Patent Application
20240189247
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. 22, 2024, is named 29539-0678001_SL.xml and is 297,563 bytes in size.
Described herein are virus-like particles (VLPs) and minimal human-derived virus-like particles (mhVLPs), including targeted human endogenous virus-like particles (theVLPs), comprising a membrane comprising a phospholipid bilayer with one or more human-derived envelope glycoproteins (env) on the external side. Optionally, a biomolecule cargo is disposed in the core of the VLPs and mhVLPs on the inside of the membrane. Preferably, the VLPs and mhVLPs do not comprise any exogenous virally derived proteins, e.g., proteins from viral gag, pro, or pol, or other viral proteins that reside inside of enveloped particles (unless the cargo comprises the viral protein(s)). In some embodiments, the VLPs and mhVLPs do not comprise any human endogenous retroviral (HERV) proteins other than the env, e.g., do not comprise gag, pol, or pro. Also described are methods of use of the VLPs and mhVLPs for delivery of the biomolecule cargo to cells.
Delivery of cargo such as proteins, nucleic acids, and/or chemicals into the cytosol of living cells has been a significant hurdle in the development of biological therapeutics.
Described herein are virus-like particles (VLPs) and minimal human-derived virus-like particles (mhVLPs), including targeted human endogenous virus-like particles (theVLPs) that are capable of packaging and delivering a wide variety of 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. The non-viral mhVLP systems described herein have the potential to be simpler, more efficient, safer, and/or less immunogenic than conventional, artificially-derived lipid/gold nanoparticles and viral particle-based delivery systems, because mhVLPs are comprised of human-derived components that are expressed in healthy human tissues in their unmodified forms, mhVLPs can also utilize but do not require chemical-based dimerizers, and mhVLPs have the ability to package and deliver cargo including, but not limited to, biomolecules including nucleic acids, e.g., 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); proteins; chemical compounds and/or molecules, and combinations of the above listed cargos (e.g., AAV particles and/or ribonucleoprotein (RNP) complexes comprising RNA and protein, e.g., guide RNA/CRISPR Cas protein complexes). The mhVLPs 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, at least because of the membrane configuration, HERV-derived envelope glycoprotein, 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, pro, or pol, and/or the mechanism of cellular entry.
Provided herein are virus-like particles (VLPs) that comprise mutant and truncated HERV glycoproteins/envelope proteins (hENV). In some embodiments, the hENV comprise a sequence that is at least 95% identical to a sequence as set forth herein, e.g., in Tables 1A, 1B, and/or 1C, optionally comprising a mutation as identified in Table 1B, and/or a truncation and/or targeting domain insertion as shown in Table 1C, or a combination thereof. In some embodiments, the truncated hENV comprises a C-terminal deletion of between 1 and 60 amino acids, or a C-terminal deletion that partially or entirely removes the intracellular domain. In some embodiments, the hENV comprises a mutation in the receptor binding domain, e.g., in an amino acid corresponding to amino acids 120-125 of the wild type HERV-W sequence set forth herein (e.g., a mutation as shown in Table 1B). In some embodiments, the hENV comprise a targeting domain that alters tropism of the particles, e.g., inserted into or fused to the N or C terminus of the hENV, e.g., as shown in Table 1C (e.g., a programmable tropism HERV env (pthENV). Optionally, linkers can be present between any or all of the parts of the fusion proteins.
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), or darpin.
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 targeting domain is inserted internally into the hENV, optionally after an amino acid corresponding to amino acid 18 or amino acid 114 of wild type HERV W. In some embodiments, the hENV further comprises one or more of: a deletion of 123 to 163 amino acids following amino acid 18; truncation of one to 50 amino acids from the C RBD mutations. 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.
Also provided herein are nucleic acids encoding the hENVs, and vectors comprising the nucleic acids, optionally operably linked to a promoter for expression of the hENV, as well as host (production) cells comprising the nucleic acids, and optionally expressing the hENV. In some embodiments, the nucleic acids are codon-optimized for expression in humans.
