Patent Application
20240191256
The instant application contains a Sequence Listing which has been submitted electronically in XML file format and is hereby incorporated by reference in its entirety. Said XML copy, created on Feb. 2, 2024, is named 29539-0683001 SL.xml and is 300,388 bytes in size.
Described herein are programmable tropism virus-like particles (ptVLPs), comprising a membrane comprising a phospholipid bilayer with one or more wild-type or mutant/truncated virus-derived envelope glycoproteins on the external side, and a targeting domain (e.g., a peptide, single chain variable fragment (scFv), nanobody, fibronectin type 3 domain (FN3), arginylglycylaspartic acid motif (RGD), single variable domain on a heavy chain/nanobody (VHH), variable domain of new antigen receptor (VNAR), darpin, or other targeting ligand). The targeting domain can optionally be fused directly to the virus-derived envelope glycoproteins(e.g., at the end or internally), and/or can be present in combination with the envelope glycoproteins as a separate membrane-anchored targeting domain fusion protein. Optionally, a biomolecule cargo is disposed in the core of the ptVLP on the inside of the membrane.
The ability to direct delivery of cargo to specific cell types is useful in a number of contexts, particularly in delivery of cargo comprising therapeutic gene editing agents.
Described herein are programmable tropism virus-like particles (ptVLPs), comprising a membrane comprising a phospholipid bilayer with one or more wild-type or mutant/truncated virus-derived glycoproteins on the external side. The virus-derived envelope glycoprotein(s) can optionally be fused directly to a targeting domain (e.g., a peptide, single chain variable fragment (scFv), nanobody, fibronectin type 3 domain (FN3), arginylglycylaspartic acid motif (RGD), single variable domain on a heavy chain/nanobody (VHH), variable domain of new antigen receptor (VNAR), darpin, or other targeting ligand), and/or can be present in combination with a membrane-anchored targeting domain. A biomolecule cargo (preferably fused to a membrane recruitment domain, such as a Pleckstrin homology domain) can be disposed in the core of the ptVLP. Preferably, the ptVLP do or do not comprise any human endogenous retroviral (HERV) proteins other than the env, e.g., do or do not comprise gag, pol, or pro (unless the cargo comprises the viral protein(s)). Exogenous virally-derived gag, pol, or pro refers to any gag, pro, pol, gag-pol, gag-pro-pol, and/or pol protein, or any other protein expressed from gag, pro, or pol, from any virus introduced into the cell.
Provided herein are fusion proteins comprising a programmable tropism glycoprotein or envelope protein (ptENV) comprising a virus-derived glycoprotein or envelope protein fused to a targeting domain, optionally wherein the targeting domain is at the C terminus of the glycoprotein or envelope protein, at the N terminus, or is inserted immediately after a signal sequence. Also provided are fusion proteins comprising a membrane-anchored targeting domain comprising a targeting domain fused to a transmembrane domain. In some embodiments, the targeting domain comprises a targeting peptide, e.g., as shown in Table A. In some embodiments, the Targeting Domain comprises a single chain variable fragment (scFv), nanobody, fibronectin type 3 domain (FN3), arginylglycylaspartic acid motif (RGD), single variable domain on a heavy chain/nanobody (VHH), variable domain of new antigen receptor (VNAR), darpin or other targeting ligand. Linkers can be present between any or all of the parts of the fusion proteins.
In some embodiments, the Targeting Domain binds to human CD19, CD4, CD34, ASGR1, TfR1, HER2, CD25, CTLA-4, HB-EGF, ACE2, Aryl hydrocarbon receptor (AhR), keratin 5 (KRT5), KRT13, Fibronectin (FN1), Amyloid precursor protein (APP), neurotrophin receptor (p75NTR), Thy-1/CD90, EpCAM, and/or CFTR.
In some embodiments, the signal sequence comprises MKCLLYLAFLFIGVNCK (SEQ ID NO: 1) or a secretion signal sequence that is derived from VSVG (e.g., MKCLLYLAFLFIGVNC, SEQ ID NO:2), or another signal sequence as known in the art or described herein.
In some embodiments, the ptENV fusion protein comprising a sequence that is at least 95% identical to a sequence set forth herein, e.g., a ptENV comprising a glycoprotein or envelope protein in Table 1, plus a targeting domain.
Further, provided herein are nucleic acids sequence encoding the fusion proteins described herein, as well as vectors comprising the nucleic acid sequence, optionally operably linked to a promoter for expression of the fusion proteins, and host cells comprising the nucleic acid sequences, and optionally expressing the fusion proteins (e.g., producer cells).
