WO2024102772A2 - Nanoparticules lipidiques modifiées en surface - Google Patents

Nanoparticules lipidiques modifiées en surface Download PDF

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Publication number
WO2024102772A2
WO2024102772A2 PCT/US2023/079009 US2023079009W WO2024102772A2 WO 2024102772 A2 WO2024102772 A2 WO 2024102772A2 US 2023079009 W US2023079009 W US 2023079009W WO 2024102772 A2 WO2024102772 A2 WO 2024102772A2
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Prior art keywords
conjugate
lnp
lipid
sequence
antibody
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WO2024102772A3 (fr
Inventor
Zhan Wang
Rui Zhang
Han GU
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Tessera Therapeutics Inc
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Tessera Therapeutics Inc
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Priority to EP23889621.1A priority Critical patent/EP4615982A2/fr
Publication of WO2024102772A2 publication Critical patent/WO2024102772A2/fr
Publication of WO2024102772A3 publication Critical patent/WO2024102772A3/fr
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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/62—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being a protein, peptide or polyamino acid
    • A61K47/65—Peptidic linkers, binders or spacers, e.g. peptidic enzyme-labile linkers
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6849—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a receptor, a cell surface antigen or a cell surface determinant
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/69—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit
    • A61K47/6921—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere
    • A61K47/6927—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere the form being a solid microparticle having no hollow or gas-filled cores
    • A61K47/6929—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere the form being a solid microparticle having no hollow or gas-filled cores the form being a nanoparticle, e.g. an immuno-nanoparticle
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/55—Fab or Fab'

Definitions

  • LNPs lipid nanoparticles
  • payloads such as nucleic acids (e.g., mRNA or siRNA).
  • LNPs are generally comprised of multiple components including an ionizable lipid, a PEGylated lipid, a helper lipid and cholesterol, all of which play important roles in effectively delivering the payload to diseased tissue. Nonetheless, substantial safety issues still remain. For instance, LNPs may accumulate and deliver payloads to cells other than the intended target, which results in potential toxicity. Accordingly, an important goal is to develop LNPs that target diseased tissue and that can be administered at nontoxic doses.
  • LNPs can be coated with targeting moieties, such as antibodies or antigen binding portions thereof, that bind to particular cellular receptors on target cells, resulting in accumulation of the payload in the targeted tissue relative to other tissue in the body.
  • targeting moieties such as antibodies or antigen binding portions thereof, that bind to particular cellular receptors on target cells, resulting in accumulation of the payload in the targeted tissue relative to other tissue in the body.
  • Different approaches have been used to introduce a targeting moiety onto the surface of an LNP. For example, one approach relies on functionalizing a preformed LNP with a targeting moiety.
  • the LNP generally includes a lipid that has polyethylene glycol (PEG) spacer functionalized with a reactive moiety such as a thiol, amine, maleimide or carboxylic acid group.
  • PEG polyethylene glycol
  • the functionalized lipid of the LNP reacts with a complementary group that is covalently bonded to a targeting moiety, hence generating a conjugate of the LNP and the targeting moiety.
  • More recent conjugation approaches using milder reactions conditions are based on biorthogonal chemistry reactions such as Click chemistry.
  • the so-called Click product formed from a Click handle on the LNP and a Click handle bonded to the target moiety links the LNP to the targeting moiety.
  • One biorthogonal approach that has been used to generate LNP/targeting moiety conjugates include copper-catalyzed Click reactions such as Huisgen 1,3-dipolar cycloaddition (CuAAC) between an azide and an alkyne.
  • CuAAC Huisgen 1,3-dipolar cycloaddition
  • the Click product can be formed between an azide and dibenzocyclooctene (DBCO), the Click product formed using an inverse electron demand Diels-alder cycloaddition (IEDDA) between a trans-cyclooctene (TCO) moiety and a tetrazine ring, or a Click product formed in a Staudinger reaction between an azide and a phosphine.
  • DBCO dibenzocyclooctene
  • IEDDA inverse electron demand Diels-alder cycloaddition
  • TCO trans-cyclooctene
  • tetrazine ring a Click product formed in a Staudinger reaction between an azide and a phosphine.
  • the conjugation approaches described above when applied to antibodies or antigen binding fragments, produce LNPs that are conjugated to the antibodies in a nonhomogeneous manner.
  • an antibody or antigen binding fragment when functionalized with a reactive group or Click handle, such functionalization occurs in a random manner, resulting in a heterogeneous population of antibodies that shows significant batch-to-batch variability.
  • the randomly modified antibodies or antigen binding fragments produce LNPs that have their surfaces modified in a random manner. The reaction between the randomly modified antibodies or antigen binding fragments with the LNPs may not occur with optimal efficiency.
  • LNPs decorated in this manner may contain a proportion of antibodies or antigen binding fragments that are incapable of efficiently binding to their target receptors on cells because of the ineffective way they were orientated on the surface of the LNP following conjugation. Furthermore, antibodies that conjugate at specific amino acid residues to the antibody or antigen binding fragment may do so in a non-optimized manner that may impair antibody binding capacity, resulting in a sub- optimal therapeutic effect. [0007] Therefore, there exists a need to develop LNPs that have surfaces modified with targeting moieties, such as antibody or antigen binding fragments, where the antibody or antigen binding fragment is linked to the LNP in a highly site-specific manner, resulting in a greater proportion of targeting moieties oriented to effectively bind their target receptor.
  • targeting moieties such as antibody or antigen binding fragments
  • the disclosure provides conjugates comprising a targeting moiety such as an antibody, Fab fragment or single chain variable fragment (ScFv) and a lipid nanoparticle (LNP) encapsulating a therapeutic agent (i.e., payload), wherein the targeting moiety, e.g., antibody, Fab fragment or the ScFv, is conjugated to the lipid nanoparticle through a linker, and wherein the linker comprises an enzyme recognition sequence.
  • a targeting moiety such as an antibody, Fab fragment or single chain variable fragment (ScFv) and a lipid nanoparticle (LNP) encapsulating a therapeutic agent (i.e., payload)
  • the targeting moiety e.g., antibody, Fab fragment or the ScFv
  • the linker comprises an enzyme recognition sequence.
  • the payload can be a small molecule, peptide or protein, siRNA or miRNA, a nucleic acid (e.g., DNA or RNA molecule, e.g., an mRNA molecule), a nucleic acid encoding components of a system for altering or modifying a genome, or combinations thereof.
  • the payload is a DNA or RNA molecule (e.g., mRNA) encoding or comprising a therapeutic agent.
  • the payload is a gene modifying system, as described herein.
  • the enzyme recognition sequence is coupled directly to a lipid of the LNP.
  • the linker does not include a spacer between the enzyme recognition sequence and the LNP, such as the product of a biorthogonal reaction (i.e., Click product).
  • the linker further comprises one or more additional amino acid residues between the antibody, Fab fragment or ScFv and the enzyme recognition sequence.
  • the amino acid residues between the antibody, Fab fragment or ScFv and the enzyme recognition sequence are selected from (GGGGS)v (SEQ ID NO: 9), (G)v (SEQ ID NO: 10), (EAAAK) V (SEQ ID NO: 11), (PAPAP) V (SEQ ID NO: 12), (AP) V (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK) V A (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • the disclosure provides conjugates comprising a targeting moiety such as an antibody, Fab fragment or single chain variable fragment (ScFv) and a lipid nanoparticle (LNP) encapsulating a therapeutic agent (i.e., payload), wherein the antibody, Fab fragment or the ScFv is conjugated to the lipid nanoparticle through a linker, and wherein the linker consists essentially of an enzyme recognition sequence.
  • the disclosure provides conjugates comprising a targeting moiety such as an antibody, Fab fragment or single chain variable fragment (ScFv) and a lipid nanoparticle (LNP) encapsulating a therapeutic agent (i.e., payload), wherein the targeting moiety, e.g.
  • the linker consists of an enzyme recognition sequence.
  • the linker further consists of one or more additional amino acid residues between the targeting moiety, e.g., antibody, Fab fragment or ScFv, and the enzyme recognition sequence.
  • amino acid residues between the targeting moiety e.g., antibody, Fab fragment or ScFv
  • the enzyme recognition sequence are selected from (GGGGS)v (SEQ ID NO: 9), (G)v (SEQ ID NO: 10), (EAAAKjv (SEQ ID NO: 11), (PAPAP) V (SEQ ID NO: 12), (AP) V (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK)vA (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • the conjugate comprises a targeting moiety such as an antibody, Fab fragment or single chain variable fragment (ScFv) and a lipid nanoparticle (LNP), wherein the C-terminus of one or more of the heavy or light chains of the antibody, the C-terminus of the heavy or light chain of the Fab fragment, or C-terminus of the ScFv is conjugated to the lipid nanoparticle through a linker, and wherein the linker comprises a sortase recognition motif.
  • the sortase recognition motif comprises an LPXT motif, wherein X is any amino acid residue.
  • the sortase recognition motif comprises an LPET (SEQ ID NO: 8) motif.
  • the linker comprises between 3 and 20 glycine residues between the sortase recognition motif and the LNP. In some such embodiments, the linker comprises 3, 4, 5, 6, 7, 8, 9 or 10 glycine residues between the sortase recognition motif and the LNP. In some embodiments, the linker comprises the sequence LPXT(G) n , wherein X is any amino acid and n is between 3 and 20 (e.g., n is 3, 4, 5, or 6). In some embodiments, the LPXT(G) n motif is coupled directly to a lipid of the LNP.
  • the linker does not include a spacer between the LPXT(G) n motif and the LNP, such as the product of a biorthogonal reaction (i.e., Click product).
  • the linker further comprises one or more additional amino acid residues between the antibody, Fab fragment or ScFv and the sortase recognition motif.
  • the amino acid residues between the antibody, Fab fragment or ScFv and the sortase recognition motif are selected from (GGGGS) V (SEQ ID NO: 9), (G) v (SEQ ID NO: 10), (EAAAK)v (SEQ ID NO: 11), (PAPAP) V (SEQ ID NO: 12), (AP) V (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK) V A (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • the conjugate comprises a targeting moiety such as an antibody, Fab fragment or single chain variable fragment (ScFv) and a lipid nanoparticle (LNP), wherein the antibody, Fab fragment or ScFv is conjugated to the lipid nanoparticle through a linker, and wherein the linker comprises a lipoic acid ligase (LplA) acceptor peptide.