Further, provided herein are virus-like particles (VLPs) comprising a hENV as described herein. Additionally provided are targeted human endogenous virus-like particle (theVLP) comprising a human endogenous retroviral (HERV) envelope protein (hENV) and a targeting domain, wherein the hENV is at least 95% identical to a sequence as set forth in Tables 1A-C, and optionally comprises a truncation of one to 50 amino acids from the C terminus and/or one or more RBD mutations, wherein the targeting domain is (i) fused at the N or C terminus, or inserted internally into the of the hENV, or (ii) is a membrane-anchored targeting domain comprising a targeting domain fused to a transmembrane domain, with optional linkers therebetween.
Optionally, a cargo is disposed in the core of the theVLP; optionally the cargo is fused to a phospholipid bilayer recruitment domain.
Also provided are minimal human-derived virus-like particles (mhVLPs), comprising a membrane comprising a phospholipid bilayer and a human endogenous retroviral (HERV) envelope protein (hENV), wherein the hENV optionally comprises one, two, or all three of: a targeting domain at the N or C terminus, or inserted internally into the protein; a truncation of one to 50 amino acids from the C terminus; and/or one or more RBD mutations; and optionally, a cargo disposed in the core of the mhVLP, wherein the cargo is optionally fused to a phospholipid bilayer recruitment domain; preferably wherein the mhVLP does not comprise an exogenous gag, pro and/or pol protein, and optionally wherein the mhVLP further comprises a separate targeting domain. In some embodiments, the mhVLPs do or do not comprise any human endogenous retroviral (HERV) proteins other than the env, e.g., do not comprise gag, pol, or pro (Grandi and Tramontano, Front Microbiol. 2018 Mar. 14; 9:462). 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.
In some embodiments, the targeting domain comprises an 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), or darpin. In some embodiments, the targeting domain is inserted internally into the hENV, optionally after an amino acid corresponding to amino acid 18 or amino acid 114 of wild type HERV W env. In some embodiments, the hENV further comprises one or more of: a deletion of 123 to 163 amino acids following amino acid 18; truncation of one to 50 amino acids from the C RBD mutations.
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 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 that is at least 95% identical to a sequence set forth herein, e.g., in Tables 2, 3, 4, and 5. In some embodiments, the cargo comprises a CRISPR-Cas protein, and the theVLP or VLP 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.
Also provided are methods of delivering a cargo to a target cell, optionally a cell in vivo or in vitro, the method comprising contacting the cell with a theVLP or mhVLP as described herein comprising the cargo.
Additionally provided herein are methods of producing a theVLP or an mhVLP, optionally comprising a cargo. The methods comprise providing a cell expressing a hENV as described herein and optionally a cargo, optionally wherein the cell does not express a human endogenous and/or exogenous any exogenous virally derived proteins, e.g., proteins from viral gag, pro, or pol, or other viral proteins that reside inside of enveloped particles (unless the cargo comprises the viral protein(s)); and maintaining the cell under conditions such that the cells produce the VLPs or mhVLPs. In some embodiments, the mhVLPs do or do not comprise any human endogenous retroviral (HERV) proteins other than the env, e.g., do not comprise gag, pol, or pro. Optionally the hENV optionally comprises one, two, or all three of: a targeting domain at the N or C terminus, or inserted internally into the protein; a truncation of one to 50 amino acids from the C terminus; and/or one or more RBD mutations, (ii) a cargo, and (iii) optionally a separate targeting domain.
In some embodiments, the methods further comprise harvesting and optionally purifying and/or concentrating the produced VLPs or mhVLPs. 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 guide RNA and/or crRNA; a nucleic acid encoding a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-Cas protein, variant, or fusion thereof; 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 Tables 2, 3, 4, and 5. In some embodiments, the cargo reagent comprises a CRISPR-Cas protein, variant, or fusion thereof and the mhVLP 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.
Also provided herein are cells expressing a hENV as described herein, and a cargo, optionally wherein the cell does not express any exogenous virally derived proteins, e.g., proteins from viral gag, pro, or pol, or other viral proteins that reside inside of enveloped particles (unless the cargo comprises the viral protein(s)). Also provided are cells expressing (i) a human endogenous retroviral (HERV) envelope protein (hENV), wherein the hENV optionally comprises one, two, or all three of: a targeting domain at the N or C terminus, or inserted internally into the protein; a truncation of one to 50 amino acids from the C terminus; and/or one or more RBD mutations, (ii) a cargo, (iii) optionally a separate targeting domain. In some embodiments, the cells do or do not express any human endogenous retroviral (HERV) proteins other than the env, e.g., do not comprise gag, pol, or pro.
