WO2019118806A1 - Non-viral production and delivery of genes - Google Patents

Non-viral production and delivery of genes Download PDF

Info

Publication number
WO2019118806A1
WO2019118806A1 PCT/US2018/065609 US2018065609W WO2019118806A1 WO 2019118806 A1 WO2019118806 A1 WO 2019118806A1 US 2018065609 W US2018065609 W US 2018065609W WO 2019118806 A1 WO2019118806 A1 WO 2019118806A1
Authority
WO
WIPO (PCT)
Prior art keywords
virus
cdsdna
dna
protelomerase
certain embodiments
Prior art date
Application number
PCT/US2018/065609
Other languages
French (fr)
Inventor
Senthil Ramu
Joel SCHNEIDER
Original Assignee
Solid Biosciences Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Solid Biosciences Inc. filed Critical Solid Biosciences Inc.
Publication of WO2019118806A1 publication Critical patent/WO2019118806A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • A61K48/0066—Manipulation of the nucleic acid to modify its expression pattern, e.g. enhance its duration of expression, achieved by the presence of particular introns in the delivered nucleic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/0012—Galenical forms characterised by the site of application
    • A61K9/0019—Injectable compositions; Intramuscular, intravenous, arterial, subcutaneous administration; Compositions to be administered through the skin in an invasive manner
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/10—Dispersions; Emulsions
    • A61K9/127—Liposomes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/14—Particulate form, e.g. powders, Processes for size reducing of pure drugs or the resulting products, Pure drug nanoparticles
    • A61K9/19—Particulate form, e.g. powders, Processes for size reducing of pure drugs or the resulting products, Pure drug nanoparticles lyophilised, i.e. freeze-dried, solutions or dispersions
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/48—Preparations in capsules, e.g. of gelatin, of chocolate
    • A61K9/50—Microcapsules having a gas, liquid or semi-solid filling; Solid microparticles or pellets surrounded by a distinct coating layer, e.g. coated microspheres, coated drug crystals
    • A61K9/51—Nanocapsules; Nanoparticles
    • A61K9/5107—Excipients; Inactive ingredients
    • A61K9/5123—Organic compounds, e.g. fats, sugars
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; CARE OF BIRDS, FISHES, INSECTS; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00—Animals characterised by species
    • A01K2227/10—Mammal
    • A01K2227/105—Murine
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; CARE OF BIRDS, FISHES, INSECTS; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00—Animals characterised by purpose
    • A01K2267/03—Animal model, e.g. for test or diseases
    • A01K2267/0306—Animal model for genetic diseases
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/53—DNA (RNA) vaccination
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2800/00—Nucleic acids vectors
    • C12N2800/20—Pseudochromosomes, minichrosomosomes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2820/00—Vectors comprising a special origin of replication system
    • C12N2820/60—Vectors comprising a special origin of replication system from viruses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1241—Nucleotidyltransferases (2.7.7)
    • C12N9/1276—RNA-directed DNA polymerase (2.7.7.49), i.e. reverse transcriptase or telomerase
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • Gene delivery to target cells for purposes such as gene therapy is well-known, particularly for the treatment of diseases such as cystic fibrosis and certain cancers.
  • the term includes the delivery or introduction into a target cell of any nucleic acid material, such as a gene or part of a gene, to correct some genetic deficiency, as well as gene vaccination and the in vitro production of commercially-useful proteins in a suitable host cell.
  • Cell delivery systems generally fall into three broad classes, namely those that involve direct injection of naked DNA or RNA, those that make use of viruses or genetically modified viruses, and those that make use of non-viral delivery agents.
  • viruses as delivery agents have the advantages of high efficiency and high cell selectivity, they have the disadvantages of toxicity, production of inflammatory responses and difficulty in dealing with large DNA fragments.
  • One aspect of the invention provides a DNA construct comprising: (1) a backbone sequence comprising sequences supporting self-replication in a eukaryotic (e.g., mammalian) or prokaryotic cell; (2) an insert comprising: (a) a DNA fragment of interest; (b) a pair of end sequences flanking the DNA fragment of interest, wherein the end sequences are inverted terminal repeats (ITRs), long terminal repeats (LTRs) or internal repeats, or telomere sequences; and, (c) a pair of protelomerase recognition sequences flanking the pair of ITR or LTR.
  • the insert or the DNA fragment of interest is configured to and capable of existing extra-chromosomally during an entire life cycle of a eukaryotic cell.
  • the ITRs are from double- stranded DNA viruses, such as AAV.
  • the AAV is any one of AAV1-AAV10.
  • the LTRs are from a DNA virus, such as HSV.
  • At least one of the protelomerase recognition sequences comprises a perfect inverted repeat DNA sequence of at least 14 bp in length, or a variant thereof.
  • At least one of the protelomerase recognition sequences comprises a 22 bp consensus sequence for a mesophilic bacteriophage perfect inverted repeat.
  • At least one of the protelomerase recognition sequences is from E. coli phage N15 (such as the one recognized by E. coli N15 TelN protelomerase), agrobacterium Klebsiella phage Phi K02, Yersinia phage PY54, Halomonas phage phiHAP-l, and Vibrio phage VP882, or Borrelia burgdorferi.
  • At least one of the protelomerase recognition sequences comprises a perfect inverted repeat at least 30, at least 40, at least 60, at least 80 or at least 100 base pairs in length.
  • the DNA fragment of interest comprises a coding sequence of interest under the control of /operably linked to a eukaryotic promoter and/or enhancer, and optionally a eukaryotic transcription termination sequence.
  • the coding sequence of interest may comprise a DNA vaccine that encodes an antigen: (1) for the treatment or prevention of conditions such as cancer, allergies, toxicity and infection by a pathogen (e.g., fungi, viruses such as Human Papilloma Viruses (HPV), HIV, HSV2/HSV1, Influenza virus (types A, B and C), Polio virus, RSV virus, Rhinoviruses, Rotaviruses, Hepatitis A virus, Norwalk Virus Group,
  • a pathogen e.g., fungi, viruses such as Human Papilloma Viruses (HPV), HIV, HSV2/HSV1, Influenza virus (types A, B and C), Polio virus, RSV virus, Rhinoviruses, Rotaviruses, Hepatitis A virus, Norwalk Virus Group,
  • Enteroviruses Astroviruses, Measles virus, Parainfluenza virus, Mumps virus, Varicella- Zoster virus, Cytomegalovirus, Epstein-Barr virus, Adenoviruses, Rubella virus, Human T- cell Lymphoma type I virus (HTLV-I), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Hepatitis D virus, Pox virus, Marburg and Ebola); bacteria (such as Mycobacterium
  • tuberculosis Chlamydia, Neisseria gonorrhoeae, Shigella, Salmonella, Vibrio cholerae, Treponema pallidum, Pseudomonas, Bordetella pertussis, Brucella, Francisella tularensis, Helicobacter pylori, Leptospira interrogans, Legionella pneumophila, Yersinia pestis,
  • Streptococcus (types A and B), Pneumococcus, Meningococcus, Haemophilus influenza (type b), Toxoplasma gondii, Campylobacteriosis, Moraxella catarrhalis, Donovanosis, and Actinomycosis); fungal pathogens (such as Candidiasis and Aspergillosis); parasitic pathogens (such as Taenia, Flukes, Roundworms, Amoebiasis, Giardiasis, Cryptosporidium, Schistosoma, Pneumocystis carinii, Trichomoniasis and Trichinosis); (2) from a member of the adenoviridae (e.g ., a human adenovirus), herpesviridae (e.g ., HSV-l, HSV-2, EBV, CMV and VZV), papovaviridae (e.g., HPV), poxyirida
  • CA 125 CA 19.9, TAG-72, BRCA-l and BRCA-2 antigen.
  • the coding sequence of interest comprises a therapeutic DNA molecule for gene therapy, wherein said therapeutic DNA molecule: (1) expresses a functional gene in a subject having a genetic disorder caused by a dysfunctional version of said functional gene (e.g., gene for Duchenne muscular dystrophy, cystic fibrosis, Gaucher’s Disease, and adenosine deaminase (ADA) deficiency, inflammatory diseases, autoimmune, chronic and infectious diseases, AIDS, cancer, neurological diseases, cardiovascular disease, hypercholesterolemia, various blood disorders (including various anaemias, thalassemia and haemophilia, and emphysema), and solid tumors); (2) encodes toxic peptides (i.e., chemotherapeutic agents such as ricin, diphtheria toxin and cobra venom factor), tumor suppressor genes (such as p53), genes coding for mRNA sequences which are antisense to transforming oncogenes, antineoplastic
  • Another aspect of the invention provides a closed-end double stranded DNA
  • cdsDNA produced by contacting the subject DNA constructs with a protelomerase that recognizes the pair of protelomerase recognition sequences.
  • the subject cdsDNA is configured to and capable of existing extra-chromosomally during an entire life cycle of a eukaryotic cell.
  • Another aspect of the invention provides a closed-end double stranded DNA
  • cdsDNA comprising: (a) a DNA fragment of interest; (b) a pair of end sequences flanking the DNA fragment of interest, wherein the end sequences are inverted terminal repeats (ITRs) (e.g., of double- stranded DNA viruses), long terminal repeats (LTRs) or internal repeats of DNA virus (such as HSV), or telomere sequences; and, (c) a pair of half protelomerase recognition sequences flanking the pair of end sequences, wherein each of said half protelomerase recognition sequences forms one closed-end of the cdsDNA.
  • ITRs inverted terminal repeats
  • LTRs long terminal repeats
  • HSV internal repeats of DNA virus
  • Another aspect of the invention provides a pharmaceutical composition comprising the subject cdsDNA.
  • the cdsDNA is encompassed by a nanoparticle, such as an LNP or a polymer-based NP.
  • the nanoparticle is SNALP (stable nucleic acid-lipid particle), AtuPLEX, DACC, DBTC, RONDEL, DPC (Dynamic PolyConjugate), SMARTICLE, DiLA 2 , or EnCore.
  • SNALP stable nucleic acid-lipid particle
  • AtuPLEX DACC
  • DBTC DBTC
  • RONDEL DPC
  • DPC Dynamic PolyConjugate
  • SMARTICLE SMARTICLE
  • DiLA 2 DiLA 2
  • EnCore EnCore
  • Another aspect of the invention provides a method of producing a cell-free closed-end double stranded DNA (cdsDNA), the method comprising: (1) isolating the subject DNA construct after amplifying the DNA construct in the eukaryotic (e.g., mammalian) or prokaryotic cell; (2) linearizing the DNA construct with an endonuclease that does not digest within the insert; (3) contacting the DNA construct with a protelomerase that recognizes the pair of protelomerase recognition sequences to release the cdsDNA; (4) after steps (2) and (3), removing linearized DNA construct or fragment thereof that are not cdsDNA with an exonuclease; (5) enriching or purifying the cdsDNA.
  • eukaryotic e.g., mammalian
  • prokaryotic cell e.g., a cell-free closed-end double stranded DNA
  • steps (2) and (3) are carried out in any order or
  • Another aspect of the invention provides a method of producing a closed-end double stranded DNA (cdsDNA), the method comprising: (1) isolating the subject DNA construct after amplifying the DNA construct in the eukaryotic (e.g ., mammalian) or prokaryotic cell; (2) contacting the DNA construct with a protelomerase that recognizes the pair of
  • protelomerase recognition sequences to release the cdsDNA; (3) enriching or purifying the cdsDNA.
  • the method further comprises encapsulating the cdsDNA in a nanoparticle (such as SNALP, AtuPLEX, DACC, DBTC, RONDEL, DPC, SMARTICLE, DiLA 2 , or EnCore).
  • a nanoparticle such as SNALP, AtuPLEX, DACC, DBTC, RONDEL, DPC, SMARTICLE, DiLA 2 , or EnCore.
  • Another aspect of the invention provides a method of delivering a target gene of interest (GOI) into a target cell, the method comprising contacting the target cell with a composition comprising the subject cdsDNA.
  • GOI target gene of interest
  • the target cell is contacted in vitro , ex vivo , or in vivo.
  • the target GOI is a wild-type, mini- or micro-dystrophin gene for treating DMD (Duchenne Muscular Dystrophy), a gene in the DMD pathway (such as follistatin or a human IgG fusion thereof, or an inhibitor of the IKKb or NF-kB pathway), or a construct related to a genetic modifier of DMA (such as SPP1 or LTBP4), and wherein the target cell is a muscle (e.g., skeletal muscle such as a tibialis anterior muscle cell, cardiac muscle, smooth muscle, or muscle in diaphragm, triceps, soleus, tibialis anterior,
  • DMD Dell Muscular Dystrophy
  • a gene in the DMD pathway such as follistatin or a human IgG fusion thereof, or an inhibitor of the IKKb or NF-kB pathway
  • a construct related to a genetic modifier of DMA such as SPP1 or LTBP4
  • the target cell is
  • At least one symptom or feature of DMD is reduced in intensity, severity, or frequency, or has delayed onset (e.g., at least one symptom or feature of DMD selected from the group consisting of muscle wasting, muscle weakness, muscle fragility, muscle necrosis, muscle fibrosis, joint contracture, skeletal deformation, cardiomyopathy, impaired swallowing, impaired bowel and bladder function, muscle ischemia, cognitive impairment, behavioral dysfunction, socialization impairment, scoliosis, and impaired respiratory function).
  • treatment results in an increase in the mass of a muscle relative to a control (e.g., an increase of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200% or 500% relative to a control).
  • treatment results in muscle regeneration, increased muscle strength, increased flexibility, increased range of motion, increased stamina, reduced fatigability, increased blood flow, improved cognition, improved pulmonary function, inflammation inhibition, reduced muscle fibrosis, and/or reduced muscle necrosis.
  • the method further comprises administering one or more additional therapeutic agents, such as anti-Fit-l antibody or fragment thereof, edasalonexent, pamrevlumab, prednisone, deflazacort, RNA modulating therapeutics, exon-skipping therapeutics and any other gene therapy.
  • additional therapeutic agents such as anti-Fit-l antibody or fragment thereof, edasalonexent, pamrevlumab, prednisone, deflazacort, RNA modulating therapeutics, exon-skipping therapeutics and any other gene therapy.
  • the target gene of interest is delivered into the target cell daily, twice weekly, weekly, monthly, bimonthly, or once every 2, 3, 4, 5, 6, 9, 12, 18, 24, 36, 60, 72 or more months.
  • a related aspect of the invention provides a use of a composition comprising any one of the subject cdsDNA, or the subject pharmaceutical composition, in the manufacture of a medicament for delivering a target gene of interest (GOI) into a target cell in vivo.
  • a composition comprising any one of the subject cdsDNA, or the subject pharmaceutical composition, in the manufacture of a medicament for delivering a target gene of interest (GOI) into a target cell in vivo.
  • GOI target gene of interest
  • FIG. 1 is a schematic illustration showing an exemplary embodiment of the non-viral production of nanoparticles encapsulating closed-end dsDNA (cdsDNA) that may be used in, for example, gene therapy to deliver a gene of interest (GOI) to a target cell in vitro , ex vivo , or in vivo to a target host organism.
  • cdsDNA closed-end dsDNA
  • the center region of the cdsDNA represented by the longest double lines in the middle, represents the GOI.
  • the pair of short bars immediately flanking the GOI represent the inverted terminal repeat (ITR) sequence of a viral genome, such as that from the Adeno Associated virus (AAV) genome.
  • ITR inverted terminal repeat
  • the pair of short bars immediately flanking the ITR-capped GOI represent the recognition or target sequence for a protelomerase, such as the 56 bp TelN protelomerase recognition sequence.
  • a protelomerase such as the 56 bp TelN protelomerase recognition sequence.
  • FIG. 2 illustrates the process by which the TelN protelomerase cleaves a dsDNA substrate to generate the cdsDNA comprising the GOI in FIG. 1.
  • the 56-bp TelN protelomerase recognition sequence (TelN site) is shown at the top of the figure.
  • TelN site The 56-bp TelN protelomerase recognition sequence
  • the 3’ of the G in the top strand to the left of the cleavage site, and the 5’ of the C in the bottom strand to the left of the cleavage site is linked by TelN to form a closed end single- stranded loop, so is the right hand side of the TelN cleavage site.
  • a dsDNA plasmid encompassing the GOI (e.g ., GFP) flanked by ITR sequences (ITR1 and ITR2), and further flanked by a pair of TelN sites (i.e ., TelN-Left and TelN-Right), protelomerase digestion releases the linear duplex encompassing the GOI flanked by the ITRs and further flanked by the TelN half sites with capped terminal single- stranded loop to form the cdsDNA.
  • ITR1 and ITR2 ITR sequences
  • TelN-Left and TelN-Right i.e ., TelN-Left and TelN-Right
  • FIG. 3 shows the generation of the cdsDNA drug substance using the methods of the invention.
  • the three bands from top to bottom in each lane, is the undigested circular plasmid encompassing the GFP as GOI; the remaining plasmid backbone; and the GOI (GFP) flanked by the ITRs with closed loop ends resulting from protelomerase digestion.
  • GFP GOI
  • FIG. 4A and 4B show that the cdsDNA so generated is biologically active to direct GFP expression in a target muscle cell in vitro.
  • the left panel of FIG. 4A is a schematic drawing showing that a circular plasmid (pCK8-GFP) is digested by protelomerase to generate a cdsDNA encoding a GFP reporter gene (“SLiD/non- viral AAV”).
  • the right panel of FIG. 4A shows a gel image in which the lane with Exonuclease Ill-digested product formed a single band (the cdsDNA), while the two other bands disappeared presumably due to Exonucleoase III digestion.
  • the cdsDNA encompassing the GFP coding sequence was then introduced into the C2C12 myotubes, and GFP expression was monitored thereafter.
  • the merged image panel in FIG. 4B includes GFP signal (expressed by the cdsDNA), the DAPI nuclear staining, and the F-actin staining.
  • FIG. 4C shows that, as control, Not I - digested same plasmid releases a dsDNA fragment consisting essentially of the GOI (GFP), but not the flanking ITRs.
  • Another control is the pCK8 GPF construct, which is a parental plasmid construct with ITR sequences flanking the identical GFP reporter gene.
  • FITC images show strong expression of cdsDNA-encoded GFP transfected to the C2C12 cells, while Not I-digested GFP dsDNA (an open-end DNA without ITR)-transfected cells have weak expression.
  • the pCK8 GFP control also yielded poor expression compared to cdsDNA-transfected cells. It was determined that transfection efficiency is about 60% for the cdsDNA-encoded GFP, and GFP expression became stronger as the myotubes matured.
  • FIG. 5A shows that the closed loop ends of the cdsDNA resulting from protelomerase digestion protects the cdsDNA from exonuclease digestion.
  • FIG. 5B shows that linearizing the plasmid backbone with an endonuclease (such as Xbal) renders the protelomerase digestion protect comprising the plasmid backbone susceptible to exonuclease digestion.
  • an endonuclease such as Xbal
  • FIG. 6 is a schematic drawing illustrating the cell-free cdsDNA drug substance manufacturing process.
  • FIG. 7A shows that the subject cdsDNA encoding a 5-repeat microdystropin protein (SLiD-MD44) is resistant to exonuclease III digestion, confirming the existence of the closed ends after protelomerase digestion.
  • FIG. 7B shows that the subject cdsDNA can express the encoded 5-repeat microdystrophin protein in vitro in C2C12 cells.
  • FIGs. 8A and 8B show in vivo expression of an exogenous microdystrophin in mdx mouse muscle tissue.
  • Mice were administered with either 40 pg of a subject cdsDNA encoding a microdystrophin minigene (SLiD-MD4), or control saline, via intramuscular electroporation (IM Electroporation).
  • IM Electroporation intramuscular electroporation
  • FIGs. 9A and 9B are enlarged sections of images shown in FIGs. 8A and 8B, respectively. Correct subcellular ( . ⁇ ? ., plasma membrane) localization by the expressed exogenous microdystrophin was shown.
  • FIG. 10 shows persistent microdystrophin minigene expression in mdx mouse receiving 60 pg of the cdsDNA construct SLiD-MD4, 7 days post IM/Electroporation.
  • Microdystrophin expression was shown as red fluorescent signals, while endogenous laminin expression was shown as green fluorescent signals.
  • compositions and methods of the invention described herein are partly based on the discovery that DNA fragment of interest flanked by a pair of end sequences, such as end sequences based on Inverted Terminal Repeats (ITRs) of certain double- stranded DNA viruses, or Long Terminal Repeats (LTRs) or internal repeats of certain DNA viruses, and further flanked by a pair of protelomerase recognition sequences, can be efficiently amplified for producing cell-free closed-end double- stranded DNA (cdsDNA) molecules encompassing such DNA fragment of interest, which cdsDNA can then be packaged into certain
  • nanoparticles such as lipid-based nanoparticles (LNPs) or polymer-based nanoparticles (NPs) as pharmaceutical compositions.
  • LNPs lipid-based nanoparticles
  • NPs polymer-based nanoparticles
  • the invention provided herein provides a means to manufacture / produce any cell- free DNA fragment of interest, such as therapeutic DNA molecules, in large quantity or scale that can be used, for example, for gene therapy without the use of any viral vectors.
  • the DNA fragment of interest can in theory be any DNA sequence, including non coding sequences, or those coding for protein, RNA (such as non-translated RNA, which may be used in RNAi, antisense inhibition, small activating RNA, or sgRNA for CRISPR/Cas, merely to name a few), etc.
  • RNA such as non-translated RNA, which may be used in RNAi, antisense inhibition, small activating RNA, or sgRNA for CRISPR/Cas, merely to name a few
  • the DNA fragment of interest is about 100 bp, 200 bp, 500 bp, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 30 kb, 50 kb, 100 kb, 150 kb, 300 kb, 500 kb, 750 kb, 1000 kb, 1500 kb, 2000 kb, 5000 kb or more in length.
  • the DNA fragment of interest encodes a functional protein, or a functional domain or portion thereof.
  • the encoded functional protein can be a protein deficient in a disease associated with / caused by lack of the functional protein.
  • the encoded functional protein may be a DMD minigene, or a full length DMD gene.
  • the DNA fragment of interest encodes an antisense
  • oligonucleotide designed to antagonize the transcription and/or translation of a target gene.
  • the DNA fragment of interest encodes an RNAi construct designed to antagonize the expression of a target gene.
  • the RNAi construct may produce an siRNA, shRNA (short hairpin RNA), or miRNA (micro RNA).
  • the DNA fragment of interest does not encode an antisense oligonucleotide designed to antagonize the transcription and/or translation of a target gene.
  • the DNA fragment of interest does not encode an RNAi construct designed to antagonize the expression of a target gene.
  • the RNAi construct may
  • siRNA short hairpin RNA
  • miRNA miRNA
  • the DNA fragment of interest encodes a small activating RNA (saRNA) designed to antagonize the expression of a target gene.
  • saRNA small activating RNA
  • Small activating RNAs are small double- stranded RNAs (dsRNA) that target gene promoters to induce transcriptional gene activation in a process known as RNAa.
  • Small dsRNAs such as siRNAs and microRNAs (miRNAs),are known to be the trigger of an evolutionary conserved RNAi, which invariably leads to gene silencing via suppression of transcription, degradation of complementary mRNA, or blocking of protein translation.
  • dsRNAs can also act as saRNA by targeting selected sequences in gene promoters.
  • the saRNAs are 21 nucleotides in length with 2 nucleotides overhang at the 3’ end of each strand.
  • Several saRNAs can be designed within a 1- to 2-kb promoter region by following a known set of rules and optionally testing in cultured cells.
  • the saRNAs are designed to target non-coding transcripts that overlap the promoter sequence of a protein coding gene.
  • saRNAs and saRNAs expressed as shRNA have been used in in vitro and in vivo experiments, including in animal models and human clinical trials to treat cancer, liver disease, ischemia, and erectile dysfunction.
  • the DNA fragment of interest is a DNA vaccine.
  • DNA vaccines typically encode a modified form of an infectious organism’s DNA.
  • DNA vaccines are administered to a subject where they then express the selected protein of the infectious organism, initiating an immune response against that protein which is typically protective.
  • DNA vaccines may also encode a tumor antigen or a neo-antigen in a cancer immunotherapy approach.
  • a DNA vaccine may comprise a nucleic acid sequence encoding an antigen for the treatment or prevention of a number of conditions including but not limited to cancer, allergies, toxicity and infection by a pathogen such as, but not limited to, fungi, viruses including Human Papilloma Viruses (HPV), HIV, HSV2/HSV1, Influenza virus (types A, B and C), Polio virus, RSV virus, Rhinoviruses, Rotaviruses, Hepatitis A virus, Norwalk Virus Group, Enteroviruses, Astroviruses, Measles virus, Parainfluenza virus, Mumps virus, Varicella-Zoster virus, Cytomegalovirus, Epstein- Barr virus, Adenoviruses, Rubella virus, Human T-cell Lymphoma type I virus (HTLV-I), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Hepatitis D virus, Pox virus, Marburg and Ebola; bacteria including Mycobacterium tuber
  • DNA vaccines may comprise a nucleic acid sequence encoding an antigen from a member of the adenoviridae (including for instance a human adenovirus), herpesviridae (including for instance HSV-I, HSV-2, EBV, CMV and VZV), papovaviridae (including for instance HPV), poxviridae (including for instance smallpox and vaccinia), parvoviridae (including for instance parvovirus B 19), reoviridae (including for instance a rotavirus), coronaviridae (including for instance SARS), flaviviridae (including for instance yellow fever, West Nile virus, dengue, hepatitis C and tick-borne encephalitis), picornaviridae (including polio, rhinovirus, and hepatitis A), togaviridae (including for instance rubella virus), filoviridae (including for instance Marburg and Ebola), paramyxoviridae (including for instance
  • the antigen may be from a pathogen responsible for a veterinary disease and in particular may be from a viral pathogen, including, for instance, a Reovirus (such as African Horse sickness or Bluetongue virus) and Herpes viruses (including equine herpes).
  • the antigen may be one from Foot and Mouth Disease virus, Tick borne encephalitis virus, dengue virus, SARS, West Nile virus and Hantaan virus.
  • the antigen may be from an immunodeficiency virus, and may, for example, be from SIV or a feline immunodeficiency virus.
  • DNA vaccines may also comprise a nucleic acid sequence encoding tumor antigens or tumor associated antigens.
  • tumor associated antigens include, but are not limited to, neo-antigens (such as those encoded by mutated genes from cancers or tumors, which neo-antigens elicit T-cell response to kill cancer / tumor cells displaying such neo antigens), cancer-testes antigens such as members of the MAGE family (MAGE 1, 2, 3 etc), NY-ESO-I and SSX-2, differentiation antigens such as tyrosinase, gplOO, PSA, Her-2 and CEA, mutated self antigens and viral tumor antigens such as E6 and/or E7 from oncogenic HPV types.
  • neo-antigens such as those encoded by mutated genes from cancers or tumors, which neo-antigens elicit T-cell response to kill cancer / tumor cells displaying such ne
  • tumor antigens include MART-I , Melan-A, p97, beta-HCG, GalNAc, MAGE-I, MAGE-2, MAGE-4, MAGE- 12, MUC1, MUC2, MUC3, MUC4, MUC18, CEA, DDC, P1A, EpCam, melanoma antigen gp75, Hker 8, high molecular weight melanoma antigen, Kl 9, Tyrl, Tyr2, members of the pMel 17 gene family, c-Met, PSM (prostate mucin antigen), PSMA (prostate specific membrane antigen), prostate secretary protein, alpha- fetoprotein, CA 125, CA 19.9, TAG-72, BRCA-I and BRCA-2 antigen.
  • the DNA fragment of interest encodes a neo-antigen, which is an antigen encoded by a mutated gene in a cancer or tumor and may only exist in the cancer or tumor.
  • neo-antigen may serve as a personalized vaccine for cancer treatment.
  • the DNA fragment of interest is a therapeutic DNA molecule, e.g., those used in gene therapy.
  • the compositions and methods of the invention described herein is a platform technology that is generally applicable for gene therapy, including all monogenic human diseases that may be corrected by provision of one or more copies of functional DNA fragment of interest encoding the defective endogenous gene causing the diseases and as targets of the gene therapy.
  • DNA molecules can be used to express a functional gene where a subject has a genetic disorder caused by a dysfunctional version of that gene.
  • diseases include Duchenne muscular dystrophy (DMD), cystic fibrosis (CF), Gaucher’s Disease, and adenosine deaminase (ADA) deficiency.
  • diseases where gene therapy may be useful include inflammatory diseases, autoimmune, chronic and infectious diseases, including such disorders as AIDS, cancer, neurological diseases, cardiovascular disease, hypercholesterolemia, various blood disorders including various anaemias, thalassemia and haemophilia, and emphysema.
  • chemotherapeutic agents such as ricin, diphtheria toxin and cobra venom factor
  • tumor suppressor genes such as p53
  • genes coding for mRNA sequences which are antisense to transforming oncogenes antineoplastic peptides such as tumor necrosis factor (TNF) and other cytokines, or transdominant negative mutants of transforming oncogenes, may be expressed.
  • TNF tumor necrosis factor
  • DNA molecules which are transcribed into an active RNA form e.g., a small interfering RNA such as siRNA, shRNA, miRNA, or a small activating RNA (saRNA)
  • DNA encoding a CRISPR/Cas component such as a Cas9 enzyme or an sgRNA.
  • the DNA fragment of interest typically comprise an expression cassette comprising one or more promoter or enhancer elements and a gene or other coding sequence which encodes an mRNA or protein of interest.
  • the DNA template comprises an expression cassette consisting of a eukaryotic promoter operably linked to a sequence encoding a protein of interest, and optionally an enhancer and/or a eukaryotic transcription termination sequence.
  • the DNA constructs of the invention may contain certain elements commonly found in some viral vectors, including ITR (inverted terminal repeat) and LTR (long terminal repeat). Such viral elements can be used as end sequences of the invention that may serve as anti-decay elements for the DNA fragment of interest. Other suitable end sequences may include telomere sequences or functional derivative or equivalent thereof.
  • the end sequences of the invention enable the cdsDNA of the invention to exist as extra-chromosomal genetic elements that are stable for a long period of time once the cdsDNA is taken up by a target cell.
  • the cdsDNA with the end sequences may be stable for 6 hrs, 12 hrs, 1 day, 3 days, 5 days, 10 days, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months,
  • the DNA fragment of interest is flanked by a pair of ITR (e.g ., ITR of double- stranded DNA virus such as AAV, including AAV1-AAV10), or LTR or internal repeats (e.g., LTR of DNA viruses such as LTR of HSV).
  • ITR e.g ., ITR of double- stranded DNA virus such as AAV, including AAV1-AAV10
  • LTR or internal repeats e.g., LTR of DNA viruses such as LTR of HSV.
  • the ITR is the ITR of any one of AAV1-AAV 10.
  • the LTR is that of HSV.
  • the pair of LTR are elements from gamma-retroviruses or lentiviruses.
  • the LTRs may comprise the U3-R-U5 regions found on either side of a retro viral pro virus.
  • U3 is the unique 3’ region at the 3’ end of viral genomic RNA (but found at both the 5’ and 3’ ends of the provirus) that contains sequences necessary for activation of viral genomic RNA transcription.
  • R is the Repeat region found within both the 5’and 3’ LTRs of retro/lentiviral vectors.
  • the Tat protein binds to this region.
  • U5 is the unique 5’ region at the 5’ end of the viral genomic RNA (but found at both the 5’ and 3’ ends of the provirus).
  • one or both ends of the DNA fragment of interest has a 5’ LTR region, which may act as an RNA pol II promoter. Transcript can begin at the beginning of its R region, is capped, and proceeds through U5 and the rest of the DNA fragment of interest.
  • a hybrid 5’ LTR may be used with a constitutive promoter such as CMV or RSV promoter.
  • the R region of the LTR may comprise a trans-activating response element TAR, and acts as a binding site for Tat (a trans-activator that binds TAR to activate transcription from the LTR promoter).
  • one or both ends of the DNA fragment of interest has a 3’ LTR region, which may terminate transcription started by 5’ LTR at the other end of the DNA fragment of interest by the addition of a poly A tract just after its R sequence.
  • transcription of the DNA fragment of interest is initiated by the 5’ LTR.
  • transcription of the DNA fragment of interest is initiated by the 3’ LTR.
  • the DNA fragment of interest itself may carry its own promoter, enhancer, other transcriptional / translational regulatory elements, polyadenylation signal and/or translation termination site.
  • the translational regulatory elements comprise WPRE, or Woodchuck hepatitis virus post-transcriptional regulatory element, which stimulates the expression of transgenes via increased nuclear export.
  • the pair of ITR are elements from adeno associated virus (AAV).
  • AAV ITR is about 145 bases each.
  • the ITRs forms a T-shaped hairpin that normally serves as the origin of viral DNA replication. It contains a D region required for packaging.
  • the method of the invention comprises a step to produce cdsDNA by contacting amplified DNA construct with a protelomerase that releases the insert, under conditions promoting production of cdsDNA.
  • a protelomerase used in the invention is any polypeptide capable of cleaving and rejoining a template comprising a protelomerase target sequence in order to produce a covalently cdsDNA molecule.
  • Enzymes having protelomerase activity have also been described as telomere resolvases (for example in Borrelia burgdorferi). The requirements for protelomerase target sequence are described below.
  • the ability of a given polypeptide to catalyze the production of cdsDNA from a template comprising a protelomerase target sequence can be determined using any suitable assay described in the art.
  • bacteriophages exist as extrachromosomal DNA comprising linear double strands with covalently closed ends. The replication of this DNA and the maintenance of the covalently closed ends (or telomeric ends) are dependent on the activity of the protelomerase.
  • An example of this catalytic activity is provided by the enzyme, TelN, from the
  • bacteriophage N15 that infects Escherichia coli.
  • TelN recognizes a specific nucleotide sequence in the circular double stranded DNA. This sequence is a slightly imperfect inverted palindromic structure termed telRL comprising two halves, telR and telL, flanking a 22 base pair inverted perfect repeat (telO). Two telRL sites are formed in the circular double stranded DNA by the initial activity of specific DNA polymerase acting on the linear prophage DNA. TelN converts this circular DNA into two identical linear prophage DNA molecules completing the replication cycle. telR and telL comprise the closed ends of the linear prophage DNA enabling the DNA to be replicated further in the same way.
  • protelomerases examples include those from bacteriophages such as phiHAP-l from Halomonas aquamarina (SEQ ID NO: 7), PY54 from Yersinia enterolytica (SEQ ID NO: 9), phiK02 from Klebsiella oxytoca (SEQ ID NO: 11) and VP882 from Vibrio sp. (SEQ ID NO: 13), and N15 from Escherichia coli (SEQ ID NO: 15), or variants of any thereof.
  • the bacteriophage N15 protelomerase (SEQ ID NO: 15) or a variant thereof is used.
  • Variants of SEQ ID NOs: 7, 9, 11, 13 and 15 include homologues or mutants thereof. Mutants include truncations, substitutions or deletions with respect to the native sequence. A variant must produce closed linear DNA from a template comprising a protelomerase target site as described above.
  • any homologues mentioned herein are typically a functional homologue and are typically at least 40% homologous to the relevant region of the native protein. Homology can be measured using known methods.
  • the UWGCG Package provides the BESTFIT program which can be used to calculate homology (for example used on its default settings) (Devereux et al (1984) Nucleic Acids Research 12, 387-395).
  • the PILEUP and BLAST algorithms can be used to calculate homology or line up sequences (typically on their default settings), for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S, F et al (1990) J Mol Biol 215:403-10. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.
  • the BLAST algorithm performs a statistical analysis of the similarity between two sequences; see e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5787.
  • One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
  • P(N) the smallest sum probability
  • a sequence is considered similar to another sequence if the smallest sum probability in comparison of the first sequence to the second sequence is less than about 1, preferably less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
  • A“protelomerase target sequence” or“protelomerase recognition sequence” is a polynucleotide (e.g., a double- stranded DNA) sequence recognized by a protelomerase for cleavage and relegation of double- stranded DNA by protelomerase to form covalently closed end dsDNA. Digestion of the protelomerase target / recognition sequence by the protelomerase creates two“half protelomerase target / recognition sequences.”
  • a protelomerase target sequence comprises a perfect palindromic sequence, i.e., a double- stranded DNA sequence having two-fold rotational symmetry, also described herein as a perfect inverted repeat.
  • Protelomerase target sequences from various mesophilic bacteriophages and a bacterial plasmid all share the common feature of comprising a perfect inverted repeat.
  • the length of the perfect inverted repeat differs depending on the specific organism.
  • the perfect inverted repeat is that from Borrelia burgdorferi, and is 14 bps in length.
  • the perfect inverted repeat is from a mesophilic