  • the conjugate comprises an antibody, wherein the C-terminus of one or more of the heavy or light chains of the antibody is bonded to the linker.
  • the conjugate comprises a Fab fragment, wherein the C-terminus of the heavy or light chain of the Fab fragment is bonded to the linker.
  • the conjugate comprises a ScFv, wherein the C-terminus of the ScFv is bonded to the linker.
  • the LplA acceptor peptide has the sequence GFEDKVWYDLDA (SEQ ID NO: 15).
  • the LplA acceptor peptide is coupled directly to a lipid of the LNP.
  • the linker does not include a spacer between the LplA acceptor peptide and the LNP, such as the product of a biorthogonal reaction (i.e., Click product).
  • the linker further comprises one or more additional amino acid residues between the targeting moiety, e.g.
  • the amino acid residues between the targeting moiety, such as an antibody, Fab fragment or ScFv, and the LplA acceptor peptide are selected from (GGGGS) V (SEQ ID NO: 9), (G) v (SEQ ID NO: 10), (EAAAK)v (SEQ ID NO: 11), (PAPAP) V (SEQ ID NO: 12), (AP)v (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK) V A (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • the enzyme recognition sequence is a transglutaminase enzyme recognition sequence (LLQG (SEQ ID NO: 16)).
  • the enzyme recognition sequence is a sequence recognized by formylglycine generating enzyme, specifically CXPXR, wherein each X is any amino acid.
  • the conjugate can comprise one or more pegylated lipid molecules.
  • the enzyme recognition sequence is covalently bonded to at least one of the pegylated lipid molecules.
  • the PEG spacer between the lipid and the enzyme recognition sequence comprises at least about 5, 10, 20, 30, 50, 50, 60, 70, 80, 90. 200, or 110 ethvlene glycol units.
  • the PEG spacer comprises about 10-120 ethylene glycol units.
  • the molecular weight of the pegylated lipid bonded to the enzyme recognition sequence is from about 500 (i.e., PEG500) to about 5,000 (i.e., PEG5000).
  • the molecular weight of the pegylated lipid bonded to the enzyme recognition sequence is from about 1,000 (i.e., PEG1000) to about 3,000 (i.e., PEG5300).
  • the lipid component of the pegylated lipid bonded to the enzyme recognition sequence is selected from DMG, DPG, DSG, DTA, DOPE, DPPE, DMPE, DSPE, sphingosine, sphingomyelin, and stearic acid.
  • the conjugate can comprise one or more cholesterol molecules.
  • the conjugate can comprise P-sitoesterol, hydroxy cholesterol, or stigmastanol.
  • the conjugate can comprise one or more non- pegylated phospholipids.
  • the non-pegylated phospholipid is selected from POPC, DOPC, DOPE, and DSPC. Such lipids are often referred to as helper lipids.
  • the LNP component comprises the ionizable lipid V003, depicted below.
  • the conjugate can comprise one or more ionizable lipids.
  • the ionizable lipids is selected from V003, V004, V005, and V040.
  • the LNP is a liposome.
  • the liposomes include phospholipids such as phosphatidylcholines, phosphatidylethanolamines, phosphatidylserines, and phosphatidylglycerols.
  • the liposomes include a stabilizer such as cholesterol.
  • the conjugate can comprise more than one targeting moiety, e.g. antibody, Fab fragment or ScFv, per LNP.
  • the conjugate can comprise more than 10 targeting moi eties, e.g., antibodies, Fab fragments or ScFvs, per LNP.
  • the conjugate can comprise more than 20 targeting moieties, e.g., antibodies, Fab fragments or ScFvs, per LNP. In some embodiments, the conjugate can comprise more than 50 targeting moieties, e.g. antibodies, Fab fragments or ScFvs, per LNP. In some embodiments, the conjugate can comprise more than 50 targeting moieties, e.g., antibodies, Fab fragments or ScFvs, per LNP. In some embodiments, the conjugate can comprise from about 50 to about 200 targeting moieties, e.g., antibodies, Fab fragments or ScFvs, per LNP. In some embodiments, the conjugate can comprise from about 100 to about 200 targeting moieties, e.g., antibodies, Fab fragments or ScFvs, per LNP.
  • the targeting moiety e.g., antibody, Fab fragment or ScFv, component of a conjugate of the disclosure can target a cell surface receptor.
  • a targeting moiety e.g., an antibody, Fab fragment or ScFv, component of a conjugate of the disclosure targets T cell receptors including, but not limited to, CD2, CD3, CD4, CD5, CD6, CD7, or CD8.
  • a targeting moiety e.g., an antibody, Fab fragment or ScFv, component of a conjugate of the disclosure targets hematopoietic stem cells (HSCs).
  • HSCs hematopoietic stem cells
  • a targeting moiety e.g., an antibody, Fab fragment or ScFv, component of a conjugate of the disclosure targets HSC receptors including, but not limited to, CD90 or CD117.
  • HSC receptors including, but not limited to, CD90 or CD117.
  • the addition of a targeting moiety to the surface of the LNP results in a targeted LNP (tLNP) that can more effectively deliver a payload to a target cell (i.e., a cell comprising a cell-surface receptor that binds to the targeting moiety) relative to the LNP without a targeting moiety.
  • a conjugate comprising a targeting moiety that binds to CD2, CD3, CD4, CD5, CD6, CD7, or CD8 comprises a targeted LNP that can deliver a payload to T cells.
  • a conjugate comprising a targeting moiety that binds to CD90 or CD117 comprises a targeted LNP that can deliver a payload to HSCs.
  • the conjugates of the disclosure can be used to deliver payloads to cells, particularly cells expressing cell-surface receptors targeted by the targeting moiety, e.g., antibody, Fab fragment or ScFv, component of the conjugates.
  • the payload is one or more nucleic acid molecule, e.g., one or more DNA molecule, one or more RNA molecule (e.g., mRNA), or combinations thereof.
  • the payload is a siRNA or a microRNA.
  • the payload is an antisense oligonucleotide (ASO).
  • the payload is a tRNA.
  • the payload is a DNA plasmid.
  • the payload is a small molecule.
  • the payload is one or more components of a CRISPR-Cas system, e.g., a CRISPR-Cas nuclease, or a nucleic acid encoding the CRISPR-Cas nuclease, and/or a guide RNA.
  • the payload is one or more components of a CRISPR-Cas9, CRISPR-Cas 12a, or CRISPR-Casl2b system.
  • conjugates of the disclosure can be used to deliver CRISPR-Cas9 genome-editing components.
  • the payload comprises a CRISPR-Cas nickase, or a nucleic acid encoding the CRISPR-Cas nickase, e.g., a CRISPR-Cas9 nickase.
  • the conjugates can deliver an mRNA that encodes Cas9 and a guide RNA.
  • the payload can be one or more components of a gene modifying system, as described herein, including a gene modifying polypeptide or a nucleic acid encoding a gene modifying polypeptide.
  • the payload can be one or more components of a heterologous gene modifying polypeptide.
  • payloads can be selected from the group consisting of small or large organic or inorganic molecules, monosaccharides, disaccharides, trisaccharides, oligosaccharides, polysaccharides, peptides, proteins, peptide analogs and derivatives thereof, peptidomimetics, nucleic acids, nucleic acid analogs and derivatives, an extract made from biological materials, or any combinations thereof.
  • the payload can be an enzyme or a nucleic acid encoding an enzyme, e.g., for enzyme replacement gene therapy.
  • the conjugates of the disclosure can be used to deliver systems that are capable of inserting a heterologous object sequence into the genome of a cell.
  • the system comprises: (A) a gene modifying polypeptide or a nucleic acid encoding the gene modifying polypeptide, wherein the gene modifying polypeptide comprises: (i) an endonuclease and/or DNA binding domain; and (ii) a reverse transcriptase (RT) domain, where (i) and (ii) are both derived from a retrotransposon (e.g., from the same retrotransposon or different retrotransposons); and (B) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.
  • a gene modifying polypeptide acts as a substantially autonomous protein machine capable of integrating a template nucleic acid sequence into a target DNA molecule (e.g., in a mammalian host cell, such as a genomic DNA molecule in the host cell), substantially without relying on host machinery.
  • the heterologous object sequence may include, e.g., a coding sequence, a regulatory sequence, a gene expression unit.
  • the gene modifying polypeptide can be a retrotransposon, e.g., selected from the retrotransposons of Table 7.
  • the gene modifying polypeptide can be a retrotransposon selected, without limitation, from the following retrotransposon classes: RTE (e g., RTE-1 MD, RTE-3 BF, and RTE-25_LMi), CR1 (e.g, CR1-1 PH), Crack (e g., Crack- 28_RF), L2 (e.g., L2-2_Dre and L2-5_GA), and Vingi (e.g., Vingi-l_Acar).
  • RTE e g., RTE-1 MD, RTE-3 BF, and RTE-25_LMi
  • CR1 e.g, CR1-1 PH
  • Crack e.g., Crack- 28_RF
  • L2 e.g., L2-2_Dre and L2-5_GA
  • Vingi e.g., Vingi-l_Acar
  • the disclosure provides a method of manufacturing a lipid nanoparticle (LNP) conjugated to a targeting moiety such as an antibody, Fab fragment or ScFv in a site-specific manner, said method comprising
  • step (ii) contacting the product of step (i) with a lipid comprising a functional group reactive with the enzyme recognition sequence in the presence of an enzyme that recognizes the enzyme recognition sequence under conditions suitable for the enzyme to ligate the targeting moiety, e.g., antibody, Fab fragment or ScFv, to the enzyme recognition sequence,
  • a lipid comprising a functional group reactive with the enzyme recognition sequence in the presence of an enzyme that recognizes the enzyme recognition sequence under conditions suitable for the enzyme to ligate the targeting moiety, e.g., antibody, Fab fragment or ScFv, to the enzyme recognition sequence
  • step (iii) inserting the product of step (ii) into a precursor LNP
  • step (iv) removing the unbound product of step (i) that did not insert into the precursor LNP in step (iii), thereby generating a lipid nanoparticle conjugated to the targeting moiety (e.g., an antibody, Fab fragment or ScFv).
