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Definitions

• eVLPs enhanced virus-like particles
• a membrane comprising a phospholipid bilayer with one or more virally-derived glycoproteins on the external side; and a cargo disposed in the core of the eVLP on the inside of the membrane, wherein the eVLP does not comprise a protein from any human endogenous or exogenous viral gag or pol, and methods of use thereof for delivery of the cargo to cells.
• eVLPs enhanced virus-like particles
• payloads e.g., biomolecules including nucleic acids (DNA, RNA) or proteins, chemical compounds including small molecules, and/or other molecules, and any combination thereof, into eukaryotic cells.
• eVLPs have the potential to be simpler, more efficient and safer than conventional, artificially-derived lipid/gold nanoparticles and viral particle-based delivery systems, at least because eVLPs have no virus-derived components except for ENV, eVLPs can utilize but do not require chemical-based dimerizers, and eVLPs have the ability to package and deliver specialty single and/or double-stranded DNA molecules (e.g., plasmid, mini circle, closed-ended linear DNA, AAV DNA, episomes, bacteriophage DNA, homology directed repair templates, etc.), single and/or double- stranded RNA molecules (e.g., single guide RNA, prime editing guide RNA, messenger RNA, transfer RNA, long non-coding RNA, circular RNA, RNA replicon, circular or linear splicing RNA, micro RNA, small interfering RNA, short hairpin RNA, piwi- interacting RNA, toehold switch RNA, RNA
• the eVLPs described herein are different from conventional retroviral particles, virus-like particles (VLPs), exosomes and other previously described extracellular vesicles that can be loaded with cargo because of the membrane configuration, vast diversity of possible cargos that are enabled by novel, innovative loading strategies, the lack of a limiting DNA/RNA length constraint, the lack of proteins derived from any viral gag or pol, and the mechanism of cellular entry.
• compositions and methods for cargo delivery that can be used with a diverse array of protein and nucleic acid molecules, including genome editing, epigenome modulation, transcriptome editing and proteome modulation reagents, that are applicable to many disease therapies.
• eVLPs that include a membrane comprising a phospholipid bilayer with one or more virally- derived glycoproteins (e.g., as shown in Table 1) on the external side; and optionally a cargo disposed in the core of the eVLP on the inside of the membrane, wherein the eVLP does not comprise any gag and/or pol protein.
• a membrane comprising a phospholipid bilayer with one or more virally- derived glycoproteins (e.g., as shown in Table 1) on the external side; and optionally a cargo disposed in the core of the eVLP on the inside of the membrane, wherein the eVLP does not comprise any gag and/or pol protein.
• a target cell e.g., a cell in vivo or in vitro.
• the methods include contacting the cell with an eVLP as described herein comprising the biomolecule and/or chemical as cargo.
• methods for producing an eVLP e.g., comprising a biomolecular cargo.
• the methods include providing a cell expressing one or more virally-derived glycoproteins (ENV) (e.g., as shown in Table 1), and a cargo biomolecule and/or chemical, wherein the cell does not express an exogenous gag and/or pol protein; and maintaining the cell under conditions such that the cells produce eVLPs.
• ENV virally-derived glycoproteins
• the methods include harvesting and optionally purifying and/or concentrating the produced eVLPs.
• the methods include using cells that have or have not been manipulated to express any exogenous proteins except for an ENV (e.g., as shown in Table 1), and, if desired, a plasma membrane recruitment domain (e.g., as shown in Table 6).
• ENV e.g., as shown in Table 1
• a plasma membrane recruitment domain e.g., as shown in Table 6
• the “empty” particles that are produced can be loaded with cargo by utilizing nucleofection, lipid, polymer, or CaCh transfection, sonication, freeze thaw, and/or heat shock of purified particles mixed with cargo.
• producer cells do not express any viral gag protein. This type of loading allows for cargo to be unmodified by fusions to plasma membrane recruitment domains and represents a significant advancement from previous VLP technology.
• cells expressing one or more virally-derived glycoproteins e.g., as shown in Table 1
• the cells are primary or stable human cell lines, e.g., Human Embryonic Kidney (HEK) 293 cells or HEK293 T cells.
• HEK Human Embryonic Kidney
• the outer surface of the particle could contain scFvs, nanobodies, darpins, and/or other targeting peptides to enable cell-specific entry.
• the biomolecule cargo is a therapeutic or diagnostic protein or nucleic acid encoding a therapeutic or diagnostic protein.
• the cargo is a chemical compound or molecule.
• the chemical molecule is a trigger for protein-protein dimerization of multimerization, such as the A/C heterodimerizer or rapamycin.
• the chemical compound is a DNA PK inhibitor, such as M3814, NU7026, or NU7441 which potently enhance homology directed repair gene editing.
• the cargo is a gene editing reagent.
• the gene editing reagent comprises a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-based genome editing or modulating protein; a nucleic acid encoding a zinc finger (ZF), transcription activator like effector (TALE), and/or CRISPR-based genome editing or modulating protein; or a ribonucleoprotein complex (RNP) comprising a CRISPR-based genome editing or modulating protein.
• ZF zinc finger
• TALE transcription activator-like effector
• RNP ribonucleoprotein complex
• the gene editing reagent is selected from the proteins listed in Tables 2, 3, 4 & 5.
• the gene editing reagent comprises a CRISPR-based genome editing or modulating protein
• the eVLP further comprises one or more guide RNAs that bind to and direct the CRISPR-based genome editing or modulating protein to a target sequence.
• the cargo comprises a covalent or non-covalent connection to a plasma membrane recruitment domain, preferably as shown in Table 6.
• Covalent connections can include direct protein-protein fusions generated from a single reading frame, inteins that can form peptide bonds, other proteins that can form covalent connections at R-groups and/or RNA splicing.
• Non-covalent connections can include DNA/DNA, DNA RNA, and/or RNA/RNA hybrids (nucleic acids base pairing to other nucleic acids via hydrogen-bonding interactions), protein domains that dimerize or multimerize with or without the need for a chemical compound/molecule to induce the protein-protein binding, single chain variable fragments, nanobodies, affibodies, proteins that bind to DNA and/or RNA, proteins with quaternary structural interactions, optogenetic protein domains that can dimerize or multimerize in the presence of certain light wavelengths, and/or naturally reconstituting split proteins.
• the cargo comprises a fusion to a dimerization domain or protein-protein binding domain that may or may not require a molecule to trigger dimerization or protein-protein binding.
• the producer cells are FDA-approved cells lines, allogenic cells, and/or autologous cells derived from a donor.
• the full or active peptide domains of human CD47 may be incorporated in the eVLP surface to reduce immunogenicity.
• AAV proteins included here are AAV REP 52, REP 78, and VPl-3.