Also provided herein are virus-like particles (VLPs) comprising the fusion proteins described herein, and optionally, a cargo disposed in the core of the VLP, wherein the cargo is optionally fused to a phospholipid bilayer recruitment domain.
Additionally provided are programmable tropism virus-like particle (ptVLP), comprising (a) a membrane comprising a phospholipid bilayer and (b) the fusion protein comprising a ptENV as described herein, or a glycoprotein or envelope protein (optionally as listed in Table 1) and the fusion protein comprising a membrane-anchored targeting domain as described herein: and (c) optionally, a cargo disposed in the core of the ptVLP, wherein the cargo is optionally fused to a phospholipid bilayer recruitment domain: and, optionally, wherein the ptVLP does not comprise an exogenous gag, pro and/or pol protein.
In some embodiments, the cargo is a therapeutic or diagnostic protein and/or nucleic acid encoding a therapeutic or diagnostic protein, and/or a chemical, optionally a small molecule therapeutic or diagnostic. In some embodiments, the cargo is a gene editing or epigenetic modulating reagent. In some embodiments, the gene editing or epigenetic modulating reagent comprises a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-Cas protein, variant, or fusion thereof: a nucleic acid encoding a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-Cas protein, variant, or fusion thereof: a guide RNA and/or crRNA: or a ribonucleoprotein complex (RNP) comprising a CRISPR-Cas protein, variant, or fusion thereof and/or optionally a guide RNA and/or crRNA.
In some embodiments, the cargo is selected from the proteins listed in Tables 2, 3, 4 & 5, or is at least 95% identical to a sequence set forth herein, e.g., in Table 2, 3, 4, or 5.
In some embodiments, the cargo comprises a CRISPR-Cas protein, and the ptVLP further comprises one or more guide RNAs and/or crRNAs that bind to and direct the CRISPR-Cas protein to a target nucleic acid sequence.
In some embodiments, the cargo comprises a fusion to a phospholipid bilayer recruitment domain, preferably as shown in Table 6, or that is at least 95% identical to a sequence set forth herein in Table 6.
Additionally, provided herein are methods for delivering a cargo to a target cell, optionally a cell in vivo or in vitro, by contacting the cell with a VLP or ptVLP as described herein comprising the cargo.
Further, provided herein are methods of producing a VLP or a ptVLP comprising a cargo by providing a cell expressing (i) a fusion protein as described herein, e.g., ptENV or a glycoprotein or envelope protein (optionally as listed in Table 1) and a separate membrane-anchored targeting domain as described herein: and optionally also expressing a cargo, optionally wherein the cell does not express an exogenous gag, pro, or pol protein: and maintaining the cell under conditions such that the cells produce the VLPs or ptVLPs.
In some embodiments, the methods include harvesting and optionally purifying and/or concentrating the produced VLPs or ptVLPs.
Also provided herein are cells expressing (i) a ptENV fusion protein as described herein, or (ii) a glycoprotein or envelope protein (optionally as listed in Table 1) and a fusion protein comprising the membrane-anchored targeting domain as described herein, part (ii): and optionally a cargo, wherein the cargo is optionally fused to a phospholipid bilayer recruitment domain: and, optionally the cell does not express an exogenous gag, pro and/or pol protein. In some embodiments, the cells are primary or stable human cell lines, e.g., Human Embryonic Kidney (HEK) 293 cells or HEK293 T cells.
In some embodiments, the cargo is a therapeutic or diagnostic protein and/or nucleic acid encoding a therapeutic or diagnostic protein, and/or a small molecule, optionally a therapeutic or diagnostic small molecule. In some embodiments, the cargo is a gene editing or epigenetic modulating reagent. In some embodiments, the gene editing or epigenetic modulating reagent comprises a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-Cas protein, variant, or fusion thereof: a nucleic acid encoding a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-Cas protein, variant, or fusion thereof: a guide RNA and/or crRNA: or a ribonucleoprotein complex (RNP) comprising a CRISPR-Cas protein, variant, or fusion thereof and optionally a guide RNA and/or crRNA.
In some embodiments, the cargo reagent is selected from the proteins listed in Tables 2, 3, 4 & 5, or that is at least 95% identical to a sequence set forth herein, e.g., in Table 2, 3, 4, or 5.
In some embodiments, the cargo reagent comprises a CRISPR-Cas protein, variant, or fusion thereof and the ptVLP further comprises one or more guide RNAs and/or crRNAs that bind to and direct the CRISPR-based genome editing or modulating protein to a target sequence.
In some embodiments, the cargo comprises a fusion to a phospholipid bilayer recruitment domain, preferably as shown in Table 6, or that is at least 95% identical to a sequence set forth herein in Table 6.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention: other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.
Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.
Therapeutic proteins and nucleic acids hold great promise, and delivery of proteins and nucleic acids to specific cell types would be of great interest, not least because it provides the possibility of reduced side effects. For example, 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 remains an important challenge for gene editing and epigenetic editing therapies.
Virus-like particles (VLPs) have been utilized to deliver mRNA and protein cargo into the cytosol of cells.2,3,25-30 VLPs have emerged as an alternative delivery modality to retroviral or lentiviral particles. VLPs can be designed to lack the ability to integrate retroviral DNA, and to package and deliver combinations of protein/RNP/DNA. However, most VLPs, including recently conceived VLPs that deliver genome editing reagents known to date, utilize HIV or other virally-derived gag or gag-pol protein fusions and viral proteases to generate retroviral-like particles.25-27,29,30 Some VLPs containing RNA-guided nucleases (RGNs) also must package and express guide RNAs from a lentiviral DNA transcript,27 and some VLPs require a viral protease in order to form functional particles and release genome editing cargo.25-27,29 Because this viral protease recognizes and cleaves at multiple amino acid motifs, it can cause damage to the protein cargo or potentially to other endogenous proteins in target recipient cells, which could be hazardous or create challenges for therapeutic applications. Most published VLP modalities that deliver genome editing proteins or RNPs to date exhibit low in vitro and in vivo gene modification efficiencies due to low packaging and transduction efficiency.25-27 The complex viral genomes utilized for these VLP 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 VLPs is not ideal for many therapeutic applications because of immunogenicity and off target concerns. In addition, most retroviral particles, such as lentiviral particles, are pseudotyped with VSVG and nearly all described VLPs that deliver genome editing reagents hitherto possess and rely upon VSVG.2,3,25-30
Described herein are various embodiments of virus-like particles with programmable tropism (ptVLPs) that can be used for cell type- or tissue-specific delivery of cargo including genome editing reagents. The ptVLPs include a targeting moiety that is either integrated into the glycoprotein (e.g., as in the sequences shown below) or separate (e.g., on the outer surface of the particle, but membrane-anchored (e.g., by connection to a transmembrane or integral membrane protein(s), GPI anchor(s) or other membrane anchor(s)).
Here, we describe methods and compositions for producing, purifying, and administering ptVLPs for in vitro and in vivo applications, e.g., of genome editing, epigenome modulation, transcriptome editing and proteome modulation. The desired editing or other modulation outcome in the target recipient cell depends on the therapeutic context and will require different gene editing or other cargos to be delivered. Streptococcus pyogenes Cas9 (SpCas9) and Acidaminococcus sp. Cas12a (AsCas12a) are two commonly used RNA-guided enzymes for editing that leverage NHEJ-mediated repair of DNA double-strand breaks (DSBs) induced by these nucleases to introduce stop codons or insertion/deletions (indels) or homology-directed repair (HDR) of the DSBs together with an exogenous DNA donor template that encodes a desired genetic alteration (e.g., precise point mutation(s) or 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.
Conventional 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 After transient transfection of production plasmid DNA constructs encoding these proteins and a viral envelope (ENV) protein, the 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 within VLPs as they bud off of the membrane into extracellular space.
In contrast, in some embodiments, proteins can be packaged into ptVLPs by fusing select human protein-derived phospholipid bilayer recruitment domains to protein-based cargo (e.g., as described in WO 2022/020800 or as shown in Table 6).
One such human protein-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, βγ-subunits of GPCRs, and PKC.41,42 Alternatively, the human Arc protein can be fused to protein-based cargo to recruit cargo to the cytosolic side of the phospholipid bilayer.43 These human protein-derived phospholipid bilayer recruitment domains, or variants thereof (e.g., as shown in Table 6) 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. Preferably, 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 protein-derived phospholipid bilayer recruitment domain localizes the cargo to the cytosolic face of the phospholipid bilayer and this protein cargo is packaged within ptVLPs that also contain and use an envelope glycoprotein to trigger budding-off of particles from the producer cell into extracellular space. These human protein-derived domains and human proteins can facilitate for localization of cargo to the cytosolic face of the plasma membrane within the ptVLP production cells, and they also allow for the cargo to localize to the nucleus of ptVLP-transduced cells without the utilization of exogenous retroviral gag/pol or chemical and/or light-based dimerization systems. The delivery of Cas9, for example, may be significantly more efficiently loaded as cargo into particles with fusion to a phospholipid bilayer recruitment domain compared to without fusion to a phospholipid bilayer recruitment domain.