  • the protelomerase recognition sequence is from E. coli N15, in which the central perfect inverted palindrome is flanked by inverted repeat sequences, i.e., forming part of a larger imperfect inverted palindrome (see FIGS. 2 and 3 in US9109250B2, incorporated herein by reference; the underlined bases indicate where the symmetry of the inverted repeats is interrupted).
  • the protelomerase target sequence comprises a double stranded palindromic (perfect inverted repeat) sequence of at least 14 base pairs in length.
  • the perfect inverted repeat sequence includes the sequences of SEQ ID NOs: 11 to 16 and variants thereof.
  • SEQ ID NO: 11 (NCATNNTANNCGNNTANNATGN) is a 22-base consensus sequence for a mesophilic bacteriophage perfect inverted repeat. Base pairs of the perfect inverted repeat are conserved at certain positions between different bacteriophages, while flexibility in sequence is possible at other positions. Thus, SEQ ID NO: 11 is a minimum consensus sequence for a perfect inverted repeat sequence for use with a bacteriophage protelomerase in the process of the present invention.
  • CCATTATACGCGCGTATAATGG is a perfect inverted repeat sequence for use with E. coli phage N15 (SEQ ID NO: 10), and Klebsiella phage Phi K02 (SEQ ID NO: 6) protelomerase s.
  • SEQ ID NO: 16 is a perfect inverted repeat sequence for use with a Borrelia burgdorferi protelomerase.
  • This perfect inverted repeat sequence is from a linear covalently closed plasmid, 1rB31.16 comprised in Borrelia burgdorferi.
  • This l4-bp sequence is shorter than the 22-bp consensus perfect inverted repeat for bacteriophages (SEQ ID NO: 11), indicating that bacterial protelomerases may differ in specific target sequence requirements to bacteriophage protelomerases. However, all protelomerase target sequences share the common structural motif of a perfect inverted repeat.
  • the perfect inverted repeat sequence may be greater than 22 bp in length depending on the requirements of the specific protelomerase used in the process of the invention. Thus, in some embodiments, the perfect inverted repeat may be at least 30, at least 40, at least 60, at least 80 or at least 100 base pairs in length. Examples of such perfect inverted repeat sequences include SEQ ID NOs: 17 to 19 and variants thereof.
  • SEQ ID Nos: 17 to 19 and variants thereof are for use respectively with
  • the perfect inverted repeat may be flanked by additional inverted repeat sequences.
  • the flanking inverted repeats may be perfect or imperfect repeats, i.e., may be completely symmetrical or partially symmetrical.
  • the flanking inverted repeats may be contiguous with or non-contiguous with the central palindrome.
  • the protelomerase target sequence may comprise an imperfect inverted repeat sequence which comprises a perfect inverted repeat sequence of at least 14 base pairs in length.
  • An example is SEQ ID NO: 24.
  • the imperfect inverted repeat sequence may comprise a perfect inverted repeat sequence of at least 22 base pairs in length.
  • An example is SEQ ID NO: 20.
  • the protelomerase target sequence comprises the sequences of any one of SEQ ID NOs: 20-24, or variants thereof.
  • sequences of SEQ ID Nos: 20 to 24 comprise perfect inverted repeat sequences as described above, and additionally comprise flanking sequences from the relevant organisms.
  • a protelomerase target sequence comprising the sequence of SEQ ID NO: 20 or a variant thereof is used in combination with E. coli N15 TelN
  • protelomerase of SEQ ID NO: 10 and variants thereof.
  • a protelomerase target sequence comprising the sequence of SEQ ID NO: 21 or a variant thereof is used in combination with Klebsiella phage Phi K02 protelomerase of SEQ ID NO: 6 and variants thereof.
  • a protelomerase target sequence comprising the sequence of SEQ ID NO: 22 or a variant thereof is used in combination with Yersinia phage PY54 protelomerase of SEQ ID NO: 4 and variants thereof.
  • a protelomerase target sequence comprising the sequence of SEQ ID NO: 23 or a variant thereof is used in combination with Vibrio phage VP882 protelomerase of SEQ ID NO: 8 and variants thereof.
  • a protelomerase target sequence comprising the sequence of SEQ ID NO: 24 or a variant thereof is used in combination with a Borrelia burgdorferi protelomerase.
  • variants of any of the palindrome or protelomerase target sequences described above include homologues or mutants thereof. Mutants include truncations, substitutions or deletions with respect to the native sequence.
  • a variant sequence is any sequence whose presence in the DNA template allows for its conversion into a closed linear DNA by the enzymatic activity of protelomerase. This can readily be determined by use of an appropriate assay for the formation of closed linear DNA. Any suitable assay described in the art may be used. An example of a suitable assay is described in Deneke et al, PNAS 97:7721-7726, 2000 (incorporated herein by reference).
  • the variant may allow for protelomerase binding and activity that is comparable to that observed with the native sequence.
  • variants of palindrome sequences described herein include truncated palindrome sequences that preserve the perfect repeat structure, and remain capable of allowing for formation of closed linear DNA.
  • variant protelomerase target sequences are modified such that they no longer preserve a perfect palindrome, provided that they are able to act as substrates for protelomerase activity.
  • candidate protelomerase target sequences can be screened for their ability to promote formation of closed end DNA using the assays described above.
  • protelomerases useful for the compositions and methods of the invention are listed below.
  • Halomonas phage phiHAP-l protelomerase nucleic acid sequence
  • CACGGTCGAG 540 ATCAACTACC ACTGGTTGAT GGAGACGGTT TACGAGCTGC
  • Halomonas phage phiHAP-l protelomerase amino acid sequence
  • AAACCATCTA CAGCTAAAAA AATAGTTAGC TTAAAAAAAA TGTACCCATC ATGGGCTAAT
  • GTTAGAGCAA 540 GGGACCGACC TACTTAACGC ATTACATTCT CTAAAAGTAA
  • ATATAAACAA 1260 TTCAAGCTGG TAAATTTCAA TCCAAAATGG ACACCTAATA
  • ADDTDAEEDE 540 IEEDFTDEEI DDTEFDVSDN ASDEDKPEDK PRFAAPIRRS EDSWLIKFEF AGKQYSWEGN 600 AESVIDAMKQ AWTENME 617 (SEQ ID NO: 4)
  • Klebsiella phage phiK02 protelomerase nucleic acid sequence SEQ ID NO: 1
  • AAACTATCAG AAAAATATCC TTTATATAGT 300 GAAGAATTAT CTTCGTGGCT
  • GCAAGCTAAA 900 AAACGCTCGG AAGATAAAGG TATATCAAGG AAAATATATA
  • CTGCAAAAGC TGGATAGCAT GATGCCAGAT 1380 TTTGCCAGGG GCGACGCCGG
  • GGTTCGTATT CATGAGACCG TGAAGCAGCT GGTGGAGCAG 1440 GACCCATCGA
  • Klebsiella phage phiK02 protelomerase amino acid sequence :
  • WKDKRDYLYK 180 LFQQGSSLLE DLNNLKVNHE VLYHLQLSSA ERTSIQQRWA
  • IVLPDEEILE 540 PMDDVDLDDE NHDDETLDDD EIEVDESEGE ELEEAGDAEE
  • MQSAWSAYFK 640 (SEQ ID NO: 6)
  • GAAGGATGCG 180 ACCAGAATCG CTCTGAGCAC CTATCGTAAG TACATGACAA
  • GAACGACGCC 900 ATCAATAAAC GCTGTGCAAA AACGCTCAAC CAAACCGCCA AGCAGTTCTT TGGCAGCGAC 960 GAGCGCGTGT TCAAAGATAG TCGTGCCATC TGGGCGCGTC TGGCTTATGA GTTGTTTTTT 1020 CAACGTGATC CGCGCTGGAA
  • telN Escherichia coli bacteriophage N15 telomerase
  • cA secondary immunity repressor
  • ACATCTATAC 900 AGCAACGATG GGCCGATGTT CTGCGCGAGA AGAAGCGTAA
  • GATCATCCAC GGTTATTGGG TTCGGTGATG GGTTCCTGCA GGCGCGGCGG AGAGCCATCC
  • TTTATCAGGC 2700 CCGAAGTTCT TCTTTCTGCC GCCAGTCCAG TGGTTCACCG
  • CTCGGTTAAA CCGAGGGTCA ATTTTTCATC ATGATCCAGC TTACGCAATG CATCAGAAGG
  • CGAGCTTCTC 3420 GCTCGGATGA TGCAATGGTG GAAAGGCGGT GGATATGGGA
  • GCATCACGAC GTTCCATCCA TTCGGTATTG TCGAC 4055 (SEQ ID NO: 9)
  • IVLPDEESVE 540 TIDEPDDESQ DDELDEDEIE LDEGGGDEPT EEEGPEEHQP
  • the amplified DNA constructs can be incubated with at least one protelomerase under conditions promoting production of closed cdsDNA.
  • the conditions that promote the cleavage and relegation of a dsDNA comprises a protelomerase target sequence to form a covalently closed end DNA with hairpin ends.
  • Conditions promoting production of closed end DNA comprise using any temperature allowing for production of closed end DNA, commonly in the range of 20 to 90°C.
  • the temperature may be in a range of 25 to 40°C, such as about 25 to about 35°C, or about 30°C.
  • Appropriate temperatures for a specific protelomerase may be selected according to the principles outlined above in relation to temperature conditions for DNA polymerases.
  • a suitable temperature for use with E. coli bacteriophage TelN protelomerase of SEQ ID NO: 10 is about 25 to about 35°C, such as about 30°C.
  • Conditions promoting production of closed end DNA also comprise the presence of a protelomerase and suitable buffering agents/pH and other factors which are required for enzyme performance or stability.
  • suitable conditions include any conditions used to provide for activity of protelomerase enzymes known in the art.
  • a suitable buffer may be 20 mM TrisHCl, pH 7.6; 5 mM CaCl2; 50 mM potassium glutamate; 0.1 mM EDTA; 1 mM Dithiothreitol (DTT).
  • Agents and conditions to maintain optimal activity and stability may also be selected from those listed for DNA polymerases.
  • All enzymes and proteins for use in the process of the invention may be produced recombinantly, for example in bacteria. Any means known to the skilled person allowing for recombinant expression may be used.
  • a plasmid or other form of expression vector comprising a nucleic acid sequence encoding the protein of interest may be introduced into bacteria, such that they express the encoded protein.
  • the vector may comprise the sequence of SEQ ID NOs: 1, 3, 5, 7 or 9 respectively.
  • the expressed protein will then typically be purified, for example by use of an affinity tag, in a sufficient quantity and provided in a form suitable for use in the process of the invention.
  • affinity tag such methodology for recombinant protein production is routinely available to the skilled person on the basis of their general knowledge. The above discussion applies to the provision of any protein discussed herein.
  • amplified DNA is purified prior to contacting with a protelomerase.
  • the process of the invention may further comprise a step of purifying amplified DNA.
  • amplified DNA is not purified prior to contacting with protelomerase.
  • the process comprises the addition of a buffer providing for protelomerase activity, i.e., to provide conditions promoting formation of closed end DNA.
  • the DNA construct of the invention may comprise more than one protelomerase target sequences, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more protelomerase target sequences.
  • Multiple protelomerase target sequences allows for excision of short closed end DNAs each comprising a DNA fragment of interest from a larger DNA molecule (such as a plasmid or a self-replicating extrachromosomal genetic element).
  • a larger DNA molecule such as a plasmid or a self-replicating extrachromosomal genetic element.
  • one or more inserts, each comprising a DNA fragment of interest flanked by its own pair of end sequences may each be further flanked on either side (outside the end sequences) by a protelomerase target sequence.
  • the same protelomerase target sequence may be shared between two adjacent inserts. The two flanking protelomerase sequences can then mediate excision of each insert from the amplified larger DNA molecule as a closed end DNA, subject to the action of protelomerase
  • the DNA construct comprises an insert having a DNA fragment of interest (such as an expression cassette) flanked on either side by a protelomerase target sequence.
  • the DNA fragment of interest e.g., expression cassette
  • the DNA fragment of interest may comprise a eukaryotic promoter operably linked to a coding sequence of interest, and optionally a eukaryotic transcription termination sequence.
  • the DNA fragment of interest e.g., expression cassette
  • the DNA fragment of interest is released from the amplified DNA construct as a closed end DNA.
  • Other sequences in the DNA construct are concomitantly deleted as a result of protelomerase digestion.
  • sequences are typically bacterial or vector sequences that may include bacterial origins of replication, bacterial selection markers (e.g ., antibiotic resistance genes), and unmethylated CpG dinucleotides. Deletion of such sequences creates a “minimal” DNA fragment of interest (e.g., expression cassette) which does not contain extraneous genetic material.
  • CpG motifs may be retained in the sequence of the product.
  • one aspect of the invention provides an in vitro process for the production of a pharmaceutical composition comprising a closed end double- stranded DNA flanked by the end sequences.
  • This process comprises: a) amplifying in a host cell (e.g., a eukaryotic or prokaryotic host cell) a DNA construct comprising at least one DNA fragment of interest (e.g., expression cassette) flanked by a pair of end sequences (such as ITR, LTR or telomere sequence that promotes stability of the cdsDNA during the life cycle of a host cell) and further flanked by a pair of protelomerase target sequences; and b) contacting amplified DNA construct produced in a) with one or more protelomerases specific for the pair of
  • a host cell e.g., a eukaryotic or prokaryotic host cell
  • a DNA construct comprising at least one DNA fragment of interest (e.g., expression cassette) flanked by a pair of end
  • protelomerase target sequences under conditions promoting cleavage of the pair of protelomerase target sequences to form a closed end double stranded DNA comprising the DNA fragment of interest.
  • the cdsDNA comprises, consists or consists essentially of a eukaryotic promoter operably linked to a coding sequence of interest, and optionally a eukaryotic transcription termination sequence, all flanked by a pair of end sequences.
  • the cdsDNA lacks bacterial or vector sequences, such as (i) bacterial origins of replication; (ii) bacterial selection markers (typically antibiotic resistance genes); and (iii) unmethylated CpG motifs.
  • the DNA fragment of interest may comprise a DNA vaccine, or a therapeutic DNA molecule encoding a gene product that can correct a defect in a target cell.
  • the DNA construct may be in the form of a plasmid or other vector typically used to house a gene for bacterial propagation, including any commercially available plasmid or other vector, such as a commercially available DNA medicine, engineered to include the flanking end sequences and the protelomerase recognition sequences.
  • the DNA construct does not contain any sequence elements required for rolling circle amplification (RCA).
  • the process of the invention may further comprise a step of purifying the cdsDNA product.
  • the purification removes undesired by-products or impurities or both.
  • Purification may be carried out by any suitable means known in the art.
  • purification may include phenol/chloroform nucleic acid extraction, or the use of a column which selectively binds nucleic acid, such as those commercially available from Qiagen.
  • the skilled person can routinely identify suitable purification techniques for use in isolation of DNA.
  • the process may further comprise its formulation as a DNA composition, for example a therapeutic DNA composition or a pharmaceutical composition comprising the cdsDNA.
  • a therapeutic DNA composition comprises a therapeutic DNA molecule of the type referred to above, e.g., a DNA fragment of interest encompassing a therapeutic function, flanked by a pair of end sequences, and further flanked by a pair of protelomerase half recognition sequences.
  • the end sequences may serve to prevent DNA decay once the cdsDNA (e.g., the therapeutic DNA molecule) is delivered inside a target cell, especially when the cdsDNA exists as an extrachromosomal genetic element that is not integrated into the host cell genome / chromosome(s).
  • Such a composition will comprise a therapeutically effective amount of the DNA fragment of interest in a form suitable for administration by a desired route, e.g., an aerosol, an injectable composition, or a formulation suitable for parenteral (i.v., i.m. etc.), oral, mucosal, or topical administration.
  • a desired route e.g., an aerosol, an injectable composition, or a formulation suitable for parenteral (i.v., i.m. etc.), oral, mucosal, or topical administration.
  • Formulation of DNA as a conventional pharmaceutical preparation may be done using standard pharmaceutical formulation chemistries and methodologies, which are available to those skilled in the art.
  • Any suitable pharmaceutically acceptable carrier or excipient may be used.
  • Auxiliary substances, such as wetting or emulsifying agents, pH buffering substances and the like, may be present in the excipient or vehicle.
  • These excipients, vehicles and auxiliary substances are generally pharmaceutical agents which may be administered without undue toxicity and which, in the case of vaccine compositions will not induce an immune response in the individual receiving the composition.
  • a suitable carrier may be a liposome.
  • compositions include, but are not limited to, liquids such as water, saline, polyethyleneglycol, hyaluronic acid, glycerol and ethanol.
  • salts can also be included therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like.
  • the preparation also contains a pharmaceutically acceptable excipient that serves as a stabilizer, particularly for peptide, protein or other like molecules if they are to be included in the composition.
  • suitable carriers that also act as stabilizers for peptides include, without limitation, pharmaceutical grades of dextrose, sucrose, lactose, trehalose, mannitol, sorbitol, inositol, dextran, and the like.
  • Other suitable carriers include, again without limitation, starch, cellulose, sodium or calcium phosphates, citric acid, tartaric acid, glycine, high molecular weight polyethylene glycols (PEGs), and combination thereof.
  • the subject cdsDNA can be delivered using a non- viral delivery system to any target cell of interest.
  • Non- viral gene delivery systems are based on the compaction of genetic material into nanometric particles by electrostatic interaction between the negatively charged phosphate backbone of DNA or RNA and cationic lipids, peptides or other polymers (Erbacher et al, Gene Therapy 6:138-145, 1999).
  • the use of non- viral transfection vectors that include lipids, as opposed to viruses, can result in lower toxicity, especially lower immunogenicity, greater safety, reduced cost, reasonably efficient targeting, and an enhanced packaging ability, e.g., the ability to deal with large fragments of nucleic acid material.
  • the subject cdsDNA is delivered using any suitable non- viral gene therapy vectors, such as those described in Yin et al., Non-viral vectors for gene-based therapy. Nature reviews Genetics, 15:541-555, 2014; or Schroeder et al., Lipid-based nanotherapeutics for siRNA delivery. J Intern Med. 267:9-21, 2010; or Zhao and Huang, Lipid nanoparticles for gene delivery. Adv Genet. 88: 13-36, 2014 (all incorporated herein by reference).
  • the cdsDNA is delivered using lipoplex for lipid-based nucleic acid complexes (see Feigner et al, Human Gene Therapy 8:511-512, 1997, incorporated by reference).
  • the term“LPD” is a form of lipopolyplex representing a formulation comprising a lipid, an integrin-(or other receptor-) binding peptide and DNA (or other nucleic acid). LPD complexes achieve transfection via an integrin- mediated or other receptor- mediated pathway. They do not necessarily need to have an overall positive charge, so undesirable serum interaction can be reduced.
  • the peptide component of LPD provides a nucleic acid packaging function, shielding the DNA or RNA from intracellular or
  • the peptide component is designed to be cell-type specific or cell- surface receptor specific.
  • the degree of specificity for integrin or other receptors can confer a degree of cell specificity to the LPD complex.
  • Specificity results from the targeting to the cell- surface receptors (for example integrin receptors), and transfection efficiencies comparable to some adenoviral vectors can be achieved (see Du et al., The role of the helper lipid on the DNA transfection efficiency of lipopolyplex formulations. Sci Rep. 4:7107, 2014; Welser et al., Gene delivery using ternary lipopolyplexes incorporating branched cationic peptides: the role of Peptide sequence and branching. Mol Pharm.
  • Multifunctional receptor-targeted nanocomplexes for the delivery of therapeutic nucleic acids to the Brain. Biomaterials. 34:9190-200, 2013; Tagalakis et al., Receptor-targeted liposome - peptide nanocomplexes for siRNA delivery. Biomaterials. 32:6302-15, 2011; Tagalakis et al., Integrin-targeted nanocomplexes for tumor specific delivery and therapy by systemic administration. Biomaterials. 32: 1370-6, 2011; Manunta et al., Nebulisation of receptor- targeted nanocomplexes for gene delivery to the airway epithelium. PLoS One.
  • the non- viral delivery comprises peptides that target human airway epithelial cells. See W002/072616 (incorporated by reference).
  • the non- viral delivery comprises peptides that target dendritic cells. See W02004/108938 (incorporated by reference).
  • the non- viral delivery is lipid/peptide vector that transfects a range of cell lines and primary cell cultures with high efficiency and low toxicity, including epithelial cells (40% efficiency), vascular smooth muscle cells (50% efficiency), endothelial cells (30% efficiency), haematopoietic cells (10% efficiency), bronchial epithelium of mouse (see Manunta et al, Nebulisation of receptor-targeted nanocomplexes for gene delivery to the airway epithelium. PLoS One. 20l l;6:e26768; Tagalakis et al., A receptor-targeted nanocomplex vector system optimized for respiratory gene transfer. Mol Ther.
  • the peptide for use in such LPD complexes or lipid/peptide complexes has two functionalities: a“head group” containing a cell surface receptor- (for example integrin) recognition sequence and a“tail” that can bind DNA non-covalently.
  • these two components of the peptide are covalently linked via a spacer in a way that does not interfere with their individual functions.
  • the peptide has a“tail” that is a polycationic nucleic acid-binding component, such as peptide described in W096/15811.
  • the lipid component of the LPD complexes are cationic lipids reported in Proc. Natl. Acad. Sci. USA 84, 7413-7417, 1987 and in US 5,264,618 (both incorporated by reference).
  • Commercially-available cationic liposome known by the trademark“Lipofectin,” which consists of the cytofectin, DOTMA 1 and the neutral lipid DOPE 2 in a 1:1 ratio, is an example of such lipid.
  • the cationic liposome formulation combines a synthetic cationic cytofectin and a neutral lipid.
  • a synthetic cationic cytofectin such as DOTMA
  • a neutral lipid such as DOTMA
  • DOTMA glycerol-skeleton
  • cholesterol such as DC-Chol 3.
  • the subject cdsDNA is formulated in lipid nanoparticles (LNPs), such as SNALP (stable nucleic acid-lipid particles).
  • LNPs lipid nanoparticles
  • Such lipid nanoparticles typically comprise one or more ionizable lipids, phospholipids, cholesterol, and PEG-lipids as carrier materials that encompass within nucleic acids (such as RNAi agents (siRNA, miRNA, shRNA), antisense oligonucleotides (ASOs), CRISPR/Cas system components (such as nucleic acids encoding the Cas9 enzyme, and sgRNA), therapeutic mRNA, genetic vaccines, or traditional DNA vectors such as plasmids).
  • nucleic acids such as RNAi agents (siRNA, miRNA, shRNA), antisense oligonucleotides (ASOs), CRISPR/Cas system components (such as nucleic acids encoding the Cas9 enzyme, and sgRNA), therapeutic
  • the subject cdsDNA is formulated in liposomes, which typically comprise one or more phospholipids, cholesterol, and PEG-lipids as carrier materials that encompass within nucleic acids, such as the ones mentioned above.
  • the subject cdsDNA is formulated in polymer-based nanoparticles (NPs), which typically comprise one or more poly-lactides (e.g ., PLGA), block copolymers (such as PEG-b-PLGA), and polysaccharides (such as chitosan and cellulose) as carrier materials that encompass within nucleic acids, such as the ones mentioned above.
  • NPs polymer-based nanoparticles
  • NPs typically comprise one or more poly-lactides (e.g ., PLGA), block copolymers (such as PEG-b-PLGA), and polysaccharides (such as chitosan and cellulose) as carrier materials that encompass within nucleic acids, such as the ones mentioned above.
  • the subject cdsDNA is formulated in SNALP (stable nucleic acid-lipid particles) that are stable lipid particles having a non-lamellar structure.
  • SNALP comprises ionizable lipids, shielding lipids (e.g., polyethylene glycol (PEG)), cholesterol, and endogenous or exogenous targeting ligands such as ApoE lipoprotein. It is a mono-lamellar (single lipid bilayer) liposome neutrally charged at physiological pH and stabilized by PEG that encapsulates the nucleic acids inside SNALP (such as the cdsDNA).
  • SNALP is suitable for delivery to various tissue and cell types.
  • the SNALP comprises ionizable cationic lipid DLinDMA (l,2-dilinoleyloxy-3- dimethylaminopropane).
  • SNALP comprises DLin-KC2-DMA and DLin-MC3-DMA, and is generated by a structure- activity relationship (SAR) study that optimized the pKa of the ionizable amino lipid head groups of the cationic lipid moiety.
  • SNALP is reLNP (rapidly eliminated LNP), such as L319, that provides biodegradability to the existing SNALP platforms and rapid elimination from plasma and tissue.
  • the subject cdsDNA is formulated as a plurality of nucleic acid-lipid particles, wherein each particle in the plurality of particles comprises: (a) a nucleic acid (e.g., the cdsDNA, which may encode a protein, an RNAi, an antisense oligonucleotide, or an mRNA); (b) a cationic lipid comprising from about 50-85 mol % (e.g., about 50-65 mol%; about 56.5-66.5 mol %; about 52-62 mol %) of the total lipid present in the particle;
  • a nucleic acid e.g., the cdsDNA, which may encode a protein, an RNAi, an antisense oligonucleotide, or an mRNA
  • a cationic lipid comprising from about 50-85 mol % (e.g., about 50-65 mol%; about 56.5-66.5 mol %; about 52-62 mol
  • a non-cationic lipid such as cholesterol or a derivative thereof, or phospholipid (such as dipalmitoylphosphatidylcholme (DPPC), distearoylphosphatidylcholine (DSPC), or a mixture thereof), or a mixture of phospholipid and cholesterol or a derivative thereof) comprising from about 13-49.5 mol % ( e.g ., about 31.5-42.5 mol % of cholesterol or a derivative thereof; or 4-10 mol % of phospholipid and 30-40 mol % cholesterol; or 5-9 mol % of phospholipid and 32-36 mol % cholesterol; or 10-30 mol % of phospholipid and 10-30 mol % of cholesterol) of the total lipid present in the particle; and (d) a conjugated lipid that inhibits aggregation of particles (e.g., PEG- lipid conjugate such as PEG-diacylglycerol (PEG-DAG) conjugate, a PEG-dialkyloxy
  • the nucleic acid-lipid particle comprises about 61.5 mol % cationic lipid, about 36.9% cholesterol or a derivative thereof, and about 1.5 mol % PEG- lipid conjugate. In certain embodiments, the nucleic acid- lipid particle comprises about 57.1 mol % cationic lipid, about 7.1 mol % phospholipid, about 34.3 mol % cholesterol or a derivative thereof, and about 1.4 mol % PEG-lipid conjugate.
  • the subject cdsDNA is formulated as a plurality of nucleic acid-lipid particles, wherein each particle in the plurality of particles comprises: (a) a nucleic acid; (b) a cationic lipid comprising from about 50 mol % to about 85 mol % (e.g., about 50 mol% to about 65 mol%, or about 50 mol% to about 60 mol%) of the total lipid present in the particle; (c) a non-cationic lipid comprising from about 13 mol % to about 49.5 mol % of the total lipid present in the particle (e.g., a mixture of a phospholipid and cholesterol or a cholesterol derivative, wherein the phospholipid comprises from about 3 mol % to about 15 mol % (or about 4 mol % to about 12 mol %) of the total lipid present in the particle; and wherein the cholesterol or derivative thereof comprises from about 30 mol % to about 40 mol % of the total lipid present in the particle
  • the subject cdsDNA is formulated as a plurality of nucleic acid-lipid particles, wherein each particle in the plurality of particles comprises: (a) a nucleic acid (such as the cdsDNA, which may encode a protein, an RNAi, an antisense
  • oligonucleotide or an mRNA
  • a cationic lipid e.g., about 10-50 mol%, about 20-50 mol%, or about 20-40 mol% of the total lipid present in the particle
  • a non-cationic lipid e.g ., about 10-60 mol%, about 20-55 mol%, or about 25-50 mol% of the total lipid present in the particle
  • a conjugated lipid that inhibits aggregation of particles e.g., about 0.5- 20 mol%, about 2-20 mol%, or about 1.5-18 mol% of the total lipid present in the particle), wherein at least about 95% of the particles in the plurality of particles have a non-lamellar morphology, or wherein at least about 95% of the particles in the plurality of particles are electron-dense.
  • the cdsDNA can encode any gene product of interest, including protein, antisense oligonucleotide, or RNAi construct (such as siRNA, aiRNA, miRNA, Dicer-substrate dsRNA, shRNA, ssRNAi oligonucleotides, and combinations thereof).
  • RNAi construct such as siRNA, aiRNA, miRNA, Dicer-substrate dsRNA, shRNA, ssRNAi oligonucleotides, and combinations thereof.
  • the cationic lipid comprises 1,2- dilinoleyloxy-N,N- dimethylaminopropane (DLinDMA), l,2-dilinolenyloxy-N,N- dimethylaminopropane
  • DLenDMA l,2-di-y-linolenyloxy-N,N-dimethylaminopropane
  • g-DLenDMA 2,2- dilinoleyl-4-(2-dimethylaminoethyl)-[l,3]-dioxolane
  • DLin-K-DMA 2,2-dilinoleyl-4- dimethylaminomethyl-[l,3]-dioxolane
  • DLin-K-DMA 2,2-dilinoleyl-4- dimethylaminomethyl-[l,3]-dioxolane
  • the cationic lipid comprises MC3, LenMC3, CP-LenMC3, y- LenMC3, CP-y-LenMC3, MC3MC, MC2MC, MC3 Ether, MC4 Ether, MC3 Amide, Pan- MC3, Pan-MC4, Pan MC5 or a mixture thereof.
  • the cationic lipid comprises N,N-dioleyl-N,N- dimethylammonium chloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N-(l-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), N- (l-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-dimethyl- 2,3-dioleyloxypropylamine (DODMA), and combinations thereof.
  • DODAC N,N-dioleyl-N,N- dimethylammonium chloride
  • DDAB N,N-distearyl-N,N-dimethylammonium bromide
  • DOTAP N-(l-(2,3-dioleoyloxy)propyl)-N,N,N-
  • the cationic lipid is any one as described in U.S. Pat. Nos. 7,799,565; 8,569,256; 9,018,187; and 9,181,545 (both incorporated herein by reference).
  • the non-cationic lipid is dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), egg phosphatidylcholine (EPC), distearoylphosphatidylcholine (DSPC), cholesterol, and combinations thereof.
  • DPPC dipalmitoylphosphatidylcholine
  • DOPE dioleoylphosphatidylethanolamine
  • POPC palmitoyloleoylphosphatidylcholine
  • EPC egg phosphatidylcholine
  • DSPC distearoylphosphatidylcholine
  • the non-cationic lipid is a phospholipid.
  • the non-cationic lipid is cholesterol or a cholesterol derivative.
  • cholesterol derivatives include, but are not limited to, cholestanol, cholestanone, cholestenone, coprostanol, cho lestery 1-2’ -hydro xyethyl ether, cholesteryl-4’- hydroxybutyl ether, and mixtures thereof.
  • the non-cationic lipid is a mixture of a phospholipid and cholesterol or a cholesterol derivative.
  • the non-cationic lipid is a phospholipid selected from the group consisting of dip almitoylphosphatidylcho line (DPPC), distearoylphosphatidylcholine (DSPC), or a mixture thereof.
  • DPPC dip almitoylphosphatidylcho line
  • DSPC distearoylphosphatidylcholine
  • the non-cationic lipid is DPPC.
  • the non-cationic lipid is a mixture of DPPC and cholesterol.
  • the conjugated lipid that inhibits aggregation of particles is a polyethyleneglycol (PEG)-lipid conjugate.
  • PEG polyethyleneglycol
  • the PEG may have an average molecular weight of from about 550 daltons to about 5,000 daltons, or an average molecular weight of about 2,000 daltons, or an average molecular weight of about 750 daltons.
  • the PEG-lipid conjugate is a member selected from the group consisting of: a PEG-diacylglycerol (PEG-DAG) conjugate, a PEG dialky loxypropyl (PEG- DAA) conjugate, a PEG-phospho lipid conjugate, a PEG- ceramide (PEG-Cer) conjugate, and a mixture thereof.
  • PEG-DAG PEG-diacylglycerol
  • PEG- DAA PEG dialky loxypropyl
  • PEG-phospho lipid conjugate PEG-phospho lipid conjugate
  • PEG-Cer PEG-ceramide
  • the PEG-lipid conjugate is a PEG-DAA conjugate, such as those described in U.S. Pat. No. 8,936,942 and 7,982,027 (incorporated by reference).
  • the PEG-DAA conjugate is a member selected from the group consisting of a PEG-didecyloxypropyl (C l0 ) conjugate, a PEG-dilauryloxypropyl (C l2 ) conjugate, a PEG-dimyristyloxypropyl (C l4 ) conjugate, a PEG-dipalmityloxypropyl (C l6 ) conjugate, a PEG-distearyloxypropyl (C l8 ) conjugate, and a mixture thereof.
  • the PEG-lipid conjugate is described in U.S. Pat. No. 7,803,397 (incorporated by reference).
  • the PEG-DAA conjugate is a PEG- dimyristyloxypropyl (CH) conjugate.
  • the nucleic acid in the particles (e.g., cdsDNA) is not substantially degraded after exposure of the particle to a nuclease at 37°C for about 20 minutes, or about 30 minutes.
  • the cdsDNA is fully encapsulated in the particles. That is, the cdsDNA is fully encapsulated within the lipid portion of the lipid particles such that the cdsDNA in the lipid particle is resistant in aqueous solution to enzymatic degradation, e.g., by a nuclease or protease.
  • the lipid particles are substantially non- toxic to mammals such as humans.
  • the particle has a lipidxdsDNA mass ratio of from about 5:1 to about 15:1.
  • the particles have a median diameter of from about 30 or 40 nm to about 150 nm.
  • the cationic lipid comprises from about 52 mol % to about 62 mol % of the total lipid present in the particle.
  • the non-cationic lipid is a mixture of a phospholipid and cholesterol or a derivative thereof comprising from about 36 mol % to about 47 mol% of the total lipid present in the particle.
  • the conjugated lipid that inhibits aggregation of the particles is a PEG-lipid conjugate comprising from about 1 mol % to about 2 mol % of the total lipid present in the particle.
  • the cationic lipid comprises from about 56.5 mol % to about 66.5 mol % of the total lipid present in the particle.
  • the non-cationic lipid is cholesterol or a derivative thereof comprising from about 31.5 mol % to about 42.5 mol% of the total lipid present in the particle.
  • the conjugated lipid that inhibits aggregation of the particles is a PEG-lipid conjugate comprising from about 1 mol % to about 2 mol % of the total lipid present in the particle.
  • the cationic lipid comprises from about 50 mol % to about 60 mol % of the total lipid present in the particle.
  • the non-cationic lipid is a mixture of a phospholipid and cholesterol or a derivative thereof comprising from about 35 mol % to about 45 mol% of the total lipid present in the particle.
  • the conjugated lipid that inhibits aggregation of the particles is a PEG-lipid conjugate comprising from about 5 mol % to about 10 mol % of the total lipid present in the particle.
  • the cationic lipid comprises from about 55 mol % to about 65 mol % of the total lipid present in the particle.
  • the non-cationic lipid is cholesterol or a derivative thereof comprising from about 30 mol % to about 40 mol% of the total lipid present in the particle.
  • the conjugated lipid that inhibits aggregation of the particles is a PEG-lipid conjugate comprising from about 5 mol % to about 10 mol % of the total lipid present in the particle.
  • greater than 95%, at least 96%, at least 97%, at least 98%, at least 99%, or greater than 99% of the particles have a non- lamellar morphology, i.e., a non bilayer structure. In certain embodiments, greater than 95%, at least 96%, at least 97%, at least 98%, at least 99%, or greater than 99% of the particles are electron-dense.
  • the non-lamellar morphology of the particles comprises an inverse hexagonal (Hu) or cubic phase structure.
  • the particles having a non-lamellar morphology are electron- dense.
  • the non-lamellar morphology of the particles can be determined by, for example, cryogenic-temperature transmission electron microscopy (cryo-TEM), X-ray diffraction, or by Differential Scanning Calorimetry (DSC), wherein no thermal transitions are seen at 5 to 75°C.
  • the lipid particles can be tailored to preferentially target particular tissues, organs, or tumors of interest. In certain other instances, it may be desirable to have a targeting moiety attached to the surface of the lipid particle to further enhance the targeting of the particle.
  • Methods of attaching targeting moieties e.g., antibodies, proteins, etc.
  • lipids such as those used in the present particles
  • the SNALP lipid particles are useful for the introduction of active agents or therapeutic agents (e.g., cdsDNA) into cells. Accordingly, the present invention also provides methods for introducing an active agent or therapeutic agent such as a cdsDNA into a cell.
  • the cell is a muscle cell, such as a skeletal muscle cell, a cardiac muscle cell, or a smooth muscle cell.
  • the muscle cell is a tibialis anterior muscle cell.
  • the methods can be carried out in vitro, ex vivo, or in vivo by first forming the particles as described above and then contacting the particles with the cells for a period of time sufficient for delivery of the active agent or therapeutic agent (e.g., cdsDNA) to the cells to occur.
  • the active agent or therapeutic agent e.g., cdsDNA
  • the SNALP lipid particles can be adsorbed to almost any cell type with which they are mixed or contacted. Once adsorbed, the particles can either be endocytosed by a portion of the cells, exchange lipids with cell membranes, or fuse with the cells. Transfer or incorporation of the active agent or therapeutic agent (e.g., cdsDNA) portion of the particle can take place via any one of these pathways. In particular, when fusion takes place, the particle membrane is integrated into the cell membrane and the contents of the particle combine with the intracellular fluid.
  • the active agent or therapeutic agent e.g., cdsDNA
  • the SNALP lipid particles can be administered either alone or in a mixture with a pharmaceutically acceptable carrier (e.g., physiological saline or phosphate buffer) selected in accordance with the route of administration and standard pharmaceutical practice.
  • a pharmaceutically acceptable carrier e.g., physiological saline or phosphate buffer
  • normal buffered saline e.g., 135-150 mM NaCl
  • suitable carriers include, e.g., water, buffered water, 0.4% saline, 0.3% glycine, and the like, including glycoproteins for enhanced stability, such as albumin, lipoprotein, globulin, etc. Additional suitable carriers are described in, e.g., REMINGTON’S PHARMACEUTICAL SCIENCES, Mack Publishing Company,
  • “carrier” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like.
  • pharmaceutically acceptable refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human.
  • the pharmaceutically acceptable carrier is generally added following lipid particle formation.
  • the lipid particle e.g., SNALP