• the capsid site where proteins can be inserted is T138 starting from the VPl amino acid counting. Dimerization domains could be inserted at this point in the capsid, for instance.
• dimerization domains included here that may or may not need a small molecule inducer are dDZFl, dDZF2, DmrA, DmrB, DmrC, FKBP, FRB, GCN4 scFv, 10x/24x GCN4, GFP nanobody and GFP.
• split inteins examples include Npu DnaE, Cfa, Vma, and Ssp DnaE.
• RNA binding proteins examples include MS2, Com, and PP7.
• Examples of synthetic DNA-binding zinc fingers included here are ZF6/10,
• proteins that multimerize as a result of quaternary structure included here are E. coli ferritin, and the other chimeric forms of ferritin.
• optogenetic “light-inducible proteins” examples include Cry2, CIBN, and Lov2-Ja.
• peptides the enhance transduction included here are L17E, Vectofusin, KALA, and the various forms of nisin.
• FIG 1 Depiction of exemplary T2eVLP/T4eVLP production and transduction for RNP/protein delivery. All eVLP expression constructs are stably integrated in the genome of the producer cell.
• Construct 1-1 corresponds to the phospholipid bilayer recruitment domain.
• 1-2 corresponds to the cargo.
• 2 corresponds to an optional guide RNA.
• 1-1 and 1-2 is translated in the cytosol where it complexes with guide RNA before it is recruited to the phospholipid bilayer.
• 3 corresponds to a virally-derived glycoprotein (VSVG).
• the virally-derived glycoprotein is expressed as a transmembrane protein on the plasma membrane and helps to drive budding of cargo-containing eVLPs from the plasma membrane to extracellular space. These particles are purified and are able to fuse with target cells and deliver cargo by interacting with surface receptors at the target cell surface.
• FIG 2 Depiction of purified eVLPs entering a target cell and delivering cargo to the cytosol.
• the phospholipid bilayer recruitment domain allows cargo to enter the target cell nucleus as long as cargo possesses a nuclear localization sequence.
• FIG 3 Cas9 RNP was delivered in VSVG-pseudotyped T2eVLPs with or without a PH domain from hPLCdl or hAKTl.
• the PH domains were fused to the N-terminus of Cas9 via a 10 amino acid glycine/serine polypeptide linker.
• HepG2, U20S, HEK293T, CFPAC1, BeWo, Jurkat, K562, and primary T cells were treated with purified and lOOx concentrated T2eVLPs for 72 hours. Percent targeted gene modification of VEGF site #3 was determined by amplicon sequencing.
• the x-axis labels correspond to the contents of each T2eVLP preparation.
• Cas9 (no fusion) lacked a PH domain fusion.
• Benzonase (Benz) was used to degrade RNA and DNA outside of VLPs, and a Benzonase treated sample was included as a control.
• FIG 4 Depiction of TleVLP/T3eVLP production. Plasmid DNA constructs involved in the transfection encode cargo, an optional guide RNA and a virally-derived glycoprotein (VSVG). Plasmids, or other types of DNA molecules, will be distributed throughout the production cell, so constructs located in the nucleus will express eVLP components and cargo, and constructs located near the plasma membrane or endosomes will be encapsulated within budding eVLPs.
• FIGs. 5A-B Exemplary TleVLP-delivered spCas9 genome editing in vitro.
• the sgRNA targets GFP Flow cytometry or T7E1 is performed 72 hours after transduction.
• the Rous sarcoma virus gag VLPs serve as controls.
• FIG 6 Exemplary TleVLP-delivered spCas9 genome editing in vitro.
• eVLPs are pseudotyped with VSVG Gene modification is measured by amplicon sequencing.
• FIG 7 Exemplary TleVLP-delivered spCas9 genome editing in vitro.
• eVLPs are pseudotyped with VSVG Gene modification is measured by amplicon sequencing.
• FIG 8 Exemplary TleVLP-delivered spCas9 base editing in vitro.
• HEK293T cells transduced with VLPs containing Rous sarcoma virus gag fused to spCas9 BE3 or Gam-BE4 with sgRNA targeted to VEGF site #2, or TleVLPs containing PLC PH fused to spCas9 BE3 or Gam-BE4 with sgRNA targeted to VEGF site #2.
• eVLPs and VLPs are pseudotyped with VSVG Gene modification is measured by amplicon sequencing.
• the Rous sarcoma virus gag VLP serves as a positive control.
• FIG 9 Exemplary TleVLP-delivered spCas9 base editing in vitro.
• HEK293T cells transduced with TleVLPs containing PLC PH fused to codon optimized spCas9 BE4 targeted to HEK site #3.
• eVLPs are pseudotyped with VSVG Gene modification is measured by amplicon sequencing.
• FIG 10 Exemplary TleVLP-delivered spCas9 base editing in vitro.
• HEK293T cells transduced with TleVLPs containing PLC PH fused to codon optimized spCas9 ABE targeted to VEGF site #3.
• eVLPs are pseudotyped with VSVG Gene modification is measured by amplicon sequencing.
• FIG 11 Exemplary TleVLP-delivered spCas9 base editing in vitro.
• eVLPs are pseudotyped with VSVG Gene modification is measured by amplicon sequencing.
• FIG 12 Exemplary TleVLP-delivered asCasl2a genome editing in vitro.
• HEK293 cells transduced with VLPs containing Rous sarcoma virus gag or TleVLPs containing PLC PH fused to asCasl2a.
• VLPs and eVLPs are targeted to FANCF site #1 by crRNA.
• Gene modification is measured by T7E1.
• the Rous sarcoma virus gag VLP serves as a positive control.
• FIG 13 Exemplary TleVLP-delivered spCas9 genome editing in vitro.
• HEK293 cells transduced with TleVLPs containing PLC PH fused to RNA binding protein MS2.
• MS2 binds to MS2 stem loops in the sgRNA, which is complexed with Cas9, and MS2 is fused to a PH domain for efficient eVLP loading.
• eVLPs are targeted to GFP site #1 by sgRNA. Gene modification is measured by T7E1.
• FIG 14 Exemplary TleVLP-delivered spCas9 genome editing in vitro.
• HEK293 cells transduced with TleVLPs containing PLC PH fused to dimerization domain (DmrC).
• DmrC dimerization domain
• eVLPs are targeted to GFP site #1 by sgRNA.
• Gene modification is measured by T7E1.
• FIG 15 Exemplary TleVLP-delivered asCas9 genome editing in vitro.
• HEK293 cells transduced with TleVLPs containing PLC PH fused to GNC4 protein domain repeats.
• An scFv binds to the GCN4 repeats, and scFvs are directly fused to Cas9.
