WO2022174004A1 - Engineered extracellular vesicles and their uses - Google Patents

Engineered extracellular vesicles and their uses Download PDF

Info

Publication number
WO2022174004A1
WO2022174004A1 PCT/US2022/016053 US2022016053W WO2022174004A1 WO 2022174004 A1 WO2022174004 A1 WO 2022174004A1 US 2022016053 W US2022016053 W US 2022016053W WO 2022174004 A1 WO2022174004 A1 WO 2022174004A1
Authority
WO
WIPO (PCT)
Prior art keywords
aptamer
sequence
protein
cells
coding sequence
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/US2022/016053
Other languages
English (en)
French (fr)
Inventor
Baisong Lu
Anthony Atala
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Wake Forest University Health Sciences
Original Assignee
Wake Forest University Health Sciences
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 Wake Forest University Health Sciences filed Critical Wake Forest University Health Sciences
Priority to US18/276,812 priority Critical patent/US20240108757A1/en
Priority to JP2023548687A priority patent/JP2024506910A/ja
Priority to EP22753385.8A priority patent/EP4291164A4/en
Priority to CA3206732A priority patent/CA3206732A1/en
Priority to AU2022220313A priority patent/AU2022220313A1/en
Publication of WO2022174004A1 publication Critical patent/WO2022174004A1/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • A61K48/0058—Nucleic acids adapted for tissue specific expression, e.g. having tissue specific promoters as part of a contruct
    • 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
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/14—Blood; Artificial blood
    • A61K35/17—Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/69—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit
    • A61K47/6901—Conjugates being cells, cell fragments, viruses, ghosts, red blood cells or viral vectors
    • 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
    • A61K9/107—Emulsions ; Emulsion preconcentrates; Micelles
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70596—Molecules with a "CD"-designation not provided for elsewhere
    • 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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • 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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • 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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • 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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/115—Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
    • 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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/62—DNA sequences coding for fusion proteins
    • 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
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • 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
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/88—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation using microencapsulation, e.g. using amphiphile liposome vesicle
    • 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
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90—Stable introduction of foreign DNA into chromosome
    • 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
    • C12N9/14—Hydrolases (3)
    • C12N9/78—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/055—Fusion polypeptide containing a localisation/targetting motif containing a signal for localisation to secretory granules (for exocytosis)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/80—Fusion polypeptide containing a DNA binding domain, e.g. Lacl or Tet-repressor
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/16—Aptamers
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPR]
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3519—Fusion with another nucleic acid
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/50—Physical structure
    • C12N2310/53—Physical structure partially self-complementary or closed
    • C12N2310/531—Stem-loop; Hairpin
    • 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
    • C12N2320/00—Applications; Uses
    • C12N2320/30—Special therapeutic applications
    • C12N2320/32—Special delivery means, e.g. tissue-specific
    • 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
    • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
    • C12N2760/00011—Details
    • C12N2760/20011—Rhabdoviridae
    • C12N2760/20211—Vesiculovirus, e.g. vesicular stomatitis Indiana virus
    • C12N2760/20222—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • 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
    • C12N2800/10—Plasmid DNA
    • C12N2800/106—Plasmid DNA for vertebrates
    • C12N2800/107—Plasmid DNA for vertebrates for mammalian