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 guide RNA or crRNA; a nucleic acid encoding a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-Cas protein, variant, or fusion thereof; or a ribonucleoprotein complex (RNP) comprising a CRISPR-Cas protein, variant, or fusion thereof and optionally a guide RNA 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 Tables 2, 3, 4, and 5. In some embodiments, the gene editing or epigenetic modulating reagent comprises a CRISPR-Cas protein, and the mhVLP further comprises one or more guide RNAs and/or crRNAs that bind to and direct the CRISPR-Cas 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. In some embodiments, the cells are primary or stable human cell lines. In some embodiments, the cells are Human Embryonic Kidney (HEK) 293 cells or HEK293 T cells.
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, but for many of these large biomolecules delivery into cells is a hurdle to clinical development. 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
Lentivirus and standard 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. In addition, the majority of 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 fully activate the fusogenicity of the ENV protein; this is believed to be essential for infectivity of viral particles and for VLPs. Without wishing to be bound by theory, it is believed that the hENV protein alone is responsible for VLP/mhVLP particle generation and the ability of VLPs/mhVLPs as described herein to efficiently deliver cargo into cells.
Human Endogenous Retroviral (HERV) Envelope Proteins (hENVs)
A number of human endogenous retroviral proteins have been described (de Parseval et al., Journal of Virology 77, 10414-10422, (2003); Heidmann et al., Proc Natl Acad Sci USA. 2017 Aug. 8; 114(32):E6642-E6651). These sequences were used to reconstruct an ancestral proviral clone termed HERV-KcoN (Lee and Bieniasz, PLoS Pathog. 2007 January; 3(1):e10). Retroviral envelope proteins are glycoprotein composed of a surface unit (SU) and a transmembrane unit (TM). In the case of HERV W env, the SU contains a receptor binding domain (RBD), a furin cleavage site (RNKR at amino acids 314-317 (SEQ ID NO: 4)), six N-glycosylation sites, and a CFFC (SEQ ID NO: 286) (CX2C at amino acids 186-189) motif (Bastida-Ruiz D, et al. Int J Mol Sci. 2016 Apr. 28; 17(5):638). The HERV W env proteins bind to receptors including the monocarboxylate transporter-1 (MCT-1, Blanco-Melo et al., eLife 6:e22519 (2017)) and Major Facilitator Superfamily Domain Containing 2 (MFSD2, Esnault et al., Proc Natl Acad Sci USA. 2008 Nov. 11; 105(45):17532-7), and can be used to pseudotype lentiviruses to infect B cells (Coquin et al., bioRxiv 816223; doi.org/10.1101/816223) and to make recombinant vesicular stomatitis virus encoding HERV-K Env as its sole attachment and fusion protein (VSV-HERVK, Robinson-McCarthy et al., PLoS Pathog. 2018 Aug. 6; 14(8):e1007123).
The N-terminal 124 amino acids of the mature HERV W env glycoprotein have been identified as the minimal receptor-binding domain (RBD, Cheynet et al., Retrovirology. 2006 Jul. 4; 3:41). Chang et al., Biol Reprod. 2004 December; 71(6):1956-62, showed that hERV W env proteins (also referred to as syncytin-1) with C terminal deletions up to amino acid 480 retained cell fusion activity. Drewlo et al., Biol. Chem., 387:1113-1120 (2006) showed that variants of hERV W env truncated after residues 483 and 515 were hyperfusogenic compared to wild-type.
Provided herein are modified human endogenous retroviral (HERV) envelope proteins (hENV), wherein the hENV comprises one, two, or all three of: a targeting domain at the N or C terminus, or inserted internally into the protein; a truncation of one to 50 amino acids from the C terminus; and one or more RBD mutations. See, e.g.,
Exemplary modified and unmodified hENVs are provided in Tables 1A-C. Combinations of the modifications shown in Tables 1B and 1C can be included.
In some embodiments, an hENV is at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% identical to a protein identified in Table 1A, and retains the ability of the reference protein to generate VLP/mhVLP particles and to efficiently promote cargo delivery into cells. 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. 48:444-453) 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.
The hENV can also include one or more mutations in the receptor binding domain (RBD) described herein, e.g., in an amino acid corresponding to amino acids 115-125 of the hERV W env protein sequence, e.g., a MUT sequence as shown in Table 1B. Other mutations (e.g., R140C in HERV K ENV) that can be included have been described, e.g., in Hanke et al., J Virol. 2009 December; 83(24):12790-800.