• eVLPs are targeted to GFP site #1 by sgRNA. Gene modification is measured by T7E1.
• FIGs. 16-40 Schematic illustrations of various exemplary eVLP configurations and possible cargo.
• Genome editing reagents such as zinc finger nucleases (ZFNs) or RNA-guided, enzymatically active/inactive DNA binding proteins such as Cas9 have undergone rapid advancements in terms of specificity and the types of edits that can be executed, but the hurdle of safe in vivo delivery still precludes efficacious gene editing therapies.
• ZFNs zinc finger nucleases
• Cas9 RNA-guided, enzymatically active/inactive DNA binding proteins
• Cas9 RNA-guided, enzymatically active/inactive DNA binding proteins
• Cas9 RNA-guided, enzymatically active/inactive DNA binding proteins
• Cas9 RNA-guided, enzymatically active/inactive DNA binding proteins
• Cas9 RNA-guided, enzymatically active/inactive DNA binding proteins
• Cas9 RNA-guided, enzymatically active/inactive DNA binding proteins
• Cas9 RNA-guided, enzymatically active/
• Retroviral particles such as lentivirus, have been developed to deliver RNA that is reverse transcribed to DNA that may or may not be integrated into genomic DNA.
• VLPs have been developed that mimic virus particles in their ability to self-assemble, but are not infectious as they lack some of the core viral genes. Both lentiviral and VLP vectors are typically produced by transiently transfecting a producer cell line with plasmids that encode all components necessary to produce lentiviral particles or VLP.
• This unintended plasmid DNA delivery can be immunogenic and cause undesirable effects, such as plasmid DNA being integrated into genomic DNA. It is important to specify the type of biomolecules/ chemicals that are to be delivered within particles, and eVLPs have been designed to possess this germane capability.
• eVLPs described herein can deliver a wide variety of cargo including DNA only, DNA+RNA+protein, or RNA+protein.
• eVLPs are the first VSVG- based VLP delivery modality that can control the form of the cargo (DNA, protein, and/or RNA).
• Previously described VSVG-based vesicles and viral particles package and deliver unwanted plasmid DNA (or other types of DNA-based gene expression constructs) introduced into particle producer cells via transient transfection in addition to the intended protein and/or RNA cargo(s).
• ENV protein on the surface of the eVLP
• the ENV protein alone is responsible for eVLP particle generation and the ability of eVLPs to efficiently deliver cargo into cells.
• Lentivirus and VLPs commonly require GAG and ENV proteins to drive particle formation via budding off of the plasma membrane of producer cells into the cell culture medium.
• retroviral ENV proteins require post-translational modifications in the form of proteolytic cleavage of the intracellular domain (ICD) of the ENV protein in order to activate the fusogenicity of the ENV protein; this is essential for viral infectivity.
• the envelope proteins described in Table 1 are all derived from viruses.
• eVLP ENV proteins do not require exogenous GAG for particle formation and they do not require ICD cleavage for fusogenicity.
• the ENV is the only virally-derived component of eVLPs, and these ENV glycoproteins on the external surface of the eVLPs are used to facilitate fusion/entry of eVLPs into the target cell because they are known to be naturally fusogenic.
• eVLPs are different from previously described viral particles, VLPs, and extracellular vesicles because eVLPs are composed of a mixture of ectosomes and exosomes which can be separated by purification, if desired.
• eVLPs are particularly suited for delivery of cargo including DNA, RNA, protein, or combinations of biomolecules and/or chemicals, such as DNA-encoded or RNP-based genome editing reagents.
• Cas9 for example, cannot efficiently cross the phospholipid bilayer to enter into cells, and has been shown to have innate and adaptive immunogenic potential. 4 8 Therefore, it is not practical or favorable to deliver Cas9 by direct injection or as an external/internal conjugate to lipid, protein or metal-based nanoparticles that have cytotoxic and immunogenic properties and often yield low levels of desired gene modifications. 9 20
• Nanoparticles that encapsulate cargo are another delivery strategy that can be used to deliver DNA, protein, RNAand RNPs into cells 9-18 Nanoparticles can be engineered for cell specificity and can trigger endocytosis and subsequent endosome lysis. However, nanoparticles can have varying levels of immunogenicity due to an artificially-derived vehicle shell. 9 20 Many nanoparticles rely on strong opposing charge distributions to maintain particle structural integrity, and the electrostatics can make it toxic and unfit for many in vivo therapeutic scenarios. 9 Nanoparticles that deliver RNA have had successes in recent clinical trials, but most have only been used to deliver siRNA or shRNA. Toxicity from such nanoparticles is still a major concern.
• Nanoparticles that deliver mRNA coding for genome editing RNPs have also been a recent success, but these create a higher number of off-target effects compared to protein delivery and RNA stability is lower than that of protein. 17 Nanoparticles that deliver genome editing RNPs and DNA have been a significant breakthrough because they can leverage both homology directed repair (HDR) and non-homologous end joining (NHEJ), but exhibit prohibitively low gene modification frequencies in vitro and in vivo, and therefore currently have limited applications in vivo as a gene editing therapeutic. 15
• HDR homology directed repair
• NHEJ non-homologous end joining
• AAV vectors are a promising delivery modality that can successfully deliver DNA into eukaryotic cells
• AAV cannot efficiently package and deliver DNA constructs larger than 4.5 kb and this precludes delivery of many CRISPR-based gene editing reagents that require larger DNA expression constructs.
• CRISPR-based gene editing reagents can be split into multiple different AAV particles, but this strategy drastically reduces delivery and editing efficiency.
• AAV and adenoviral vectors can have varying levels of immunogenicity.
• inverted-terminal repeats (ITRs) in the AAV DNA construct can promote the formation of spontaneous episomes leading to prolonged expression of genome editing reagents and increased off-target effects. ITRs can also promote the undesired integration of AAV DNA into genomic DNA. 21 24 Recently, VLPs have been utilized to deliver mRNA and protein cargo into the cytosol of cells. 2 ⁇ 3 ⁇ 25 30 VLPs have emerged as a substitute delivery modality for retroviral particles. VLPs can be designed to lack the ability to integrate retroviral DNA, and to package and deliver protein/RNP/DNA.
• VLPs including recently conceived VLPs that deliver genome editing reagents known to date, utilize HIV or other virally-derived gag-pol protein fusions and viral proteases to generate retroviral-like particles. 25 27 ⁇ 29 ’ 30 Secondly, some VLPs containing RGNs also must package and express guide RNAs from a lentiviral DNA transcript. 27 Thirdly, some VLPs require a viral protease in order to form functional particles and release genome editing cargo. 25 27 ⁇ 29 Since this viral protease recognizes and cleaves at multiple amino acid motifs, it can cause damage to the protein cargo which could be hazardous for therapeutic applications.