Definitions

  • compositions and methods of using same for eukaryotic gene editing are described.
  • sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named 1293190_seqlist.txt, created on February 7, 2022, and having a size of 121 KB and is filed concurrently with the specification.
  • sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.
  • CRISPR-based genome editing effectors is important to reduce off-target effects and immune responses.
  • Extracellular vesicles (EVs) have been explored for Cas9 ribonucleoprotein (RNP) delivery.
  • RNP Cas9 ribonucleoprotein
  • the efficiency of these EVs as a RNP delivery vehicle was limited.
  • compositions and methods for efficient packing of functional RNPs into EVs are necessary.
  • plasmid systems and extracellular vesicles for the delivery of nucleic acid sequences (e.g., mRNA sequence encoding a heterologous polypeptide) and heterologous polypeptides to a cell.
  • nucleic acid sequences e.g., mRNA sequence encoding a heterologous polypeptide
  • heterologous polypeptides to a cell.
  • a plasmid system comprising: (a) a first mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence, wherein the nucleic acid sequence comprises: (i) a nucleic acid sequence encoding a CRISPR- associated endonuclease; and (ii) a guide RNA (gRNA) coding sequence, wherein the gRNA coding sequence comprises at least one aptamer coding sequence; and (b) a second mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence encoding a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence of the first mammalian expression plasmid.
  • the plasmid system further comprises an envelope plasmid
  • the CRISPR-associated endonuclease is a Cas9 protein, a Cpfl protein or a derivative of either.
  • the CRISPR-associated endonuclease is a catalytically impaired CRISPR-associated endonuclease.
  • the catalytically impaired CRISPR-associated endonuclease coding sequence encodes a Cas9 D10A protein.
  • the nucleic acid sequence of the first mammalian expression plasmid encodes a nucleic acid sequence encoding an adenosine base pair editor (ABE), wherein the ABE is a fusion protein comprising an adenosine deaminase and the catalytically impaired CRISPR-associated endonuclease.
  • ABE adenosine base pair editor
  • the adenine base editor is ABE 7.10 or ABE8.
  • the at least one aptamer coding sequence encodes an aptamer sequence bound specifically by an ABP selected from the group consisting of MS2 coat protein, PP7 coat protein, lambda N RNA-binding domain, or Com protein.
  • the aptamer sequence is an MS2 aptamer sequence, PP7 aptamer sequence, BoxB aptamer sequence or a com aptamer sequence.
  • the fusion protein comprises a first ABP fused to the N- terminus of CD63 and a second ABP fused to the C-terminus of CD63, wherein the first and second ABP are the same.
  • the first and second ABP is a Com binding protein.
  • the sgRNA coding sequence comprises at least one aptamer coding sequence inserted into the tetraloop or the ST2 loop of the sgRNA coding sequence. In some embodiments, the sgRNA coding sequence comprises at least one com aptamer sequence inserted into the tetraloop or the ST2 loop of the gRNA coding sequence.
  • an extracellular vesicle comprising: (a) a ribonucleotide protein (RNP) complex comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; and (b) a fusion protein comprising CD63 and at least one aptamer binding protein (ABP), wherein the ABP binds to the at least one aptamer coding sequence.
  • the extracellular vesicle further comprises a VSV-G protein.
  • the CRISPR-associated endonuclease is a Cas9 protein, a Cpfl protein or a derivative of either.
  • the CRISPR-associated endonuclease is a catalytically impaired CRISPR-associated endonuclease.
  • the catalytically impaired CRISPR-associated endonuclease coding sequence encodes a Cas9 D10A protein.
  • the RNP comprises an adenine base pair editor (ABE), wherein the ABE is a fusion protein comprising an adenosine deaminase and the catalytically impaired CRISPR-associated endonuclease.
  • the adenine base editor is ABE 7.10 or ABE8.
  • the at least one aptamer coding sequence encodes an aptamer sequence bound specifically by an ABP selected from the group consisting of MS2 coat protein, PP7 coat protein, lambda N RNA-binding domain, or Com protein.
  • the aptamer sequence is an MS2 aptamer sequence or a com aptamer sequence.
  • the fusion protein comprises a first ABP fused to the N- terminus of CD63 and a second ABP fused to the C-terminus of CD63, wherein the first and second ABP are the same.
  • the first and second ABP is a Com binding protein.
  • the sgRNA coding sequence comprises at least one aptamer coding sequence inserted into the tetraloop or the ST2 loop of the sgRNA coding sequence. In some embodiments, the sgRNA coding sequence comprises at least one com aptamer sequence inserted into the tetraloop or the ST2 loop of the gRNA coding sequence. In some embodiments, the extracellular vesicle is an exosome or a microvesicle.
  • a method of producing an extracellular vesicle comprising: (a) transfecting a plurality of eukaryotic cells with the first mammalian expression plasmid and the second mammalian expression plasmid of any of the plasmid systems described herein; and (b) culturing the transfected eukaryotic cells for sufficient time for extracellular vesicles to be produced.
  • the method further comprises transfecting the plurality of eukaryotic cells with the envelope plasmid of any of the plasmid systems described herein.
  • the extracellular vesicle comprises: (a) a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; and (b) a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence.
  • a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence
  • a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence.
  • the extracellular vesicle comprises: (a) a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; (b) a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the aptamer coding sequence; and(c) a VSV-G protein.
  • a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence
  • a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the aptamer coding sequence
  • ABS aptamer binding protein
  • the plurality of eukaryotic cells are mammalian cells.
  • the method further comprises isolating the extracellular vesicles from the cultured transfected eukaryotic cells.
  • extracellular vesicle made by any of the methods provided herein.
  • a method of modifying a genomic target sequence in a cell comprising transducing a plurality of eukaryotic cells with a plurality of extracellular vesicles, wherein the plurality of extracellular vesicles comprises an extracellular vesicles described herein, wherein the RNP binds to the genomic target sequence in genomic DNA of the cell, thereby modifying the genomic target sequence.
  • the plurality of eukaryotic cells are mammalian cells.
  • the plurality of eukaryotic cells are cells present in a subject.
  • the subject is a human subject.
  • the subject is injected with the plurality of extracellular vesicles.
  • a cell containing any of the plasmid systems described herein A cell modified using any of the methods for modifying a cell described herein is also provided.
  • a method for treating a disease in a subject comprising: a) obtaining cells from the subject; b) modifying the cells of the subject using any of the methods for modifying a cell described herein; and c) administering the modified cells to the subject.
  • the disease is cancer.
  • the disease is sickle cell anemia.
  • the cells are T cells.
  • the present application includes the following figures.
  • the figures are intended to illustrate certain embodiments and/or features of the compositions and methods, and to supplement any description(s) of the compositions and methods.
  • the figures do not limit the scope of the compositions and methods, unless the written description expressly indicates that such is the case.
  • FIG. 1 A illustrates a fusion protein comprising Com and CD63 according to certain aspects of this disclosure.
  • Com was fused to the N-terminus, C-terminus or both termini of CD63 with linker peptide in between.
  • the sequences for linker 1 and linker 2 were “GGHNSGGGGGQSPGPAA” (SEQ ID NO: 115) and
  • FIG. IB is a diagram showing the recruitment of Cas9 or ABE RNPs into exosomes according to certain aspects of this disclosure.
  • RNPs associate with Com-CD63-Com on the plasma membrane through com/Com interaction and then enter the endosome system via endocytosis (step 1).
  • the early endosomes become multivesicular bodies (MVB) following the inward budding of the outer endosomal membrane (step 2).
  • the intraluminal vesicles are released into the medium as exosomes when the membranes of MVBs fuse with the cell membrane (step 3).
  • Com is drawn as a monomer but may function as a homodimer.
  • FIG. 1C shows the recruitment of Cas9 RNPs into microvesicles (step 4) according to certain aspects of this disclosure.
  • FIG. 2A is a Western blot showing expression of Com and CD63 fusion proteins according to certain aspects of this disclosure. Plasmid DNA for CD63, CD63-Com, Com- CD63 and Com-CD63-Com expression were transfected into HEK293T cells and the expression of CD63 or CD63 -fusion proteins were detected by anti-CD63 antibody. GAPDH was detected for loading control.
  • FIG. 2B shows flow cytometry detection of gene editing activities according to certain aspects of this disclosure.
  • 2.5x10 4 HBB-IL2RG GFP reporter cells were treated with RNP-enriched EVs secreted by 0.6 million cells in 48 hours.
  • the RNPs w ere //.2//G-targeting SaCas9 RNPs (n 6).
  • FIG. 2C shows that vesicular stomatitis virus- G (VSV-G) improves gene editing activity of the EV-delivered RNPs according to certain aspects of this disclosure.
  • VSV-G vesicular stomatitis virus- G
  • IL2RG- targeting SaCas9 RNPs were packaged into EVs with or without VSV-G protein.
  • ## p ⁇ 0.01 compared with the group without VSV-G; ***, p ⁇ 0.0001 when compared with all other conditions (Tukey posttests following ANOVA).
  • FIG. 1 vesicular stomatitis virus- G
  • FIG. 2D shows detection of gene editing activities of EV-delivered SpCas9 RNPs by flow cytometry according to certain aspects of this disclosure.
  • HBB-IL2RG GFP reporter cells 2.5xl0 4
  • the RNPs were IL2RG- targeting SpCas9 RNPs.
  • FIG. 3 shows optimization of DNA ratios for most efficient production of RNP loaded EVs according to certain aspects of this disclosure.
  • the indicated amount of pCom- CD63-Com and pX601 -Tetra-com-//.2/RG DNA was used in transfection for making the RNP- loaded EVs.
  • FIG. 4 is a Western blot showing detection of VSV-G and VSV-G-Com fusion protein according to certain aspects of this disclosure. Control cells were mock transfected.
  • FIG. 5A is a schematic of sgRNA driven by RNA polymerase II promoter and flanked by the Hammerhead (HH) ribozyme and hepatitis delta virus (HDV) ribozyme. The sgRNAs were //.2//G-targeting sgRNAs for SaCas9 and SpCas9.
  • FIG. 5B is a comparision of gene editing activities of EV delivered SaCas9 or SpCas9 RNPs (targeting IL2RG and DMD exon 53 respectively), with or without extra sgRNA, according to certain aspects of this disclosure.
  • RNP-loaded EVs were prepared with and without the respective plasmid DNA shown in FIG. 5A.
  • Gene editing activities were assayed in HBB-IL2RG GFP reporter cells by flow cytometry.
  • FIG. 6A shows enrichment of SaCas9 RNPs in EVs according to certain aspects of this disclosure.
  • Com-CD63-Com, SaCas9 and IL2RG sgRNA with and without com modification were co- expressed in 5x10 6 HEK293T cells, EVs were collected for 48 hours. One-fifth of the EVs were analyzed by Western blot. Numbers under protein bands were estimated protein mass (ng) based on protein standards.
  • FIG. 6B shows enrichment of SpCas9 RNPs and ABE into EVs according to certain aspects of this disclosure.
  • IL2RG and Site 5 were targeted for SpCas9 and ABE respectively.
  • Experimental conditions were similar as in FIG. 6A.
  • FIG. 6C shows Com and com dependent enrichment of sgRNA into EVs according to certain aspects of this disclosure.
  • sgRNA was unmodified (com-) or with a com replacing the Tetra loop (com+).
  • CD63 was overexpressed instead.
  • RNAs were extracted from EVs and the sgRNA was detected by RT-qPCR using primers Scid-g2F and sgRNA-R3. ***, p ⁇ 0.000l when compared with all other conditions (Tukey posttests following ANOVA).
  • FIG. 7A is a Western blot analysis of proteins in EVs according to certain aspects of this disclosure.
  • EVs were collected from cells with or without //.2/RG-targeting SaCas9 RNPs. l/20 th of the EVs secreted by 1 million cells, in 48 hours, and were loaded.
  • FIG. 7B shows transmission electric microscopy analysis of EVs according to certain aspects of this disclosure.
  • FIG. 7C shows nanoparticle tracking analysis of EV particle concentrations according to certain aspects of this disclosure.
  • FIG. 7D shows nanoparticle tracking analysis of EV size distribution according to certain aspects of this disclosure. EVs secreted by 5 million cells in 48 hours were re-suspended in 500 pi PBS for analysis in FIGS. 7B, 7C and 7D.
  • FIG. 8A is a Western blot of degradation of EV delivered SpCas9 RNPs according to certain aspects of this disclosure.
  • the arrow indicates the position of SpCas9 protein.
  • the asterisk indicates a nonspecific band as the indication of similar loading. EVs secreted by
  • FIG. 8B shows densitometry analysis (IMAGEJ) of Cas9 protein levels, at various times, according to certain aspects of this disclosure. Half-life was estimated using one phase decay (GraphPad Prism 5).
  • FIG. 8C is a Western blot of degradation of EV delivered SaCas9 RNPs according to certain aspects of this disclosure.
  • the arrow indicates the position of SaCas9 protein.
  • the asterisk indicates a nonspecific band as the indication of similar loading. EVs secreted by 0.2 million cells in 48 hours were added to 2.5xl0 4 HEK293T cells.
  • FIG. 9A is a diagram showing an exemplary strategy to detect co-targeting of two loci according to certain aspects of this disclosure.
  • the primers, 50-F, 51-R and 53- R used for PCR detection of deletions are also shown.
  • the solid boxes indicate hDMD exons 51 to 53. Distances between primers before sequence removal are listed.
  • FIG. 9B shows that co-packaged SaCas9 RNPs targeting different loci were more efficient in multiplex genome editing, according to certain aspects of this disclosure.
  • FIG. 9C shows that SaCas9 RNPs and SpCas9 RNPs could be co-packaged in EVs for efficient multiplex genome editing, according to certain aspects of this disclosure. Definitions
  • the transitional phrase "consisting essentially of' (and grammatical variants) is to be interpreted as encompassing the recited materials or steps "and those that do not materially affect the basic and novel characteristic(s)" of the claimed invention. See In re Herz, 537 F.2d 549, 551-52, 190 U.S.P.Q. 461, 463 (CCPA 1976) (emphasis in the original); see also MPEP ⁇ 2111.03. Thus, the term “consisting essentially of' as used herein should not be interpreted as equivalent to "comprising.”
  • nucleic acid refers to deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) (e.g., mRNA) and polymers thereof in either single- or double- stranded form. It is understood that when an RNA is described, its corresponding DNA is also described, wherein uridine is represented as thymidine. Similarly, when a DNA is described, its corresponding RNA is also described wherein thymidine is represented by uridine.
  • nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides.
  • a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated.
  • degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res.
  • polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.
  • the term “gene” can refer to the segment of DNA involved in producing or encoding a polypeptide chain. It may include regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons). Alternatively, the term “gene” can refer to the segment of DNA involved in producing or encoding a non-translated RNA, such as an rRNA, tRNA, guide RNA, or micro RNA.
  • heterologous refers to what is not normally found in nature.
  • heterologous polypeptide refers to a polypeptide not normally found in a given cell in nature.
  • a heterologous polypeptide may be: (a) foreign to its host cell (i.e., is exogenous to the cell); or (b) naturally found in the host cell (i.e., endogenous) but present at an unnatural quantity in the cell (i.e., greater or lesser quantity than naturally found in the host cell).
  • heterologous promoter refers to a promoter sequence not normally found in a given cell in nature or not normally found operably linked to polynucleotide expressing a given protein.