The hENV can include targeting domains as described herein.
In some embodiments, the hENV is used in place of an ENV protein in a standard VLP, e.g., those VLPs described in previous publications.29,39,40 In some embodiments, the VLPs or mhVLPs or theVLPs can be composed of a mixture of ectosomes and exosomes that can be separated by purification, if desired. In part because of the above mentioned design simplifications and optimizations, VLPs/mhVLPs/theVLPs as described herein are particularly suited for delivery of cargo including but not limited to DNA, RNA, protein, and/or combinations of biomolecules and/or chemicals, such as DNA-encoded or RNP-based genome editing reagents.
Provided herein are VLPs/mhVLPs/theVLPs that include targeting domains that bind to antigens on target cells to alter tropism of the VLPs/mhVLPs/theVLPs. A number of such antigens are known in the art. Exemplary antigens include CD19,73 asialoglycoprotein receptor 1 (ASGR1),74 Transferrin receptor (TfR),75 HER2,76 CD34,77 CD4,78 CD25,79 CTLA-4,80 HB-EGF,81 ACE2,82 Aryl hydrocarbon receptor (AhR),83 keratin 5 (KRT5),84 keratin 17 (KRT17),85 keratin 14 (KRT14),86 keratin 13 (KRT13),87 Neural cell adhesion molecule L1,88 Fibronectin (FN1),89,90,91 Amyloid precursor protein (APP),92 Programmed cell death protein 1 (PD-1),93,94 neurotrophin receptor (p75NTR),95 Thy-1/CD90,96 EpCAM,97 and/or CFTR.98
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.63-69
Targeting domains can also include peptides, e.g., as shown in Table A. The targeting domains can be inserted into the sequence of an hENV protein such that it will be displayed on the surface of the VLP/mhVLP membrane, as described herein, or can be present as a separate molecule anchored on the outside of the VLP/mhVLP/theVLP membrane. Thus, fusion proteins comprising (i) a targeting domain and an envelope glycoprotein (programmable tropism HERV envelope protein (e.g., also referred to as a pthENV)), 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 hENV 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),99 CD9,100 CD63,100 CD81,100 CD86, Notch,73 CD28.101 CD8,102 or CD4.103 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.,
plasmodium
falciparum
plasmodium
falciparum
Preferably, the membrane anchored targeting domains and the hENV 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.
Conventional VLPs that have been engineered to encapsulate and deliver protein-based cargo commonly fuse the cargo to the INT, GAG or GAG-PRO-POL polyprotein.25-27,29,30,39,40 After transient transfection of production plasmid DNA constructs encoding the GAG/GAG-PRO-POL-fused cargo 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 the mhVLPs/theVLPs by fusing select phospholipid bilayer recruitment domains, preferably human protein-derived phospholipid bilayer recruitment domains to protein-based cargo (e.g., 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 mhVLPs/theVLPs 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 mhVLP/theVLP production cells, and they also allow for the cargo to localize to the nucleus of mhVLP/theVLP-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.
mhVLP-Mediated Delivery of DNAs, Proteins and RNAs
The VLPs, mhVLPs, and theVLPs described herein (e.g., comprising hENV proteins) can package and deliver biomolecule cargo. “Cargo” refers to 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, DNA and RNA, RNP, combinations of DNA and protein(s), or protein(s), 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 can include, 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, VLPs/mhVLPs/theVLPs can also package and deliver a combination of DNA and RNA, e.g., when VLPs/mhVLPs/theVLPs 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 mhVLPs/theVLPs and another fraction in the cytosol/near the plasma membrane could be encapsulated and delivered in mhVLPs. 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 U.S. Pat. No. 9,393,257B2; and International Publication WO2014134412A1) (CRISPR Cas proteins are described, for example, in 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).37,38,70-72 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., Grunewald et al., Nat Biotechnol. 2022 Sep. 26. doi: 10.1038/s41587-022-01473-1; and Liu et al., Nat Biotechnol. 2022 September; 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 KOX1, or amino acids 1-36 of the Mad mSIN3 interaction domain (SID); see Beerli et al., PNAS USA 95:14628-14633 (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 VLPs/mhVLPs/theVLPs. 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, mhVLP 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, mhVLP/VLP/theVLP 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, mhVLP/VLP/theVLP 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 mhVLP/VLP/theVLP cargo). This example is especially pertinent when combined with mhVLPs 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, mhVLPs/VLPs/theVLPs as described herein 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. This can be accomplished by overexpressing the Yamanaka factors and a hENV(s) in the producer cell. In addition, mhVLPs/VLPs/theVLPs can be used to deliver mitochondria. This can be accomplished by overexpressing a hENV in the producer cell. Particle populations that are within a certain size range will be enriched with mitochondria.