Provided herein are VLPs that include targeting domains that bind to antigens on target cells (e.g., ptVLPs) to alter tropism of the VLPs. A number of such antigens are known in the art. Exemplary antigens include CD19,70 asialoglycoprotein receptor 1 (ASGR1),71 Transferrin receptor (TfR),72 HER2,73 CD34,74 CD4,75 CD25,76 CTLA-4,77 HB-EGF,78 ACE2,79 Aryl hydrocarbon receptor (AhR),80 keratin 5 (KRT5),81 keratin 17 (KRT17),82 keratin 14 (KRT14),83 keratin 13 (KRT13),84 Neural cell adhesion molecule L1,85 Fibronectin (FN1),86,87,88 Amyloid precursor protein (APP),89 Programmed cell death protein 1 (PD-1),90,91 neurotrophin receptor (p75NTR),92 Thy-1/CD90,93 EpCAM,94 and/or CFTR.95
ptVLP targeting domains can include single chain variable fragment (scFv), nanobody, fibronectin type 3 domain (FN3), arginylglycylaspartic acid motif (RGD), single variable domain on a heavy chain/nanobody (VHH), variable domain of new antigen receptor (VNAR), darpin, or other targeting ligand that binds to an antigen on a target cell.47-53
Targeting domains can also include peptides, e.g., as shown in Table A.
The targeting domains can be inserted into the sequence of an envelope protein such that it will be displayed on the surface of the ptVLP, as described herein, or can be present as a separate molecule anchored on the outside of the ptVLP membrane. Thus fusion proteins comprising (i) a targeting domain and an envelope glycoprotein, or (ii) a targeting domain and a membrane anchor are provided herein, as well as nucleic acids encoding the fusion proteins. In some embodiments, the targeting domain is inserted into an ENV protein between the signal sequence and the transmembrane domain, optionally replacing some or most of the N terminus of the ENV, including the RBD.
Membrane anchors can be any transmembrane (TM) domain, such as a TM from Platelet-derived growth factor receptor (PDGFR),96 CD9,97 CD63,97 CD81,97 CD86, Notch,70 CD28.98 CD8,99 or CD4.100 In general, the membrane anchored targeting domain fusion proteins will comprise, from N terminus to C terminus, the following a secretion signal sequence—optional linker—targeting domain—optional linker—transmembrane domain (see, e.g.,
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Preferably, the membrane anchored targeting domains and the ptENV comprise an N-terminal signal sequence; the original signal sequence can be used or can be replaced with a heterologous signal sequence. Exemplary signal sequences include the one from the VSV-G protein, e.g., MKCLLYLAFLFIGVNCK (SEQ ID NO: 1) and/or any other secretion signal sequence that is derived from VSVG (e.g., MKCLLYLAFLFIGVNC, SEQ ID NO:2) or a homolog thereof, or from a transmembrane protein and/or a synthetic/engineered signal sequence. A number of secretory signal peptide sequences are known in the art, including human signal sequences, examples of which are shown in Table B (Table adapted from novoprolabs. com/support/articles/commonly-used-leader-peptide-sequences-forefficient-secretion-of-a-recombinant-protein-expressed-in-mammalian-cells-201804211337.html).
In some embodiments, another signal sequence that promotes secretion is used, e.g., as described in Table 5 of U.S. Ser. No. 10/993,967; von Heijne, J Mol Biol. 1985 Jul. 5; 184(1)99-105; Kober et al., Biotechnol. Bioeng. 2013; 110 1164-1173; Tsuchiya et al., Nucleic Acids Research Supplement No. 3 261-262 (2003).
In general, the signal peptide is cleaved by a signal peptidase after the nascent protein is inserted into the membrane, as part of the secretory pathway processing inherent to cells.
ptVLP-Mediated Delivery of DNAs, Proteins and RNAs
The ptVLPs described herein can package and deliver biomolecule cargo. ptVLP. “Cargo” refers to a any payload that can be delivered, including chemicals, e.g., small molecule compounds, and biomolecules, including DNA, RNA, peptide nucleic acid (PNA), 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 modulating, 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. Other exemplary nucleic acids can include 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, crRNA, tracrRNA, 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, RNAs that can be bound by RNA binding proteins, bacteriophage RNA, or internal ribosomal entry site containing RNA). Combinations of the above cargos (e.g., AAV particles and/or ribonucleoprotein (RNP) complexes comprising RNA and protein, e.g., guide RNA/CRISPR Cas protein complexes) can also be included.
As used herein, “small molecules” refers to small organic or inorganic molecules of molecular weight below about 3,000 Daltons. In general, 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).
In some embodiments, the cargo is limited by the diameter of the particles, e.g., which in some embodiments can range from 30 nm to 500 nm.
