nt. In some cases, the guide sequence has a length of 18 nt. In some cases, the guide sequence has a length of 19 nt. In some cases, the guide sequence has a length of 20 nt. In some cases, the guide sequence has a length of 21 nt. In some cases, the guide sequence has a length of 22 nt. In some cases, the guide sequence has a length of 23 nt. In some cases, the guide sequence has a length of 24 nt.
The guide sequence of a type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) can have 100% complementarity with a corresponding length of target nucleic acid sequence. The guide sequence can have less than 100% complementarity with a corresponding length of target nucleic acid sequence. For example, the guide sequence of a type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) can have 1, 2, 3, 4, or 5 nucleotides that are not complementary to the target nucleic acid sequence. For example, in some cases, where a guide sequence has a length of 25 nucleotides, and the target nucleic acid sequence has a length of 25 nucleotides, in some cases, the target nucleic acid-binding segment has 100% complementarity to the target nucleic acid sequence. As another example, in some cases, where a guide sequence has a length of 25 nucleotides, and the target nucleic acid sequence has a length of 25 nucleotides, in some cases, the target nucleic acid-binding segment has 1 non-complementary nucleotide and 24 complementary nucleotides with the target nucleic acid sequence. As another example, in some cases, where a guide sequence has a length of 25 nucleotides, and the target nucleic acid sequence has a length of 25 nucleotides, in some cases, the target nucleic acid-binding segment has 2 non-complementary nucleotides and 23 complementary nucleotides with the target nucleic acid sequence.
The duplex-forming segment of a type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) (e.g., of a targeter RNA or an activator RNA) can, in some cases, have a length of from 15 nt to 25 nt (e.g., 15 nt, 16 nt, 17 nt, 18 nt, 19 nt, 20 nt, 21 nt, 22 nt, 23 nt, 24 nt, or 25 nt).
In some cases, the RNA duplex of a type V or type VI CRISPR/Cas guide RNA (e.g., cpf1 guide RNA) can have a length of from 5 base pairs (bp) to 40 bp (e.g., from 5 to 35 bp, 5 to 30 bp, 5 to 25 bp, 5 to 20 bp, 5 to 15 bp, 5-12 bp, 5-10 bp, 5-8 bp, 6 to 40 bp, 6 to 35 bp, 6 to 30 bp, 6 to 25 bp, 6 to 20 bp, 6 to 15 bp, 6 to 12 bp, 6 to 10 bp, 6 to 8 bp, 7 to 40 bp, 7 to 35 bp, 7 to 30 bp, 7 to 25 bp, 7 to 20 bp, 7 to 15 bp, 7 to 12 bp, 7 to 10 bp, 8 to 40 bp, 8 to 35 bp, 8 to 30 bp, 8 to 25 bp, 8 to 20 bp, 8 to 15 bp, 8 to 12 bp, 8 to 10 bp, 9 to 40 bp, 9 to 35 bp, 9 to 30 bp, 9 to 25 bp, 9 to 20 bp, 9 to 15 bp, 9 to 12 bp, 9 to 10 bp, 10 to 40 bp, 10 to 35 bp, 10 to 30 bp, 10 to 25 bp, 10 to 20 bp, 10 to 15 bp, or 10 to 12 bp).
As an example, a duplex-forming segment of a Cpf1 guide RNA can comprise a nucleotide sequence selected from (5′ to 3′): AAUUUCUACUGUUGUAGAU (SEQ ID NO:18), AAUUUCUGCUGUUGCAGAU (SEQ ID NO:19), AAUUUCCACUGUUGUGGAU (SEQ ID NO:20), AAUUCCUACUGUUGUAGGU (SEQ ID NO:21), AAUUUCUACUAUUGUAGAU (SEQ ID NO:22), AAUUUCUACUGCUGUAGAU (SEQ ID NO:23), AAUUUCUACUUUGUAGAU (SEQ ID NO:24), and AAUUUCUACUUGUAGAU (SEQ ID NO:25). The guide sequence can then follow (5′ to 3′) the duplex forming segment.
A non-limiting example of an activator RNA (e.g. tracrRNA) of a C2c1 guide RNA (dual guide or single guide) is an RNA that includes the nucleotide sequence GAAUUUUUCAACGGGUGUGCCAAUGGCCACUUUCCAGGUGGCAAAGCCCGUUG A GCUUCUCAAAAAG (SEQ ID NO:26). In some cases, a C2c guide RNA (dual guide or single guide) is an RNA that includes the nucleotide sequence In some cases, a C2c guide RNA (dual guide or single guide) is an RNA that includes the nucleotide sequence GUCUAGAGGACAGAAUUUUUCAACGGGUGUGCCAAUGGCCACUUUCCAGGUG GC AAAGCCCGUUGAGCUUCUCAAAAAG (SEQ ID NO:27). In some cases, a C2c1 guide RNA (dual guide or single guide) is an RNA that includes the nucleotide sequence UCUAGAGGACAGAAUUUUUCAACGGGUGUGCCAAUGGCCACUUUCCAGGUGGC A AAGCCCGUUGAGCUUCUCAAAAAAG (SEQ ID NO:28). A non-limiting example of an activator RNA (e.g. tracrRNA) of a C2c1 guide RNA (dual guide or single guide) is an RNA that includes the nucleotide sequence ACUUUCCAGGCAAAGCCCGU UGAGCUUCUCAAAAAG (SEQ ID NO:29). In some cases, a duplex forming segment of a C2c1 guide RNA (dual guide or single guide) of an activator RNA (e.g. tracrRNA) includes the nucleotide sequence AGCUUCUCA (SEQ ID NO:30) or the nucleotide sequence GCUUCUCA (SEQ ID NO:31) (the duplex forming segment from a naturally existing tracrRNA.
A non-limiting example of a targeter RNA (e.g. crRNA) of a C2c1 guide RNA (dual guide or single guide) is an RNA with the nucleotide sequence CUGAGAAGUGGCACNNNNNNNNNNNNNNNNNNNN (SEQ ID NO:32), where the Ns represent the guide sequence, that will vary depending on the target sequence, and although 20 Ns are depicted a range of different lengths are acceptable. In some cases, a duplex forming segment of a C2c1 guide RNA (dual guide or single guide) of a targeter RNA (e.g. crRNA) includes the nucleotide sequence CUGAGAAGUGGCAC (SEQ ID NO:33) or includes the nucleotide sequence CUGAGAAGU (SEQ ID NO:34) or includes the nucleotide sequence UGAGAAGUGGCAC (SEQ ID NO:35) or includes the nucleotide sequence UGAGAAGU (SEQ ID NO:36).
Examples and guidance related to type V or type VI CRISPR/Cas endonucleases and guide RNAs (as well as information regarding requirements related to protospacer adjacent motif (PAM) sequences present in targeted nucleic acids) can be found in the art (see, e.g., Zetsche et al. (2015) Cell, 163(3): 759-771; Makarova et al. (2015)Nat. Rev. Microbiol. 13(11): 722-736; Shmakov et al. (2015) Mol. Cell. 60(3): 385-397, and the like).
Target Cells
Because the polyrotaxane (PRX) carriers described herein are effective to deliver complexed nucleic acids in vivo, the target nucleic acid (e.g., target genomic DNA) can be located within a eukaryotic cell in vivo.
In some cases a target cell (a cell into which a class 2 CRISPR/Cas endonuclease and a pair of corresponding CRISPR/Cas guide RNAs can be introduced) is a cell of a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal); a cell of a mammal (e.g., a cell of a rodent such as a mouse or rat, a cell of a non-human primate, a cell of a human, etc.); and the like. In some cases, a target cell (a cell into which a class 2 CRISPR/Cas endonuclease and a pair of corresponding CRISPR/Cas guide RNAs can be introduced) is a mammalian cell (e.g., a human cell or a non-human mammalian cell).
The cell(s) targeted in vivo, can be any type of cell of interest (e.g., a stem cell, e.g. an embryonic stem (ES) cell, a hematopoietic stem cell, a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.), a somatic cell, a muscle cell, an in in vivo embryonic cell of an embryo at any stage, e.g., a 1-cell, 2-cell, 4-cell, 8-cell, etc. stage zebrafish embryo; etc.).
In some cases, the cell is a pericyte. A pericyte is a multipotent stem cell that is located within the blood vessels of skeletal muscle.
Thus, in some cases, a target cell (a cell into which a class 2 CRISPR/Cas endonuclease and a pair of corresponding CRISPR/Cas guide RNAs can be introduced) is a pericyte (e.g., see Dellavalle et al. (2007) Nat. Cell Biol. 9(3): 255-267). In some cases, the cell is a type 2 pericyte (e.g., which can form myotubes and can be characterized by positive expression for nestin (PDGFRB+ CD146+ NG2+)). In some cases, is a muscle stem cell. In some cases, the cell is a myogenic precursor cell.
The foregoing cells and/or tissues are illustrative and non-limiting. Using the teachings provided herein, nucleic acid constructs can be delivered in vivo to essentially any desired cell.
Illustrative Modification of Mutant Dystrophin.
Duchenne Muscular Dystrophy (DMD) is a muscle genetic disorder in boys, resulting in loss of ambulation and premature death due to frame-shifting mutations in the DMD gene resulting in the loss of dystrophin protein in muscle. Currently, no cure has been found. Dystrophin stabilizes the dystrophin-glycoprotein complex (DGC) and loss of functional dystrophin leads to the degradation of DGC components, muscle membrane damage, and dysfunctional muscle stem cells. DMD can lead to wheelchair dependence, life threatening infection, cardiomyopathy, and the like.
One approach to the treatment of DMD described in PCT Pub. No: WO 2017/139505 (PCT/US2017/017255, which is incorporated herein by reference for the constructs and sequences described therein) involves the use of CRISPR to restore the reading frame for DMD. By restoring the reading frame, DMD can be switched to a milder phenotype, Becker's muscular dystrophy (BMD).
Accordingly, in certain embodiments the CRISPR components encoded by the plasmid that is complexed with the polyrotaxane carrier(s) described herein are designed to modify a mutant dystrophin gene in the genome of a cell (e.g., a human cell), e.g., as described in PCT/US2017/017255. In various embodiments, the PRX carrier introduced into the cell carries: (a) a nucleic acid comprising a nucleotide sequence encoding the class 2 CRISPR/Cas endonuclease; and (b) one or more nucleic acids comprising nucleotide sequences encoding the first and/or second CRISPR/Cas guide RNAs. In certain embodiments, the first CRISPR/Cas guide RNA comprises a guide sequence that hybridizes to a target sequence within intron 44 of the mutant dystrophin gene, and the second CRISPR/Cas guide RNA comprises a guide sequence that hybridizes to a target sequence within intron 55 of the mutant dystrophin gene (see, e.g., FIG. 5). In this illustrative, but non-limiting embodiment, introduction of these components into the cell by the PRX carrier/plasmid complex results in deletion of a greater than 330 kilobase region of the mutant dystrophin gene comprising exons 45-55 (e.g., in some cases due to non-homologous end-joining (NHEJ)).
Thus, in some cases, the subject methods result in cleavage of the cell's genome in introns 44 and 55 of the mutant dystrophin gene and deletion of a greater than 330-kilobase region of the mutant dystrophin gene comprising exons 45-55. The subject methods thus result in deletion of a greater than 330-kilobase region of the mutant dystrophin gene, where the deleted region comprises exons 45-55 (e.g., such that the remaining sequence encode a dystrophin mRNA missing exons 45-55, e.g., remaining sequence of intron 44 and remaining sequence of intron 55 become a single intron, and exon 44 is therefore spliced directly to exon 56). Thus, in some cases, the deleted region includes intron sequence and the remaining sequence also includes intron sequence.
In some cases, the subject methods result in a genomic deletion of greater than 330 kilobases (kb). In some cases, the subject methods result in a genomic deletion of 400 kilobases (kb) or more (e.g., 450 kb or more, 500 kb or more, 550 kb or more, 600 kb or more, 650 kb or more, 700 kb or more, etc.). For example, in some cases, the target sequence within intron 44 and the target sequence within intron 55 are separated from each other by greater than 330 kilobases (kb). In some cases, the target sequence within intron 44 and the target sequence within intron 55 are separated from each other by 400 kb or more (e.g., 450 kb or more, 500 kb or more, 550 kb or more, 600 kb or more, 650 kb or more, 700 kb or more, etc.). In some cases, the target sequence within intron 44 and the target sequence within intron 55 are separated from each other by 700 kb or more.
Thus, in some cases, the guide sequence of the first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) has 100% complementarity over 20 contiguous nucleotides with a target sequence corresponding to intron 44 of the human dystrophin gene (e.g., a target sequence within intron 44 of the human dystrophin gene, a target sequence within a mouse dystrophin gene, etc.), and the guide sequence of the second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) has 100% complementarity over 20 contiguous nucleotides with a target sequence corresponding to intron 55 of the human dystrophin gene (e.g., a target sequence within intron 55 of the human dystrophin gene, a target sequence within a mouse dystrophin gene, etc.). In some such cases, the target sequence corresponding to intron 44 and the target sequence corresponding to intron 55 are separated from each other by greater than 330 kilobases (kb). In some cases, the target sequence corresponding to intron 44 and the target sequence corresponding to intron 55 are separated from each other by 400 kilobases (kb) or more (e.g., 450 kb or more, 500 kb or more, 550 kb or more, 600 kb or more, 650 kb or more, 700 kb or more, etc.). In some cases, the target sequence within intron 44 and the target sequence within intron 55 are separated from each other by 700 kb or more. Examples guide RNAs (e.g., guide sequences of guide RNAs) and target sequences that can be used to accomplish such genomic deletions in human cells are provided in Tables 4 and 5 (see also FIGS. 23 and 24 in PCT/US2017/017255).







TABLE 4







Illustrative, but non-limiting examples, of guide sequences of


guide RNAs and non-complementary strands of target sequences that 


can be used to accomplish genomic deletion of a mutant dystrophin 


gene in human cells. Note PCT/US2017/017255 SEQ ID shown in 


parenthiticals)


















Followed
SEQ


Intron
Site

Length
Sequence
by PAM
ID NO





44
1
Non-
20 nt
GTGGTGTCCTTTGAATATGC
AGG
37(1140)



(44C1)
complementary
17 nt
GTGTCCTTTGAATATGC
AGG
38(1145)




strand of target








sequence






 




Guide
20 nt
GUGGUGUCCUUUGAAUAUGC

39(1150)




Sequence of
17 nt
GUGUCCUUUGAAUAUGC

40(1155)




Guide RNA






 



2
Non-
20 nt
AGATTGTCCAGGATATAATT
TGG
41(1141)



(44C2)
complementary
17 nt
TTGTCCAGGATATAATT
TGG
42(1146)




strand of target








sequence






 




Guide
20 nt
AGAUUGUCCAGGAUAUAAUU

43(1151)




Sequence of
17 nt
UUGUCCAGGAUAUAAUU

44(1156)




Guide RNA






 



3
Non-
20 nt
TTAGCAACCAAATTATATCC
TGG
45(1142)



(44C3)
complementary
17 nt
GCAACCAAATTATATCC
TGG
46(1147)




strand of target








sequence






 




Guide
20 nt
UUAGCAACCAAAUUAUAUCC

47(1152)




Sequence of
17 nt
GCAACCAAAUUAUAUCC

48(1157)




Guide RNA






 



4
Non-
20 nt
GTTGAAATTAAACTACACAC
TGG
49(1143)



(44C4)
complementary
17 nt
GAAATTAAACTACACAC
TGG
50(1148)




strand of target








sequence






 




Guide
20 nt
GUUGAAAUUAAACUACACAC

51(1153)




Sequence of
17 nt
GAAAUUAAACUACACAC

52(1158)




Guide RNA






 



5
Non-
20 nt
ATCTTTACCTGCATATTCAA
AGG
53(1144)



(44C5)
complementary
17 nt
TTTACCTGCATATTCAA
AGG
54(1149)




strand of target








sequence






 




Guide
20 nt
AUCUUUACCUGCAUAUUCAA

55(1154)




Sequence of
17 nt
UUUACCUGCAUAUUCAA

56(1159)




Guide RNA






 


55
1
Non-
20 nt
TACACATTTTTAGGCTTGAC
AGG
57(1160)



(55C1)
complementary
17 nt
ACATTTTTAGGCTTGAC
AGG
58(1165)




strand of target








sequence






 




Guide
20 nt
UACACAUUUUUAGGCUUGAC

59(1170)




Sequence of
17 nt
ACAUUUUUAGGCUUGAC

60(1175)




Guide RNA






 



2
Non-
20 nt
CATTCCTGGGAGTCTGTCAT
GGG
61(1161)



(55C2)
complementary
17 nt
TCCTGGGAGTCTGTCAT
GGG
62(1166)




strand of target








sequence






 




Guide
20 nt
CAUUCCUGGGAGUCUGUCAU

63(1171)




Sequence of
17 nt
UCCUGGGAGUCUGUCAU

64(1176)




Guide RNA






 



3
Non-
20 nt
TGTATGATGCTATAATACCA
AGG
65(1162)



(55C3)
complementary
17 nt
ATGATGCTATAATACCA
AGG
66(1167)




strand of target








sequence






 




Guide
20 nt
UGUAUGAUGCUAUAAUACCA

67(1172)




Sequence of
17 nt
AUGAUGCUAUAAUACCA

68(1177)




Guide RNA






 



4
Non-
20 nt
GTGGAAAGTACATAGGACCT
TGG
69(1163)



(55C4)
complementary
17 nt
GAAAGTACATAGGACCT
TGG
70(1168)




strand of target








sequence






 




Guide
20 nt
GUGGAAAGUACAUAGGACCU

71(1173)




Sequence of
17 nt
GAAAGUACAUAGGACCU

72(1178)




Guide RNA






 



5
Non-
20 nt
TCTTATCATAACTCTTACCA
AGG
73(1164)



(55C5)
complementary
17 nt
TATCATAACTCTTACCA
AGG
74(1169)




strand of target








sequence






 




Guide
20 nt
UCUUAUCAUAACUCUUACCA

75(1174)




Sequence of
17 nt
UAUCAUAACUCUUACCA

76(1179)




Guide RNA









Table 5 shows example guide sequences of guide RNAs and non-complementary strands of target sequences that can be used to accomplish genomic deletions of a mutant dystrophin gene in human cells.

