In some embodiments, mhVLPs/VLPs/theVLPs as described herein could deliver dominant-negative forms of proteins in order to elicit a therapeutic effect.
mhVLPs/VLPs/theVLPs as described herein 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, mhVLPs/VLPs/theVLPs as described herein 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 Such fusion proteins, mhVLPs, 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. mhVLPs/VLPs/theVLPs as described herein 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 1E which has been linked to tumorigenesis.48
mhVLPs/VLPs/theVLPs as described herein can be indicated for treatments that involve targeted disruption of proteins. For example, mhVLPs/VLPs/theVLPs as described herein 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.49-51 Such fusion proteins, mhVLPs/VLPs/theVLPs as described herein, and methods of making and using the same are provided herein.
In addition, the targeting of targeted small molecules is limited to proteins of a certain size that contain binding pockets which 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 mhVLPs that can deliver specifically to cancer cells scFvs that bind to and disrupt the function of multiple RAS isoforms.49-51 VLP/mhVLP/theVLP composition, production, purification and applications mhVLPs/VLPs/theVLPs as described herein can be produced from producer cell lines that are either transiently transfected with at least one plasmid/polynucleic acid construct or stably expressing construct(s) that have been integrated into the producer cell line genomic DNA. In some embodiments, for mhVLPs/theVLPs, e.g., if a single plasmid is used in the transfection, it should comprise sequences encoding one or more transmembrane HERV envelope glycoproteins (with or without specified mutation(s)/truncations and/or targeting domain fusions) (e.g., unmodified HERV envelopes are shown in Table 1A) or a transmembrane HERV envelope glycoprotein with or without specified mutation(s)/truncations 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. Preferably, 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 also be combined in a single plasmid):
In addition, four or more plasmids could be used in the transient transfection. These four or more plasmids can include the following (any two or more components listed here can also be combined in a single plasmid):
If it is desired to deliver a type of DNA molecule other than plasmid(s), 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. Alternatively, for mhVLPs/theVLPs, the producer cell line can be made to stably express the constructs (1 through 3) described in the transfection above.
As stated earlier, in some embodiments, the methods include using cells that have or have not been manipulated to express any exogenous proteins except for a targeted HERV envelope with or without targeting domain fusion or HERV envelope with associated targeting domain in trans with or without specified mutation(s)/truncation(s) (e.g., as shown in Tables 1A-C), and, if desired, a plasma membrane recruitment domain (e.g., as shown in Table 6). 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 some 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 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; IRES; 2A peptide; an insulator sequence; or another sequence that increases or controls expression (e.g., an inducible promoter element).
Preferably, 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. 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. mhVLPs/theVLPs can be produced from cells that have been derived from patients (autologous mhVLPs/theVLPs) and other FDA-approved cell lines (allogenic mhVLPs/theVLPs) as long as these cells can be transfected with DNA constructs that encode the aforementioned mhVLP/theVLP 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 may 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 mhVLP/theVLP components in a constitutive and/or inducible fashion can be used for production of mhVLPs/theVLPs. mhVLPs/theVLPs can be produced from cells that have been derived from patients (autologous mhVLPs/theVLPs) and other FDA-approved cell lines (allogenic mhVLPs/theVLPs) if these cells have been converted into stable cell lines that express the aforementioned mhVLP/theVLP components.
Also provided herein are the producer cells themselves.