• VHP modalities that deliver genome editing proteins to date exhibit low in vitro and in vivo gene modification efficiencies due to low packaging and transduction efficiency.
• 25 27 Fifthly, the complex viral genomes utilized for these VHP components possess multiple reading frames and employ RNA splicing that could result in spurious fusion protein products being delivered. 25 - 27 ⁇ 29 ⁇ 30
• the presence of reverse transcriptase, integrase, capsid and a virally-derived envelope protein in these VHPs is not ideal for most therapeutic applications because of immunogenicity and off target editing concerns.
• Extracellular vesicles are another delivery modality that can package and deliver cargo within exosomes and ectosomes. 3 1 ⁇ 32 Similar to VHPs, extracellular vesicles are comprised of a phospholipid bilayer from a mammalian cell. Unlike VHPs, extracellular vesicles lack viral components and therefore have limited immunogenicity. Whereas VHPs have a great ability to enter cells due to external fusogenic glycoproteins (VSVG) extracellular vesicles mainly rely on cellular uptake via micropinocytosis and this limits the delivery efficiency of extracellular vesicles.
• VSVG fusogenic glycoproteins
• eVLPs are a safer and more effective alternative than previously described VLPs, extracellular vesicles, AAVs and nanoparticles-especially for delivery of genome editing reagents-because eVLPs are composed of all human components except for a virally- derived glycoprotein that has been demonstrated to be safe in humans in a clinical trial of a HIV-1 gag vaccine (VSVG), 33 eVLPs lack all other retroviral components besides a safe glycoprotein, eVLPs have the ability to deliver DNA+RNP, or RNP alone while other previously described VLPs cannot prevent transient transfection DNA from being unintentionally packaged and delivered, eVLPs can deliver specialty DNA molecules while previously described VLPs, nanoparticles and AAVs cannot or do not, and eVLPs can be produced with cells that have been derived from patients (autologous eVLPs) and other FDA-approved cell lines (allogenic eVLPs) to further reduce the risks of adverse immune reactions.
• autologous eVLPs
• eVLPs for in vitro and in vivo applications, e.g., of genome editing, epigenome modulation, transcriptome editing and proteome modulation.
• the desired editing outcome depends on the therapeutic context and will require different gene editing reagents.
• Casl2a (functionalize) are two of the most popular RNA-guided enzymes for editing that leverages NHEJ for introducing stop codons or deletions, or HDR for causing insertions.
• Cas9-deaminase fusions also known as base editors, are the current standard for precise editing of a single nucleotide without double stranded DNA cleavage. 37 ⁇ 38 Importantly, these methods address the phenomenon of inadvertent DNA delivery in VLPs and the first to control for the type of biomolecule to be delivered (DNA, RNA, and/or protein) thereby increasing the types of therapeutic in vivo genome modifications that are possible and minimizing deleterious off target effects.
• Section 1 eVLP-mediated delivery of DNAs, proteins and RNAs
• VLPs that have been engineered to encapsulate and deliver protein- based cargo commonly fuse cargo to the INT or GAG polyprotein 25 27 ⁇ 29 ⁇ 30 ’ 39 ’ 40
• these protein fusions are translated in the cytosol of conventional VLP production cell lines, the gag matrix is acetylated and recruited to the cell membrane, and the gag fusions are encapsulated (transient transfection DNA is also unintentionally encapsulated) within VLPs as VLPs bud off of the membrane into extracellular space.
• the eVLPs described herein can package protein-based cargo by integrating all production DNA into the genomic DNA of production cell lines. Once cell lines are created, protein delivery eVLPs can be produced in a constitutive or inducible fashion. Proteins are packaged into eVLP by fusing select human-derived phospholipid bilayer recruitment domains to protein-based cargo (e.g., as shown in Table 6).
• One such human-derived phospholipid bilayer recruitment domain used for this purpose is a human pleckstrin homology (PH) domain. PH domains interact with phosphatidylinositol lipids and proteins within biological membranes, such as PIP2, PIP3, bg-subunits of GPCRs, and PKC.
• the human Arc protein can be fused to protein-based cargo to recruit cargo to the cytosolic side of the phospholipid bilayer.
• These human-derived phospholipid bilayer recruitment domains can be fused to the N-terminus or C-terminus of protein-based cargo via polypeptide linkers of variable length regardless of the location or locations of one or more nuclear localization sequence(s) (NLS) within the cargo.
• the linker between protein-based cargo and the phospholipid bilayer recruitment domain is a polypeptide linker 5-20, e.g., 8-12, e.g., 10, amino acids in length primarily composed of glycines and serines.
• the human- derived phospholipid bilayer recruitment domain localizes the cargo to the phospholipid bilayer and this protein cargo is packaged within eVLPs that utilize a glycoprotein to trigger budding off of particles from the producer cell into extracellular space (FIG 1).
• These human-derived domains and proteins can facilitate for localization of cargo to the cytosolic face of the plasma membrane within the eVLP production cells, and they also allow for cargo to localize to the nucleus of eVLP -transduced cells without the utilization of exogenous retroviral gag/pol or chemical and/or light- based dimerization systems (FIG 2).
• eVLPs can also package and deliver a combination of DNA and RNA if eVLPs are produced via transient transfection of a production cell line. DNA that is transfected into cells will possess size-dependent mobility such that a fraction of the transfected DNA will remain in the cytosol while another fraction of the transfected DNA will localize to the nucleus. 44 46 One fraction of the transfected DNA in the nucleus will expressed components needed to create eVLPs and the other fraction in the cytosol/near the plasma membrane will be encapsulated and delivered in eVLPs (FIG
• Cargo refers to a any payload that can be delivered, including chemicals, e.g., small molecule compounds, and biomolecules, including DNA, RNA, RNP, proteins, and combinations thereof, including combinations of DNA and RNP, RNP, combinations of DNA and proteins, or proteins, as well as viruses and portions thereof, e.g., for therapeutic or diagnostic use, or for the applications of genome editing, epigenome modulation, and/or transcriptome modulation.
• chemicals e.g., small molecule compounds, and biomolecules, including DNA, RNA, RNP, proteins, and combinations thereof, including combinations of DNA and RNP, RNP, combinations of DNA and proteins, or proteins, as well as viruses and portions thereof, e.g., for therapeutic or diagnostic use, or for the applications of genome editing, epigenome modulation, and/or transcriptome modulation.
• RNA in this context includes, for example, single guide RNA (sgRNA), Clustered Regularly Interspaced Palindromic Repeat (CRISPR) RNA (crRNA), and/or mRNA coding for cargo.