In some embodiments, the cargo can include a combination of DNA and RNA, e.g., when ptVLPs 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 A fraction of the transfected DNA in the nucleus will express components encoded on these plasmids needed to create ptVLPs and another fraction in the cytosol/near the plasma membrane will be encapsulated and delivered in ptVLPs. See, e.g., FIGS. 1-4 of WO 2022/020800.
Cargo developed for applications of genome or gene editing also includes CRISPR-Cas nucleases and fusions and variants thereof, e.g., prime editors, and base editors. Nucleases include ZFNs and Transcription activator-like effector nucleases (TALENs) that comprise a FokI or AcuI nuclease domain; and CRISPR Cas proteins 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 U.S. Pat. No. 9,393,257B2; and International Publication WO2014134412A1) (CRISPR Cas proteins are described, for example, in United States Patent Publications U.S. Pat. No. 8,697,359B1; US20180208976A1; and International Publications WO2014093661A2; WO2017184786A8).34-36 Base editors can include any CRISPR based nuclease orthologs (wt, nickase, or catalytically inactive (CI)), e.g., as shown in Table 2, fused at the N-terminus to a nucleotide deaminase or nucleoside deaminase or a functional derivative thereof (e.g., as shown in Table 3), or comprising a deaminase domain inlaid internally, 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; US20180312825A1; U.S. Ser. No. 10/113,163B2; and International Publications WO2015089406A1; WO2018218188A2; WO2017070632A2; WO2018027078A8; WO2018165629A1; WO 2018/218166).37,38 In addition, prime editors are also compatible with mVLP delivery modalities (Prime editors are described, for example, in Anzalone et al., Nature. 2019 December; 576(7785)149-157). Prime editors can be delivered, e.g., as fusions of Cas nickase to a reverse transcriptase or as separate components (see, e.g., Granewald et al., Nat Biotechnol. 2022 Sep. 26. doi 10.1038/s41587-022-01473-1; and Liu et al., Nat Biotechnol. 2022 Sep; 40(9)1388-1393).
Cargo designed for the purposes of epigenome modulating includes CRISPR Cas proteins, zinc fingers (ZFs) and TALEs fused to an epigenome/epigenetic modulating agent or combination of epigenome/epigenetic modulating agent or a functional derivative thereof connected together by one or more variable length polypeptide linkers. Exemplary epigenetic modulating agents include CRISPR-Cas proteins (e.g., nickases or catalytically inactive Cas) fused to DNA methylases, histone acetyltransferases, and deacetylases, as well as transcriptional activators or repressors (see, e.g., Tables 2 & 4). Examples include, e.g., transcriptional repressors (e.g., KRAB, ERD, SID, and others, e.g., amino acids 473-530 of the ets2 repressor factor (ERF) repressor domain (ERD), amino acids 1-97 of the KRAB domain of KOXI, or amino acids 1-36 of the Mad mSIN3 interaction domain (SID); see Beerli et al., PNAS USA 9514628-14633 (1998)) or silencers such as Heterochromatin Protein 1 (HP1, also known as swi6), e.g., HP1α or HP1β; proteins or peptides that could recruit long non-coding RNAs (lncRNAs) fused to a fixed RNA binding sequence such as those bound by the MS2 coat protein, endoribonuclease Csy4, or the lambda N protein; enzymes that modify the methylation state of DNA (e.g., DNA methyltransferase (DNMT) or TET proteins); or enzymes that modify histone subunits (e.g., histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (e.g., for methylation of lysine or arginine residues) or histone demethylases (e.g., for demethylation of lysine or arginine residues)) In some embodiments, the sequence of the cargo is at least 95% identical to a sequence set forth herein.
sgRNAs can complex with genome editing reagents during the packaging process to be co-delivered within ptVLPs. Also, linear or circular RNAs encoding cargo or edits that are to be installed by a prime editor could be co-packaged with genome editing reagents that are fused to RNA binding proteins, such as MS2, PP7, COM, or TAR hairpin binding protein (TBP) or human SLBP. Cargo designed for the purposes of transcriptome editing includes CRISPR Cas proteins or any functional derivatives thereof (e.g., as shown in Table 5) or CRISPR Cas proteins or any functional derivatives thereof (e.g., as shown in Table 5) fused to nucleotide deaminases or nucleoside deaminases (e.g., as shown 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., WO2014005219; U.S. Ser. No. 10/137,206; US20180339166; U.S. Pat. No. 5,892,020A; EP2134841B1; WO2007020965A1. For example, 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. In the mammalian inner ear, ptVLP 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 β-catenin (β-catenin Ser 33 edited to Tyr, Pro, or Cys) in order to better stabilize β-catenin could help reverse hearing loss.