  • the targeting moiety e.g., an antibody, Fab fragment or ScFv.
  • the enzyme recognition sequence can be directly to the targeting moiety, e.g., antibody, Fab fragment or ScFv, or can be bonded or bonded through a linker comprising one or more amino acid residues.
  • Particular amino acid residues added that can be covalently attached to the antibody, Fab fragment or ScFv include, but are not limited to from (GGGGS) V (SEQ ID NO: 9), (G) v (SEQ ID NO: 10), (EAAAK)v (SEQ ID NO: 11), (PAPAP) V (SEQ ID NO: 12), (AP)v (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK) V A (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • the disclosure provides a method of manufacturing a surface-modified lipid nanoparticle (LNP) conjugated to a targeting moiety such as an antibody, Fab fragment or ScFv in a site-specific manner, said method comprising
  • step (i) covalently bonding a peptide with a sortase recognition site to one or more C- terminus of the targeting moiety, e.g., antibody or Fab fragment, or to the C-terminus of the ScFv; (ii) contacting the product of step (i) with a lipid covalently bound to three or more glycine residues in the presence of a sortase enzyme under conditions suitable for the sortase enzyme to ligate the targeting moiety, e.g., antibody, Fab fragment or ScFv, to the lipid;
  • step (iii) inserting the product of step (ii) into a precursor LNP
  • step (iv) removing the unbound product of step (i) that did not insert into the precursor LNP in step (iii), thereby generating a lipid nanoparticle conjugated to the targeting moiety (e.g., an antibody, Fab fragment or ScFv).
  • the targeting moiety e.g., an antibody, Fab fragment or ScFv.
  • the peptide with the sortase recognition motif can be directly bonded to a C -terminus of the targeting moiety, e.g., antibody, Fab fragment or ScFv, or can be bonded or bonded through a linker comprising one or more amino acid residues.
  • Particular amino acid residues added that can be covalently attached to a C-terminus of the targeting moiety include, but are not limited to from (GGGGS) V (SEQ ID NO: 9), (G) v (SEQ ID NO: 10), (EAAAK) V (SEQ ID NO: 11), (PAPAP)v (SEQ ID NO: 12), (AP) V (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK)vA (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • step (ii) i.e., the sortase-catalyzed reaction
  • step (ii) is carried out in the presence of sortase A5.
  • step (ii) is carried out in the presence of the sortase enzyme Streptococcus pyogenes sortase A (SpSrtA WT).
  • the disclosure provides a method of manufacturing a lipid nanoparticle conjugated to a targeting moiety such as an antibody, Fab fragment or ScFv in a site-specific manner, said method comprising
  • step (ii) contacting the product of step (i) with a lipid comprising a carboxylic acid group in the presence of a lipoic acid ligase under conditions suitable for lipoic acid ligase to ligate the targeting moiety, e.g., antibody, Fab fragment or ScFv to the lipid;
  • a lipoic acid ligase under conditions suitable for lipoic acid ligase to ligate the targeting moiety, e.g., antibody, Fab fragment or ScFv to the lipid
  • step (iii) inserting the product of step (ii) into a precursor LNP
  • step (iv) removing the unbound product of step (i) that did not insert into the precursor LNP in step (iii), thereby generating a lipid nanoparticle conjugated to the targeting moiety (e.g., an antibody, Fab fragment or ScFv).
  • the targeting moiety e.g., an antibody, Fab fragment or ScFv.
  • the LplA acceptor peptide can be directly bonded to the targeting moiety, e.g., antibody, Fab fragment or ScFv, or can be bonded or bonded through a linker comprising one or more amino acid residues.
  • Particular amino acid residues added that can be covalently attached to the antibody, Fab fragment or ScFv include, but are not limited to from (GGGGS) V (SEQ ID NO: 9), (G) v (SEQ ID NO: 10), (EAAAK)v (SEQ ID NO: 11), (PAPAP) V (SEQ ID NO: 12), (AP)v (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK) V A (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • the LplA acceptor peptide is covalently bonded to one or more C-terminus of the antibody or Fab fragment. In other embodiments of step (i) the LplA acceptor peptide is covalently bonded to the C-terminus of the ScFv.
  • the disclosure provides a method of manufacturing a lipid nanoparticle conjugated to a targeting moiety such as an antibody, Fab fragment or ScFv in a site-specific manner, said method comprising
  • an enzyme recognition sequence site e.g., sortase recognition motif or LplA acceptor peptide
  • the targeting moiety e.g., antibody, Fab fragment or ScFv
  • step (ii) contacting the product of step (i) with a lipid comprising a functional group reactive with the enzyme recognition sequence (e.g., a sortase recognition motif or a LplA acceptor peptide) in the presence of an enzyme that recognizes the enzyme recognition sequence under conditions suitable for the enzyme to ligate the targeting moiety, e.g., antibody, Fab fragment or ScFv, to the enzyme recognition sequence,
  • the enzyme recognition sequence e.g., a sortase recognition motif or a LplA acceptor peptide
  • step (iii) contacting the product of step (ii) with other lipid components, thereby generating a lipid nanoparticle conjugated to the targeting moiety (e.g., an antibody, Fab fragment or ScFv).
  • the targeting moiety e.g., an antibody, Fab fragment or ScFv.
  • the enzyme recognition sequence can be directly to the targeting moiety, e.g., antibody, Fab fragment or ScFv, or can be bonded or bonded through a linker comprising one or more amino acid residues.
  • Particular amino acid residues added that can be covalently attached to the antibody, Fab fragment or ScFv include, but are not limited to from (GGGGS) V (SEQ ID NO: 9), (G) v (SEQ ID NO: 10), (EAAAK)v (SEQ ID NO: 11), (PAPAP) V (SEQ ID NO: 12), (AP)v (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK) V A (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • FIG. 1 shows a general schematic of a manufacturing process of the disclosure to generate a surface-modified LNP.
  • FIG. 2 shows a schematic of a sortase A5 catalyzed transpeptidation reaction to conjugate a GGG-lipid to a Fab fragment modified with a sortase recognition motif.
  • FIG. 3 shows a schematic to insert a lipidated Fab fragment comprising a sortase recognition motif into a precursor LNP to generate a surface-modified LNP.
  • FIG. 4 shows a schematic of conjugating a precursor LNP to a Fab fragment via a linker comprising a sortase recognition motif.
  • FIG. 5 shows a schematic of a lipoic acid ligase catalyzed reaction to conjugate a lipid to a Fab fragment modified with a LplA acceptor peptide.
  • FIG. 6 shows a schematic to insert a lipidated Fab fragment comprising a LplA acceptor peptide into a precursor LNP to generate a surface-modified LNP.
  • FIG. 7 shows a schematic of conjugating a precursor LNP to a Fab fragment via a linker comprising a LplA acceptor peptide.
  • FIG. 8 shows an example of a lipoic acid ligase catalyzed reaction between a Fab fragment covalently bonded to a LplA acceptor peptide and a carboxylic acid.
  • Antigen binding domain refers to that portion of a targeting moiety, e.g., an antibody or a chimeric antigen receptor which binds an antigen.
  • an antigen binding domain binds to a cell surface antigen of a cell.
  • an antigen binding domain binds an antigen characteristic of a cancer, e.g., a tumor associated antigen in a neoplastic cell.
  • an antigen binding domain binds an antigen characteristic of an infectious disease, e.g. a virus associated antigen in a virus infected cell.
  • an antigen binding domain binds an antigen characteristic of a cell targeted by a subject’s immune system in an autoimmune disease, e.g., a self-antigen.
  • an antigen binding domain is or comprises an antibody or antigen-binding portion thereof.
  • an antigen binding domain is or comprises an scFv or Fab.
  • domain refers to a structure of a biomolecule that contributes to a specified function of the biomolecule.
  • a domain may comprise a contiguous region (e.g., a contiguous sequence) or distinct, non-contiguous regions (e.g., non-contiguous sequences) of a biomolecule.
  • protein domains include, but are not limited to, an endonuclease domain, a DNA binding domain, a reverse transcriptase domain; an example of a domain of a nucleic acid is a regulatory domain, such as a transcription factor binding domain.
  • Exogenous when used with reference to a biomolecule (such as a nucleic acid sequence or polypeptide) means that the biomolecule was introduced into a host genome, cell, or organism by the hand of man.
  • a nucleic acid that is as added into an existing genome, cell, tissue, or subject using recombinant DNA techniques or other methods is exogenous to the existing nucleic acid sequence, cell, tissue or subject.
  • Expression cassette refers to a nucleic acid construct comprising nucleic acid elements sufficient for the expression of the nucleic acid molecule of the instant invention.
  • gRNA spacer A “gRNA spacer”, as used herein, refers to a portion of a nucleic acid that has complementarity to a target nucleic acid and can, together with a gRNA scaffold, target a Cas protein to the target nucleic acid.
  • gRNA scaffold refers to a portion of a nucleic acid that can bind a Cas protein and can, together with a gRNA spacer, target the Cas protein to the target nucleic acid.
  • the gRNA scaffold comprises a crRNA sequence, tetraloop, and tracrRNA sequence.
  • Gene modifying polypeptide A “gene modifying polypeptide,” and “retrotransposon gene modifying polypeptide” as used herein interchangeably to refer to a polypeptide comprising a retrotransposase reverse transcriptase domain and a retrotransposase endonuclease domain, or a polypeptide comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity to said domains, which is capable of integrating a nucleic acid sequence (e.g., a sequence provided on a template nucleic acid) into a target DNA molecule (e.g., in a mammalian host cell, such as a genomic DNA molecule in the host cell).
  • a nucleic acid sequence e.g., a sequence provided on a template nucleic acid
  • the endonuclease domain is a catalytically inactive endonuclease domain.
  • the retrotransposase reverse transcriptase domain and a retrotransposase endonuclease domain are derived from the same retrotransposase.
  • the gene modifying polypeptide is capable of integrating the sequence substantially without relying on host machinery.
  • the gene modifying polypeptide integrates a sequence into a random position in a genome, and in some embodiments, the gene modifying polypeptide integrates a sequence into a specific target site.
  • a gene modifying polypeptide includes one or more domains that, collectively, facilitate 1) binding the template nucleic acid, 2) binding the target DNA molecule, and 3) facilitate integration of the at least a portion of the template nucleic acid into the target DNA.