• sgRNA single guide RNA
• CRISPR Clustered Regularly Interspaced Palindromic Repeat
• crRNA Clustered Regularly Interspaced Palindromic Repeat
• small molecules refers to small organic or inorganic molecules of molecular weight below about 3,000 Daltons.
• small molecules useful for the invention have a molecular weight of less than 3,000 Daltons (Da).
• the small molecules can be, e.g., from at least about 100 Da to about 3,000 Da (e.g., between about 100 to about 3,000 Da, about 100 to about 2500 Da, about 100 to about 2,000 Da, about 100 to about 1,750 Da, about 100 to about 1,500 Da, about 100 to about 1,250 Da, about 100 to about 1,000 Da, about 100 to about 750 Da, about 100 to about 500 Da, about 200 to about 1500, about 500 to about 1000, about 300 to about 1000 Da, or about 100 to about 250 Da).
• Nucleases include Fokl and Acul ZFNs and Transcription activator- like effector nucleases (TALENs) and CRISPR based nucleases or a functional derivative thereof (e.g., as shown in Table 2)
• ZFNs are described, for example, in United States Patent Publications 20030232410; 20050208489; 20050026157; 20050064474; 20060188987; 20060063231; and International Publication WO 07/014275
• TALENs are described, for example, in United States Patent Publication US9393257B2; and International Publication WO2014134412A1
• CRISPR based nucleases are described, for example, in United States Patent Publications US8697359B1; US20180208976A1; and International Publications WO201409
• Base editors that are described by this work include any CRISPR based nuclease orthologs (wt, nickase, or catalytically inactive (Cl)), e.g., as shown in Table 2, fused at the N-terminus to a deaminase or a functional derivative thereof (e.g., as shown in Table 3) with or without a fusion at the C-terminus to one or multiple uracil glycosylase inhibitors (UGIs) using polypeptide linkers of variable length (Base editors are described, for example, in United States Patent Publications US20150166982A1 ; US20180312825 Al; US10113163B2; and International Publications W02015089406A1; WO2018218188A2; W02017070632A2; W02018027078A8; WO2018165629A1).
• CRISPR based nuclease orthologs wt, nickase, or catalytically inactive (
• Prime editors are also compatible with eVLP delivery modalities (Prime editors are described, for example, in PMTD: 31634902). sgRNAs complex with genome editing reagents during the packaging process, and are co-delivered within eVLPs. To date, this concept has been validated in vitro by experiments that demonstrate the TleVLP or T2eVLP delivery of RGN and Cl RGN fused to deaminase and UGI (base editor) as protein for the purposes of site specific editing of exogenous and endogenous sites (FIGs. 3, 5, 6, 7, 8, 9, 10, 11 & 12).
• TleVEPs have been used to deliver Cas9 RNP to U20S and HEK293 cells for the purposes of editing exogenous GFP, and endogenous HEK site #3and VEGF site #2 & #3 (FIGs. 4, 5, 6 & 7).
• TleVEPs have been used to deliver BE3 and BE4 RNP to HEK293T cells for the purpose of base editing endogenous VEGF site #2 & #3 and HEK site #3 (FIGs. 8, 9, 10 & 11).
• TleVEPs have also been used to deliver Casl2a RNP to HEK293 cells for the purposes of editing endogenous FANCF site #1 (FIG 12).
• Cargo designed for the purposes of epigenome modulation includes the Cl CRISPR based nucleases, zinc fingers (ZFs) and TALEs fused to an epigenome modulator or combination of epigenome modulators or a functional derivative thereof connected together by one or more variable length polypeptide linkers (Tables 2 & 4).
• T1-T4 cargo designed for the purposes of transcriptome editing includes CRISPR based nucleases or any functional derivatives thereof in Table 5 or Cl CRISPR based nucleases or any functional derivatives thereof in Table 5 fused to deaminases in Table 3 by one or more variable length polypeptide linkers.
• the cargo can also include any therapeutically or diagnostically useful protein, DNA, RNP, or combination of DNA, protein and/or RNP. See, e.g., W02014005219; US10137206; US20180339166; US5892020A; EP2134841B1; W02007020965A1.
• cargo encoding or composed of nuclease or base editor proteins or RNPs or derivatives thereof can be delivered to retinal cells for the purposes of correcting a splice site defect responsible for Leber Congenital Amaurosis type 10.
• eVLP delivery of base editing reagents or HDR promoting cargo to sensory cells such as cochlear supporting cells and hair cells for the purposes of editing b-catenin (b- catenin Ser 33 edited to Tyr, Pro, or Cys) in order to better stabilize b-catenin could help reverse hearing loss.
• eVLP delivery of RNA editing reagents or proteome perturbing reagents could cause a transitory reduction in cellular levels of one or more specific proteins of interest (potentially at a systemic level, in a specific organ or a specific subset of cells, such as a tumor), and this could create a therapeutically actionable window when secondary drug(s) could be administered (this secondary drug is more effective in the absence of the protein of interest or in the presence of lower levels of the protein of interest).
• eVLP delivery of RNA editing reagents or proteome perturbing reagents could trigger targeted degradation of MAPK and PI3K/AKT proteins and related mRNAs in vemurafenib/dabrafenib-resistant BRAF- driven tumor cells, and this could open a window for the administration of vemurafenib/dabrafenib because BRAF inhibitor resistance is temporarily abolished (resistance mechanisms based in the MAPK/PI3K/AKT pathways are temporarily downregulated by eVLP cargo).
• This example is especially pertinent when combined with eVLPs that are antigen inducible and therefore specific for tumor cells.
• eVLPs could be used deliver factors, e.g., including the Yamanaka factors Oct3/4, Sox2, Klf4, and c-Myc, to cells such as human or mouse fibroblasts, in order to generate induced pluripotent stem cells.
• factors e.g., including the Yamanaka factors Oct3/4, Sox2, Klf4, and c-Myc, to cells such as human or mouse fibroblasts, in order to generate induced pluripotent stem cells.
• eVLPs could deliver dominant-negative forms of proteins in order to elicit a therapeutic effect.
• eVLPs that are antigen-specific i.e., tumor-antigen specific
• Tumor antigens are known in the art and include
• pancreatic cancer patients present with unresectable disease. Around 30% of patients with unresectable pancreatic tumors will die from local disease progression, so it is desirable to treat locally advanced pancreatic tumors with ablative radiation, but the intestinal tract cannot tolerate high doses of radiation needed to cause tumor ablation. Selective radioprotection of the intestinal tract enables ablative radiation therapy of pancreatic tumors while minimizing damage done to the surrounding gastrointestinal tract.
• eVLPs could be loaded with dCas9 fused to the transcriptional repressor KRAB and guide RNA targeting EGLN. EGLN inhibition has been shown to significantly reduce gastrointestinal toxicity from ablative radiation treatments because it causes selective radioprotection of the gastrointestinal tract but not the pancreatic tumor. 47
• fusion proteins, eVLPs, and methods of making and using the same are provided herein.