  • the particle can be diluted into pharmaceutically acceptable carriers such as normal buffered saline.
  • the concentration of particles in the pharmaceutical formulations can vary widely, i.e., from less than about 0.05%, usually at or at least about 2 to 5%, to as much as about 10 to 90% by weight, and will be selected primarily by fluid volumes, viscosities, etc., in
  • concentration may be increased to lower the fluid load associated with treatment. This may be particularly desirable in patients having atherosclerosis-associated congestive heart failure or severe hypertension.
  • particles composed of irritating lipids may be diluted to low concentrations to lessen inflammation at the site of administration.
  • compositions of the present invention may be sterilized by conventional, well-known sterilization techniques.
  • Aqueous solutions can be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration.
  • the compositions can contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, and calcium chloride.
  • the particle suspension may include lipid- protective agents which protect lipids against free-radical and lipid-peroxidative damages on storage. Lipophilic free-radical quenchers, such as alphatocopherol, and water-soluble iron- specific chelators, such as ferrioxamine, are suitable.
  • a therapeutically effective amount of the lipid particle may be administered to the mammal.
  • cells are removed from a patient, the lipid particles are delivered in vitro (e.g., using a SNALP described herein), and the cells are reinjected into the patient.
  • nucleic acid-lipid particles such as those described in PCT Publication Nos. WO 05/007196, WO 05/121348, WO 05/120152, and WO 04/002453, the disclosures of which are herein incorporated by reference in their entirety for all purposes.
  • the present invention also provides fully encapsulated lipid particles that protect the nucleic acid from nuclease degradation in serum, are non- immunogenic, are small in size, and are suitable for repeat dosing.
  • administration can be in any manner known in the art, e.g., by injection, oral administration, inhalation (e.g., intranasal or intratracheal), transdermal application, or rectal administration. Administration can be accomplished via single or divided doses.
  • the pharmaceutical compositions can be administered parenterally, i.e., intraarticularly, intravenously, intraperitoneally, subcutaneously, or intramuscularly. In some embodiments, the pharmaceutical compositions are administered intravenously,
  • lipid particles can be administered by direct injection at the site of disease or by injection at a site distal from the site of disease (see, e.g., Culver, HUMAN GENE
  • the SNALP lipid particles are administered intravenously, at least about 5%, 10%, 15%, 20%, or 25% of the total injected dose of the particles is present in plasma about 8, 12, 24, 36, or 48 hours after injection. In other embodiments, more than about 20%, 30%, 40% and as much as about 60%, 70% or 80% of the total injected dose of the lipid particles is present in plasma about 8, 12, 24, 36, or 48 hours after injection. In certain instances, more than about 10% of a plurality of the particles is present in the plasma of a mammal about 1 hour after administration. In certain other instances, the presence of the lipid particles is detectable at least about 1 hour after administration of the particle. In certain embodiments, the presence of a therapeutic agent such as a nucleic acid is detectable in cells of the lung, liver, tumor, or at a site of inflammation at about 8, 12, 24, 36, 48, 60, 72 or 96 hours after administration.
  • a therapeutic agent such as a nucleic acid is detectable in cells of the lung, liver, tumor, or at a site of
  • compositions of the present invention can be made into aerosol formulations (i.e ., they can be“nebulized”) to be administered via inhalation (e.g., intranasally or intratracheally) (see, Brigham et al., Am. J. Sci., 298:278 (1989)). Aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen, and the like.
  • the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles.
  • Methods for delivering nucleic acid compositions directly to the lungs via nasal aerosol sprays have been described, e.g., in U.S. Patent Nos. 5,756,353 and 5,804,212.
  • the delivery of drugs using intranasal microparticle resins and lysophosphatidyl-glycerol compounds (U.S. Patent 5,725,871) are also well-known in the pharmaceutical arts.
  • transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is described in U.S. Patent No. 5,780,045.
  • Formulations suitable for parenteral administration include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives.
  • compositions are preferably administered, for example, by intravenous infusion, orally, topically, intraperitoneally, intravesically, or intrathecally.
  • the lipid particle formulations are formulated with a suitable pharmaceutical carrier.
  • a suitable pharmaceutical carrier may be employed in the compositions and methods of the present invention. Suitable formulations for use in the present invention are found, for example, in REMINGTON’S PHARMACEUTICAL SCIENCES, Mack Publishing Company, Philadelphia, PA, l7th ed. (1985).
  • a variety of aqueous carriers may be used, for example, water, buffered water, 0.4% saline, 0.3% glycine, and the like, and may include glycoproteins for enhanced stability, such as albumin, lipoprotein, globulin, etc.
  • compositions can be sterilized by conventional liposomal sterilization techniques, such as filtration.
  • the compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.
  • These compositions can be sterilized using the techniques referred to above or, alternatively, they can be produced under sterile conditions.
  • the resulting aqueous solutions may be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration.
  • the lipid particles disclosed herein may be delivered via oral administration to the individual.
  • the particles may be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, pills, lozenges, elixirs, mouthwash, suspensions, oral sprays, syrups, wafers, and the like (see, e.g., U.S. Patent Nos. 5,641,515, 5,580,579, and 5,792,451, the disclosures of which are herein incorporated by reference in their entirety for all purposes).
  • These oral dosage forms may also contain the following: binders, gelatin; excipients, lubricants, and/or flavoring agents.
  • the unit dosage form When the unit dosage form is a capsule, it may contain, in addition to the materials described above, a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit. Of course, any material used in preparing any unit dosage form should be pharmaceutically pure and substantially non-toxic in the amounts employed.
  • these oral formulations may contain at least about 0.1% of the lipid particles or more, although the percentage of the particles may, of course, be varied and may conveniently be between about 1% or 2% and about 60% or 70% or more of the weight or volume of the total formulation.
  • the amount of particles in each therapeutically useful composition may be prepared is such a way that a suitable dosage will be obtained in any given unit dose of the compound.
  • Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such
  • Formulations suitable for oral administration can consist of: (a) liquid solutions, such as an effective amount of a packaged therapeutic agent such as nucleic acid (e.g ., cdsDNA) suspended in diluents such as water, saline, or PEG 400; (b) capsules, sachets, or tablets, each containing a predetermined amount of a therapeutic agent such as nucleic acid (e.g., cdsDNA), as liquids, solids, granules, or gelatin; (c) suspensions in an appropriate liquid; and (d) suitable emulsions.
  • a packaged therapeutic agent such as nucleic acid (e.g ., cdsDNA) suspended in diluents such as water, saline, or PEG 400
  • diluents such as water, saline, or PEG 400
  • capsules, sachets, or tablets each containing a predetermined amount of a therapeutic agent such as nucleic acid (e
  • Tablet forms can include one or more of lactose, sucrose, mannitol, sorbitol, calcium phosphates, corn starch, potato starch, microcrystalline cellulose, gelatin, colloidal silicon dioxide, talc, magnesium stearate, stearic acid, and other excipients, colorants, fillers, binders, diluents, buffering agents, moistening agents, preservatives, flavoring agents, dyes, disintegrating agents, and pharmaceutically compatible carriers.
  • Lozenge forms can comprise a therapeutic agent such as nucleic acid (e.g., cdsDNA) in a flavor, e.g., sucrose, as well as pastilles comprising the therapeutic agent in an inert base, such as gelatin and glycerin or sucrose and acacia emulsions, gels, and the like containing, in addition to the therapeutic agent, carriers known in the art.
  • a therapeutic agent such as nucleic acid (e.g., cdsDNA) in a flavor, e.g., sucrose, as well as pastilles comprising the therapeutic agent in an inert base, such as gelatin and glycerin or sucrose and acacia emulsions, gels, and the like containing, in addition to the therapeutic agent, carriers known in the art.
  • lipid particles can be incorporated into a broad range of topical dosage forms.
  • a suspension containing nucleic acid-lipid particles such as SNALP can be formulated and administered as gels, oils, emulsions, topical creams, pastes, ointments, lotions, foams, mousses, and the like.
  • lipid particles of the invention When preparing pharmaceutical preparations of the lipid particles of the invention, it is preferable to use quantities of the particles which have been purified to reduce or eliminate empty particles or particles with therapeutic agents such as nucleic acid associated with the external surface.
  • hosts include mammalian species, such as primates (e.g ., humans and chimpanzees as well as other nonhuman primates), canines, felines, equines, bo vines, ovines, caprines, rodents (e.g., rats and mice), lagomorphs, and swine.
  • primates e.g ., humans and chimpanzees as well as other nonhuman primates
  • canines felines, equines, bo vines, ovines, caprines
  • rodents e.g., rats and mice
  • lagomorphs e.g., swine.
  • the amount of particles administered will depend upon the ratio of therapeutic agent (e.g., nucleic acid) to lipid, the particular therapeutic agent (e.g., nucleic acid) used, the disease or disorder being treated, the age, weight, and condition of the patient, and the judgment of the clinician, but will generally be between about 0.01 and about 50 mg per kilogram of body weight, preferably between about 0.1 and about 5 mg/kg of body weight per administration (e.g., injection).
  • the delivery of therapeutic agents such as nucleic acids can be to any cell grown in culture, whether of plant or animal origin, vertebrate or invertebrate, and of any tissue or type.
  • the cells are animal cells, more preferably mammalian cells, and most preferably human cells (e.g., tumor cells or hepatocytes).
  • the concentration of particles varies widely depending on the particular application, but is generally between about 1 pmole and about 10 mmol.
  • Treatment of the cells with the lipid particles is generally carried out at physiological temperatures (about 37°C) for periods of time from about 1 to 48 hours, preferably from about 2 to 4 hours.
  • a lipid particle suspension is added to 60- 80% confluent plated cells having a cell density of from about 10 to about 10 cells/ml, more preferably about 2 x 10 4 cells/ml.
  • the concentration of the suspension added to the cells is preferably of from about 0.01 to 0.2 pg/ml, more preferably about 0.1 pg/ml.
  • tissue culture of cells may be required, it is well-known in the art.
  • Freshney Culture of Animal Cells, a Manual of Basic Technique, 3rd Ed., Wiley-Liss, New York (1994), Kuchler et ah, Biochemical Methods in Cell Culture and Virology, Dowden, Hutchinson and Ross, Inc. (1977), and the references cited therein provide a general guide to the culture of cells.
  • Cultured cell systems often will be in the form of monolayers of cells, although cell suspensions are also used.
  • an ERP assay is described in detail in U.S. Patent Publication No. 20030077829, the disclosure of which is herein incorporated by reference in its entirety for all purposes. More particularly, the purpose of an ERP assay is to distinguish the effect of various cationic lipids and helper lipid components of SNALP or other lipid particle based on their relative effect on binding/uptake or fusion with/destabilization of the endosomal membrane. This assay allows one to determine quantitatively how each component of the SNALP or other lipid particle affects delivery efficiency, thereby optimizing the SNALP or other lipid particle.
  • an ERP assay measures expression of a reporter protein (e.g., luciferase, b-galactosidase, green fluorescent protein (GFP), etc.), and in some instances, a SNALP formulation optimized for an expression plasmid will also be appropriate for encapsulating an interfering RNA.
  • a SNALP formulation optimized for an expression plasmid will also be appropriate for encapsulating an interfering RNA.
  • an ERP assay can be adapted to measure downregulation of transcription or translation of a target sequence in the presence or absence of an interfering RNA (e.g., siRNA).
  • compositions and methods of the present invention are used to treat a wide variety of cell types, in vivo and in vitro.
  • Suitable cells include, but are not limited to, hepatocytes, reticuloendothelial cells (e.g., monocytes, macrophages, etc.), fibroblast cells, endothelial cells, platelet cells, other cell types infected and/or susceptible of being infected with viruses, hematopoietic precursor (stem) cells, keratinocytes, skeletal, cardiac, and smooth muscle cells, osteoblasts, neurons, quiescent lymphocytes, terminally differentiated cells, slow or noncycling primary cells, parenchymal cells, lymphoid cells, epithelial cells, bone cells, and the like.
  • hematopoietic precursor (stem) cells keratinocytes, skeletal, cardiac, and smooth muscle cells
  • osteoblasts neurons
  • quiescent lymphocytes terminally differentiated cells, slow or noncycling primary cells, parenchymal
  • an active agent or therapeutic agent such as a cdsDNA is delivered to cancer cells (e.g., cells of a solid tumor) including, but not limited to, liver cancer cells, lung cancer cells, colon cancer cells, rectal cancer cells, anal cancer cells, bile duct cancer cells, small intestine cancer cells, stomach (gastric) cancer cells, esophageal cancer cells, gallbladder cancer cells, pancreatic cancer cells, appendix cancer cells, breast cancer cells, ovarian cancer cells, cervical cancer cells, prostate cancer cells, renal cancer cells, cancer cells of the central nervous system, glioblastoma tumor cells, skin cancer cells, lymphoma cells, choriocarcinoma tumor cells, head and neck cancer cells, osteogenic sarcoma tumor cells, and blood cancer cells.
  • cancer cells e.g., cells of a solid tumor
  • cancer cells e.g., cells of a solid tumor
  • cancer cells e.g., cells of a solid tumor
  • cancer cells e.g., cells
  • lipid particles such as SNALP encapsulating a nucleic acid (e.g ., a cdsDNA) is suited for targeting cells of any cell type.
  • the methods and compositions can be employed with cells of a wide variety of vertebrates, including mammals, such as, e.g., canines, felines, equines, bo vines, ovines, caprines, rodents (e.g., mice, rats, and guinea pigs), lagomorphs, swine, and primates (e.g. monkeys, chimpanzees, and humans).
  • AtuPLEX is a multi-lamellar (multiple lipid bilayer) and positively-charged siRNA- lipoplex that combines siRNA with three-lipid liposomes. This can be modified to deliver the subject cdsDNA for various purposes.
  • the liposomes contain proprietary cationic lipids AtuFectOl, co-lipids (fusogenic or stabilizing), and PEGylated lipids, to form a nanoparticle structure with nucleic acid (siRNA or cdsDNA) embedded within multiple lipid bilayers of the particle.
  • the subject cdsDNA is formulated in a composition comprising a pharmaceutically acceptable carrier and a compound according to formula (I):
  • Rl and R2 are each and independently selected from the group comprising alkyl
  • n is any integer between 1 and 4;
  • R3 is an acyl selected from the group comprising lysyl, ornithyl, 2,4-diaminobutyryl, histidyl and an acyl moiety according to formula (II),
  • Rl and R2 are each and independently selected from the group comprising lauryl, myristyl, palmityl and oleyl.
  • Rl is lauryl and R2 is myristyl; or Rl is palmityl and R2 is oleyl.
  • m is 1 or 2.
  • Y is selected from the group consisting of halogenids, acetate, and trifluoroacetate.
  • the compound is selected from the group consisting of:
  • the composition further comprises a pharmaceutically active component selected from the group consisting of peptides, proteins, oligonucleotides, polynucleotides, and nucleic acids.
  • the composition further comprises at least one helper lipid component selected from the group consisting of phospholipids and steroids.
  • the helper lipid component may be selected from the group consisting of l,2-diphytanoyl-sn- glycero-3-phosphoethanolamine and l,2-dioleyl-sn-glycero-3-phosphoethanolamine.
  • the content of the helper lipid component is from about 20 mol % to about 80 mol % of the overall lipid content of the composition.
  • At least one helper lipid comprises a moiety which is selected from the group consisting of a PEG, a HEG, a polyhydroxyethyl starch (polyHES), and a polypropylene.
  • the helper lipid comprising the PEG moiety is selected from the group consisting of l,2-distearoyl-sn-glycero-3-phosphoethanolamine, l,2-dialkyl-sn-glycero-3- phosphoethanolamine, and Ceramide-PEG.
  • the composition comprising: a) 50 mol % of P-arginyl-2,3- diamino propionic acid-N-palmityl-N-oleyl-amide trihydrochloride, 48 mol % of 1,2- diphytanoyl-sn-glycero-3-phosphoethanolamine, and 2 mol % l,2-distearoyl-sn-glycero-3- phosphoethanolamine-PEG2000; or b) P-arginyl-2, 3-diamino propionic acid-N-palmityl-N- oleyl-amide trihydrochloride, 49 mol % l,2-diphytanoyl-sn-glycero-3-phosphoethanolamine, and 1 mol % l,2-distearoyl-sn-glycero-3-phosphoethanolamine-PEG2000.
  • the composition comprises: a) 50 mol % of P-arginyl-2,3- diamino propionic acid-N-palmityl-N-oleyl-amide trihydrochloride, 48 mol % of 1,2- diphytanoyl-sn-glycero-3-phosphoethanolamine, and 2 mol % N(Carbonyl- methoxypolyethylenglycol-2000)- 1 ,2-distearoyl-sn-glycero-3-pho-sphoethanolamine; or b)
  • the composition comprises: a) 50 mol % of P-L-arginyl-2,3- L-diamino propionic acid-N-palmityl-N-oleyl-amide trihydrochloride, 48 mol % of 1,2- diphytanoyl-sn-glycero-3-phosphoethanolamine, and 2 mol % N(Carbonyl- methoxypolyethylenglycol-2000)- 1 ,2-distearoyl-sn-glycero-3-pho-sphoethano lamine; or b)
  • DACC is a lipid delivery system that includes AtuFectOl (see above) and is used to embed siRNAs into a multiple lipid bilayer structure. This system can also be modified to deliver the subject cdsDNA for various purposes.
  • DACC While closely related to the AtuPLEX system, DACC has significantly different biopharmaceutical properties, and delivers nucleic acids to the pulmonary vascular endothelium.
  • DBTC DBTC
  • DBTC is a lipid delivery system that delivers siRNA to hepatocytes and the hepatic vascular system of the liver parenchyma, rather than merely targeting liver hepatocytes. This system can also be modified to deliver the subject cdsDNA for various purposes.
  • the DBTC nanoparticles consist of a synthetic delivery system containing (i) a linear, cyclodextrin-based polymer (CDP), (ii) a human transferrin protein (hTf) targeting ligand displayed on the exterior of the nanoparticle to engage Tf receptors (hTfR) on the surface of the cancer cells, (iii) a hydrophilic polymer (polyethylene glycol (PEG) used to promote nanoparticle stability in biological fluids), and (iv) siRNA designed to reduce the expression of a target gene.
  • CDP linear, cyclodextrin-based polymer
  • hTf human transferrin protein
  • hTfR Tf receptors
  • siRNA designed to reduce the expression of a target gene. See Davis et al, Nature 464(7291): 1067-1070, 2010 (incorporated by reference). This system can be modified by replacing the siRNA component with the subject cdsDNA.
  • the system can also be modified by replacing targeting moiety such that delivery to other specific tissue sites can be accomplished.
  • targeting moiety for delivery to skeletal or cardiac muscle cells, the TfR can be replaced with a natural ligand for a receptor on skeletal or cardiovascular cells, or an antibody or fragment thereof specific for a marker on the skeletal or cardiovascular cells.
  • the targeting moiety can also be derived from viruses that have the natural tropism desired (e.g ., adenovirus type 5 knob protein for cardiomyocyte delivery). The same strategy can be used for any of the other targeted delivery of
  • nanoparticles have been shown to be well tolerated in multi-dosing studies in non-human primates, and can be systemically delivered to treat, for example, solid tumor.
  • RONDEL stands for RNAi/Oligonucleotide Nanoparticle Delivery. It is a platform that has been used in delivery of siRNA in clinical trials for treating solid tumors.
  • RONDEL is a non-liposomal polymer-based nanoparticle re-optimized for in vivo siRNA delivery. It has four components that self-assemble into nanoparticles: (i) siRNA strands (which can be replaced with the cdsDNA of the invention), (ii) cyclodextrin-containing polymers (CDPs), (iii) polythethylene glycol (PEG) as steric stabilization agents, and (iv) human transferrin (Tf).
  • Tf is a targeting ligand for binding to transferrin receptors (TfR) that are typically
  • the CDPs are linear polycationic oligomers containing positively charged amidine groups alternating with sugar (cyclodextrin) moieties.
  • the positively charged CDP polymer associates with the negatively charged backbone of nucleic acids (such as cdsDNA) to form nanoparticles less than 100 nm in diameter, with the nucleic acid at their cores and
  • Components (iii) and (iv) associate non-covalently with the hydrophobic cores in the CDP via a hydrophobic adamantine group covalently bound to one end of the PEG.
  • the resulting complex is a nucleic acid containing
  • PEG stabilizer
  • PEG-targeting ligands such as TfR
  • DPC Dynamic PolyConjugates
  • PBAVE amphipathic endosomolytic polymer poly(butyl amino vinyl ether)
  • the PEG and targeting ligands are released in the acidic environment of the endosome to trigger endosomal release.
  • the disulfide linkage is cleaved to release the nucleic acid (e.g., cdsDNA). See US Patent No. 8,501,930 (incorporated herein by reference).
  • An improved version of the DPC system takes advantage of atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT) to produce polymers that are homogeneous and amenable to large scale manufacturing.
  • ATRP atom transfer radical polymerization
  • RAFT reversible addition-fragmentation chain transfer
  • the nucleic acid within is not attached to the DPC polymer. Instead, the nucleic acid -cholesterol conjugate is co-injected with a melittin-like peptide that has reversibly masked
  • SMARTICLES are amphoteric liposomes that are pH dependent charge-transitioning particles that provide therapeutic nucleic acids (e.g., cdsDNA) to cells by local or systemic administration. SMARTICLES are stable in blood and distribute in the same manner as conventional liposomes, but become positively charged when they cross cell membranes, leading to delivery of the nucleic acid payload within sites of inflammation, tumors, liver, and spleen.
  • nucleic acids e.g., cdsDNA
  • DiLA Di-alkylated Amino Acids
  • cdsDNA therapeutic nucleic acid
  • DiLA is Histidine-containing Di-alkylated Amino Acid based system that allows one to modify key aspects of the delivery system such as charge, linker and acyl chains to optimize the properties of the liposome.
  • DiLA allows one to optimize delivery to a target tissue of interest, and permits inclusion of peptides to improve a variety of delivery characteristics such as encapsulation of nanoparticles, cellular uptake, endosomal release and cell/tissue targeting.
  • peptides an amino acid-based amphoteric liposomal delivery system for systemic administration of siRNA. Mol. Ther. 19:1141-1151, 2011 (incorporated by reference).
  • U.S. Patent Nos. 8,501,824, and 7,959,505 are examples of the delivery systemic administration of siRNA.
  • EnCore is a nanoparticle system developed for delivery of nucleic acid payloads (such as cdsDNA), for delivering to the liver and solid tumors.
  • EnCore contains a lipid-nucleic acid core surrounded by an envelope of a different lipid mixture that mediates accumulation, internalization, and release of nucleic acid payload into the target cell. This sub- structured particle is designed for preferential accumulation in tumors and provides high levels of payload delivery. See U.S. Patent No. 7,371,404 (incorporated herein by reference).
  • Polyrotaxane or PRX is a type of interlocked macromolecule made of multiple a- cyclodextrin rings, a PEG chain, and two bulky stoppers to physically prevent the rings from dethreading.
  • PRX can self-assemble and condense nucleic acid into nanostructures.
  • PRX has been demonstrated in mdx mice to successfully deliver plasmid, and data showed abundant plasmid distribution in most muscle tissues. Thus PRX can also be used to deliver the subject cdsDNA.
  • the process of the invention is partially carried out in an in vitro cell-free
  • the process is partly carried out in the absence of a host cell, and typically comprises use of purified enzymatic components. Accordingly, processing by protelomerase and other downstream operations are typically carried out by contacting the reaction components in solution in a suitable container.
  • particular components may be provided in immobilized form, such as attached to a solid support.
  • the process of the invention may be carried out at any scale. However, it is preferred that the process is carried out to produce any DNA fragment of interest at a commercial or industrial scale, i.e., generating amplified DNA fragment of interest in mg or greater quantities.
  • the process generates at least 1 mg, at least 10 mg, at least 20 mg, at least 50 mg, or at least 100 mg of DNA fragment of interest.
  • the final cdsDNA product may also be generated in mg or greater quantities.
  • the process generates at least one mg, at least 2 mg, at least 5 mg, at least 10 mg, at least 20 mg, at least 50 mg, or at least 100 mg of cdsDNA.
  • the LNPs and polymer NPs of the invention encompassing the subject cdsDNA can be manufactured using any art-recognized methods.
  • the LNPs and polymer LPs can be manufactured using commercially available services and/or equipments, such as those provided by Precision Nanosystems (Vancouver, British Columbia).
  • the LNPs and NPs are prepared using the NanoAsseblr platform of Precision Nanosystems.
  • the NanoAsseblr platform utilizes microfluidic mixing for the controlled, tuned and fully scalable manufacture of nanomedicines, including the LNPs and polymer NPs of the invention. It enables the rapid and controlled manufacture of nanomedicines (liposomes, lipid nanoparticles, polymeric nanoparticles) via custom- engineered microfluidic mixing cartridges that allow millisecond mixing of nanoparticle components at the nano litre scale.
  • the platform allows users to control size by process and composition, and adjust parameters such as mixing ratio, flow rate and lipid composition in order to fine-tune nanoparticle size and encapsulation efficiency.
  • This system has been used in conjunction with the Neuro9TM Transfection kit (a Non viral transfection kit by Precision Nanosystems, Vancouver, British Columbia) to deliver siRNA and mRNA and pDNA to primary neurons both in vitro and in vivo , and achieve 95% cell transfection efficiency and 90% knockdown in transfected cells, with no observable toxicity.
  • Neuro9TM Transfection kit a Non viral transfection kit by Precision Nanosystems, Vancouver, British Columbia
  • Neuro9TM encapsulates and protects nucleic acids in a synthetic lipid nanoparticle (LNP) that mimics endogenous low density lipoproteins (LDLs), which are taken up naturally by cells like neurons, astrocytes and iPSCs.
  • LNP synthetic lipid nanoparticle
  • LDLs low density lipoproteins
  • Neuro9 is pH-sensitive and engineered to release its contents into the cytoplasm.
  • the Neuro9TM Transfection kit and related products can also be used to deliver the subject cdsDNA to specific target cells such as neurons.
  • the LNPs and polymer NPs of the invention are produced at a scaled up quantity of about 10 mL to 1 L, or up to 5 L, or up to 10 L, or up to 15 L, or up to 20 L, or up to 25 L, or up to 50 L or more LNPs and NPs formulations.
  • the scale-up can be through microfluidic reactor parallelization, similar to the arraying of transistors on an integrated chip.
  • the manufacture process is controlled by software or semi- / fully automated.
  • the manufacture is carried out in the NanoAssemblr Spark, which has an operating nanoparticle formulation volume of 25 - 250 pL.
  • the manufacture is carried out in the NanoAssemblr
  • Benchtop system which is designed for rapid prototyping of novel nanoparticle formulations of 1 to l5mL, and has software control that enables the control of input mixing parameters for optimizing particle characteristics such as size and encapsulation efficiency.
  • the manufacture is carried out in the NanoAssemblr Blaze system suitable for clinical development.
  • the system can manufacture between 10 mL and 1
  • the manufacture is carried out in the NanoAssemblr Scale-Up system developed for manufacturing clinical trial nanoparticle materials in the cGMP environment. It provides seamless scale-up of formulations developed on the NanoAssemblr Benchtop and Blaze platforms. Processes developed on pre-clinical instruments are directly transferred to scale-up using identical microfluidic mixers connected in parallel. Parallel mixers enable the execution of identical processes producing a single large volume batch in less time.
  • the Scale-up System with 8 microfluidic mixers running in parallel can produce nanoparticle formulation volumes suitable for early stage clinical trials.
  • the invention further provides a kit comprising components required to carry out the process of the invention.
  • This kit comprises at least one protelomerase, and optionally instructions for use in a process as described herein.
  • the kit may comprise two, three, four, five or more different protelomerase s.
  • the protelomerases may be selected from any of SEQ ID NOs: 2, 4, 6, 8 or 10 or variants of any thereof.
  • the kit comprises E. coli N15 TelN (SEQ ID NO: 10) or a variant thereof.
  • the kit may also comprise suitable buffers and other factors which are required for protelomerase enzyme performance or stability as described above.
  • a Pucl9 backbone plasmid construct was prepared for amplifying a GFP reporter gene, including a GFP coding sequence under the control of a mammalian promoter and comprising a polyA coding sequence.
  • the GFP reporter gene is flanked by a pair of AAV2 ITR sequences, ITR1 and ITR2, respectively. Each ITR can be separated from the GFP reporter gene via Not I digestion due to the presence of Not I recognition sequences between the ITRs and the GFP reporter gene.
  • the ITR-flanked GFP reporter gene is further flanked by two TelN recognition sequences, TelN-Left and TelN- Right.
  • the plasmid Upon amplification and harvesting of the plasmid comprising the GFP construct, the plasmid was digested with the N6 protelomerase TelN to resolve the GFP construct into two cdsDNA, one comprising essentially the GFP reporter gene flanked by the ITRs, and further flanked by two half-sites of the TelN recognition sequences.
  • the other cdsDNA comprises the rest of the plasmid backbone, flanked by the two half-sites of the TelN recognition sequences. See gel electrophoresis results in FIG. 3.
  • the GFP-containing cdsDNA can be recovered from the gel, or purified from the TelN digestion reaction directly for further use.
  • Purified cdsDNA comprising the GFP reporter gene (FIG. 4A) was transfected into C2C12 myotubes using standard molecular biology techniques, and GFP expression in the C2C12 myotubes (see FIG. 4B) was monitored over time.
  • Not I digested cdsDNA was similarly transfected into the C2C12 myotubes, so is a pCK8-GFP construct with an identical GFP reporter gene that is not flanked by the ITRs.
  • FITC images show strong expression of cdsDNA-encoded GFP transfected to the C2C12 cells, while Not I-digested GFP dsDN A- transfected cells have weak expression.
  • the pCK8 GFP control also yielded poor expression compared to cdsDNA-transfected cells.
  • Example 1 To test the integrity of the cdsDNA, the plasmid construct of Example 1 was digested with TelN and/or exonuclease under several conditions, and the digestion products were resolved on gel electrophoresis. See FIGs. 5A and 5B.
  • cdsDNA constructs of the invention can be used to express an exogenous transgene in vitro , in C2C12 cells were transfected by a cdsDNA construct named SLiD-MD44 using the VIAFECTTM Transfection Reagent (Promega Corp., WI) according to the manufacturer’s recommendation.
  • SLiD-MD44 encodes a 5-repeat microdystrophin protein that contains, from N- to C- terminus, the N-terminal actin binding domain, Hinge region 1 (Hl), specctrin-like repeats Rl, R16, R17, R23, and R24, Hinge region 4 (H4), and the C-terminal dystroglycan binding domain of the human full-length dystrophin protein.
  • Hl Hinge region 1
  • H4 specctrin-like repeats
  • Rl, R16, R17, R23, and R24 Hinge region 4
  • H4 Hinge region 4
  • C-terminal dystroglycan binding domain of the human full-length dystrophin protein The protein sequence of this 5-repeat microdystrophin and the related dystrophin minigene are described in WO2016/115543 (incorporated herein by reference).
  • FIG. 7A shows that the subject cdsDNA is resistant to exonuclease III digestion. Restriction and protelomerase digestion of the plasmid comprising the 5-repeat
  • microdystrophin protein coding sequence (SLiD-MD44) generated multiple bands resolved on electrophoresis, only one of the bands matching the expected size of the subject cdsDNA (i.e., MD44) appeared resistant to exonuclease III digestion, confirming the co-valently linked terminal structures in the protelomerase digestion product.
  • the isolated cdsDNA SLiD-MD44 was then transfected into cultured C2C12 cells using the VIAFECTTM Transfection Reagent, and immunofluorescent staining was used to reveal the cytoskeleton (anti-F-actin antibody staining), the nuclei (Haematoxylin staining), and any expressed 5-repeat microdystrophin protein (anti-DysB antibody). It is apparent that C2C12 cells transfected by the subject cdsDNA encoding a 5-repeat microdystrophin protein had robust expression of the 5-repeat microdystrophin protein. Meanwhile, control transfection with no DNA generated no signal when the same anti-DysB antibody was used.
  • cdsDNA constructs of the invention can be used to express an exogenous transgene in vivo, specifically, expression of an exogenous microdystrophin gene in the mdx mouse model of DMD.
  • a cdsDNA construct named SLiD-MD4 was prepared to encoding a 5-repeat microdystrophin as in Example 4. About 40 pg of SLiD-MD4 cdsDNA was then introduced into an mdx mouse via intramuscular electroporation (IM Electroporation). As a control, saline solution was used instead of the SLiD-MD4 cdsDNA construct.
  • Purified SLiD-MD4 cdsDNA construct was formulated in 150 mM of NaCl at 2 pg/pF, and was stored at -20°C till use.
  • Hyaluronidase (Sigma, H-4272) was formulated in PBS at 2 mg/mL, and 1 mL aliquots were stored at -20°C till use.
  • SLiD-MD4 and hyaluronidase stocks were thawed.
  • An mdx mouse was anesthetized through inhalation of 2-3% isoflurane.
  • Mouse hindlegs were shaved at where tibialis anterior muscles are.
  • a 50 pL of hyaluronidase was then injected directly into the tibialis anterior muscle by entering at the middle of the muscle with a 0.3 mL tuberculin syringe. Materials were injected slowly, and the needle was retracted slowly after injection.
  • SLiD-MD4 cdsDNA- containing construct in 30 pL was injected directly into the tibialis anterior muscle by entering the needle at the middle of the muscle with a tuberculin syringe. Materials were injected slowly, and the needle was retracted slowly after injection. Immediately after the DNA injection, the mdx mouse underwent electroporation using a BTX AgilePulse ID
  • Electroporator and a 5 mm, 4-needle-array electrode (BTX, 47-0045).
  • the DNA injection site was positioned in between the 2 parallel arrays of needles, which were inserted through skin and into the tibialis anterior muscle until the estimated load reading is ⁇ 3000 ohms. Perform electroporation using the following setting.
  • Tibialis anterior muscles were collected 7 days after injection for analysis.
  • Immunofluorescent staining using the anti-DysB mouse monoclonal antibody was then used to verify microdystrophin expression in muscle tissues isolated from the mdx mouse electroporated by the SLiD-MD4 cdsDNA construct.
  • the antibody was raised against residues 321-494 of the human dystrophin protein.
  • FIG. 8B shows wide-spread fluorescent signal representing robust dystrophin expression in mdx mouse receiving the SLiD-MD4 cdsDNA construct through IM
  • FIG. 9B An enlarged portion of FIG. 8B is shown in FIG. 9B, in which dystrophin expression was observed along the correct subcellular localization around the plasma membrane, suggesting that the exogenous microdystrophin is not only successfully and widely expressed in the muscle tissue of the mdx mouse, but is also likely to be functional due to the correct folding and correct subcellular localization.
  • control mouse receiving saline control through the same procedure only had background level signal. See FIG. 8A, and similarly enlarged section in FIG. 9A.
  • FIG. 10 shows that the expression of the exogenous microdystrophin gene persisted after 7 days post IM electroporation.
  • 60 pg of the same SLiD-MD4 cdsDNA construct was used in mdx mouse via IM electroporation.
  • Immuno staining was performed 7 days post electroporation, using both an anti-DysB monoclonal antibody labeled by a red fluorescent signal, and an anti- laminin monoclonal antibody labeled by a green fluorescent signal.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Genetics & Genomics (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Epidemiology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Animal Behavior & Ethology (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • Organic Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Wood Science & Technology (AREA)
  • Optics & Photonics (AREA)
  • Plant Pathology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Dispersion Chemistry (AREA)
  • Nanotechnology (AREA)
  • Dermatology (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