PCT/U52017/



Target seq; gRNA seq
SEQ ID
017255


Name
(w/out PAM)
NO
SEQ ID NO


















44C1
gtggtgtcct ttgaatatgc
77
1140


 



gugguguccu uugaauaugc
78
1150


 


44C1
agattgtcca ggatataatt
79
1141


 



agauugucca ggauauaauu
80
1151


 


44C1
ttagcaacca aattatatcc
81
1142


 



uuagcaacca aauuauaucc
82
1152


 


44C1
gttgaaatta aactacacac
83
1143


 



guugaaauua aacuacacac
84
1153


 


44C1
atctttacct gcatattcaa
85
1144


 



aucuuuaccu gcauauucaa
86
1154


 


44C6md
ctctgcattg ttttggcctc
87
1136


 



cucugcauug uuuuggccuc
88
1223


 


44C7m
tcctccaaag agtagaatgg
89
1137


 



uccuccaaag aguagaaugg
90
1224


 


44C8m
gccctaaact tacactgttc
91
1138


 



gcccuaaacu uacacuguuc
92
1225


 


44r1-3
aaagatagat tagattgtcc
93
1139


 



aaagauagau uagauugucc
94
1226


 


44r1-7
gttgctaaat tacatagttt
95
1180


 



guugcuaaau uacauaguuu
96
1227


 


44r1-1
tgttgcaata gtcaatcaag
97
1181


 



uguugcaaua gucaaucaag
98
1228


 


44r2-2
atactgatta agacagatga
99
1182


 



auacugauua agacagauga
100
1229


 


44r2-3
aatactgatt aagacagatg
101
1183


 



aauacugauu aagacagaug
102
1230


 


44r3-1
ctctatacaa atgccaacgc
103
1184


 



cucuauacaa augccaacgc
104
1231


 


44r3-2
acttgcatgc acaccagcgt
105
1185


 



acuugcaugc acaccagcgu
106
1232


 


44r3-3
ttgggctaat gtagcataat
107
1186


 



uugggcuaau guagcauaau
108
1233


 


44r3-4
gcgttggcat ttgtatagag
109
1187


 



gcguuggcau uuguauagag
110
1234


 


44r3-5
tgggctaatg tagcataatg
111
1188


 



ugggcuaagu agcauaaug
112
1235


 


44r3-6
tttgggctaa tgtagcataa
113
1189


 



uuugggcuaa uguagcauaa
114
1236


 


44r3-7
gcttaactcc ttaatattaa
115
1190


 



gcuuaacucc uuaauauuaa
116
1237


 


44r3-8
tcttctatat taaagcagat
117
1191


 



ucuucuauau uaaagcagau
118
1238


 


44r3-9
cttctatatt aaagcagatt
119
1192


 



cuucuauauu aaagcagauu
120
1239


 


44r4-1
aatatataac taccttgggt
121
1193


 



aauauauaac uaccuugggu
122
1240


 


44r4-2
acctccattc tactctttgg
123
1194


 



accuccauuc uacucuuugg
124
1241


 


44r4-3
tttcaatgat atccaaccca
125
1195


 



uuucaaugau auccaaccca
126
1242


 


44r4-5
agtacctcca ttctactctt
127
1196


 



aguaccucca uucuacucuu
128
1243


 


44r4-6
ctatcctcca aagagtagaa
129
1197


 



cuauccucca aagaguagaa
130
1244


 


44r4-7
ttttgctaca tatttcaggc
131
1198


 



uuuugcuaca uauuucaggc
132
1245


 


44r4-8
tttgctacat atttcaggct
133
1199


 



uuugcuacau auuucaggcu
134
1246


 


44r4-9
gggttggata tcattgaaaa
135
1200


 



ggguuggaua ucauugaaaa
136
1247


 


44r4-10
atatttcagg ctgggtttct
137
1201


 



auauuucagg cuggguucu
138
1248


 


44r4-11
ttgaaatata taactacctt
139
1202


 



uugaaauaua uaacuaccuu
140
1249


 


44r4-12
attgaaatat ataactacct
141
1203


 



auugaaauau auaacuaccu
142
1250


 


44r5-1
gtgagtagtg gggcacttta
143
1204


 



gugaguagug gggcacuuua
144
1251


 


44r5-2
tgtatgtaga aggttaacta
145
1205


 



uguauguaga agguuaacua
146
1252


 


44r5-3
gagcctaata aatgtacaat
147
1206


 



gagccuaaua aauguacaau
148
1253


 


44r5-4
ttgtatgtag aaggttaact
149
1207


 



uuguauguag aagguuaacu
150
1254


 


44r5-5
caatttgttt tgatgtaact
151
1208


 



caauuuguuu ugaguaacu
152
1255


 


44r6-1
tgccttctga aatagtccag
153
1209


 



ugccuucuga aauaguccag
154
1256


 


44r6-3
gttaataggg aaacagcata
155
1210


 



guuaauaggg aaacagcaua
156
1257


 


44r6-4
aacaatgcag agttaattgt
157
1211


 



aacaaugcag aguuaauugu
158
1258


 


447-1
gaacatgttg agtagacaca
159
1212


 



gaacauguug aguagacaca
160
1259


 


44r7-2
tttatcatct gtgtctattc
161
1213


 



uuuaucaucu gugucuauuc
162
1260


 


44r7-3
tctttacttt cttgactata
163
1214


 



ucuuuacuuu cuugacuaua
164
1261


 


448-1
aatattctca aacctcgttc
165
1215


 



aauauucuca aaccucguuc
166
1262


 


44r8-3
attaactgtg ttccagaacg
167
1216


 



auuaacugug uuccagaacg
168
1263


 


44r8-4
taactgcttc tttggatgac
169
1217


 



uaacugcuuc uuuggaugac
170
1264


 


44r8-5
gaccagaaca gtgtaagttt
171
1218


 



gaccagaaca guguaaguuu
172
1265


 


44r8-6
accagaacag tgtaagttta
173
1219


 



accagaacag uguaaguuua
174
1266


 


44r8-7
ctactttttc cccactactg
175
1220


 



cuacuuuuuc cccacuacug
176
1267


 


44r8-8
tggaacacag ttaattcact
177
1221


 



uggaacacag uuaauucacu
178
1268


 


44r8-9
gtgttgttta actgcttctt
179
1222


 



guguuguuua acugcuucuu
180
1269


 


55C1
tacacatttt taggcttgac
181
1160


 



uacacauuuu uaggcuugac
182
1170


 


55C2
cattcctggg agtctgtcat
183
1161


 



cauuccuggg agucugucau
184
1171


 


55C3
tgtatgatgc tataatacca
185
1162


 



uguaugaugc uauaauacca
186
1172


 


55C4
gtggaaagta cataggacct
187
1163


 



guggaaagua cauaggaccu
188
1173


 


55C5
tcttatcata actcttacca
189
1164


 



ucuuaucaua acucuuacca
190
1174


 


55C6d
aactgtcagt tgcatattcc
191
1270


 



aacugucagu ugcauauucc
192
1318


 


55C7d
cagaaaggaa tgctggtacc
193
1271


 



cagaaaggaa ugcugguacc
194
1319


 


55C8d
tctgcctaca caatgaatgg
195
1272


 



ucugccuaca caaugaaugg
196
1320


 


55C9d
cacagatcaa tccaattgtt
197
1273


 



cacagaucaa uccaauuguu
198
1321


 


55r1-5
ttgacaggtg gaaagtacat
199
1274


 



uugacaggug gaaaguacau
200
1322


 


55r1-6
acatttttag gcttgacagg
201
1275


 



acauuuuuag gcuugacagg
202
1323


 


55r1-8
ctctcccatg acagactccc
203
1276


 



cucucccaug acagacuccc
204
1324


 


55r1-9
ttggtaagag ttatgataag
205
1277


 



uugguaagag uuaugauaag
206
1325


 


55r1-10
aacacaaatt aagttcacct
207
1278


 



aacacaaauu aaguucaccu
208
1326


 


55r2-1
aggatcagtg ctgtagtgcc
209
1279


 



aggaucagug cuguagugcc
210
1327


 


55r2-2
ggccgtttat tattattgac
211
1280


 



ggccguuuau uauuauugac
212
1328


 


55r2-3
tctcaggatt gctatgcaac
213
1281


 



ucucaggauu gcuaugcaac
214
1329


 


55r2-4
caggaagaca taccatgtaa
215
1282


 



caggaagaca uaccauguaa
216
1330


 


55r2-5
agcagggctc tttcagtttc
217
1283


 



agcagggcuc uuucaguuuc
218
1331


 


55r2-6
taacattttc agcttgaacc
219
1284


 



uaacauuuuc agcuugaacc
220
1332


 


55r2-7
tcaagctgaa aatgttacac
221
1285


 



ucaagcugaa aauguuacac
222
1333


 


55r2-8
gtaacatttt cagcttgaac
223
1286


 



guaacauuuu cagcuugaac
224
1334


 


55r2-9
cagaatgaat tttggagcac
225
1287


 



cagaaugaau uuuggagcac
226
1335


 


55r2-10
tttattatta ttgactggtg
227
1288


 



uuuauuauua uugacuggug
228
1336


 


55r2-11
agaagaatct gacctttaca
229
1289


 



agaagaaucu gaccuuuaca
230
1337


 


55r2-12
gcagggctct ttcagtttct
231
1290


 



gcagggcucu uucaguuucu
232
1338


 


55r3-1
ctaaacagta gccaggcgtg
233
1291


 



cuaaacagua gccaggcgug
234
1339


 


55r3-2
cgcctggcta ctgtttagtg
235
1292


 



cgccuggcua cuguuuagug
236
1340


 


55r3-3
ctccgcacta aacagtagcc
237
1293


 



cuccgcacua aacaguagcc
238
1341


 


55r3-4
gtagccaggc gtgtggatgt
239
1294


 



guagccaggc guguggaugu
240
1342


 


55r3-6
cttggctttg actattctgc
241
1295


 



cuuggcuuug acuauucugc
242
1343


 


55r3-7
agtagccagg cgtgtggatg
243
1296


 



aguagccagg cguguggaug
244
1344


 


55r3-8
tcctcccaca tccacacgcc
245
1297


 



uccucccaca uccacacgcc
246
1345


 


55r3-10
ttggctttga ctattctgct
247
1298


 



uuggcuuuga cuauucugcu
248
1346


 


55r3-11
ataatgtctc tggcttgtaa
249
1299


 



auaaugucuc uggcuuguaa
250
1347


 


55r3-12
tggtacccgg cagctctctg
251
1300


 



ugguacccgg cagcucucug
252
1348


 


55r3-13
gtgggaggaa cctcaaagag
253
1301


 



gugggaggaa ccucaaagag
254
1349


 


55r3-14
tgactattct gctgggaaca
255
1302


 



ugacuauucu gcugggaaca
256
1350


 


55r3-15
ctctctgagg aatgttccct
257
1303


 



cucucugagg aauguucccu
258
1351


 


55r3-16
aacattcctc agagagctgc
259
1304


 



aacauuccuc agagagcugc
260
1352


 


55r4-2
attctgaagc tccaaacaat
261
1305


 



auucugaagc uccaaacaau
262
1353


 


55r4-3
taaattactc tgctaaagta
263
1306


 



uaaauuacuc ugcuaaagua
264
1354


 


55r5-1
agtacaaacc aggtttgtac
265
1307


 



aguacaaacc agguuuguac
266
1355


 


55r5-2
atatccttcc agtacaaacc
267
1308


 



auauccuucc aguacaaacc
268
1356


 


55r5-3
caaaccaggt ttgtactgga
269
1309


 



caaaccaggu uuguacugga
270
1357


 


55r5-4
ggcagctaaa gcatcactga
271
1310


 



ggcagcuaaa gcaucacuga
272
1358


 


55r5-5
atctctgagt agtacaaacc
273
1311


 



aucucugagu aguacaaacc
274
1359


 


55r5-6
gtgtcccatt ctctttgact
275
1312


 



gugucccauu cucuuugacu
276
1360


 


55r5-7
tgtgtcccat tctctttgac
277
1313


 



ugugucccau ucucuuugac
278
1361


 


55r5-8
ttctgaatgt tgaacaagta
279
1314


 



uucugaaugu ugaacaagua
280
1362


 


55r5-9
gtctcccagt caaagagaat
281
1315


 



gucucccagu caaagagaau
282
1363


 


55r5-10
attctctttg actgggagac
283
1316


 



auucucuuug acugggagac
284
1364


 


55r5-11
tctttgactg ggagacaggc
285
1317


 



ucuuugacug ggagacaggc
286
1365





The full sequence of the gRNA is the above sequence in the Table plus the rest of the scaffold sequence: gttttagagctaGAAAtagcaagttaaaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO :287)