  • Gene modifying polypeptides include both naturally occurring polypeptides as well as engineered variants of the foregoing, e.g., having one or more amino acid substitutions to the naturally occurring sequence.
  • Gene modifying polypeptides also include heterologous constructs, e.g., where one or more of the domains recited above are heterologous to each other, whether through a heterologous fusion (or other conjugate) of otherwise wild-type domains, as well as fusions of modified domains, e.g., by way of replacement or fusion of a heterologous sub-domain or other substituted domain.
  • Exemplary gene modifying polypeptides, and systems comprising them and methods of using them, that can be used in the methods provided herein are described, e.g., in WO/2021/178717, including Tables 10, 11, X, 3 A, 3B, and Z1 therein.
  • a gene modifying polypeptide integrates a sequence into a gene. In some embodiments, a gene modifying polypeptide integrates a sequence into a sequence outside of a gene.
  • a “gene modifying system,” as used herein, refers to a system comprising a gene modifying polypeptide and a template nucleic acid.
  • Gene modifying system refers to a system comprising a gene modifying polypeptide, or a nucleic acid (e.g., an mRNA) encoding the gene modifying polypeptide, and a template nucleic acid.
  • a gene modifying system refers to a system comprising a gene modifying polypeptide, or a nucleic acid (e.g., an mRNA) encoding the gene modifying polypeptide, and a template nucleic acid.
  • heterologous when used to describe a first element in reference to a second element means that the first element and second element do not exist in nature disposed as described.
  • a heterologous polypeptide, nucleic acid molecule, construct or sequence refers to (a) a polypeptide, nucleic acid molecule or portion of a polypeptide or nucleic acid molecule sequence that is not native to a cell in which it is expressed, (b) a polypeptide or nucleic acid molecule or portion of a polypeptide or nucleic acid molecule that has been altered or mutated relative to its native state, or (c) a polypeptide or nucleic acid molecule with an altered expression as compared to the native expression levels under similar conditions.
  • a heterologous regulatory sequence e.g., promoter, enhancer
  • a heterologous domain of a polypeptide or nucleic acid sequence e.g., a DNA binding domain of a polypeptide or nucleic acid encoding a DNA binding domain of a polypeptide
  • a heterologous nucleic acid molecule may exist in a native host cell genome, but may have an altered expression level or have a different sequence or both.
  • heterologous nucleic acid molecules may not be endogenous to a host cell or host genome but instead may have been introduced into a host cell by transformation (e.g., transfection, electroporation), wherein the added molecule may integrate into the host genome or can exist as extra-chromosomal genetic material either transiently (e.g., mRNA) or semi- stably for more than one generation (e.g., episomal viral vector, plasmid or other selfreplicating vector).
  • a domain is heterologous relative to another domain, if the first domain is not naturally comprised in the same polypeptide as the other domain (e.g., a fusion between two domains of different proteins from the same organism).
  • heterologous gene modifying polypeptide refers to a polypeptide comprising a retroviral reverse transcriptase, or a polypeptide comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity to a retroviral reverse transcriptase, which is capable of integrating a nucleic acid sequence (e.g., a sequence provided on a template nucleic acid) into a target DNA molecule (e.g., in a mammalian host cell, such as a genomic DNA molecule in the host cell).
  • a nucleic acid sequence e.g., a sequence provided on a template nucleic acid
  • target DNA molecule e.g., in a mammalian host cell, such as a genomic DNA molecule in the host cell.
  • the heterologous gene modifying polypeptide is capable of integrating the sequence substantially without relying on host machinery.
  • the heterologous gene modifying polypeptide integrates a sequence into a random position in a genome, and in some embodiments, the heterologous gene modifying polypeptide integrates a sequence into a specific target site.
  • the sequence that is integrated comprises a deletion, substitution, or insertion relative to the target DNA molecule.
  • a heterologous gene modifying polypeptide includes one or more domains that, collectively, facilitate 1) binding the template nucleic acid, 2) binding the target DNA molecule, and 3) facilitate integration of the at least a portion of the template nucleic acid into the target DNA.
  • Heterologous gene modifying polypeptides include both naturally occurring polypeptides as well as engineered variants of the foregoing, e.g., having one or more amino acid substitutions to the naturally occurring sequence.
  • Heterologous gene modifying polypeptides also include heterologous constructs, e.g., where one or more of the domains recited above are heterologous to each other, whether through a heterologous fusion (or other conjugate) of otherwise wild-type domains, as well as fusions of modified domains, e.g., by way of replacement or fusion of a heterologous sub-domain or other substituted domain.
  • heterologous gene modifying polypeptides and systems comprising them and methods of using them, that can be used in the methods provided herein are described, e.g., in PCT/US2021/020948, which is incorporated herein by reference with respect to heterologous gene modifying polypeptides that comprise a retroviral reverse transcriptase domain.
  • a heterologous gene modifying polypeptide integrates a sequence into a gene.
  • a heterologous gene modifying polypeptide integrates a sequence into a sequence outside of a gene.
  • a “heterologous gene modifying system,” as used herein, refers to a system comprising a heterologous gene modifying polypeptide and a template nucleic acid.
  • Mutation or Mutated when applied to nucleic acid sequences means that nucleotides in a nucleic acid sequence may be inserted, deleted or changed compared to a reference (e.g., native) nucleic acid sequence. A single alteration may be made at a locus (a point mutation) or multiple nucleotides may be inserted, deleted, or changed at a single locus. In addition, one or more alterations may be made at any number of loci within a nucleic acid sequence.
  • a nucleic acid sequence may be mutated by any method known in the art. In some embodiments a mutation occurs naturally. In some embodiments a desired mutation can be produced by a system described herein.
  • Nucleic acid molecule refers to both RNA and DNA molecules including, without limitation, complementary DNA (“cDNA”), genomic DNA (“gDNA”), and messenger RNA (“mRNA”), and also includes synthetic nucleic acid molecules, such as those that are chemically synthesized or recombinantly produced, such as RNA templates, as described herein.
  • the nucleic acid molecule can be double-stranded or single-stranded, circular, or linear. If single-stranded, the nucleic acid molecule can be the sense strand or the antisense strand.
  • nucleic acid comprising SEQ ID NO: 1 refers to a nucleic acid, at least a portion which has either (i) the sequence of SEQ ID NO: 1, or (ii) a sequence complimentary to SEQ ID NO: 1. The choice between the two is dictated by the context in which SEQ ID NO: 1 is used. For instance, if the nucleic acid is used as a probe, the choice between the two is dictated by the requirement that the probe be complementary to the desired target.
  • Nucleic acid sequences of the present disclosure may be modified chemically or biochemically or may contain non-natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more naturally occurring nucleotides with an analog, inter-nucleotide modifications such as uncharged linkages (for example, methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages (for example, phosphorothioates, phosphorodithioates, etc.), pendant moieties, (for example, polypeptides), intercalators (for example, acridine, psoralen, etc.), chelators, alkylators, and modified linkages (for example, alpha anomeric nucleic acids, etc.).
  • uncharged linkages for example, methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.
  • RNA molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions.
  • Such molecules are known in the art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of a molecule, e.g., peptide nucleic acids (PNAs).
  • PNAs peptide nucleic acids
  • Other modifications can include, for example, analogs in which the ribose ring contains a bridging moiety or other structure such as modifications found in “locked” nucleic acids (LNAs).
  • the nucleic acids are in operative association with additional genetic elements, such as tissue-specific expression-control sequence(s) (e.g., tissue-specific promoters and tissue-specific microRNA recognition sequences), as well as additional elements, such as inverted repeats (e.g., inverted terminal repeats, such as elements from or derived from viruses, e.g., AAV ITRs) and tandem repeats, inverted repeats/direct repeats, homology regions (segments with various degrees of homology to a target DNA), untranslated regions (UTRs) (5', 3', or both 5' and 3' UTRs), and various combinations of the foregoing.
  • tissue-specific expression-control sequence(s) e.g., tissue-specific promoters and tissue-specific microRNA recognition sequences
  • additional elements such as inverted repeats (e.g., inverted terminal repeats, such as elements from or derived from viruses, e.g., AAV ITRs) and tandem repeats, inverted repeats/direct repeats
  • nucleic acid elements of the systems provided by the invention can be provided in a variety of topologies, including single-stranded, double-stranded, circular, linear, linear with open ends, linear with closed ends, and particular versions of these, such as doggybone DNA (dbDNA), closed-ended DNA (ceDNA).
  • dbDNA doggybone DNA
  • ceDNA closed-ended DNA
  • Primer binding site sequence refers to a portion of a template RNA capable of binding to a region comprised in a target nucleic acid sequence.
  • a PBS sequence is a nucleic acid sequence comprising at least 3, 4, 5, 6, 7, or 8 bases with 100% identity to the region comprised in the target nucleic acid sequence.
  • the primer region comprises at least 5, 6, 7, 8 bases with 100% identity to the region comprised in the target nucleic acid sequence.
  • a template RNA comprises a PBS sequence and a heterologous object sequence
  • the PBS sequence binds to a region comprised in a target nucleic acid sequence, allowing a reverse transcriptase domain to use that region as a primer for reverse transcription, and to use the heterologous object sequence as a template for reverse transcription.
  • the disclosure provides conjugates comprising a targeting moiety and a lipid nanoparticle (LNP) encapsulating a therapeutic agent (i.e., payload), wherein the targeting moiety is conjugated to the lipid nanoparticle through a linker, and wherein the linker comprises an enzyme recognition sequence.
  • a targeting moiety is conjugated to the lipid nanoparticle through a linker
  • the linker comprises an enzyme recognition sequence.
  • the enzyme recognition sequence is a sortase recognition motif or a LplA acceptor peptide.
  • the payload can be a small molecule, peptide or protein, siRNA or miRNA, a nucleic acid (e.g., mRNA) encoding a therapeutic agent, a nucleic acid encoding components of a system for altering a genome, or combinations thereof.
  • the enzyme recognition sequence is coupled directly to a lipid of the LNP. In such embodiments, the linker would not include a spacer between the enzyme recognition sequence and the LNP, such as the product of a biorthogonal reaction (i.e., Click product).
  • the targeting moiety is an antibody or an antigen binding fragment thereof.