In another application, ptVLP 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). For example, ptVLP 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 ptVLP cargo). This example is especially pertinent when combined with ptVLPs that are antigen inducible and therefore specific for tumor cells. Alternatively, the transitory reduction in cellular levels of a specific protein of interest may itself have therapeutic benefit.
In some embodiments, ptVLPs 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 or to deliver factors that induce forward differentiation or trans-differentiation into a specific cell-type.
In some embodiments, ptVLPs could deliver dominant-negative forms of proteins in order to elicit a therapeutic effect.
ptVLPs that are antigen-specific (e.g., tumor-antigen specific) could be targeted to cancer cells in order to deliver proapoptotic proteins BIM, BID, PUMA, NOXA, BAD, BIK, BAX, BAK and/or HRK in order to trigger apoptosis of cancer cells. Tumor antigens are known in the art.
90% of 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. To this end, ptVLPs 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.54 Such fusion proteins, ptVLPs, 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. ptVLPs could deliver single chain variable fragment (scFv) antibodies to the cytosol of cells that bind to and disrupt cytosolic steroid receptors. For example, 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 that has been linked to tumorigenesis.55
ptVLPs can be indicated for treatments that involve targeted disruption of proteins. For example, ptVLPs can be utilized for targeting and disrupting proteins in the cytosol of cells by delivering antibodies/scFvs to the cytosol of cells. Classically, 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.56-58 Such fusion proteins, ptVLPs, and methods of making and using the same are included herein.
In addition, the targeting of targeted small molecules is limited to proteins of a certain size that contain binding pockets that are relevant to catalytic function or protein-protein interactions. 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. For example, RAS oncoproteins are implicated across a multitude of cancer subtypes, and RAS is one of the most frequently observed oncogenes in cancer. For instance, 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 ptVLPs that can deliver specifically to cancer cells scFvs that bind to and disrupt the function of multiple RAS isoforms.56-58
ptVLP Composition, Production, Purification and Applications
ptVLPs 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. This, in some embodiments, the ptVLPs described herein can be produced and package protein-based cargo by integrating all production DNA constructs into the genomic DNA of production cell lines. Once cell lines (e.g., production lines) are created, protein delivery ptVLPs can be produced in a constitutive or inducible fashion.
Alternatively, some or all of the components for producing ptVLPs can be transiently expressed. In some embodiments, for ptVLPs, a single plasmid is used in the transfection that comprises sequences encoding one or more transmembrane envelope glycoproteins (with or without specified mutation(s)/truncation(s) and/or targeting domain fusions, e.g., as described herein) (e.g., unmodified envelopes are shown in Table 1) or a transmembrane envelope glycoprotein with or without specified mutation(s)/truncation(s) with a membrane-anchored targeting domain in trans, 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 at least one guide RNA, if necessary.
In some embodiments, two to three plasmids are used in the transient transfection. These two to three plasmids can include the following (any two or more components listed here can be combined in a single plasmid)
In some embodiments, the methods for producing ptVLPs can include using cells that have or have not been manipulated to express any exogenous proteins except for a targeted viral envelope protein comprising a targeting domain fusion or viral envelope with associated targeting domain in trans with or without specified mutation(s)/truncation(s) (e.g., as shown in Table 1), and, if desired, a plasma membrane recruitment domain (e.g., as shown in Table 6); in other words, no cargo is expressed. In this embodiment, the “empty” particles that are produced can be loaded with cargo and/or small molecules by utilizing incubation, nucleofection, lipid, polymer, or CaCl2) transfection, sonication, freeze thaw, and/or heat shock of purified particles mixed with cargo. In all embodiments, producer cells do not express any exogenous 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 technologies.
The plasmids, or other types of specialty DNA molecules known in the art or described herein, 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; IRES; 2A peptide; an insulator sequence; or another sequence that increases or controls expression (e.g., an inducible promoter element).
Appropriate producer cell lines can include primary or stable human cell lines refractory to the effects of transfection reagents and fusogenic effects due to virally-derived glycoproteins. Examples of 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. For example, such cells could be selected for their ability to grow as adherent cells, or suspension cells. In some embodiments, the producer cells can be cultured in classical DMEM under serum conditions, serum-free conditions, or exosome-free serum conditions. ptVLPs can be produced from cells that have been derived from patients (autologous ptVLPs) and other FDA-approved cell lines (allogenic ptVLPs) as long as these cells can be transfected with DNA constructs that encode the aforementioned ptVLP production components by various techniques known in the art.