In various embodiments, the CRISPR components (e.g., (a) a class 2 CRISPR/Cas endonuclease, e.g., Cas9, Cpf1, etc.; and/or (b) first and second corresponding guide RNAs, e.g., Cas9 guide RNAs, a Cpf1 guide RNAs, etc.) can be delivered to a cell using the polyrotaxane carriers described herein as DNA, or RNA. Thus, for example, a class 2 CRISPR/Cas endonuclease (e.g., Cas9) can be introduced into a cell as a DNA and/or RNA encoding the endonuclease and guide RNA(s). The CRISPR/Cas guide RNA can be introduced into a cell as RNA, or as DNA encoding the guide RNA.
In some cases, the encoded class 2 CRISPR/Cas endonuclease (e.g., a Cas9 protein) is encoded as a fusion protein that is fused to a heterologous polypeptide (also referred to as a“fusion partner”). In some cases, a class 2 CRISPR/Cas endonuclease is fused to an amino acid sequence (a fusion partner) that provides for subcellular localization, e.g., the fusion partner is a subcellular localization sequence (e.g., one or more nuclear localization signals (NLSs) for targeting to the nucleus, two or more NLSs, three or more NLSs, etc.). In some embodiments, a class 2 CRISPR/Cas endonuclease is fused to an amino acid sequence (a fusion partner) that provides a tag (e.g., the fusion partner is a detectable label) for ease of tracking and/or purification (e.g., a fluorescent protein, e.g., green fluorescent protein (GFP), YFP, RFP, CFP, mCherry, tdTomato, and the like; a histidine tag, e.g., a 6×His tag; a hemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like). In some embodiments, the fusion partner can provide for increased or decreased stability (i.e., the fusion partner can be a stability control peptide, e.g., a degron, which in some cases is controllable (e.g., a temperature sensitive or drug controllable degron sequence).
In some cases the class 2 CRISPR/Cas endonuclease encoded by the plasmid includes a “Protein Transduction Domain” or PTD (also known as a CPP—cell penetrating peptide), which refers to a polypeptide that facilitates traversing a lipid bilayer, micelle, cell membrane, organelle membrane, or vesicle membrane. A PTD attached to another molecule, which can range from a small polar molecule to a large macromolecule and/or a nanoparticle, facilitates the molecule traversing a membrane and can facilitate translocation of the CRISPR/Cas endojnuclease into the cell nucleus. In some embodiments, the PTD, when present, is covalently linked to the amino terminus or to the carboxyl terminus of the class 2 CRISPR/Cas endonuclease (e.g., a Cas9 protein). In some cases, the PTD is inserted internally in the class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) (i.e., is not at the N- or C-terminus of the class 2 CRISPR/Cas endonuclease). In some cases, a subject class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) includes (is conjugated to, is fused to) one or more PTDs (e.g., two or more, three or more, four or more PTDs). In some cases a PTD includes a nuclear localization signal (NLS) (e.g, in some cases 2 or more, 3 or more, 4 or more, or 5 or more NLSs).
In some cases, the nucleic acid encoding the class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) also encodes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, or 5 or more NLSs). In some embodiments, a PTD is covalently linked to the construct. Examples of PTDs include but are not limited to a minimal undecapeptide protein transduction domain (corresponding to residues 47-57 of HIV-1 TAT comprising YGRKKRRQRRR (SEQ ID NO:288); a polyarginine sequence comprising a number of arginines sufficient to direct entry into a cell (e.g., 3, 4, 5, 6, 7, 8, 9, 10, or 10−50 arginines); a VP22 domain (Zender et al. (2002) Cancer Gene Ther. 9(6): 489-496); a Drosophila Antennapedia protein transduction domain (Noguchi et al. (2003) Diabetes 52(7): 1732-1737); a truncated human calcitonin peptide (Trehin et al. (2004) Pharm. Res. 21:1248-1256); polylysine (Wender et al. (2000) Proc. Nal. Acad. Sci. USA, 97:13003-13008); RRQRRTSKLMKR (SEQ ID NO:289); Transportan GWTLNSAGYLLGKINLKALAALAKKIL (SEQ ID NO:290); KALAWEAKLAKALAKALAKHLAKALAKALKCEA (SEQ ID N0:291); and RQIKIWFQNRRMKWKK (SEQ ID NO:292). Exemplary PTDs include but are not limited to, YGRKKRRQRRR (SEQ ID NO:293), RKKRRQRRR (SEQ ID NO:294); an arginine homopolymer of from 3 arginine residues to 50 arginine residues. Exemplary PTD domain amino acid sequences include, but are not limited to, any of the following: YGRKKRRQRRR (SEQ ID NO:295); RKKRRQRR (SEQ ID NO:296); YARAAARQARA (SEQ ID NO:297); THRLPRRRRRR (SEQ ID NO:298); and GGRRARRRRRR (SEQ ID NO:299). In some embodiments, the PTD is an activatable CPP (ACPP) (Aguilera et al. (2009) Integr Biol (Camb) 1(5-6): 371-381). ACPPs comprise a polycationic CPP (e.g., Arg9 or “R9”) connected via a cleavable linker to a matching polyanion (e.g., Glu9 or “E9”), which reduces the net charge to nearly zero and thereby inhibits adhesion and uptake into cells. Upon cleavage of the linker, the polyanion is released, locally unmasking the polyarginine and its inherent adhesiveness, thus “activating” the ACPP to traverse the membrane.
A class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) can have multiple (1 or more, 2 or more, 3 or more, etc.) fusion partners in any combination of the above. As an illustrative example, a class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) can have a fusion partner that provides for tagging (e.g., GFP), and can also have a subcellular localization sequence (e.g., one or more NLSs). In some cases, such a fusion protein might also have a tag for ease of tracking and/or purification (e.g., a histidine tag, e.g., a 6×His tag; a hemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like). As another illustrative example, class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) can have one or more NLSs (e.g., two or more, three or more, four or more, five or more, 1, 2, 3, 4, or 5 NLSs). In some cases a fusion partner (or multiple fusion partners, e.g., 1, 2, 3, 4, or 5 NLSs) (e.g., an NLS, a tag, a fusion partner providing an activity, etc.) is located at or near the C-terminus of the class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein). In some cases a fusion partner (or multiple fusion partners, e.g., 1, 2, 3, 4, or 5 NLSs) (e.g., an NLS, a tag, a fusion partner providing an activity, etc.) is located at the N-terminus of the class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein). In some cases the class 2 CRISPR/Cas endonuclease (e.g., Cas9 protein) has a fusion partner (or multiple fusion partners, e.g., 1, 2, 3, 4, or 5 NLSs) (e.g., an NLS, a tag, a fusion partner providing an activity, etc.) at both the N-terminus and C-terminus.
Guide RNAs for Modification of Dystrophin.
In some embodiments a subject CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) targets a target sequence depicted in Table 4 (also provided in FIG. 23 of PCT/US2017/017255) (e.g., also see Table 3 of PCT/US2017/017255). In some embodiments, a subject CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) targets a target sequence depicted in Table 5 (also provided in FIG. 24 in PCT/US2017/017255).
Table 5 provides examples of (i) target sequences (non-complementary strand) of target DNA, and (ii) guide sequences of CRISPR/Cas guide RNAs (e.g., for CRISPR/Cas proteins such as S. pyogenes Cas9 that have a PAM requirement of NGG in the non-complementary strand), where the first targeted sequence is within intron 44 of the human dystrophin gene and the second targeted sequence is within intron 55 of the human dystrophin gene. A guide sequence that is targeted to a target sequence within intron 44 of the human dystrophin gene is referred to as a “44” series guide sequence; and a guide sequence that is targeted to a target sequence within intron 55 of the human dystrophin gene is referred to as a “55” series guide sequence.
For example, in some cases, the non-complementary strand of target sequence that is targeted by a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1140-1144 (PCT/US2017/017255 numbering in Table 5) (which sequences are 20 nucleotides long and are within intron 44 of the human dystrophin gene). In some cases, the non-complementary strand of target sequence that is targeted by a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1145-1149 (PCT/US2017/017255 numbering in Table 4, supra.) (which sequences are 17 nucleotides long and are within intron 44 of the human dystrophin gene). In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1150-1154 (PCT/US2017/017255 numbering in Table 4, supra.) (which sequences are 20 nucleotides long and hybridize to a target sequence within intron 44 of the human dystrophin gene). In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1155-1159 (PCT/US2017/017255 numbering in Table 4, supra.) (which sequences are 17 nucleotides long and hybridize to a target sequence within intron 44 of the human dystrophin gene). In some cases, the non-complementary strand of target sequence that is targeted by a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1136-1139 (PCT/US2017/017255 numbering in Table 5, supra.) and SEQ ID NOs: 1180-1222 (PCT/US2017/017255 numbering in Table 5, supra.) (which sequences are within intron 44 of the human dystrophin gene). In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1223-1269 (PCT/US2017/017255 numbering in Table 5, supra.) (which sequences hybridize to a target sequence within intron 44 of the human dystrophin gene).
In some embodiments, the non-complementary strand of target sequence that is targeted by a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1160-1164 (PCT/US2017/017255 numbering in Table 4, supra.) (which sequences are 20 nucleotides long and are within intron 55 of the human dystrophin gene). In some cases, the non-complementary strand of target sequence that is targeted by a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1165-1169 (PCT/US2017/017255 numbering in Table 4, supra.) (which sequences are 17 nucleotides long and are within intron 55 of the human dystrophin gene). In some cases, a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1170-1174 (PCT/US2017/017255 numbering in Table 4, supra.) (which sequences are 20 nucleotides long and hybridize to a target sequence within intron 55 of the human dystrophin gene). In some cases, a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1175-1179 (PCT/US2017/017255 numbering in Table 5, supra.) (which sequences are 17 nucleotides long and hybridize to a target sequence within intron 55 of the human dystrophin gene). In some cases, the non-complementary strand of target sequence that is targeted by a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1270-1317 (PCT/US2017/017255 numbering in Table 5, supra.) (which sequences are within intron 55 of the human dystrophin gene). In some cases, a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1318-1365 (PCT/US2017/017255 numbering in Table 5, supra.) (which sequences hybridize to a target sequence within intron 55 of the human dystrophin gene).
In some cases, the non-complementary strand of target sequence that is targeted by a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1140-1144 (PCT/US2017/017255 numbering in Table 5, supra.) (which sequences are 20 nucleotides long and are within intron 44 of the human dystrophin gene), and the non-complementary strand of target sequence that is targeted by a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1160-1164 (PCT/US2017/017255 numbering in Table 4, supra.) (which sequences are 20 nucleotides long and are within intron 55 of the human dystrophin gene).
In some cases, the non-complementary strand of target sequence that is targeted by a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1136-1139 and SEQ ID NOs: 1180-1222 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are within intron 44 of the human dystrophin gene), and the non-complementary strand of target sequence that is targeted by a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1270-1317 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 20 nucleotides long and are within intron 55 of the human dystrophin gene).
In some cases, the non-complementary strand of target sequence that is targeted by a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1145-1149 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 17 nucleotides long and are within intron 44 of the human dystrophin gene), and the non-complementary strand of target sequence that is targeted by a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a sequence selected from SEQ ID NOs: 1165-1169 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 17 nucleotides long and are within intron 55 of the human dystrophin gene).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1150-1154 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 20 nucleotides long and hybridize to a target sequence within intron 44 of the human dystrophin gene), and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1170-1174 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 20 nucleotides long and hybridize to a target sequence within intron 55 of the human dystrophin gene).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1150-1154 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 20 nucleotides long and hybridize to a target sequence within intron 44 of the human dystrophin gene), and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1170-1174 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 20 nucleotides long and hybridize to a target sequence within intron 55 of the human dystrophin gene).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1223-1269 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences hybridize to a target sequence within intron 44 of the human dystrophin gene), and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1318-1365 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences hybridize to a target sequence within intron 55 of the human dystrophin gene).
In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaataaggctagtccgttatca acttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO:16 (SEQ ID NO:1366 in PCT/US2017/017255)), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguua ucaacuugaaaaaguggcaccgagucggugcUU UUUU (SEQ ID NO:300, SEQ ID NO:1367 in PCT/US2017/017255)).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1223; and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1320. In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO:16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguua ucaacuugaaaaaguggcaccgagucggugcUU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1224 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID N0:1320 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagtta aaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugc UU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1225 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1320 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaata aggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugc UU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1153 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1172 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaataagg ctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugc UU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1153 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1171 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaat aaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugc UU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1152 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1172 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaataag gctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaag gcuaguccguuaucaacuugaa aaaguggcaccg agucggugcUU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1152 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1171 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaataag gctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaa ggcuaguccguuaucaac uugaaaaaguggc accgagucggugcUU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1150 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1172 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaataag gctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugc UU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1150 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1171 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaata aggctagtccgtta tcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugc UU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1150 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1174 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gttttagagctaGAAAtagcaagttaaaata aggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugc UU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1152 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.); and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence comprising the nucleotide sequence set forth in SEQ ID NO:1174 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.). In some cases, the duplex-forming portion of a guide RNA suitable for use herein comprises the sequence: gtttagagctaGAAAtagcaagtta aaataaggctag tccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 16), or guuuuagagcuaGAAAuagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugc UU UUUU (SEQ ID NO:300).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1155-1159 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 17 nucleotides long and hybridize to a target sequence within intron 44 of the human dystrophin gene), and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes a sequence selected from SEQ ID NOs: 1175-1179 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (which sequences are 17 nucleotides long and hybridize to a target sequence within intron 55 of the human dystrophin gene).
In some cases, the non-complementary strand of target sequence that is targeted by a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes the sequence set forth in SEQ ID NO:1143 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (within intron 44), and the non-complementary strand of target sequence that is targeted by a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes the sequence set forth in SEQ ID NO:1162 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (within intron 55). In some cases, the non-complementary strand of target sequence that is targeted by a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes the sequence set forth in SEQ ID NO:1148 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (within intron 44), and the non-complementary strand of target sequence that is targeted by a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes the sequence set forth in SEQ ID NO:1167 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (within intron 55).