  • the targeting moiety is a Fab fragment, a scFv, a D ARPIN, a VHH domain antibody, a FN3 domain, a nanobody, a single domain antibody or a Centyrin.
  • the targeting moiety is a folate moiety, an antibiotic mimetic, a polynucleotide (such as a DNA or RNA apatamer), a carbohydrate, a vitamin or a N- Acetylgalactosamine (GalNac).
  • the targeting moiety is a ligand that binds to a receptor on the surface of a cell.
  • the ligand can be a natural ligand for the receptor. In some embodiments, the ligand can be a synthetic ligand for the receptor.
  • the targeting moiety is a small molecule, e.g., a small molecule ligand for a receptor on the surface of a cell. In some embodiments, the targeting moiety is a peptide or polypeptide, e.g., a peptide or polypeptide ligand for a receptor on the surface of a cell. In some embodiments, the peptide or polypeptide is linear. In other embodiments, the peptide or polypeptide is circular.
  • the targeting moiety is a cytokine, e.g., such that the cytokine targeting moiety binds to a cytokine receptor on the surface of a cell. Conjugation of a targeting moiety to the LNP creates a targeted LNP (tLNP).
  • tLNP targeted LNP
  • the linker consists essentially of the enzyme recognition sequence. In other embodiments, the linker consists of the enzyme recognition sequence. [0058] In some such embodiments the linker further consists of one or more additional amino acid residues between the targeting moiety, e.g., antibody, Fab fragment or ScFv, and the enzyme recognition sequence.
  • the disclosure provides a method of manufacturing a lipid nanoparticle (LNP) conjugated to a targeting moiety, said method comprising
  • step (ii) contacting the product of step (i) with a lipid comprising a functional group reactive with the enzyme recognition sequence in the presence of an enzyme that recognizes the enzyme recognition sequence under conditions suitable for the enzyme to ligate the targeting moiety to the enzyme recognition sequence,
  • step (iii) inserting the product of step (ii) into a precursor LNP
  • step (iv) removing the unbound product of step (i) that did not insert into the precursor LNP in step (iii), thereby generating a lipid nanoparticle conjugated to the targeting moiety.
  • the enzyme recognition sequence can be directly bonded to the targeting moiety, e.g., antibody, Fab fragment or ScFv, or bonded through a linker comprising one or more amino acid residues.
  • Particular amino acid residues added that can be covalently attached to the antibody, Fab fragment or ScFv include, but are not limited to (GGGGS)v (SEQ ID NO: 9), (G) v (SEQ ID NO: 10), (EAAAK) V (SEQ ID NO: 11), (PAPAP)v (SEQ ID NO: 12), (AP) V (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK)vA (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • the targeting moiety is an antibody, a Fab fragment, a scFv, a D ARPIN, a VHH domain antibody, a FN3 domain, a nanobody, a single domain antibody or a Centyrin.
  • the targeting moiety is a folate moiety, an antibiotic mimetic, a polynucleotide (such as a DNA or RNA apatamer), a carbohydrate, a vitamin or a N- Acetylgalactosamine (GalNac).
  • the targeting moiety is a protein
  • the targeting moiety is covalently bonded to the C-terminus of the targeting moiety in step (i).
  • the enzyme recognition sequence can be covalently bonded to one or more C-terminus of the antibody of Fab fragment in step (i).
  • the enzyme recognition sequence can be bonded to the C-terminus of the heavy chain of the antibody of Fab fragment.
  • the conjugation efficiency achieved by step (i) the disclosed method is greater than 50%, greater than 60%, greater than 70%, greater than 80%, or greater than 90%. In some embodiments, the conjugation efficiency achieved by the disclosed method is from about 60% to about 95%. In some embodiments, the conjugation efficiency achieved by the disclosed methods are from about 70% to about 85%.
  • FIG. 1 shows a general schematic of a manufacturing process of the disclosure when the targeting moiety is a Fab fragment.
  • a precursor LNP is formed from various lipid components (e.g., ionizable lipid, helper lipid, sterol, payload)
  • a Fab fragment bound to a lipid via an enzyme recognition sequence, as disclosed herein is inserted into the precursor LNP.
  • the unbound lipid/Fab fragments are removed, thereby generating the surface- modified LNP encapsulating a payload (e.g., mRNA).
  • a payload e.g., mRNA
  • the disclosure provides a method of manufacturing a surface-modified lipid nanoparticle (LNP) conjugated to a targeting moiety, e.g., an antibody, Fab fragment or ScFv in a site-specific manner, said method comprising
  • step (ii) contacting the product of step (i) with a lipid covalently bound to three or more glycine residues in the presence of a sortase enzyme under conditions suitable for the sortase enzyme to ligate the targeting moiety, e.g., antibody, Fab fragment or ScFv to the lipid;
  • a sortase enzyme under conditions suitable for the sortase enzyme to ligate the targeting moiety, e.g., antibody, Fab fragment or ScFv to the lipid
  • step (iii) inserting the product of step (ii) into a precursor LNP
  • step (iv) removing the unbound product of step (i) that did not insert into the precursor LNP in step (iii), thereby generating a lipid nanoparticle conjugated to the targeting moiety (e.g., an antibody, Fab fragment or ScFv).
  • the sortase recognition motif bonded to the C-terminus of the targeting moiety e.g., antibody, Fab fragment or ScFv
  • the sortase recognition motif bonded to the C-terminus of the targeting moiety e.g., antibody, Fab fragment or ScFv
  • the sortase recognition motif bonded to the C-terminus of the targeting moiety e.g., antibody, Fab fragment or ScFv
  • the sortase recognition motif bonded to the C-terminus of the targeting moiety e.g., antibody, Fab fragment or ScFv
  • the glycine (G) of the LPXTG (SEQ ID NO: 17) motif can be bonded to one or more (e.g.,
  • step (ii) i.e., the sortase-catalyzed reaction
  • step (ii) is carried out in the presence of sortase A5.
  • Sortase A5 is an engineered pentamutant variant of the wildtype sortase from Staphylococcus aureus that is significantly more active than the wild-type sortase. See U.S. patent No. 9,267,227.
  • the sortase recognition site bond to the targeting moiety, e.g., antibody, Fab fragment or ScFv, in step (i) has the sequence LPXTG (SEQ ID NO: 17), where X is any amino acid residue.
  • step (ii) sortase A catalyzes the transpeptidation reaction between the LPXTG (SEQ ID NO: 17) recognition motif and a glycine residue by cleaving the sortase recognition site between the threonine and the glycine residues.
  • FIG. 2 shows a schematic of reacting a Fab fragment modified with a sortase recognition motif and a GGG-lipid through a Sortase A5 transpeptidation reaction.
  • step (ii) is carried out in the presence of the sortase enzyme Streptococcus pyogenes sortase A (SpSrtA WT).
  • the sortase recognition site bond to the targeting moiety, e.g., antibody, Fab fragment or ScFv in step (i) has the sequence LPXTA (SEQ ID NO: 18), where X is any amino acid residue.
  • SpSrtA catalyzes the transpeptidation reaction between the LPXTA recognition motif and a glycine residue by cleaving the sortase recognition site between the threonine and the alanine residues.
  • the lipidated targeting moiety can be inserted into a precursor LNP.
  • FIG. 3 shows a schematic to insert a lipidated Fab fragment comprising a sortase recognition motif into a precursor LNP to generate a surface-modified LNP.
  • FIG. 4 depicts a schematic of conjugating a precursor LNP to a Fab fragment via a linker comprising a sortase recognition motif.
  • the Fab fragment has been covalently modified at a C-terminus with the residues LPXTG-HHHHHH (SEQ ID NO: 96).
  • the modified Fab fragment is then reacted in a sortase mediated transpeptidation reaction with a lipid covalently bound to three or more glycine (G) residues.
  • G glycine
  • the disclosure provides a method of manufacturing a lipid nanoparticle conjugated to a targeting moiety such as an antibody, Fab fragment or ScFv in a site-specific manner, said method comprising
  • step (ii) contacting the product of step (i) with a lipid comprising a carboxylic acid group in the presence of a lipoic acid ligase under conditions suitable for lipoic acid ligase to ligate the antibody, Fab fragment or ScFv to the lipid;
  • step (iii) inserting the product of step (ii) into a precursor LNP
  • step (iv) removing the unbound product of step (i) that did not insert into the precursor LNP in step (iii), thereby generating a lipid nanoparticle conjugated to the targeting moiety (e.g., an antibody, Fab fragment or ScFv).
  • the targeting moiety e.g., an antibody, Fab fragment or ScFv.
  • step (ii) i.e., the lipoic acid ligase catalyzed reaction
  • step (ii) is carried out in the presence of a mutated lipoic acid ligase, wherein the tryptophan reside (W) at position of the lipoic acid ligase is mutated.
  • W37 mutants are described in Cohen et al., 2012, ChemBioChem, 13, 888-894.
  • the mutant lipoic acid ligase is selected from W37V, W37I, W37T, W37L, W37C, W37A, and W37G.
  • FIG. 5 shows a schematic of a lipoic acid ligase catalyzed reaction to conjugate a lipid to a Fab fragment.
  • the carboxylic acid in step (ii) is a C3-C20 carboxylic acid.
  • the carboxylic acid in step (ii) is a fatty acid, for instance a C7-C19 fatty acid.
  • the fatty acid is selected from decanoic acid, palmitic acid, lauric acid or octanoic acid.
  • the carboxylic acid in step (ii) has the formula COOH-R-Click handle, where R includes two lipid tales.
  • R includes two lipid tales.
  • the carboxylic acid as shown below, wherein n 1 — 120.
  • the lipidated targeting moiety can be inserted into a precursor LNP.
  • FIG. 6 shows a schematic to insert a lipidated Fab fragment comprising a LplA acceptor peptide into a precursor LNP to generate a surface-modified LNP.
  • FIG. 7 shows a schematic of conjugating a precursor LNP to a Fab fragment via a linker comprising a LplA acceptor peptide.
  • R represents a lipid molecule.
  • the lysine (K) residue of the LplA acceptor peptide reacts with the carboxylic acid group of the lipid in the lipoic acid ligase catalyzed reaction.
  • the resultant lipidated Fab fragment is then inserted into a precursor LNP, hence generating a conjugate.