  • Treating refers to any indicia of success in the treatment or amelioration or prevention of the disease, condition, or disorder, including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the disease condition more tolerable to the patient; slowing in the rate of degeneration or decline; or making the final point of degeneration less debilitating.
  • the treatment or amelioration of symptoms can be based on objective or subjective parameters; including the results of an examination by a physician.
  • the term “treating” includes the administration of the compounds or agents of the present disclosure to prevent or delay, to alleviate, or to arrest or inhibit development of the symptoms or conditions associated with a disease, condition or disorder as described herein.
  • therapeutic effect refers to the reduction, elimination, or prevention of the disease, symptoms of the disease, or side effects of the disease in the subject.
  • “Treating” or “treatment” using the methods of the present disclosure includes preventing the onset of symptoms in a subject that can be at increased risk of a disease or disorder associated with a disease, condition or disorder as described herein, but does not yet experience or exhibit symptoms, inhibiting the symptoms of a disease or disorder (slowing or arresting its development), providing relief from the symptoms or side effects of a disease (including palliative treatment), and relieving the symptoms of a disease (causing regression).
  • Treatment can be prophylactic (to prevent or delay the onset of the disease, or to prevent the manifestation of clinical or subclinical symptoms thereof) or therapeutic suppression or alleviation of symptoms after the manifestation of the disease or condition.
  • treatment includes preventative (e.g., prophylactic), curative, or palliative treatment.
  • a “promoter” is defined as one or more a nucleic acid control sequences that direct transcription of a nucleic acid.
  • a promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element.
  • a promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription.
  • Polypeptide “peptide,” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. All three terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymers. As used herein, the terms encompass full-length proteins, truncated proteins, and fragments thereof, and amino acid chains, wherein the amino acid residues are linked by covalent peptide bonds. As used throughout, the term “fusion polypeptide” or “fusion protein” is a polypeptide comprising two or more proteins or fragments thereof. In some embodiments, a linker comprising about 3 to 10 amino acids can be positioned between any two proteins or fragments thereof to help facilitate proper folding of the proteins upon expression.
  • identity refers to a sequence that has at least 60% sequence identity to a reference sequence.
  • percent identity can be any integer from 60% to 100%.
  • Exemplary embodiments include at least: 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, as compared to a reference sequence using the programs described herein; preferably BLAST using standard parameters, as described below.
  • sequences having at 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to any nucleotide or polypeptide sequence set forth herein, for example, any one of SEQ ID NOs: 1- 49, can be used in the compositions and methods provided herein.
  • a nucleic acid sequence can comprise, consist of, or consist essentially of any nucleic acid sequence described herein.
  • a polypeptide can comprise, consist of, or consist essentially of, any polypeptide sequence described herein.
  • For sequence comparison typically one sequence acts as a reference sequence to which test sequences are compared.
  • a “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, about 20 to 50, about 20 to 100, about 50 to about 200 or about 100 to about 150, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
  • Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Add. APL. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (U.S.A.) 85: 2444 (1988), by computerized implementations of these algorithms (e.g., BLAST), or by manual alignment and visual inspection.
  • HSPs high scoring sequence pairs
  • T is referred to as the neighborhood word score threshold (Altschul et al, supra).
  • These initial neighborhood word hits acts as seeds for initiating searches to find longer HSPs containing them.
  • the word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always ⁇ 0). Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment.
  • the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)).
  • 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 nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.01, more preferably less than about 10-5, and most preferably less than about 10-20.
  • subject an individual.
  • the subject is a mammal, such as a primate, and, more specifically, a human.
  • Non-human primates are subjects as well.
  • subject includes domesticated animals, such as cats, dogs, etc., livestock (for example, cattle, horses, pigs, sheep, goats, etc.) and laboratory animals (for example, ferret, chinchilla, mouse, rabbit, rat, gerbil, guinea pig, etc.).
  • livestock for example, cattle, horses, pigs, sheep, goats, etc.
  • laboratory animals for example, ferret, chinchilla, mouse, rabbit, rat, gerbil, guinea pig, etc.
  • veterinary uses and medical uses and formulations are contemplated herein.
  • the term does not denote a particular age or sex. Thus, adult and newborn subjects, whether male or female, are intended to be covered.
  • patient or subject may be used interchangeably and can refer to a subject afflicted with a
  • An “expression cassette” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular polynucleotide sequence in a host cell.
  • An expression cassette may be part of a plasmid, viral genome, or nucleic acid fragment.
  • an expression cassette includes a polynucleotide to be transcribed, operably linked to a promoter, followed by a transcription termination signal sequence.
  • An expression cassette may or may not include specific regulatory sequences, such as 5’ or 3’ untranslated regions from human globin genes.
  • a “reporter gene” encodes proteins that are readily detectable due to their biochemical characteristics, such as enzymatic activity or chemifluorescent features. These reporter proteins can be used as selectable markers.
  • One specific example of such a reporter is green fluorescent protein. Fluorescence generated from this protein can be detected with various commercially-available fluorescent detection systems. Other reporters can be detected by staining.
  • the reporter can also be an enzyme that generates a detectable signal when contacted with an appropriate substrate.
  • the reporter can be an enzyme that catalyzes the formation of a detectable product. Suitable enzymes include, but are not limited to, proteases, nucleases, lipases, phosphatases and hydrolases.
  • the reporter can encode an enzyme whose substrates are substantially impermeable to eukaryotic plasma membranes, thus making it possible to tightly control signal formation.
  • suitable reporter genes that encode enzymes include, but are not limited to, CAT (chloramphenicol acetyl transferase; Alton and Vapnek (1979) Nature 282: 864-869); luciferase (lux); b-galactosidase; LacZ; b - glucuronidase; and alkaline phosphatase (Toh, et al. (1980) Eur. J. Biochem. 182: 231-238; and Hall et al. (1983) J. Mol. Appl. Gen. 2: 101), each of which are incorporated by reference herein in its entirety.
  • Other suitable reporters include those that encode for a particular epitope that can be detected with a labeled antibody that specifically recognizes the epitope.
  • CRISPR/Cas refers to a widespread class of bacterial systems for defense against foreign nucleic acid.
  • CRISPR/Cas systems are found in a wide range of eubacterial and archaeal organisms.
  • CRISPR/Cas systems include type I, II, and III sub-types.
  • the CRISPR/Cas system classification as described in by Makarova, et al. defines five types and 16 subtypes based on shared characteristics and evolutionary similarity. These are grouped into two large classes based on the structure of the effector complex that cleaves genomic DNA.
  • the Type II CRISPR/Cas system was the first used for genome engineering, with Type V following in 2015.
  • Wild-type type II CRISPR/Cas systems utilize an RNA-mediated nuclease Cas protein or homolog (referred to herein as a “CRISPR-associated endonuclease”) in complex with guide RNA to recognize and cleave foreign nucleic acid.
  • Cas9 proteins also use an activating RNA (also referred to as a transactivating or tracr RNA).
  • Guide RNAs having the activity of either a guide RNA or both a guide RNA and an activating RNA, depending on the type of CRISPR-associated endonuclease used therewith, are also known in the art.
  • sgRNA single guide RNA
  • sgRNAs synthetic guide RNAs that do not contain an activating RNA sequence
  • the terms sgRNA and gRNA are used interchangeably to refer to an RNA molecule that complexes with a CRISPR-associated endonuclease and localizes the ribonucleoprotein complex to a target DNA sequence.
  • the CRISPR-associated endonuclease can be a catalytically impaired nuclease.
  • catalytically impaired refers to decreased CRISPR-associated endonuclease enzymatic activity for cleaving one or both strands of DNA.
  • Examples of catalytically impaired CRISPR-associated endonuclease include but are not limited to catalytically impaired Cas9, catalytically impaired Cpfl and catalytically impaired C2c2.
  • the catalytically impaired CRISPR- associated endonuclease is a the catalytically impaired Cas9, for example Cas9 D10A, which cleaves or nicks only one strand of DNA.
  • the CRISPR-associated endonuclease may be a catalytically impaired CRISPR-associated endonuclease, wherein the endonuclease cannot cleave both strands of a double-stranded DNA molecule, i.e., cannot make a double-stranded break.
  • Modifications include, but are not limited to, altering one or more amino acids to inactivate the nuclease activity or the nuclease domain.
  • D10A and/or H840A mutations can be made in Cas9 from Streptococcus pyogenes to reduce or inactivate Cas9 nuclease activity.
  • a catalytically impaired Cas9 may include polypeptide sequences modified to reduce nuclease activity or removal of a polypeptide sequence or sequences to reduce nuclease activity.
  • the catalytically impaired Cas9 retains the ability to bind to DNA even though the nuclease activity has been inactivated.
  • a catalytically impaired Cas9 includes the polypeptide sequence or sequences required for DNA binding but includes modified nuclease sequences or lacks nuclease sequences responsible for nuclease activity.
  • the Cas9 protein is a full-length Cas9 sequence from S. pyogenes lacking the polypeptide sequence of the RuvC nuclease domain and/or the HNH nuclease domain and retaining the DNA binding function.
  • the Cas9 protein sequences have at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98% or 99% identity to Cas9 polypeptide sequences lacking the RuvC nuclease domain and/or the HNH nuclease domain and retains DNA binding function.
  • activity in the context of sgRNA activity, or RNP activity, i.e., RNP activity of a complex comprising: (1) a gRNA and (2) a CRISPR-associated endonuclease, refers to the ability of a sgRNA to bind to a target genetic element. Typically, activity also refers to the ability of an RNP (i.e., and sgRNA complexed with a CRISPR- associated endonuclease) to edit the genome of a cell. In some examples, activity refers to the ability of an ABE RNP (i.e., an sgRNA complexed with an ABE) to edit base pairs, i.e., perform an A to G change in one strand of DNA.
  • ABE RNP i.e., an sgRNA complexed with an ABE
  • editing in the context of editing of a genome of a cell refers to inducing a structural change in the sequence of the genome at a target genomic region, for example, cleaving a genomic sequence and inserting a donor sequence into the genome of a cell, at the cleavage site, via homology directed repair (HDR), or cleaving a sequence and allowing repair via non-homologus end joining (NHEJ).
  • HDR homology directed repair
  • NHEJ non-homologus end joining
  • editing is performed by an ABE.
  • the editing can take the form of an A to G change in one strand of DNA (or a T to C change on the opposite strand of DNA) at a target genomic region.
  • the nucleotide sequence can encode a polypeptide or a fragment thereof. See, for example, Gaudelli et al., “Programmable base editing of A-T to G-C in genomic DNA without DNA cleavage,” Nature 551: 464-471 (2017).
  • an adenine base editor or “ABE” refers to a fusion protein comprising an adenosine deaminase and a catalytically impaired CRISPR-associated endonuclease.
  • the adenosine deaminase is a tadA enzyme that deaminates adenine on a single-strand of DNA to form inosine. See, Gaudelli et al, (2017).
  • the ABE is a fusion protein comprising a catalytically impaired CRISPR-associated endonuclease and one or more copies, for example, two, three, four copies, etc. of an adenosine deaminase.
  • the ABE comprises the fusion protein is encoded by a nucleic acid sequence comprising SEQ ID NO: 27.
  • the ABE comprises SEQ ID NO: 28.
  • RNPs ribonucleoprotein complex
  • a crRNA e.g., guide RNA or single guide RNA
  • tracrRNA trans-activating crRNA
  • a CRISPR-associated endonuclease and a guide RNA or (4) a combination thereof (e.g., a complex containing the CRISPR-associated endonuclease and the catalytically impaired Cas9 protein, a tracrRNA, and a crRNA guide).
  • the CRISPR- associated endonuclease is catalytically impaired. In some embodiments, the catalytically impaired CRISPR-associate endonuclease is fused to an adenosine deaminase.
  • a “cell” can be any eukaryotic cell, for example, human T cell or a cell capable of differentiating into a T cell, for example, a T cell that expresses a TCR receptor molecule. These include hematopoietic stem cells and cells derived from hematopoietic stem cells. Populations of cells, for example, populations of cells comprising viral particles or genetically modified cells made by any of the genomic editing methods provided herein, are also provided.
  • hematopoietic stem cell refers to a type of stem cell that can give rise to a blood cell. Hematopoietic stem cells can give rise to cells of the myeloid or lymphoid lineages, or a combination thereof. Hematopoietic stem cells are predominantly found in the bone marrow, although they can be isolated from peripheral blood, or a fraction thereof. Various cell surface markers can be used to identify, sort, or purify hematopoietic stem cells. In some cases, hematopoietic stem cells are identified as c-kit+ and lin-.
  • human hematopoietic stem cells are identified as CD34+, CD59+, Thy 1/CD90+, CD381o/-, C- kit/CD117+, lin-. In some cases, human hematopoietic stem cells are identified as CD34-, CD59+, Thyl/CD90+, CD381o/-, C-kit/CD117+, lin-. In some cases, human hematopoietic stem cells are identified as CD133+, CD59+, Thyl/CD90+, CD381o/-, C-kit/CD117+, lin-.
  • mouse hematopoietic stem cells are identified as CD341o/-, SCA-1+, Thyl+/lo, CD38+, C-kit +, lin-.
  • the hematopoietic stem cells are CD150+CD48-CD244-.
  • the phrase “hematopoietic cell” refers to a cell derived from a hematopoietic stem cell. The hematopoietic cell may be obtained or provided by isolation from an organism, system, organ, or tissue (e.g., blood, or a fraction thereof).
  • an hematopoietic stem cell can be isolated and the hematopoietic cell obtained or provided by differentiating the stem cell.
  • Hematopoietic cells include cells with limited potential to differentiate into further cell types. Such hematopoietic cells include, but are not limited to, multipotent progenitor cells, lineage-restricted progenitor cells, common myeloid progenitor cells, granulocyte-macrophage progenitor cells, or megakaryocyte-erythroid progenitor cells.
  • Hematopoietic cells include cells of the lymphoid and myeloid lineages, such as lymphocytes, erythrocytes, granulocytes, monocytes, and thrombocytes.
  • the hematopoietic cell is an immune cell, such as a T cell, B cell, macrophage, a natural killer (NK) cell or dendritic cell.
  • the cell is an innate immune cell.
  • T cell refers to a lymphoid cell that expresses a T cell receptor molecule.
  • T cells include human alpha beta (ab) T cells and human gamma delta (gd) T cells.
  • T cells include, but are not limited to, naive T cells, stimulated T cells, primary T cells (e.g., uncultured), cultured T cells, immortalized T cells, helper T cells, cytotoxic T cells, memory T cells, regulatory T cells, natural killer T cells, combinations thereof, or sub populations thereof.
  • T cells can be CD4+, CD8+, or CD4+ and CD8+.
  • T cells can also be CD4-, CD8-, or CD4- and CD8-.
  • T cells can be helper cells, for example helper cells of type TH1, TH2, TH3, TH9, TH17, or TFH.
  • T cells can be cytotoxic T cells.
  • Regulatory T cells can be FOXP3+ or FOXP3-.