In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes the sequence set forth in SEQ ID NO:1153 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (targets intron 44), and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes the sequence set forth in SEQ ID NO:1172 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (targets intron 55). In some cases, a first CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes the sequence set forth in SEQ ID NO:1158 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (targets intron 44), and a second CRISPR/Cas guide RNA (e.g., a Cas9 guide RNA) includes a guide sequence that includes the sequence set forth in SEQ ID NO:1177 (PCT/US2017/017255 numbering in Tables 4 and/or Table 5, supra.) (targets intron 55).
Nucleic Acids to be Complexed with PRX Carriers
As noted above, the polyrotaxane carriers described herein are effective to delivery large nucleic acids in vivo to cells. Thus, in various embodiments, the nucleic acids carriers by the multi-arm PRX include nucleic acids (RNA or DNA) encoding one or more of: (i) a class 2 CRISPR/Cas endonuclease (e.g., a Cas9 protein), (ii) a first CRISPR/Cas guide RNA (that hybridizes to intron 44, e.g., as described elsewhere herein), and (iii) a second CRISPR/Cas guide RNA (e.g., that hybridizes to intron 55, e.g., as described elsewhere herein). In some cases, one nucleic acid (e.g., an expression vector) encodes the first and second CRISPR/Cas guide RNAs. In some cases, the same nucleic acid (e.g., expression vector) also encodes the class 2 CRISPR/Cas endonuclease.
Many vectors, e.g. plasmids, cosmids, minicircles, are available and can be delivered using the carriers described herein. The vectors comprising the nucleic acid(s) may be maintained episomally, e.g. as plasmids, minicircle DNAs, or they may be integrated into the target cell genome, through homologous recombination or random integration.
In various embodiments the polyrotaxane carriers described herein are effective to deliver vectors directly to the subject cells. In other words, cells can be contacted with the carriers described herein, e.g., via local injection of the carrier, by nasal administration, by systemic administration, and the like.
In certain embodiments the vectors (e.g., plasmids) complexed with the carriers can include suitable promoters for driving expression, that is, transcriptional activation, of the nucleic acid of interest. In other words, the nucleic acid of interest (e.g., a heterologous nucleic acid, a nucleotide sequence encoding the first CRISPR/Cas guide RNA, a nucleotide sequence encoding the second CRISPR/Cas guide RNA, a nucleotide sequence encoding a class 2 CRISPR/Cas endonuclease, etc.) can be operably linked to a promoter (e.g., a promoter operable in the target cell). This may include ubiquitously acting promoters, for example, the CMV-R-actin promoter, the EF-1 alpha promoter, and the like, or inducible promoters, such as promoters that are active in particular cell populations or that respond to the presence of drugs such as tetracycline. By transcriptional activation, it is intended that transcription will be increased above basal levels in the target cell by at least about 10-fold, by at least about 100-fold, more usually by at least about 1000-fold. Expression vectors may include nucleic acid sequences that encode for selectable markers in the target cells, so as to identify cells that have taken up the introduced nucleic acid.
As noted above, a promoter can be a constitutively active promoter (i.e., a promoter that is constitutively in an active/“ON” state), it may be an inducible promoter (i.e., a promoter whose state, active/“ON” or inactive/“OFF”, is controlled by an external stimulus, e.g., the presence of a particular temperature, compound, or protein), it may be a spatially restricted promoter (i.e., transcriptional control element, enhancer, etc.)(e.g., tissue specific promoter, cell type specific promoter, etc.), and it may be a temporally restricted promoter (i.e., the promoter is in the “ON” state or “OFF” state during specific stages of embryonic development or during specific stages of a biological process, e.g., hair follicle cycle in mice).
Tissue-specific promoters are known in the art. Non-limiting examples of tissue-specific promoters are muscle cell-specific promoters. Suitable muscle-specific promoters include, e.g., a desmin promoter; an α-myosin heavy chain promoter; a myosin light chain-2 promoter; a cardiac troponin C promoter; a muscle creatine kinase promoter; an a-actinin promoter; a cardiac troponin I promoter; and the like (see, e.g., Pacak et al. (2008) Genet. Vaccines Ther. 6:13).
Suitable promoters can be derived from viruses and can therefore be referred to as viral promoters, or they can be derived from any organism, including prokaryotic or eukaryotic organisms. Suitable promoters can be used to drive expression by any RNA polymerase (e.g., pol I, pol II, pol III). Illustrative promoters include, but are not limited to the SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6) (see, e.g., Miyagishi et al. (2002), Nat. Biotechnol. 20: 497-500), an enhanced U6 promoter (e.g., Xia et al., (2003) Nucleic Acids Res. 31(17)), a human HI promoter (HI), and the like.
Examples of inducible promoters include, but are not limited to T7 RNA polymerase promoter, T3 RNA polymerase promoter, Isopropyl-beta-D-thiogalactopyranoside (IPTG)-regulated promoter, lactose induced promoter, heat shock promoter, Tetracycline-regulated promoter, Steroid-regulated promoter, Metal-regulated promoter, estrogen receptor-regulated promoter, etc. Inducible promoters can therefore be regulated by molecules including, but not limited to, doxycycline; RNA polymerase, e.g., T7 RNA polymerase; an estrogen receptor; an estrogen receptor fusion; etc.
As noted above, in certain embodiments the nucleic acid (e.g., a nucleic acid encoding a class 2 CRISPR/Cas endonuclease, and/or a CRISPR/Cas guide RNA may be introduced into cells by the multi-arm polyrotaxane carriers described herein as RNA.
Kits
In certain embodiments kits are provided for practice of the methods described herein. In certain embodiments, the kits comprise a container containing a polyrotaxane carrier as described herein. In certain embodiments, the kit further comprises a container containing a nucleic acid that is to be delivered to said mammal. In certain embodiments, the nucleic acid is in a container separate from the container containing said carrier. In certain embodiments, the nucleic acid comprises a nucleic acid as described and/or claimed herein. In certain embodiments, the nucleic acid comprises a plasmid encoding a CRISPR/Cas9 and one or more guide RNAs as described herein. In certain embodiments, the nucleic acid is provided as a complex with the carrier, e.g., as described and/or claimed herein.
In addition to above-mentioned components, a subject kit can further include instructions for using the components of the kit to practice the subject methods. The instructions for practicing the subject methods are generally recorded on a suitable recording medium. For example, the instructions may be printed on a substrate, such as paper or plastic, etc. As such, the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof (i.e., associated with the packaging or subpackaging) etc. In other embodiments, the instructions are present as an electronic storage data file present on a suitable computer readable storage medium, e.g. CD-ROM, diskette, flash drive, etc. In yet other embodiments, the actual instructions are not present in the kit, but means for obtaining the instructions from a remote source, e.g. via the internet, are provided. An example of this embodiment is a kit that includes a web address where the instructions can be viewed and/or from which the instructions can be downloaded. As with the instructions, this means for obtaining the instructions is recorded on a suitable substrate.
EXAMPLES
The following examples are offered to illustrate, but not to limit the claimed invention.
Example 1
Development of Multi-Arm Polyrotaxane (PRX) Nucleic Acid Delivery Vehicles
Methods and Reagents During the Nano DMD Study
Mice
All animal work was conducted under protocols approved by the UCLA Animal Research Committee in the Office of Animal Research Oversight. hDMD (Tg(DMD)72Thoen/J, 018900), C57BL/10 mdx (001801), and mdxD2 (D1.B10-Dmdmdx/J, 013141) mice were obtained from Jackson Laboratories. hDMD del45 mdx and hDMD del45 mdxD2 mice were generated as described (Young et al. 2017).
Cell Culture
Primary hDMD or hDMD del45 mdx myoblasts were obtained from 11-13 day old pups by dissociation of muscle tissue using dispase and collagenase II. Fibroblasts were removed by repeated pre-plating. Myoblasts were maintained in F-10 HAM with 20% FBS, 5 ng/ml bFGF and 1% penicillin/streptomycin (P/S). Myoblasts were differentiated to form myotubes (at >85% confluence) in DMEM with 2% horse serum, 1% insulin-transferrin-selenium (ITS) and 1% P/S.
CRISPR Plasmid
gRNAs for the exon 45-55 deletion (44C4, 55C3) from Young et al. 2016 were cloned into px333 (Addgene 64073, Andrea Ventura) in tandem using BbsI and BsaI.
PRX Synthesis
Synthesis of G1 PRX Prototype.
Briefly, the procedures could be divided into three steps, namely, (i) Preparation of an inclusion complex between PEG and α-CDs to form polyseudorotaxane. (ii) Synthesis of polyrotaxane by ending the α-CD complexed PEG chain with big blocking group benzyloxycarbonyl tyrosine; (iii) Modification of α-CDs in the polyrotaxane with positively charged amine groups by reaction with N,N-dimethylethylenediamine (DMAE). Briefly, PEG-diamine (Mw 3000, Polysciences) powder (160 mg) was added to a saturated solution of a-CDs (5 g in 35 ml H2O). After stirring at rt. for 24 h, then white precipitate was collected by centrifugation and dried in vacuum at 60° C. to obtain an inclusion complex. The product was confirmed by 1H-NMR in DMSO-d6. The number of a-CDs per PEG chain is calculated by comparing the value for the area of the resonance peak due to C(1)H of a-CD with that of the resonance peak due to the methylene protons of PEG. Next, the polyseudorotaxane inclusion complex (1.9 g) was added in the mixture of Z-L-Tyr (0.82 g), BOP reagent (1.15 g), HOBt (0.35 g) and DIEA (0.45 ml) which dissolved in 10 ml DMF. The mixture suspension was stirred at rt. for 24 h. Then, the Pour the suspension was precipitated into 100 ml diethyl ether and the precipitate was collected by centrifugation. The precipitate was further washed by stirring three times in succession in abundant acetone, methanol and water. The precipitate was dried in vacuum at 60° C. to obtain a Z-L-Tyr-capped polyrotaxane (PRX). The product was confirmed by 1H-NMR in DMSO-d6. The number of a-CDs per PEG chain is calculated by comparing the value for the area of the resonance peak due to C(1)H of a-CD with that of the resonance peak due to the methylene protons of PEG. PRX (0.8 g) was dissolved in 15 ml dry DMSO and CDI (2.3 g) was add to the solution later. The mixture was stirred for 3 h under nitrogen atmosphere, and then DMEDA (5.6 ml) was slowly added to the solution. After stirring overnight at rt., the reaction mixture was precipitated into 500 ml diethyl ether and the precipitate was collected by centrifugation. The precipitate was further washed by stirring in succession in abundant ether and acetone. In order to completely remove the unreacted CDI and DMEDA, the product was dialyzed against water (2-3 d) using dialysis membrane (Mw cutoff. 3,400). Finally the solution was lyophilized to obtain solid DMAE modified PRX (G1-PRX). The product was confirmed by 1H-NMR in DMSO-d6. The numbers of a-CDs and DMAE groups per PEG chain are calculated by comparing, respectively, values for the areas of the resonance peaks due to C(1)H of α-CD, and to CH3 of DMAE, with the area of the resonance peak due to the methylene protons of PEG.
Synthesis of G2 PRX Prototype.
Briefly, the procedures could be divided into four steps, namely, (i) Preparation of a diamino-PEG with disulfide linkages at both terminals; (ii) Preparation of an inclusion complex between SS-PEG-diamine and α-CDs to form SS-polyseudorotaxane. (iii) Synthesis of polyrotaxane by ending the α-CD complexed PEG chain with big blocking group benzyloxycarbonyl tyrosine; (iv) Modification of α-CDs in the polyrotaxane with positively charged amine groups by reaction with N,N-dimethylethylenediamine (DMAE). PEG di(OPSS) (Mw 3000, Polysciences) powder (400 mg) was dissolved in 20 mL 0.1 M PBS (pH=8.0) and the solution was degassed by bubbling nitrogen gas for 15 min. 2-aminoethanethiol (0.54 g was added to the solution and stirred for 10 min under nitrogen atmosphere. The reaction mixture was dialyzed (2-3 d) against 3% NaCl aq and then water, sequentially, using Spectra/Por dialysis membrane (Mw cutoff. 1,000). The solution was finally lyophilized to obtain PEG-SS-diamine as a white powder. The product was confirmed by 1H-NMR in DMSO-d6. Then PEG-SS-diamine powder (50 mg) was added to a saturated solution of a-CDs (1.6 g in 12 ml H2O). After stirring at rt. for 24 h, then white precipitate was collected by centrifugation and dried in vacuum at 60° C. to obtain an inclusion complex (SS-polyseudorotaxane). The product was confirmed by 1H-NMR in DMSO-d6. The number of a-CDs per PEG chain is calculated by comparing the value for the area of the resonance peak due to C(1)H of a-CD with that of the resonance peak due to the methylene protons of PEG. Next, the SS-polyseudorotaxane inclusion complex (0.36 g) was added in the mixture of Z-L-Tyr (0.64 g), BOP reagent (0.23 g), HOBt (0.07 g) and DIEA (0.09 ml) which dissolved in 2 ml DMF. The mixture suspension was stirred at rt. for 24 h. Then, the Pour the suspension was precipitated into 50 ml diethyl ether and the precipitate was collected by centrifugation. The precipitate was further washed by stirring three times in succession in abundant acetone, methanol and water. The precipitate was dried in vacuum at 60° C. to obtain a Z-L-Tyr-capped SS-polyrotaxane (SS-PRX). The product was confirmed by 1H-NMR in DMSO-d6. The number of a-CDs per PEG chain is calculated by comparing the value for the area of the resonance peak due to C(1)H of a-CD with that of the resonance peak due to the methylene protons of PEG. Finally, SS-PRX (0.1 g) was dissolved in 2 ml dry DMSO and CDI (0.25 g) was add to the solution later. The mixture was stirred for 3 h under nitrogen atmosphere, and then DMEDA (0.66 ml) was slowly added to the solution. After stirring overnight at rt., the reaction mixture was precipitated into 500 ml diethyl ether and the precipitate was collected by centrifugation. The precipitate was further washed by stirring in succession in abundant ether and acetone. In order to completely remove the unreacted CDI and DMEDA, the product was dialyzed against water (2-3 d) using dialysis membrane (Mw cutoff: 3,400). Finally, the solution was lyophilized to obtain solid DMAE modified SS-PRX (G2-PRX). The product was confirmed by 1H-NMR in DMSO-d6. The numbers of α-CDs and DMAE groups per PEG chain are calculated by comparing, respectively, values for the areas of the resonance peaks due to C(1)H of α-CD, and to CH3 of DMAE, with the area of the resonance peak due to the methylene protons of PEG.
Synthesis of G3 PRX Prototype.
Briefly, the procedures could be divided into four steps, namely, (i) Block two arms of 4-arm-PEG-tetramine by bulk group, e.g. FITC; (ii) Preparation of an inclusion complex between the partly blocked 4-arm-PEG and α-CDs to form 2/4-arm-polyseudorotaxane. (iii) Synthesis of 2/4-arm-polyrotaxane by ending the α-CD complexed PEG chain with big blocking group benzyloxycarbonyl tyrosine; (iv) Modification of α-CDs in the 2/4-arm-polyrotaxane with positively charged amine groups by reaction with N,N-dimethylethylenediamine (DMAE). 4-arm-PEG-tetramine (Mw 10, 000, JenKem Technology USA) powder (100 mg) was dissolved in 2 mL 0.1 M PBS (pH=8.0) and then 7.8 mg FITC in 0.1 mL DMF was added to the solution. The mixture was stirred at rt. for overnight. The reaction mixture was purified by centrifugal filter (cutoff, 3 K). Finally the solution was lyophilized to obtain 4-arm-PEG with two arms blocked by FITC (2/4-arm-PEG-diamine). Then the 2/4-arm-PEG-diamine powder (65 mg) was added to a saturated solution of a-CDs (0.625 g in 4 ml H2O). After stirring at rt. for 24 h, then white precipitate was collected by centrifugation and dried in vacuum at 60° C. to obtain an inclusion complex (2/4-arm-polyseudorotaxane). The product was confirmed by 1H-NMR in DMSO-d6. The number of a-CDs per PEG chain is calculated by comparing the value for the area of the resonance peak due to C(1)H of a-CD with that of the resonance peak due to the methylene protons of PEG. Next, the 2/4-arm-polyseudorotaxane inclusion complex (240 mg) was added in the mixture of Z-L-Tyr (0.082 g), BOP reagent (0.115 g), HOBt (0.035 g) and DIEA (0.045 ml) which dissolved in 1 ml DMF. The mixture suspension was stirred at rt. for 24 h. Then, the Pour the suspension was precipitated into 50 ml diethyl ether and the precipitate was collected by centrifugation. The precipitate was further washed by stirring three times in succession in abundant acetone, methanol and water. The precipitate was dried in vacuum at 60° C. to obtain a Z-L-Tyr-capped 2/4-arm-polyrotaxane (2/4-arm-PRX). The product was confirmed by 1H-NMR in DMSO-d6. The number of a-CDs per PEG chain is calculated by comparing the value for the area of the resonance peak due to C(1)H of a-CD with that of the resonance peak due to the methylene protons of PEG. 2/4-arm-PRX PRX (0.1 g) was dissolved in 2 ml dry DMSO and CDI (0.364 g) was add to the solution later. The mixture was stirred for 3 h under nitrogen atmosphere, and then DMEDA (1 ml) was slowly added to the solution. After stirring overnight at rt., the reaction mixture was precipitated into 50 ml diethyl ether and the precipitate was collected by centrifugation. The precipitate was further washed by stirring in succession in abundant ether and acetone. In order to completely remove the unreacted CDI and DMEDA, the product was dialyzed against water (2-3 d) using dialysis membrane (Mw cutoff. 3,400). Finally, the solution was lyophilized to obtain solid DMAE modified 2/4-arm-PRX (G3-PRX). The product was confirmed by 1H-NMR in DMSO-d6. The numbers of a-CDs and DMAE groups per PEG chain are calculated by comparing, respectively, values for the areas of the resonance peaks due to C(1)H of a-CD, and to CH3 of DMAE, with the area of the resonance peak due to the methylene protons of PEG.
Synthesis of G4 PRX Prototype.