The invention described herein pertains to the production of closed-end double- stranded DNA (cdsDNA) that can be easily amplified and produced in large quantity, for use in, for example, therapeutic use, such as gene therapy.

Description

NON- VIRAL PRODUCTION AND DELIVERY OF GENES
REFERENCE TO RELATED APPLICATION
This application claims the benefit of the filing date to U.S. Provisional Application No. 62/598,532, filed on December 14, 2017, the entire contents of which are incorporated herein by reference.
BACKGROUND OF THE INVENTION
Gene delivery to target cells for purposes such as gene therapy is well-known, particularly for the treatment of diseases such as cystic fibrosis and certain cancers. The term includes the delivery or introduction into a target cell of any nucleic acid material, such as a gene or part of a gene, to correct some genetic deficiency, as well as gene vaccination and the in vitro production of commercially-useful proteins in a suitable host cell.
Cell delivery systems generally fall into three broad classes, namely those that involve direct injection of naked DNA or RNA, those that make use of viruses or genetically modified viruses, and those that make use of non-viral delivery agents. Although viruses as delivery agents have the advantages of high efficiency and high cell selectivity, they have the disadvantages of toxicity, production of inflammatory responses and difficulty in dealing with large DNA fragments.
Thus, there is a need to provide improved cell delivery systems, including non-viral delivery of any DNA fragment of interest.
SUMMARY OF THE INVENTION
One aspect of the invention provides a DNA construct comprising: (1) a backbone sequence comprising sequences supporting self-replication in a eukaryotic (e.g., mammalian) or prokaryotic cell; (2) an insert comprising: (a) a DNA fragment of interest; (b) a pair of end sequences flanking the DNA fragment of interest, wherein the end sequences are inverted terminal repeats (ITRs), long terminal repeats (LTRs) or internal repeats, or telomere sequences; and, (c) a pair of protelomerase recognition sequences flanking the pair of ITR or LTR. In certain embodiments, the insert or the DNA fragment of interest is configured to and capable of existing extra-chromosomally during an entire life cycle of a eukaryotic cell.
In certain embodiments, the ITRs are from double- stranded DNA viruses, such as AAV. In certain embodiments, the AAV is any one of AAV1-AAV10. In certain embodiments, the LTRs are from a DNA virus, such as HSV.
In certain embodiments, at least one of the protelomerase recognition sequences comprises a perfect inverted repeat DNA sequence of at least 14 bp in length, or a variant thereof.
In certain embodiments, at least one of the protelomerase recognition sequences comprises a 22 bp consensus sequence for a mesophilic bacteriophage perfect inverted repeat.
In certain embodiments, at least one of the protelomerase recognition sequences is from E. coli phage N15 (such as the one recognized by E. coli N15 TelN protelomerase), agrobacterium Klebsiella phage Phi K02, Yersinia phage PY54, Halomonas phage phiHAP-l, and Vibrio phage VP882, or Borrelia burgdorferi.
In certain embodiments, at least one of the protelomerase recognition sequences comprises a perfect inverted repeat at least 30, at least 40, at least 60, at least 80 or at least 100 base pairs in length.
In certain embodiments, the DNA fragment of interest comprises a coding sequence of interest under the control of /operably linked to a eukaryotic promoter and/or enhancer, and optionally a eukaryotic transcription termination sequence.
In certain embodiments, the coding sequence of interest may comprise a DNA vaccine that encodes an antigen: (1) for the treatment or prevention of conditions such as cancer, allergies, toxicity and infection by a pathogen (e.g., fungi, viruses such as Human Papilloma Viruses (HPV), HIV, HSV2/HSV1, Influenza virus (types A, B and C), Polio virus, RSV virus, Rhinoviruses, Rotaviruses, Hepatitis A virus, Norwalk Virus Group,
Enteroviruses, Astroviruses, Measles virus, Parainfluenza virus, Mumps virus, Varicella- Zoster virus, Cytomegalovirus, Epstein-Barr virus, Adenoviruses, Rubella virus, Human T- cell Lymphoma type I virus (HTLV-I), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Hepatitis D virus, Pox virus, Marburg and Ebola); bacteria (such as Mycobacterium
tuberculosis, Chlamydia, Neisseria gonorrhoeae, Shigella, Salmonella, Vibrio cholerae, Treponema pallidum, Pseudomonas, Bordetella pertussis, Brucella, Francisella tularensis, Helicobacter pylori, Leptospira interrogans, Legionella pneumophila, Yersinia pestis,
Streptococcus (types A and B), Pneumococcus, Meningococcus, Haemophilus influenza (type b), Toxoplasma gondii, Campylobacteriosis, Moraxella catarrhalis, Donovanosis, and Actinomycosis); fungal pathogens (such as Candidiasis and Aspergillosis); parasitic pathogens (such as Taenia, Flukes, Roundworms, Amoebiasis, Giardiasis, Cryptosporidium, Schistosoma, Pneumocystis carinii, Trichomoniasis and Trichinosis); (2) from a member of the adenoviridae ( e.g ., a human adenovirus), herpesviridae ( e.g ., HSV-l, HSV-2, EBV, CMV and VZV), papovaviridae (e.g., HPV), poxyiridae (e.g., smallpox and vaccinia), parvoviridae (e.g., parvovirus B19), reoviridae (e.g., a rotavirus), coronaviridae (e.g., SARS), flaviviridae (e.g., yellow fever, West Nile virus, dengue, hepatitis C and tick-borne encephalitis), picornaviridae (e.g., polio, rhino virus, and hepatitis A), togaviridae (e.g., rubella virus), filoviridae (e.g., Marburg and Ebola), paramyxoviridae (e.g., a parainfluenza virus, respiratory syncytial virus, mumps and measles), rhabdoviridae (e.g., rabies virus), bunyaviridae (e.g., Hantaan virus), orthomyxoviridae (e.g., influenza A, B and C viruses), retroviridae (e.g., HIV and HTLV) and hepadnaviridae (e.g., hepatitis B); (3) from a pathogen responsible for a veterinary disease, such as a viral pathogen, a Reo virus (e.g., African Horse sickness or Bluetongue virus) and Herpes viruses (e.g., equine herpes), a Foot and Mouth Disease virus, a Tick borne encephalitis virus, a dengue virus, SARS, a West Nile virus and a Hantaan virus; (4) from an immunodeficiency virus, such as SIV or a feline immunodeficiency virus; (5) that is a neo-antigen (e.g., encoded by mutated genes in cancers / tumors), a tumor antigen, such as testes antigen (e.g., members of the MAGE family (MAGE 1, 2, 3 etc), NY-ESO-l and SSX-2), differentiation antigens (e.g., tyrosinase, gplOO, PSA, Her-2 and CEA), mutated self antigens, and viral tumor antigens (e.g., E6 and/or E7 from oncogenic HPV types), MART-l, Melan-A, p97, beta-HCG, GalNAc, MAGE-l, MAGE-2, MAGE-4, MAGE- 12, MUC1, MUC2, MUC3, MUC4, MUC18, CEA, DDC, P1A, EpCam, melanoma antigen gp75, Hker 8, high molecular weight melanoma antigen, K19, Tyrl, Tyr2, members of the pMel 17 gene family, c-Met, PSM (prostate mucin antigen), PSMA (prostate specific membrane antigen), prostate secretary protein, alpha- fetoprotein,
CA 125, CA 19.9, TAG-72, BRCA-l and BRCA-2 antigen.
In certain embodiments, the coding sequence of interest comprises a therapeutic DNA molecule for gene therapy, wherein said therapeutic DNA molecule: (1) expresses a functional gene in a subject having a genetic disorder caused by a dysfunctional version of said functional gene (e.g., gene for Duchenne muscular dystrophy, cystic fibrosis, Gaucher’s Disease, and adenosine deaminase (ADA) deficiency, inflammatory diseases, autoimmune, chronic and infectious diseases, AIDS, cancer, neurological diseases, cardiovascular disease, hypercholesterolemia, various blood disorders (including various anaemias, thalassemia and haemophilia, and emphysema), and solid tumors); (2) encodes toxic peptides (i.e., chemotherapeutic agents such as ricin, diphtheria toxin and cobra venom factor), tumor suppressor genes (such as p53), genes coding for mRNA sequences which are antisense to transforming oncogenes, antineoplastic peptides such as tumor necrosis factor (TNF) and other cytokines, or transdominant negative mutants of transforming oncogenes; (3) encodes an active RNA form (e.g., a small interfering RNA (siRNA, miRNA, shRNA), or a small activating RNA (saRNA); or, (4) encodes a CRISPR/Cas component (such as a Cas9 enzyme or an sgRNA).
Another aspect of the invention provides a closed-end double stranded DNA
(cdsDNA) produced by contacting the subject DNA constructs with a protelomerase that recognizes the pair of protelomerase recognition sequences. In certain embodiments, the subject cdsDNA is configured to and capable of existing extra-chromosomally during an entire life cycle of a eukaryotic cell.
Another aspect of the invention provides a closed-end double stranded DNA
(cdsDNA) comprising: (a) a DNA fragment of interest; (b) a pair of end sequences flanking the DNA fragment of interest, wherein the end sequences are inverted terminal repeats (ITRs) (e.g., of double- stranded DNA viruses), long terminal repeats (LTRs) or internal repeats of DNA virus (such as HSV), or telomere sequences; and, (c) a pair of half protelomerase recognition sequences flanking the pair of end sequences, wherein each of said half protelomerase recognition sequences forms one closed-end of the cdsDNA. In certain embodiments, the cdsDNA or the DNA fragment of interest is configured to and capable of existing extra-chromosomally during an entire life cycle of a eukaryotic cell.
Another aspect of the invention provides a pharmaceutical composition comprising the subject cdsDNA.
In certain embodiments, the cdsDNA is encompassed by a nanoparticle, such as an LNP or a polymer-based NP.
In certain embodiments, the nanoparticle is SNALP (stable nucleic acid-lipid particle), AtuPLEX, DACC, DBTC, RONDEL, DPC (Dynamic PolyConjugate), SMARTICLE, DiLA2, or EnCore.
Another aspect of the invention provides a method of producing a cell-free closed-end double stranded DNA (cdsDNA), the method comprising: (1) isolating the subject DNA construct after amplifying the DNA construct in the eukaryotic (e.g., mammalian) or prokaryotic cell; (2) linearizing the DNA construct with an endonuclease that does not digest within the insert; (3) contacting the DNA construct with a protelomerase that recognizes the pair of protelomerase recognition sequences to release the cdsDNA; (4) after steps (2) and (3), removing linearized DNA construct or fragment thereof that are not cdsDNA with an exonuclease; (5) enriching or purifying the cdsDNA.
In certain embodiments, steps (2) and (3) are carried out in any order or
simultaneously, both after step (1).
Another aspect of the invention provides a method of producing a closed-end double stranded DNA (cdsDNA), the method comprising: (1) isolating the subject DNA construct after amplifying the DNA construct in the eukaryotic ( e.g ., mammalian) or prokaryotic cell; (2) contacting the DNA construct with a protelomerase that recognizes the pair of
protelomerase recognition sequences to release the cdsDNA; (3) enriching or purifying the cdsDNA.
In certain embodiments, the method further comprises encapsulating the cdsDNA in a nanoparticle (such as SNALP, AtuPLEX, DACC, DBTC, RONDEL, DPC, SMARTICLE, DiLA2, or EnCore).
Another aspect of the invention provides a method of delivering a target gene of interest (GOI) into a target cell, the method comprising contacting the target cell with a composition comprising the subject cdsDNA.
In certain embodiments, the target cell is contacted in vitro , ex vivo , or in vivo.
In certain embodiments, the target GOI is a wild-type, mini- or micro-dystrophin gene for treating DMD (Duchenne Muscular Dystrophy), a gene in the DMD pathway (such as follistatin or a human IgG fusion thereof, or an inhibitor of the IKKb or NF-kB pathway), or a construct related to a genetic modifier of DMA (such as SPP1 or LTBP4), and wherein the target cell is a muscle (e.g., skeletal muscle such as a tibialis anterior muscle cell, cardiac muscle, smooth muscle, or muscle in diaphragm, triceps, soleus, tibialis anterior,
gastrocnemius, extensor digitorum longus, rectus abdominus, quadriceps, and combinations thereof, or muscle as described in Table 1 of W02017152090A2, incorporated by reference). In certain embodiments, at least one symptom or feature of DMD is reduced in intensity, severity, or frequency, or has delayed onset (e.g., at least one symptom or feature of DMD selected from the group consisting of muscle wasting, muscle weakness, muscle fragility, muscle necrosis, muscle fibrosis, joint contracture, skeletal deformation, cardiomyopathy, impaired swallowing, impaired bowel and bladder function, muscle ischemia, cognitive impairment, behavioral dysfunction, socialization impairment, scoliosis, and impaired respiratory function). In certain embodiments, treatment results in an increase in the mass of a muscle relative to a control (e.g., an increase of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200% or 500% relative to a control). In certain embodiments, treatment results in muscle regeneration, increased muscle strength, increased flexibility, increased range of motion, increased stamina, reduced fatigability, increased blood flow, improved cognition, improved pulmonary function, inflammation inhibition, reduced muscle fibrosis, and/or reduced muscle necrosis. In certain embodiments, the method further comprises administering one or more additional therapeutic agents, such as anti-Fit-l antibody or fragment thereof, edasalonexent, pamrevlumab, prednisone, deflazacort, RNA modulating therapeutics, exon-skipping therapeutics and any other gene therapy.
In certain embodiments, the target gene of interest (GOI) is delivered into the target cell daily, twice weekly, weekly, monthly, bimonthly, or once every 2, 3, 4, 5, 6, 9, 12, 18, 24, 36, 60, 72 or more months.
A related aspect of the invention provides a use of a composition comprising any one of the subject cdsDNA, or the subject pharmaceutical composition, in the manufacture of a medicament for delivering a target gene of interest (GOI) into a target cell in vivo.
It is contemplated that any one or more of the embodiments described herein, including those described only in the examples or only under one aspect of the invention, can be combined with any one or more embodiments unless explicitly disclaimed or improper.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic illustration showing an exemplary embodiment of the non-viral production of nanoparticles encapsulating closed-end dsDNA (cdsDNA) that may be used in, for example, gene therapy to deliver a gene of interest (GOI) to a target cell in vitro , ex vivo , or in vivo to a target host organism. The center region of the cdsDNA, represented by the longest double lines in the middle, represents the GOI. The pair of short bars immediately flanking the GOI represent the inverted terminal repeat (ITR) sequence of a viral genome, such as that from the Adeno Associated virus (AAV) genome. The pair of short bars immediately flanking the ITR-capped GOI represent the recognition or target sequence for a protelomerase, such as the 56 bp TelN protelomerase recognition sequence. Once the cdsDNA is digested by the protelomerase, the two ends of the dsDNA are converted to closed-end single stranded DNA loop, as the product of the protelomerase digestion, thus forming the cdsDNA molecule. The cdsDNA molecule is then packaged / assembled / prepared / manufactured into nanoparticles of suitable materials, which nanoparticles can be introduced into a target cell or cells inside a target organism for expression of the GOI.
FIG. 2 illustrates the process by which the TelN protelomerase cleaves a dsDNA substrate to generate the cdsDNA comprising the GOI in FIG. 1. The 56-bp TelN protelomerase recognition sequence (TelN site) is shown at the top of the figure. Upon cleavage by TelN at the middle of the TelN site, the 3’ of the G in the top strand to the left of the cleavage site, and the 5’ of the C in the bottom strand to the left of the cleavage site is linked by TelN to form a closed end single- stranded loop, so is the right hand side of the TelN cleavage site. Thus in a dsDNA plasmid encompassing the GOI ( e.g ., GFP) flanked by ITR sequences (ITR1 and ITR2), and further flanked by a pair of TelN sites ( i.e ., TelN-Left and TelN-Right), protelomerase digestion releases the linear duplex encompassing the GOI flanked by the ITRs and further flanked by the TelN half sites with capped terminal single- stranded loop to form the cdsDNA.
FIG. 3 shows the generation of the cdsDNA drug substance using the methods of the invention. The three bands, from top to bottom in each lane, is the undigested circular plasmid encompassing the GFP as GOI; the remaining plasmid backbone; and the GOI (GFP) flanked by the ITRs with closed loop ends resulting from protelomerase digestion.
FIG. 4A and 4B show that the cdsDNA so generated is biologically active to direct GFP expression in a target muscle cell in vitro. The left panel of FIG. 4A is a schematic drawing showing that a circular plasmid (pCK8-GFP) is digested by protelomerase to generate a cdsDNA encoding a GFP reporter gene (“SLiD/non- viral AAV”). The right panel of FIG. 4A shows a gel image in which the lane with Exonuclease Ill-digested product formed a single band (the cdsDNA), while the two other bands disappeared presumably due to Exonucleoase III digestion. The cdsDNA encompassing the GFP coding sequence was then introduced into the C2C12 myotubes, and GFP expression was monitored thereafter.
The merged image panel in FIG. 4B includes GFP signal (expressed by the cdsDNA), the DAPI nuclear staining, and the F-actin staining.
FIG. 4C shows that, as control, Not I - digested same plasmid releases a dsDNA fragment consisting essentially of the GOI (GFP), but not the flanking ITRs. Another control is the pCK8 GPF construct, which is a parental plasmid construct with ITR sequences flanking the identical GFP reporter gene. Though transfected cells displayed the same morphology under the phase contrast microscope, FITC images show strong expression of cdsDNA-encoded GFP transfected to the C2C12 cells, while Not I-digested GFP dsDNA (an open-end DNA without ITR)-transfected cells have weak expression. The pCK8 GFP control also yielded poor expression compared to cdsDNA-transfected cells. It was determined that transfection efficiency is about 60% for the cdsDNA-encoded GFP, and GFP expression became stronger as the myotubes matured.
FIG. 5A shows that the closed loop ends of the cdsDNA resulting from protelomerase digestion protects the cdsDNA from exonuclease digestion.
FIG. 5B shows that linearizing the plasmid backbone with an endonuclease (such as Xbal) renders the protelomerase digestion protect comprising the plasmid backbone susceptible to exonuclease digestion.
FIG. 6 is a schematic drawing illustrating the cell-free cdsDNA drug substance manufacturing process.
FIG. 7A shows that the subject cdsDNA encoding a 5-repeat microdystropin protein (SLiD-MD44) is resistant to exonuclease III digestion, confirming the existence of the closed ends after protelomerase digestion.
FIG. 7B shows that the subject cdsDNA can express the encoded 5-repeat microdystrophin protein in vitro in C2C12 cells.
FIGs. 8A and 8B show in vivo expression of an exogenous microdystrophin in mdx mouse muscle tissue. Mice were administered with either 40 pg of a subject cdsDNA encoding a microdystrophin minigene (SLiD-MD4), or control saline, via intramuscular electroporation (IM Electroporation). Expression of microdystrophin in muscle was verified by immuno staining using an anti-DysB monoclonal antibody raised against a spectrin repeat found in the microdystrophin minigene.
FIGs. 9A and 9B are enlarged sections of images shown in FIGs. 8A and 8B, respectively. Correct subcellular ( .<?., plasma membrane) localization by the expressed exogenous microdystrophin was shown.
FIG. 10 shows persistent microdystrophin minigene expression in mdx mouse receiving 60 pg of the cdsDNA construct SLiD-MD4, 7 days post IM/Electroporation.
Microdystrophin expression was shown as red fluorescent signals, while endogenous laminin expression was shown as green fluorescent signals.
DETAILED DESCRIPTION OF THE INVENTION
1. Overview
The compositions and methods of the invention described herein are partly based on the discovery that DNA fragment of interest flanked by a pair of end sequences, such as end sequences based on Inverted Terminal Repeats (ITRs) of certain double- stranded DNA viruses, or Long Terminal Repeats (LTRs) or internal repeats of certain DNA viruses, and further flanked by a pair of protelomerase recognition sequences, can be efficiently amplified for producing cell-free closed-end double- stranded DNA (cdsDNA) molecules encompassing such DNA fragment of interest, which cdsDNA can then be packaged into certain
nanoparticles, such as lipid-based nanoparticles (LNPs) or polymer-based nanoparticles (NPs) as pharmaceutical compositions.
The invention provided herein provides a means to manufacture / produce any cell- free DNA fragment of interest, such as therapeutic DNA molecules, in large quantity or scale that can be used, for example, for gene therapy without the use of any viral vectors.
Different aspects of the invention are described in more details in separate sections below.
2. DNA Fragment of Interest
The DNA fragment of interest can in theory be any DNA sequence, including non coding sequences, or those coding for protein, RNA (such as non-translated RNA, which may be used in RNAi, antisense inhibition, small activating RNA, or sgRNA for CRISPR/Cas, merely to name a few), etc.
In certain embodiments, the DNA fragment of interest is about 100 bp, 200 bp, 500 bp, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 30 kb, 50 kb, 100 kb, 150 kb, 300 kb, 500 kb, 750 kb, 1000 kb, 1500 kb, 2000 kb, 5000 kb or more in length.
In certain embodiments, the DNA fragment of interest encodes a functional protein, or a functional domain or portion thereof. For example, the encoded functional protein can be a protein deficient in a disease associated with / caused by lack of the functional protein. The encoded functional protein may be a DMD minigene, or a full length DMD gene.
In certain embodiments, the DNA fragment of interest encodes an antisense
oligonucleotide designed to antagonize the transcription and/or translation of a target gene.
In certain embodiments, the DNA fragment of interest encodes an RNAi construct designed to antagonize the expression of a target gene. The RNAi construct may produce an siRNA, shRNA (short hairpin RNA), or miRNA (micro RNA).
In certain embodiments, the DNA fragment of interest does not encode an antisense oligonucleotide designed to antagonize the transcription and/or translation of a target gene.
In certain embodiments, the DNA fragment of interest does not encode an RNAi construct designed to antagonize the expression of a target gene. The RNAi construct may
- Si - produce an siRNA, shRNA (short hairpin RNA), or miRNA (micro RNA).
In certain embodiments, the DNA fragment of interest encodes a small activating RNA (saRNA) designed to antagonize the expression of a target gene.
Small activating RNAs (saRNAs) are small double- stranded RNAs (dsRNA) that target gene promoters to induce transcriptional gene activation in a process known as RNAa. Small dsRNAs, such as siRNAs and microRNAs (miRNAs),are known to be the trigger of an evolutionary conserved RNAi, which invariably leads to gene silencing via suppression of transcription, degradation of complementary mRNA, or blocking of protein translation.
dsRNAs can also act as saRNA by targeting selected sequences in gene promoters.
In certain embodiments, the saRNAs are 21 nucleotides in length with 2 nucleotides overhang at the 3’ end of each strand. Several saRNAs can be designed within a 1- to 2-kb promoter region by following a known set of rules and optionally testing in cultured cells.
In certain embodiments, the saRNAs are designed to target non-coding transcripts that overlap the promoter sequence of a protein coding gene.
Both chemically synthesized saRNAs and saRNAs expressed as shRNA have been used in in vitro and in vivo experiments, including in animal models and human clinical trials to treat cancer, liver disease, ischemia, and erectile dysfunction.
In certain embodiments, the DNA fragment of interest is a DNA vaccine. DNA vaccines typically encode a modified form of an infectious organism’s DNA. DNA vaccines are administered to a subject where they then express the selected protein of the infectious organism, initiating an immune response against that protein which is typically protective. DNA vaccines may also encode a tumor antigen or a neo-antigen in a cancer immunotherapy approach.
A DNA vaccine may comprise a nucleic acid sequence encoding an antigen for the treatment or prevention of a number of conditions including but not limited to cancer, allergies, toxicity and infection by a pathogen such as, but not limited to, fungi, viruses including Human Papilloma Viruses (HPV), HIV, HSV2/HSV1, Influenza virus (types A, B and C), Polio virus, RSV virus, Rhinoviruses, Rotaviruses, Hepatitis A virus, Norwalk Virus Group, Enteroviruses, Astroviruses, Measles virus, Parainfluenza virus, Mumps virus, Varicella-Zoster virus, Cytomegalovirus, Epstein- Barr virus, Adenoviruses, Rubella virus, Human T-cell Lymphoma type I virus (HTLV-I), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Hepatitis D virus, Pox virus, Marburg and Ebola; bacteria including Mycobacterium tuberculosis, Chlamydia, Neisseria gonorrhoeae, Shigella, Salmonella, Vibrio cholerae, Treponema pallidum, Pseudomonas, Bordetella pertussis, Brucella, Francisella tularensis, Helicobacter pylori, Leptospira interrogans, Legionella pneumophila, Yersinia pestis, Streptococcus (types A and B), Pneumococcus, Meningococcus, Haemophilus influenza (type b), Toxoplasma gondii, Campylobacteriosis, Moraxella catarrhalis, Donovanosis, and Actinomycosis; fungal pathogens including Candidiasis and Aspergillosis; parasitic pathogens including Taenia, Flukes, Roundworms, Amoebiasis, Giardiasis, Cryptosporidium, Schistosoma, Pneumocystis carinii, Trichomoniasis and Trichinosis. DNA vaccines may comprise a nucleic acid sequence encoding an antigen from a member of the adenoviridae (including for instance a human adenovirus), herpesviridae (including for instance HSV-I, HSV-2, EBV, CMV and VZV), papovaviridae (including for instance HPV), poxviridae (including for instance smallpox and vaccinia), parvoviridae (including for instance parvovirus B 19), reoviridae (including for instance a rotavirus), coronaviridae (including for instance SARS), flaviviridae (including for instance yellow fever, West Nile virus, dengue, hepatitis C and tick-borne encephalitis), picornaviridae (including polio, rhinovirus, and hepatitis A), togaviridae (including for instance rubella virus), filoviridae (including for instance Marburg and Ebola), paramyxoviridae (including for instance a parainfluenza virus, respiratory syncytial virus, mumps and measles), rhabdoviridae (including for instance rabies virus), bunyaviridae (including for instance Hantaan virus), orthomyxoviridae (including for instance influenza A, B and C viruses), retroviridae (including for instance HIV and HTLV) and hepadnaviridae (including for instance hepatitis B).
The antigen may be from a pathogen responsible for a veterinary disease and in particular may be from a viral pathogen, including, for instance, a Reovirus (such as African Horse sickness or Bluetongue virus) and Herpes viruses (including equine herpes). The antigen may be one from Foot and Mouth Disease virus, Tick borne encephalitis virus, dengue virus, SARS, West Nile virus and Hantaan virus. The antigen may be from an immunodeficiency virus, and may, for example, be from SIV or a feline immunodeficiency virus.
DNA vaccines may also comprise a nucleic acid sequence encoding tumor antigens or tumor associated antigens. Examples of tumor associated antigens include, but are not limited to, neo-antigens (such as those encoded by mutated genes from cancers or tumors, which neo-antigens elicit T-cell response to kill cancer / tumor cells displaying such neo antigens), cancer-testes antigens such as members of the MAGE family (MAGE 1, 2, 3 etc), NY-ESO-I and SSX-2, differentiation antigens such as tyrosinase, gplOO, PSA, Her-2 and CEA, mutated self antigens and viral tumor antigens such as E6 and/or E7 from oncogenic HPV types. Further examples of particular tumor antigens include MART-I , Melan-A, p97, beta-HCG, GalNAc, MAGE-I, MAGE-2, MAGE-4, MAGE- 12, MUC1, MUC2, MUC3, MUC4, MUC18, CEA, DDC, P1A, EpCam, melanoma antigen gp75, Hker 8, high molecular weight melanoma antigen, Kl 9, Tyrl, Tyr2, members of the pMel 17 gene family, c-Met, PSM (prostate mucin antigen), PSMA (prostate specific membrane antigen), prostate secretary protein, alpha- fetoprotein, CA 125, CA 19.9, TAG-72, BRCA-I and BRCA-2 antigen.
In certain embodiments, the DNA fragment of interest encodes a neo-antigen, which is an antigen encoded by a mutated gene in a cancer or tumor and may only exist in the cancer or tumor. Such neo-antigen may serve as a personalized vaccine for cancer treatment.
In certain embodiments, the DNA fragment of interest is a therapeutic DNA molecule, e.g., those used in gene therapy. It should be noted that the compositions and methods of the invention described herein is a platform technology that is generally applicable for gene therapy, including all monogenic human diseases that may be corrected by provision of one or more copies of functional DNA fragment of interest encoding the defective endogenous gene causing the diseases and as targets of the gene therapy.
For example, such DNA molecules can be used to express a functional gene where a subject has a genetic disorder caused by a dysfunctional version of that gene. Examples of such diseases include Duchenne muscular dystrophy (DMD), cystic fibrosis (CF), Gaucher’s Disease, and adenosine deaminase (ADA) deficiency.
Other diseases where gene therapy may be useful include inflammatory diseases, autoimmune, chronic and infectious diseases, including such disorders as AIDS, cancer, neurological diseases, cardiovascular disease, hypercholesterolemia, various blood disorders including various anaemias, thalassemia and haemophilia, and emphysema.
For the treatment of solid tumors, genes encoding toxic peptides ( i.e .,
chemotherapeutic agents such as ricin, diphtheria toxin and cobra venom factor), tumor suppressor genes such as p53, genes coding for mRNA sequences which are antisense to transforming oncogenes, antineoplastic peptides such as tumor necrosis factor (TNF) and other cytokines, or transdominant negative mutants of transforming oncogenes, may be expressed.
Other types of therapeutic DNA molecules are also contemplated, including, for example, DNA molecules which are transcribed into an active RNA form (e.g., a small interfering RNA such as siRNA, shRNA, miRNA, or a small activating RNA (saRNA)); or DNA encoding a CRISPR/Cas component (such as a Cas9 enzyme or an sgRNA).
In embodiments directed to production of DNA molecules having therapeutic utility, the DNA fragment of interest typically comprise an expression cassette comprising one or more promoter or enhancer elements and a gene or other coding sequence which encodes an mRNA or protein of interest. In particular embodiments directed to generation of DNA vaccine molecules or DNA molecules for gene therapy, the DNA template comprises an expression cassette consisting of a eukaryotic promoter operably linked to a sequence encoding a protein of interest, and optionally an enhancer and/or a eukaryotic transcription termination sequence.
3. LTR and ITR
Although the composition and methods of the invention described herein do not rely on any viral vectors for the delivery of DNA fragment of interest, the DNA constructs of the invention may contain certain elements commonly found in some viral vectors, including ITR (inverted terminal repeat) and LTR (long terminal repeat). Such viral elements can be used as end sequences of the invention that may serve as anti-decay elements for the DNA fragment of interest. Other suitable end sequences may include telomere sequences or functional derivative or equivalent thereof.
The end sequences of the invention enable the cdsDNA of the invention to exist as extra-chromosomal genetic elements that are stable for a long period of time once the cdsDNA is taken up by a target cell. The cdsDNA with the end sequences may be stable for 6 hrs, 12 hrs, 1 day, 3 days, 5 days, 10 days, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months,
3 months, 4 months, 5 months, 6 months, 9 months, 12 months, 2 years, 3 years, 5 years, 10 years or more, or may be stable for the entire life cycle of the target cell, such as a skeletal, cardiac, or smooth muscle cell.
In certain embodiments, the DNA fragment of interest is flanked by a pair of ITR ( e.g ., ITR of double- stranded DNA virus such as AAV, including AAV1-AAV10), or LTR or internal repeats (e.g., LTR of DNA viruses such as LTR of HSV). In certain embodiments, the ITR is the ITR of any one of AAV1-AAV 10. In certain embodiments, the LTR is that of HSV.
In certain embodiments, the pair of LTR are elements from gamma-retroviruses or lentiviruses. The LTRs may comprise the U3-R-U5 regions found on either side of a retro viral pro virus.
In certain embodiments, U3 is the unique 3’ region at the 3’ end of viral genomic RNA (but found at both the 5’ and 3’ ends of the provirus) that contains sequences necessary for activation of viral genomic RNA transcription.
In certain embodiments, R is the Repeat region found within both the 5’and 3’ LTRs of retro/lentiviral vectors. The Tat protein binds to this region.
In certain embodiments, U5 is the unique 5’ region at the 5’ end of the viral genomic RNA (but found at both the 5’ and 3’ ends of the provirus).
In certain embodiments, one or both ends of the DNA fragment of interest has a 5’ LTR region, which may act as an RNA pol II promoter. Transcript can begin at the beginning of its R region, is capped, and proceeds through U5 and the rest of the DNA fragment of interest. In certain embodiments, a hybrid 5’ LTR may be used with a constitutive promoter such as CMV or RSV promoter.
In certain embodiments, the R region of the LTR may comprise a trans-activating response element TAR, and acts as a binding site for Tat (a trans-activator that binds TAR to activate transcription from the LTR promoter).
In certain embodiments, one or both ends of the DNA fragment of interest has a 3’ LTR region, which may terminate transcription started by 5’ LTR at the other end of the DNA fragment of interest by the addition of a poly A tract just after its R sequence.
In certain embodiments, transcription of the DNA fragment of interest is initiated by the 5’ LTR.
In certain embodiments, transcription of the DNA fragment of interest is initiated by the 3’ LTR.
In certain embodiments, alternatively or in addition, the DNA fragment of interest itself may carry its own promoter, enhancer, other transcriptional / translational regulatory elements, polyadenylation signal and/or translation termination site.
In certain embodiments, the translational regulatory elements comprise WPRE, or Woodchuck hepatitis virus post-transcriptional regulatory element, which stimulates the expression of transgenes via increased nuclear export.
In certain embodiments, the pair of ITR are elements from adeno associated virus (AAV). The AAV ITR is about 145 bases each. The ITRs forms a T-shaped hairpin that normally serves as the origin of viral DNA replication. It contains a D region required for packaging.
4. Protelomerase and Protelomerase Recognition Sequences