  • the disclosure provides a method of manufacturing a lipid nanoparticle conjugated to a targeting moiety, e.g., antibody, Fab fragment or ScFv, in a sitespecific manner, said method comprising
  • step (ii) contacting the product of step (i) with a lipid comprising a functional group reactive with the enzyme recognition sequence (e.g., a sortase recognition motif or a LplA acceptor peptide) in the presence of an enzyme that recognizes the enzyme recognition sequence under conditions suitable for the enzyme to ligate the antibody, Fab fragment or ScFv to the enzyme recognition sequence,
  • the enzyme recognition sequence e.g., a sortase recognition motif or a LplA acceptor peptide
  • step (iii) contacting the product of step (ii) with other lipid components, thereby generating a lipid nanoparticle conjugated to the targeting moiety, e.g., antibody, Fab fragment or ScFv.
  • the targeting moiety e.g., antibody, Fab fragment or ScFv.
  • Conjugates prepared by site-specific methods disclosed herein have a high density of the targeting agent on the surface of the LNP.
  • the conjugate can comprise more than one targeting moiety (e.g., antibody, Fab fragment or ScFv) per LNP.
  • the conjugate can comprise more than 10 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP.
  • the conjugate can comprise more than 20 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP.
  • the conjugate can comprise more than 30 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP.
  • the conjugate can comprise more than 50 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP. In some embodiments, the conjugate can comprise more than 50 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP. In some embodiments, the conjugate can comprise more than 100 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP. In some embodiments, the conjugate can comprise from about 50 to about 200 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP.
  • targeting moieties e.g., antibodies, Fab fragments or ScFvs
  • the conjugate can comprise from about 100 to about 200 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP. In some embodiments, the conjugate can comprise from about 100 to about 230 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP. In some embodiments, the conjugate can comprise from about 10 to about 150 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP. In some embodiments, the conjugate can comprise from about 10 to about 30 targeting moieties (e.g., antibodies, Fab fragments or ScFvs) per LNP
  • the enzyme recognition site will be bonded at a specific site of the targeting moiety.
  • the enzyme recognition sequence can be bonded to the C-terminus, N-terminus or framework region of one of the formats described above.
  • the targeting moiety is bonded to the enzyme recognition sequence in a site-specific manner. Accordingly, the LNPs formed following insertion of the lipidated targeting moiety are site- selectively modified at their surfaces, which has distinct advantages, as disclosed herein.
  • a C-terminus of the antibody, Fab fragment, scFv, a DARPIN, VHH domain antibody, FN3 domain, or nanobody, single domain antibody or Centyrin is bonded to the enzyme recognition sequence.
  • the enzyme recognition sequence can be bonded to one or more C-terminus of the targeting moiety.
  • the enzyme recognition sequence can be bonded to the C-terminus of one or both of the heavy chains and/or one or both of the light chains.
  • the enzyme recognition sequence bonds to a heavy chain C-terminus of an antibody or Fab fragment.
  • the conjugate comprises a protein targeting moiety as set forth above (e.g., antibody, Fab fragment or ScFv) and a lipid nanoparticle (LNP), wherein a C- terminus of the targeting moiety is conjugated to the lipid nanoparticle through a linker, and wherein the linker comprises a sortase recognition motif.
  • the C- terminus of one or more of the heavy or light chains of the antibody, the C-terminus of the heavy or light chain of the Fab fragment, or C-terminus of the ScFv is conjugated to the lipid nanoparticle through the linker.
  • the sortase recognition motif comprises an LPXT motif, wherein X is any amino acid residue.
  • the sortase recognition motif comprises an LPET motif.
  • the linker comprises 3 or more glycine residues between the sortase recognition motif and the LNP. In some embodiments, the linker comprises between 3 and 20 glycine residues. In some embodiments, the linker comprises between 3 and 10 glycine residues. In some such embodiments, the linker comprises 3, 4, 5, or 6 glycine residues.
  • the linker further consists of one or more additional amino acid residues between the targeting moiety, e.g., antibody, Fab fragment or ScFv, and the sortase recognition motif.
  • the amino acid residues between the targeting moiety e.g., Targeting moiety-LPXT(G) n -Click product-LNP antibody, Fab fragment or ScFv and the enzyme recognition sequence are selected from (GGGGS)v (SEQ ID NO: 9), (G)v (SEQ ID NO: 10), (EAAAK (SEQ ID NO: 11), (PAPAP) V (SEQ ID NO: 12), (AP) V (SEQ ID NO: 13) and A(EAAAK) U ALEA(EAAAK)vA (SEQ ID NO: 14), wherein u is 1-10 and v is 1-10.
  • the conjugate comprises a protein targeting moiety as set forth above (e.g., antibody, Fab fragment or ScFv) and a lipid nanoparticle (LNP), wherein a C- terminus of the targeting moiety is conjugated to the lipid nanoparticle through a linker, and wherein the linker consists of the sequence LPXT(G) n (SEQ ID NO: 19), wherein X is any amino acid and n is between 3 and 20 (e.g., n is between 3 and 15, between 3 anlO, between 3 and 5 or between 3 and 5).
  • a protein targeting moiety as set forth above (e.g., antibody, Fab fragment or ScFv) and a lipid nanoparticle (LNP), wherein a C- terminus of the targeting moiety is conjugated to the lipid nanoparticle through a linker, and wherein the linker consists of the sequence LPXT(G) n (SEQ ID NO: 19), wherein X is any amino acid and n is between
  • the C-terminus of one or more of the heavy or light chains of the antibody, the C-terminus of the heavy or light chain of the Fab fragment, or C-terminus of the ScFv is conjugated to the lipid nanoparticle through the linker.
  • X is E.
  • the LPXT(G) n motif is coupled directly to a lipid of the LNP.
  • the linker does not include a spacer between the enzyme recognition sequence and the LNP, such as the product of a biorthogonal reaction (i.e., Click product).
  • the conjugates have the structure Targeting moiety- LPXT(G) n -Click product-LNP, e.g., Antibody-LPXT(G) n -LNP, Fab fragment- LPXT(G) n - LNP, or ScFv- LPXT(G) n -LNP, wherein X is any amino acid residues and n is between 3 and 20 (e.g., between 3 and 10 or between 3 and 6).
  • the leucine (L) residue of the sortase recognition motif is bonded to at least one C -terminus of the antibody or Fab fragment or to the C-terminus of the ScFv.
  • X is E.
  • the conjugates have the moiety liked to the antibody (or Fab fragment or ScFv) has the following amino acid residues: LPETGGG (SEQ ID NO: 20), LPETGGGG (SEQ ID NO: 21), LPETGGGGG (SEQ ID NO: 22), LPETAGGG (SEQ ID NO: 23) or LPETGGGGGG (SEQ ID NO: 24).
  • the conjugates have the structure Targeting moiety- LPXT(G) n -Click product-LNP, e.g.
  • the leucine (L) residue of the sortase recognition motif is bonded to at least one C -terminus of the antibody or Fab fragment or to the C-terminus of the ScFv through the linker Z.
  • Z comprises one or more amino acid residues.
  • Z is Z is GG, GGG, GGGG (SEQ ID NO: 25), GGGGG (SEQ ID NO: 26), GGGGGG (SEQ ID NO: 27), and GGGGGGG (SEQ ID NO: 28) or GGGGGS (SEQ ID NO: 29).
  • the conjugate comprises a protein targeting moiety as set forth above (e.g., antibody, Fab fragment or ScFv), conjugated to the lipid nanoparticle through a linker, and wherein the linker comprises a lipoic acid ligase (LplA) acceptor peptide.
  • the conjugate comprises an antibody, wherein the C-terminus of one or more of the heavy or light chains of the antibody is bonded to the linker.
  • the conjugate comprises a Fab fragment, the C-terminus of the heavy or light chain of the Fab fragment is bonded to the linker.
  • the conjugate comprises a ScFv, wherein the C-terminus of the ScFv is bonded to the linker.
  • the LplA acceptor peptide has the sequence GFEDKVWYDLDA (SEQ ID NO: 15).
  • the LplA acceptor peptide is coupled directly to a lipid of the LNP.
  • the linker does not include a spacer between the LplA acceptor peptide and the LNP, such as the product of a biorthogonal reaction (i.e., Click product).
  • the conjugate has the structure Targeting moiety-LPXT(G) n - Click product-LNP, e.g. Antibody- LplA acceptor peptide— LNP, Fab fragment- LplA acceptor peptide- -LNP, or ScFv- LplA acceptor peptide— LNP.
  • the glycine (G) residue of the LplA acceptor peptide is bonded to the antibody, Fab fragment or ScFv.
  • the glycine (G) residue of the LplA acceptor peptide is bonded to a C- terminus of the antibody, Fab fragment or ScFv.
  • the lysine (K) residue of the LplA acceptor peptide is covalently linked to a lipid in the nanoparticle (FIG.7).
  • the conjugates have the structure Targeting moiety-LPXT(G) n , Click product-LNP, e.g. Antibody- LplA acceptor peptide -LNP, Fab fragment- LplA acceptor peptide -LNP, or ScFv- LplA acceptor peptide -LNP.
  • the conjugates have the structure Targeting moiety-LPXT(G) n -Click product-LNP, e.g.
  • the glycine (G) residue of the LplA acceptor peptide is bonded to at least one C -terminus of the antibody or Fab fragment or to the C-terminus of the ScFv through the linker Z.
  • Z comprises one or more amino acid residues.
  • Z is (GGGGS) V , (SEQ ID: NO. 9), (G)v (SEQ ID: NO. 10), (EAAAK) V (SEQ ID: NO. 11), (PAPAP) V (SEQ ID: NO. 912), (AP) V (SEQ ID: NO. 13) and A(EAAAK) U ALEA(EAAAK) V A (SEQ ID: NO. 14), wherein u is 1-10 and v is 1-10.
  • Z is GG, GGG, GGGG (SEQ ID NO: 25), GGGGG (SEQ ID NO: 26), GGGGGG (SEQ ID NO: 27), and GGGGGGG (SEQ ID NO: 28) or GGGGGS (SEQ ID NO: 29).
  • the enzyme recognition sequence is a transglutaminase enzyme recognition sequence (LLQG) (SEQ ID NO: 16).