Briefly, the procedures could be divided into five steps, namely, (i) Block two arms of 4-arm-PEG-tetramine by bulk group, e.g. FITC; (ii) Preparation of an inclusion complex between the partly blocked 4-arm-PEG and α-CDs to form 2/4-arm-polyseudorotaxane. (iii) Synthesis of 2/4-arm-polyrotaxane by ending the α-CD complexed PEG chain with big blocking group benzyloxycarbonyl tyrosine; (iv) Modification of α-CDs in the 2/4-arm-polyrotaxane with pyridyldithiol groups (v) introduce cleavable cationic charge by reaction with N,N-dimethylethylenediamine (DMAE). Briefly, 4-arm-PEG-tetramine (Mw 10, 000, JenKem Technology USA) powder (100 mg) was dissolved in 2 mL 0.1 M PBS (pH=8.0) and then 7.8 mg FITC in 0.1 mL DMF was added to the solution. The mixture was stirred at rt. for overnight. The reaction mixture was purified by centrifugal filter (cutoff, 3 K). Finally, the solution was lyophilized to obtain 4-arm-PEG with two arms blocked by FITC (2/4-arm-PEG-diamine). Then the 2/4-arm-PEG-diamine powder (65 mg) was added to a saturated solution of a-CDs (0.625 g in 4 ml H2O). After stirring at rt. for 24 h, then white precipitate was collected by centrifugation and dried in vacuum at 60° C. to obtain an inclusion complex (2/4-arm-polyseudorotaxane). The product was confirmed by 1H-NMR in DMSO-d6. The number of a-CDs per PEG chain is calculated by comparing the value for the area of the resonance peak due to C(1)H of a-CD with that of the resonance peak due to the methylene protons of PEG. Next, the 2/4-arm-polyseudorotaxane inclusion complex (240 mg) was added in the mixture of Z-L-Tyr (0.082 g), BOP reagent (0.115 g), HOBt (0.035 g) and DIEA (0.045 ml) which dissolved in 1 ml DMF. The mixture suspension was stirred at rt. for 24 h. Then, the Pour the suspension was precipitated into 50 ml diethyl ether and the precipitate was collected by centrifugation. The precipitate was further washed by stirring three times in succession in abundant acetone, methanol and water. The precipitate was dried in vacuum at 60° C. to obtain a Z-L-Tyr-capped 2/4-arm-polyrotaxane (2/4-arm-PRX). The product was confirmed by 1H-NMR in DMSO-d6. The number of a-CDs per PEG chain is calculated by comparing the value for the area of the resonance peak due to C(1)H of a-CD with that of the resonance peak due to the methylene protons of PEG. 2/4-arm-PRX PRX (0.1 g) was dissolved in 2 ml dry DMSO and CDI (0.364 g) was add to the solution later. The mixture was stirred for 3 h under nitrogen atmosphere, and then pyridyldithiol-cysteamine (0.1 g) was slowly added to the solution. After stirring overnight at rt., the reaction mixture was precipitated into 50 ml diethyl ether and the precipitate was collected by centrifugation. The precipitate was further washed by stirring in succession in abundant ether and acetone. In order to completely remove the unreacted CDI and pyridyldithiol-cysteamine, the product was repeated concentrated by centrifugal filter unit (Mw cutoff. 3,000). The solution was lyophilized and the product was confirmed by 1H-NMR in DMSO-d6.
PRX Delivery in Muscle Cells In Vitro
Myoblasts were seeded at 1.2×105 cells/cm2 for growth conditions or 1.7×105 cells/cm2 for differentiation where the media was changed to differentiation media the following day. PRX complexed with pmax GFP (Lonza), an mCherry/luciferase plasmid or px333 44C4+55C3 was added to the cells (plasmid 1 ug/mL, PRX 10 ug/ml). For trafficking studies, the particles were labeled with FITC and the plasmid labeled with Cy3 using Label IT® TrackerTM kit (Mirus Bio) Media was changed every 2-3 days. Imaging for GFP or mCherry was done at timepoints between 24 hrs-21 days. For CRISPR delivery, cells were harvested at day 7, 14 or 21 and pelleted for genomic DNA extraction using the Quick gDNA mini prep kit (Zymo Research) and analyzed with the deletion PCR described below. 4 μL Lipofectamine (Life Technologies) per 1 μg plasmid DNA and 3 ul ViaFect (Promega) per 1 ug plasmid DNA were used as controls for plasmid transfection.
PRX Delivery In Vivo
50 or 100 ug px333 44C4+55C3 plasmid complexed with PRX was injected systemically into the tail vein of mdx or hDMD del45 mdxD2 mice. For biodistribution studies, the plasmid was labeled with Cy3 using Label IT® TrackerTM kit (Mirus Bio) and mice were sacrificed 24 hrs later. Muscles and organs were imaged with IVIS imaging. Muscles were flash frozen in isopentane and cryosectioned at 10 μm for staining and imaging. For short term efficacy studies, mice were dosed 2×/wk for 3 wks. For short term systemic efficacy studies, 50 or 100 μg px333 44C4+55C3 plasmid complexed with PRX was injected into the tail vein of hDMD del45 mdxD2 mice (2nd backcross) at 11 wks of age. Mice were dosed 4 times over 2.5 wks. Muscles were harvested and flash frozen in isopentane after  ̃5 wks (34 days).
CRISPR Exon 45-55 Deletion PCR
For determining if the exon 45-55 deletion occurred, individual PCR reactions containing primers flanking the deletion (del) or internal to the deletion (undel) was performed with AccuPrime Taq High Fidelity (Life Technologies) or Herculase II Fusion Polymerase (Agilent Genomics). PCR products were run on a 2% agarose gel and visualized with ethidium bromide staining.
Immunostaining Muscle Sections
Cryosections were stained as described in Young et al. 2016. Anti-laminin (1:200, rabbit, Sigma) primary antibody was used with an Alexa Fluor 647 secondary. For dystrophin staining, sections were fixed in cold acetone for 1-2 mins, then TrueBlack (Biotium, 20-fold diluted in 70% ethanol) was added for 30 s−1 min, then blocking buffer (PBS with 5% horse serum and 10% goat serum) was added for at least 1 hr, followed by the M.O.M. kit (Vector Labs) according to the manufacturer's protocol. Primary antibodies MANDYS106 (1:60) MANEX55/56B (1:100), laminin (1:200) were added overnight. The following day secondary antibodies at 1:250 were added for 1.5 hrs.
Example 2
Use of PRX Nanocarrier to Deliver Various Plasmids in Cancer Cells
In addition to DMD, we have achieved some progresses for large plasmid delivery in non-muscle cells, such as cancer cells. In this regard, we have used our PRX carriers for comparison against commercial transfection reagent in a range of cancer cell types to provide proof-of-principle demonstration of the wider utility of our platform, including for melanoma, pancreatic cancer and colon cancer, etc. The PRX delivery systems described herein find use in numerous other fields, such as infectious disease, organ transplantation, liver disease, cardiovascular disease and other non-DMD rare diseases (e.g. Huntington's Disease) etc. To illustrate these possibilities, two plasmids were tested as payloads, namely a pmaxGFP plasmid and CRISPR/Cas9 knockout plasmid (FIG. 14). The latter is a commercial K-Ras CRISPR/Cas9 KO Plasmid (h) that is designed to disrupt gene expression by causing a double-strand break in a 5′ constitutive exon within the human KRAS gene. The K-Ras CRISPR/Cas9 KO Plasmid (h) consists of a pool of 3 plasmids, each encoding the Cas9 nuclease and a target-specific 20 nt guide RNA designed for maximum knockout efficiency. Since there is a GFP sequence in the K-Ras CRISPR/Cas9 KO Plasmid, the expression of GFP protein in an indicative of the success of gene editing. The effect of GFP plasmid laden G3 PRX was tested in murine B16 melanoma cells (FIG. 15). The effect of K-Ras CRISPR/Cas9 KO Plasmid loaded G3 PRX was tested in Kras-mutated human pancreatic cancer (Panc-1) and colon cancer (HCT116) cells (FIG. 16). This suggests that G3 PRX allows a sufficient CRISPR/Cas9 KO plasmid delivery in Panc-1 cells as compared to HCT116 cells in which transfection efficient is relatively low.
We also studied the intracellular localization of red-labeled PRX in relation to lysosomal co-staining by green fluorescent labeled anti-LAMP-1 antibody. Confocal microscopy confirmed high percentage co-localization of the red-labeled PRX particles with the green-labeled lysosomes at early time point (not shown). At 24 hrs post incubation, we continued to demonstrate >63% G3 PRX has escaped from the acidic lysosomal compartment, presumably due to the proton sponge effect (FIG. 17, left panel). In a subsequent confocal study we demonstrated that less than 15% CRISPR plasmid can be released from G3 PRX particles after entrance into the lysosome, which inspired us to further improve the plasmid intracellular release in cancer cells (FIG. 17, right panel). One solution is to use the G4 PRX.
An important consideration in the use of positively charged nanocarrier is its potential cytotoxicity. Although no cytotoxicity was seen with the PRX nanocarriers, commercially available transfection reagent such as Lipofectamine 2000 is relatively toxic to the cells.
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Example 3
Development of Self-Assembled Multi-Arm Polyrotaxanes Nanocarriers for Systemic Plasmid Delivery In Vivo
Polyrotaxane (PRX) has been extensively studied for gene delivery. Classic PRX exhibits a linear structure in which the amine-functionalized α-cyclodextrin (CD) is threaded along the entire polyethylene glycol (PEG) backbone. While the classic PRX is promising in vitro, the in vivo implementation is limited due to unfavorable pharmacokinetics (PK), which can be partially explained by the formation of unprotected cationic surface and lack of functional PEG after CD threading. Herein, we developed a multi-arm PRX platform, which has been designed for protective loading and improved PK, allowing intravenous (IV) delivery of nucleic acid. A key design is to introduce cationic CDs onto a multi-arm backbone in a spatially selective fashion. This was achieved by the controlled protection of PEG arms using protective group with steric hindrance. The optimal carrier was obtained through iterative rounds of experimentation to determine the appropriate features, such as charge density, the degree of PEGlyation and polymer backbone size, etc. Post IV injection, the multi-arm design significantly enhanced the biodistribution and circulatory half-life. We also used our PRX to formulate an IL-12 plasmid for cancer immunogene therapy in a solid tumor (colon cancer) model, leading to efficacious and safe anti-tumor effect in vivo.
Introduction
Polyrotaxanes (PRX) are supramolecular inclusion complex assembled from the threading of macrocycles onto a polymer backbone. PRXs are excellent carriers for the delivery of nucleic acids due to their advantageous properties (Mellet et al. (2011) Chem. Soc. Rev. 40: 1586), such as effective and spontaneous nucleic acid (e.g., plasmid) and polymer self-assembly, protective nucleic acids encapsulation, tunability of condensation/decondensation by choosing various types/densities of amine groups, functionalizability of PRX through the introduction of cleavable linkers for controlling intracellular gene delivery, etc. (Ooya et al. (2006) J. Am. Chem. Soc. 128: 3852). Moreover, these materials are very biocompatible due to the intrinsic safety of polyethylene glycol (PEG) and cyclodextrin sugar rings (Li & Loh (2008) Adv. Drug Deliv. Rev. 60: 1000). The general structure of the classic PRX carrier (Yamashita et al. (2006) Nat. Protocol. 1: 2861; Badwaik et al. (2016) Biomaterials, 84: 86; Tamura & Yui (2013) Biomaterials, 34: 2480; Kayashima et al. (2010) J. Immunol. 185: 698; Morille et al. (2008) Biomaterials, 29: 3477) involves the threading of cationically-rendered cyclodextrin (α-CD) along the linear PEG polymer backbone, capable of condensing DNA to sub-200 nm polyplex (Scheme S1 shown in FIG. 24). The reported in vitro transfection efficiency by linear PRXs was competent with polyethylene imine (PEI) but with no apparent cytotoxicity (Li & Loh (2008)Adv. Drug Deliv. Rev. 60: 1000). The in vitro effectiveness was achieved by systemic tuning of the cationic charge and molecular weight of these linear PRXs.[7] While the classic PRXs are promising in vitro (Yamashita et al. (2006)Nat. Protocol. 1: 2861; Badwaik et al. (2016) Biomaterials, 84: 86; Tamura & Yui (2013) Biomaterials, 34: 2480; Kayashima et al. (2010) J. Immunol. 185: 698; Morille et al. (2008) Biomaterials, 29: 3477), they are rarely tested in vivo. The utilization of the linear PRXs is limited at intact organism level, partially because the inclusion complex largely reduces the availability of PEG on the nano surface (see, e.g., Scheme 1 in FIG. 23). As a result, these PRX nano particulates lead to rapid formation of protein corona and can be effectively removed by the phagocytic cells in the reticuloendothelial system (RES) organs. Moreover, there is a possibility that the colloidal instability of these low- or non-PEG protected PRX nanocarriers could lead to agglomeration in the circulation and therefore excluded the plasmid payload from the intended “target site” (Suk et al. (2016) Adv. Drug Deliv. Rev., 99: 28).
As described in this example, our aim was to develop an in vivo effective PRX platform, that can address the above challenges. A major innovation is the creative use of multi-arm PEG backbone with spatially selective threading of α-CD, resulting in available PEG arms after inclusion complexation, which serves as a safeguard for in vivo administration, including intravenous (IV) injection (FIG. 18, panel A). Inspired by the previous studies in which CD-based polymer was optimized across multiple structural parameters (Popielarski et al. (2003) Bioconjug. Chem. 14: 672; Reineke & Davis (2003) Bioconjug. Chem., 14: 247), we generated a series of multi-arm PRX analogues through tuning the key design features. This allowed us to establish nano quantitative structure-activity relationship (QSAR) and multi-variants design features to iteratively improve biodistribution, pharmacokinetics (PK), transfection efficiency and safety of PRX nanocarriers. In order to determine the best PRX phenotype, we have systemically dissected the role of cationic charge density, level of available free PEG moieties, size of PEG backbones via cellular test of reporter plasmid transfection. We also test the optimal multi-arm PRX delivery system using a reporter plasmid and a therapeutic plasmid in normal and disease mouse models.
To demonstrate the therapeutic impact of our PRX, we constructed an interleukin-12 (IL-12) encoding IV formulation to solid tumor (e.g., colon cancer). Although IL-12 is an important anti-tumor cytokine, the direct administration of recombinant IL-12 (rIL-12) was pharmacologically abandoned due to serious side effects including patient deaths, attributed to its unfavorable PK profile (Tugues et al. (2015) Cell Death & Diff 22: 237 Tugues et al. (2015) Cell Death & Diff 22: 237). Researchers have developed various advanced delivery mechanisms (e.g., adenovirus (Sangro et al. (2004) J. Clin. Oncol. 22: 1389), gene gun (Rakhmilevich et al. (1996) Proc. Natl. Acad. Sci. USA, 93: 6291), electroporation (Daud et al. (2008) J. Clin. Oncol. 26: 5896), and nanoparticles (Dass et al. (2010) J. Pharm. & Pharm. Sci. 13: 472)) to improve the PK and safety of IL-12 immunotherapy. Some of them include nano formulations for IL-12 plasmid (pIL-12) delivery, administrated intratumorally (IT) or intraperitoneally (IP), which have resulted in early stage clinical trials in skin cancer (Daud et al. (2008) J. Clin. Oncol. 26: 5896) and ovarian cancer (that is usually confined in peritoneal cavity) (Edwards, ClinicalTrials.gov Identifier: NCT00003439 2004). However, for a deep seated solid tumor that metastasizes hematogenously and lymphatically to distant organs (e.g., colon cancer), there is a need to implement IL-12 therapy through systemic administration with additional consideration of toxicity reduction and tumor targeting. We have demonstrated that IV injected multi-arm PRX significantly improved the PK and biodistribution at a colon cancer site in mice, leading to efficacious and safe anti-tumor effect in vivo. Our data suggests that the presence of PRX/pIL-12 nano complex in colon cancer becomes a sustained source of continuous replenishment of IL-12 without major toxicity.
Results and Discussion
Development and Optimization of Multi-Arm (i.e. 4-Arm) PRX Gene Delivery Platform
Classic linear PRX gene carriers were established based on the supramolecular assembly of CD rings threading along the entire linear PEG backbone, followed by introducing bulky end-caps and further functionalization of CD molecules by various amine groups (Ooya et al. (2006) J. Am. Chem. Soc. 128: 3852). When combining negatively charged nucleic acid with linear PRX, the self-assembly process is instantaneous and mediated by the electrostatic interaction between nucleic acid and cationic CDs, which distribute non-selectively along —(O—CH2—CH2)— repeating units in the PEG backbone (see Scheme S1 in FIG. 24) (Id.). While an ideal scenario would be to use such a linear PRX for gene delivery in vivo, the linear PRX is unlikely to make therapeutic delivery possible, especially for IV treatment. From a nanomaterial property perspective, the net outcome using linear PRX is the formation of none or low PEGylated but cationic nano particulates, which are generally inefficient for systemic application because of non-specific binding, short t1/2 and unwanted macrophage uptake (Ogris et al. (1999) Gene Ther., 6: 595). It is also found that IV-injected cationic nanoparticles typically ended up in the lung (Morille et al. (2008) Biomaterials, 29: 3477). In this example, we describe an IV-injectable multi-arm PRX platform with a group of optimal design features, allowing for the introduction of cationic CDs onto multi-arm PEG backbone in a spatially selective fashion (see, FIG. 18, panel A). Our hypothesis is that spatially selective CD threading into multi-arm PRX maintains the availability of functional PEG, which is the safeguard for improved PK profile, and therefore suitable for systemic gene delivery in vivo.
For proof-of-principle, we used commercially available 4-arm PEG as a precursor to make representative multi-arm PRXs. Generally speaking, the synthesis of the 4-arm PRX consists of the following 4 steps (FIG. 18, panel B and Table 6). 4-arm PEG-amine was selectively end-capped with bulky groups (i.e., fluorescein group) by controlling the feed ratio between 4-arm PEG-tetra-amine and fluorescein-NHS (“I” in FIG. 18, panel B). Subsequently, the modified 4-arm PEG was added to a saturated aqueous solution of α-CD. α-CD selectively threaded onto the PEG arms ended with free amine and formed inclusion complex. The steric hindrance of bulky end-caps would prevent α-CD from threading onto the occupied arms and resulted in CD-free PEG arms (“II” in FIG. 18, panel B). This was followed by an amide coupling reaction to introduce Z-L-tyrosine to the amine terminals, which prevented the de-threading of α-CD (“III” in FIG. 18, panel B). Finally, amine functionalization was achieved by introducing N,N-dimethylethylenediamine (DMEA) to α-CD via carbonyldiimidazole (CDI) activation to generate cationic 4-arm polyrotaxane (4-arm PRX) (“IV”, FIG. 18, panel B). Detailed synthesis procedures were described in the method section.