The method of the invention comprises a step to produce cdsDNA by contacting amplified DNA construct with a protelomerase that releases the insert, under conditions promoting production of cdsDNA.
A protelomerase used in the invention is any polypeptide capable of cleaving and rejoining a template comprising a protelomerase target sequence in order to produce a covalently cdsDNA molecule. Enzymes having protelomerase activity have also been described as telomere resolvases (for example in Borrelia burgdorferi). The requirements for protelomerase target sequence are described below. The ability of a given polypeptide to catalyze the production of cdsDNA from a template comprising a protelomerase target sequence can be determined using any suitable assay described in the art.
Protelomerase enzymes have been described in bacteriophages. In some lysogenic bacteria, bacteriophages exist as extrachromosomal DNA comprising linear double strands with covalently closed ends. The replication of this DNA and the maintenance of the covalently closed ends (or telomeric ends) are dependent on the activity of the protelomerase. An example of this catalytic activity is provided by the enzyme, TelN, from the
bacteriophage N15 that infects Escherichia coli. TelN recognizes a specific nucleotide sequence in the circular double stranded DNA. This sequence is a slightly imperfect inverted palindromic structure termed telRL comprising two halves, telR and telL, flanking a 22 base pair inverted perfect repeat (telO). Two telRL sites are formed in the circular double stranded DNA by the initial activity of specific DNA polymerase acting on the linear prophage DNA. TelN converts this circular DNA into two identical linear prophage DNA molecules completing the replication cycle. telR and telL comprise the closed ends of the linear prophage DNA enabling the DNA to be replicated further in the same way.
Examples of suitable protelomerases include those from bacteriophages such as phiHAP-l from Halomonas aquamarina (SEQ ID NO: 7), PY54 from Yersinia enterolytica (SEQ ID NO: 9), phiK02 from Klebsiella oxytoca (SEQ ID NO: 11) and VP882 from Vibrio sp. (SEQ ID NO: 13), and N15 from Escherichia coli (SEQ ID NO: 15), or variants of any thereof. In certain embodiments, the bacteriophage N15 protelomerase (SEQ ID NO: 15) or a variant thereof is used.
Variants of SEQ ID NOs: 7, 9, 11, 13 and 15 include homologues or mutants thereof. Mutants include truncations, substitutions or deletions with respect to the native sequence. A variant must produce closed linear DNA from a template comprising a protelomerase target site as described above.
Any homologues mentioned herein are typically a functional homologue and are typically at least 40% homologous to the relevant region of the native protein. Homology can be measured using known methods. For example the UWGCG Package provides the BESTFIT program which can be used to calculate homology (for example used on its default settings) (Devereux et al (1984) Nucleic Acids Research 12, 387-395). The PILEUP and BLAST algorithms can be used to calculate homology or line up sequences (typically on their default settings), for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S, F et al (1990) J Mol Biol 215:403-10. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.
The BLAST algorithm performs a statistical analysis of the similarity between two sequences; see e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5787. One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a sequence is considered similar to another sequence if the smallest sum probability in comparison of the first sequence to the second sequence is less than about 1, preferably less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
A“protelomerase target sequence” or“protelomerase recognition sequence” (used interchangeably herein) is a polynucleotide (e.g., a double- stranded DNA) sequence recognized by a protelomerase for cleavage and relegation of double- stranded DNA by protelomerase to form covalently closed end dsDNA. Digestion of the protelomerase target / recognition sequence by the protelomerase creates two“half protelomerase target / recognition sequences.”
In certain embodiments, a protelomerase target sequence comprises a perfect palindromic sequence, i.e., a double- stranded DNA sequence having two-fold rotational symmetry, also described herein as a perfect inverted repeat.
Protelomerase target sequences from various mesophilic bacteriophages and a bacterial plasmid all share the common feature of comprising a perfect inverted repeat. The length of the perfect inverted repeat differs depending on the specific organism.
In certain embodiments, the perfect inverted repeat is that from Borrelia burgdorferi, and is 14 bps in length.
In certain embodiments, the perfect inverted repeat is from a mesophilic
bacteriophage, and is 22 bps or greater in length.
In certain embodiments, the protelomerase recognition sequence is from E. coli N15, in which the central perfect inverted palindrome is flanked by inverted repeat sequences, i.e., forming part of a larger imperfect inverted palindrome (see FIGS. 2 and 3 in US9109250B2, incorporated herein by reference; the underlined bases indicate where the symmetry of the inverted repeats is interrupted).
In certain embodiments, the protelomerase target sequence comprises a double stranded palindromic (perfect inverted repeat) sequence of at least 14 base pairs in length. In certain embodiments, the perfect inverted repeat sequence includes the sequences of SEQ ID NOs: 11 to 16 and variants thereof.
SEQ ID NO: 11 (NCATNNTANNCGNNTANNATGN) is a 22-base consensus sequence for a mesophilic bacteriophage perfect inverted repeat. Base pairs of the perfect inverted repeat are conserved at certain positions between different bacteriophages, while flexibility in sequence is possible at other positions. Thus, SEQ ID NO: 11 is a minimum consensus sequence for a perfect inverted repeat sequence for use with a bacteriophage protelomerase in the process of the present invention.
Within the consensus defined by SEQ ID NO: 11, SEQ ID NO: 12
(CCATTATACGCGCGTATAATGG) is a perfect inverted repeat sequence for use with E. coli phage N15 (SEQ ID NO: 10), and Klebsiella phage Phi K02 (SEQ ID NO: 6) protelomerase s.
Also within the consensus defined by SEQ ID NO: 11, SEQ ID NOs: 13 to 15:
GCATACTACGCGCGTAGTATGC ( SEQ ID NO : 13 ) ,
CCATACTATACGTATAGTATGG ( SEQ ID NO : 14 ) ,
GCATACTATACGTATAGTATGC ( SEQ ID NO : 15 ) ,
are perfect inverted repeat sequences for use respectively with protelomerases from Yersinia phage PY54 (SEQ ID NO: 4), Halomonas phage phiHAP-l (SEQ ID NO: 2), and Vibrio phage VP882 (SEQ ID NO: 8).
SEQ ID NO: 16 (ATTATATATATAAT) is a perfect inverted repeat sequence for use with a Borrelia burgdorferi protelomerase. This perfect inverted repeat sequence is from a linear covalently closed plasmid, 1rB31.16 comprised in Borrelia burgdorferi. This l4-bp sequence is shorter than the 22-bp consensus perfect inverted repeat for bacteriophages (SEQ ID NO: 11), indicating that bacterial protelomerases may differ in specific target sequence requirements to bacteriophage protelomerases. However, all protelomerase target sequences share the common structural motif of a perfect inverted repeat.
The perfect inverted repeat sequence may be greater than 22 bp in length depending on the requirements of the specific protelomerase used in the process of the invention. Thus, in some embodiments, the perfect inverted repeat may be at least 30, at least 40, at least 60, at least 80 or at least 100 base pairs in length. Examples of such perfect inverted repeat sequences include SEQ ID NOs: 17 to 19 and variants thereof.
GGCATACTATACGTATAGTATGCC (SEQ ID NO: 17)
ACCTATTTCAGCATACTACGCGCGTAGTATGCTGAAATAGGT (SEQ ID NO:
18)
CCTATATTGGGCCACCTATGTATGCACAGTTCGCCCATACTATACGTATAGTATGGG CGAACTGTGCATACATAGGTGGCCCAATATAGG (SEQ ID NO: 19)
SEQ ID NOs: 17 to 19 and variants thereof are for use respectively with
protelomerases from Vibrio phage VP882 (SEQ ID NO: 8), Yersinia phage PY54 (SEQ ID NO: 4) and Halomonas phage phi HAP-l (SEQ ID NO: 2).
The perfect inverted repeat may be flanked by additional inverted repeat sequences. The flanking inverted repeats may be perfect or imperfect repeats, i.e., may be completely symmetrical or partially symmetrical. The flanking inverted repeats may be contiguous with or non-contiguous with the central palindrome.
In certain embodiments, the protelomerase target sequence may comprise an imperfect inverted repeat sequence which comprises a perfect inverted repeat sequence of at least 14 base pairs in length. An example is SEQ ID NO: 24.
In certain embodiments, the imperfect inverted repeat sequence may comprise a perfect inverted repeat sequence of at least 22 base pairs in length. An example is SEQ ID NO: 20.
In certain embodiments, the protelomerase target sequence comprises the sequences of any one of SEQ ID NOs: 20-24, or variants thereof.
TATCAGCACACAATTGCCCATTATACGCGCGTATAATGGACTATTGTGTGCTGATA
(SEQ ID NO: 20)
ATGCGCGCATCCATTATACGCGCGTATAATGGCGATAATACA (SEQ ID NO:
21) TAGTCACCTATTTCAGCATACTACGCGCGTAGTATGCTGAAATAGGTTACTG (SEQ ID NO: 22)
GGGATCCCGTTCCATACATACATGTATCCATGTGGCATACTATACGTATAGTATGCC GATGTTACATATGGTATCATTCGGGATCCCGTT (SEQ ID NO: 23)
TACTAAATAAATATTATATATATAATTTTTTATTAGTA (SEQ ID NO: 24)
The sequences of SEQ ID NOs: 20 to 24 comprise perfect inverted repeat sequences as described above, and additionally comprise flanking sequences from the relevant organisms.
In certain embodiments, a protelomerase target sequence comprising the sequence of SEQ ID NO: 20 or a variant thereof is used in combination with E. coli N15 TelN
protelomerase of SEQ ID NO: 10 and variants thereof.
In certain embodiments, a protelomerase target sequence comprising the sequence of SEQ ID NO: 21 or a variant thereof is used in combination with Klebsiella phage Phi K02 protelomerase of SEQ ID NO: 6 and variants thereof.
In certain embodiments, a protelomerase target sequence comprising the sequence of SEQ ID NO: 22 or a variant thereof is used in combination with Yersinia phage PY54 protelomerase of SEQ ID NO: 4 and variants thereof.
In certain embodiments, a protelomerase target sequence comprising the sequence of SEQ ID NO: 23 or a variant thereof is used in combination with Vibrio phage VP882 protelomerase of SEQ ID NO: 8 and variants thereof.
In certain embodiments, a protelomerase target sequence comprising the sequence of SEQ ID NO: 24 or a variant thereof is used in combination with a Borrelia burgdorferi protelomerase.
Variants of any of the palindrome or protelomerase target sequences described above include homologues or mutants thereof. Mutants include truncations, substitutions or deletions with respect to the native sequence. A variant sequence is any sequence whose presence in the DNA template allows for its conversion into a closed linear DNA by the enzymatic activity of protelomerase. This can readily be determined by use of an appropriate assay for the formation of closed linear DNA. Any suitable assay described in the art may be used. An example of a suitable assay is described in Deneke et al, PNAS 97:7721-7726, 2000 (incorporated herein by reference). In certain embodiments, the variant may allow for protelomerase binding and activity that is comparable to that observed with the native sequence.
Examples of variants of palindrome sequences described herein include truncated palindrome sequences that preserve the perfect repeat structure, and remain capable of allowing for formation of closed linear DNA.
In certain embodiments, variant protelomerase target sequences are modified such that they no longer preserve a perfect palindrome, provided that they are able to act as substrates for protelomerase activity.
It should be understood that the skilled person would readily be able to identify suitable protelomerase target sequences for use in the invention on the basis of the structural principles outlined above.
In certain embodiments, candidate protelomerase target sequences can be screened for their ability to promote formation of closed end DNA using the assays described above.
Certain exemplary sequences of the protelomerases useful for the compositions and methods of the invention are listed below.
Halomonas phage phiHAP-l protelomerase nucleic acid sequence:
ATGAGCGGTG AGTCACGTAG AAAGGTCGAT TTAGCGGAAT TGATAGAGTG GTTGCTCAGC 60 GAGATCAAAG AGATCGACGC CGATGATGAG ATGCCACGTA AAGAGAAAAC CAAGCGCATG
120 GCGCGGCTGG CACGTAGCTT CAAAACGCGC CTGCATGATG ACAAGCGCCG
CAAGGATTCT 180 GAGCGGATCG CGGTCACGAC CTTTCGCCGC TACATGACAG
AAGCGCGCAA GGCGGTGACT 240 GCGCAGAACT GGCGCCATCA CAGCTTCGAC
CAGCAGATCG AGCGGCTGGC CAGCCGCTAC 300 CCGGCTTATG CCAGCAAGCT
GGAAGCGCTC GGCAAGCTGA CCGATATCAG CGCCATTCGT 360 ATGGCCCACC
GCGAGCTGCT CGACCAGATC CGCAACGATG ACGACGCTTA TGAGGACATC 420
CGGGCGATGA AGCTGGACCA TGAAATCATG CGCCACCTGA CGTTGAGCTC TGCACAGAAA
480 AGCACGCTGG CTGAAGAGGC CAGCGAGACG CTGGAAGAGC GCGCGGTGAA
CACGGTCGAG 540 ATCAACTACC ACTGGTTGAT GGAGACGGTT TACGAGCTGC
TGAGTAACCG GGAGAGAATG 600 GTCGATGGGG AGTATCGCGG CTTTTTCAGT
TACCTAGCGC TTGGGCTGGC GCTGGCCACC 660 GGGCGTCGCT CGATCGAGGT
GCTGAAGACC GGACGGATCA CGAAGGTGGG CGAGTATGAG 720 CTGGAGTTCA
GCGGCCAGGC GAAAAAGCGC GGCGGCGTCG ACTATAGCGA GGCTTACCAC 780
ATTTATACCC TGGTGAAAGC TGACCTGGTG ATCGAAGCGT GGGATGAGCT TCGCTCGCTG
840 CCGGAAGCTG CTGAGCTGCA GGGCATGGAC AACAGCGATG TGAACCGCCG
CACGGCGAAG 900 ACGCTCAACA CGCTCACTAA GCGGATCTTT AACAACGATG
AGCGCGTTTT CAAGGACAGC 960 CGGGCGATCT GGGCGCGGCT GGTGTTTGAG CTGCACTTCT CGCGCGACAA GCGCTGGAAG 1020 AAAGTCACCG AGGACGTGTT CTGGCGTGAG ATGCTGGGGC ATGAGGACAT GGATACACAG 1080 CGCAGCTACC
GCGCCTTTAA AATCGACTAC GACGAGCCGG ATCAAGCCGA CCAGGAAGAT 1140
TACGAACACG CTAGCCGCCT CGCCGCGCTG CAGGCGCTGG ACGGCCATGA GCAGCTTGAG
1200 AGCAGCGACG CCCAGGCGCG TGTGCATGCC TGGGTGAAAG CGCAGATCGA
GCAGGAGCCT 1260 GACGCGAAAA TTACGCAGTC TCTGATCAGC CGGGAGCTGG
GCGTTTATCG CCCTGCCATA 1320 AAAGCGTACC TGGAGCTGGC GCGAGAGGCG
CTCGACGCGC CGAACGTCGA TCTGGACAAG 1380 GTCGCGGCGG CAGTGCCGAA
GGAAGTAGCC GAGGCGAAGC CCCGGCTGAA CGCCCACCCA 1440 CAAGGGGATG
GCAGGTGGGT CGGGGTGGCT TCAATCAACG GGGTGGAAGT TGCACGGGTG 1500
GGCAACCAGG CAGGCCGGAT CGAAGCGATG AAAGCGGCCT ATAAAGCGGC GGGTGGGCGC
1560 TGA 1563 (SEQ ID NO: 1)
Halomonas phage phiHAP-l protelomerase amino acid sequence:
MSGESRRKVD LAELIEWLLS EIKEIDADDE MPRKEKTKRM ARLARSFKTR LHDDKRRKDS 60 ERIAVTTFRR YMTEARKAVT AQNWRHHSFD QQIERLASRY PAYASKLEAL GKLTDISAIR
120 MAHRELLDQI RNDDDAYEDI RAMKLDHEIM RHLTLSSAQK STLAEEASET
LEERAVNTVE 180 INYHWLMETV YELLSNRERM VDGEYRGFFS YLALGLALAT
GRRSIEVLKT GRITKVGEYE 240 LEFSGQAKKR GGVDYSEAYH IYTLVKADLV
IEAWDELRSL PEAAELQGMD NSDVNRRTAK 300 TLNTLTKRIF NNDERVFKDS
RAIWARLVFE LHFSRDKRWK KVTEDVFWRE MLGHEDMDTQ 360 RSYRAFKIDY
DEPDQADQED YEHASRLAAL QALDGHEQLE SSDAQARVHA WVKAQIEQEP 420
DAKITQSLIS RELGVYRPAI KAYLELAREA LDAPNVDLDK VAAAVPKEVA EAKPRLNAHP
480 QGDGRWVGVA SINGVEVARV GNQAGRIEAM KAAYKAAGGR 520 (SEQ ID NO: 2)
Yersinia phage PY54 protelomerase nucleic acid sequence:
ATGAAAATCC ATTTTCGCGA TTTAGTTAGT GGTTTAGTTA AAGAGATCGA TGAAATAGAA 60 AAATCAGACC GGGCGCAGGG TGACAAAACT CGGCGTTATC AGGGCGCGGC CAGAAAGTTC
120 AAAAATGCCG TGTTTATGGA TAAACGGAAA TATCGCGGTA ACGGTATGAA
GAATAGAATA 180 TCGTTAACAA CATTTAATAA ATATTTAAGT CGAGCACGTT
CTCGGTTTGA AGAAAGGCTT 240 CACCATAGTT TTCCTCAATC TATAGCAACT
ATCTCAAATA AATATCCTGC ATTCAGCGAA 300 ATAATAAAAG ATCTGGATAA
TAGACCCGCT CATGAAGTTA GAATAAAACT TAAAGAATTA 360 ATAACTCATC
TTGAATCCGG TGTTAATTTA TTAGAAAAAA TAGGTAGCTT AGGGAAAATA 420
AAACCATCTA CAGCTAAAAA AATAGTTAGC TTAAAAAAAA TGTACCCATC ATGGGCTAAT
480 GATCTAGATA CTTTAATTAG TACTGAAGAT GCTACAGAAT TACAACAAAA
GTTAGAGCAA 540 GGGACCGACC TACTTAACGC ATTACATTCT CTAAAAGTAA
ACCATGAAGT TATGTATGCA 600 TTAACGATGC AGCCTTCTGA CAGAGCTGCA TTAAAAGCTA GGCATGACGC TGCCCTTCAC 660 TTTAAAAAGC GTAACATCGT ACCTATCGAT TATCCCGGCT ATATGCAACG AATGACGGAC 720 ATACTACATC
TTCCAGATAT AGCTTTTGAA GATTCGATGG CATCACTTGC CCCTTTAGCA 780
TTTGCTCTAG CAGCTGCTAG CGGTCGCAGA CAAATTGAAA TACTAATTAC TGGTGAGTTT
840 GACGCCAAAA ATAAAAGCAT CATTAAATTT TCTGGACAAG CAAAAAAAAG
AATGGCCGTT 900 TCAGGTGGAC ATTATGAAAT ATACAGTCTA ATTGACTCAG
AGCTATTCAT TCAACGGTTA 960 GAGTTTTTAC GTTCTCATAG CTCAATACTT
CGATTACAAA ATTTGGAAAT AGCACATGAT 1020 GAACATCGTA CTGAACTATC
TGTTATTAAC GGTTTTGTAG CCAAACCTTT AAATGATGCA 1080 GCAAAACAGT
TCTTTGTCGA TGACAGAAGA GTATTTAAAG ATACCCGTGC AATTTACGCT 1140
CGCATAGCAT ATGAAAAATG GTTTAGAACA GATCCTCGCT GGGCGAAGTG CGACGAAGAT
1200 GTTTTCTTCT CTGAATTATT AGGCCATGAC GACCCAGATA CTCAGCTGGC
ATATAAACAA 1260 TTCAAGCTGG TAAATTTCAA TCCAAAATGG ACACCTAATA
TATCAGATGA AAACCCTCGG 1320 TTAGCTGCAC TTCAAGAGCT TGACAATGAT
ATGCCCGGCC TAGCACGTGG CGATGCGGCA 1380 GTTCGCATAC ATGAGTGGGT
TAAAGAGCAA CTGGCGCAGA ACCCTGCGGC AAAAATAACT 1440 GCATACCAAA
TCAAGAAAAA TTTAAATTGT CGAAATGACT TGGCCAGCCG ATACATGGCA 1500
TGGTGTGCTG ACGCGCTAGG GGTTGTTATT GGTGATGATG GACAGGCAAG GCCAGAAGAA
1560 CTCCCACCAT CGCTCGTGCT TGATATTAAC GCTGATGACA CTGACGCTGA
AGAAGATGAA 1620 ATAGAGGAAG ACTTTACTGA TGAGGAAATA GACGACACCG
AATTCGACGT ATCAGATAAC 1680 GCCAGTGATG AAGATAAGCC CGAAGATAAA
CCTCGCTTTG CAGCACCAAT TCGTAGAAGT 1740 GAGGACTCTT GGCTGATTAA
ATTTGAATTT GCTGGCAAGC AATATAGCTG GGAGGGTAAT 1800 GCCGAAAGTG
TTATCGATGC GATGAAACAA GCATGGACTG AAAATATGGA GTAA 1854 (SEQ ID NO:
3)
Yersinia phage PY54 protelomerase amino acid sequence:
MKIHFRDLVS GLVKEIDEIE KSDRAQGDKT RRYQGAARKF KNAVFMDKRK YRGNGMKNRI 60 SLTTFNKYLS RARSRFEERL HHSFPQSIAT ISNKYPAFSE IIKDLDNRPA HEVRIKLKEL
120 ITHLESGVNL LEKIGSLGKI KPSTAKKIVS LKKMYPSWAN DLDTLISTED
ATELQQKLEQ 180 GTDLLNALHS LKVNHEVMYA LTMQPSDRAA LKARHDAALH
FKKRNIVPID YPGYMQRMTD 240 ILHLPDIAFE DSMASLAPLA FALAAASGRR
QIEILITGEF DAKNKSIIKF SGQAKKRMAV 300 SGGHYEIYSL IDSELFIQRL
EFLRSHSSIL RLQNLEIAHD EHRTELSVIN GFVAKPLNDA 360 AKQFFVDDRR
VFKDTRAIYA RIAYEKWFRT DPRWAKCDED VFFSELLGHD DPDTQLAYKQ 420
FKLVNFNPKW TPNISDENPR LAALQELDND MPGLARGDAA VRIHEWVKEQ LAQNPAAKIT
480 AYQIKKNLNC RNDLASRYMA WCADALGVVI GDDGQARPEE LPPSLVLDIN
ADDTDAEEDE 540 IEEDFTDEEI DDTEFDVSDN ASDEDKPEDK PRFAAPIRRS EDSWLIKFEF AGKQYSWEGN 600 AESVIDAMKQ AWTENME 617 (SEQ ID NO: 4)
Klebsiella phage phiK02 protelomerase nucleic acid sequence:
ATGCGTAAGG TGAAAATTGG TGAGCTAATC AATTCGCTTG TGAGCGAGGT CGAGGCAATC 60 GATGCCTCTG ATCGTCCGCA AGGCGATAAA ACGAAGAAAA TTAAAGCCGC AGCATTAAAA
120 TATAAGAATG CATTATTTAA TGACAAAAGA AAGTTTCGCG GTAAAGGTTT
AGAAAAAAGA 180 ATTTCTGCCA ACACGTTCAA CTCGTATATG AGTCGGGCAA
GGAAAAGATT TGATGATAGA 240 TTGCATCATA ACTTTGAAAA GAATGTAATT
AAACTATCAG AAAAATATCC TTTATATAGT 300 GAAGAATTAT CTTCGTGGCT
TTCTATGCCT GCGGCATCAA TTAGACAGCA TATGTCAAGA 360 TTGCAAGCCA
AGCTAAAAGA GATAATGCCA TTGGCAGAAG ACTTATCCAA TATAAAGATT 420
GGTACAAAAA ATAGCGAAGC AAAAATAAAT AAACTCGCTA ATAAATATCC TGAATGGCAA
480 TTCGCTATTA GTGATTTAAA TAGCGAAGAT TGGAAGGATA AAAGAGATTA
TCTTTATAAA 540 CTATTCCAAC AAGGTTCTTC GCTCCTGGAA GACTTGAATA
ACCTGAAAGT AAACCATGAG 600 GTTCTCTATC ATCTGCAGCT TAGTTCTGCC
GAGCGAACCT CTATCCAGCA GCGCTGGGCC 660 AACGTCCTCA GCGAGAAAAA
GCGCAACGTT GTCGTGATTG ACTATCCGCG CTATATGCAG 720 GCCATCTACG
ATATAATCAA CAAGCCTATA GTTTCGTTCG ATTTGACTAC TCGTCGTGGT 780
ATGGCCCCGC TGGCGTTCGC CCTTGCCGCG CTATCTGGTC GCCGAATGAT TGAAATCATG
840 CTCCAGGGTG AATTTTCCGT CGCAGGTAAA TATACAGTAA CATTCCTGGG
GCAAGCTAAA 900 AAACGCTCGG AAGATAAAGG TATATCAAGG AAAATATATA
CCTTATGCGA CGCTACTTTA 960 TTTGTTAGTT TGGTAAATGA ACTTCGCTCA
TGCCCCGCTG CTGCGGATTT TGATGAAGTA 1020 ATAAAAGGAT ATGGCGAAAA
TGACACTCGC TCAGAAAATG GGCGTATTAA TGCAATTCTC 1080 GCTACAGCTT
TTAATCCGTG GGTAAAAACT TTCTTAGGCG ATGACCGCCG CGTTTATAAA 1140
GATAGCCGCG CTATTTACGC CCGTATTGCC TATGAAATGT TCTTCCGCGT TGACCCTCGG
1200 TGGAAGAATG TTGATGAGGA TGTATTCTTC ATGGAGATTC TCGGCCATGA
CGATGAAAAC 1260 ACCCAACTGC ACTATAAGCA GTTTAAATTG GCTAACTTCT
CCAGAACATG GCGACCAAAT 1320 GTCGGCGAGG AGAATGCCCG CCTAGCGGCG
CTGCAAAAGC TGGATAGCAT GATGCCAGAT 1380 TTTGCCAGGG GCGACGCCGG
GGTTCGTATT CATGAGACCG TGAAGCAGCT GGTGGAGCAG 1440 GACCCATCGA
TAAAAATCAC AAACAGCACC CTGCGACCGT TTAACTTCAG TACCAGGCTG 1500
ATTCCTCGCT ACCTGGAGTT TGCCGCCGAT GCATTGGGCC AGTTCGTCGG TGAAAATGGG
1560 CAATGGCAAC TGAAGGATGA GGCGCCTGCA ATAGTCCTGC CTGATGAGGA
AATTCTTGAG 1620 CCTATGGACG ACGTCGATCT CGATGACGAA AACCATGATG
ATGAAACGCT GGATGACGAT 1680 GAGATCGAAG TGGACGAAAG CGAAGGAGAG
GAACTGGAGG AAGCGGGCGA CGCTGAAGAG 1740 GCCGAGGTGG CTGAACAGGA
AGAGAAGCAC CCTGGCAAGC CAAACTTTAA AGCGCCGAGG 1800 GATAATGGCG ATGGTACCTA CATGGTGGAA TTTGAATTCG GTGGCCGTCA TTACGCCTGG 1860
TCCGGTGCCG CCGGTAATCG GGTAGAGGCA ATGCAATCTG CCTGGAGTGC CTACTTCAAG
1920 TGA 1923 (SEQ ID NO: 5)
Klebsiella phage phiK02 protelomerase amino acid sequence:
MRKVKIGELI NSLVSEVEAI DASDRPQGDK TKKIKAAALK YKNALFNDKR KFRGKGLEKR 60 ISANTFNSYM SRARKRFDDR LHHNFEKNVI KLSEKYPLYS EELSSWLSMP AASIRQHMSR
120 LQAKLKEIMP LAEDLSNIKI GTKNSEAKIN KLANKYPEWQ FAISDLNSED
WKDKRDYLYK 180 LFQQGSSLLE DLNNLKVNHE VLYHLQLSSA ERTSIQQRWA
NVLSEKKRNV VVIDYPRYMQ 240 AIYDIINKPI VSFDLTTRRG MAPLAFALAA
LSGRRMIEIM LQGEFSVAGK YTVTFLGQAK 300 KRSEDKGISR KIYTLCDATL
FVSLVNELRS CPAAADFDEV IKGYGENDTR SENGRINAIL 360 ATAFNPWVKT
FLGDDRRVYK DSRAIYARIA YEMFFRVDPR WKNVDEDVFF MEILGHDDEN 420
TQLHYKQFKL ANFSRTWRPN VGEENARLAA LQKLDSMMPD FARGDAGVRI HETVKQLVEQ
480 DPSIKITNST LRPFNFSTRL IPRYLEFAAD ALGQFVGENG QWQLKDEAPA
IVLPDEEILE 540 PMDDVDLDDE NHDDETLDDD EIEVDESEGE ELEEAGDAEE
AEVAEQEEKH PGKPNFKAPR 600 DNGDGTYMVE FEFGGRHYAW SGAAGNRVEA
MQSAWSAYFK 640 (SEQ ID NO: 6)
Vibrio phage VP882 protelomerase nucleic acid sequence:
ATGAGCGGCG AAAGTAGACA AAAGGTAAAC CTCGAGGAGT TAATAAATGA GCTCGTCGAG 60 GAGGTGAAAA CCATCGATGA CAATGAGGCG ATTACTCGGT CTGAAAAAAC CAAGTTGATC
120 ACCAGGGCGG CGACTAAATT CAAGACCAAG CTGCACGACG ATAAGCGCCG
GAAGGATGCG 180 ACCAGAATCG CTCTGAGCAC CTATCGTAAG TACATGACAA
TGGCCAGGGC AGCAGTTACT 240 GAGCAGAACT GGAAACACCA CAGTCTCGAG
CAGCAGATAG AGCGGCTGGC CAAAAAGCAC 300 CCGCAATACG CTGAGCAGCT
GGTGGCCATC GGGGCCATGG ATAACATCAC CGAGTTGCGC 360 CTGGCGCATC
GCGACCTCCT GAAGAGCATC AAGGACAACG ATGAAGCCTT CGAGGATATC 420
CGCAGCATGA AGTTAGACCA CGAGGTAATG CGCCATCTGA CGCTACCCAG TGCGCAAAAG
480 GCGAGACTGG CAGAGGAAGC CGCCGAGGCG TTGACCGAGA AGAAAACCGC
CACGGTCGAC 540 ATCAACTATC ACGAGCTGAT GGCCGGCGTG GTGGAGCTGT
TGACCAAGAA GACCAAGACG 600 GTCGGCAGCG ACAGCACCTA CAGCTTCAGC
CGGCTGGCGC TTGGTATTGG CCTGGCTACC 660 GGTCGTCGTT CTATCGAGAT
ACTGAAGCAG GGCGAGTTCA AAAAGGTGGA TGAGCAGCGG 720 CTCGAGTTCT
CTGGCCAAGC GAAAAAGCGC GGCGGTGCCG ACTATTCAGA GACCTATACC 780
ATTTACACCC TGGTCGACTC CGACCTGGTA CTGATGGCGC TGAAGAACCT GCGAGAGTTG
840 CCAGAAGTTC GCGCACTGGA TGAGTACGAC CAACTGGGCG AGATTAAGCG
GAACGACGCC 900 ATCAATAAAC GCTGTGCAAA AACGCTCAAC CAAACCGCCA AGCAGTTCTT TGGCAGCGAC 960 GAGCGCGTGT TCAAAGATAG TCGTGCCATC TGGGCGCGTC TGGCTTATGA GTTGTTTTTT 1020 CAACGTGATC CGCGCTGGAA
AAAGAAAGAC GAGGACGTTT TCTGGCAGGA GATGCTGGGC 1080 CACGAGGACA
TCGAGACTCA GAAAGCCTAT AAGCAATTCA AGGTCGACTA CAGCGAACCT 1140
GAGCAGCCGG TGCACAAGCC TGGCAAATTT AAGAGCAGAG CTGAAGCCCT CGCGGCGCTC
1200 GACTCAAATG AGGACATTAC CACCCGCTCA TCCATGGCCA AGATCCACGA
CTGGGTGAAA 1260 GAGCGTATTG CGGAAGACCC CGAGGCGAAC ATCACACAGT
CACTCATCAC CCGGGAACTG 1320 GGCTCAGGCC GTAAGGTGAT CAAGGACTAC
CTCGACCTGG CTGACGATGC CCTTGCTGTG 1380 GTGAATACTC CTGTCGATGA
CGCAGTCGTC GAGGTTCCAG CTGATGTGCC GGCAGCAGAA 1440 AAACAGCCGA
AGAAAGCGCA GAAGCCCAGA CTCGTGGCTC ACCAGGTTGA TGATGAGCAC 1500
TGGGAAGCCT GGGCGCTGGT GGAAGGCGAG GAGGTGGCCA GGGTGAAAAT CAAGGGCACC
1560 CGCGTTGAGG CAATGACAGC CGCATGGGAG GCCAGCCAAA AGGCACTCGA TGACTAA 1617 (SEQ ID NO: 7)
Vibrio phage VP882 protelomerase amino acid sequence:
MSGESRQKVN LEELINELVE EVKTIDDNEA ITRSEKTKLI TRAATKFKTK LHDDKRRKDA 60 TRIALSTYRK YMTMARAAVT EQNWKHHSLE QQIERLAKKH PQYAEQLVAI GAMDNITELR
120 LAHRDLLKSI KDNDEAFEDI RSMKLDHEVM RHLTLPSAQK ARLAEEAAEA
LTEKKTATVD 180 INYHELMAGV VELLTKKTKT VGSDSTYSFS RLALGIGLAT
GRRSIEILKQ GEFKKVDEQR 240 LEFSGQAKKR GGADYSETYT IYTLVDSDLV
LMALKNLREL PEVRALDEYD QLGEIKRNDA 300 INKRCAKTLN QTAKQFFGSD
ERVFKDSRAI WARLAYELFF QRDPRWKKKD EDVFWQEMLG 360 HEDIETQKAY
KQFKVDYSEP EQPVHKPGKF KSRAEALAAL DSNEDITTRS SMAKIHDWVK 420
ERIAEDPEAN ITQSLITREL GSGRKVIKDY LDLADDALAV VNTPVDDAVV EVPADVPAAE
480 KQPKKAQKPR LVAHQVDDEH WEAWALVEGE EVARVKIKGT RVEAMTAAWE ASQKALDD 538 (SEQ ID NO: 8)
Escherichia coli bacteriophage N15 telomerase (telN) and secondary immunity repressor (cA) nucleic acid sequence:
CATATGCACT ATATCATATC TCAATTACGG AACATATCAG CACACAATTG CCCATTATAC 60 GCGCGTATAA TGGACTATTG TGTGCTGATA AGGAGAACAT AAGCGCAGAA CAATATGTAT
120 CTATTCCGGT GTTGTGTTCC TTTGTTATTC TGCTATTATG TTCTCTTATA
GTGTGACGAA 180 AGCAGCATAA TTAATCGTCA CTTGTTCTTT GATTGTGTTA
CGATATCCAG AGACTTAGAA 240 ACGGGGGAAC CGGGATGAGC AAGGTAAAAA
TCGGTGAGTT GATCAACACG CTTGTGAATG 300 AGGTAGAGGC AATTGATGCC
TCAGACCGCC CACAAGGCGA CAAAACGAAG AGAATTAAAG 360 CCGCAGCCGC
ACGGTATAAG AACGCGTTAT TTAATGATAA AAGAAAGTTC CGTGGGAAAG 420 GATTGCAGAA AAGAATAACC GCGAATACTT TTAACGCCTA TATGAGCAGG GCAAGAAAGC
480 GGTTTGATGA TAAATTACAT CATAGCTTTG ATAAAAATAT TAATAAATTA
TCGGAAAAGT 540 ATCCTCTTTA CAGCGAAGAA TTATCTTCAT GGCTTTCTAT
GCCTACGGCT AATATTCGCC 600 AGCACATGTC ATCGTTACAA TCTAAATTGA
AAGAAATAAT GCCGCTTGCC GAAGAGTTAT 660 CAAATGTAAG AATAGGCTCT
AAAGGCAGTG ATGCAAAAAT AGCAAGACTA ATAAAAAAAT 720 ATCCAGATTG
GAGTTTTGCT CTTAGTGATT TAAACAGTGA TGATTGGAAG GAGCGCCGTG 780
ACTATCTTTA TAAGTTATTC CAACAAGGCT CTGCGTTGTT AGAAGAACTA CACCAGCTCA
840 AGGTCAACCA TGAGGTTCTG TACCATCTGC AGCTAAGCCC TGCGGAGCGT
ACATCTATAC 900 AGCAACGATG GGCCGATGTT CTGCGCGAGA AGAAGCGTAA
TGTTGTGGTT ATTGACTACC 960 CAACATACAT GCAGTCTATC TATGATATTT
TGAATAATCC TGCGACTTTA TTTAGTTTAA 1020 ACACTCGTTC TGGAATGGCA CCTTTGGCCT TTGCTCTGGC TGCGGTATCA GGGCGAAGAA 1080 TGATTGAGAT AATGTTTCAG GGTGAATTTG CCGTTTCAGG AAAGTATACG GTTAATTTCT 1140 CAGGGCAAGC TAAAAAACGC TCTGAAGATA AAAGCGTAAC CAGAACGATT TATACTTTAT
1200 GCGAAGCAAA ATTATTCGTT GAATTATTAA CAGAATTGCG TTCTTGCTCT GCTGCATCTG 1260 ATTTCGATGA GGTTGTTAAA GGATATGGAA AGGATGATAC AAGGTCTGAG AACGGCAGGA 1320 TAAATGCTAT TTTAGCAAAA GCATTTAACC CTTGGGTTAA ATCATTTTTC GGCGATGACC 1380 GTCGTGTTTA TAAAGATAGC CGCGCTATTT ACGCTCGCAT CGCTTATGAG ATGTTCTTCC 1440 GCGTCGATCC ACGGTGGAAA AACGTCGACG AGGATGTGTT CTTCATGGAG ATTCTCGGAC 1500 ACGACGATGA GAACACCCAG CTGCACTATA AGCAGTTCAA GCTGGCCAAC TTCTCCAGAA
1560 CCTGGCGACC TGAAGTTGGG GATGAAAACA CCAGGCTGGT GGCTCTGCAG AAACTGGACG 1620 ATGAAATGCC AGGCTTTGCC AGAGGTGACG CTGGCGTCCG TCTCCATGAA ACCGTTAAGC 1680 AGCTGGTGGA GCAGGACCCA TCAGCAAAAA TAACCAACAG CACTCTCCGG GCCTTTAAAT 1740 TTAGCCCGAC GATGATTAGC CGGTACCTGG AGTTTGCCGC TGATGCATTG GGGCAGTTCG 1800 TTGGCGAGAA CGGGCAGTGG CAGCTGAAGA TAGAGACACC TGCAATCGTC CTGCCTGATG 1860 AAGAATCCGT TGAGACCATC GACGAACCGG ATGATGAGTC CCAAGACGAC GAGCTGGATG
1920 AAGATGAAAT TGAGCTCGAC GAGGGTGGCG GCGATGAACC AACCGAAGAG GAAGGGCCAG 1980 AAGAACATCA GCCAACTGCT CTAAAACCCG TCTTCAAGCC TGCAAAAAAT AACGGGGACG 2040 GAACGTACAA GATAGAGTTT GAATACGATG GAAAGCATTA TGCCTGGTCC GGCCCCGCCG 2100 ATAGCCCTAT GGCCGCAATG CGATCCGCAT GGGAAACGTA CTACAGCTAA AAGAAAAGCC 2160 ACCGGTGTTA ATCGGTGGCT TTTTTATTGA GGCCTGTCCC TACCCATCCC CTGCAAGGGA 2220 CGGAAGGATT AGGCGGAAAC TGCAGCTGCA ACTACGGACA TCGCCGTCCC GACTGCAGGG
2280 ACTTCCCCGC GTAAAGCGGG GCTTAAATTC GGGCTGGCCA ACCCTATTTT TCTGCAATCG 2340 CTGGCGATGT TAGTTTCGTG GATAGCGTTT CCAGCTTTTC AATGGCCAGC TCAAAATGTG 2400 CTGGCAGCAC CTTCTCCAGT TCCGTATCAA
TATCGGTGAT CGGCAGCTCT CCACAAGACA 2460 TACTCCGGCG ACCGCCACGA
ACTACATCGC GCAGCAGCTC CCGTTCGTAG ACACGCATGT 2520 TGCCCAGAGC
CGTTTCTGCA GCCGTTAATA TCCGGCGCAC GTCGGCGATG ATTGCCGGGA 2580
GATCATCCAC GGTTATTGGG TTCGGTGATG GGTTCCTGCA GGCGCGGCGG AGAGCCATCC
2640 AGACGCCGCT AACCCATGCG TTACGGTACT GAAAACTTTG TGCTATGTCG
TTTATCAGGC 2700 CCGAAGTTCT TCTTTCTGCC GCCAGTCCAG TGGTTCACCG
GCGTTCTTAG GCTCAGGCTC 2760 GACAAAAGCA TACTCGCCGT TTTTCCGGAT
AGCTGGCAGA ACCTCGTTCG TCACCCACTT 2820 GCGGAACCGC CAGGCTGTCG
TCCCCTGTTT CACCGCGTCG CGGCAGCGGA GGATTATGGT 2880 GTAGAGACCA
GATTCCGATA CCACATTTAC TTCCCTGGCC ATCCGATCAA GTTTTTGTGC 2940
CTCGGTTAAA CCGAGGGTCA ATTTTTCATC ATGATCCAGC TTACGCAATG CATCAGAAGG
3000 GTTGGCTATA TTCAATGCAG CACAGATATC CAGCGCCACA AACCACGGGT
CACCACCGAC 3060 AAGAACCACC CGTATAGGGT GGCTTTCCTG AAATGAAAAG
ACGGAGAGAG CCTTCATTGC 3120 GCCTCCCCGG ATTTCAGCTG CTCAGAAAGG
GACAGGGAGC AGCCGCGAGC TTCCTGCGTG 3180 AGTTCGCGCG CGACCTGCAG
AAGTTCCGCA GCTTCCTGCA AATACAGCGT GGCCTCATAA 3240 CTGGAGATAG
TGCGGTGAGC AGAGCCCACA AGCGCTTCAA CCTGCAGCAG GCGTTCCTCA 3300
ATCGTCTCCA GCAGGCCCTG GGCGTTTAAC TGAATCTGGT TCATGCGATC ACCTCGCTGA
3360 CCGGGATACG GGCTGACAGA ACGAGGACAA AACGGCTGGC GAACTGGCGA
CGAGCTTCTC 3420 GCTCGGATGA TGCAATGGTG GAAAGGCGGT GGATATGGGA
TTTTTTGTCC GTGCGGACGA 3480 CAGCTGCAAA TTTGAATTTG AACATGGTAT
GCATTCCTAT CTTGTATAGG GTGCTACCAC 3540 CAGAGTTGAG AATCTCTATA
GGGGTGGTAG CCCAGACAGG GTTCTCAACA CCGGTACAAG 3600 AAGAAACCGG
CCCAACCGAA GTTGGCCCCA TCTGAGCCAC CATAATTCAG GTATGCGCAG 3660
ATTTAACACA CAAAAAAACA CGCTGGCGCG TGTTGTGCGC TTCTTGTCAT TCGGGGTTGA
3720 GAGGCCCGGC TGCAGATTTT GCTGCAGCGG GGTAACTCTA CCGCCAAAGC
AGAACGCACG 3780 TCAATAATTT AGGTGGATAT TTTACCCCGT GACCAGTCAC
GTGCACAGGT GTTTTTATAG 3840 TTTGCTTTAC TGACTGATCA GAACCTGATC
AGTTATTGGA GTCCGGTAAT CTTATTGATG 3900 ACCGCAGCCA CCTTAGATGT
TGTCTCAAAC CCCATACGGC CACGAATGAG CCACTGGAAC 3960 GGAATAGTCA
GCAGGTACAG CGGAACGAAC CACAAACGGT TCAGACGCTG CCAGAACGTC 4020
GCATCACGAC GTTCCATCCA TTCGGTATTG TCGAC 4055 (SEQ ID NO: 9)
Escherichia coli bacteriophage N15 telomerase amino acid sequence:
MSKVKIGELI NTLVNEVEAI DASDRPQGDK TKRIKAAAAR YKNALFNDKR KFRGKGLQKR 60 ITANTFNAYM SRARKRFDDK LHHSFDKNIN KLSEKYPLYS EELSSWLSMP TANIRQHMSS 120 LQSKLKEIMP LAEELSNVRI GSKGSDAKIA RLIKKYPDWS FALSDLNSDD WKERRDYLYK 180 LFQQGSALLE ELHQLKVNHE VLYHLQLSPA ERTSIQQRWA
DVLREKKRNV VVIDYPTYMQ 240 SIYDILNNPA TLFSLNTRSG MAPLAFALAA
VSGRRMIEIM FQGEFAVSGK YTVNFSGQAK 300 KRSEDKSVTR TIYTLCEAKL
FVELLTELRS CSAASDFDEV VKGYGKDDTR SENGRINAIL 360 AKAFNPWVKS
FFGDDRRVYK DSRAIYARIA YEMFFRVDPR WKNVDEDVFF MEILGHDDEN 420
TQLHYKQFKL ANFSRTWRPE VGDENTRLVA LQKLDDEMPG FARGDAGVRL HETVKQLVEQ
480 DPSAKITNST LRAFKFSPTM ISRYLEFAAD ALGQFVGENG QWQLKIETPA
IVLPDEESVE 540 TIDEPDDESQ DDELDEDEIE LDEGGGDEPT EEEGPEEHQP
TALKPVFKPA KNNGDGTYKI 600 EFEYDGKHYA WSGPADSPMA AMRSAWETYY S 631 (SEQ ID NO: 10)
The amplified DNA constructs can be incubated with at least one protelomerase under conditions promoting production of closed cdsDNA. The conditions that promote the cleavage and relegation of a dsDNA comprises a protelomerase target sequence to form a covalently closed end DNA with hairpin ends. Conditions promoting production of closed end DNA comprise using any temperature allowing for production of closed end DNA, commonly in the range of 20 to 90°C. The temperature may be in a range of 25 to 40°C, such as about 25 to about 35°C, or about 30°C. Appropriate temperatures for a specific protelomerase may be selected according to the principles outlined above in relation to temperature conditions for DNA polymerases. A suitable temperature for use with E. coli bacteriophage TelN protelomerase of SEQ ID NO: 10 is about 25 to about 35°C, such as about 30°C.
Conditions promoting production of closed end DNA also comprise the presence of a protelomerase and suitable buffering agents/pH and other factors which are required for enzyme performance or stability. Suitable conditions include any conditions used to provide for activity of protelomerase enzymes known in the art. For example, where E. coli bacteriophage TelN protelomerase is used, a suitable buffer may be 20 mM TrisHCl, pH 7.6; 5 mM CaCl2; 50 mM potassium glutamate; 0.1 mM EDTA; 1 mM Dithiothreitol (DTT). Agents and conditions to maintain optimal activity and stability may also be selected from those listed for DNA polymerases.
All enzymes and proteins for use in the process of the invention may be produced recombinantly, for example in bacteria. Any means known to the skilled person allowing for recombinant expression may be used. A plasmid or other form of expression vector comprising a nucleic acid sequence encoding the protein of interest may be introduced into bacteria, such that they express the encoded protein. For example, for expression of SEQ ID NOs: 2, 4, 6, 8 or 10, the vector may comprise the sequence of SEQ ID NOs: 1, 3, 5, 7 or 9 respectively. The expressed protein will then typically be purified, for example by use of an affinity tag, in a sufficient quantity and provided in a form suitable for use in the process of the invention. Such methodology for recombinant protein production is routinely available to the skilled person on the basis of their general knowledge. The above discussion applies to the provision of any protein discussed herein.
In certain embodiments, amplified DNA is purified prior to contacting with a protelomerase. Thus, the process of the invention may further comprise a step of purifying amplified DNA. In certain embodiments, amplified DNA is not purified prior to contacting with protelomerase. In some embodiments, the process comprises the addition of a buffer providing for protelomerase activity, i.e., to provide conditions promoting formation of closed end DNA.
5. DNA Constructs
The DNA construct of the invention may comprise more than one protelomerase target sequences, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more protelomerase target sequences. Multiple protelomerase target sequences allows for excision of short closed end DNAs each comprising a DNA fragment of interest from a larger DNA molecule (such as a plasmid or a self-replicating extrachromosomal genetic element). For example, one or more inserts, each comprising a DNA fragment of interest flanked by its own pair of end sequences, may each be further flanked on either side (outside the end sequences) by a protelomerase target sequence. The same protelomerase target sequence may be shared between two adjacent inserts. The two flanking protelomerase sequences can then mediate excision of each insert from the amplified larger DNA molecule as a closed end DNA, subject to the action of protelomerase.
In one embodiment, the DNA construct comprises an insert having a DNA fragment of interest (such as an expression cassette) flanked on either side by a protelomerase target sequence. In one embodiment, the DNA fragment of interest (e.g., expression cassette) may comprise a eukaryotic promoter operably linked to a coding sequence of interest, and optionally a eukaryotic transcription termination sequence. In this embodiment, following amplification of the DNA construct, and contacting with the protelomerase, the DNA fragment of interest (e.g., expression cassette) is released from the amplified DNA construct as a closed end DNA. Other sequences in the DNA construct are concomitantly deleted as a result of protelomerase digestion. Such sequences are typically bacterial or vector sequences that may include bacterial origins of replication, bacterial selection markers ( e.g ., antibiotic resistance genes), and unmethylated CpG dinucleotides. Deletion of such sequences creates a “minimal” DNA fragment of interest (e.g., expression cassette) which does not contain extraneous genetic material.
In some embodiments, particularly where the closed end DNA product is a DNA vaccine, CpG motifs may be retained in the sequence of the product.
Thus one aspect of the invention provides an in vitro process for the production of a pharmaceutical composition comprising a closed end double- stranded DNA flanked by the end sequences. This process comprises: a) amplifying in a host cell (e.g., a eukaryotic or prokaryotic host cell) a DNA construct comprising at least one DNA fragment of interest (e.g., expression cassette) flanked by a pair of end sequences (such as ITR, LTR or telomere sequence that promotes stability of the cdsDNA during the life cycle of a host cell) and further flanked by a pair of protelomerase target sequences; and b) contacting amplified DNA construct produced in a) with one or more protelomerases specific for the pair of
protelomerase target sequences, under conditions promoting cleavage of the pair of protelomerase target sequences to form a closed end double stranded DNA comprising the DNA fragment of interest.
In certain embodiments, the cdsDNA comprises, consists or consists essentially of a eukaryotic promoter operably linked to a coding sequence of interest, and optionally a eukaryotic transcription termination sequence, all flanked by a pair of end sequences.
In certain embodiments, the cdsDNA lacks bacterial or vector sequences, such as (i) bacterial origins of replication; (ii) bacterial selection markers (typically antibiotic resistance genes); and (iii) unmethylated CpG motifs.