  • the transglutaminase enzyme recognition sequence (LLQG) (SEQ ID NO: 16) is also referred to as Q-tag.
  • the Q-tag may be present on or can be inserted at one or more locations of antibody, Fab fragment or ScFv, for instance at a C-terminus.
  • the transglutamine enzyme catalyzes the reaction between a sidechain amide group on the Q-tag and an alkyl-primary amine on a component of the LNP (e.g., a lipid), thus linking the antibody to the LNP through an amide bond.
  • the enzyme recognition sequence is a sequence recognized by formylglycine generating enzyme, specifically CXPXR, wherein each X is any amino acid.
  • the CXPXR sequence can be inserted at one or more locations of antibody, Fab fragment or ScFv, for instance at a C-terminus.
  • the formylglycine generating enzyme converts the cysteine thiol of CXPXR into an aldehyde group, which can be reacted with an aminooxy or hydrazine group covalently bonded to a component of the LNP.
  • the targeting moiety component of a conjugate of the disclosure can target a cell surface antigen or receptor.
  • the targeting moiety component of a conjugate by targeting a cell surface antigen or receptor on a cell, enhances delivery of a payload, e.g., a therapeutic payload, formulated in the LNP component of the conjugate.
  • the conjugates described herein deliver a payload to more target cells and/or deliver greater amounts of payload to target cells relative to a conjugate lacking a targeting moiety.
  • Enhanced delivery of a therapeutic payload to a target cell e.g., to an immune cell or a diseased or malfunctional cell, using a targeted conjugate (LNP) as described herein can improve treatment of a disease or ailment in a patient.
  • LNP targeted conjugate
  • the targeting moiety component of a conjugate of the disclosure targets T cell receptors including, but not limited to, CD2, CD3, CD4, CD5, CD6, CD7 or CD8.
  • the targeting moiety component of a conjugate of the disclosure targets hematopoietic stem cells (HSCs).
  • HSCs hematopoietic stem cells
  • the targeting moiety component of a conjugate of the disclosure targets HSC receptors including, but not limited to, CD90 or CD 117.
  • the targeting moiety component of a conjugate binds to CD8, TCR alpha, TCR beta, CD10, CD33, CD34, CD68, CD19, CD62L, CD25, CXCR3, CCR2, CCR3, CCR4, CCR5, CCR6, or CCR7, o a combination thereof.
  • the targeting moiety binds to CD4+ or CD8+ T cell. In other embodiments, the targeting moiety binds to a natural killer (NK) cell. In other embodiments, the targeting moiety binds to a hematopoietic stem cell. In other embodiments, the targeting moiety binds to a lymphoid progenitor cell. In other embodiments, the targeting moiety binds to a myeloid cell. In other embodiments, the targeting moiety binds to a macrophage.
  • NK natural killer
  • the targeting moiety binds to a hematopoietic stem cell. In other embodiments, the targeting moiety binds to a lymphoid progenitor cell. In other embodiments, the targeting moiety binds to a myeloid cell. In other embodiments, the targeting moiety binds to a macrophage.
  • the conjugates of the disclosure can be used to deliver specific payloads to cells, particularly cells expressing cell-surface receptors targeted by the targeting moiety, e.g., antibody, Fab fragment or ScFv, component of the conjugates.
  • the payload is an RNA.
  • the payload is an mRNA.
  • the payload is a siRNA or a microRNA (miRNA).
  • the payload is an antisense oligonucleotide (ASO).
  • the payload is a tRNA.
  • the payload is a DNA vector, for example, a DNA plasmid, close-ended DNA (ceDNA), or a small circular DNA (e.g., a nanoplasmid).
  • the payload is a small molecule.
  • the payload is a guide RNA.
  • the payload is a peptide or protein.
  • the conjugates disclosed herein can include two or more payloads of the same or different payload class, for example, selected from any two or more of mRNA, guide RNA, siRNA, miRNA, ASO, DNA vector, small molecule, peptide, and protein.
  • the conjugates disclosed herein can be used to deliver a therapeutic of interest to a cell.
  • the conjugates disclosed herein can be used to deliver a nucleic acid (e.g., mRNA) encoding a vaccine.
  • the conjugates disclosed herein can be used to deliver a nucleic acid (e.g., mRNA) encoding an enzyme.
  • the conjugates disclosed herein can be used to deliver a nucleic acid (e.g., a DNA or RNA molecule) encoding a chimeric antigen receptor (CAR) to T cells.
  • CAR chimeric antigen receptor
  • the conjugates described herein may be used to target and modify immune cells.
  • the conjugates may be used to modify T cells.
  • T- cells may include any subpopulation of T-cells, e.g., CD4+, CD8+, gamma-delta, naive T cells, stem cell memory T cells, central memory T cells, or a mixture of subpopulations.
  • the conjugates may be used to deliver or modify a T-cell receptor (TCR) in a T cell.
  • TCR T-cell receptor
  • the conjugates may be used to deliver at least one chimeric antigen receptor (CAR) to T-cells.
  • CAR chimeric antigen receptor
  • the conjugates can be used to deliver a CAR or a nucleic acid (e.g., a DNA or RNA, such as mRNA) encoding a CAR to T-cells.
  • the conjugates may be used to deliver at least one CAR, a nucleic acid (e.g., a DNA or RNA, such as mRNA) encoding a CAR to natural killer (NK) cells.
  • the conjugates can be used to deliver at least one CAR or a nucleic acid (e.g., a DNA or RNA, such as mRNA) encoding a CAR to natural killer T (NKT) cells.
  • the conjugates may be used to deliver at least one CAR or a nucleic acid (e.g., a DNA or RNA, such as mRNA) encoding a CAR to a progenitor cell, e.g., a progenitor cell of T, NK, or NKT cells.
  • a progenitor cell e.g., a progenitor cell of T, NK, or NKT cells.
  • cells modified with at least one CAR e.g., CAR-T cells, CAR-NK cells, CAR-NKT cells
  • a combination of cells modified with at least one CAR e.g., a mixture of CAR-NK/T cells
  • the immune cells comprise a CAR specific to a tumor or a pathogen antigen selected from a group consisting of AChR (fetal acetylcholine receptor), ADGRE2, AFP (alpha fetoprotein), BAFF-R, BCMA, CAIX (carbonic anhydrase IX), CCR1, CCR4, CEA (carcinoembryonic antigen), CD3, CD5, CD8, CD7, CD10, CD13, CD14, CD15, CD19, CD20, CD22, CD30, CD33, CLLI, CD34, CD38, CD41, CD44, CD49f, CD56, CD61, CD64, CD68, CD70,CD74, CD99,CD117, CD123, CD133, CD138, CD44v6, CD267, CD269, CDS, CLEC12A, CS1, EGP-2 (epithelial glycoprotein-2), EGP-40 (epithelial glycoprotein-40), EGFR
  • AChR fetal acetylcholine receptor
  • a conjugate as described herein is administered to an immune cell, e.g., a T-cell, NK cell, NKT cell, or progenitor cell ex vivo or in vitro to deliver a therapeutic payload (e.g., a gene modifying system) and then the cells are delivered to a patient.
  • a therapeutic payload e.g., a gene modifying system
  • immune cells e.g., T-cells, NK cells, NKT cells, or progenitor cells are modified ex vivo or in vitro and then delivered to a patient.
  • a nucleic acid e.g., DNA or RNA, such as mRNA
  • RNA e.g., DNA or RNA, such as mRNA
  • immune cells e.g., T-cells, NK cells, NKT cells, or progenitor cells are modified in vivo in the patient.
  • the patient is a human patient.
  • the targeting moiety is a T-cell targeting moiety, for example, an antibody, Fab fragment or ScFv, that binds to a T-cell antigen selected from the group consisting of CD2, CD3, CD4, CD5, CD7, CD8, CD28, CD137, CD45, T-cell receptor (TCR)p,TCR-a, TCR-a/p, TCR-y/5, PD1 , CTLA4, TIM3, LAG3, CD18, IL-2 receptor, CDl la, TLR2, TLR4, TLR5, IL-7 receptor, or IL-15 receptor.
  • a T-cell antigen selected from the group consisting of CD2, CD3, CD4, CD5, CD7, CD8, CD28, CD137, CD45, T-cell receptor (TCR)p,TCR-a, TCR-a/p, TCR-y/5, PD1 , CTLA4, TIM3, LAG3, CD18, IL-2 receptor, CDl la, TLR2, TLR4, TLR5, IL-7 receptor, or IL-15 receptor
  • a conjugate as described herein is administered to an HSC (e.g., a LT-HSC) or a HSC progenitor ex vivo or in vitro to deliver a therapeutic payload (e.g., a gene modifying system) and then the cells are delivered to a patient.
  • a conjugate as described herein is administered to an HSC (e.g., a LT-HSC) or a HSC progenitor in vivo to deliver a therapeutic payload (e.g., a gene modifying system).
  • HSCs e.g., LT-HSCs
  • HSC progenitor cells are modified ex vivo or in vitro and then delivered to a patient.
  • HSCs e.g., LT-HSCs
  • HSC progenitor cells are modified in vivo in the patient.
  • the patient is a human patient.
  • the targeting moiety is an HSC targeting moiety, for example, an antibody, Fab fragment or ScFv, that binds to an HSC antigen selected from CD90 and CD117.
  • a conjugate as disclosed herein can be introduced into cells, tissues and multicellular organisms.
  • the system or components of the system are delivered to the cells via mechanical means or physical means.
  • the cells are human cells.
  • a conjugate described herein is delivered to a tissue or cell from or in the cerebrum, cerebellum, adrenal gland, ovary, pancreas, parathyroid gland, hypophysis, testis, thyroid gland, breast, spleen, tonsil, thymus, lymph node, bone marrow, lung, cardiac muscle, esophagus, stomach, small intestine, colon, liver, salivary gland, kidney, prostate, blood, or other cell or tissue type.
  • a conjugate described herein is used to treat a disease, such as a cancer, inflammatory disease, infectious disease, genetic defect, or other disease.
  • a cancer can be cancer of the cerebrum, cerebellum, adrenal gland, ovary, pancreas, parathyroid gland, hypophysis, testis, thyroid gland, breast, spleen, tonsil, thymus, lymph node, bone marrow, lung, cardiac muscle, esophagus, stomach, small intestine, colon, liver, salivary gland, kidney, prostate, blood, or other cell or tissue type, and can include multiple cancers.