  • T cells can be alpha/beta T cells or gamma/delta T cells.
  • the T cell is a CD4+CD25hiCD1271o regulatory T cell.
  • the T cell is a regulatory T cell selected from the group consisting of type 1 regulatory (Trl), TH3, CD8+CD28-, Tregl7, and Qa-1 restricted T cells, or a combination or sub-population thereof.
  • the T cell is a FOXP3+ T cell. In some cases, the T cell is a CD4+CD251oCD127hi effector T cell. In some cases, the T cell is a CD4+CD251oCD127hiCD45RAhiCD45RO- naive T cell.
  • a T cell can be a recombinant T cell that has been genetically manipulated.
  • the phrase “primary” in the context of a primary cell is a cell that has not been transformed or immortalized. Such primary cells can be cultured, sub-cultured, or passaged a limited number of times (e.g., cultured 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 times). In some cases, the primary cells are adapted to in vitro culture conditions. In some cases, the primary cells are isolated from an organism, system, organ, or tissue, optionally sorted, and utilized directly without culturing or sub-culturing. In some cases, the primary cells are stimulated, activated, or differentiated. For example, primary T cells can be activated by contact with (e.g., culturing in the presence of) CD3, CD28 agonists, IL-2, IFN- g, or a combination thereof.
  • extracellular vesicle refers to membrane-hound vesicles that are naturally released from eukaryotic cells.
  • EVs are cell-derived vesicles, re., a lipid bilayer delimited particles, comprising a membrane that encloses an internal space (lumen).
  • Generally EVs range in diameter from 20 nmto 1000 nm.
  • EVs include, but are not limited to, exosomes and microvesicles. EVs are released by cells and found in most biological fluids including urine, plasma, cerebrospinal fluid, saliva etc. as well, as in tissue culture conditioned media
  • nucleic acid sequences e.g., mRNA sequences
  • RNPs eukaryotic cells
  • nucleic acid sequences e.g., mRNA sequences
  • RNPs can be efficiently packaged in EVs and delivered to eukaryotic cells.
  • components, systems, methods of manufacture, and methods for efficient delivery to cells of RNPs comprising (1) a CRISPR-associated endonuclease and (2) an sgRNA, via EVs, are provided.
  • the EVs described herein have a limited half-life, thus reducing the risk of RNA and DNA off-target mediated mutagenesis. Delivery of RNPs into eukaryotic cells allows for efficient delivery, for example, in cells that are difficult to transfect, such as primary cells while reducing off-target effects.
  • plasmid systems that are used to deliver CRISPR component coding sequences, i.e., an sgRNA and a CRISPR-associated endonuclease, into mammalian cells being used to generate the EVs of this disclosure.
  • CRISPR component coding sequences i.e., an sgRNA and a CRISPR-associated endonuclease
  • a plasmid system comprising: (a) a first mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence, wherein the nucleic acid sequence comprises: (i) a nucleic acid sequence encoding a CRISPR-associated endonuclease; and (ii) a guide RNA (gRNA) coding sequence, wherein the gRNA coding sequence comprises at least one aptamer coding sequence; and (b) a second mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence encoding a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence of the first mammalian expression plasmid.
  • the plasmid system further comprises an envelope plasmid comprising a first mammalian expression
  • the first mammalian expression plasmid of the systems provided herein comprises CRISPR component coding sequences, e.g., the coding sequence for a CRISPR-associated endonuclease and a gRNA.
  • the gRNA coding sequence comprises at least one aptamer coding sequence.
  • the at least one aptamer coding sequence may be positioned at the 5’ end or the 3’ end of the gRNA.
  • the at least one aptamer coding sequence may be inserted at an internal position within the gRNA such as, for example, at one or more of the loops formed in the folded gRNA.
  • the at least one aptamer coding sequence may be positioned at the tetra loop, the stem loop 2 (ST2), or the 3’ end of the gRNA.
  • a spacer of 1-30 nucleotides may be positioned between the gRNA the at least one aptamer coding sequence, or flanking the at least one aptamer coding sequence.
  • the sgRNA coding sequence comprises at least one aptamer coding sequence inserted into the tetraloop or the ST2 loop of the sgRNA coding sequence.
  • the sgRNA coding sequence comprises at least one com aptamer sequence inserted into the tetraloop or the ST2 loop of the gRNA coding sequence.
  • the first mammalian expression plasmid comprises at least one aptamer coding sequence that encodes an aptamer sequence that is bound specifically by an aptamer-binding protein (ABP) encoded by the second mammalian expression plasmid of the system.
  • an aptamer sequence is an RNA sequence that forms a tertiary loop structure that is specifically bound by an ABP.
  • ABPs are RNA-binding proteins or RNA-binding protein domains.
  • Suitable aptamer coding sequences include polynucleotide sequences that encode known bacteriophage aptamer sequences.
  • Exemplary aptamer coding sequences include those encoding the aptamer sequences provided above in Table 1.
  • the aptamers are bound by a dimer of ABP.
  • These aptamer sequences are RNA sequences known to be bound specifically by bacteriophage proteins.
  • the at least one aptamer coding sequence encodes an aptamer sequence bound specifically by an ABP selected from the group consisting of MS2 coat protein, PP7 coat protein, lambda N RNA-binding domain, or Com protein.
  • the at least one aptamer coding sequence is a com aptamer and the ABP is a Com protein.
  • the first mammalian expression vector comprises a sgRNA that comprises one aptamer coding sequence downstream thereof.
  • the gRNA may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 aptamer coding sequences.
  • the gRNA may comprise two aptamer coding sequences in tandem.
  • the two or more tandem aptamer coding sequences are the same.
  • the two or more tandem aptamer coding sequences are different.
  • a sgRNA is a single guide RNA sequence that interacts with a CRISPR-associated endonuclease (a CRISPR site-directed nuclease) and specifically binds to or hybridizes to a target nucleic acid within the genome of a cell (genomic target sequence), such that the sgRNA and the CRISPR-associated endonuclease co-localize to the target nucleic acid in the genome of the cell.
  • Each sgRNA includes a DNA targeting sequence or protospacer sequence of about 10 to 50 nucleotides in length that specifically binds to or hybridizes to a target DNA sequence in the genome.
  • the DNA targeting sequence may be about
  • the DNA targeting sequence may be about 15-30 nucleotides, about 15-25 nucleotides, about 10-25 nucleotides, or about 18-23 nucleotides. In one example, the DNA targeting sequence is about 20 nucleotides.
  • the sgRNA comprises a crRNA sequence and a transactivating crRNA (tracrRNA) sequence. In some embodiments, the sgRNA does not comprise a tracrRNA sequence.
  • the DNA targeting sequence is designed to complement (e.g., perfectly complement) or substantially complement (e.g., having 1-4 mismatches) to the target DNA sequence.
  • the DNA targeting sequence can incorporate wobble or degenerate bases to bind multiple genetic elements.
  • the 19 nucleotides at the 3’ or 5’ end of the binding region are perfectly complementary to the target genetic element or elements.
  • the binding region can be altered to increase stability. For example, non-natural nucleotides, can be incorporated to increase RNA resistance to degradation.
  • the binding region can be altered or designed to avoid or reduce secondary structure formation in the binding region.
  • the binding region can be designed to optimize G-C content.
  • G-C content is preferably between about 40% and about 60% (e.g., 40%, 45%, 50%, 55%, 60%).
  • the binding region can be selected to begin with a sequence that facilitates efficient transcription of the sgRNA.
  • the binding region can begin at the 5’ end with a G nucleotide.
  • the binding region can contain modified nucleotides such as, without limitation, methylated or phosphorylated nucleotides.
  • complementary refers to base pairing between nucleotides or nucleic acids, for example, and not to be limiting, base pairing between a sgRNA and a target sequence.
  • Complementary nucleotides are, generally, A and T (or A and U), and G and C.
  • the guide RNAs described herein can comprise sequences, for example, DNA targeting sequence that are perfectly complementary or substantially complementary (e.g., having 1-4 mismatches) to a genomic sequence.
  • the sgRNA includes a sgRNA constant region that interacts with or binds to the CRISPR-associated endonuclease.
  • the constant region of an sgRNA can be from about 75 to 250 nucleotides in length.
  • the constant region is a modified constant region comprising one, two, three, four, five, six, seven, eight, nine, ten or more nucleotide substitutions in the stem, the stem loop, a hairpin, a region in between hairpins, and/or the nexus of a constant region.
  • a modified constant region that has at least 80%, 85%, 90%, or 95% activity, as compared to the activity of the natural or wild-type sgRNA constant region from which the modified constant region is derived, may be used in the constructs described herein.
  • modifications should not be made at nucleotides that interact directly with a CRISPR-associated endonuclease or at nucleotides that are important for the secondary structure of the constant region.
  • the CRISPR-associated endonuclease encoded on the first mammalian expression plasmid of any of the systems described herein are RNA-guided site-directed nucleases.
  • the CRISPR-associated endonuclease can be a Cas9 polypeptide (Type II) or a Cpfl polypeptide (Type V). See, for example, Abudayyeh et al., Science 2016 August 5; 353(6299):aaf5573; Fonfara et al. Nature 532: 517-521 (2016), and Zetsche et al., Cell 163(3): p. 759-771, 22 October 2015.
  • Cas9 polypeptide means a Cas9 protein, or a fragment or derivative thereof, identified in any bacterial species that encodes a Type II CRISPR/Cas system. See, for example, Makarova et al. Nature Reviews, Microbiology, 9: 467-477 (2011), including supplemental information, hereby incorporated by reference in its entirety.
  • CRISPR-associated endonucleases such as Cas9 and Cas9 homologs
  • Cas9 and Cas9 homologs are found in a wide variety of eubacteria, including, but not limited to bacteria of the following taxonomic groups: Actinobacteria, Aquificae, Bacteroidetes- Chlorobi, Chlamydiae-Verrucomicrobia, Chlroflexi, Cyanobacteria, Firmi cutes, Proteobacteria, Spirochaetes, and Thermotogae.
  • An exemplary Cas9 protein is the Streptococcus pyogenes Cas9 protein (SpCas9).
  • Cas9 protein is the Staphylococcus aureus Cas9 protein (SaCas9). Additional Cas9 proteins and homologs thereof are described in, e.g., Chylinksi, et al., RNA Biol. 2013 May 1; 10(5): 726-737 ; Nat. Rev. Microbiol. 2011 June; 9(6): 467-477; Hou, et al., Proc Natl Acad Sci USA. 2013 Sep 24;110(39): 15644-9; Sampson et al., Nature. 2013 May 9;497(7448):254-7; and Jinek, et al., Science. 2012 Aug 17;337(6096):816-21.
  • the Cas9 nuclease domains can be optimized for efficient activity or enhanced stability in the host cell.
  • Other CRISPR-associated endonucleases include Cpfl (See, e.g., Zetsche et al., Cell, Volume 163, Issue 3, p759-771, 22 October 2015) and homologs thereof.
  • Full-length Cas9 is an endonuclease comprising a recognition domain and two nuclease domains (HNH and RuvC, respectively) that creates double-stranded breaks in DNA sequences.
  • HNH is linearly continuous
  • RuvC is separated into three regions, one left of the recognition domain, and the other two right of the recognition domain flanking the HNH domain.
  • Cas9 is targeted to a genomic site in a cell by interacting with a guide RNA that hybridizes to a 20-nucleotide DNA sequence that immediately precedes an NGG motif recognized by Cas9. This results in a double-strand break in the genomic DNA of the cell.
  • a Cas9 nuclease that requires an NGG protospacer adjacent motif (PAM) immediately 3’ of the region targeted by the guide RNA can be utilized.
  • Cas9 proteins with orthogonal PAM motif requirements can be utilized to target sequences that do not have an adjacent NGG PAM sequence.
  • Exemplary Cas9 proteins with orthogonal PAM sequence specificities include, but are not limited to those described in Esvelt et al., Nature Methods 10: 1116-1121 (2013).
  • Various Cas9 nucleases can be utilized in the methods described herein.
  • a Cas9 nuclease that requires an NGG protospacer adjacent motif (PAM) immediately 3’ of the region targeted by the guide RNA, such as SpCas9 can be utilized.
  • Such Cas9 nucleases can be targeted to any region of a genome that contains an NGG sequence.
  • a Cas9 nuclease that requires an NNGRRT (SEQ ID NO: 106) or NNGRR(N) (SEQ ID NO: 107) PAM immediately 3’ of the region targeted by the guide RNA, such as SaCas9 can be utilized.
  • Cas9 proteins with orthogonal PAM motif requirements can be utilized to target sequences that do not have an adjacent NGG PAM sequence.
  • Exemplary Cas9 proteins with orthogonal PAM sequence specificities include, but are not limited to those described in Nature Methods 10, 1116-1121 (2013), and those described in Zetsche et al., Cell, Volume 163, Issue 3, p759-771, 22 October 2015. [0089] Any of the CRISPR-associated endonucleases described herein can be catalytically impaired. In some cases, the catalytically impaired CRISPR-associated endonuclease is a Cas9 nickase, for example, Cas9 D10A . In some instances, Cas9 10A is encoded by SEQ ID NO: 21. In some instances, the Cas9 10A comprises SEQ ID NO: 22.
  • Cas9 nickase is bound to target nucleic acid as part of a complex with a guide RNA, a single strand break or nick is introduced into the target nucleic acid.
  • a pair of Cas9 nickases, each bound to a structurally different guide RNA, can be targeted to two proximal sites of a target genomic region.
  • Exemplary Cas9 nickases include Cas9 nucleases having a D10A or H840A mutation.
  • the nucleic acid sequence of the first mammalian expression plasmid encodes a nucleic acid sequence encoding an adenosine base pair editor (ABE), wherein the ABE is a fusion protein comprising an adenosine deaminase and the catalytically impaired CRISPR-associated endonuclease.
  • ABE adenosine base pair editor
  • the adenine base editor is ABE 7.10 or ABE8.
  • the plasmid systems described herein comprise a second mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence encoding a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence of the first mammalian expression plasmid.
  • a second mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence encoding a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence of the first mammalian expression plasmid.
  • ABSP aptamer binding protein
  • the fusion protein comprises an ABP fused to the N-terminus of CD63 and/or an ABP fused to the C-terminus of CD63.
  • the fusion protein comprises a first ABP fused to the N-terminus of CD63 and a second ABP fused to the C-terminus of CD63, wherein the first and second ABP are the same.
  • the fusion protein comprises a first ABP fused to the N-terminus of CD63 and a second ABP fused to the C-terminus of CD63, wherein the first and second ABP are different.
  • the first and second ABP is Com which binds to the com aptamer in the first mammalian expression plasmid.
  • CD63 CD63 antigen, or a fragment thereof, is a member of the transmembrane 4 superfamily of proteins, also known as the tetraspanin family.
  • CD63 is a cell- surface protein, characterized by the presence of four hydrophobic domains, that is found on the cell surface of extracellular vesicles.
  • An exemplary amino acid sequence for CD63 is set forth as SEQ ID NO: 43.
  • SEQ ID NO 43 is encoded by SEQ ID NO: 42. It is understood that any of the isoforms of CD63 or a fragment thereof can be used in the compositions and methods described herein.
  • Exemplary CD63 isoform protein sequences are set forth under GenBank Accession Nos.
  • NP_001244318.1 NP_001771.1, NP_001254627.1, NP_001244319.1, NP_001244320.1, NP_001244329.1, NP_001244330.1, NP_001244321.1, and
  • the mammalian expression plasmids comprise a eukaryotic promoter operably linked to the nucleic acid sequence encoding the CRISPR-endonuclease, the sgRNA coding squence or the CD63-ABP fusion protein.
  • the systems described herein also can include an envelope plasmid having an envelope coding sequence that encodes a viral envelope glycoprotein.
  • the Env nucleotide sequence may encode VSV-G.
  • the envelope coding sequence is operably linked to a eukaryotic promoter.
  • the eukaryotic promoter is a RNA polymerase II promoter.
  • VSV-G vesicular stomatitis virus G