• Unbound steroid receptors reside in the cytosol. After binding to ligands, these receptors will translocate to the nucleus and initiate transcription of response genes.
• eVLPs could deliver single chain variable fragment (scFv) antibodies to the cytosol of cells that bind to and disrupt cytosolic steroid receptors.
• scFv single chain variable fragment
• the scFv could bind to the glucocorticoid receptor and prevent it from binding dexamethasone, and this would prevent transcription of response genes, such as metallothionein IE which has been linked to tumorigenesis.
• 48 eVLPs can be indicated for treatments that involve targeted disruption of proteins.
• eVLPs can be utilized for targeting and disrupting proteins in the cytosol of cells by delivering antibodies/scFvs to the cytosol of cells.
• Delivery of antibodies through the plasma membrane to the cytosol of cells has been notoriously difficult and inefficient.
• This mode of protein inhibition is similar to how a targeted small molecule binds to and disrupts proteins in the cytosol and could be useful for the treatment of a diverse array of diseases. 49-51
• Such fusion proteins, eVLPs, and methods of making and using the same are
• scFvs are not hampered by these limitations because scFvs can be generated that bind to many different moieties of a protein in order to disrupt catalysis and interactions with other proteins.
• RAS oncoproteins are implicated across a multitude of cancer subtypes, and RAS is one of the most frequently observed oncogenes in cancer.
• the International Cancer Genome Consortium found KRAS to be mutated in 95% of their Pancreatic Adenocarcinoma samples.
• RAS isoforms are known to activate a variety of pathways that are dysregulated in human cancers, like the PI3K and MAPK pathways. Despite the aberrant roles RAS plays in cancer, no efficacious pharmacologic direct or indirect small molecule inhibitors of RAS have been developed and approved for clinical use.
• One strategy for targeting RAS could be eVLPs that can deliver specifically to cancer cells scFvs that bind to and disrupt the function of multiple RAS isoforms. 49-51
• Section 2 eVLP composition, production, purification and applications eVLPs can be produced from producer cell lines that are either transiently transfected with at least one plasmid or stably expressing constructs that have been integrated into the producer cell line genomic DNA.
• a single plasmid if used in the transfection, it should comprise sequences encoding one or more virally-derived glycoproteins (e.g., as shown in Table 1), cargo (e.g., a therapeutic protein or a gene editing reagent such as a zinc finger, transcription activator-like effector (TALE), and/or CRISPR-based genome editing/modulating protein and/or RNP such as those found in Tables 2, 3, 4 & 5), with or without fusion to a plasma membrane recruitment domain (e.g., as shown in Table 6), and a guide RNA, if necessary.
• a therapeutic protein or a gene editing reagent such as a zinc finger, transcription activator-like effector (TALE), and/or CRISPR-based genome editing/modulating protein and/or RNP such as those found in Tables 2, 3, 4 & 5
• TALE transcription activator-like effector
• RNP CRISPR-based genome editing/modulating protein and/or RNP
• a guide RNA if
• a plasmid comprising sequences encoding a therapeutic protein or a genome editing reagent, with or without a fusion to a plasma membrane recruitment domain.
• a plasmid comprising one or more virally-derived glycoproteins (e.g., as listed in Table 1).
• plasmid 1 If the genome editing reagent from plasmid 1 requires one or more guide RNAs, a plasmid comprising one or more guide RNAs apposite for the genome editing reagent in plasmid 1.
• the above- mentioned transfection can be performed with double-stranded closed-end linear DNA, episome, mini circle, double-stranded oligonucleotide and/or other specialty DNA molecules.
• the producer cell line can be made to stably express the constructs (1 through 3) described in the transfection above.
• the methods include using cells that have or have not been manipulated to express any exogenous proteins except for a viral envelope (e.g., as shown in Table 1), and, if desired, a plasma membrane recruitment domain (e.g., as shown in Table 6).
• the “empty” particles that are produced can be loaded with cargo by utilizing nucleofection, lipid, polymer, or CaCh transfection, sonication, freeze thaw, and/or heat shock of purified particles mixed with cargo.
• producer cells do not express any gag protein. This type of loading allows for cargo to be unmodified by fusions to plasma membrane recruitment domains and represents a significant advancement from previous VLP technology.
• the plasmids, or other types of specialty DNA molecules known in the art or described above, can also preferably include other elements to drive expression or translation of the encoded sequences, e.g., a promoter sequence; an enhancer sequence, e.g., 5’ untranslated region (UTR) or a 3’ UTR; a polyadenylation site; an insulator sequence; or another sequence that increases or controls expression (e.g., an inducible promoter element).
• a promoter sequence e.g., an enhancer sequence, e.g., 5’ untranslated region (UTR) or a 3’ UTR
• UTR untranslated region
• insulator sequence e.g., insulator sequence
• another sequence that increases or controls expression e.g., an inducible promoter element
• appropriate producer cell lines are primary or stable human cell lines refractory to the effects of transfection reagents and fusogenic effects due to virally- derived glycoproteins.
• appropriate cell lines include Human Embryonic Kidney (HEK) 293 cells, HEK293 T/17 SF cells kidney-derived Phoenix- AMPHO cells, and placenta-derived BeWo cells.
• HEK Human Embryonic Kidney
• HEK293 T/17 SF cells kidney-derived Phoenix- AMPHO cells
• placenta-derived BeWo cells could be selected for their ability to grow as adherent cells, or suspension cells.
• the producer cells can be cultured in classical DMEM under serum conditions, serum-free conditions, or exosome-free serum conditions.
• eVLPs e.g., T1 and T3eVLPs
• T1 and T3eVLPs can be produced from cells that have been derived from patients (autologous eVLPs) and other FDA-approved cell lines (allogenic eVLPs) as long as these cells can be transfected with DNA constructs that encode the aforementioned eVLP production components by various techniques known in the art.
• the DNA constructs can be designed to overexpress proteins in the producer cell lines.
• the plasmid backbones for example, used in the transfection can be familiar to those skilled in the art, such as the pCDNA3 backbone that employs the CMV promoter for RNA polymerase II transcripts or the U6 promoter for RNA polymerase III transcripts.
• Various techniques known in the art may be employed for introducing nucleic acid molecules into producer cells.
• Such techniques include chemical-facilitated transfection using compounds such as calcium phosphate, cationic lipids, cationic polymers, liposome-mediated transfection, such as cationic liposome like LIPOFECTAMINE (LIPOFECTAMINE 2000 or 3000 and TransIT-X2), polyethyleneimine, non-chemical methods such as electroporation, particle bombardment, or microinjection.