TABLE 6







Detailed steps and intermediate products in the synthesis of 4-arm PRX, 


as shown in FIG. 18, panel B.















Catalytic







materials/







Reaction

Yield












Starting Materials
solution
Product
%















Step 1
4-arm PEG
NHS-
NHS-
Occupied 4-arm
>90%



tetra-amine
Fluores-
Fluorescein
PEG





cein





Step 2
Occupied 4-
A-CD
Water
4-arm 
95%



arm PEG


polypseudo-







rotaxane



Step 3
2/4 CD 4-arm
Z-Tyr
BOP, HOBt,
4-arm 
70%



pseudorotaxane

DIEA, DMF
polyrotaxane



Step 4
4-arm
DMEA
CDI, DMSO
4-arm 
56%



polyrotaxane


polyrotaxane-







DMEA









Since multiple design features are involved in the synthesis of 4-arm PRX, we decide to perform iterative optimization to obtain the appropriate design features to make the therapeutic PRX carrier (Reineke & Davis (2003) Bioconjug. Chem. 14: 255). Since charge density on the non-viral carriers is one the most important variants that governs self-assembly and the delivery performances of polyplex (Pack et al. (2005) Nat. Rev. Drug Discov. 4: 581), our first attempt was to explore the effect of charge density per α-CD in 4-arm PRX while keep other structural parameters the same. For ease of experimentation, the abiotic characterization and in vitro transfection efficiency were first determined by a tdTomato reporter plasmid (Addgene plasmid 30530, MW=5.5 kbp). We prepared a library of 4-arm PRXs with different amine density per α-CD by adjusting the molar feed ratio of CDI to α-CD ranging from 5:1 to 30:1. The molecular weight (i.e., 10 kDa) and the number of protective groups (i.e., 2 out of 4 arms are protected) in 4-arm PEG precursors were not changed at this stage. The charge density was determined by 1H-NMR spectra (FIG. 18, panel C and FIG. 26A). The integration of —CH3 peak (2.35 ppm) from DMAE divided by C1(H) peak (5.15 ppm) from α-CD gave the number of tertiary amines per α-CD. This allowed us to obtain a list of PRXs with amine density values of  ̃1,  ̃3 and  ̃6 per α-CD sugar ring (FIG. 18, panel C).
To compare the effectiveness of in vitro transfection, MC38 colon adenocarcinoma cells were used as a cellular model that allowed us to visualize tdTomato expression using various PRX carriers. Four-arm PRXs with 3 different charge densities were complexed with tdTomato plasmid at various N/P ratios ranging from 0.5:1 to 20:1. MC38 cells were treated with various polyplexes for 72 h, before the tdTomato+ cells were identified by fluorescence microscopy. The heat map in FIG. 18, panel D provided a semi-quantitative display of the impact of charge density and N/P ratio on the transfection efficiency in vitro. Compared to PRX with lower charge density, the best reporter expression was obtained with 4-arm PRX at 6 amines per α-CD. The optimum N/P ratio to achieve sufficient reporter expression was 3:1 for the PRX with 6 amines per α-CD, and shifted to higher values with decreasing charge density. Comparing the transfection results at their optimum N/P, 4-arm PRX with 6 amines per α-CD revealed significant increase over 3 amines per α-CD, while the 4-arm PRX with 1 amine per α-CD barely transfected MC38 cells. Since decreasing the charge density negatively affected the transfection efficiency, the following experimentation was performed at the fixed charge density, i.e., 6 amines per α-CD.
The second design feature to optimize was the level of free PEG moieties. By manipulation of the number of bulky end-caps on 4-arm PEG backbone, we constructed 3 different PRXs with α-CD threading onto 1 out of 4 arms (1/4 CD), 2 out of 4 arms (2/4 D) or 3 out 4 arms (3/4CD), respectively (FIG. 19, panel A). To start with, 4-arm PEG tetra-amines were selectively functionalized with NHS-fluorescein, as illustrated in FIG. 25, panel A. Synthesis success was confirmed by MALDI-TOF-MS (FIG. 26, panel B) and 1H-NMR spectroscopy (FIG. 25, panel B). As demonstrated, the increase of average molecular weight in 4-arm PEG was associated with increasing degree of end-capping. For example, the experimental molecular weight of 2/4CD 4-arm PRX (10680 Da) was in close accordance with the theoretical molecular weight (10629 Da) (FIG. 19, panel B). As the inclusion complex was formed in a saturated aqueous solution of α-CD, the number of α-CD on 4-arm PRX was directly related to the availability of free PEG arms. From 1H-NMR spectra, the integration of C1(H) peak (5.15 ppm) from α-CD and —CH2CH2O— peak from PEG was used to calculate the total number of α-CD per PRX polymer. As demonstrated in FIG. 19, panel C and FIG. 26, panel B, an average of 37α-CDs per polymer was resulted for 3/4CD PRX, while the total number of α-CDs decreased to 26 per 2/4CD PRX and 13 per 1/4CD PRX, due to the increased level of free PEG moieties (FIG. 19, panel C). While the degree of free PEG moieties on PRX/plasmid nano particulates requires additional PK and biodistribution assessment in vivo, it suffices to perform tdTomato plasmid in vitro screening at this stage to exclude inefficient candidate in vitro (FIG. 19, panel D). We did not pursue 1/4CD PRX because it exhibited the lowest transfection efficiency in MC38 cells. The result was in line with previous study, which suggested the excessive level of free PEG moieties could impede the access of polycation to plasmid DNA and reduce gene expression (Mishra et al. (2004) Eur. J Cell Biol. 83: 97). Furthermore, 3/4CD PRX and 2/4CD PRX resulted in comparable tdTomato gene expression, and no significant difference was observed in terms of optimum N/P ratio. Since the additional PEG arm on 2/4CD PRX did not compromise transfection efficiency, we focused on 2/4CD PRX in order to achieve sufficient level of free PEG moieties, which is a favorable feature for IV administration.
Moreover, we also optimized the molecular weight of the 4-arm PEG backbone in PRXs. In this case, 3 PRXs were constructed from 5 kDa, 10 kDa and 20 kDa 4-arm PEG backbone structures, and characterized by 1H-NMR spectroscopy (FIG. 19, panel E and FIG. 26, panel C). The number of α-CDs per PRX polymer was positively correlated with the size of the 4-arm PEG backbone. 5 kDa 4-arm PRX required higher N/P ratio for tdTomato transfection compared to PRXs with 10 kDa or 20 kDa PEG backbone (FIG. 27), with >4-fold reduction in transfection efficiency at optimum N/P ratio. The results suggested that the in vitro delivery performance of 4-arm PRX was molecular weight-dependent, which can be explained by the reduced level of plasmid condensation by low-molecular weight polycations. The molecular-weight dependent transfection efficiency was also reported with other polycations including poly(lysine) (Ward et al. (2001) Blood, 97: 2221), polyethyleneimine (Fischer et al. 91999) Pharmaceut. Res. 16: 1273), etc. In addition to MC38 cells, we also demonstrated abundant tdTomato expression in B16 melanoma cells (FIG. 27, panel C) and normal cells (not shown) treated by tdTomato plasmid laden 4-arm PRX. The results suggested that the 4-arm PRX platform could accommodate multiple cell types. A separate MTS cytotoxicity assay demonstrated that 4-arm PRX was devoid of toxicity in MC38 cells up N/P ratio of 100:1 for 72 h (FIG. 28).
In general, the direct in vitro transfection study of 4-arm PRX analogues provided further insights into the role of multiple design features along the polymer structure. Our optimized PRXs exhibit the following characteristics, i.e., 4-arm PEG backbone with a molecular weight of 10 kDa, 2 out 4 arms protected,  ̃26 CD rings per PRX molecule, and  ̃6 amines per CD ring. We are aware of other design features yet to be optimized, including the type of cyclodextrin derivatives, the type of cationic functional groups, bulky end-caps with additional functionalities, etc. However, we decided to generate in vivo data at this point because the decision making of these parameters may require in vivo data input, including disease-specific considerations. The features of optimized 4-arm PRX were summarized in FIG. 20, panel A, and the self-assembly of PRX/plasmid was confirmed by AFM topographs. The polyplex nanoparticles formed by optimized 4-arm PRX and plasmid had a hydrodynamic size of 172±8.7 nm (PDI=0.18), with an average zeta potential of 15.3±3.2 mV.
Improved Pharmacokinetics (PK) and Biodistribution in Plasmid Delivery by 4-Arm PRX Compared to Linear PRX Nanocarrier
In order to determine whether the 4-arm design improved the biodistribution and PK profile post IV injection, comparative analysis on PK parameters was performed in C57BL/6 mice. To quantify plasmid concentration in the blood, plasmid was covalently labeled by Cy3 fluorescent probe. Animals were IV injected with Cy3-plasmid laden 4-arm PRX at dose of 5 mg plasmid/kg (PRX dose: 15 mg/kg). The control is the nano assembly formed by linear PRX complexed with the same amount of plasmid, which exhibited similar level of gene packaging capabilities (FIG. 29) and in vitro transfection efficiency (FIG. 30). Plasma was collected at the indicated time points (0.083, 1, 2, 4, 8 and 24 h). The plasmid concentration in each sample was calculated based on the fluorescence intensity using plasmid standard curve, and expressed as total ID/mL (total injection dose per mL) (FIG. 20, panel B). The 1st measurement at 0.083 h represents Cmax. The PK parameters of each formulation were assessed using PKSolver software (Zhang et al. (2010) Comp. Meth. Prog. Biomed. 99: 306). When delivered by linear PRX, >90% ID/mL declined 5 min post injection, which can be reflected by AUC and Cmax results. This clearly contrasted with 4-arm PRX, which maintained an AUC of 73.5% ID/mL-h (compared to 8.8% ID/mL·h in the case of linear PRX). Four-arm PRX significantly prolonged the circulatory t/2 of plasmid from <0.083 h to 5.8 h in mice. To further corroborate this phenomena, we incubated plasmid laden 4-arm PRX or linear PRX with a representative opsonin protein (mouse immunoglobulin IgG) abiotically. Compared to linear PRX, native gel electrophoresis demonstrated significantly reduced IgG binding to 4-arm PRX nanoparticles (FIG. 31). However, we found the retardation of IgG by linear PRX, which suggested significant opsonization in biological solutions such as serum (Owens & Peppas (2006) Int. J. Pharmaceut. 307: 93). Presumably, the reduced interaction between 4-arm PRX particle and opsonin protein contributed to its prolonged circulatory t/2 and enhanced PK profile in vivo.
The improved PK and prolonged t1/2 prompted us to consider the use of such carrier for targeted gene delivery at solid tumor site, which is colon cancer in this case. It is generally believed that IV-injected nanoparticles tend to accumulate in solid tumor partially due to the abnormal tumor vasculature and enlarged tumor fenestration, a.k.a. enhanced permeability and retention (EPR) effect (Maeda et al. (2000) J. Control. Release, 65: 271). In order to determine whether the redesigned PRX carrier improves plasmid delivery and tumor targeting, imaging studies were performed in C57BL/6 mice model bearing subcutaneous MC38 tumor. To determine the biodistribution, ex vivo imaging of the tumors and major organs was performed 24 h post IV injection of Cy3-labeled plasmid PRX (FIG. 20, panel C). The radiance efficiency of labeled plasmid in tumors and other organs was quantified by IVIS software and normalized to control. The majority of plasmid delivered by linear PRX was entrapped in lung, the most typical off-target organ for cationic gene carrier (Morille et al. (2008) Biomaterials, 29: 3477), but barely distributed in tumor presumably due to non-specific binding and rapid clearance of opsonin-attached linear PRX particles (FIG. 20, panel B). However, when delivered by 4-arm PRX, minimized distribution in lung was observed (similar to control mice), and abundant plasmid uptake was shifted to the tumor site (FIG. 20, panel C). The liver was still a major site of plasmid distribution, a phenomena commonly observed for IV injected nanoparticles subjected to sequestration by Kupffer cells (Moghimi et al. (2001) Pharmacol. Rev. 53: 283). Hardly any plasmid was detected in the heart, spleen or kidney. The Cy-3 labelling of plasmid allowed the visualization of the abundance of plasmid at tumor site. To facilitate the interpretation on intratumoral particle distribution, the tumor blood vessels were stained with CD31 immunofluorescence (FIG. 20, panel D). We demonstrated higher plasmid abundance at the tumor site for 4-arm PRX. The CD31 staining suggested the plasmid laden 4-arm-PRX traveled from blood vessels and accessed the tumor tissue. In addition, perinuclear distribution of plasmid was confirmed. Furthermore, we performed an in vivo reporter transfection study with IV injected tdTomato plasmid laden 4-arm PRX and linear PRX in MC38 tumor bearing mice. Western blot identification of protein expression from tumor extracts was performed 7 days post injection (FIG. 32). As expected, hardly any tdTomato expression was detected in MC38 tumors receiving linear PRX. However, tdTomato signals were identified in 4-arm PRX treated tumor, which demonstrated the feasibility of systemic delivery of plasmid by 4-arm PRX that leads to successful protein expression at tumor site. Collectively, careful tuning of the free PEG moieties on 4-arm PRX effectively enhanced the PK profile and distribution, and did not significantly compromise gene packaging properties or transfection efficiency. Given this background, we continued to use this optimized 4-arm PRX for therapeutic IL-12 plasmid delivery in the same syngeneic MC38 colon cancer model.
Systemic Delivery of Interleukinin-12 Plasmid by 4-Arm PRX Leads to Efficacious Anti-Tumor Effect Through Concurrent Activation of Innate and Adaptive Immunity
To demonstrate the therapeutic impact of our PRX, we used the optimized carrier to deliver an IL-12 plasmid (pIL-12), which encodes a potent cytokine that bridges the innate and adaptive immunity in solid tumor, including colon cancer (Tugues et al. (2015) Cell Death & Diff 22: 237). IL-12 targets natural killer (NK) cells and T lymphocytes, effectively stimulating their activity and the secretion of IFN-γ (a cytokine coordinating anticancer defense) (Lasek et al. (2014) Cancer Immunol. Immunotherap. 63: 419). Moreover, IL-12 has proven to be very effective in various solid tumor models for both immunogenic (e.g., CT26 colon cancer (Melero et al. (1999) Gene Therap. 6: 1779), RENCA renal cancer (Brunda et al. (1993) J. Exp. Med. 178: 1223)) and poorly immunogenic tumor models (e.g., LLC lung cancer (Cui et al. (1997) Science, 278: 1623), B16 melanoma (Tahara et al. (1994) Canc. Res. 54: 182)) in mice. While there is high level of awareness and interest in using IL-12 for solid tumor treatment, practical use of IL-12 as a cancer therapy requires novel delivery mechanism because recombinant IL-12 (rIL-12) protein did not meet the successful criteria in patients because of serious side effects. The adverse effects in human and preclinical models include fatal pulmonary, hepatic, intestinal and hematopoietic toxicities (Car et al. (1999) Toxicol. Path., 27: 58). This seems to be true for both IP (Lenzi, ClinicalTrials.gov Identifier: NCT00003046, 2004) and IV (Carson, ClinicalTrials.gov Identifier: NCT01468896, 2011) administration of rIL-12 in solid tumor patients. An important lesson from rIL-12's failures is that IL-12 protein appears to elicit more potent antitumor responses when existing directly in the tumor whereabouts, rather than systemically (Lasek et al. (2014) Cancer Immunol. Immunotherap. 63: 419). To address the challenges in IL-12 immunotherapy, we investigated the IV-injectable 4-arm PRX as a delivery carrier for plasmid encoding IL-12 (pIL-12, MW=4.8 kbp, InvivoGen). The 1st set of animal experiment is a short-term study, in which pIL-12 (MW=4.8 kbp, InvivoGen) laden 4-arm PRX was IV injected once (5 mg plasmid/kg) into mice bearing subcutaneous MC38 tumor. 3 or 7 days post single IV injection, tumors and major organs were harvested for ELISA detection of IL-12 (p70). At both time points, significantly enhanced IL-12 production was observed in PRX group compared to saline control at tumor site (FIG. 21, panel A). In most normal organs, such as spleen, lung, kidney and heart where rIL-12 leads to toxicity (Ryffel (1997) Clin. Immunol. Immunopath. 83: 18) no significantly elevated IL-12 was detected (FIG. 33). Importantly, IV pIL-12 PRX did not generate detectable IL-12 level in serum, which is crucial in reducing systemic off-target toxicity (Car et al. (1999) Toxicol. Path., 27: 58). With a view to elucidate any nonspecific IL-12 stimulation (presumably related to the general immunogenicity of bacteria-derived plasmid) (Dow et al. (1999) J. Immunol. 163: 1552), tumor mice receiving tdTomato plasmid laden 4-arm PRX (pC 4-arm PRX) were used as an additional control. Our data demonstrated that no significant secretion of IL-12 was found in tumors receiving IV pC laden PRX. This finding is in agreement with literature (Lohr et al. (2001) Canc. Res. 61: 3281). Moreover, the time-dependency of IL-12 expression at the tumor site provides the rationale for planning the injection regimen in the following proof-of-principle efficacy study.
For the anti-tumor efficacy study, we subcutaneously implanted luciferase-expressing MC38-luc cells to C57BL/6 mice. Following tumor growth to 5-8 mm in size, the mice received IV injections of 5 mg plasmid/kg twice per week, 5 injections in total (FIG. 21, panel B). Control mice received IV injection with saline or pC laden 4-arm PRX. Tumor growth was monitored in situ by IVIS bioluminescence imaging (FIG. 21, panel B), followed by euthanization of animals on day 21. Quantitative expression of tumor growth by IVIS (the intensity of tumor signals normalized to day 1), demonstrated significantly slower tumor growth when treated by pIL-12 laden 4-arm PRX, compared to saline or pC controls. Representative tumor images after euthanizing the animal on day 21 (FIG. 34) further revealed the anti-tumor effect.
Shown in the schematic FIG. 21, panel C, as a potent inducer of anti-tumor immunity, IL-12 directly augments the proliferation and cytolytic potential of NK cells and promotes the development of CD8+ T cells in tumor microenvironment, including colon cancer (Caruso et al. (1996) Proc. Natl. Acad. Sci. USA, 93: 11302). In addition, the anti-angiogenesis function by IL-12 contributes pivotally to the tumoricidal efficacy (Colombo & Trinchieri (2002) Cytokine & Growth Factor Rev. 13: 155). To dissect the immunomodulatory effect elicited by IL-12 expression, the tumor tissues (day 21) were used for IHC and multi-parameter flow cytometry analysis (Lu et al. (2017) Nat. Comm. 8: 1811). IHC staining for CD8, NK1.1 and IFN-γ+ showed that pIL-12 laden 4-arm PRX resulted in significantly enhanced recruitment of CD8+ T cells along with NK cells (FIG. 21, panel D). These findings were corroborated by flow cytometry (FIG. 21, panel D and FIG. 35), suggesting that pIL-12 4-arm PRX enhanced the CD45+CD3+CD8+ TILs populations (by 1.8-fold) and CD45+NK1.1 populations (by 4-fold) compared to saline or pC treated groups. As a central effector in IL-12-mediated anti-tumor immunity, significantly increased IFN-γ release was revealed by IHC staining of pIL-12 4-arm PRX treated tumor section (FIG. 21, panel D). Phenotypic identification of CD45+CD8+IFN-γ+ and CD45+NK1.1+IFN-γ+ population suggested the recruited NK cells and CD8+ T cells were the sources for IFN-γ+ production. Furthermore, immunofluorescence staining of CD31+ blood vessels (FIG. 21, panel E), demonstrated distinct anti-angiogenesis effect in tumor sections treated by pIL-12 laden 4-arm PRX.
pIL-12 Laden 4-Arm PRX Improves Toxicity Profiles in Mice Compared to rIL-12
The major reason for the rIL12 failure is its safety issue, which is a key concern for IL-12 immunotherapy. Rapid buildup of rIL12 systemically leads to significant toxicity, including a severe impact on hepatic serum enzymes, leukopenia, pulmonary edema and interstitial macrophage infiltrates in lung tissues, etc (Car et al. (1999) Toxicol. Path., 27: 58). The possibility of reducing IL-12 toxicity by encapsulated plasmid delivery is one of the major objectives of this study. In order to address IL-12 toxicity through IV plasmid delivery, in a separate experiment, we performed IV injections following exactly the same treatment regimen as the tumor inhibition study in normal C57BL/6 mice. We preferred normal mice in this case because the late stage tumor burden may introduce a large standard deviation within the same group, leading to complexity for data interpretation. The pIL-12 laden PRX did not elicit adverse effects after repetitive IV injections in the most parameters in the blood biochemistry measurement, such as liver function enzymes (e.g., AST, ALT, ALP), kidney panel (BUN and creatinine) at both 7 days and 21 (FIG. 22, panel A). Transit and moderate decrease of white blood cells, lymphocytes and neutrophils were observed in mice receiving pIL-12 4-arm PRX on day 7; however, these abnormalities were reversible at day 21 without medication. For comparison, we also included IV injection of rIL-12 at a rodent therapeutic dose (100 μg/kg) in the literature (Brunda et al. (1993) J. Exp. Med. 178: 1223). This allowed for the demonstration of severe and extensive abnormalities in multiple organs in animals treated with rIL-12, similar to the side effects in the human (Leonard et al. (1997) Blood, 90: 2541). Different from pIL-12 PRX, rIL-12 induced adverse changes were persistent, up to 21 days post treatment. Moreover, major organs, such as the lung, kidneys, heart and spleen were collected from the same safety animal experiment. Animals receiving treatment with rIL-12 showed sign of pulmonary toxicities, such as pulmonary edema and interstitial thickening in H&E staining of lung section (FIG. 22, panel B). In contrast, no damage was seen in the lungs of animals treated with saline and pIL-12 laden PRX. In rIL-12 group, histological assessment of kidney tissues showed glomerular swelling and edema of Bowman's space in the glomeruli of the kidneys (FIG. 22, panel B). However, this histological alteration was not found in other groups or accompanied by urea and electrolyte disturbances.