Production of Cargo-Loaded mhVLPs theVLPs and Compositions
Preferably mhVLPs/theVLPs are harvested from cell culture medium supernatant 36-48 hours post-transfection, or when mhVLPs/theVLPs 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 m, e.g., through 0.45 pore size polyvinylidene fluoride hydrophilic membrane (Millipore Millex-HV) or 0.8 m 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×g 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 mhVLPs/theVLPs 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, mhVLP/theVLP-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 mhVLP/theVLP 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, mhVLPs/theVLPs 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 mhVLPs/theVLPs 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 mhVLPs/theVLPs. Transduction-enhancing reagents that can be mixed into the purified and concentrated mhVLP/theVLP 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 mhVLPs/theVLPs in an appropriate carrier are applied to the cells to be transduced, transduction efficiency can be further increased by centrifugation. Preferably, the plate containing mhVLPs/theVLPs 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 mhVLPs/theVLPs 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 mhVLPs/theVLPs and do not prevent mhVLP/theVLP 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.
The compositions comprising cargo-loaded mhVLPs/theVLPs 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. 48:444-453) 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 sapiens: AIDv solubility variant lacking N-terminal RNA-binding
Homo sapiens: AIDv solubility variant lacking N-terminal RNA-binding
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
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: Tet
Homo sapiens: Dnmt3a
MALPYHIFLFTVLLPSFTLTAPPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSLSKGTPTFTAHTHMP
RNCYHSATLCMHANTHYWTGKMINPSCPGGLGVTVCWTYFTQTGMSDGGGVQNKAREKHVKEVISQLTR
VHGTSSPYKGLDLSKLHETLRTHTRIVSLENTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPEQWN
NFSTEINTTSVLVGPLVSNLEITHTSNLTCVKFSNTTYTTNSQCIRWVTPPTQIVCLPSGIFFVCGTSA
YRCLNGSSESMCFLSFLVPPMTIYTEQDLYSYVISKPRNKRVPILPFVIGAGVLGALGTGIGGITTSTQ
FYYKLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIV
TEKVKEIRDRIQRRAEELRNTGPWGLLSQWMPWILPFLGPLAAIILLLLFGPCIFNLLVNFVSSRIEAV
KLQMEPKMQSKTKIYRRPLDRPASPRSDVNDIKGTPPEEISAAQPLLRPNSAGSS
MALPYHIFLFTVLLPSFTLTAPPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSLSKGTPTFTAHTHMP
RNCYHSATLCMHANTHYWTGKMINPSCPGGLGVTVCWTYFTQTGMSDGGGVKNKAREKHVKEVISQLTR
VHGTSSPYKGLDLSKLHETLRTHTRIVSLENTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPEQWN
NFSTEINTTSVLVGPLVSNLEITHTSNLTCVKFSNTTYTTNSQCIRWVTPPTQIVCLPSGIFFVCGTSA
YRCLNGSSESMCFLSFLVPPMTIYTEQDLYSYVISKPRNKRVPILPFVIGAGVLGALGTGIGGITTSTQ
FYYKLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIV
TEKVKEIRDRIQRRAEELRNTGPWGLLSQWMPWILPFLGPLAAIILLLLFGPCIENLLVNFVSSRIEAV
KLQMEPKMQSKTKIYRRPLDRPASPRSDVNDIKGTPPEEISAAQPLLRPNSAGSS
MALPYHIFLFTVLLPSFTLTAPPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSLSKGTPTFTAHTHMP
RNCYHSATLCMHANTHYWTGKMINPSCPGGLGVTVCWTYFTQTGMSNGGGVQRQAREKHVKEVISQLTR
VHGTSSPYKGLDLSKLHETLRTHTRIVSLENTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPEQWN
NFSTEINTTSVLVGPLVSNLEITHTSNLTCVKFSNTTYTTNSQCIRWVTPPTQIVCLPSGIFFVCGTSA
YRCLNGSSESMCFLSFLVPPMTIYTEQDLYSYVISKPRNKRVPILPFVIGAGVLGALGTGIGGITTSTQ
FYYKLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIV
TEKVKEIRDRIQRRAEELRNTGPWGLLSQWMPWILPFLGPLAAIILLLLFGPCIFNLLVNFVSSRIEAV