• compounds such as calcium phosphate, cationic lipids, cationic polymers, liposome-mediated transfection, such as cationic liposome like LIPOFECTAMINE (LIPOFECTAMINE 2000 or 3000 and TransIT-X2), polyethyleneimine, non-chemical methods such as electroporation, particle bombardment, or microinjection.
• T2 and T4eVLPs can be produced from cells that have been derived from patients (autologous eVLPs) and other FDA-approved cell lines (allogenic eVLPs) if these cells have been converted into stable cell lines that express the aforementioned eVLP components.
• eVLPs are harvested from cell culture medium supernatant 36-48 hours post-transfection, or when eVLPs are at the maximum concentration in the medium of the producer cells (the producer cells are expelling particles into the media and at some point in time, the particle concentration in the media will be optimal for harvesting the particles).
• Supernatant can be purified by any known methods in the art, such as centrifugation, ultracentrifugation, precipitation, ultrafiltration, and/or chromatography.
• the supernatant is first filtered, e.g., to remove particles larger than 1 pm, e.g., through 0.45 pore size polyvinylidene fluoride hydrophilic membrane (Millipore Millex-HV) or 0.8pm pore size mixed cellulose esters hydrophilic membrane (Millipore Millex-AA).
• the supernatant can be further purified and concentrated, e.g., using ultracentrifugation, e.g., at a speed of 80,000 to 100,000xg at a temperature between 1°C and 5°C for 1 to 2 hours, or at a speed of 8,000 to 15,000 g at a temperature between 1°C and 5°C for 10 to 16 hours.
• the eVLPs are concentrated in the form of a centrifugate (pellet), which can be resuspended to a desired concentration, mixed with transduction-enhancing reagents, subjected to a buffer exchange, or used as is.
• eVLP-containing supernatant can be filtered, precipitated, centrifuged and resuspended to a concentrated solution.
• PEG polyethylene glycol
• Purified particles are stable and can be stored at 4°C for up to a week or -80°C for years without losing appreciable activity.
• eVLPs are resuspended or undergo buffer exchange so that particles are suspended in an appropriate carrier.
• buffer exchange can be performed by ultrafiltration (Sartorius Vivaspin 500 MWCO 100,000).
• An exemplary appropriate carrier for eVLPs to be used for in vitro applications would preferably be a cell culture medium that is suitable for the cells that are to be transduced by eVLPs.
• Transduction-enhancing reagents that can be mixed into the purified and concentrated eVLP solution for in vitro applications include reagents known by those familiar with the art (Miltenyi Biotec Vectofusin- 1 , Millipore Polybrene, Takara Retronectin, Sigma Protamine Sulfate, and the like).
• transduction efficiency can be further increased by centrifugation.
• the plate containing eVLPs applied to cells can be centrifuged at a speed of 1,150 g at room temperature for 30 minutes. After centrifugation, cells are returned into the appropriate cell culture incubator (humidified incubator at 37°C with 5% CO2).
• An appropriate carrier for eVLPs to be administered to a mammal, especially a human would preferably be a pharmaceutically acceptable composition.
• a “pharmaceutically acceptable composition” refers to a non-toxic semisolid, liquid, or aerosolized filler, diluent, encapsulating material, colloidal suspension or formulation auxiliary of any type. Preferably, this composition is suitable for injection. These may be in particular isotonic, sterile, saline solutions (monosodium or disodium phosphate, sodium, potassium, calcium or magnesium chloride and and similar solutions or mixtures of such salts), or dry, especially freeze-dried compositions which upon addition, depending on the case, of sterilized water or physiological saline, permit the constitution of injectable solutions.
• Another appropriate pharmaceutical form would be aerosolized particles for administration by intranasal inhalation or intratracheal intubation.
• the pharmaceutical forms suitable for injectable use include sterile aqueous solutions or suspensions.
• the solution or suspension may comprise additives which are compatible with eVLPs and do not prevent eVLP entry into target cells.
• the form must be sterile and must be fluid to the extent that the form can be administered with a syringe. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
• An example of an appropriate solution is a buffer, such as phosphate buffered saline.
• solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
• the parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
• compositions suitable for injectable use can include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
• suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, NJ) or phosphate buffered saline (PBS).
• the composition must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
• the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof.
• the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
• Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
• isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition.
• Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, aluminum monostearate and gelatin.
• Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
• dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and the required other ingredients from those enumerated above.
• the preferred methods of preparation are vacuum drying and freeze- drying, which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile- filtered solution thereof.
• compositions comprising cargo-loaded eVLPs can be included in a container, pack, or dispenser together with instructions for administration.
• PEI polyethylenimine
• HEK293T cells were split to reach a confluency of 70%-90% at time of transfection and are cultured in 10% FBS DMEM media.
• Cargo vectors such as one encoding a CMV promoter driving expression of a hPLC51 PH fusion to codon optimized Cas9 were co-transfected with a U6 promoter-sgRNA encoding plasmid and the VSV-G envelope plasmid pMD2.G (Addgene #12259). Transfection reactions were assembled in reduced serum media (Opti-MEM; GIBCO #31985-070).
• eVLP particle production on 10 cm plates 7.5 pg PH-Cas9 expressing plasmid, 7.5 pg sgRNA- expression plasmid and 5 pg pMD2.G were mixed in 1 mL Opti-MEM, followed by addition of 27.5pl PEI MAX. After 20-30 min incubation at room temperature, the transfection reactions were dispersed dropwise over the HEK293T cells. eVLPs were harvested at 48-72 hours post-transfection.
• eVLP supernatants were filtered using 0.45 pm cellulose acetate or 0.8 pm PES membrane filters and transferred to polypropylene Beckman ultracentrifuge tubes that are used with the SW28 rotor (Beckman Coulter #326823). Each ultracentrifuge tube is filled with eVLP-containing supernatant from 3 10 cm plates to reach an approximate final volume of 35-37.5 ml. eVLP supernatant underwent ultracentrifugation at approximately 100,000 xg, or 25,000 rpm, at 4°C for 2 hours.
• eVLPs were added dropwise to cells that were seeded in a 24-well plate 24 hours prior to transduction.
• Polybrene (5-10 pg/mL in cell culture medium; Sigma-Aldrich #TR-1003-G) was supplemented to enhance transduction efficiency, if necessary.
• Vectofusin-1 (10 pg/mL in cell culture medium, Miltenyi Biotec #130-111-163) was supplemented to enhance transduction efficiency, if necessary.
• the 24- well plate was centrifuged at 1,150 xg for 30 min at room temperature to enhance transduction efficiency, if necessary.
• Cas9 RNP was delivered in VSVG-pseudotyped VLPs with or without a fusion to a PH domain.