For IL-12, there is continuous interest and critical need to improve PK and safety, with a hope to practically implement safe and efficacious cancer immunotherapy. Other strategies have immerged including developing tumor-targeting IL-12 derivatives (NHS-IL-12) (Fallon et al. (2014) Oncotarget, 5: 1869) and IL-12 gene therapeutics (Hemandez-Alcoceba et al. (2016) Immunother. 8: 179). GEN-1 (Thaker et al. (2017) Gynecologic Oncol. 147: 283) formulated with IL-12 plasmid and PEG-PEI-cholesterol lipopolymer, is designed for IP administration in ovarian cancer. Unlike ovarian cancer that primarily disseminates within the peritoneal cavity with massive ascites (Lengyel (2010) Am. J Pathol. 177: 1053), colon cancer is a deep-seated solid tumor that metastasizes to lung and liver (Sadahiro et al. (2014) J. Clin. Oncol. 43: 444; Leake (2014) Nat. rev. Gastroentrol. & Amp Hepatology, 11: 270). While local injection of IL-12 might lead to systemic anti-cancer immunity, safe and effective IV-injectable formulation is still the preferred route for pIL-12 delivery from tumor targeting perspective (Hallaj-Nezhadi & Lotfipour (2010) J. Pharm. Pharm. Sci. 13: 472). Further studies are needed to investigate the capability of metastasis management.
While our current formulation (that relies on passive targeting principle to biodistribute at colon cancer site) has led to promising data, we can also include tumor targeting ligand such as iRGD peptide (Liu et al. (2017) J. Clin. Invest. 127: 2007). However, we also consider the design complexity and the cost increase of each component in terms of clinical application. Moreover, preclinical and clinical data have suggested the benefit of IL-12 combination because repeated IL-12 dosing may activate various immunosuppressive mechanisms (Lasek & Zagozdzon, in Interleukin 12: Antitumor Activity and Immunotherapeutic Potential in Oncology, Springer, 2016, 43). Thus, it is also interesting to look at the effect of pIL-12 PRX monotherapy or combined with treatments such as other cytokines (e.g., IL-2) (Addison et al. (1998) Gene therapy, 5: 1400), neoadjuvant chemotherapeutic agents (e.g., oxaliplatin, doxorubicin and paclitaxel) (Kayashima et al. (2010) J. Immunol. 185: 698) and checkpoint inhibitors (e.g., anti-PD-1, anti-PD-L1, anti-CTL4 and IDO inhibitors) (Fallon et al. (2017) Oncotarget, 8: 20558).
The multifunctional properties of multi-arm PRX can be further tuned to accommodate different clinical needs. In Scheme 1 (see FIG. 23), we included the list of structural design features and their possible impacts. Fine-tuning of cationic entities and their spatial arrangement, as well as other components along PRX structure, can make this delivery platform available for multiple APIs, including large plasmid (e.g., CRISPR/Cas9 plasmid for gene editing). However, while the use of multi-arm PRX platform is practical for these purposes, it is necessary to consider the disease-specific complexity that may require extra optimization and re-design of the carrier.
To conclude, we have established a multi-functional multi-arm PRX platform that is suitable for systemic nucleic acid delivery in vivo. Our comprehensive biodistribution and PK analyses demonstrated the spatially selective design of inclusion complexation of CD rings in multi-arm PRX polymer maintains appropriate degree of PEGylation, which play a key role for the improved t/2 and bioavailability. When delivering a pIL-12 plasmid to a colon tumor site, we also demonstrated a protective and effective plasmid self-assembly, which led to efficacious and safe immunogene therapy at intact animal level.
Materials and Experimental Methods
Materials
α-Cyclodextrin, triethylamine (TEA), Z-L-tyrosine, Benzotriazol-1-yl-oxy-tris(dimethylamino) phosphonium hexafluorophosphate (BOP), 1-hydroxybenzotriazole (HOBt,) N,N-diisopropylethylamine (DIEA), 1,1′-carbonyldiimidazole (CDI), N,N-dimethylethylenediamine (DMAE), dimethylformamide (DMF), dimethyl sulfoxide (DMSO) were purchased from Sigma Aldrich. Four-arm PEG tetra-amine hydrochloride salt with different molecular weight (5 kDa, 10 kDa or 20 kDa) and linear PEG-diamine hydrochloride salt (3.5 kDa) were purchased from Jen Kem Technology. NHS-fluorescein and Snakeskin dialysis tubing (MWCO=3.5 kDa or 10 kDa) were purchased from Thermo Fisher. Plasmid pUNO1-mIL12 (p40p35) (designated as pIL-12) encoding mouse IL-12 p70, was provided by InvivoGen. Plasmid encoding tdTomato reporter protein was provided by Addgene (Addgene plasmid 30530). MatrigelTM matrix basement membrane was purchased from BD Bioscience, USA. Centrifugal filter units (MWCO=3 kDa, 10 kDa, 100 kDa) were purchased from EMD Millipore.
Synthesis of 4-Arm PRX Analogues
4-Arm-PEG Backbone with End-Caps.
4-arm PEG tetra-amine hydrochloride salt 10 kDa (103 mg) was dissolved in DMF (5 mL) with TEA (6 mg) before NHS-fluorecein was added and stirred at room temperature for 24 h. The amount of NHS-fluorecein was manipulated to achieve different number of fluorescein end-caps, i.e., 4.7 mg NHS-fluorecein for 1-occupied 4-arm PEG amine (4-arm PEG:NHS-fluorescein=1:1 molar ratio), 9.5 mg NHS-fluorecein for 2-occupied 4-arm PEG amine (4-arm PEG:NHS-fluorescein=1:2 molar ratio) and 14.2 mg NHS-fluorecein for 3-occupied 4-arm PEG amine (4-arm PEG:NHS-fluorescein=1:3 molar ratio), respectively. The resulting solution was precipitated in cold diethyl ether, dissolved in DI water and purified by repeated washing with DI water in centrifugal filter units (MWCO=3 kDa), and lyophilized (Labconco FreeZone). To detect the average molecular weight after modification, 4-arm PEG amine compounds with different number of fluorescein end-caps were dissolved in THF/H2 O (1:1, v/v) at a concentration of 10 mg/mL for MALDI-TOF (Bruker Ultraflex). Fluorescein occupied 4-arm PEG amine compounds were dissolved in deuterated water for 1H-NMR spectroscopy.
4-Arm Polypseudorotaxane.
Fluorescein occupied 4-arm PEG amine (100 mg) was added to a saturated solution of α-CDs (1.01 g in 7 mL of DI water) and stirred at room temperature for 24 h, resulting in supramolecular polypseudorotaxane formed from α-CDs threading onto 4-arm PEG backbone. The precipitate was collected via centrifugation at 3,000 rcf for 10 min and lyophilized to obtain 4-arm polypseudorotaxane as yellow powder.
4-Arm Polyrotaxane.
To prevent the de-threading of α-CDs, bulky end caps (Z-tyrosine) were further introduced to 4-arm polypseudorotaxane. An example was given here for 2/4CD 4-arm polypseudorotaxane preparation. Z-L-tyrosine-OH (126 mg), HOBt (54 mg), BOP (177 mg) and DIEA (69 μL) were dissolved in 2.5 mL anhydrous DMF. 370 mg polypseudorotaxane was then added and the reaction was stirred at room temperature for 24 h. The mixture was precipitated in 50 mL diethyl ether, and sequentially washed by acetone (50 mL), methanol (50 mL) and DI water (15 mL). Each washing steps were 2 h at room temperature under constant stirring and the precipitate was collected via centrifugation at 3,000 rcf for 10 min. After the last washing step, the 4-arm polyrotaxane was lyophilized. 1H-NMR was performed in DMSO-d6 to characterize the product.
4-Arm Polyrotaxane-DMAE.
An example was given here for the synthesis of 2/4CD 4-arm PRX with 6 amines per CD. Z-L-Tyrosine capped 2/4CD 4-arm polyrotaxane (100 mg) was dissolved in dry DMSO (2 mL). CDI (364 mg, 30 molar excessive to α-CDs) was added and the reaction was stirred for 3 h under nitrogen atmosphere. DMAE (1 mL) was then added dropwise to the solution, and the reaction was further stirred overnight at room temperature. The resulting mixture was precipitated in diethyl ether, and washed sequentially by acetone (50 mL) and methanol (50 mL). Each washing steps were 2 h at room temperature under constant stirring and the precipitate was collected via centrifugation at 3,000 rcf for 10 min. The precipitate was redissolved in DI water and dialyzed against DI water for 72 h (MWCO=3 kDa). The final product of 4-arm PRX was lyophilized as yellow powder. The density of amine functionalization on α-CD was manipulated via tuning the feed ratio between CDI and α-CDs in 4-arm polyrotaxane. CDI at 5 molar excessive to α-CDs resulted in 4-arm PRX with 1 amine group per CD, and CDI at 20 molar excessive to α-CDs resulted in 3 amine groups per CD, respectively. The purified 4-arm PRX was lyophilized and 1H-NMR characterization was performed in deuterated water to characterize the product. In addition, 2/4CD 4-arm polyrotaxane-DMAE with 5 kDa or 20 kDa 4-arm PEG backbone were synthesized, following the same procedures and molar ratio between reactants for 2/4CD 4-arm polyrotaxane-DMAE (6 amines per α-CD) with 10 kDa backbone.
Synthesis of Linear PRX
The synthesis of linear PRX was performed as previously reported (Yamashita et al. (2006) Nat. Protocol. 1: 2861). 100 mg of linear PEG-diamine hydrochloride salt (3.5 kDa) was dissolved in a saturated solution of α-CDs (1.01 g in 7 mL of DI water) and stirred for 24 h at room temperature to give linear polypseudorotaxane as white precipitate. The precipitate was collected via centrifugation at 3,000 rcf for 10 min and lyophilized. The lyophilized white powder (190 mg) was then dissolved in a mixture solution of Z-L-tyrosine-OH (82 mg), HOBt (35 mg), BOP (115 mg) and DIEA (45 μL) in 0.5 mL anhydrous DMF. The reaction was stirred at room temperature for 24 h. The mixture was precipitated in 50 mL diethyl ether, and sequentially washed by acetone (50 mL), methanol (50 mL) and DI water (50 mL). The dried precipitate (108 mg) was dissolved in 2 mL dry DMSO and CDI (300 mg) was added. The reaction was stirred for 3 h under nitrogen atmosphere. DMAE (1 mL) was then added dropwise to the solution, and the reaction was further stirred overnight at room temperature. The resulting mixture was precipitated in diethyl ether and washed in succession in acetone (50 mL), methanol (50 mL). The precipitate was redissolved in DI water, dialyzed against DI water for 72 h (MWCO=3 kDa) and lyophilized to result in linear PRX.
Physicochemical Characterization of Plasmid Laden 4-Arm PRX
The size and ζ-potential of plasmid laden 4-arm PRX were measured by a ZETAPALS instrument (Brookhaven Instruments Corporation), with an equivalent plasmid concentration of 1 μg/mL. The morphology of plasmid laden 4-arm PRX was visualized by atomic force microscope (AFM). Plasmid laden 4-arm PRX was directly added to mica substrate (1 cm×1 cm), and free plasmid was premixed with 5 mM MgCl2-HEPES buffer before addition to mica substrate. The equivalent concentration of plasmid was 0.2 μg/mL. The samples were dried with nitrogen gas and imaged on Bruker Dimension FastScan AFM. DNA gel retardation assay was performed with Precast agarose gel (Sigma Aldrich). Plasmid DNA was complexed with 4-arm PRX analogues in multiple N/P ratio, with a constant plasmid concentration of 50 μg/mL. Samples were loaded in gel loading buffer (Sigma Aldrich), running in TBE buffer at 50 V for 30 min, followed by visualization on gel imaging system (MultiImage II AlphaImager HP, Alpha Innotech).
In Vitro Cell Culture and Transfection
To facilitate bioluminescence imaging of tumor growth, MC38 colon adenocarcinoma cells were permanently transfected with a luciferase-lentiviral vector in the UCLA vector core facility, as previously described (Meng et al. (2015) ACS Nano, 9: 3540). Limiting dilution was performed to generate monoclonal MC38 cells. MC38 cells were cultured in DMEM, supplemented with 10% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, and 2 mM L-glutamine. 24 h prior to transfection, MC38 cells were seeded at 1×104 cells/well on 96-well plates. Plasmid encoding tdTomato reporter protein was complexed with 4-arm PRX analogues in multiple N/P ratios and incubated with MC38 cells (1 μg plasmid/mL) in medium containing 10% FBS. MC38 cells were further incubated for 72 h and the expression of tdTomato was examined on a fluorescence microscope (Observer D1, Zeiss). For pIL-12 transfection, optimized 4-arm PRX or linear PRX were complexed with pIL-12 and incubated with MC38 cells (1 μg plasmid/mL) for 72 h. The supernatant of cell culture media were collected and subjected to ELISA detection of IL-12 p70 protein with DuoSet ELISA kit (R&D Systems). Untreated MC 38-luc cells or MC38 cells treated with control plasmid (pC) laden 4-arm PRX were also detected as control. For real-time qPCR detection, total RNA was isolated from MC38 cells with RNeasy Mini Kit (Qiagen), and then reverse-transcribed with iTaq University SYBR Green Supermix (Biorad). The following primers were used: IL12: forward, 5′-AAC CTC ACC TGT ACA CGC C-3′ (SEQ ID NO:301), reverse, 5′-CAA GTC CAT GTT TCT TTG CAC G-3′ (SEQ ID NO:302); β-actin, forward, 5′-AGA GCT ACG AGC TGC CTG AC-3′ (SEQ ID NO:303), reverse, 5′-AGC ACT GTG TTG GCG TAC AG-3′ (SEQ ID NO:304). The ACT for IL-12 mRNA was divided by that of β-actin to give the fold increase of gene expression, and then normalized to untreated control to obtain the relative IL-12 expression.
Native Gel Electrophoresis
Mouse immunoglobulin (IgG) was prepared as 10 μg/μL aqueous solution and incubated with pIL-12 laden optimized 4-arm PRX or linear PRX (plasmid concentration 1 μg/μL) for 30 min at 37° C. The treated IgG solutions were directly loaded in 4-16% NativePAGE gel system (10 μg IgG per lane) for 100 min at 150 V. The protein bands were visualized by Coomassie blue stainingN. The intensity of IgG band was semi-quantified by Image J software.
In Vivo Biodistribution and PK Study
Female C57BL/6 mice ( ̃8 weeks) were purchased from The Jackson Laboratory and maintained under pathogen-free conditions. All animal experiments were performed with protocols approved by the UCLA Animal Research Committee. To study the PK profile, Cy3-labeled plasmid was prepared with Label IT® TrackerTM kit (Mirus Bio) according to manufacturer's instruction. Normal C57BL/6 mice received single IV injection of Cy3-plasmid laden 4-arm PRX or linear PRX (5 mg plasmid/kg). This is equivalent to PRX dose of 15 mg/kg. Plasma was collected at the indicated time points (0.083, 1, 2, 4, 8 and 24 h). The fluorescence intensity of plasma samples were detected on microplate reader (M5e, Molecular Device), with Ex/Em of 544 nm/590 nm. The plasmid concentration in the sample was calculated based on the fluorescence intensity using the standard curve of plasmid. The PK profiles of Cy3-labeled plasmid were assessed using PKsolver software (Zhang et al. (2010) Computer methods and programs in biomedicine, 99: 306). We continued to perform biodistribution study in a subcutaneous tumor bearing mice model. Female C57BL/6 mice were subcutaneously inoculated in the right flank with MC38 cells (1×106 cells/mouse). The animals were maintained under pathogen-free conditions and all animal experiments were approved by the UCLA Animal Research Committee. Following tumor growth to 8-10 mm in size, mice were IV injected with Cy3-labeled plamid laden 4-arm PRX, or linear PRX (5 mg plasmid/kg). 24 h post IV injection, the mice were sacrificed to collect tumors and the major organs (heart, liver, spleen, lung and kidney). Ex-vivo imaging was performed on IVIS system (Xenogen) with Ex/Em of 535 nm/575-650 nm. Tumor tissues were then embedded in OCT reagents and cryo-sectioned. CD31 immuno-fluorescence staining was performed to locate the blood vessels as we shown before (Meng et al. (2011) ACS Nano, 5: 4131). The intratumoral distribution of Cy3-labeled plasmid was visualized by confocal microscopy (SP8-SMD, Leica).
ELISA and Western Blot Analysis for Short-Term In Vivo Efficacy Study.
To study the short-term efficacy, C57/BL6 mice bearing subcutaneous MC38 tumors were IV injected with pIL-12 laden 4-arm PRX (5 mg plasmid/kg), tdTomato plasmid laden 4-arm PRX (as non-functional control) or saline. To validate the in vivo transfection efficacy, western blot detection of tdTomato reporter protein was performed in MC38 tumors 7 days post IV injection. The snap-freezed MC38 tumors were weighed and homogenized in RIPA buffer (Cell Signaling Technology) supplemented with protease inhibitor cocktail (Roche Diagnostics), followed by centrifugation at 10,000 rcf for 20 min. Western blot was performed according to published procedures (Lu et al. (2017) Nat. Comm. 8: 1811). Briefly, electrophoresis was performed on 4-12% SDS-PAGE gel (Invitrogen), and the proteins were subsequently transferred to a PVDF membrane. After blocking in 5% BSA, the membrane was overlaid with primary antibodies including anti-mCherry (ab167453, Abcam) to detect tdTomato and anti-vinculin XP® mAb (Cell Signaling Technology) as loading control. Staining with HRP-conjugated secondary antibodies was sequentially performed and the blots were developed by the addition of the ECL solution.
To detect the IL-12 expression in vivo, 3 and 7 days post IV injection, the mice were sacrificed, and tumors, major organs (heart, liver, spleen, lung and kidney) were collected and snap-freezed in liquid nitrogen. Serum was also collected for IL-12 detection. For ELISA detection of IL-12, the snap-freezed MC38 tumors and major organs were weighed, cut into pieces and suspended in tissue extraction reagent I (Invitrogen) supplemented with protease inhibitor cocktail (Roche Diagnostics). Tissue samples were then homogenized on ice and centrifuged at 10,000 rcf for 20 min. Serum samples were centrifuged at 3,000 rpm for 10 min before testing. The above procedures were all performed at 4° C. The IL-12 p70 protein level in tissue extracts and plasma was determined by Quantikine ELISA Kit (R&D Systems).
In Vivo Antitumor Efficacy Study
Female C57BL/6 mice were subcutaneously inoculated in the right flank with MC38-luc cells (1×106 cells/mouse). Following tumor growth to 5-8 mm in size, C57BL/6 mice were randomly assigned to 3 groups (n=4), and received IV injection of pIL-12 laden 4-arm PRX, pC laden 4-arm PRX as non-functional control, or saline twice per week (5 mg plasmid/kg/injection, 5 injections in total). To monitor the tumor burden weekly, mice received intraperitoneal injection of 75 mg/kg D-Luciferin for 8 min, before IVIS detection of bioluminescent signal from tumor site. Quantitative expression of tumor growth was obtained by normalizing the bioluminescent radiance of tumor to day 1. The size of the tumor were also measured by caliper and plotted vs. time. The size of tumor was calculated as π/6×length×width2, in which a represented width of the rumor and b represented the length of the tumor. The animals were sacrificed on day 21, and the tumor tissues were collected for further analysis.
Flow Cytometry Analysis
Right after tissue collection on day 21, the treated MC38 tumors were cut into smaller pieces digested in DMEM with 0.5 mg/mL collagenase type I (Worthington Biochemical Corporation) at 37° C. for 1 h. The digested tissues were gently meshed though a 70 μm cell strainer and treated by ACK lysing buffer (Gibco) as per manufacturer's instructions. The harvested cells were washed twice and resuspended in stain buffer (BD Pharmigen), and incubated with FcBlock (TruStain fcXTM anti-mouse CD16/32, clone 93, BioLegend) to avoid nonspecific binding. Staining was then performed with primary antibodies for 30 min at 4° C. The following anti-mouse antibodies were purchased from eBiosciences: CD45-eFluor 450 (clone 30-F11), CD8α-Alexa Flour 488 (clone 53-6.7), NK1.1-PerCP-Cyanine 5.5 (clone PK136), CD3e-APC-eFlour780 (clone 17A2). For the staining of intracellular Interferon-γ, the cell were treated with intracellular fixation and permeabilization kit (eBioscience) as per manufacturer's instruction, and stained with anti-Interferon-γ-APC (clone XMG1.2, eBioscience). After washing, cells were analyzed on a flow cytometer (LSRII, BD Biosciences). The data were processed by FlowJo software (Tree Star). Dead cells and doublets were excluded based on forward and side scatter.
Immunohistochemistry (IHC) Analysis
MC38 Tumor tissues harvested on day 21 were fixed in 10% formalin solution. Tissue sectioning and IHC staining were performed by the UCLA Jonsson Comprehensive Cancer Center Translational Pathology Core Laboratory. Briefly, the slides were deparaffinized, incubated in 3% methanol-hydrogen peroxide, followed by incubation with 10 mM EDTA at 95° C. using the Decloaking NxGen Chamber (Biocare Medical, DC2012). The slides were incubated with individual primary antibodies for 1 h including anti-CD8 (eBioscience, 4SM15, 1/100), anti-NK1.1 (Bioss, bs4682R, 1/100), anti-IFN-γ (Abcam, ab9657, 1/200) or anti-IL-12p70 (Novus Biologics, NBP1-85564, 1/100). After washing, the slides were further incubated with HRP-conjugated secondary antibodies at room temperature for 30 min. After rinsing with PBST, the slides were incubated with 3,3′-diaminobenzidine and counterstained with hematoxylin. The slides were scanned by an Aperio AT Turbo Digital Pathology Scanner (Leica Biosystems).
Immunofluorescence Staining
To determine the density of CD31-positive blood vessels and evaluate the anti-angiogenesis effect, the treated MC38 tumor tissues harvested on day 21 were embedded with OCT reagent and cyro-sectioned. The sections were stained with anti-CD31 monoclonal antibody (Clone 390, BD Pharmingen) at 4° C. overnight. After removal of the primary antibody and washing in PBS 3 times, the Alexa Fluor® 647 secondary antibody was added and incubated for 1 h at room temperature, and counter-stained with DAPI. The stained slides were examined with a confocal microscope (SP8-SMD, Leica).
Safety Profile of pIL-12 Laden 4-Arm PRX
IV injection of pIL-12 laden 4-arm PRX, pC laden 4-arm PRX as non-functional control or saline was performed in non-tumor bearing C57BL/6 mice. The dose and injection scheme was the same as the antitumor efficacy study. For comparison, we also included IV mouse rIL-12 at a therapeutic dose (100 μg/kg). Mice were sacrificed on day 7 and day 21, blood and major organs (heart, liver, spleen, and lung) were collected. Major organs were fixed in 10% formalin, followed by paraffin embedding. Tissue sections were stained by Haemotoxylin and Eosin (H&E) for histological analysis. Blood chemistry test were also performed by Pathology & Laboratory Medicine Services from UCLA Division of Laboratory Animal Medicine (DLAM).
Statistical Analysis
Comparative analysis of the differences between groups was performed using the two-sided Student's t-test (Excel software, Microsoft). A statistically significant difference was determined at p<0.05. Values were expressed as mean±SD of multiple determinations, as stated in the figure legends.
It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