In addition, if it is desirable, more than one genome editing reagent encoded in polynucleic acid construct(s) can be included in the transfection. 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 can be employed for introducing polynucleic 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.
A human producer cell line that stably expresses the necessary ptVLP components in a constitutive and/or inducible fashion can be used for production of ptVLPs. ptVLPs can be produced from cells that have been derived from patients (autologous ptVLPs) and other FDA-approved cell lines (allogenic ptVLPs) if these cells have been converted into stable cell lines that express the aforementioned ptVLP components.
Also provided herein are the producer cells themselves.
Production of Cargo-Loaded ptVLPs and Compositions
Preferably ptVLPs are harvested from cell culture medium supernatant 36-48 hours post-transfection, or when ptVLPs 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, tangential flow filtration, and/or chromatography. In some embodiments, the supernatant is first filtered, e.g., to remove particles larger than 1 μm, e.g., through 0.45 pore size polyvinylidene fluoride hydrophilic membrane (Millipore Millex-HV) or 0.8 μm pore size mixed cellulose esters hydrophilic membrane (Millipore Millex-AA). After filtration, the supernatant can be further purified and concentrated, e.g., using ultracentrifugation, e.g., at a speed of 80,000 to 100,000 xg 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. After this centrifugation step, the ptVLPs 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. In some embodiments, ptVLP-containing supernatant can be filtered, precipitated, centrifuged and resuspended to a concentrated solution. For example, polyethylene glycol (PEG), e.g., PEG 8000, or antibody-bead conjugates that bind to ptVLP surface proteins or membrane components can be used to precipitate particles. 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.
Preferably, ptVLPs are resuspended or undergo buffer exchange so that particles are suspended in an appropriate carrier. In some embodiments, buffer exchange can be performed by ultrafiltration (e.g., Sartorius Vivaspin 500 MWCO 100,000). An exemplary appropriate carrier for ptVLPs 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 ptVLPs. Transduction-enhancing reagents that can be mixed into the purified and concentrated ptVLP solution for in vitro applications include reagents known by those familiar with the art (e.g., Miltenyi Biotec Vectofusin-1, Millipore Polybrene, Takara Retronectin, Sigma Protamine Sulfate, and the like). After ptVLPs in an appropriate carrier are applied to the cells to be transduced, transduction efficiency can be further increased by centrifugation. Preferably, the plate containing ptVLPs 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 (e.g., humidified incubator at 37° C. with 5% CO2).
An appropriate carrier for ptVLPs 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 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 ptVLPs and do not prevent ptVLP entry into target cells. In all cases, 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.
Methods of formulating suitable pharmaceutical compositions are known in the art, see, e.g., Remington The Science and Practice of Pharmacy, 21st ed., 2005; and the books in the series Drugs and the Pharmaceutical Sciences a Series of Textbooks and Monographs (Dekker, NY). For example, 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.
Pharmaceutical 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. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, 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. In many cases, it will be preferable to include 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. Generally, 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. In the case of sterile powders for the preparation of sterile injectable solutions, 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 ptVLPs as described herein can be included in a container, pack, or dispenser together with instructions for administration.
E. coli TadA
In some embodiments, the sequence of a protein or nucleic acid used in a composition or method described herein is at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% identical to a sequence set forth herein. To determine the percent identity of two amino acid sequences, or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In a preferred embodiment, the length of a reference sequence aligned for comparison purposes is at least 80% of the length of the reference sequence, and in some embodiments is at least 90% or 100%. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. For example, the percent identity between two amino acid sequences can be determined using the Needleman and Wunsch ((1970) J. Mol. Biol. 48444-453) algorithm which has been incorporated into the GAP program in the GCG software package (available on the world wide web at gcg.com), using the default parameters, e.g., a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