• T2eVLPs containing Cas9 with or without PH fusion and VEGF-targeting sgRNA were applied to HepG2, U20S, HEK293T, CFPAC1, BeWo, Jurkat, K562, and primary T cells for 48 hours.
• Gene modification frequencies of the target site within VEGF were obtained by amplicon sequencing.
• FIG. 3 demonstrates that fusion to PH domains from hPLCdl or hAKTl significantly enhanced delivery/editing efficiency of Cas9 in T2eVLPs.
• Gag fusions to Cas9 or PH fusions to Cas9 with guide RNA targeting GFP were packaged in VLPs or T1 eVLPs, respectively.
• U20S or HEK293 cell line stably expressing a single copy of GFP were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, Cas9 fusions and guide RNA expressing plasmids.
• Particle purification and concentration was performed by PVDF filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by T7E1 and flow cytometry. The results are shown in FIGs. 5A-B.
• hPLC51 PH fusions to codon optimized Cas9 with guide RNA targeting HEK site #3 or VEGF site #2 were packaged in TleVFPs.
• U20S cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM, 10% FBS) 48 hours after transfection of VSVG, Cas9 fusions and guide RNA expressing plasmids.
• Particle purification and concentration was performed by filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by amplicon sequencing.
• hPLC51 left graph
• hAkt PH right graph
• fusions to codon optimized Cas9 with guide RNA targeting VEGF site #3 were packaged in TleVFPs.
• U20S cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM, 10% FBS) 48 hours after transfection of VSVG, Cas9 fusions and guide RNA expressing plasmids. Particle purification and concentration was performed by filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by amplicon sequencing.
• gag fusions to the N or C terminus of Cas9-based base editors (BE3 and BE4) or PH fusions to the N or C terminus of BE3 and BE4 with guide RNA targeting VEGF site #2 were packaged in VFPs and eVFPs, respectively.
• HEK293T cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, base editor fusions and guide RNA expressing plasmids. Particle purification and concentration was performed by filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by amplicon sequencing.
• hPLC51 fusions to the N terminus of Cas9-based base editors (codon optimized BE4) with guide RNA targeting HEK site #3 were packaged in eVFPs.
• HEK293T cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, base editor fusions and guide RNA expressing plasmids.
• Particle purification and concentration was performed by filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by amplicon sequencing.
• DMEM HEK293T cell culture media
• hPLC51 fusions to the N terminus of Cas9-based base editors (codon optimized ABE) with guide RNA targeting VEGF site #3 were packaged in eVLPs.
• HEK293T cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, base editor fusions and guide RNA expressing plasmids.
• Particle purification and concentration was performed by filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by amplicon sequencing.
• hPLC51 fusions to the N terminus of Cas9-based base editors (codon optimized ABE) with guide RNA targeting HEK site #3 were packaged in eVLPs.
• HEK293T cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, base editor fusions and guide RNA expressing plasmids.
• Particle purification and concentration was performed by filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by amplicon sequencing.
• gag fusions to Casl2a or hPLC51 PH fusions to Casl2a with guide RNA targeting FANCF site #1 were packaged in VLPs and eVLPs, respectively.
• HEK293 cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, Casl2a fusions and guide RNA expressing plasmids. Particle purification and concentration was performed by PVDF filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by T7E1.
• hPLC51 PH fusions to MS2 with MS2-stem loop guide RNA targeting GFP site #1 were packaged in eVLPs with Cas9.
• HEK293 cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, Cas9, PH-MS2 fusions and MS2 stem loop guide RNA expressing plasmids.
• Particle purification and concentration was performed by PVDF filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by T7E1.
• hPLC51 PH fusions to DmrC with guide RNA targeting GFP site #1 and Cas9 fused to DmrA repeats were packaged in eVLPs.
• HEK293 cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, DmrA-Cas9, PH-DmrC fusions and guide RNA expressing plasmids.
• Particle purification and concentration was performed by PVDF filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by T7E1.
• HEK293 cells were treated with these particles that were previously purified from HEK293T cell culture media (DMEM) 48 hours after transfection of VSVG, scFv-Cas9, PH-GCN4 fusions and guide RNA expressing plasmids. Particle purification and concentration was performed by PVDF filtration and ultracentrifugation at 100,000xg for 2 hours. Gene modification frequencies were determined by T7E1.
• FIGs. 16-40 show various non-limiting examples of eVLP configurations and possible cargo.
• BaEVTR Baboon Endogenous Retrovirus glycoprotein
• RVGIHLCIKLKHTKKRQIYTDIEMNRLGK SEQ ID NO:14
• RVGIHLCIKLKHTKKRQIYTDIEMNRLGK SEQ ID NO:15
• MLV ENV Amphotrophic Murine Leukemia Virus
• Rattus norvegicus & synthetic APOBEC1-XTEN L8-nspCas9-UGI-SV40 NLS
• Homo sapiens AIDv solubility variant lacking N-terminal RNA-binding region
• Homo sapiens AIDv solubility variant lacking N-terminal RNA-binding region and the C-terminal poorly structured region
• Rattus norvegicus APOBEC1
• Mus musculus APOBEC3 catalytic domain
• Homo sapiens APOBEC3G catalytic domain
• Streptococcus pyogenes spCas9 Bipartite NLS
• Staphylococcus aureus saCas9
• Campylobacter jejuni c/Cas9
• Neisseria meningitidis nme Cas9
• hPDPKI Pleckstrin homology domain of Homo sapiens PDPK1
• HSV Herpes simplex virus
• HSV Herpes simplex virus
• Baculovirus envelope glycoprotein GP64 Baculovirus envelope glycoprotein GP64
• AAV2 REP52
• NGVYSEPRPIGTRYLTRNL (SEQ ID NO:66)
• MIKIATRKYLGKQNVYDIGVERDHNFALKNGFIASNCFN SEQ ID N0:81
• VLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQ FLLANQVVVHN (SEQ ID NO:85)
• VPTIVMVDAYKRYK (SEQ ID NO:88)
• MS2 (N55K) RNA Binding Protein
• MS2 (N55K)(V29I) RNA Binding Protein
• Bacteriophage PP7 PP7 RNA Binding Protein
• Bacteriophage Mu COM RNA Binding Protein
• Truncated WT ADAR2 (E488Q) VLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGT
• AIA GIYGGSGSGAGSGSPAGGGAPGSGGGSKAERMGFTEVTPVTGASLR
• AIA GIYGGSGSGAGSGSPAGGGAPGSGGGSKAERMGFTEVTPVTGASLR
• Lactococcus lactis Nisin A
• ITSKSLCTPGCKTGILMTCPLKTATCGCHFG SEQ ID NO: 138

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