  • SEQ ID NO: 45 An exemplary VSV-G amino acid sequence is set forth as SEQ ID NO: 45.
  • SEQ ID NO: 45 is encoded by SEQ ID NO: 44.
  • GenBank Accession Nos. CAC47944.1 Another exemplary VSV-G protein sequence is set forth under GenBank Accession Nos. CAC47944.1.
  • RNA polymerase II promoter is operably linked to the CRISPR-associated endonuclease coding sequence and a RNA polymerase III promoter is operably linked to the gRNA coding sequence.
  • the RNA polymerase II promoter sequence is selected from a mammalian species.
  • the RNA polymerase III promoter sequences is selected from a mammalian species. For example, these promoter sequences can be selected from a human, cow, sheep, buffalo, pig, or mouse, to name a few.
  • the RNA polymerase II promoter sequence is a CMV, FEla, or SV40 sequence.
  • the RNA polymerase III promoter sequence is a U6 or an HI sequence.
  • the RNA polymerase II sequence is a modified RNA polymerase II sequence.
  • the RNA polymerase II sequences having at least 80%, 85%, 90%, 95%, or 99% identity to a wild-type RNA polymerase II promoter sequence from any mammalian species can be used in the constructs provided herein.
  • the RNA polymerase III sequence is a modified RNA polymerase III sequence.
  • the RNA polymerase III sequences having at least 80%, 85%, 90%, 95%, or 99% identity to a wild-type RNA polymerase III promoter sequence from any mammalian species can be used in the constructs provided herein.
  • the identity can be calculated after aligning the two sequences so that the identity is at its highest level, as described above.
  • the eukaryotic promoter is an inducible or regulatable promoter.
  • Coding sequences transcribed from a RNA pol II promoter include a poly(A) signal and a transcription terminator sequence downstream of the coding sequence.
  • Commonly used mammalian terminators include the sequence motif AAUAAA (SEQ ID NO: 108) which promotes both polyadenylation and termination.
  • Coding sequences transcribed from a RNA pol III promoter include a simple run of T residues downstream of the coding sequence as a terminator sequence.
  • the role of the terminator, a sequence-based element is to define the end of a transcriptional unit (such as a gene) and initiate the process of releasing the newly synthesized RNA from the transcription machinery. Terminators are found downstream of the gene to be
  • transcribed and typically occur directly after any 3’ regulatory elements, such as the polyadenylation or poly(A) signal.
  • the mammalian expression plasmid may also include at least one polynucleotide sequence encoding a RNA-stabilizing sequence positioned downstream of the CRISPR component coding sequence or the aptamer coding sequence if positioned downstream of the CRISPR component coding sequence.
  • the polynucleotide sequence encoding the RNA-stabilizing sequence is transcribed downstream of the CRISPR/Cas system component coding sequence and stabilizes the longevity of the transcribed RNA sequence.
  • the polynucleotide sequence encoding the RNA-stabilizing sequence is positioned downstream of the catalytically impaired CRISPR-associated endonuclease coding sequence.
  • the polynucleotide sequence encoding the RNA-stabilizing sequence is positioned downstream of the gRNA coding sequence.
  • An exemplary RNA- stabilizing sequence is the sequence of the 3’ UTR of human beta globin gene as set forth in SEQ ID NO: 17 (DNA) and SEQ ID NO: 18 (RNA).
  • the RNA- stabilizing sequence comprises two or more copies of SEQ ID NO: 17.
  • Other RNA-stabilizing sequences are described in Hayashi, T. et al., Developmental Dynamics 239(7):2034-2040 (2010) and Newbury, S. et al., Cell 48(2):297-310 (1987).
  • a spacer of 1-30 nucleotides may be positioned between the CRISPR component coding sequence and the at least one polynucleotide sequence encoding RNA-stabilizing sequence.
  • any of the mammalian expression plasmids described herein may comprise one or more expression cassettes.
  • the first mammalian expression plasmid comprises a first expression cassette that encodes the CRISPR-associated endonuclease and a second expression cassette that encodes the gRNA comprising at least one aptamer.
  • the mammalian expression plasmid may also comprise a reporter gene.
  • kits include the components of the systems described in this disclosure.
  • the kits include one or more of the plasmids described herein.
  • EVs for example, EVs made by any of the systems and methods described herein.
  • the EVs are exosomes and/or microvesicles. Extracellular vesicles made by any of the methods described herein are also provided. A plurality of EVs is also provided.
  • the EVs contain (a) a ribonucleotide protein (RNP) complex comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; and (b) a fusion protein comprising CD63 and at least one aptamer binding protein (ABP), wherein the ABP binds to the at least one aptamer coding sequence.
  • RNP ribonucleotide protein
  • the extracellular vesicle further comprises a VSV-G protein.
  • Any of the first mammalian expression plasmids described herein wherein at least one aptamer is attached or inserted into the gRNA sequence, can be used to generate EVs containing RNPs. These EVs are useful to transduce eukaryotic cells of interest.
  • one or more first mammalian expression plasmids wherein each of the expression plasmids targets a different site in the genome of cell are used to generate EVs that contain one or more RNPs that target one or more sites in the genome of the cell.
  • a first mammalian expression plasmid comprising a sgRNA that targets site A in the genome of the cell and a first mammalian expression plasmid comprising a sgRNA that targets site B in the genome of a cell can be transduced into cells with the second mammalian expression plasmid encoding a CD63-ABP fusion protein, to generate EVs comprising RNPs that target site A and RNPs that target site B.
  • EVs that target three or more, four or more, five or more, or six or more sites in the genome can be generated using similar methods.
  • the EVs may comprise a fusion protein comprising one or more ABPs.
  • the EVs contain CD63 or a fragment thereof, fused with at least one ABP.
  • the fusion protein comprises an ABP fused to the N-terminus of CD63 and/or an ABP fused to the C-terminus of CD63.
  • the fusion protein comprises a first ABP fused to the N-terminus of CD63 and a second ABP fused to the C-terminus of CD63, wherein the first and second ABP are the same.
  • the fusion protein comprises a first ABP fused to the N-terminus of CD63 and a second ABP fused to the C- terminus of CD63, wherein the first and second ABP are different.
  • the first and second ABP is Com, which binds to the com aptamer that is attached or inserted in the gRNA.
  • the fusion protein comprises two or more ABPs in tandem, fused to the N-terminus of CD63 and/or the C-terminus of CD63.
  • An ABP is a polypeptide sequence that binds to an RNA aptamer sequence.
  • suitable ABPs include bacteriophage RNA-binding proteins that bind specifically to known RNA aptamer sequences, which are RNA sequences that form stem-loop structures.
  • Exemplary non-viral aptamer binding protein include MS2 coat protein, PP7 coat protein, lambda N peptide, and Com protein.
  • the lambda N peptide may be amino acids 1-22 of the lambda N protein, which are the RNA-binding domain of the protein. Information about these ABP and the aptamer sequences to which they bind is provided above in Table 1.
  • gRNA generally comprises a DNA targeting sequence and a constant region that interacts with the CRISPR-associated endonuclease.
  • the gRNA may comprise a transactivating crRNA (tracrRNA) sequence.
  • the gRNA may comprise a tracrRNA where it is to be used in conjunction with a Cas9 protein or derivative.
  • the gRNA does not comprise a tracrRNA sequence.
  • the gRNA may not comprise a tracrRNA sequence where it is to be used in conjunction with a Cpfl protein or derivative.
  • the gRNA comprises at least one aptamer sequence.
  • the at least one aptamer sequence may be positioned at the 5’ end or the 3’ end of the gRNA.
  • the at least one aptamer sequence may be inserted at an internal position within the gRNA such as, for example, at one or more of the loops formed in the folded gRNA.
  • the at least one aptamer sequence may be positioned at the tetra loop, the stem loop 2 (ST2), or the 3’ end of the gRNA.
  • a spacer of 1-30 ribonucleotides may be positioned between the gRNA and the at least one aptamer sequence, or flanking the at least one aptamer sequence.
  • a method of producing an extracellular vesicle comprising: (a) transfecting a plurality of eukaryotic cells with the first mammalian expression plasmid (i.e., a plasmid encoding a CRISPR-associated endonuclease and a sgRNA) and the second mammalian expression plasmid (i.e., a plasmid encoding a CD63-ABP fusion protein) of any of the plasmid systems described herein; and (b) culturing the transfected eukaryotic cells for sufficient time for extracellular vesicles to be produced.
  • the method further comprises transfecting the plurality of eukaryotic cells with the envelope plasmid (i.e., a plasmid encoding VSV-G
  • the extracellular vesicle comprises: (a) a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; and (b) a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence.
  • a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence
  • a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence.
  • the extracellular vesicle comprises: (a) a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; (b) a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the aptamer coding sequence; and(c) a VSV-G protein.
  • a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence
  • a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the aptamer coding sequence
  • ABS aptamer binding protein
  • the plurality of eukaryotic cells are mammalian cells.
  • the method further comprises isolating the extracellular vesicles from the cultured transfected eukaryotic cells.
  • Methods for isolating EVs are known in the art. See, for example, Konoshenko et al. “Isolation of Extracellular Vesicles: General Methodologies and Latest Trends,” Hindawi BioMed Research International Vol. 2018, Article ID 8545347; and Furi et al. “Extracellular vesicle isolation: present and future,” Ann Transl. Med. 5(12): 263 (2017).
  • the eukaryotic cells are selected from the group consisting of HEK293T cells, C2C12 cells, primary myoblasts, neural stem cells, pluripotent stem cells, and mesenchymal stem cells.
  • eukaryotic cells comprising a target genomic sequence of interest to be modified are transduced with EVs that contain a fusion protein comprising CD63, or a fragment thereof, fused to at least one aptamer-binding protein (ABP) and an RNP comprising (1) a gRNA and (2) a CRISPR-associated endonuclease.
  • EVs that contain a fusion protein comprising CD63, or a fragment thereof, fused to at least one aptamer-binding protein (ABP) and an RNP comprising (1) a gRNA and (2) a CRISPR-associated endonuclease.
  • ABSP aptamer-binding protein
  • the EVs contain (1) a fusion protein comprising CD63, or a fragment thereof, fused to at least one aptamer-binding protein (ABP); (2) an RNP comprising (a) a gRNA and (b) a CRISPR-associated endonuclease; and (3) an envelope protein or a fragment thereof (for example VSV-G or a fragment thereof.
  • VSV-G facilitates entry of EVs into transduced cells.
  • the CRISPR-associated endonuclease is catalytically impaired.
  • the catalytically impaired CRISPR-associated endonuclease is fused to an adenosine deaminase as part of an ABE.
  • CRISPR-associated endonucleases including catalytically impaired CRISPR-associate endonucleases are described above.
  • the gene editing methods provided herein result in increased editing efficiency by the CRISPR-associated endonuclease or ABE.
  • editing efficiency can be increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or greater, as compared to editing efficiency when RNPs are delivered using non-EV delivery.
  • the increase in gene editing efficiency is a two-fold, a four-fold, a ten-fold, a twenty -fold, a fifty-fold increase or greater.
  • the increase is relative to lentiviral delivery of RNPs.
  • the transduction efficiency of delivering RNPs into cells, using the EVs described herein is increased as compared to non-EV delivery.
  • transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or greater, as compared to transduction efficiency when RNPs are delivered to cells using non-EV delivery.
  • the increase in transduction efficiency is a two-fold, a four-fold, a ten-fold, a twenty -fold, a fifty-fold increase or greater.
  • the increase is relative to lentiviral delivery of RNPs.
  • the gene editing methods provided herein result in reduced guide independent RNA off-target gene editing events, for example, those associated CRISPR- associated endonuclesase or ABEs.
  • guide-independent RNA off-target activity can be reduced by at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or greater, as compared to RNA off-target activity when RNPs are delivered using non-EV delivery.
  • guide independent DNA off-target gene editing events are also reduced.
  • guide-dependent DNA off-target activity can be reduced by at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 90%, 95%, 99% or greater when RNPs are delivered using non-EV delivery.
  • the transduced eukaryotic cells are mammalian cells.
  • the eukaryotic cells may be in vitro cultured cells.
  • the eukaryotic cells may ex vivo cells obtained from a subject.
  • the eukaryotic cells are present in a subject.
  • subject is meant an individual.
  • the subject is a mammal, such as a primate, and, more specifically, a human. Non-human primates are subjects as well.
  • the term subject includes domesticated animals, such as cats, dogs, etc., livestock (for example, cattle, horses, pigs, sheep, goats, etc.) and laboratory animals (for example, ferret, chinchilla, mouse, rabbit, rat, gerbil, guinea pig, etc.).
  • livestock for example, cattle, horses, pigs, sheep, goats, etc.
  • laboratory animals for example, ferret, chinchilla, mouse, rabbit, rat, gerbil, guinea pig, etc.
  • patient or subject may be used interchangeably and can refer to a subject afflicted with a disease or disorder.
  • the EVs provided by this disclosure may be injected into a subject according to known, routine methods.
  • the viral particles of the system are injected intravenously (IV), intraperitoneally (IP), intramuscularly, or into a specific organ.
  • the EVs may also be implanted, for example, into a tumor.
  • the provided methods are for modifying a target loci of interest, the method comprising transducing a plurality of eukaryotic cells with a plurality of EVs, wherein the plurality of EVs comprise a fusion protein comprising CD63 or a fragment thereof, fused to at least one ABP; and a ribonucleotide protein (RNP) complex comprising (1) a gRNA and (2) a CRISPR-associated endonuclease, wherein the RNP binds to the genomic target sequence in genomic DNA of the cell and the CRISPR-associated endonuclease alters the genomic DNA of the cell.
  • RNP ribonucleotide protein
  • EVs comprising two or more RNPs wherein each RNP targets a different locus can be used to modify two or more loci of interest in a eukaryotic cells.
  • the RNPs are packaged into the EVs via the interaction of an aptamer sequence attached to or inserted into a gRNA sequence that forms a complex with the catalytically impaired CRISPR-associated endonuclease.
  • the methods described can be used with any CRISPR-associated endonuclease that requires a constant region of an sgRNA for function.
  • CRISPR-associated endonuclease that requires a constant region of an sgRNA for function.
  • These include, but are not limited to RNA- guided site-directed nucleases. Examples include nucleases present in any bacterial species that encodes a Type II or V CRISPR/Cas system. Suitable CRISPR-associated endonucleases are described throughout this disclosure.
  • the site-directed nuclease can be a catalytically impaired Cas9 polypeptide, a catalytically impaired Cpfl polypeptide, a catalytically impaired Cas9 nickase or derivatives thereof.
  • the sgRNA is targeted to specific regions at or near a gene.
  • the sgRNA can be targeted to a region where single base changes are necessary, for example, to correct a single base mutation in the human beta-globin gene that causes sickle cell anemia.
  • the sgRNA allows the RNPs described herein to a specific site in the genomic sequence of a cell. Once the RNP binds to the specific site in the genomic sequence, the CRISPR-associated endonuclease cleaves one or more strands of the DNA at the specific site.
  • the ABE catalyzes adenosine (A) to inosine formation in one strand, while the catalytically impaired endonuclease, for example, Cas9 D10A nicks the opposite strand, i.e., the non-edited strand.