The DNA fragment of interest may comprise a DNA vaccine, or a therapeutic DNA molecule encoding a gene product that can correct a defect in a target cell.
The DNA construct may be in the form of a plasmid or other vector typically used to house a gene for bacterial propagation, including any commercially available plasmid or other vector, such as a commercially available DNA medicine, engineered to include the flanking end sequences and the protelomerase recognition sequences.
In certain embodiments, the DNA construct does not contain any sequence elements required for rolling circle amplification (RCA). 6. Pharmaceutical Formulations and Delivery
Following production of the cdsDNA by the action of protelomerase, the process of the invention may further comprise a step of purifying the cdsDNA product.
In certain embodiments, the purification removes undesired by-products or impurities or both.
Purification may be carried out by any suitable means known in the art. For example, purification may include phenol/chloroform nucleic acid extraction, or the use of a column which selectively binds nucleic acid, such as those commercially available from Qiagen. The skilled person can routinely identify suitable purification techniques for use in isolation of DNA.
Once the cdsDNA has been generated and purified in a sufficient quantity, the process may further comprise its formulation as a DNA composition, for example a therapeutic DNA composition or a pharmaceutical composition comprising the cdsDNA.
A therapeutic DNA composition comprises a therapeutic DNA molecule of the type referred to above, e.g., a DNA fragment of interest encompassing a therapeutic function, flanked by a pair of end sequences, and further flanked by a pair of protelomerase half recognition sequences. The end sequences may serve to prevent DNA decay once the cdsDNA (e.g., the therapeutic DNA molecule) is delivered inside a target cell, especially when the cdsDNA exists as an extrachromosomal genetic element that is not integrated into the host cell genome / chromosome(s). Such a composition will comprise a therapeutically effective amount of the DNA fragment of interest in a form suitable for administration by a desired route, e.g., an aerosol, an injectable composition, or a formulation suitable for parenteral (i.v., i.m. etc.), oral, mucosal, or topical administration.
Formulation of DNA as a conventional pharmaceutical preparation may be done using standard pharmaceutical formulation chemistries and methodologies, which are available to those skilled in the art. Any suitable pharmaceutically acceptable carrier or excipient may be used. Auxiliary substances, such as wetting or emulsifying agents, pH buffering substances and the like, may be present in the excipient or vehicle. These excipients, vehicles and auxiliary substances are generally pharmaceutical agents which may be administered without undue toxicity and which, in the case of vaccine compositions will not induce an immune response in the individual receiving the composition. A suitable carrier may be a liposome.
Pharmaceutically acceptable excipients include, but are not limited to, liquids such as water, saline, polyethyleneglycol, hyaluronic acid, glycerol and ethanol.
Pharmaceutically acceptable salts can also be included therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like.
In certain embodiments, the preparation also contains a pharmaceutically acceptable excipient that serves as a stabilizer, particularly for peptide, protein or other like molecules if they are to be included in the composition. Examples of suitable carriers that also act as stabilizers for peptides include, without limitation, pharmaceutical grades of dextrose, sucrose, lactose, trehalose, mannitol, sorbitol, inositol, dextran, and the like. Other suitable carriers include, again without limitation, starch, cellulose, sodium or calcium phosphates, citric acid, tartaric acid, glycine, high molecular weight polyethylene glycols (PEGs), and combination thereof. A thorough discussion of pharmaceutically acceptable excipients, vehicles and auxiliary substances is available in REMINGTON’S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. 1991), incorporated herein by reference.
The subject cdsDNA can be delivered using a non- viral delivery system to any target cell of interest. Non- viral gene delivery systems are based on the compaction of genetic material into nanometric particles by electrostatic interaction between the negatively charged phosphate backbone of DNA or RNA and cationic lipids, peptides or other polymers (Erbacher et al, Gene Therapy 6:138-145, 1999). The use of non- viral transfection vectors that include lipids, as opposed to viruses, can result in lower toxicity, especially lower immunogenicity, greater safety, reduced cost, reasonably efficient targeting, and an enhanced packaging ability, e.g., the ability to deal with large fragments of nucleic acid material.
In certain embodiments, the subject cdsDNA is delivered using any suitable non- viral gene therapy vectors, such as those described in Yin et al., Non-viral vectors for gene-based therapy. Nature reviews Genetics, 15:541-555, 2014; or Schroeder et al., Lipid-based nanotherapeutics for siRNA delivery. J Intern Med. 267:9-21, 2010; or Zhao and Huang, Lipid nanoparticles for gene delivery. Adv Genet. 88: 13-36, 2014 (all incorporated herein by reference).
In certain embodiments, the cdsDNA is delivered using lipoplex for lipid-based nucleic acid complexes (see Feigner et al, Human Gene Therapy 8:511-512, 1997, incorporated by reference). The term“LPD” is a form of lipopolyplex representing a formulation comprising a lipid, an integrin-(or other receptor-) binding peptide and DNA (or other nucleic acid). LPD complexes achieve transfection via an integrin- mediated or other receptor- mediated pathway. They do not necessarily need to have an overall positive charge, so undesirable serum interaction can be reduced. The peptide component of LPD provides a nucleic acid packaging function, shielding the DNA or RNA from intracellular or
extracellular degradation, endosomal or otherwise. The lipid components mediate
interactions with endosomal lipid bilayers by membrane fusion or permeabilisation, reducing endosomal or lysosomal degradation and allowing trafficking of the nucleic acid cargo the cytoplasm.
In certain embodiments, the peptide component is designed to be cell-type specific or cell- surface receptor specific. For example the degree of specificity for integrin or other receptors can confer a degree of cell specificity to the LPD complex. Specificity results from the targeting to the cell- surface receptors (for example integrin receptors), and transfection efficiencies comparable to some adenoviral vectors can be achieved (see Du et al., The role of the helper lipid on the DNA transfection efficiency of lipopolyplex formulations. Sci Rep. 4:7107, 2014; Welser et al., Gene delivery using ternary lipopolyplexes incorporating branched cationic peptides: the role of Peptide sequence and branching. Mol Pharm. 10:127- 41, 2013; Meng et al., Inhibition of neointimal hyperplasia in a rabbit vein graft model following non- viral transfection with human iNOS cDNA. Gene Ther. 20:979-86, 2013; Manunta et al, Airway deposition of nebulized gene delivery nanocomplexes monitored by radioimaging agents. Am J Respir Cell Mol Biol. 49:471-80, 2013; Kenny et al.,
Multifunctional receptor-targeted nanocomplexes for the delivery of therapeutic nucleic acids to the Brain. Biomaterials. 34:9190-200, 2013; Tagalakis et al., Receptor-targeted liposome - peptide nanocomplexes for siRNA delivery. Biomaterials. 32:6302-15, 2011; Tagalakis et al., Integrin-targeted nanocomplexes for tumor specific delivery and therapy by systemic administration. Biomaterials. 32: 1370-6, 2011; Manunta et al., Nebulisation of receptor- targeted nanocomplexes for gene delivery to the airway epithelium. PLoS One. 6:e26768, 2011; Grosse et al., Tumor- specific gene transfer with receptor-mediated nanocomplexes modified by polyethylene glycol shielding and endosomally cleavable lipid and peptide linkers. F ASEB J. 24:2301-13, 2010).
In certain embodiments, the non- viral delivery comprises peptides that target human airway epithelial cells. See W002/072616 (incorporated by reference).
In certain embodiments, the non- viral delivery comprises peptides that target dendritic cells. See W02004/108938 (incorporated by reference).
In certain embodiments, the non- viral delivery is lipid/peptide vector that transfects a range of cell lines and primary cell cultures with high efficiency and low toxicity, including epithelial cells (40% efficiency), vascular smooth muscle cells (50% efficiency), endothelial cells (30% efficiency), haematopoietic cells (10% efficiency), bronchial epithelium of mouse (see Manunta et al, Nebulisation of receptor-targeted nanocomplexes for gene delivery to the airway epithelium. PLoS One. 20l l;6:e26768; Tagalakis et al., A receptor-targeted nanocomplex vector system optimized for respiratory gene transfer. Mol Ther. 2008; 16:907- 15; Jenkins et al., Formation of LID vector complexes in water alters physicochemical properties and enhances pulmonary gene expression in vivo, Gene Therapy 2003, 10, 1026- 34), rat lung (Jenkins et al. , An integrin-targeted non-viral vector for pulmonary gene therapy, Gene Therapy 2000, 7, 393-400), and pig lung (Manunta et al, Airway deposition of nebulized gene delivery nanocomplexes monitored by radioimaging agents. Am J Respir Cell Mol Biol. 2013;49:471-80; Cunningham et al., Evaluation of a porcine model for pulmonary gene transfer using a novel synthetic vector, J Gene Med 2002, 4, 438-46), and with efficiency comparable to that of an adenoviral vector (Jenkins et al, 2000, as above).
In certain embodiments, the peptide for use in such LPD complexes or lipid/peptide complexes has two functionalities: a“head group” containing a cell surface receptor- (for example integrin) recognition sequence and a“tail” that can bind DNA non-covalently. In certain embodiments, these two components of the peptide are covalently linked via a spacer in a way that does not interfere with their individual functions. In certain embodiments, the peptide has a“tail” that is a polycationic nucleic acid-binding component, such as peptide described in W096/15811.
In certain embodiments, the lipid component of the LPD complexes are cationic lipids reported in Proc. Natl. Acad. Sci. USA 84, 7413-7417, 1987 and in US 5,264,618 (both incorporated by reference). Commercially-available cationic liposome, known by the trademark“Lipofectin,” which consists of the cytofectin, DOTMA 1 and the neutral lipid DOPE 2 in a 1:1 ratio, is an example of such lipid.
In certain embodiments, the cationic liposome formulation combines a synthetic cationic cytofectin and a neutral lipid. Some, for example, are based on the glycerol-skeleton (such as DOTMA) or on cholesterol, such as DC-Chol 3.
In certain embodiments, the subject cdsDNA is formulated in lipid nanoparticles (LNPs), such as SNALP (stable nucleic acid-lipid particles). Such lipid nanoparticles typically comprise one or more ionizable lipids, phospholipids, cholesterol, and PEG-lipids as carrier materials that encompass within nucleic acids (such as RNAi agents (siRNA, miRNA, shRNA), antisense oligonucleotides (ASOs), CRISPR/Cas system components (such as nucleic acids encoding the Cas9 enzyme, and sgRNA), therapeutic mRNA, genetic vaccines, or traditional DNA vectors such as plasmids).
In certain embodiments, the subject cdsDNA is formulated in liposomes, which typically comprise one or more phospholipids, cholesterol, and PEG-lipids as carrier materials that encompass within nucleic acids, such as the ones mentioned above.
In certain embodiments, the subject cdsDNA is formulated in polymer-based nanoparticles (NPs), which typically comprise one or more poly-lactides ( e.g ., PLGA), block copolymers (such as PEG-b-PLGA), and polysaccharides (such as chitosan and cellulose) as carrier materials that encompass within nucleic acids, such as the ones mentioned above.
Certain specific types of LNPs, liposomes and polymer NPs are exemplified below. SNALP
In certain embodiments, the subject cdsDNA is formulated in SNALP (stable nucleic acid-lipid particles) that are stable lipid particles having a non-lamellar structure. SNALP comprises ionizable lipids, shielding lipids (e.g., polyethylene glycol (PEG)), cholesterol, and endogenous or exogenous targeting ligands such as ApoE lipoprotein. It is a mono-lamellar (single lipid bilayer) liposome neutrally charged at physiological pH and stabilized by PEG that encapsulates the nucleic acids inside SNALP (such as the cdsDNA). SNALP is suitable for delivery to various tissue and cell types.
In certain embodiments, the SNALP comprises ionizable cationic lipid DLinDMA (l,2-dilinoleyloxy-3- dimethylaminopropane). In certain embodiments, SNALP comprises DLin-KC2-DMA and DLin-MC3-DMA, and is generated by a structure- activity relationship (SAR) study that optimized the pKa of the ionizable amino lipid head groups of the cationic lipid moiety. In certain embodiments, SNALP is reLNP (rapidly eliminated LNP), such as L319, that provides biodegradability to the existing SNALP platforms and rapid elimination from plasma and tissue.
In certain embodiments, the subject cdsDNA is formulated as a plurality of nucleic acid-lipid particles, wherein each particle in the plurality of particles comprises: (a) a nucleic acid (e.g., the cdsDNA, which may encode a protein, an RNAi, an antisense oligonucleotide, or an mRNA); (b) a cationic lipid comprising from about 50-85 mol % (e.g., about 50-65 mol%; about 56.5-66.5 mol %; about 52-62 mol %) of the total lipid present in the particle;
(c) a non-cationic lipid (such as cholesterol or a derivative thereof, or phospholipid (such as dipalmitoylphosphatidylcholme (DPPC), distearoylphosphatidylcholine (DSPC), or a mixture thereof), or a mixture of phospholipid and cholesterol or a derivative thereof) comprising from about 13-49.5 mol % ( e.g ., about 31.5-42.5 mol % of cholesterol or a derivative thereof; or 4-10 mol % of phospholipid and 30-40 mol % cholesterol; or 5-9 mol % of phospholipid and 32-36 mol % cholesterol; or 10-30 mol % of phospholipid and 10-30 mol % of cholesterol) of the total lipid present in the particle; and (d) a conjugated lipid that inhibits aggregation of particles (e.g., PEG- lipid conjugate such as PEG-diacylglycerol (PEG-DAG) conjugate, a PEG-dialkyloxypropyl (PEG-DAA) conjugate, or a mixture thereof) comprising from about 0.5-10 mol % (e.g. about 0.5-2 mol%, or about 1-2 mol%) of the total lipid present in the particle, optionally wherein at least about 95% of the particles in the plurality of particles have a non- lamellar morphology. In certain embodiments, the nucleic acid-lipid particle comprises about 61.5 mol % cationic lipid, about 36.9% cholesterol or a derivative thereof, and about 1.5 mol % PEG- lipid conjugate. In certain embodiments, the nucleic acid- lipid particle comprises about 57.1 mol % cationic lipid, about 7.1 mol % phospholipid, about 34.3 mol % cholesterol or a derivative thereof, and about 1.4 mol % PEG-lipid conjugate.
In certain embodiments, the subject cdsDNA is formulated as a plurality of nucleic acid-lipid particles, wherein each particle in the plurality of particles comprises: (a) a nucleic acid; (b) a cationic lipid comprising from about 50 mol % to about 85 mol % (e.g., about 50 mol% to about 65 mol%, or about 50 mol% to about 60 mol%) of the total lipid present in the particle; (c) a non-cationic lipid comprising from about 13 mol % to about 49.5 mol % of the total lipid present in the particle (e.g., a mixture of a phospholipid and cholesterol or a cholesterol derivative, wherein the phospholipid comprises from about 3 mol % to about 15 mol % (or about 4 mol % to about 12 mol %) of the total lipid present in the particle; and wherein the cholesterol or derivative thereof comprises from about 30 mol % to about 40 mol % of the total lipid present in the particle); and (d) a conjugated lipid that inhibits aggregation of particles comprising from about 0.5 mol % to about 10 mol % (e.g., about 0.5 mol % to about 2 mol %, or about 5 mol % to about 10 mol %) of the total lipid present in the particle, wherein at least about 95% of the particles in the plurality of particles have a non- lamellar morphology.
In certain embodiments, the subject cdsDNA is formulated as a plurality of nucleic acid-lipid particles, wherein each particle in the plurality of particles comprises: (a) a nucleic acid (such as the cdsDNA, which may encode a protein, an RNAi, an antisense
oligonucleotide, or an mRNA); (b) a cationic lipid (e.g., about 10-50 mol%, about 20-50 mol%, or about 20-40 mol% of the total lipid present in the particle); (c) a non-cationic lipid ( e.g ., about 10-60 mol%, about 20-55 mol%, or about 25-50 mol% of the total lipid present in the particle); and (d) a conjugated lipid that inhibits aggregation of particles (e.g., about 0.5- 20 mol%, about 2-20 mol%, or about 1.5-18 mol% of the total lipid present in the particle), wherein at least about 95% of the particles in the plurality of particles have a non-lamellar morphology, or wherein at least about 95% of the particles in the plurality of particles are electron-dense.
The cdsDNA can encode any gene product of interest, including protein, antisense oligonucleotide, or RNAi construct (such as siRNA, aiRNA, miRNA, Dicer-substrate dsRNA, shRNA, ssRNAi oligonucleotides, and combinations thereof).
In certain embodiments, the cationic lipid comprises 1,2- dilinoleyloxy-N,N- dimethylaminopropane (DLinDMA), l,2-dilinolenyloxy-N,N- dimethylaminopropane
(DLenDMA), l,2-di-y-linolenyloxy-N,N-dimethylaminopropane (g-DLenDMA), 2,2- dilinoleyl-4-(2-dimethylaminoethyl)-[l,3]-dioxolane (DLin-K-C2-DMA), 2,2-dilinoleyl-4- dimethylaminomethyl-[l,3]-dioxolane (DLin-K-DMA), or a mixture thereof.
In certain embodiments, the cationic lipid comprises MC3, LenMC3, CP-LenMC3, y- LenMC3, CP-y-LenMC3, MC3MC, MC2MC, MC3 Ether, MC4 Ether, MC3 Amide, Pan- MC3, Pan-MC4, Pan MC5 or a mixture thereof.
In certain embodiments, the cationic lipid comprises N,N-dioleyl-N,N- dimethylammonium chloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N-(l-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), N- (l-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-dimethyl- 2,3-dioleyloxypropylamine (DODMA), and combinations thereof.
In certain embodiments, the cationic lipid is any one as described in U.S. Pat. Nos. 7,799,565; 8,569,256; 9,018,187; and 9,181,545 (both incorporated herein by reference).
In certain embodiments, the non-cationic lipid is dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), egg phosphatidylcholine (EPC), distearoylphosphatidylcholine (DSPC), cholesterol, and combinations thereof.
In certain embodiments, the non-cationic lipid is a phospholipid.
In certain embodiments, the non-cationic lipid is cholesterol or a cholesterol derivative. Examples of cholesterol derivatives include, but are not limited to, cholestanol, cholestanone, cholestenone, coprostanol, cho lestery 1-2’ -hydro xyethyl ether, cholesteryl-4’- hydroxybutyl ether, and mixtures thereof.
In certain embodiments, the non-cationic lipid is a mixture of a phospholipid and cholesterol or a cholesterol derivative.
In certain embodiments, the non-cationic lipid is a phospholipid selected from the group consisting of dip almitoylphosphatidylcho line (DPPC), distearoylphosphatidylcholine (DSPC), or a mixture thereof.
In certain embodiments, the non-cationic lipid is DPPC.
In certain embodiments, the non-cationic lipid is a mixture of DPPC and cholesterol.
In certain embodiments, the conjugated lipid that inhibits aggregation of particles is a polyethyleneglycol (PEG)-lipid conjugate. For example, the PEG may have an average molecular weight of from about 550 daltons to about 5,000 daltons, or an average molecular weight of about 2,000 daltons, or an average molecular weight of about 750 daltons.
In certain embodiments, the PEG-lipid conjugate is a member selected from the group consisting of: a PEG-diacylglycerol (PEG-DAG) conjugate, a PEG dialky loxypropyl (PEG- DAA) conjugate, a PEG-phospho lipid conjugate, a PEG- ceramide (PEG-Cer) conjugate, and a mixture thereof.
In certain embodiments, the PEG-lipid conjugate is a PEG-DAA conjugate, such as those described in U.S. Pat. No. 8,936,942 and 7,982,027 (incorporated by reference).
In certain embodiments, the PEG-DAA conjugate is a member selected from the group consisting of a PEG-didecyloxypropyl (Cl0) conjugate, a PEG-dilauryloxypropyl (Cl2) conjugate, a PEG-dimyristyloxypropyl (Cl4) conjugate, a PEG-dipalmityloxypropyl (Cl6) conjugate, a PEG-distearyloxypropyl (Cl8) conjugate, and a mixture thereof. In certain embodiments, the PEG-lipid conjugate is described in U.S. Pat. No. 7,803,397 (incorporated by reference).
In certain embodiments, the PEG-DAA conjugate is a PEG- dimyristyloxypropyl (CH) conjugate.
In certain embodiments, the nucleic acid in the particles (e.g., cdsDNA) is not substantially degraded after exposure of the particle to a nuclease at 37°C for about 20 minutes, or about 30 minutes.
In certain embodiments, the cdsDNA is fully encapsulated in the particles. That is, the cdsDNA is fully encapsulated within the lipid portion of the lipid particles such that the cdsDNA in the lipid particle is resistant in aqueous solution to enzymatic degradation, e.g., by a nuclease or protease. In certain other embodiments, the lipid particles are substantially non- toxic to mammals such as humans.
In certain embodiments, the particle has a lipidxdsDNA mass ratio of from about 5:1 to about 15:1.
In certain embodiments, the particles have a median diameter of from about 30 or 40 nm to about 150 nm.
In certain embodiments, the cationic lipid comprises from about 52 mol % to about 62 mol % of the total lipid present in the particle.
In certain embodiments, the non-cationic lipid is a mixture of a phospholipid and cholesterol or a derivative thereof comprising from about 36 mol % to about 47 mol% of the total lipid present in the particle.
In certain embodiments, the conjugated lipid that inhibits aggregation of the particles is a PEG-lipid conjugate comprising from about 1 mol % to about 2 mol % of the total lipid present in the particle.
In certain embodiments, the cationic lipid comprises from about 56.5 mol % to about 66.5 mol % of the total lipid present in the particle.
In certain embodiments, the non-cationic lipid is cholesterol or a derivative thereof comprising from about 31.5 mol % to about 42.5 mol% of the total lipid present in the particle.
In certain embodiments, the conjugated lipid that inhibits aggregation of the particles is a PEG-lipid conjugate comprising from about 1 mol % to about 2 mol % of the total lipid present in the particle.
In certain embodiments, the cationic lipid comprises from about 50 mol % to about 60 mol % of the total lipid present in the particle.
In certain embodiments, the non-cationic lipid is a mixture of a phospholipid and cholesterol or a derivative thereof comprising from about 35 mol % to about 45 mol% of the total lipid present in the particle.
In certain embodiments, the conjugated lipid that inhibits aggregation of the particles is a PEG-lipid conjugate comprising from about 5 mol % to about 10 mol % of the total lipid present in the particle.
In certain embodiments, the cationic lipid comprises from about 55 mol % to about 65 mol % of the total lipid present in the particle. In certain embodiments, the non-cationic lipid is cholesterol or a derivative thereof comprising from about 30 mol % to about 40 mol% of the total lipid present in the particle.
In certain embodiments, the conjugated lipid that inhibits aggregation of the particles is a PEG-lipid conjugate comprising from about 5 mol % to about 10 mol % of the total lipid present in the particle.
In certain embodiments, greater than 95%, at least 96%, at least 97%, at least 98%, at least 99%, or greater than 99% of the particles have a non- lamellar morphology, i.e., a non bilayer structure. In certain embodiments, greater than 95%, at least 96%, at least 97%, at least 98%, at least 99%, or greater than 99% of the particles are electron-dense.
In certain embodiments, the non-lamellar morphology of the particles comprises an inverse hexagonal (Hu) or cubic phase structure.
In certain embodiments, the particles having a non-lamellar morphology are electron- dense. The non-lamellar morphology of the particles can be determined by, for example, cryogenic-temperature transmission electron microscopy (cryo-TEM), X-ray diffraction, or by Differential Scanning Calorimetry (DSC), wherein no thermal transitions are seen at 5 to 75°C.
Methods of making the SNALP and delivering of the SNALP are known in the art, see for example, US7901708, US9492386, W02009127060A1 and W02012000104A1 (incorporated herein by reference).
The lipid particles can be tailored to preferentially target particular tissues, organs, or tumors of interest. In certain other instances, it may be desirable to have a targeting moiety attached to the surface of the lipid particle to further enhance the targeting of the particle. Methods of attaching targeting moieties (e.g., antibodies, proteins, etc.) to lipids (such as those used in the present particles) are known to those of skill in the art.
Once formed, the SNALP lipid particles are useful for the introduction of active agents or therapeutic agents (e.g., cdsDNA) into cells. Accordingly, the present invention also provides methods for introducing an active agent or therapeutic agent such as a cdsDNA into a cell.
In some instances, the cell is a muscle cell, such as a skeletal muscle cell, a cardiac muscle cell, or a smooth muscle cell. In certain embodiments, the muscle cell is a tibialis anterior muscle cell.
The methods can be carried out in vitro, ex vivo, or in vivo by first forming the particles as described above and then contacting the particles with the cells for a period of time sufficient for delivery of the active agent or therapeutic agent (e.g., cdsDNA) to the cells to occur.
The SNALP lipid particles can be adsorbed to almost any cell type with which they are mixed or contacted. Once adsorbed, the particles can either be endocytosed by a portion of the cells, exchange lipids with cell membranes, or fuse with the cells. Transfer or incorporation of the active agent or therapeutic agent (e.g., cdsDNA) portion of the particle can take place via any one of these pathways. In particular, when fusion takes place, the particle membrane is integrated into the cell membrane and the contents of the particle combine with the intracellular fluid.
The SNALP lipid particles can be administered either alone or in a mixture with a pharmaceutically acceptable carrier (e.g., physiological saline or phosphate buffer) selected in accordance with the route of administration and standard pharmaceutical practice.
Generally, normal buffered saline (e.g., 135-150 mM NaCl) will be employed as the pharmaceutically acceptable carrier. Other suitable carriers include, e.g., water, buffered water, 0.4% saline, 0.3% glycine, and the like, including glycoproteins for enhanced stability, such as albumin, lipoprotein, globulin, etc. Additional suitable carriers are described in, e.g., REMINGTON’S PHARMACEUTICAL SCIENCES, Mack Publishing Company,
Philadelphia, PA, l7th ed. (1985). As used herein,“carrier” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The phrase“pharmaceutically acceptable” refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human.
The pharmaceutically acceptable carrier is generally added following lipid particle formation. Thus, after the lipid particle (e.g., SNALP) is formed, the particle can be diluted into pharmaceutically acceptable carriers such as normal buffered saline.
The concentration of particles in the pharmaceutical formulations can vary widely, i.e., from less than about 0.05%, usually at or at least about 2 to 5%, to as much as about 10 to 90% by weight, and will be selected primarily by fluid volumes, viscosities, etc., in
accordance with the particular mode of administration selected. For example, the
concentration may be increased to lower the fluid load associated with treatment. This may be particularly desirable in patients having atherosclerosis-associated congestive heart failure or severe hypertension. Alternatively, particles composed of irritating lipids may be diluted to low concentrations to lessen inflammation at the site of administration.
The pharmaceutical compositions of the present invention may be sterilized by conventional, well-known sterilization techniques. Aqueous solutions can be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration. The compositions can contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, and calcium chloride. Additionally, the particle suspension may include lipid- protective agents which protect lipids against free-radical and lipid-peroxidative damages on storage. Lipophilic free-radical quenchers, such as alphatocopherol, and water-soluble iron- specific chelators, such as ferrioxamine, are suitable.
In certain other embodiments, a therapeutically effective amount of the lipid particle may be administered to the mammal. In other instances, cells are removed from a patient, the lipid particles are delivered in vitro (e.g., using a SNALP described herein), and the cells are reinjected into the patient.
Systemic delivery for in vivo therapy, e.g., delivery of a therapeutic nucleic acid to a distal target cell via body systems such as the circulation, has been achieved using nucleic acid-lipid particles such as those described in PCT Publication Nos. WO 05/007196, WO 05/121348, WO 05/120152, and WO 04/002453, the disclosures of which are herein incorporated by reference in their entirety for all purposes. The present invention also provides fully encapsulated lipid particles that protect the nucleic acid from nuclease degradation in serum, are non- immunogenic, are small in size, and are suitable for repeat dosing.
For in vivo administration, administration can be in any manner known in the art, e.g., by injection, oral administration, inhalation (e.g., intranasal or intratracheal), transdermal application, or rectal administration. Administration can be accomplished via single or divided doses. The pharmaceutical compositions can be administered parenterally, i.e., intraarticularly, intravenously, intraperitoneally, subcutaneously, or intramuscularly. In some embodiments, the pharmaceutical compositions are administered intravenously,
intramuscularly, or intraperitoneally by a bolus injection (see, e.g., U.S. Patent No.
5,286,634). Intracellular nucleic acid delivery has also been discussed in Straubringer et al. , Methods Enzymol., 101:512 (1983); Mannino et al, Biotechniques, 6:682 (1988); Nicolau et al, Crit. Rev. Ther. Drug Carrier Syst., 6:239 (1989); and Behr, Acc. Chem. Res., 26:21 (1993). Still other methods of administering lipid-based therapeutics are described in, for example, U.S. Patent Nos. 3,993,754; 4,145,410; 4,235,871; 4,224,179; 4,522,803; and 4,588,578. The lipid particles can be administered by direct injection at the site of disease or by injection at a site distal from the site of disease (see, e.g., Culver, HUMAN GENE
THERAPY, Mary Ann Liebert, Inc., Publishers, New York. pp.70-71(1994)). The disclosures of the above-described references are herein incorporated by reference in their entirety for all purposes.
In embodiments where the SNALP lipid particles are administered intravenously, at least about 5%, 10%, 15%, 20%, or 25% of the total injected dose of the particles is present in plasma about 8, 12, 24, 36, or 48 hours after injection. In other embodiments, more than about 20%, 30%, 40% and as much as about 60%, 70% or 80% of the total injected dose of the lipid particles is present in plasma about 8, 12, 24, 36, or 48 hours after injection. In certain instances, more than about 10% of a plurality of the particles is present in the plasma of a mammal about 1 hour after administration. In certain other instances, the presence of the lipid particles is detectable at least about 1 hour after administration of the particle. In certain embodiments, the presence of a therapeutic agent such as a nucleic acid is detectable in cells of the lung, liver, tumor, or at a site of inflammation at about 8, 12, 24, 36, 48, 60, 72 or 96 hours after administration.
The compositions of the present invention, either alone or in combination with other suitable components, can be made into aerosol formulations ( i.e ., they can be“nebulized”) to be administered via inhalation (e.g., intranasally or intratracheally) (see, Brigham et al., Am. J. Sci., 298:278 (1989)). Aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen, and the like.
In certain embodiments, the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles. Methods for delivering nucleic acid compositions directly to the lungs via nasal aerosol sprays have been described, e.g., in U.S. Patent Nos. 5,756,353 and 5,804,212. Likewise, the delivery of drugs using intranasal microparticle resins and lysophosphatidyl-glycerol compounds (U.S. Patent 5,725,871) are also well-known in the pharmaceutical arts. Similarly, transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is described in U.S. Patent No. 5,780,045. The disclosures of the above-described patents are herein incorporated by reference in their entirety for all purposes. Formulations suitable for parenteral administration, such as, for example, by intraarticular (in the joints), intravenous, intramuscular, intradermal, intraperitoneal, and subcutaneous routes, include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. In the practice of this invention, compositions are preferably administered, for example, by intravenous infusion, orally, topically, intraperitoneally, intravesically, or intrathecally.
Generally, when administered intravenously, the lipid particle formulations are formulated with a suitable pharmaceutical carrier. Many pharmaceutically acceptable carriers may be employed in the compositions and methods of the present invention. Suitable formulations for use in the present invention are found, for example, in REMINGTON’S PHARMACEUTICAL SCIENCES, Mack Publishing Company, Philadelphia, PA, l7th ed. (1985). A variety of aqueous carriers may be used, for example, water, buffered water, 0.4% saline, 0.3% glycine, and the like, and may include glycoproteins for enhanced stability, such as albumin, lipoprotein, globulin, etc. Generally, normal buffered saline (135-150 mM NaCl) will be employed as the pharmaceutically acceptable carrier, but other suitable carriers will suffice. These compositions can be sterilized by conventional liposomal sterilization techniques, such as filtration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc. These compositions can be sterilized using the techniques referred to above or, alternatively, they can be produced under sterile conditions. The resulting aqueous solutions may be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration.
In certain applications, the lipid particles disclosed herein may be delivered via oral administration to the individual. The particles may be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, pills, lozenges, elixirs, mouthwash, suspensions, oral sprays, syrups, wafers, and the like (see, e.g., U.S. Patent Nos. 5,641,515, 5,580,579, and 5,792,451, the disclosures of which are herein incorporated by reference in their entirety for all purposes). These oral dosage forms may also contain the following: binders, gelatin; excipients, lubricants, and/or flavoring agents. When the unit dosage form is a capsule, it may contain, in addition to the materials described above, a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit. Of course, any material used in preparing any unit dosage form should be pharmaceutically pure and substantially non-toxic in the amounts employed.