## Claims

1. A polyrotaxane carrier for in vivo delivery of a nucleic acid, said carrier comprising:
a multi-arm polyethylene glycol (PEG) backbone comprising 4 arms;
at least one cyclic compound having a cavity, where an arm of said multi-arm PEG backbone is threaded into the cavity of said cyclic compound forming an inclusion complex;
a bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound where said moiety inhibits dethreading of the cyclodextrin from the arm(s) of said backbone;
where two arms of said PEG backbone are free of cyclic compounds; and
where said carrier has a net positive charge.

2. The carrier of claim 1, wherein:
said PEG backbone has a molecular weight ranging from about 1.0 to about 10 kDA per arm; and/or
said PEG backbone comprise about 22 to about 227 ethylene oxides per arm; and/or
said PEG backbone has a molecular weight of about 2.5 kDa per arm.

3. The carrier of claim 1, wherein:
the arm(s) threaded into said cyclic compound(s) each bear on average from about 5 to about 110 cyclic compounds; and/or
the arm(s) threaded into said cyclic compound(s) each bear, on average, about 20 cyclic compounds per arm.

4. The carrier of claim 1, wherein:
said cyclic compound comprise a compound selected from the group consisting of a cyclodextrin, a crown ether, a cucurbituril and a cyclofructan; and/or
said cyclic compound comprises a cyclodextrin; and/or
said cyclic compound comprises a cyclodextrin selected from the group consisting of an α-cyclodextrin, a ß-cyclodextrin, a γ-cyclodextrin, a hydroxypropylated α-cyclodextrin, a hydroxypropylated ß-cyclodextrin, a hydroxypropoylated γ-cyclodextrin, a dimethylcyclodextrin, a chemically modified cyclodextrin (e.g., carboxyl modified cyclodextrin); and/or
said cyclic compound comprises a cucurbituril; and/or
said cyclic compound comprises a cucurbituril selected from the group consisting of cucurbit[5]uril, cucurbit[6]uril, cucurbit[7]uril, cucurbit[8]uril, cucurbit[9]uril, cucurbit[10]uril, and a chemically modified cucubituril; and/or
said cyclic compound comprises a cucurbit[6]uril (CB[6]).

5. The carrier of claim 1, wherein:
said cyclic compound(s) are substituted with one or more nucleophilic groups; and/or
said cyclic compound(s) are substituted with one or more amine groups or groups derived from an amine group; and/or
said cyclic compound(s) are substituted with one or more groups selected from the group consisting of a primary amine, a secondary amine, a tertiary amine, and an imine group; and/or
said cyclic compound(s) are substituted with one or more primary amines; and/or
the number of nucleophilic group substituted on the cyclic compound(s) ranges from 1 up to about 20 substitutions per cyclic compound; and/or
the cyclic compounds are substituted with nucleophilic groups to provide a positive zeta potential for said carrier ranging from about +1V or from about +5 mV up to about +50 m V, or up to about +25 mV.

6. The carrier of claim 1, wherein:
the bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound(s) comprises a compound having a 3 dimensional size greater than the internal diameter of the cyclic compound(s); and/or
the bulky moiety capping the terminal of the arm(s) threaded into said cyclic the bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound(s) comprises a moiety selected from the group consisting of Z-tyrosine, phenylalanine, a group having at least one benzene ring, and a group having at least one tertiary butyl; and/or
the bulky moiety capping the terminal of the arm(s) threaded into said cyclic the bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound(s) comprises a moiety selected from the group consisting of a Z-tyrosine, phenylaline, a benzyloxycarbonyl (Z) group, a 9-fluorenylmethyloxycarbonyl (Fmoc) group, a benzyl ester (OBz) group, a tertiary butylcarbonyl (Boc) group, and an amino acid-tertiary butyl ester (OBu) group; and/or
the bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound(s) comprises a Z-tyrosine.

7. A polyrotaxane carrier for in vivo delivery of a nucleic acid, said carrier comprising:
a multi-arm polyethylene glycol (PEG) backbone comprising at least three arms;
at least one cyclic compound having a cavity, where an arm of said multi-arm PEG backbone is threaded into the cavity of said cyclic compound forming an inclusion complex;
a bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound where said moiety inhibits dethreading of the cyclodextrin from the arm(s) of said backbone;
where at least one arm of said PEG backbone is free of cyclic compounds;
where said carrier has a net positive charge;
where:
at least one arm not threaded into said cyclic compound is terminated with a protecting group, and/or a fluorophore, and/or a targeting moiety; and/or
at least one arm not threaded into said cyclic compound are terminated with a protecting group selected from the group consisting of dansyl, acetyl, amide, and 3 to 20 carbon alkyl groups, Fmoc, Tboc, 9-fluoreneacetyl group, 1-fluorenecarboxylic group, 9-florenecarboxylic group, 9-fluorenone-1-carboxylic group, benzyloxycarbonyl, Xanthyl (Xan), Trityl (Trt), 4-methyltrityl (Mtt), 4-methoxytrityl (Mmt), 4-methoxy-2,3,6-trimethyl-benzenesulphonyl (Mtr), Mesitylene-2-sulphonyl (Mts), 4,4-dimethoxybenzhydryl (Mbh),Tosyl (Tos), 2,2,5,7,8-pentamethyl chroman-6-sulphonyl (Pmc), 4-methylbenzyl (MeBzl), 4-methoxybenzyl (MeOBzl), Benzyloxy (BzlO), Benzyl (Bzl), Benzoyl (Bz), 3-nitro-2-pyridinesulphenyl (Npys), 1-(4,4-dimentyl-2,6-diaxocyclohexylidene)ethyl (Dde), 2,6-dichlorobenzyl (2,6-DiCl-Bzl), 2-chlorobenzyloxycarbonyl (2-Cl-Z), 2-bromobenzyloxycarbonyl (2-Br-Z), Benzyloxymethyl (Bom), t-butoxycarbonyl (Boc), cyclohexyloxy (cHxO),t-butoxymethyl (Bum), t-butoxy (tBuO), t-Butyl (tBu), Acetyl (Ac), and Trifluoroacetyl (TFA); and/or
at least one arm not threaded into said cyclic compound is attached to a fluorophore; and/or
at least one arm not threaded into said cyclic compound is attached to a targeting moiety that specifically or preferentially binds to a cell; and/or
at least one arm not threaded into said cyclic compound is attached to a at least one arm not threaded into said cyclic compound is attached to a targeting moiety selected from the group consisting of an antibody, a receptor ligand, a nucleic acid aptamer, a peptide aptamer, neural cell adhesion molecule (NCAM), a cell penetrating peptide (CPP), a peptide aptamer, and a lectin; and/or
at least one arm not threaded into said cyclic compound is attached to a at least one arm not threaded into said cyclic compound is attached to a targeting moiety comprising a ligand that binds a receptor where said ligand is selected from the group consisting of transferrin, mannose, glucose, and folic acid; and/or
at least one arm not threaded into said cyclic compound is attached to a targeting moiety comprising transferrin.

8. The carrier of claim 1, wherein:
said bulky moiety is attached to an arm of said backbone by a cleavable linkage; and/or
said one or more nucleophilic groups are attached to said cyclic compounds by a cleavable linkage.

9. The carrier of claim 1, wherein:
said carrier is complexed with a nucleic acid; and/or
said carrier is complexed with an RNA; and/or
said carrier is complexed with a DNA; and/or
said carrier is complexed with a plasmid; and/or
said carrier is complexed with a plasmid that encodes a heterologous gene or cDNA; and/or
said carrier is complexed with a plasmid that encodes a class 2 CRISPR/Cas endonuclease and a guide RNA; and/or
the N/P ratio of said carrier complexed to a nucleic acid ranges from about 0.01:1 up to about 100:1, or from about 2:1 up to about 50:1, or up to about 40:1, or up to about 30:1, or up to about 25:1, or ranges from about 2:1 up to about 25:1; and/or
the N/P ratio of said carrier complexed to a nucleic acid is about 10:1.

10. A pharmaceutical formulation comprising:
a polyrotaxane carrier of claim 7; and
a pharmaceutically acceptable carrier.

11. A construct for the treatment of Duchenne Muscular Dystrophy, said construct comprising:
a polyrotaxane carrier comprising:
a multi-arm polyethylene glycol (PEG) backbone comprising at least three arms;
at least one cyclic compound having a cavity, where an arm of said multi-arm PEG backbone is threaded into the cavity of said cyclic compound forming an inclusion complex;
a bulky moiety capping the terminal of the arm(s) threaded into said cyclic compound where said moiety inhibits dethreading of the cyclodextrin from the arm(s) of said backbone;
where at least one arm of said PEG backbone is free of cyclic compounds; and
where said carrier has a net positive charge; and
where said carrier is complexed with a plasmid encoding a class 2 CRISPR/Cas endonuclease, and a guide RNA that hybridizes to a target sequence within intron 44 of a mutant dystrophin gene, and/or a second CRISPR/Cas guide RNA guide sequence that hybridizes to a target sequence within intron 55 of the mutant dystrophin gene.

12. The construct of claim 11, wherein:
the first CRISPR/Cas guide RNA comprises a guide sequence having 100% complementarity over 17 or more contiguous nucleotides with a first target sequence corresponding to intron 44 of the human dystrophin gene, and/or
the second CRISPR/Cas guide RNA comprises a guide sequence having 100% complementarity over 17 or more contiguous nucleotides with a second target sequence corresponding to intron 55 of the human dystrophin gene.

13. The construct of claim 11, wherein:
the class 2 CRISPR/Cas endonuclease is a type II CRISPR/Cas endonuclease; and/or
the class 2 CRISPR/Cas endonuclease is a type II CRISPR/Cas endonuclease wherein the class 2 CRISPR/Cas endonuclease is a Cas9 protein and the corresponding CRISPR/Cas guide RNA is a Cas9 guide RNA; and/or
the guide sequence of the first CRISPR/Cas guide RNA comprises the 17 nucleotide sequence GAAAUUAAACUACACAC (SEQ ID NO:304) (SEQ ID NO:1158 in PCT/US2017/017255), and the guide sequence of the second CRISPR/Cas guide RNA comprises the 17 nucleotide sequence AUGAUGCUAUAAUACCA (SEQ ID NO:305) (SEQ ID NO:1177 in PCT/US2017/017255); and/or
the guide sequence of the first CRISPR/Cas guide RNA comprises the 20 nucleotide sequence GUUGAAAUUAAACUACACAC (SEQ ID NO:306) (SEQ ID NO:1153 in PCT/US2017/017255) and the guide sequence of the second CRISPR/Cas guide RNA comprises the 20 nucleotide sequence UGUAUGAUGCUAUAAUACCA (SEQ ID NO:307) (SEQ ID NO:1172 in PCT/US2017/017255).

14. A pharmaceutical formulation comprising:
a polyrotaxane construct of claim 11; and
a pharmaceutically acceptable carrier.

15. The carrier of claim 7, wherein said carrier is complexed with a nucleic acid.

16. The carrier of claim 15, wherein said carrier is complexed with a plasmid.

17. The carrier of claim 15, wherein the N/P ratio of said carrier complexed to a nucleic acid ranges from about 0.01:1 up to about 100:1, or from about 2:1 up to about 50:1, or up to about 40:1, or up to about 30:1, or up to about 25:1, or ranges from about 2:1 up to about 25:1.

18. The carrier of claim 17, wherein the N/P ratio of said carrier complexed to a nucleic acid is about 10:1.

19. The carrier of claim 1, wherein:
said PEG backbone has a molecular weight ranging from about 1.0 to about 10 kDA per arm; and/or
said PEG backbone comprise about 22 to about 227 ethylene oxides per arm; and/or
said PEG backbone has a molecular weight of about 2.5 kDa per arm.

20. The carrier of claim 1, wherein:
the arm(s) threaded into said cyclic compound(s) each bear on average from about 5 to about 110 cyclic compounds; and/or
the arm(s) threaded into said cyclic compound(s) each bear, on average, about 20 cyclic compounds per arm.

21. A pharmaceutical formulation comprising:
a polyrotaxane carrier of claim 1; and
a pharmaceutically acceptable carrier.