  • endonuclease for example, Cas9 D10A
  • inosine is read as guanosine by polymerase enzymes
  • DNA repair and replication mechanism replace the original A-T base pair with a G-C base pair at the target site. See, Gaudelli et al. (2017).
  • the modifications to the system components as described in this disclosure do not impair how the system components function following transduction into eukaryotic cells. Rather, the components may function similarly or better than unmodified components upon transduction into eukaryotic cells.
  • the CD63-ABP fusion proteins in the EVs may not interfere with the EV transduction of eukaryotic cells.
  • the RNPs packaged in the EVs comprise at least one aptamer sequence
  • the at least one aptamer sequence may not interfere with the EV transduction of eukaryotic cells.
  • the EV containing the CD63-ABP fusion protein may result in greater gene editing upon transduction into eukaryotic cells relative to EVs that do not comprise CD63-ABP fusion protein.
  • the eukaryotic cells can be in vitro, ex vivo or in vivo.
  • the cell is a primary cell (isolated from a subject).
  • a primary cell is a cell that has not been transformed or immortalized.
  • Such primary cells can be cultured, sub-cultured, or passaged a limited number of times (e.g., cultured 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 times).
  • the primary cells are adapted to in vitro culture conditions.
  • the primary cells are isolated from an organism, system, organ, or tissue, optionally sorted, and utilized directly without culturing or sub-culturing.
  • the primary cells are stimulated, activated, or differentiated.
  • the cells are cultured under conditions effective for expanding the population of modified cells.
  • cells modified by any of the methods provided herein are purified.
  • cells are removed from a subject, modified using any of the methods described herein and re administered to the patient.
  • the cells are cultured for a sufficient amount of time to allow for gene editing to occur, such that a pool of cells expressing a detectable phenotype can be selected from the plurality of transduced cells.
  • the phenotype can be, for example, cell growth, survival, or proliferation.
  • the phenotype is cell growth, survival, or proliferation in the presence of an agent, such as a cytotoxic agent, an oncogene, a tumor suppressor, a transcription factor, a kinase (e.g., a receptor tyrosine kinase), a gene (e.g., an exogenous gene) under the control of a promoter (e.g., a heterologous promoter), a checkpoint gene or cell cycle regulator, a growth factor, a hormone, a DNA damaging agent, a drug, or a chemotherapeutic.
  • the phenotype can also be protein expression, RNA expression, protein activity, or cell motility, migration, or invasiveness.
  • the selecting the cells on the basis of the phenotype comprises fluorescence activated cell sorting, affinity purification of cells, or selection based on cell motility.
  • the selecting the cells can also comprise analysis of the genomic DNA of the cells such as by amplification, sequencing, SNP analysis, etc.
  • Sequencing methods include, but are not limited to, shotgun sequencing, bridge PCR, Sanger sequencing (including microfluidic Sanger sequencing), pyrosequencing, massively parallel signature sequencing, nanopore DNA sequencing, single molecule real-time sequencing (SMRT) (Pacific Biosciences, Menlo Park, CA), ion semiconductor sequencing, ligation sequencing, sequencing by synthesis (Illumina, San Diego, Ca), Polony sequencing, 454 sequencing, solid phase sequencing, DNA nanoball sequencing, heliscope single molecule sequencing, mass spectroscopy sequencing, pyrosequencing, Supported Oligo Ligation Detection (SOLiD) sequencing, DNA microarray sequencing, RNAP sequencing, tunneling currents DNA sequencing, and any other DNA sequencing method identified in the future.
  • One or more of the sequencing methods described herein can be used in high throughput sequencing methods. As used herein, the term “high
  • Any of the methods and compositions described herein can be used to treat a disease (e.g., cancer, a blood disorder (for example, sickle cell anemia or beta thalassemia), an infectious disease, an autoimmune disease, transplantation rejection, graft vs. host disease or other inflammatory disorder) in a subject.
  • a disease e.g., cancer, a blood disorder (for example, sickle cell anemia or beta thalassemia), an infectious disease, an autoimmune disease, transplantation rejection, graft vs. host disease or other inflammatory disorder
  • the cancer to be treated is selected from a cancer of B-cell origin, breast cancer, gastric cancer, neuroblastoma, osteosarcoma, lung cancer, colon cancer, chronic myeloid cancer, leukemia (e.g., acute myeloid leukemia, chronic lymphocytic leukemia (CLL) or acute lymphocytic leukemia (ALL)), prostate cancer, colon cancer, renal cell carcinoma, liver cancer, kidney cancer, ovarian cancer, stomach cancer, testicular cancer, rhabdomyosarcoma, and Hodgkin's lymphoma.
  • the cancer of B-cell origin is selected from the group consisting of B-lineage acute lymphoblastic leukemia, B-cell chronic lymphocytic leukemia, and B-cell non-Hodgkin's lymphoma.
  • the cells of the subject are modified in vivo, for example, by delivering any of the EVs described herein to the subject. See, for example, Murphy et al. Experimental and Molecular Medicine 51: 1-12 (2019)).
  • the EVs can be targeted to a cell or tissue by modification of the EVs to include a binding moiety that binds to a target, for example, a tumor antigen on a tumor cell.
  • a desired ligand can be linked to the EVs via association with polyethylene glycol (PEG), such that the PEGylated EVs coated with the desired ligand can be specifically targeted to a cell-surface target. See, for example, Rocco et al.
  • PEG polyethylene glycol
  • an effective amount of any of the EVs described herein are administered to the subject.
  • an "effective amount" is an amount sufficient to effect beneficial or desired results.
  • An effective amount can be administered in one or more administrations, applications or dosages.
  • the EVs are delivered in a pharmaceutical composition.
  • such pharmaceutical compositions are formulated for in use in vivo, ex vivo or in vitro using pharmaceutically acceptable excipients.
  • the dosage of EVs administered to a subject will depend the disease or the symptoms to be treated or alleviated, the administration route, as well as various other parameters of relevance known to a skilled person.
  • the amount of EVs to be administered to the subject can be determined by quantitating an EV protein, for example, CD63, with a bicinchoninic acid (BCA) method.
  • the amount of protein to be delivered to the subject can be determined by Western blot detection of the CRISPR-associated endonuclease, for example, Cas9, in EVs, respectively. It is understood that populations of EVs are also provided herein.
  • the EV concentration in any of the compositions described herein may be expressed in many different ways, for instance amount of EV protein per unit (often volume) or per dose, number of EVs or particles per unit (often volume, per subject, per kg of body weight, etc.).
  • a composition comprising from about 10 6 to about 10 25 EVs can be administered to a subject in one or more doses.
  • a composition comprising 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , 10 14 , 10 15 , 10 16 , 10 17 , 10 18 , 10 19 , 10 20 , 10 21 , 10 22 , 10 23 , 10 24 , 10 25 or any other amount of EVs, in between these amounts, can be administered to the subject in one or more administrations.
  • the method of treating a disease in a subject comprises: a) obtaining cells from the subject; b) modifying the cells using any of the methods provided herein; and c) administering the modified cells to the subject.
  • the modified cells are expanded and/or differentiated prior to administering the modified cells to the subject.
  • modification occurs by contacting eukaryotic cells with any of the EVs described herein, wherein the RNP (i.e., a complex comprising a CRISPR-associated endonuclease and a gRNA) delivered by the EV into the cell binds to a site in the genome targeted by the sgRNA, and modifies the genome the cell.
  • the RNP i.e., a complex comprising a CRISPR-associated endonuclease and a gRNA
  • the cells are modified to, for example, correct a mutation, insert a functional copy of a gene, insert a nucleic acid sequence encoding a tumor antigen, edit a base, or otherwise alter the genomic sequence of the cells to treat the disease.
  • the disease is selected from the group consisting of cancer, a blood disorder (for example, sickle cell anemia or beta thalassemia), an infectious disease, an autoimmune disease, transplantation rejection, graft vs. host disease or other inflammatory disorder in a subject.
  • a blood disorder for example, sickle cell anemia or beta thalassemia
  • infectious disease for example, an autoimmune disease, transplantation rejection, graft vs. host disease or other inflammatory disorder in a subject.
  • the cells obtained form the subject are modified to express a tumor specific antigen.
  • tumor- specific antigen means an antigen that is unique to cancer cells or is expressed more abundantly in cancer cells than in in non-cancerous cells.
  • the cells obtained from the subject are T cells.
  • the modified cells are expanded prior to administration to the subject.
  • a single component may be replaced by multiple components, and multiple components may be replaced by a single component, to provide an element or structure or to perform a given function or functions. Except where such substitution would not be operative to practice certain embodiments of the disclosure, such substitution is considered within the scope of the disclosure.
  • Exemplary embodiments of the invention include:
  • a plasmid system comprising: (a) a first mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence, wherein the nucleic acid sequence comprises: (i) a nucleic acid sequence encoding a CRISPR-associated endonuclease; and (ii) a guide RNA (gRNA) coding sequence, wherein the gRNA coding sequence comprises at least one aptamer coding sequence; and (b) a second mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence encoding a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence of the first mammalian expression plasmid.
  • a first mammalian expression plasmid comprising a eukaryotic promoter operably linked
  • VSV G vesicular stomatis virus G
  • the CRISPR-associated endonuclease is a Cas9 protein, a Cpfl protein or a derivative of either.
  • CRISPR-associated endonuclease coding sequence encodes a Cas9 D10A protein.
  • nucleic acid sequence of the first mammalian expression plasmid encodes a nucleic acid sequence encoding an adenosine base pair editor (ABE), wherein the ABE is a fusion protein comprising an adenosine deaminase and the catalytically impaired CRISPR-associated endonuclease.
  • ABE adenosine base pair editor
  • aptamer sequence is an MS2 aptamer sequence, a pp7 aptamer, Box-B aptamer, or a com aptamer sequence.
  • fusion protein comprises a first ABP fused to the N-terminus of CD63 and a second ABP fused to the C- terminus of CD63, wherein the first and second ABP are the same.
  • sgRNA coding sequence comprises at least one aptamer coding sequence inserted into the tetraloop or the ST2 loop of the sgRNA coding sequence.
  • sgRNA coding sequence comprises at least one com aptamer sequence inserted into the tetraloop or the ST2 loop of the gRNA coding sequence.
  • An extracellular vesicle comprising:(a) a ribonucleotide protein (RNP) complex comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; and (b) a fusion protein comprising CD63 and at least one aptamer binding protein (ABP), wherein the ABP binds to the at least one aptamer coding sequence.
  • RNP ribonucleotide protein
  • ABP aptamer binding protein
  • CRISPR-associated endonuclease is a catalytically impaired CRISPR-associated endonuclease.
  • CRISPR-associated endonuclease coding sequence encodes a Cas9 D10A protein.
  • ABE adenine base pair editor
  • sgRNA coding sequence comprises at least one aptamer coding sequence inserted into the tetraloop or the ST2 loop of the sgRNA coding sequence.
  • a method of producing an extracellular vesicle comprising:
  • the extracellular vesicle comprises: (a) a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; and (b) a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence.
  • the extracellular vesicle comprises:
  • a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) a gRNA comprising at least one aptamer coding sequence; (b) a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the aptamer coding sequence; and(c) a VSV-G protein.
  • a method of modifying a genomic target sequence in a cell comprising transducing a plurality of eukaryotic cells with a plurality of extracellular vesicles, wherein the plurality of extracellular vesicles comprise an extracellular vesicle according to any one of embodiments 14-27, wherein the RNP binds to the genomic target sequence in genomic DNA of the cell, thereby modifying the genomic target sequence.
  • a method for treating a disease in a subject comprising:
  • a plasmid system comprising: (a) a first mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence, wherein the nucleic acid sequence comprises: (i) a nucleic acid sequence encoding a heterologous polypeptide; and (ii) at least one aptamer coding sequence; and (b) a second mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence encoding a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence of the first mammalian expression plasmid.
  • a first mammalian expression plasmid comprising a eukaryotic promoter operably linked to a nucleic acid sequence
  • the nucleic acid sequence comprises: (i) a nucleic acid sequence
  • nucleic acid sequence of the first mammalian expression plasmid encodes a CRISPR-associated endonuclease and further comprises a guide RNA (gRNA) coding sequence.
  • gRNA guide RNA
  • nucleic acid sequence encoding the heterologous polypeptide comprises the at least one aptamer coding sequence.
  • gRNA coding sequence comprises the at least one aptamer coding sequence.
  • plasmid system of any of embodiments 1-49, further comprising an envelope plasmid comprising a nucleic acid sequence encoding vesicular stomatis virus G (VSV G) protein.
  • VSV G vesicular stomatis virus G
  • CRISPR-associated endonuclease coding sequence encodes a Cas9 D10A protein.
  • nucleic acid sequence of the first mammalian expression plasmid encodes a nucleic acid sequence encoding an adenosine base pair editor (ABE), wherein the ABE is a fusion protein comprising an adenosine deaminase and the catalytically impaired CRISPR-associated endonuclease.
  • ABE adenosine base pair editor
  • fusion protein comprises a first ABP fused to the N-terminus of CD63 and a second ABP fused to the C-terminus of CD63, wherein the first and second ABP are the same.
  • sgRNA coding sequence comprises at least one aptamer coding sequence inserted into the tetraloop or the ST2 loop of the sgRNA coding sequence.
  • sgRNA coding sequence comprises at least one com aptamer sequence inserted into the tetraloop or the ST2 loop of the gRNA coding sequence.
  • An extracellular vesicle comprising: (a) a mRNA encoding a heterologous polypeptide and at least one aptamer coding sequence; and (b) a fusion protein comprising CD63 and at least one aptamer binding protein (ABP), wherein the ABP binds to the at least one aptamer coding sequence.
  • ABP aptamer binding protein
  • a method of producing an extracellular vesicle comprising:
  • nucleic acid sequence encoding the heterologous polypeptide comprises the at least one aptamer coding sequence.
  • gRNA coding sequence comprises the at least one aptamer coding sequence
  • RNA encoding the heterologous polypeptide and the at least one aptamer sequence (a) an mRNA encoding the heterologous polypeptide and the at least one aptamer sequence; and (b) a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the at least one aptamer coding sequence.
  • ABSP aptamer binding protein
  • a RNP comprising: (i) a CRISPR-associated endonuclease; and (ii) the gRNA comprising at least one aptamer coding sequence; (b) a fusion protein comprising CD63 and at least one aptamer binding protein, wherein the aptamer binding protein (ABP) binds to the aptamer coding sequence; and (c) a VSV-G protein.
  • a method of modifying a genomic target sequence in a cell comprising transducing a plurality of eukaryotic cells with a plurality of extracellular vesicles, wherein the plurality of extracellular vesicles comprise an extracellular vesicle according to any one of embodiments 62-66 and 76, wherein the RNP binds to the genomic target sequence in genomic DNA of the cell, thereby modifying the genomic target sequence.