Typically, these oral formulations may contain at least about 0.1% of the lipid particles or more, although the percentage of the particles may, of course, be varied and may conveniently be between about 1% or 2% and about 60% or 70% or more of the weight or volume of the total formulation. Naturally, the amount of particles in each therapeutically useful composition may be prepared is such a way that a suitable dosage will be obtained in any given unit dose of the compound. Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such
pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.
Formulations suitable for oral administration can consist of: (a) liquid solutions, such as an effective amount of a packaged therapeutic agent such as nucleic acid ( e.g ., cdsDNA) suspended in diluents such as water, saline, or PEG 400; (b) capsules, sachets, or tablets, each containing a predetermined amount of a therapeutic agent such as nucleic acid (e.g., cdsDNA), as liquids, solids, granules, or gelatin; (c) suspensions in an appropriate liquid; and (d) suitable emulsions. Tablet forms can include one or more of lactose, sucrose, mannitol, sorbitol, calcium phosphates, corn starch, potato starch, microcrystalline cellulose, gelatin, colloidal silicon dioxide, talc, magnesium stearate, stearic acid, and other excipients, colorants, fillers, binders, diluents, buffering agents, moistening agents, preservatives, flavoring agents, dyes, disintegrating agents, and pharmaceutically compatible carriers. Lozenge forms can comprise a therapeutic agent such as nucleic acid (e.g., cdsDNA) in a flavor, e.g., sucrose, as well as pastilles comprising the therapeutic agent in an inert base, such as gelatin and glycerin or sucrose and acacia emulsions, gels, and the like containing, in addition to the therapeutic agent, carriers known in the art.
In another example of their use, lipid particles can be incorporated into a broad range of topical dosage forms. For instance, a suspension containing nucleic acid-lipid particles such as SNALP can be formulated and administered as gels, oils, emulsions, topical creams, pastes, ointments, lotions, foams, mousses, and the like.
When preparing pharmaceutical preparations of the lipid particles of the invention, it is preferable to use quantities of the particles which have been purified to reduce or eliminate empty particles or particles with therapeutic agents such as nucleic acid associated with the external surface.
The methods of the present invention may be practiced in a variety of hosts. Preferred hosts include mammalian species, such as primates ( e.g ., humans and chimpanzees as well as other nonhuman primates), canines, felines, equines, bo vines, ovines, caprines, rodents (e.g., rats and mice), lagomorphs, and swine.
The amount of particles administered will depend upon the ratio of therapeutic agent (e.g., nucleic acid) to lipid, the particular therapeutic agent (e.g., nucleic acid) used, the disease or disorder being treated, the age, weight, and condition of the patient, and the judgment of the clinician, but will generally be between about 0.01 and about 50 mg per kilogram of body weight, preferably between about 0.1 and about 5 mg/kg of body weight per administration (e.g., injection).
For in vitro applications, the delivery of therapeutic agents such as nucleic acids (e.g., cdsDNA) can be to any cell grown in culture, whether of plant or animal origin, vertebrate or invertebrate, and of any tissue or type. In preferred embodiments, the cells are animal cells, more preferably mammalian cells, and most preferably human cells (e.g., tumor cells or hepatocytes).
Contact between the cells and the lipid particles, when carried out in vitro, takes place in a biologically compatible medium. The concentration of particles varies widely depending on the particular application, but is generally between about 1 pmole and about 10 mmol. Treatment of the cells with the lipid particles is generally carried out at physiological temperatures (about 37°C) for periods of time from about 1 to 48 hours, preferably from about 2 to 4 hours.
In one embodiment, a lipid particle suspension is added to 60- 80% confluent plated cells having a cell density of from about 10 to about 10 cells/ml, more preferably about 2 x 104 cells/ml. The concentration of the suspension added to the cells is preferably of from about 0.01 to 0.2 pg/ml, more preferably about 0.1 pg/ml.
To the extent that tissue culture of cells may be required, it is well-known in the art. For example, Freshney, Culture of Animal Cells, a Manual of Basic Technique, 3rd Ed., Wiley-Liss, New York (1994), Kuchler et ah, Biochemical Methods in Cell Culture and Virology, Dowden, Hutchinson and Ross, Inc. (1977), and the references cited therein provide a general guide to the culture of cells. Cultured cell systems often will be in the form of monolayers of cells, although cell suspensions are also used.
Using an Endosomal Release Parameter (ERP) assay, the delivery efficiency of the SNALP or other lipid particle of the invention can be optimized. An ERP assay is described in detail in U.S. Patent Publication No. 20030077829, the disclosure of which is herein incorporated by reference in its entirety for all purposes. More particularly, the purpose of an ERP assay is to distinguish the effect of various cationic lipids and helper lipid components of SNALP or other lipid particle based on their relative effect on binding/uptake or fusion with/destabilization of the endosomal membrane. This assay allows one to determine quantitatively how each component of the SNALP or other lipid particle affects delivery efficiency, thereby optimizing the SNALP or other lipid particle. Usually, an ERP assay measures expression of a reporter protein (e.g., luciferase, b-galactosidase, green fluorescent protein (GFP), etc.), and in some instances, a SNALP formulation optimized for an expression plasmid will also be appropriate for encapsulating an interfering RNA. In other instances, an ERP assay can be adapted to measure downregulation of transcription or translation of a target sequence in the presence or absence of an interfering RNA (e.g., siRNA). By comparing the ERPs for each of the various SNALP or other lipid particles, one can readily determine the optimized system, e.g., the SNALP or other lipid particle that has the greatest uptake in the cell.
The compositions and methods of the present invention are used to treat a wide variety of cell types, in vivo and in vitro. Suitable cells include, but are not limited to, hepatocytes, reticuloendothelial cells (e.g., monocytes, macrophages, etc.), fibroblast cells, endothelial cells, platelet cells, other cell types infected and/or susceptible of being infected with viruses, hematopoietic precursor (stem) cells, keratinocytes, skeletal, cardiac, and smooth muscle cells, osteoblasts, neurons, quiescent lymphocytes, terminally differentiated cells, slow or noncycling primary cells, parenchymal cells, lymphoid cells, epithelial cells, bone cells, and the like.
In particular embodiments, an active agent or therapeutic agent such as a cdsDNA is delivered to cancer cells (e.g., cells of a solid tumor) including, but not limited to, liver cancer cells, lung cancer cells, colon cancer cells, rectal cancer cells, anal cancer cells, bile duct cancer cells, small intestine cancer cells, stomach (gastric) cancer cells, esophageal cancer cells, gallbladder cancer cells, pancreatic cancer cells, appendix cancer cells, breast cancer cells, ovarian cancer cells, cervical cancer cells, prostate cancer cells, renal cancer cells, cancer cells of the central nervous system, glioblastoma tumor cells, skin cancer cells, lymphoma cells, choriocarcinoma tumor cells, head and neck cancer cells, osteogenic sarcoma tumor cells, and blood cancer cells.
In vivo delivery of lipid particles such as SNALP encapsulating a nucleic acid ( e.g ., a cdsDNA) is suited for targeting cells of any cell type. The methods and compositions can be employed with cells of a wide variety of vertebrates, including mammals, such as, e.g., canines, felines, equines, bo vines, ovines, caprines, rodents (e.g., mice, rats, and guinea pigs), lagomorphs, swine, and primates (e.g. monkeys, chimpanzees, and humans).
AtuPLEX
AtuPLEX is a multi-lamellar (multiple lipid bilayer) and positively-charged siRNA- lipoplex that combines siRNA with three-lipid liposomes. This can be modified to deliver the subject cdsDNA for various purposes.
The liposomes contain proprietary cationic lipids AtuFectOl, co-lipids (fusogenic or stabilizing), and PEGylated lipids, to form a nanoparticle structure with nucleic acid (siRNA or cdsDNA) embedded within multiple lipid bilayers of the particle.
Thus in certain embodiments, the subject cdsDNA is formulated in a composition comprising a pharmaceutically acceptable carrier and a compound according to formula (I):
Figure imgf000049_0001
wherein Rl and R2 are each and independently selected from the group comprising alkyl;
n is any integer between 1 and 4;
R3 is an acyl selected from the group comprising lysyl, ornithyl, 2,4-diaminobutyryl, histidyl and an acyl moiety according to formula (II),
Figure imgf000049_0002
wherein m is any integer from 1 to 3 and Y is a pharmaceutically acceptable anion. In certain embodiments, Rl and R2 are each and independently selected from the group comprising lauryl, myristyl, palmityl and oleyl.
In certain embodiments, Rl is lauryl and R2 is myristyl; or Rl is palmityl and R2 is oleyl.
In certain embodiments, m is 1 or 2.
In certain embodiments, Y is selected from the group consisting of halogenids, acetate, and trifluoroacetate.
In certain embodiments, the compound is selected from the group consisting of:
Figure imgf000050_0001
In certain embodiments, the composition further comprises a pharmaceutically active component selected from the group consisting of peptides, proteins, oligonucleotides, polynucleotides, and nucleic acids.
In certain embodiments, the composition further comprises at least one helper lipid component selected from the group consisting of phospholipids and steroids. For example, the helper lipid component may be selected from the group consisting of l,2-diphytanoyl-sn- glycero-3-phosphoethanolamine and l,2-dioleyl-sn-glycero-3-phosphoethanolamine. In certain embodiments, the content of the helper lipid component is from about 20 mol % to about 80 mol % of the overall lipid content of the composition. In certain embodiments, at least one helper lipid comprises a moiety which is selected from the group consisting of a PEG, a HEG, a polyhydroxyethyl starch (polyHES), and a polypropylene. In certain embodiments, the helper lipid comprising the PEG moiety is selected from the group consisting of l,2-distearoyl-sn-glycero-3-phosphoethanolamine, l,2-dialkyl-sn-glycero-3- phosphoethanolamine, and Ceramide-PEG.
In certain embodiments, the composition comprising: a) 50 mol % of P-arginyl-2,3- diamino propionic acid-N-palmityl-N-oleyl-amide trihydrochloride, 48 mol % of 1,2- diphytanoyl-sn-glycero-3-phosphoethanolamine, and 2 mol % l,2-distearoyl-sn-glycero-3- phosphoethanolamine-PEG2000; or b) P-arginyl-2, 3-diamino propionic acid-N-palmityl-N- oleyl-amide trihydrochloride, 49 mol % l,2-diphytanoyl-sn-glycero-3-phosphoethanolamine, and 1 mol % l,2-distearoyl-sn-glycero-3-phosphoethanolamine-PEG2000.
In certain embodiments, the composition comprises: a) 50 mol % of P-arginyl-2,3- diamino propionic acid-N-palmityl-N-oleyl-amide trihydrochloride, 48 mol % of 1,2- diphytanoyl-sn-glycero-3-phosphoethanolamine, and 2 mol % N(Carbonyl- methoxypolyethylenglycol-2000)- 1 ,2-distearoyl-sn-glycero-3-pho-sphoethanolamine; or b)
50 mol % of P-arginyl-2, 3-diamino propionic acid-N-palmityl-N-oleyl-amide
trihydrochloride, 49 mol % l,2-diphytanoyl-sn-glycero-3-phosphoethanolamine, and 1 mol % N(Carbonyl-methoxypolyethylenglycol-2000)-l,2-distearoyl-sn-glycero-3-pho- spho ethano lamine .
In certain embodiments, the composition comprises: a) 50 mol % of P-L-arginyl-2,3- L-diamino propionic acid-N-palmityl-N-oleyl-amide trihydrochloride, 48 mol % of 1,2- diphytanoyl-sn-glycero-3-phosphoethanolamine, and 2 mol % N(Carbonyl- methoxypolyethylenglycol-2000)- 1 ,2-distearoyl-sn-glycero-3-pho-sphoethano lamine; or b)
50 mol % of P-L-arginyl-2,3-L-diamino propionic acid-N-palmityl-N-oleyl-amide trihydrochloride, 49 mol % l,2-diphytanoyl-sn-glycero-3-phosphoethanolamine, and 1 mol % N(Carbonyl-methoxypolyethylenglycol-2000)-l,2-distearoyl-sn-glycero-3-pho- spho ethano lamine .
Further suitable lipid compositions for producing the multiple lipid bilayers of the particle are described in U.S. Pat. Nos. 8,357,722, 8,017,804, and 9,486,538 (all incorporated by reference).
DACC
DACC is a lipid delivery system that includes AtuFectOl (see above) and is used to embed siRNAs into a multiple lipid bilayer structure. This system can also be modified to deliver the subject cdsDNA for various purposes.
While closely related to the AtuPLEX system, DACC has significantly different biopharmaceutical properties, and delivers nucleic acids to the pulmonary vascular endothelium. DBTC
DBTC is a lipid delivery system that delivers siRNA to hepatocytes and the hepatic vascular system of the liver parenchyma, rather than merely targeting liver hepatocytes. This system can also be modified to deliver the subject cdsDNA for various purposes.
The DBTC nanoparticles consist of a synthetic delivery system containing (i) a linear, cyclodextrin-based polymer (CDP), (ii) a human transferrin protein (hTf) targeting ligand displayed on the exterior of the nanoparticle to engage Tf receptors (hTfR) on the surface of the cancer cells, (iii) a hydrophilic polymer (polyethylene glycol (PEG) used to promote nanoparticle stability in biological fluids), and (iv) siRNA designed to reduce the expression of a target gene. See Davis et al, Nature 464(7291): 1067-1070, 2010 (incorporated by reference). This system can be modified by replacing the siRNA component with the subject cdsDNA. The system can also be modified by replacing targeting moiety such that delivery to other specific tissue sites can be accomplished. For example, for delivery to skeletal or cardiac muscle cells, the TfR can be replaced with a natural ligand for a receptor on skeletal or cardiovascular cells, or an antibody or fragment thereof specific for a marker on the skeletal or cardiovascular cells. The targeting moiety can also be derived from viruses that have the natural tropism desired ( e.g ., adenovirus type 5 knob protein for cardiomyocyte delivery). The same strategy can be used for any of the other targeted delivery of
nanoparticles described herein.
These nanoparticles have been shown to be well tolerated in multi-dosing studies in non-human primates, and can be systemically delivered to treat, for example, solid tumor.
RONDEL
RONDEL stands for RNAi/Oligonucleotide Nanoparticle Delivery. It is a platform that has been used in delivery of siRNA in clinical trials for treating solid tumors. RONDEL is a non-liposomal polymer-based nanoparticle re-optimized for in vivo siRNA delivery. It has four components that self-assemble into nanoparticles: (i) siRNA strands (which can be replaced with the cdsDNA of the invention), (ii) cyclodextrin-containing polymers (CDPs), (iii) polythethylene glycol (PEG) as steric stabilization agents, and (iv) human transferrin (Tf). Tf is a targeting ligand for binding to transferrin receptors (TfR) that are typically
upregulated on cancer cells. But this component can be replaced by any targeting moiety, such as antibody or antibody fragments specific for muscle cells or other target tissues. The CDPs are linear polycationic oligomers containing positively charged amidine groups alternating with sugar (cyclodextrin) moieties. The positively charged CDP polymer associates with the negatively charged backbone of nucleic acids (such as cdsDNA) to form nanoparticles less than 100 nm in diameter, with the nucleic acid at their cores and
cyclodextrin groups on their surfaces. Components (iii) and (iv) associate non-covalently with the hydrophobic cores in the CDP via a hydrophobic adamantine group covalently bound to one end of the PEG. The resulting complex is a nucleic acid containing
nanoparticle coated with PEG (stabilizer) and PEG-targeting ligands (such as TfR).
DPC
DPC (Dynamic PolyConjugates) is a class of non-liposomal, polymer conjugate-based nucleic acid ( e.g ., siRNA or cdsDNA) delivery platform. DPCs are small nanoparticles, 5-20 nm in size, containing the amphipathic endosomolytic polymer poly(butyl amino vinyl ether) (PBAVE), to which shielding agents (e.g., PEG) and targeting ligands are reversibly attached, and the nucleic acids are attached via a hydro lysable disulfide linker. While the membrane disrupting PBAVE polymer is masked by the PEG side chains, the PEG and targeting ligands are released in the acidic environment of the endosome to trigger endosomal release. Once in the reducing environment of the cytoplasm, the disulfide linkage is cleaved to release the nucleic acid (e.g., cdsDNA). See US Patent No. 8,501,930 (incorporated herein by reference).
An improved version of the DPC system takes advantage of atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT) to produce polymers that are homogeneous and amenable to large scale manufacturing. The nucleic acid within is not attached to the DPC polymer. Instead, the nucleic acid -cholesterol conjugate is co-injected with a melittin-like peptide that has reversibly masked
endosomolytic properties, similar to the PBAVE polymer.
SMARTICLES
SMARTICLES are amphoteric liposomes that are pH dependent charge-transitioning particles that provide therapeutic nucleic acids (e.g., cdsDNA) to cells by local or systemic administration. SMARTICLES are stable in blood and distribute in the same manner as conventional liposomes, but become positively charged when they cross cell membranes, leading to delivery of the nucleic acid payload within sites of inflammation, tumors, liver, and spleen.
DiLA2
DiLA (Di-alkylated Amino Acids) is a platform for creating liposome formulations from dialkylated amino acids for delivery of therapeutic nucleic acid (such as cdsDNA).
DiLA is Histidine-containing Di-alkylated Amino Acid based system that allows one to modify key aspects of the delivery system such as charge, linker and acyl chains to optimize the properties of the liposome. For example, DiLA allows one to optimize delivery to a target tissue of interest, and permits inclusion of peptides to improve a variety of delivery characteristics such as encapsulation of nanoparticles, cellular uptake, endosomal release and cell/tissue targeting. See Adami el al., An amino acid-based amphoteric liposomal delivery system for systemic administration of siRNA. Mol. Ther. 19:1141-1151, 2011 (incorporated by reference). Also see U.S. Patent Nos. 8,501,824, and 7,959,505 (incorporated herein by reference).
EnCore
EnCore is a nanoparticle system developed for delivery of nucleic acid payloads (such as cdsDNA), for delivering to the liver and solid tumors. EnCore contains a lipid-nucleic acid core surrounded by an envelope of a different lipid mixture that mediates accumulation, internalization, and release of nucleic acid payload into the target cell. This sub- structured particle is designed for preferential accumulation in tumors and provides high levels of payload delivery. See U.S. Patent No. 7,371,404 (incorporated herein by reference).
PRX
Polyrotaxane or PRX is a type of interlocked macromolecule made of multiple a- cyclodextrin rings, a PEG chain, and two bulky stoppers to physically prevent the rings from dethreading. PRX can self-assemble and condense nucleic acid into nanostructures. PRX has been demonstrated in mdx mice to successfully deliver plasmid, and data showed abundant plasmid distribution in most muscle tissues. Thus PRX can also be used to deliver the subject cdsDNA.
The process of the invention is partially carried out in an in vitro cell-free
environment, such as the protelomerase digestion and the downstream purification and formulation steps. Thus, the process is partly carried out in the absence of a host cell, and typically comprises use of purified enzymatic components. Accordingly, processing by protelomerase and other downstream operations are typically carried out by contacting the reaction components in solution in a suitable container. Optionally, particular components may be provided in immobilized form, such as attached to a solid support.
It should be understood that the process of the invention may be carried out at any scale. However, it is preferred that the process is carried out to produce any DNA fragment of interest at a commercial or industrial scale, i.e., generating amplified DNA fragment of interest in mg or greater quantities. In certain embodiments, the process generates at least 1 mg, at least 10 mg, at least 20 mg, at least 50 mg, or at least 100 mg of DNA fragment of interest. The final cdsDNA product may also be generated in mg or greater quantities. In certain embodiments, the process generates at least one mg, at least 2 mg, at least 5 mg, at least 10 mg, at least 20 mg, at least 50 mg, or at least 100 mg of cdsDNA.
7. Large Scale Manufacture
The LNPs and polymer NPs of the invention encompassing the subject cdsDNA can be manufactured using any art-recognized methods. In certain embodiments, the LNPs and polymer LPs can be manufactured using commercially available services and/or equipments, such as those provided by Precision Nanosystems (Vancouver, British Columbia).
In certain embodiments, the LNPs and NPs are prepared using the NanoAsseblr platform of Precision Nanosystems. The NanoAsseblr platform utilizes microfluidic mixing for the controlled, tuned and fully scalable manufacture of nanomedicines, including the LNPs and polymer NPs of the invention. It enables the rapid and controlled manufacture of nanomedicines (liposomes, lipid nanoparticles, polymeric nanoparticles) via custom- engineered microfluidic mixing cartridges that allow millisecond mixing of nanoparticle components at the nano litre scale. The platform allows users to control size by process and composition, and adjust parameters such as mixing ratio, flow rate and lipid composition in order to fine-tune nanoparticle size and encapsulation efficiency.
This system has been used in conjunction with the Neuro9™ Transfection kit (a Non viral transfection kit by Precision Nanosystems, Vancouver, British Columbia) to deliver siRNA and mRNA and pDNA to primary neurons both in vitro and in vivo , and achieve 95% cell transfection efficiency and 90% knockdown in transfected cells, with no observable toxicity.
Neuro9™ encapsulates and protects nucleic acids in a synthetic lipid nanoparticle (LNP) that mimics endogenous low density lipoproteins (LDLs), which are taken up naturally by cells like neurons, astrocytes and iPSCs. Neuro9 is pH-sensitive and engineered to release its contents into the cytoplasm. The Neuro9™ Transfection kit and related products can also be used to deliver the subject cdsDNA to specific target cells such as neurons.
In certain embodiments, the LNPs and polymer NPs of the invention are produced at a scaled up quantity of about 10 mL to 1 L, or up to 5 L, or up to 10 L, or up to 15 L, or up to 20 L, or up to 25 L, or up to 50 L or more LNPs and NPs formulations. The scale-up can be through microfluidic reactor parallelization, similar to the arraying of transistors on an integrated chip. In certain embodiments, the manufacture process is controlled by software or semi- / fully automated.
In certain embodiments, the manufacture is carried out in the NanoAssemblr Spark, which has an operating nanoparticle formulation volume of 25 - 250 pL.
In certain embodiments, the manufacture is carried out in the NanoAssemblr
Benchtop system, which is designed for rapid prototyping of novel nanoparticle formulations of 1 to l5mL, and has software control that enables the control of input mixing parameters for optimizing particle characteristics such as size and encapsulation efficiency.
In certain embodiments, the manufacture is carried out in the NanoAssemblr Blaze system suitable for clinical development. The system can manufacture between 10 mL and 1
L.
In certain embodiments, the manufacture is carried out in the NanoAssemblr Scale-Up system developed for manufacturing clinical trial nanoparticle materials in the cGMP environment. It provides seamless scale-up of formulations developed on the NanoAssemblr Benchtop and Blaze platforms. Processes developed on pre-clinical instruments are directly transferred to scale-up using identical microfluidic mixers connected in parallel. Parallel mixers enable the execution of identical processes producing a single large volume batch in less time. The Scale-up System with 8 microfluidic mixers running in parallel can produce nanoparticle formulation volumes suitable for early stage clinical trials.
8. Kits
The invention further provides a kit comprising components required to carry out the process of the invention. This kit comprises at least one protelomerase, and optionally instructions for use in a process as described herein. The kit may comprise two, three, four, five or more different protelomerase s. The protelomerases may be selected from any of SEQ ID NOs: 2, 4, 6, 8 or 10 or variants of any thereof. In certain embodiments, the kit comprises E. coli N15 TelN (SEQ ID NO: 10) or a variant thereof.
The kit may also comprise suitable buffers and other factors which are required for protelomerase enzyme performance or stability as described above. EXAMPLES
Example 1 Generation of cdsDNA Encompassing Gene of Interest
A Pucl9 backbone plasmid construct was prepared for amplifying a GFP reporter gene, including a GFP coding sequence under the control of a mammalian promoter and comprising a polyA coding sequence. In the plasmid construct, the GFP reporter gene is flanked by a pair of AAV2 ITR sequences, ITR1 and ITR2, respectively. Each ITR can be separated from the GFP reporter gene via Not I digestion due to the presence of Not I recognition sequences between the ITRs and the GFP reporter gene. The ITR-flanked GFP reporter gene is further flanked by two TelN recognition sequences, TelN-Left and TelN- Right.
Upon amplification and harvesting of the plasmid comprising the GFP construct, the plasmid was digested with the N6 protelomerase TelN to resolve the GFP construct into two cdsDNA, one comprising essentially the GFP reporter gene flanked by the ITRs, and further flanked by two half-sites of the TelN recognition sequences. The other cdsDNA comprises the rest of the plasmid backbone, flanked by the two half-sites of the TelN recognition sequences. See gel electrophoresis results in FIG. 3.
The GFP-containing cdsDNA can be recovered from the gel, or purified from the TelN digestion reaction directly for further use.
Example 2 Expression of cdsDNA-Encoded Gene of Interest
Purified cdsDNA comprising the GFP reporter gene (FIG. 4A) was transfected into C2C12 myotubes using standard molecular biology techniques, and GFP expression in the C2C12 myotubes (see FIG. 4B) was monitored over time.
As a control, Not I digested cdsDNA was similarly transfected into the C2C12 myotubes, so is a pCK8-GFP construct with an identical GFP reporter gene that is not flanked by the ITRs.
Though transfected cells displayed the same morphology under the phase contrast microscope, FITC images show strong expression of cdsDNA-encoded GFP transfected to the C2C12 cells, while Not I-digested GFP dsDN A- transfected cells have weak expression. The pCK8 GFP control also yielded poor expression compared to cdsDNA-transfected cells.
It was determined that transfection efficiency is about 60% for the cdsDNA-encoded GFP, and GFP expression became stronger as the myotubes matured. See FIG. 4C. Example 3 cdsDNA-Encoded Gene of Interest is Protected from Exonuclease Digestion
To test the integrity of the cdsDNA, the plasmid construct of Example 1 was digested with TelN and/or exonuclease under several conditions, and the digestion products were resolved on gel electrophoresis. See FIGs. 5A and 5B.
In FIG. 5A, in the first lane to the right of the size marker, 4 pg of circular plasmid DNA was digested with TelN in the absence of exonuclease, and the results showed that only the two expected cdsDNA products were present, one representing the cdsDNA comprising the GFP reporter gene.
In the lane to its right, the same experiment was carried out, except that exonuclease was added. The results showed that both cdsDNA products were resistant to exonuclease digestion, consistent with the expectation that the closed-end of the TelN digestion products protected the cdsDNA from exonuclease digestion.
However, when the input DNA is not circular but instead linearized prior to protelomerase digestion, the linearized plasmid backbone is not resistant to exonuclease digestion, while the cdsDNA (marked as SFiD in the figure) remained resistant to
exonuclease.
In a similar set of experiments, the results of which were shown in FIG. 5B, 2 pg of input plasmid DNA was used instead, with increasing amounts of exonucleases, except that the input plasmid DNA was first linearized with Xba I, which digests the plasmid construct of Example 1 once outside the GFP construct and the TelN recognition sites. As a result of TelN digestion, the cdsDNA comprising the GFP construct is intact, while the would-be cdsDNA encompassing the rest of the plasmid backbone was bisected by the Xba I digestion, resulting in two linear dsDNA with only one closed-end. Such digestion products were susceptible to exonuclease digestion. See the 3rd - the 5th lanes to the right of the size marker in FIG. 5B.
This experiment demonstrates that, in a manufacture process outlines in FIG. 6, after the protelomerase digestion, exonuclease can be used to remove the contaminating plasmid backbone cdsDNA, thus facilitating the purification of the cdsDNA encompassing the GOI.
Example 4 In vitro Expression of cdsDNA-Encoded Microdystrophin in Cells
This example demonstrates that the cdsDNA constructs of the invention can be used to express an exogenous transgene in vitro , in C2C12 cells were transfected by a cdsDNA construct named SLiD-MD44 using the VIAFECT™ Transfection Reagent (Promega Corp., WI) according to the manufacturer’s recommendation.
SLiD-MD44 encodes a 5-repeat microdystrophin protein that contains, from N- to C- terminus, the N-terminal actin binding domain, Hinge region 1 (Hl), specctrin-like repeats Rl, R16, R17, R23, and R24, Hinge region 4 (H4), and the C-terminal dystroglycan binding domain of the human full-length dystrophin protein. The protein sequence of this 5-repeat microdystrophin and the related dystrophin minigene are described in WO2016/115543 (incorporated herein by reference).
FIG. 7A shows that the subject cdsDNA is resistant to exonuclease III digestion. Restriction and protelomerase digestion of the plasmid comprising the 5-repeat
microdystrophin protein coding sequence (SLiD-MD44) generated multiple bands resolved on electrophoresis, only one of the bands matching the expected size of the subject cdsDNA (i.e., MD44) appeared resistant to exonuclease III digestion, confirming the co-valently linked terminal structures in the protelomerase digestion product.
The isolated cdsDNA SLiD-MD44 was then transfected into cultured C2C12 cells using the VIAFECT™ Transfection Reagent, and immunofluorescent staining was used to reveal the cytoskeleton (anti-F-actin antibody staining), the nuclei (Haematoxylin staining), and any expressed 5-repeat microdystrophin protein (anti-DysB antibody). It is apparent that C2C12 cells transfected by the subject cdsDNA encoding a 5-repeat microdystrophin protein had robust expression of the 5-repeat microdystrophin protein. Meanwhile, control transfection with no DNA generated no signal when the same anti-DysB antibody was used.
Example 5 In vivo Expression of cdsDNA-Encoded Microdystrophin in mdx Mice
This example demonstrates that the cdsDNA constructs of the invention can be used to express an exogenous transgene in vivo, specifically, expression of an exogenous microdystrophin gene in the mdx mouse model of DMD.
A cdsDNA construct named SLiD-MD4 was prepared to encoding a 5-repeat microdystrophin as in Example 4. About 40 pg of SLiD-MD4 cdsDNA was then introduced into an mdx mouse via intramuscular electroporation (IM Electroporation). As a control, saline solution was used instead of the SLiD-MD4 cdsDNA construct.
Purified SLiD-MD4 cdsDNA construct was formulated in 150 mM of NaCl at 2 pg/pF, and was stored at -20°C till use. Hyaluronidase (Sigma, H-4272) was formulated in PBS at 2 mg/mL, and 1 mL aliquots were stored at -20°C till use.
For electroporation, SLiD-MD4 and hyaluronidase stocks were thawed. An mdx mouse was anesthetized through inhalation of 2-3% isoflurane. Mouse hindlegs were shaved at where tibialis anterior muscles are. A 50 pL of hyaluronidase was then injected directly into the tibialis anterior muscle by entering at the middle of the muscle with a 0.3 mL tuberculin syringe. Materials were injected slowly, and the needle was retracted slowly after injection. About 2 hours after hyaluronidase injection, 60 pg of SLiD-MD4 cdsDNA- containing construct in 30 pL was injected directly into the tibialis anterior muscle by entering the needle at the middle of the muscle with a tuberculin syringe. Materials were injected slowly, and the needle was retracted slowly after injection. Immediately after the DNA injection, the mdx mouse underwent electroporation using a BTX AgilePulse ID
Electroporator and a 5 mm, 4-needle-array electrode (BTX, 47-0045). The DNA injection site was positioned in between the 2 parallel arrays of needles, which were inserted through skin and into the tibialis anterior muscle until the estimated load reading is < 3000 ohms. Perform electroporation using the following setting.
Figure imgf000060_0001
Tibialis anterior muscles were collected 7 days after injection for analysis.
Immunofluorescent staining using the anti-DysB mouse monoclonal antibody (Leica Biosystems, Prod. Code: NCL-DYSB) was then used to verify microdystrophin expression in muscle tissues isolated from the mdx mouse electroporated by the SLiD-MD4 cdsDNA construct. The antibody was raised against residues 321-494 of the human dystrophin protein.
FIG. 8B shows wide-spread fluorescent signal representing robust dystrophin expression in mdx mouse receiving the SLiD-MD4 cdsDNA construct through IM
electroporation. An enlarged portion of FIG. 8B is shown in FIG. 9B, in which dystrophin expression was observed along the correct subcellular localization around the plasma membrane, suggesting that the exogenous microdystrophin is not only successfully and widely expressed in the muscle tissue of the mdx mouse, but is also likely to be functional due to the correct folding and correct subcellular localization. In contrast, control mouse receiving saline control through the same procedure only had background level signal. See FIG. 8A, and similarly enlarged section in FIG. 9A.
FIG. 10 shows that the expression of the exogenous microdystrophin gene persisted after 7 days post IM electroporation. In this experiment, 60 pg of the same SLiD-MD4 cdsDNA construct was used in mdx mouse via IM electroporation. Immuno staining was performed 7 days post electroporation, using both an anti-DysB monoclonal antibody labeled by a red fluorescent signal, and an anti- laminin monoclonal antibody labeled by a green fluorescent signal.