Rattus norvegicus & synthetic APOBEC1-XTEN L8-nspCas9-UGI-SV40 NLS
Homo sapiens AID
Homo sapiensAIDv solubility variant lacking N-terminal RNA-binding region
Homo sapiens AIDv solubility variant lacking N-terminal RNA-binding region
Rattus norvegicus APOBEC1
Mus musculus APOBEC3
Mus musculus APOBEC3 catalytic domain
Homo sapiens APOBEC3A
Homo sapiens APOBEC3G
Homo sapiens APOBEC3G catalytic domain
Homo sapiens APOBEC3H
Homo sapiens APOBEC3F
Homo sapiens APOBEC3F catalytic domain
Escherichia coli TadA
Homo sapiens Adar1
Homo sapiens Adar2
Streptococcus pyogenes Cas9 Bipartite NLS
Staphylococcus aureus Cas9
Campylobacter jejuni Cas9
Neisseria meningitidis Cas9
Acidaminococcus sp. Cas12a
Lachnospiraceae bacterium Cas12a
Leptotrichia shahii Cas13a
Leptotrichia wadei Cas13a
Homo sapiens P65
Homo sapiens KRAB
Homo sapiens MeCP2
Homo sapiens Tet1
Homo sapiens Dnmt3a
Vesicular stomatitis virus Glycoprotein (VSVG) WT
Vesicular stomatitis virus Glycoprotein (VSVG) (K47A)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47E)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47G)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47Q)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47W)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47A)(R354A)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47E) (R354A)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47G) (R354A)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47Q) (R354A)
Vesicular stomatitis virus Glycoprotein (VSVG) (K47W) (R354A)
Vesicular stomatitis virus Glycoprotein (VSVG truncation) (F421 Truncation)
Vesicular stomatitis virus Glycoprotein (VSVG truncation) (F448 Truncation)
Tupaia Paramyxovirus Hemagglutinin (TPMV H) WT
Tupaia Paramyxovirus Hemagglutinin (TPMV H) delta 32
Tupaia Paramyxovirus Hemagglutinin (TPMV H) delta 32 with targeting
Tupaia Paramyxovirus Hemagglutinin (TPMV H) delta 80
Tupaia Paramyxovirus Hemagglutinin (TPMV H) delta 80 with targeting
Tupaia Paramyxovirus Fusion (TPMV F) WT
Tupaia Paramyxovirus Fusion (TPMV F) delta 32
The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
ptVLP particles were produced in HEK293T cells by using polyethylenimine (PEI) to transfect plasmids into these cells. PEI is Polyethylenimine 25 kD linear (Polysciences #23966-2). To make a stock ‘PEI MAX’ solution, Ig of PEI was added to 1 L endotoxin-free dH2O that was previously heated to ˜80° C. and cooled to room temperature. This mixture was neutralized to pH 7.1 by addition of TON NaOH and filter sterilized with 0.22 μm polyethersulfone (PES). PEI MAX solution was stored at −20° C.
HEK293T cells were split to reach a confluency of 70%-90% at time of transfection and are cultured in 10% FBS DMEM media. Plasmid vectors encoding cargo, e.g., one encoding a CMV promoter driving expression of a fusion protein comprising hPLCδ1 PH domain linked to codon optimized Cas9, were co-transfected with plasmids encoding a U6 promoter driving expression of a Cas9 sgRNA, a membrane-anchored targeting moiety, and a mutated VSV-G envelope plasmid. Transfection reactions were assembled in reduced serum media (Opti-MEM; GIBCO #31985-070). For ptVLP particle production on 10 cm plates, 7.5 μg PH-Cas9 expressing plasmid, 7.5 μg sgRNA-expression plasmid and 5 μg programmed tropism ENV expressing plasmid were mixed in 1 mL Opti-MEM, followed by addition of 27.5 μl PEI MAX. After 20-30 min incubation at room temperature, the transfection reactions were dispersed dropwise over the HEK293T cells.
ptVLPs were harvested at 48-72 hours post-transfection. To do this, ptVLP supernatants were filtered using 0.45 μm PVDF or cellulose acetate or 0.8 μm 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 ptVLP-containing supernatant from three 10 cm plates to reach an approximate final volume of 35-37.5 ml. ptVLP supernatant underwent ultracentrifugation at approximately 100,000 xg, or 25,000 rpm, at 4° C. for 2 hours. After ultracentrifugation, supernatants were decanted and ptVLP pellets resuspended in DMEM 10% FBS media such that they were now approximately 1,000 times more concentrated than they were before ultracentrifugation. ptVLPs were added dropwise to cells that were seeded in a 24-well plate 24-hours prior to transduction. Polybrene (5-10 μg/mL in cell culture medium; Sigma-Aldrich #TR-1003-G) was supplemented to enhance transduction efficiency, if necessary. Vectofusin-1 (10 μg/mL in cell culture medium, Miltenyi Biotec #130-111-163) was supplemented to enhance transduction efficiency, if necessary. Immediately following the addition of ptVLPs, the 24-well plate was centrifuged at 1,150×g for 30 min at room temperature to enhance transduction efficiency, if necessary.
ptVLPs (illustrated in
For
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
This application claims the benefit of U.S. Provisional Patent Application Ser. No. 63/425,894, filed on Nov. 16, 2022. The entire contents of the foregoing are hereby incorporated by reference.
This invention was made with Government support under Grant Nos. GM118158 awarded by the National Institutes of Health. The Government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 63425894 | Nov 2022 | US |