  • a method for treating a disease in a subject comprising: a) obtaining cells from the subject; b) modifying the cells of the subject using the method of any one of embodiments 77-81; and c) administering the modified cells to the subject.
  • Plasmids CD63-pEGFP-C2 (Addgene #62964) and pMD2.G (Addgene #12259) were purchased from Addgene. Plasmids generated for the studies described herein are provided in Table 2. Gene synthesis was done by GenScript Inc. (Piscataway NJ). All constructs generated were confirmed by Sanger sequencing. Sequence information for primers, oligoes, and synthesized DNA fragments is in Table 3. Target sequences for sgRNAs are listed in Table 4. All constructs generated were confirmed by Sanger sequencing. Sequence information for primers and oligonucleotides are listed in Tables 3 and 4.
  • any of the constructs described herein can include one or more introns, for example, between the promoter sequence and a nucleic acid encoding a polypeptide sequence (e.g., CD63, ABE etc.), to facilitate expression of one or more polypeptides sequences in the construct.
  • a polypeptide sequence e.g., CD63, ABE etc.
  • GFP reporter assays for gene editing activities HEK293T derived HBB-IL2RG EGFP reporter cells with target sequences for human beta hemoglobin (HBB) sickle cell mutant and human IL2RG (Javidi-Parsijani et al. PLoS One 12, e0177444 (2017)), and DMD reporter cells with target sequence from human DMD exon 53 (Lyu et al., PLoS One 15, e0239468 (2020)) were used to detect gene editing activities of Cas9 RNPs targeting HBB, IL2RG, and DMD exon 53, respectively.
  • the GFP-reporter cells expressed no EGFP due to the disruption of the EGFP reading frame by the insertion of the respective target sequences right after the start codon of EGFP coding sequence.
  • INDELs formed after gene editing may restore the EGFP reading frame, resulting in EGFP expression.
  • GFP-positive cells were analyzed by fluorescence microscopy or flow cytometry (BD Biosciences, Accuri C6 (San Jose, CA)).
  • RNP-enriched extracellular vesicles were produced by co-transfection of three plasmids into HEK293T cells: plasmid DNA expressing a fusion protein between ABP Com and CD63, pDM2.G expressing VSV-G, and the target plasmid expressing the gene editing effector (SaCas9, SpCas9 or ABE) and the respective gene-specific sgRNA (See Table 2 for various target plasmids). Briefly, 5 million actively proliferating HEK293T cells grown in 10-cm dishes were incubated with 5 ml Opti- MEM ® medium.
  • 3 ⁇ g of Com-CD63-Com fusion protein expressing plasmid, 3 pg pMD2.G, and 12 pg target plasmid DNA were mixed in 0.5 ml Opti-MEM ® medium.
  • Fifty -four pi of Fugene HD (Promega (Madison, WI)) or 54 pg of polyethylenimine (Synchembio, Cat. No. SH-35421, Chicago, IL) were mixed in 0.5 ml Opti-MEM ® medium.
  • the DNA mixture and the transfection reagent mixture were then mixed and incubated at room temperature for 15 mins, before they were added to the cells in Opti-MEM ® medium.
  • the medium was changed into 10 ml Opti-MEM ® medium and the RNP-enriched EVs were collected 72 hr after transfection.
  • the amounts of DNA and transfection reagent were scaled based on tissue culture surface area.
  • EV concentration Ultracentrifugation was used to concentrate EVs from tissue culture medium following procedures described in Lu et al. (PloS One 12, e eOl 85992 (2017)). Briefly, the cell culture medium was centrifuged at 1000 c g for 30 minutes at 4°C to remove cell debris. The supernatant was centrifuged at 120,000 c g for 70 minutes at 4°C.
  • the pellet was washed once with PBS and centrifuged again under the same conditions.
  • the resulting pellet containing the EVs was resuspended in PBS.
  • EVs from 10 ml supernatants were resuspended in 500 pi (20X concentration) for in vitro experiments. These EVs can be stored at -80°C or be used immediately.
  • Nanoparticle tracking analysis of EVs Hydrodynamic diameters and concentrations of EVs were measured using the Nanosight NS500 instrument (Malvern Instruments, UK) using the instrument’s software (version NTA3.2). The instrument was primed using phosphate buffered saline (PBS), pH 7.4 and the temperature was maintained at 25 °C. Accurate particle tracking was verified using 50 nm and 100 nm polystyrene nanoparticle standards (Malvern Instruments) prior to examining samples. Concentrated samples containing EVs were serial diluted 1000 fold in PBS. The linear range for quantification of EV concentration in each sample fell between 10-40,000 fold dilutions. Therefore, all samples were diluted 1,000-fold in PBS. Five independent measurements (60 sec each) were obtained for each sample in triplicate. Data are reported as the mean (multiplied by dilution factor for concentration determination) of these measurements ⁇ standard error of the mean.
  • EV mediated RNP delivery RNP enriched EVs concentrated from supernatant of 0.6-20 million cells were added to 2.5xl0 4 cells grown in Opti-MEM (Cat. No. 11058021, ThermoFisher, Waltham, MA) in 24-well plates. It is important that the medium had low serum, since the presence of FBS in the medium inhibits EV mediated RNP delivery. After incubation for 12-24 hours, the medium was changed to DMEM medium with 10% FBS. Thirty-six hours after EV treatment, gene editing was analyzed by flow cytometry, fluorescent microscopy or next generation sequencing (NGS).
  • NGS next generation sequencing
  • HEK293T cells (2.5xl0 4 ) were grown in RMPI1640 medium with 0.5% FBS in 24-well plates to limit proliferation. The cells were treated with RNP-loaded EVs at different times, but were collected at the same time. EVs secreted by 0.2 million cells in 48 hours ( ⁇ 8xl0 9 vesicles) were added to each well. Just before EV treatment, the medium was changed to Opti-MEM ® medium.
  • the cells were collected at 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, and 48 hr after EV addition, washed twice with PBS buffer, and lysed in Laemmli buffer for Western blot analysis.
  • CD9 antibody SBI, Cat. EXOAB-CD9A-1, 1:1000 (Palo Alto, C A)
  • VS V-G antibody Sigma, Cat. V4888, 1:1000
  • CD63 antibody Abeam, Cat. ab68418, 1:1000
  • GRP 94 antibody CST, Cat. 20292T, 1:1000 (Danvers, MA)
  • anti- Rabbit IgG H+L
  • Chemiluminescent reagents (Pierce ECL Western blotting substrate, Cat.32106 (Waltham, MA)) were used to visualize the protein signals under the LAS-3000 system (Fujifilm (Valhalla, NY)). Densitometry (ImageJ software (Version 1.49), National Institutes of Health, imagej.nih.gov/ij/index.html) was used to quantitate protein amount based on Western blotting images. [0236] RT-qPCR and qPCR analyses. A RNeasy ® Plus Mini Kit (QIAGEN Cat No. 74136 (Hilden, Germany)) was used to isolate RNA from collected EVs.
  • QuantiTect ® Reverse Transcription Kit (QIAGEN) was used to reverse-transcribe the RNA to cDNA.
  • sgRNA-Fl and sgRNA-R3 were used as primers in SYBRTM Green based RT-qPCR.
  • ABE-g5-onF and g5-ABE-R were used as qPCR primers to detect base editing at site 5.
  • PCR was run on an ABI 7500 instrument. Primer information is included in Table 3.
  • Transmission electron microscopy was performed at the Cellular Imaging Shared Resource of Wake Forest Institution Health Center (Winston-Salem, NC). Collected EVs were (about 6.0 x 10 11 vesicles/ml) stained with uranyl acetate. The particles were absorbed on plain carbon grids, dried and observed under a FEI Tecnai G2 30 electron microscope (FEI, Hillsboro, OR). The diameters of the particles were measured with NIH ImageJ software (Version 1.49).
  • Genomic DNA was isolated from cultured cells with the DNeasy Blood & Tissue Kit (Qiagen). The DNA region containing the target sequences were amplified by the proofreading HotStart® ReadyMix from KAPA Biosystems (Wilmington, MA). PCR primers used for amplifying each target sequence were listed in Table 3. The purified PCR products were shipped to Genewiz Inc. (Morrisville, NC) to perform next generation sequencing using the Amplicon EZ service. Usually 50,000 reads/amplicon were obtained. Analysis of insertions and deletions (INDEL) was done with the online Cas-Analyzer software 28 and CRISPRESS0229, which gave very similar results.
  • INDEL Analysis of insertions and deletions
  • CD63 is a tetraspan transmembrane protein with the N- and C-termini in the cytoplasm. Com was fused to the N- terminus, the C-terminus, or both termini of CD63 (Fig. 1 A), so that Com faces the cytoplasmic side of the plasma membrane. It was hypothesized that, during exosome generation, Cas9 or ABE RNPs would be enriched in exosomes via interactions between CD63-Com, com-sgRNA, and Cas9 (Fig. IB).
  • RNPs can also be enriched in microvesicles via the outward budding and fission of membrane vesicles from the cell surface (Fig. 1C).
  • Fig. 1C membrane vesicles from the cell surface
  • Com-CD63, CD63-Com or Com-CD63-Com was co-expressed with VSV-G, SaCas9 and com modified IL2RG-targeting sgRNA 12 in HEK293T cells.
  • the EVs were collected from the supernatant of the transfected cells and concentrated by ultracentrifugation.
  • the resuspended EVs were added to the medium of HBB-IL2RG GFP reporter cells described previously (Javidi-Parsijani 2017)) . These cells expressed no EGFP due to the disruption of the EGFP reading frame by the insertion of the 119 nt HBB sickle mutation and IL2RG target sequences right after the start codon of EGFP coding sequence.
  • INDELs formed after gene editing may restore the EGFP reading frame, resulting in EGFP expression.
  • Com-CD63-Com was used in further experiments since it generated EV-associated RNPs with the highest gene editing activities. Different ratios of Com-CD63-Com and Cas9 RNP expressing plasmid DNA were tested and the best activities were obtained when they were at a mass ratio of 1:4 (Fig. 3).
  • VSV-G was co-expressed in the EV production cells to help the EVs escape from the endosome system in recipient cells.
  • EV-associated RNPs were generated in the absence of VSV-G. These RNPs generated background levels of GFP-positive reporter cells (Fig. 2C). Whether fusing Com to the C-terminus of VSV-G could further increase gene editing activity was tested. This fusion greatly decreased gene editing activity of the EV-associated RNPs. Two possibilities might underlie this observation: 1) fusing Com to the C-terminus of VSV-G decreased the expression of VSV-G by over 50% (Fig. 4); and 2) doing so might interfere with VSV-G’ s fusogenic activity.
  • RNPs can be enriched in and functionally delivered by EVs.
  • the aptamer com, ABP Com and, optionally, VSV-G protein could be used for functional delivery of RNPs by EVs.
  • SpCas9 RNPs could be packaged and delivered by EVs was ablso tested.
  • Replacing the ST2 loop with com aptamer best preserves the functions of SpCas9 sgRNAs and enables efficient delivery of SpCas9 RNPs by lentivirus-like particles. Therefore, similarly modified sgRNA were used to package SpCas9 RNPs into EVs.
  • Various Com- CD63 fusion proteins, VSV-G, SpCas9, and ST2-com modified IL2RG-targeting sgRNA were co expressed in HEK293T cells. The resultant EVs were applied to HBB-IL2RG GFP reporter cells.
  • SpCas9 RNPs were efficiently packaged by Com-CD63-Com, and both the ABP and aptamer were needed for best gene editing activities (Fig. 2D).
  • an ABP/aptamer interaction can be used to package SpCas9 RNPs into EVs.
  • Adenine base editor (ABE) RNPs targeting ABE site 5 (GRCh38.pl3, chromosome 20, 32752960-32752979) 31 were packaged in EVs.
  • the data show that EVs can also enrich and deliver ABE RNPs.
  • Nuclear export of sgRNAs driven by U6 promoter can be inefficient.
  • RNA polymerase II promoter-driven sgRNA that was flanked by the Hammerhead (HH) ribozyme and hepatitis delta virus (HDV) ribozyme were used in some studies.
  • This design has been shown to generate mature sgRNA after ribozyme cleavage (Yoshioka et ak, Sci Rep 5, 18341 (2015).
  • This design only slightly increased the gene editing activities of the EV-delivered RNPs (Fig. 5). This suggested that sgRNA nuclear export was not a limiting factor in these studies. It is possible that aptamer modified sgRNA provides an active enrichment mechanism to recruit sgRNAs into membrane vesicles.
  • Example 7 Single preparation of RNP-enriched EVs for multiplex gene editing
  • each CD63 molecule is fused to two Com molecules, and each EV may have more than one Com-CD63-Com molecule, it was reasoned that EVs could be ideal for delivering RNPs for simultaneously targeting multiple loci.
  • EVs loaded with RNPs targeting DMD intron 50, RNPs targeting DMD intron 51, and RNPs targeting both introns were prepared.
  • EVs loaded with RNPs targeting both introns were prepared in a single EV preparation simply by using half of each target plasmid DNA.
  • the two individually packaged RNPs were used together to compare with the co-packaged RNPs for exon 51 removal. All RNP- loaded EVs were prepared in parallel and similarly concentrated. PCR was used to detect exon 51 removal: a 2645 bp would be amplified with primers DMD50-F and DMD51-R2 without exon 51 removal (Fig.9A), otherwise a 284 bp product would be amplified. A 284 bp amplicon was observed in cells treated with the co-packaged RNPs, but not in cells treated with the two individually packaged RNPs (Fig. 9B). DNA sequencing confirmed that the ⁇ 284bp amplicon was the result of deleting the sequences between the two sgRNAs. This experiment showed that one single preparation can produce EVs loaded with RNPs targeting more than one locus, and doing so is more efficient for multiplex gene targeting.
  • RNP- loaded EVs produced by 40 million cells in 48 hours were concentrated and injected into each TA muscle of del52hDMD/mdx mice. One week later, the mice were sacrificed and the TA muscles were collected to examine for target gene editing. Genomic DNA was isolated from the TA muscle and the target DNA region was amplified for NGS analysis. Up to 0.2% INDEL rates (316 of 157982 reads) were observed in the RNP injected muscle, and 0% INDEL rate was observed in the PBS injected muscle (0 of 51302 reads, p ⁇ 0.0001 by Chi-square tests). The INDELs were all around the predicted cleavage site.
  • VSV-G could be important for genome editing activity for the EV delivered RNPs.
  • the most likely explanation is that VSV-G helps the escape of the RNPs from the endosome system in recipient cells. Based on the studies described herein, it is likely that an intact and free C-terminus is important for V SV -G to induce endosome escape.
  • an EV-mediated RNP delivery system Advantages of an EV-mediated RNP delivery system are that RNPs targeting more than one loci and RNPs with Cas9 proteins from different species can be enriched in EVs in a single RNP preparation. As demonstrated herein, co-packaging of SaCas9 and SpCas9 RNPs is possible. It is expected that Cas9 proteins from other species may also be co-packaged as long as the com aptamer can be inserted into their sgRNA. In addition, the co-packaged RNPs are more active than the combination of the individually packaged RNPs for multiplex genome editing. These features make EVs an ideal delivery tool for multiplex genome editing, which is needed in many situations, including knockout of antigens to reduce the risk of immuno- rejection, eradicating HIV pro viral DNA from a genome, and enhancing response in cancer therapy.
  • EVs may be more suitable for systemic delivery, for example, as compared to virus-like particles, which tend to be inactivated by complement system in circulation. Also, EVs have the ability to cross the blood brain barrier, thus expanding therapeutic potential.
  • RNPs can be efficiently and functionally packaged into EVs. EV-delivered RNPs show high on-target gene editing activities.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Biomedical Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Plant Pathology (AREA)
  • Cell Biology (AREA)
  • Immunology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Epidemiology (AREA)
  • Animal Behavior & Ethology (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Virology (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Hematology (AREA)
  • Developmental Biology & Embryology (AREA)
  • Toxicology (AREA)
  • Analytical Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Dispersion Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Mycology (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)
PCT/US2022/016053 2021-02-12 2022-02-11 Engineered extracellular vesicles and their uses Ceased WO2022174004A1 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
US18/276,812 US20240108757A1 (en) 2021-02-12 2022-02-11 Engineered extracellular vesicles and their uses
JP2023548687A JP2024506910A (ja) 2021-02-12 2022-02-11 操作された細胞外小胞およびそれらの使用
EP22753385.8A EP4291164A4 (en) 2021-02-12 2022-02-11 MANIPULATED EXTRACELLULAR VESILES AND THEIR USES
CA3206732A CA3206732A1 (en) 2021-02-12 2022-02-11 Engineered extracellular vesicles and their uses
AU2022220313A AU2022220313A1 (en) 2021-02-12 2022-02-11 Engineered extracellular vesicles and their uses