KLQMEPKMQSKTKIYRRPLDRPASPRSDVNDIKGTPPEEISAAQPLLRPNSAGSS
MALPYHIFLFTVLLPSFTLTAPPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSLSKGTPTFTAHTHMP
RNCYHSATLCMHANTHYWTGKMINPSCPGGLGVTVCWTYFTQTGMSNGGGVQDQAREKHVKEVISQLTR
VHGTSSPYKGLDLSKLHETLRTHTRIVSLENTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPEQWN
NFSTEINTTSVLVGPLVSNLEITHTSNLTCVKFSNTTYTTNSQCIRWVTPPTQIVCLPSGIFFVCGTSA
YRCLNGSSESMCFLSFLVPPMTIYTEQDLYSYVISKPRNKRVPILPFVIGAGVLGALGTGIGGITTSTQ
TEKVKEIRDRIQRRAEELRNTGPWGLLSQWMPWILPFLGPLAAIILLLLFGPCIFNLLVNFVSSRIEAV
KLQMEPKMQSKTKIYRRPLDRPASPRSDVNDIKGTPPEEISAAQPLLRPNSAGSS
MALPYHIFLFTVLLPSFTLTAPPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSLSKGTPTFTAHTHMP
RNCYHSATLCMHANTHYWTGKMINPSCPGGLGVTVCWTYFTQTGMSDGGGVQRQAREKHVKEVISQLTR
VHGTSSPYKGLDLSKLHETLRTHTRIVSLENTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPEQWN
NFSTEINTTSVLVGPLVSNLEITHTSNLTCVKFSNTTYTTNSQCIRWVTPPTQIVCLPSGIFFVCGTSA
YRCLNGSSESMCFLSFLVPPMTIYTEQDLYSYVISKPRNKRVPILPFVIGAGVLGALGTGIGGITTSTQ
FYYKLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIV
TEKVKEIRDRIQRRAEELRNTGPWGLLSQWMPWILPFLGPLAAIILLLLFGPCIFNLLVNFVSSRIEAV
KLQMEPKMQSKTKIYRRPLDRPASPRSDVNDIKGTPPEEISAAQPLLRPNSAGSS
The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
The following methods were used in the Examples below. mhVLP or theVLP particles were produced in HEK293T cells by using jetPRIME® (Polyplus) or 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 is stored at −20° C.
HEK293T cells were split to reach a confluency of 70%-90% at time of transfection and cultured in 2% FBS DMEM media. Plasmid vectors encoding cargo, e.g., encoding a CMV promoter driving expression of a hPLCδ1 or hAKT (E17K) PH domain fused to codon optimized Cas9-based ABE8e were co-transfected with plasmids encoding a U6 promoter driving expression of a sgRNA and another expressing the VSV-G envelope or hENV from a CMV promoter. Transfection reactions were assembled in JETPRIME buffer. For mhVLP particle production on 300 cm2 T300 flasks, 19 μg PH-ABE8e expressing plasmid, 30 μg sgRNA-expression plasmid and 15 μg hENV expressing plasmid were mixed in 2 mL of JetPrime buffer, followed by addition of 4.6 μl/μg JetPrime. After 10 min incubation at room temperature, the transfection reactions were dispersed dropwise over the HEK293T cells.
Alternatively, if PEI was used for mhVLP particle production on 10 cm plates, 7.5 μg PH-ABE8e expressing plasmid, 7.5 μg sgRNA-expression plasmid and 5 μg hENV expressing plasmid were mixed in 1 mL Opti-MEM reduced serum media (Opti-MEM; GIBCO #31985-070), 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. In the following examples, JETPRIME was used for transfection.
mhVLPs were harvested at 48 hours post-transfection and a media swap of 36 ml 2% DMEM is performed 18 hours-post transfection. 48-hours-post transfection, mhVLP supernatants were filtered using 0.45 m PVDF membrane filters and PEG precipitated (PEG-it, System Biosciences). The following examples employ PEG precipitation.
Alternatively, 0.45 um PVDF clarified harvest was transferred to polypropylene Beckman ultracentrifuge tubes that are used with the SW28 rotor (Beckman Coulter #326823). Each ultracentrifuge tube was filled with mhVLP-containing supernatant from three 10 cm plates or 1 T300 flask to reach an approximate final volume of 35-37.5 ml with a 1.5-3 ml 10% sucrose cushion. mhVLP supernatant underwent ultracentrifugation at approximately 100,000×g, or 25,000 rpm, at 4° C. for 2 hours.