Claims

WE CLAIM:
1. A DNA construct comprising:
(1) a backbone sequence comprising sequences supporting self-replication in a eukaryotic (e.g., mammalian) or prokaryotic cell;
(2) an insert comprising:
(a) a DNA fragment of interest;
(b) a pair of end sequences flanking the DNA fragment of interest,
wherein the end sequences are inverted terminal repeats (ITRs) of double- stranded DNA viruses, long terminal repeats (LTRs) or internal repeats of DNA virus (such as HSV), or telomere sequences; and,
(c) a pair of protelomerase recognition sequences flanking the pair of ITR or LTR.
2. The DNA construct of claim 1, wherein at least one of said protelomerase recognition sequences comprises a perfect inverted repeat DNA sequence of at least 14 bp in length, or a variant thereof.
3. The DNA construct of claim 1, wherein at least one of said protelomerase recognition sequences comprises a 22 bp consensus sequence for a mesophilic bacteriophage perfect inverted repeat.
4. The DNA construct of claim 1, wherein at least one of said protelomerase recognition sequences is from E. coli phage N15 (such as the one recognized by E. coli N15 TelN protelomerase), agrobacterium Klebsiella phage Phi K02, Yersinia phage PY54, Halomonas phage phiHAP-l, and Vibrio phage VP882, or Borrelia burgdorferi.
5. The DNA construct of claim 1, wherein at least one of said protelomerase recognition sequences comprises a perfect inverted repeat at least 30, at least 40, at least 60, at least 80 or at least 100 base pairs in length.
6. The DNA construct of claim 1, wherein said DNA fragment of interest comprises a coding sequence of interest under the control of /operably linked to a eukaryotic promoter and/or enhancer, and optionally a eukaryotic transcription termination sequence.
7. The DNA construct of claim 6, wherein said coding sequence of interest comprises a DNA vaccine that encodes an antigen: (1) for the treatment or prevention of conditions such as cancer, allergies, toxicity and infection by a pathogen ( e.g ., fungi, viruses such as Human Papilloma Viruses (HPV), HIV, HSV2/HSV1, Influenza virus (types A, B and C), Polio virus, RSV virus, Rhinoviruses, Rotaviruses, Hepatitis A virus, Norwalk Virus Group, Enteroviruses, Astroviruses, Measles virus, Parainfluenza virus,
Mumps virus, Varicella- Zoster virus, Cytomegalovirus, Epstein-Barr virus, Adenoviruses, Rubella virus, Human T-cell Lymphoma type I virus (HTLV-I), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Hepatitis D virus, Pox virus, Marburg and Ebola); bacteria (such as Mycobacterium tuberculosis, Chlamydia, Neisseria gonorrhoeae, Shigella, Salmonella, Vibrio cholerae, Treponema pallidum, Pseudomonas, Bordetella pertussis, Brucella, Francisella tularensis, Helicobacter pylori, Leptospira interrogans, Legionella
pneumophila, Yersinia pestis, Streptococcus (types A and B), Pneumococcus, Meningococcus, Haemophilus influenza (type b), Toxoplasma gondii,
Campylobacteriosis, Moraxella catarrhalis, Donovanosis, and Actinomycosis); fungal pathogens (such as Candidiasis and Aspergillosis); parasitic pathogens (such as Taenia, Flukes, Roundworms, Amoebiasis, Giardiasis,
Cryptosporidium, Schistosoma, Pneumocystis carinii, Trichomoniasis and Trichinosis);
(2) from a member of the adenoviridae (e.g., a human adenovirus), herpesviridae (e.g., HSV-l, HSV-2, EBV, CMV and VZV), papovaviridae (e.g., HPV), poxyiridae (e.g., smallpox and vaccinia), parvoviridae (e.g., parvovirus B19), reoviridae (e.g., a rotavirus), coronaviridae (e.g., SARS), flaviviridae (e.g., yellow fever, West Nile virus, dengue, hepatitis C and tick-borne encephalitis), picornaviridae (e.g., polio, rhino virus, and hepatitis A), togaviridae (e.g., rubella virus), filoviridae (e.g., Marburg and Ebola), paramyxoviridae (e.g., a parainfluenza virus, respiratory syncytial virus, mumps and measles), rhabdoviridae (e.g., rabies virus), bunyaviridae (e.g., Hantaan virus), orthomyxoviridae (e.g., influenza A, B and C viruses), retro viridae (e.g., HIV and HTLV) and hepadnaviridae (e.g., hepatitis B);
(3) from a pathogen responsible for a veterinary disease, such as a viral pathogen, a Reo virus (e.g., African Horse sickness or Bluetongue virus) and Herpes viruses (e.g., equine herpes), a Foot and Mouth Disease virus, a Tick borne encephalitis virus, a dengue virus, SARS, a West Nile virus and a Hantaan virus;
(4) from an immunodeficiency virus, such as SIV or a feline immunodeficiency virus;
(5) that is a neo-antigen ( e.g ., encoded by mutated genes in cancers / tumors), a tumor antigen, such as testes antigen (e.g., members of the MAGE family (MAGE 1, 2, 3 etc), NY-ESO-l and SSX-2), differentiation antigens (e.g., tyrosinase, gplOO, PSA, Her-2 and CEA), mutated self antigens, and viral tumor antigens (e.g., E6 and/or E7 from oncogenic HPV types), MART-l, Melan-A, p97, beta-HCG, GalNAc, MAGE-l, MAGE-2, MAGE-4, MAGE- 12, MUC1, MUC2, MUC3, MUC4, MUC18, CEA, DDC, P1A, EpCam, melanoma antigen gp75, Hker 8, high molecular weight melanoma antigen, K19, Tyrl, Tyr2, members of the pMel 17 gene family, c-Met, PSM (prostate mucin antigen), PSMA (prostate specific membrane antigen), prostate secretary protein, alpha- fetoprotein, CA 125, CA 19.9, TAG-72, BRCA-l and BRCA-2 antigen.
8. The DNA construct of claim 6, wherein said coding sequence of interest comprises a therapeutic DNA molecule for gene therapy, wherein said therapeutic DNA molecule:
(1) expresses a functional gene in a subject having a genetic disorder caused by a dysfunctional version of said functional gene (e.g., gene for Duchenne muscular dystrophy, cystic fibrosis, Gaucher’s Disease, and adenosine deaminase (ADA) deficiency, inflammatory diseases, autoimmune, chronic and infectious diseases, AIDS, cancer, neurological diseases, cardiovascular disease, hypercholesterolemia, various blood disorders (including various anaemias, thalassemia and haemophilia, and emphysema), and solid tumors);
(2) encodes toxic peptides (i.e., chemotherapeutic agents such as ricin, diphtheria toxin and cobra venom factor), tumor suppressor genes (such as p53), genes coding for mRNA sequences which are antisense to transforming oncogenes, antineoplastic peptides such as tumor necrosis factor (TNF) and other cytokines, or transdominant negative mutants of transforming oncogenes;
(3) encodes an active RNA form (e.g., a small interfering RNA (siRNA, miRNA, shRNA), or a small activating RNA (saRNA); or, (4) encodes a CRISPR/Cas component (such as a Cas9 enzyme or an sgRNA).
9. A closed-end double stranded DNA (cdsDNA) produced by contacting the DNA
construct of any one of claims 1-8 with a protelomerase that recognizes said pair of protelomerase recognition sequences.
10. A closed-end double stranded DNA (cdsDNA) comprising:
(a) a DNA fragment of interest;
(b) a pair of end sequences flanking the DNA fragment of interest, wherein the end sequences are inverted terminal repeats (ITRs) of double- stranded DNA viruses, long terminal repeats (LTRs) or internal repeats of DNA virus (such as HSV), or telomere sequences; and,
(c) a pair of half protelomerase recognition sequences flanking the pair of end sequences, wherein each of said half protelomerase recognition sequences forms one closed-end of said cdsDNA.
11. A pharmaceutical composition comprising the cdsDNA of claim 9 or 10.
12. The pharmaceutical composition of claim 11, wherein said cdsDNA is encompassed by a nanoparticle.
13. The pharmaceutical composition of claim 12, wherein said nanoparticle is SNALP (stable nucleic acid-lipid particle), AtuPLEX, DACC, DBTC, RONDEL, DPC (Dynamic PolyConjugate), SMARTICLE, DiLA2, or EnCore.
14. A method of producing a cell-free closed-end double stranded DNA (cdsDNA), the method comprising:
(1) isolating the DNA construct of any one of claims 1-8 after amplifying said DNA construct in said eukaryotic ( e.g ., mammalian) or prokaryotic cell;
(2) linearizing the DNA construct with an endonuclease that does not digest
within the insert;
(3) contacting the DNA construct with a protelomerase that recognizes said pair of protelomerase recognition sequences to release the cdsDNA;
(4) after steps (2) and (3), removing linearized DNA construct or fragment thereof that are not cdsDNA with an exonuclease;
(5) enriching or purifying the cdsDNA.
15. The method of claim 14, wherein steps (2) and (3) are carried out in any order or simultaneously, both after step (1).
16. A method of producing a closed-end double stranded DNA (cdsDNA), the method comprising:
(1) isolating the DNA construct of any one of claims 1-8 after amplifying said DNA construct in said eukaryotic ( e.g ., mammalian) or prokaryotic cell;
(2) contacting the DNA construct with a protelomerase that recognizes said pair of protelomerase recognition sequences to release the cdsDNA;
(3) enriching or purifying the cdsDNA.
17. The method of any one of claims 14-16, further comprising encapsulating the
cdsDNA in a nanoparticle (such as SNALP, AtuPLEX, DACC, DBTC, RONDEL, DPC, SMARTICLE, DiLA2, or EnCore).
18. A method of delivering a target gene of interest (GOI) into a target cell, the method comprising contacting the target cell with a composition comprising the cdsDNA of claim 10.
19. The method of claim 18, wherein the target cell is contacted in vitro , ex vivo , or in vivo.
20. The method of claim 18, wherein the target GOI is a wild-type, mini- or micro
dystrophin gene or a gene in a DMA pathway or related to a genetic modifier of DMD, and wherein the target cell is a muscle (e.g., skeletal muscle such as a tibialis anterior muscle cell, cardiac muscle, or smooth muscle) cell in a human.
21. Use of a composition comprising the cdsDNA of claim 10, or the pharmaceutical
composition of any one of claims 11-13, in the manufacture of a medicament for delivering a target gene of interest (GOI) into a target cell in vivo.
PCT/US2018/065609 2017-12-14 2018-12-14 Non-viral production and delivery of genes WO2019118806A1 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762598532P 2017-12-14 2017-12-14
US62/598,532 2017-12-14

Publications (1)

Publication Number Publication Date
WO2019118806A1 true WO2019118806A1 (en) 2019-06-20

Family

ID=65234649

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2018/065609 WO2019118806A1 (en) 2017-12-14 2018-12-14 Non-viral production and delivery of genes

Country Status (2)

Country Link
TW (1) TW201936201A (en)
WO (1) WO2019118806A1 (en)

Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2020092904A1 (en) * 2018-11-02 2020-05-07 Nikegen, Llc Recombinant parvoviral vectors and method of making and use thereof
CN112143726A (en) * 2020-09-08 2020-12-29 华东理工大学 Escherichia coli-affinity phage symbiotic biofilm immobilized display method
WO2021123062A1 (en) * 2019-12-20 2021-06-24 Keygene N.V. Ngs library preparation using covalently closed nucleic acid molecule ends
WO2021152146A1 (en) * 2020-01-31 2021-08-05 Tyris Therapeutics, S.L. Process for the production of closed linear dna
WO2021257595A1 (en) 2020-06-15 2021-12-23 Research Institute At Nationwide Children's Hospital Adeno-associated virus vector delivery for muscular dystrophies
CN114231596A (en) * 2021-12-12 2022-03-25 徐州医科大学 Gene detection method based on CRISPR/dcas9 and magnetic nano material and application
WO2022156188A1 (en) * 2021-01-22 2022-07-28 Nanjing GenScript Biotech Co., Ltd. Method for producing target dna sequence and cloning vector
US11535868B2 (en) 2020-04-29 2022-12-27 Bristol-Myers Squibb Company Miniaturized dystrophins having spectrin fusion domains and uses thereof
EP4108263A2 (en) 2021-06-02 2022-12-28 Research Institute at Nationwide Children's Hospital Recombinant adeno-associated virus products and methods for treating limb girdle muscular dystrophy 2a
EP4124348A1 (en) * 2021-07-30 2023-02-01 4basebio UK Ltd Nanoparticles for cell delivery
WO2023006985A1 (en) * 2021-07-30 2023-02-02 4Basebio Uk Ltd Nanoparticles and peptides for the delivery of cargos to muscle cells

Citations (37)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US3993754A (en) 1974-10-09 1976-11-23 The United States Of America As Represented By The United States Energy Research And Development Administration Liposome-encapsulated actinomycin for cancer chemotherapy
US4145410A (en) 1976-10-12 1979-03-20 Sears Barry D Method of preparing a controlled-release pharmaceutical preparation, and resulting composition
US4224179A (en) 1977-08-05 1980-09-23 Battelle Memorial Institute Process for the preparation of liposomes in aqueous solution
US4235871A (en) 1978-02-24 1980-11-25 Papahadjopoulos Demetrios P Method of encapsulating biologically active materials in lipid vesicles
US4522803A (en) 1983-02-04 1985-06-11 The Liposome Company, Inc. Stable plurilamellar vesicles, their preparation and use
US4588578A (en) 1983-08-08 1986-05-13 The Liposome Company, Inc. Lipid vesicles prepared in a monophase
US5264618A (en) 1990-04-19 1993-11-23 Vical, Inc. Cationic lipids for intracellular delivery of biologically active molecules
US5286634A (en) 1989-09-28 1994-02-15 Stadler Joan K Synergistic method for host cell transformation
WO1996015811A1 (en) 1994-11-17 1996-05-30 Imperial College Of Science, Technology & Medicine Internalisation of dna, using conjugates of poly-l-lysine and an integrin receptor ligand
US5580579A (en) 1995-02-15 1996-12-03 Nano Systems L.L.C. Site-specific adhesion within the GI tract using nanoparticles stabilized by high molecular weight, linear poly (ethylene oxide) polymers
US5641515A (en) 1995-04-04 1997-06-24 Elan Corporation, Plc Controlled release biodegradable nanoparticles containing insulin
US5725871A (en) 1989-08-18 1998-03-10 Danbiosyst Uk Limited Drug delivery compositions comprising lysophosphoglycerolipid
US5756353A (en) 1991-12-17 1998-05-26 The Regents Of The University Of California Expression of cloned genes in the lung by aerosol-and liposome-based delivery
US5780045A (en) 1992-05-18 1998-07-14 Minnesota Mining And Manufacturing Company Transmucosal drug delivery device
US5792451A (en) 1994-03-02 1998-08-11 Emisphere Technologies, Inc. Oral drug delivery compositions and methods
US5804212A (en) 1989-11-04 1998-09-08 Danbiosyst Uk Limited Small particle compositions for intranasal drug delivery
WO2002072616A2 (en) 2001-03-14 2002-09-19 Ich Productions Limited Transfection complexes
US20030077829A1 (en) 2001-04-30 2003-04-24 Protiva Biotherapeutics Inc.. Lipid-based formulations
WO2004002453A1 (en) 2002-06-28 2004-01-08 Protiva Biotherapeutics Ltd. Method and apparatus for producing liposomes
WO2004108938A2 (en) 2003-06-06 2004-12-16 Ich Productions Limited Peptide ligands of dendritic cells for nucleic acid vector targeting
WO2005007196A2 (en) 2003-07-16 2005-01-27 Protiva Biotherapeutics, Inc. Lipid encapsulated interfering rna
WO2005120152A2 (en) 2004-06-07 2005-12-22 Protiva Biotherapeutics, Inc. Cationic lipids and methods of use
WO2005121348A1 (en) 2004-06-07 2005-12-22 Protiva Biotherapeutics, Inc. Lipid encapsulated interfering rna
US7371404B2 (en) 2001-02-21 2008-05-13 Novosom Ag Amphoteric liposomes and their use
WO2009127060A1 (en) 2008-04-15 2009-10-22 Protiva Biotherapeutics, Inc. Novel lipid formulations for nucleic acid delivery
WO2010086626A1 (en) * 2009-01-30 2010-08-05 Touchlight Genetics Limited Production of closed linear dna
US7803397B2 (en) 2003-09-15 2010-09-28 Protiva Biotherapeutics, Inc. Polyethyleneglycol-modified lipid compounds and uses thereof
US7959505B2 (en) 2005-11-22 2011-06-14 Labtronix Concept Inc. Evaluation-structure base game feature persisting over a number of outcomes
US8017804B2 (en) 2004-05-05 2011-09-13 Silence Therapeutics Ag Lipids, lipid complexes and use thereof
WO2012000104A1 (en) 2010-06-30 2012-01-05 Protiva Biotherapeutics, Inc. Non-liposomal systems for nucleic acid delivery
WO2012017210A1 (en) * 2010-08-04 2012-02-09 Touchlight Genetics Limited Production of closed linear dna using a palindromic sequence
US8501824B2 (en) 2007-05-04 2013-08-06 Marina Biotech, Inc. Amino acid lipids and uses thereof
US8501930B2 (en) 2010-12-17 2013-08-06 Arrowhead Madison Inc. Peptide-based in vivo siRNA delivery system
US8569256B2 (en) 2009-07-01 2013-10-29 Protiva Biotherapeutics, Inc. Cationic lipids and methods for the delivery of therapeutic agents
US9018187B2 (en) 2009-07-01 2015-04-28 Protiva Biotherapeutics, Inc. Cationic lipids and methods for the delivery of therapeutic agents
WO2016115543A2 (en) 2015-01-16 2016-07-21 University Of Washington Novel micro-dystrophins and related methods of use
WO2017152090A2 (en) 2016-03-04 2017-09-08 Shire Human Genetic Therapies, Inc. Recombinant follistatin-fc fusion proteins and use in treating duchenne muscular dystrophy

Patent Citations (46)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US3993754A (en) 1974-10-09 1976-11-23 The United States Of America As Represented By The United States Energy Research And Development Administration Liposome-encapsulated actinomycin for cancer chemotherapy
US4145410A (en) 1976-10-12 1979-03-20 Sears Barry D Method of preparing a controlled-release pharmaceutical preparation, and resulting composition
US4224179A (en) 1977-08-05 1980-09-23 Battelle Memorial Institute Process for the preparation of liposomes in aqueous solution
US4235871A (en) 1978-02-24 1980-11-25 Papahadjopoulos Demetrios P Method of encapsulating biologically active materials in lipid vesicles
US4522803A (en) 1983-02-04 1985-06-11 The Liposome Company, Inc. Stable plurilamellar vesicles, their preparation and use
US4588578A (en) 1983-08-08 1986-05-13 The Liposome Company, Inc. Lipid vesicles prepared in a monophase
US5725871A (en) 1989-08-18 1998-03-10 Danbiosyst Uk Limited Drug delivery compositions comprising lysophosphoglycerolipid
US5286634A (en) 1989-09-28 1994-02-15 Stadler Joan K Synergistic method for host cell transformation
US5804212A (en) 1989-11-04 1998-09-08 Danbiosyst Uk Limited Small particle compositions for intranasal drug delivery
US5264618A (en) 1990-04-19 1993-11-23 Vical, Inc. Cationic lipids for intracellular delivery of biologically active molecules
US5756353A (en) 1991-12-17 1998-05-26 The Regents Of The University Of California Expression of cloned genes in the lung by aerosol-and liposome-based delivery
US5780045A (en) 1992-05-18 1998-07-14 Minnesota Mining And Manufacturing Company Transmucosal drug delivery device
US5792451A (en) 1994-03-02 1998-08-11 Emisphere Technologies, Inc. Oral drug delivery compositions and methods
WO1996015811A1 (en) 1994-11-17 1996-05-30 Imperial College Of Science, Technology & Medicine Internalisation of dna, using conjugates of poly-l-lysine and an integrin receptor ligand
US5580579A (en) 1995-02-15 1996-12-03 Nano Systems L.L.C. Site-specific adhesion within the GI tract using nanoparticles stabilized by high molecular weight, linear poly (ethylene oxide) polymers
US5641515A (en) 1995-04-04 1997-06-24 Elan Corporation, Plc Controlled release biodegradable nanoparticles containing insulin
US7371404B2 (en) 2001-02-21 2008-05-13 Novosom Ag Amphoteric liposomes and their use
WO2002072616A2 (en) 2001-03-14 2002-09-19 Ich Productions Limited Transfection complexes
US20030077829A1 (en) 2001-04-30 2003-04-24 Protiva Biotherapeutics Inc.. Lipid-based formulations
US9492386B2 (en) 2002-06-28 2016-11-15 Protiva Biotherapeutics, Inc. Liposomal apparatus and manufacturing methods
WO2004002453A1 (en) 2002-06-28 2004-01-08 Protiva Biotherapeutics Ltd. Method and apparatus for producing liposomes
US7901708B2 (en) 2002-06-28 2011-03-08 Protiva Biotherapeutics, Inc. Liposomal apparatus and manufacturing methods
WO2004108938A2 (en) 2003-06-06 2004-12-16 Ich Productions Limited Peptide ligands of dendritic cells for nucleic acid vector targeting
WO2005007196A2 (en) 2003-07-16 2005-01-27 Protiva Biotherapeutics, Inc. Lipid encapsulated interfering rna
US7982027B2 (en) 2003-07-16 2011-07-19 Protiva Biotherapeutics, Inc. Lipid encapsulated interfering RNA
US8936942B2 (en) 2003-09-15 2015-01-20 Protiva Biotherapeutics, Inc. Polyethyleneglycol-modified lipid compounds and uses thereof
US7803397B2 (en) 2003-09-15 2010-09-28 Protiva Biotherapeutics, Inc. Polyethyleneglycol-modified lipid compounds and uses thereof
US9486538B2 (en) 2004-05-05 2016-11-08 Silence Therapeutics Gmbh Lipids, lipid complexes and use thereof
US8357722B2 (en) 2004-05-05 2013-01-22 Silence Therpeutics AG Lipids, lipid complexes and use thereof
US8017804B2 (en) 2004-05-05 2011-09-13 Silence Therapeutics Ag Lipids, lipid complexes and use thereof
WO2005121348A1 (en) 2004-06-07 2005-12-22 Protiva Biotherapeutics, Inc. Lipid encapsulated interfering rna
WO2005120152A2 (en) 2004-06-07 2005-12-22 Protiva Biotherapeutics, Inc. Cationic lipids and methods of use
US7799565B2 (en) 2004-06-07 2010-09-21 Protiva Biotherapeutics, Inc. Lipid encapsulated interfering RNA
US9181545B2 (en) 2004-06-07 2015-11-10 Protiva Biotherapeutics, Inc. Lipid encapsulating interfering RNA
US7959505B2 (en) 2005-11-22 2011-06-14 Labtronix Concept Inc. Evaluation-structure base game feature persisting over a number of outcomes
US8501824B2 (en) 2007-05-04 2013-08-06 Marina Biotech, Inc. Amino acid lipids and uses thereof
WO2009127060A1 (en) 2008-04-15 2009-10-22 Protiva Biotherapeutics, Inc. Novel lipid formulations for nucleic acid delivery
US9109250B2 (en) 2009-01-30 2015-08-18 Vanessa Hill Production of closed linear DNA
WO2010086626A1 (en) * 2009-01-30 2010-08-05 Touchlight Genetics Limited Production of closed linear dna
US9018187B2 (en) 2009-07-01 2015-04-28 Protiva Biotherapeutics, Inc. Cationic lipids and methods for the delivery of therapeutic agents
US8569256B2 (en) 2009-07-01 2013-10-29 Protiva Biotherapeutics, Inc. Cationic lipids and methods for the delivery of therapeutic agents
WO2012000104A1 (en) 2010-06-30 2012-01-05 Protiva Biotherapeutics, Inc. Non-liposomal systems for nucleic acid delivery
WO2012017210A1 (en) * 2010-08-04 2012-02-09 Touchlight Genetics Limited Production of closed linear dna using a palindromic sequence
US8501930B2 (en) 2010-12-17 2013-08-06 Arrowhead Madison Inc. Peptide-based in vivo siRNA delivery system
WO2016115543A2 (en) 2015-01-16 2016-07-21 University Of Washington Novel micro-dystrophins and related methods of use
WO2017152090A2 (en) 2016-03-04 2017-09-08 Shire Human Genetic Therapies, Inc. Recombinant follistatin-fc fusion proteins and use in treating duchenne muscular dystrophy

Non-Patent Citations (39)

* Cited by examiner, † Cited by third party
Title
"REMINGTON'S PHARMACEUTICAL SCIENCES", 1985, MACK PUBLISHING COMPANY
"REMINGTON'S PHARMACEUTICAL SCIENCES", 1991, MACK PUB. CO.
ADAMI ET AL.: "An amino acid-based amphoteric liposomal delivery system for systemic administration of siRNA", MOL. THER., vol. 19, 2011, pages 1141 - 1151, XP055261119, DOI: doi:10.1038/mt.2011.56
ALTSCHUL S. F., J MOL EVOL, vol. 36, 1993, pages 290 - 300
ALTSCHUL, S, F ET AL., J MOL BIOL, vol. 215, 1990, pages 403 - 10
BEHR, ACC. CHEM. RES., vol. 26, 1993, pages 21
BRIGHAM ET AL., AM. J. SCI., vol. 298, 1989, pages 278
CULVER: "HUMAN GENE THERAPY", 1994, MARYANN LIEBERT, INC., pages: 70 - 71
CUNNINGHAM ET AL.: "Evaluation of a porcine model for pulmonary gene transfer using a novel synthetic vector", J GENE MED, vol. 4, 2002, pages 438 - 46
DAVIS ET AL., NATURE, vol. 464, no. 7291, 2010, pages 1067 - 1070
DENEKE ET AL., PNAS, vol. 97, 2000, pages 7721 - 7726
DEVEREUX ET AL., NUCLEIC ACIDS RESEARCH, vol. 12, 1984, pages 387 - 395
DU ET AL.: "The role of the helper lipid on the DNA transfection efficiency of lipopolyplex formulations", SCI REP., vol. 4, 2014, pages 7107
ERBACHER ET AL., GENE THERAPY, vol. 6, 1999, pages 138 - 145
FEIGNER ET AL., HUMAN GENE THERAPY, vol. 8, 1997, pages 511 - 512
FRESHNEY: "Culture of Animal Cells, a Manual of Basic Technique", 1994, WILEY-LISS
GROSSE ET AL.: "Tumor-specific gene transfer with receptor-mediated nanocomplexes modified by polyethylene glycol shielding and endosomally cleavable lipid and peptide linkers", F ASEB J., vol. 24, 2010, pages 2301 - 13
JENKINS ET AL.: "An integrin-targeted non-viral vector for pulmonary gene therapy", GENE THERAPY, vol. 7, 2000, pages 393 - 400
JENKINS ET AL.: "Formation of LID vector complexes in water alters physicochemical properties and enhances pulmonary gene expression in vivo", GENE THERAPY, vol. 10, 2003, pages 1026 - 34, XP008063708, DOI: doi:10.1038/sj.gt.3301963
KARLIN; ALTSCHUL, PROC. NATL. ACAD. SCI. USA, vol. 90, 1993, pages 5873 - 5787
KENNY ET AL.: "Multifunctional receptor-targeted nanocomplexes for the delivery of therapeutic nucleic acids to the Brain", BIOMATERIALS, vol. 34, 2013, pages 9190 - 200, XP028714753, DOI: doi:10.1016/j.biomaterials.2013.07.081
KUCHLER ET AL.: "Biochemical Methods in Cell Culture and Virology, Dowden", 1977, HUTCHINSON AND ROSS, INC.
MANNINO ET AL., BIOTECHNIQUES, vol. 6, 1988, pages 682
MANUNTA ET AL.: "Airway deposition of nebulized gene delivery nanocomplexes monitored by radioimaging agents", AM J RESPIR CELL MOL BIOL, vol. 49, 2013, pages 471 - 80
MANUNTA ET AL.: "Airway deposition of nebulized gene delivery nanocomplexes monitored by radioimaging agents", AM J RESPIR CELL MOL BIOL., vol. 49, 2013, pages 471 - 80
MANUNTA ET AL.: "Nebulisation of receptor-targeted nanocomplexes for gene delivery to the airway epithelium", PLOS ONE, vol. 6, 2011, pages e26768
MENG ET AL.: "Inhibition of neointimal hyperplasia in a rabbit vein graft model following non-viral transfection with human iNOS cDNA", GENE THER., vol. 20, 2013, pages 979 - 86
NAFISEH NAFISSI ET AL: "Construction and Characterization of an in-vivo Linear Covalently Closed DNA Vector Production System", MICROBIAL CELL FACTORIES,, vol. 11, no. 1, 6 December 2012 (2012-12-06), pages 154, XP021136155, ISSN: 1475-2859, DOI: 10.1186/1475-2859-11-154 *
NICOLAU ET AL., CRIT. REV. THER. DRUG CARRIER SYST., vol. 6, 1989, pages 239
OOI ET AL: "Recombineering linear DNA that replicate stably in E. coli", PLASMID, NEW YORK,NY, US, vol. 59, no. 1, 7 November 2007 (2007-11-07), pages 63 - 71, XP022428066, ISSN: 0147-619X, DOI: 10.1016/J.PLASMID.2007.09.002 *
PROC. NATL. ACAD. SCI. USA, vol. 84, 1987, pages 7413 - 7417
SCHROEDER ET AL., LIPID-BASED NANOTHERAPEUTICS FOR SIRNA DELIVERY. J INTERN MED., vol. 267, 2010, pages 9 - 21
STRAUBRINGER ET AL., METHODS ENZYMOL., vol. 101, 1983, pages 512
TAGALAKIS ET AL.: "A receptor-targeted nanocomplex vector system optimized for respiratory gene transfer", MOL THER., vol. 16, 2008, pages 907 - 15
TAGALAKIS ET AL.: "Biomaterials", RECEPTOR-TARGETED LIPOSOME - PEPTIDE NANOCOMPLEXES FOR SIRNA DELIVERY, vol. 32, 2011, pages 6302 - 15
TAGALAKIS ET AL.: "Integrin-targeted nanocomplexes for tumor specific delivery and therapy by systemic administration", BIOMATERIALS, vol. 32, 2011, pages 1370 - 6, XP027537935
WELSER ET AL.: "Gene delivery using ternary lipopolyplexes incorporating branched cationic peptides: the role of Peptide sequence and branching", MOL PHARM, vol. 10, 2013, pages 127 - 41
YIN ET AL., NON-VIRAL VECTORS FOR GENE-BASED THERAPY. NATURE REVIEWS GENETICS, vol. 15, 2014, pages 541 - 555
ZHAO; HUANG: "Lipid nanoparticles for gene delivery", ADV GENET., vol. 88, 2014, pages 13 - 36

Cited By (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2020092904A1 (en) * 2018-11-02 2020-05-07 Nikegen, Llc Recombinant parvoviral vectors and method of making and use thereof
WO2021123062A1 (en) * 2019-12-20 2021-06-24 Keygene N.V. Ngs library preparation using covalently closed nucleic acid molecule ends
WO2021152146A1 (en) * 2020-01-31 2021-08-05 Tyris Therapeutics, S.L. Process for the production of closed linear dna
US11535868B2 (en) 2020-04-29 2022-12-27 Bristol-Myers Squibb Company Miniaturized dystrophins having spectrin fusion domains and uses thereof
WO2021257595A1 (en) 2020-06-15 2021-12-23 Research Institute At Nationwide Children's Hospital Adeno-associated virus vector delivery for muscular dystrophies
CN112143726B (en) * 2020-09-08 2022-09-13 华东理工大学 Escherichia coli-affinity phage symbiotic biofilm immobilized display method
CN112143726A (en) * 2020-09-08 2020-12-29 华东理工大学 Escherichia coli-affinity phage symbiotic biofilm immobilized display method
WO2022156188A1 (en) * 2021-01-22 2022-07-28 Nanjing GenScript Biotech Co., Ltd. Method for producing target dna sequence and cloning vector
EP4108263A2 (en) 2021-06-02 2022-12-28 Research Institute at Nationwide Children's Hospital Recombinant adeno-associated virus products and methods for treating limb girdle muscular dystrophy 2a
EP4124348A1 (en) * 2021-07-30 2023-02-01 4basebio UK Ltd Nanoparticles for cell delivery
WO2023007017A1 (en) * 2021-07-30 2023-02-02 4Basebio Uk Ltd Nanoparticles for cell delivery
WO2023006985A1 (en) * 2021-07-30 2023-02-02 4Basebio Uk Ltd Nanoparticles and peptides for the delivery of cargos to muscle cells
CN114231596A (en) * 2021-12-12 2022-03-25 徐州医科大学 Gene detection method based on CRISPR/dcas9 and magnetic nano material and application
CN114231596B (en) * 2021-12-12 2023-11-21 徐州医科大学 Gene detection method based on CRISPR/dcas9 and magnetic nano material and application thereof

Also Published As

Publication number Publication date
TW201936201A (en) 2019-09-16

Similar Documents

Publication Publication Date Title
WO2019118806A1 (en) Non-viral production and delivery of genes
US20230365950A1 (en) Compositions and methods of use of crispr-cas systems in nucleotide repeat disorders
US8569065B2 (en) Compositions and methods for the delivery of biologically active RNAs
Zhang et al. Cationic compounds used in lipoplexes and polyplexes for gene delivery
US20220290186A1 (en) Gene editing using a modified closed-ended dna (cedna)
US9890391B2 (en) RNA vector with an open reading frame, an albumin 3′-UTR, and a histone stem loop
JP2022546597A (en) Lipid nanoparticle compositions comprising closed-end DNA and cleavable lipids and methods of their use
US20130164845A1 (en) Compositions and Methods for the Delivery of Biologically Active RNAs
JP2020530463A (en) Peptides and nanoparticles for intracellular delivery of viruses
WO2020186150A2 (en) Non-viral dna vectors and uses thereof for expressing phenylalanine hydroxylase (pah) therapeutics
Khoshandam et al. Clinical applications of the CRISPR/Cas9 genome-editing system: Delivery options and challenges in precision medicine
Shi et al. Chemically Modified Platforms for Better RNA Therapeutics
EP1871889B1 (en) A process for producing modified reconstituted sendai viral envelope specific for drug and/or gene delivery to liver cells
Yang et al. Viral and Nonviral Cancer Gene Therapy
WO2024040222A1 (en) Cleavable closed-ended dna (cedna) and methods of use thereof
Kwok The challenges and current advances in delivering RNAi as therapeutics
Iemsam-Arng et al. Gene and ribonucleic acid therapy
JP3095248B2 (en) Nucleic acid carrier
Viola Nucleic acid delivery: reports from the search of the Magic Bullet

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 18839976

Country of ref document: EP

Kind code of ref document: A1

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 18839976

Country of ref document: EP

Kind code of ref document: A1