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202163148872P 2021-02-12 2021-02-12
US63/148,872 2021-02-12

Publications (1)

Publication Number Publication Date
WO2022174004A1 true WO2022174004A1 (en) 2022-08-18

Family

ID=82837296

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2022/016053 Ceased WO2022174004A1 (en) 2021-02-12 2022-02-11 Engineered extracellular vesicles and their uses

Country Status (6)

Country Link
US (1) US20240108757A1 (https=)
EP (1) EP4291164A4 (https=)
JP (1) JP2024506910A (https=)
AU (1) AU2022220313A1 (https=)
CA (1) CA3206732A1 (https=)
WO (1) WO2022174004A1 (https=)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN116218906A (zh) * 2023-01-31 2023-06-06 安可来(重庆)生物医药科技有限公司 一种rna编辑器表达质粒、外泌体适配子融合表达质粒以及一种靶向基因rna编辑方法
EP4118203A4 (en) * 2020-03-11 2024-03-27 The Broad Institute, Inc. NEW ENZYMES CASES AND METHODS FOR SPECIFICITY AND ACTIVITY PROFILING
WO2024172152A1 (ja) * 2023-02-17 2024-08-22 国立大学法人 東京大学 細胞外小胞の運命記録システム
WO2024259973A1 (zh) * 2023-06-21 2024-12-26 安徽省立医院(中国科学技术大学附属第一医院) 装载蛋白或多肽的细胞外囊泡递送平台及其应用

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015002956A1 (en) * 2013-07-01 2015-01-08 Ohio State Innovation Foundation Exosome delivery system
WO2019213257A1 (en) * 2018-05-01 2019-11-07 Wake Forest University Health Sciences Lentiviral-based vectors and related systems and methods for eukaryotic gene editing
WO2020099682A1 (en) 2018-11-16 2020-05-22 Evox Therapeutics Ltd Extracellular vesicles for replacement of urea cycle proteins & nucleic acids
US20200308571A1 (en) * 2019-02-04 2020-10-01 The General Hospital Corporation Adenine dna base editor variants with reduced off-target rna editing
US20200390700A1 (en) * 2015-09-28 2020-12-17 Northwestern University Targeted extracellular vesicles comprising membrane proteins with engineered glycosylation sites

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021095842A1 (ja) * 2019-11-15 2021-05-20 国立大学法人 東京大学 バーコード化された細胞外小胞のライブラリー

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015002956A1 (en) * 2013-07-01 2015-01-08 Ohio State Innovation Foundation Exosome delivery system
US20200390700A1 (en) * 2015-09-28 2020-12-17 Northwestern University Targeted extracellular vesicles comprising membrane proteins with engineered glycosylation sites
WO2019213257A1 (en) * 2018-05-01 2019-11-07 Wake Forest University Health Sciences Lentiviral-based vectors and related systems and methods for eukaryotic gene editing
WO2020099682A1 (en) 2018-11-16 2020-05-22 Evox Therapeutics Ltd Extracellular vesicles for replacement of urea cycle proteins & nucleic acids
US20200308571A1 (en) * 2019-02-04 2020-10-01 The General Hospital Corporation Adenine dna base editor variants with reduced off-target rna editing

Non-Patent Citations (41)

* Cited by examiner, † Cited by third party
Title
"GenBank", Database accession no. XP _024305051.1
ABUDAYYEH ET AL., SCIENCE, vol. 353, no. 6299, 5 August 2016 (2016-08-05), pages 5573
ALTONVAPNEK, NATURE, vol. 282, 1979, pages 864 - 869
ALTSCHUL ET AL., NUCLEIC ACIDS RES, vol. 25, 1977, pages 3389 - 3402
ALTSCHUL, J. MOL. BIOL., vol. 215, 1990, pages 403 - 410
BATZER ET AL., NUCLEIC ACID RES, vol. 19, no. 5081, 1991
CHYLINKSI ET AL., RNA BIOL, vol. 10, no. 5, 1 May 2013 (2013-05-01), pages 726 - 737
ESVELT ET AL., NATURE METHODS, vol. 10, 2013, pages 1116 - 1121
FONFARA ET AL., NATURE, vol. 532, 2016, pages 517 - 521
FURI ET AL.: "Extracellular vesicle isolation: present and future", ANN TRANSL. MED., vol. 5, no. 12, 2017, pages 263
GAUDELLI ET AL.: "Programmable base editing of A-T to G-C in genomic DNA without DNA cleavage", NATURE, vol. 551, 2017, pages 464 - 471
HALL ET AL., J. MOL. APPL. GEN., vol. 2, 1983, pages 101
HAYASHI, T. ET AL., DEVELOPMENTAL DYNAMICS, vol. 239, no. 7, 2010, pages 2034 - 2040
HERZ, vol. 537, no. 549, pages 551 - 52
HOU ET AL., PROC NATL ACAD SCI, vol. 110, no. 39, 24 September 2013 (2013-09-24), pages 15644 - 9
JAVIDI-PARSIJANI ET AL., PLOS ONE, vol. 12, 2017, pages 0177444
JINEK ET AL., SCIENCE, vol. 337, no. 6096, 17 August 2012 (2012-08-17), pages 816 - 21
KARLINALTSCHUL, PROC. NAT'L. ACAD. SCI., vol. 90, 1993, pages 5873 - 5787
KONOSHENKO ET AL.: "Isolation of Extracellular Vesicles: General Methodologies and Latest Trends", HINDAWI BIOMED RESEARCH INTERNATIONAL, vol. 2018
KOSTYUSHEV ET AL., INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 21, no. 19, pages 7362
LU ET AL., PLOS ONE, vol. 12, 2017, pages 0185992
LYU ET AL., PLOS ONE, vol. 15, 2020, pages 0239468
MAKAROVA ET AL., NAT REV MICROBIOL, vol. 13, no. 11, November 2015 (2015-11-01), pages 722 - 36
MAKAROVA ET AL., NATURE REVIEWS, MICROBIOLOGY, vol. 9, 2011, pages 467 - 477
MURPHY ET AL., EXPERIMENTAL AND MOLECULAR MEDICINE, vol. 51, 2019, pages 1 - 12
NAT. REV. MICROBIOL., vol. 9, no. 6, June 2011 (2011-06-01), pages 467 - 477
NEEDLEMANWUNSCH, J. MOL. BIOL., vol. 48, 1970, pages 443
NEWBURY, S. ET AL., CELL, vol. 48, no. 2, 1987, pages 297 - 310
OHTSUKA ET AL., J. BIOL. CHEM., vol. 260, 1985, pages 2605 - 2608
PEARSONLIPMAN, PROC. NATL. ACAD. SCI., vol. 85, 1988, pages 2444
ROCCO ET AL., STEM CELLS INTERNATIONAL, vol. 2016, 2016, pages 12
ROSSOLINI ET AL., MOL. CELL. PROBES, vol. 8, 1994, pages 91 - 98
SAMPSON ET AL., NATURE, vol. 497, no. 7448, 9 May 2013 (2013-05-09), pages 254 - 7
See also references of EP4291164A4
SMITHWATERMAN, ADD. APL. MATH., vol. 2, 1981, pages 482
TOH ET AL., EUR. J. BIOCHEM., vol. 182, 1980, pages 231 - 238
VELTROP, M. ET AL., PLOS ONE, vol. 13, 2018, pages 0193289
YAO XINGANG, LYU PIN, YOO KYUNG, YADAV MANISH KUMAR, SINGH RAVI, ATALA ANTHONY, LU BAISONG: "Engineered extracellular vesicles as versatile ribonucleoprotein delivery vehicles for efficient and safe CRISPR genome editing", JOURNAL OF EXTRACELLULAR VESICLES, TAYLOR & FRANCIS, UK, vol. 10, no. 5, 16 March 2021 (2021-03-16), UK , XP055897973, ISSN: 2001-3078, DOI: 10.1002/jev2.12076 *
YE ET AL., BIOMATERIALS SCIENCE, vol. 8, no. 10, 2020, pages 2966 - 2976
YOSHIOKA ET AL., SCI REP, vol. 5, 2015, pages 18341
ZETSCHE ET AL., CELL, vol. 163, no. 3, 22 October 2015 (2015-10-22), pages 759 - 771

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4118203A4 (en) * 2020-03-11 2024-03-27 The Broad Institute, Inc. NEW ENZYMES CASES AND METHODS FOR SPECIFICITY AND ACTIVITY PROFILING
CN116218906A (zh) * 2023-01-31 2023-06-06 安可来(重庆)生物医药科技有限公司 一种rna编辑器表达质粒、外泌体适配子融合表达质粒以及一种靶向基因rna编辑方法
WO2024172152A1 (ja) * 2023-02-17 2024-08-22 国立大学法人 東京大学 細胞外小胞の運命記録システム
WO2024259973A1 (zh) * 2023-06-21 2024-12-26 安徽省立医院(中国科学技术大学附属第一医院) 装载蛋白或多肽的细胞外囊泡递送平台及其应用

Also Published As

Publication number Publication date
EP4291164A1 (en) 2023-12-20
AU2022220313A1 (en) 2023-08-17
CA3206732A1 (en) 2022-08-18
US20240108757A1 (en) 2024-04-04
EP4291164A4 (en) 2024-11-13
AU2022220313A9 (en) 2024-10-17
JP2024506910A (ja) 2024-02-15

Similar Documents

Publication Publication Date Title
US20240108757A1 (en) Engineered extracellular vesicles and their uses
AU2020266587B2 (en) Novel OMNI-50 CRISPR nuclease
JP2020537541A (ja) 脂質ナノ粒子を用いるインビトロでのｍｒｎａの送達方法
WO2021248016A2 (en) Novel omni-59, 61, 67, 76, 79, 80, 81, and 82 crispr nucleases
JP2024531217A (ja) 遺伝子改変高忠実度ｏｍｎｉ－５０ヌクレアーゼバリアント
EP4119166A1 (en) Composition for inducing apoptosis of cells having genomic sequence variation and method for inducing apoptosis of cells by using composition
EP4587571A2 (en) Immune cells having co-expressed tgfbr shrnas
US20230405116A1 (en) Vectors, systems and methods for eukaryotic gene editing
CN119585419A (zh) 工程化t细胞
WO2023102407A9 (en) Engineered high activity omni-79 nuclease variants
JP2023546694A (ja) 新規のｏｍｎｉ５６、５８、６５、６８、７１、７５、７８及び８４ｃｒｉｓｐｒヌクレアーゼ
KR20240155953A (ko) 진핵 유전자 편집을 위한 조성물, 시스템 및 방법
EP4304663A1 (en) Strategies for knock-ins at c3 safe harbor sites
US20260091113A1 (en) Biallelic Knockout of CTLA4
AU2024206494A1 (en) Omni xl 1-22 crispr nucleases
WO2025221789A1 (en) Compositions and methods for use in car/tcr cell therapies
WO2024064607A9 (en) Biallelic knockout of tet2
WO2024206125A1 (en) Use of prime editing for treating sickle cell disease
CN118647365A (zh) 巨核细胞来源的细胞外囊泡的生物标志物

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: 22753385

Country of ref document: EP

Kind code of ref document: A1

ENP Entry into the national phase

Ref document number: 3206732

Country of ref document: CA

WWE Wipo information: entry into national phase

Ref document number: 2023548687

Country of ref document: JP

ENP Entry into the national phase

Ref document number: 2022220313

Country of ref document: AU

Date of ref document: 20220211

Kind code of ref document: A

WWE Wipo information: entry into national phase

Ref document number: 2022753385

Country of ref document: EP

NENP Non-entry into the national phase

Ref country code: DE

ENP Entry into the national phase

Ref document number: 2022753385

Country of ref document: EP

Effective date: 20230912