After ultracentrifugation, supernatants were decanted and mhVLP pellets resuspended in DMEM 2% FBS media, or other media appropriate for the culturing of the target recipient cells, to be up to 2,000 times more concentrated than they were before ultracentrifugation. mhVLPs 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) can be supplemented to enhance transduction efficiency, if necessary. Vectofusin-1 (10 μg/mL in cell culture medium, Miltenyi Biotec #130-111-163) can be supplemented to enhance transduction efficiency, if necessary. Immediately following the addition of mhVLPs, the 24-well plate can be centrifuged at 1,150×g for 30 min at room temperature to enhance transduction efficiency, if necessary (“Spinduction”). The following examples did not employ transduction enhancers or “spinduction.”
mhVLPs were produced by transient plasmid transfection of HEK293T cells (
mhVLPs and one eVLP (WO 2022/020800) were produced by transient transfection of producer cells (
mhVLPs were produced by transient transfection of producer cells (
mhVLPs were produced by transient transfection of producer cells (
mhVLPs were produced by transient transfection of producer cells (
The following methods were used in the example below. mhVLP particles were produced in HEK293T cells by using jetPRIME® (Polyplus) or 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 10N NaOH and filter sterilized with 0.22 m polyethersulfone (PES). PEI MAX is stored at −20° C.
HEK293T cells were split to reach a confluency of 70%-90% at time of transfection and are cultured in 2% FBS DMEM media. Plasmid vectors encoding cargo, e.g., encoding a CMV promoter driving expression of a hPLCδ1 or hAKT (E17K) PH domain fused to codon optimized Cas9-based ABE8e were co-transfected with plasmids encoding a U6 promoter driving expression of a sgRNA and another expressing the the VSV-G envelope or hENV from a CMV promoter. Transfection reactions were assembled in JetPrime buffer. For mhVLP particle production on 300 cm2 T300 flasks, 19 μg PH-ABE8e expressing plasmid, 30 μg sgRNA-expression plasmid and 15 μg hENV expressing plasmid were mixed in 2 mL of JetPrime buffer, followed by addition of 4.6 μl/μg JetPrime. After 10 min incubation at room temperature, the transfection reactions were dispersed dropwise over the HEK293T cells.
Alternatively, if PEI is used for mhVLP particle production on 10 cm plates, 7.5 μg PH-ABE8e expressing plasmid, 7.5 μg sgRNA-expression plasmid and 5 μg hENV expressing plasmid are mixed in 1 mL Opti-MEM reduced serum media (Opti-MEM; GIBCO #31985-070), followed by addition of 27.5 μl PEI MAX. After 20-30 min incubation at room temperature, the transfection reactions are dispersed dropwise over the HEK293T cells. In the following example, JetPrime was used for transfection.
mhVLPs were harvested at 48 hours post-transfection and a media swap of 36 ml 2% DMEM is performed 18 hours-post transfection. 48-hours-post transfection, mhVLP supernatants were filtered using 0.45 m PVDF membrane filters and PEG precipitated (PEG-it, System Biosciences). The following example employs PEG precipitation.
Alternatively, 0.45 um PVDF clarified harvest can be transferred to polypropylene Beckman ultracentrifuge tubes that are used with the SW28 rotor (Beckman Coulter #326823). Each ultracentrifuge tube is filled with mhVLP-containing supernatant from three 10 cm plates or 1 T300 flask to reach an approximate final volume of 35-37.5 ml with a 1.5-3 ml 10% sucrose cushion. mhVLP supernatant can undergo ultracentrifugation at approximately 100,000×g, or 25,000 rpm, at 4° C. for 2 hours.
After ultracentrifugation, supernatants were decanted and mhVLP pellets resuspended in DMEM 2% FBS media, or other media appropriate for the culturing of the target recipient cells, to be up to 2,000 times more concentrated than they were before ultracentrifugation. mhVLPs 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) can be supplemented to enhance transduction efficiency, if necessary. Vectofusin-1 (10 μg/mL in cell culture medium, Miltenyi Biotec #130-111-163) can be supplemented to enhance transduction efficiency, if necessary. Immediately following the addition of mhVLPs, the 24-well plate can be centrifuged at 1,150×g for 30 min at room temperature to enhance transduction efficiency, if necessary (“Spinduction”). The following example do not employ transduction enhancers or “spinduction.”
mhVLPs were produced by transient transfection of producer cells (
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. 63/425,900, 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 No. GM118158 awarded by the National Institutes of Health. The Government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 63425900 | Nov 2022 | US |