  • a conjugate described herein is administered by enteral administration (e.g. oral, rectal, gastrointestinal, sublingual, sublabial, or buccal administration).
  • a conjugate system described herein is administered by parenteral administration (e.g., intravenous, intramuscular, subcutaneous, intradermal, epidural, intracerebral, intracerebroventricular, epicutaneous, nasal, intra-arterial, intraarticular, intracavernous, intraocular, intraosseous infusion, intraperitoneal, intrathecal, intrauterine, intravaginal, intravesical, perivascular, or transmucosal administration).
  • a conjugate described herein is administered by topical administration (e.g., transdermal administration).
  • a conjugate described herein is used to treat a disease, disorder, or condition.
  • a conjugate described herein, or component or portion thereof is used to treat a disease, disorder, or condition listed in any of Tables 1-6.
  • the conjugate described herein, or component or portion thereof is used to treat a disease, disorder, or condition in a human patient.
  • a conjugate described herein is used to treat a hematopoietic stem cell (HSC) disease, disorder, or condition, e.g., as listed in Table 1.
  • HSC hematopoietic stem cell
  • a conjugate described herein is used to treat a kidney disease, disorder, or condition, e.g., as listed in Table 2.
  • a conjugate described herein is used to treat a liver disease, disorder, or condition, e.g., as listed in Table 3.
  • a conjugate described herein is used to treat a lung disease, disorder, or condition, e.g., as listed in Table 4.
  • a conjugate described herein is used to treat a skeletal muscle disease, disorder, or condition, e.g., as listed in Table 5.
  • a conjugate described herein is used to treat a skin disease, disorder, or condition, e.g., as listed in Table 6.
  • the conjugates (targeted LNPs) described herein can be used to deliver payloads (e.g., comprising therapeutic agents) to cells, such as, but not limited to, immune cells (e.g., T cells) or HSCs (e.g., LT-HSCs) or HSC progenitors.
  • payloads e.g., comprising therapeutic agents
  • cells such as, but not limited to, immune cells (e.g., T cells) or HSCs (e.g., LT-HSCs) or HSC progenitors.
  • the payload is one or more nucleic acids.
  • the payload is one or more RNA molecules.
  • the payload is an mRNA (e.g., an mRNA encoding an enzyme).
  • the RNA molecule is a non-coding RNA (ncRNA).
  • the payload is an RNA template (for example, an RNA template for reverse transcription, e.g., Target Primed Reverse Transcription (TPRT)).
  • TPRT Target Primed Reverse Transcription
  • the payload is a siRNA or a microRNA (miRNA).
  • the payload comprises a guide RNA for a CRISPR-Cas system.
  • the payload is a tRNA. In other embodiments, the payload is an antisense oligonucleotide (ASO). In other embodiments, the payload is a DNA molecule, for example, a DNA plasmid, closed-ended DNA (ceDNA), or a small circular DNA (e.g., a minicircle or nanoplasmid). Nucleic acid payloads can be linear, circular, covalently closed, single-stranded, double-stranded, or hybrid RNA/DNA molecules. In other embodiments, the payload is a small molecule. In some embodiments, the payload is a peptide or protein.
  • the conjugates disclosed herein can include two or more payloads, for example, selected from RNA (such as mRNA, ncRNA, guide RNA, siRNA, miRNA), an ASO, DNA vector, small molecule, peptide, or protein.
  • RNA such as mRNA, ncRNA, guide RNA, siRNA, miRNA
  • ASO ASO
  • DNA vector small molecule, peptide, or protein.
  • the conjugates (targeted LNPs) described herein can be used to deliver a therapeutic of interest to a cell, such as, but not limited to an immune cell (e.g., a T cell), HSC or HSC progenitor.
  • the conjugate (targeted LNP) contains a payload that is a therapeutic agent.
  • the therapeutic agent can be a therapeutic peptide or protein, a nucleic acid comprising a therapeutic agent, or a nucleic acid encoding a therapeutic agent.
  • the therapeutic agent can be a genetic medicine (e.g., for gene therapy or gene editing), wherein the therapeutic agent is capable of modifying, altering or effecting a change in the genomic DNA of a cell such as, but not limited to, an immune cell, such as a T cell, an HSC (e.g., LT-HSC) or HSC progenitor in the subject).
  • the therapeutic agent is a gene therapy agent or gene editing agent.
  • the therapeutic agent is a gene modifying polypeptide, as described herein.
  • the therapeutic agent is a gene modifying system, as described herein.
  • the therapeutic agent can be a peptide or protein, such as an enzyme, or a nucleic acid (e.g., mRNA or DNA) encoding the peptide or protein (e.g., an enzyme).
  • the enzyme can be or comprise a nuclease, recombinase, integrase, transposase, retrotransposase, helicase, transcriptase, polymerase, reverse transcriptase, deaminase, methylase, demethylase, or ligase, or can have a combination of enzymatic activities thereof.
  • the therapeutic agent can be a peptide or protein, or a nucleic acid encoding the peptide or protein, for use as a replacement gene therapy.
  • the therapeutic agent can be a peptide or protein, or a nucleic acid encoding the peptide or protein, for use in modifying or altering the genome or epigenome of a cell, such as, but not limited to, an immune cell, such as a T cell, an HSC or HSC progenitor of a subject.
  • the therapeutic agent can comprise one or more components of a system for modifying or altering the genome or epigenome of a cell such as, but not limited to, an immune cell such as a T cell, an HSC or HSC progenitor of a subject.
  • the system for modifying or altering the genome or epigenome of a cell of a subject comprises one or more proteins, one or more nucleic acids (e.g., RNA and/or DNA), or combinations thereof.
  • the therapeutic agent can be a fusion protein, e.g., a fusion protein comprising a nuclease (e.g., an endonuclease such as Cas9 or a functional portion thereof) and a protein domain comprising recombinase, integrase, transposase, retrotransposase, helicase, transcriptase, polymerase, reverse transcriptase, deaminase, methylase, demethylase, or ligase activity.
  • a nuclease e.g., an endonuclease such as Cas9 or a functional portion thereof
  • a protein domain comprising recombinase, integrase, transposase, retrotransposase, helicase, transcriptase, polymerase, reverse transcriptase, deaminase, methylase, demethylase, or ligase activity.
  • the therapeutic agent can be one or more components of a ribonucleoprotein (RNP) complex for modifying or altering the genome or epigenome of a cell such as, but not limited to, an immune cell, such as a T cell, an HSC or HSC progenitor.
  • RNP ribonucleoprotein
  • the therapeutic agent can be a protein, or a nucleic acid (e.g., mRNA) encoding the protein, and/or an RNA molecule (e.g., a gRNA or RNA comprising a gRNA) for guiding the protein to a particular location in the genome or epigenome, wherein the protein is capable of modifying or altering the genome or epigenome as a nuclease, recombinase, integrase, transposase, helicase, transcriptase, polymerase, reverse transcriptase, deaminase, methylase, demethylase, or ligase, or combinations thereof.
  • a nucleic acid e.g., mRNA
  • an RNA molecule e.g., a gRNA or RNA comprising a gRNA
  • the therapeutic agent comprises a nuclease (e.g., an endonuclease) or a nucleic acid encoding the nuclease (e.g., an endonuclease).
  • the nuclease cleaves DNA to create a double stranded break, leading to the introduction of insertion and/or deletion (indel) mutations in DNA, e.g., genomic DNA.
  • the nuclease is a nickase (i.e., it cleaves a single stand of DNA).
  • the nuclease is mutated such that it is inactive or comprises reduced nuclease activity.
  • the nuclease is a CRISPR-Cas protein. In some embodiments, the nuclease is a recombinant nuclease. In some embodiments, the nuclease is a restriction endonuclease, meganuclease, homing endonuclease, zinc finger nuclease (ZFN), or a transcription activator-like effector nuclease (TALEN).
  • CRISPR-Cas protein In some embodiments, the nuclease is a recombinant nuclease. In some embodiments, the nuclease is a restriction endonuclease, meganuclease, homing endonuclease, zinc finger nuclease (ZFN), or a transcription activator-like effector nuclease (TALEN).
  • the conjugates (targeted LNPs) of the disclosure can be used to deliver gene editing components into cells.
  • the conjugates described herein can be used to deliver a therapeutic agent comprising a CRISPR-Cas system or a component thereof into a cell.
  • the therapeutic agent comprises a Class 1 (type I, type III, or type IV) CRISPR-Cas protein or a nucleic acid encoding the CRISPR- Cas protein.
  • the therapeutic agent comprises a Class 2 (type II, type V, or type VI) CRISPR -Cas protein or a nucleic acid encoding the CRISPR-Cas protein.
  • the therapeutic agent comprises a CRISPR-Cas9 system, or a nucleic acid encoding one or more components of the CRISPR-Cas9 system.
  • the therapeutic agent comprises a CRISPR-Casl2 system (e.g., a Casl2a system), or a nucleic acid encoding one or more components of the CRISPR-Casl2 system.
  • the conjugates described herein can comprise two RNA molecules, such as an RNA comprising a guide RNA (gRNA) and an mRNA encoding a CRISPR-Cas protein.
  • the Cas is Cas9 or Casl2a.
  • the Cas is Cas9. In some embodiments, the Cas is Casl2a. In some embodiments, the gRNA is a single guide RNA (sgRNA). In some embodiments, the LNPs, e.g., targeted LNPs, comprise a payload consisting of or comprising a Cas9 or an mRNA encoding a Cas9.
  • the therapeutic agent comprises one of the following CRISPR- Cas proteins or a nucleic acid (e.g., mRNA) encoding one of the following CRISPR-Cas proteins: Cas9 (e.g., dCas9 and nCas9), Casl2a/Cpfl, Casl2b/C2cl, Casl2c/C2c3, Casl2d/CasY, Casl2e/CasX, Casl2g, Casl2h, or Casl2i.
  • the therapeutic agent comprises an S. pyogenes or an S.
  • thermophilus Cas9 or a functional fragment thereof, or a nucleic acid encoding the Cas9 or functional fragment thereof.
  • the therapeutic agent comprises a Cas9 sequence, e.g., as described in Chylinski, Rhun, and Charpentier (2013) RNA Biology 10:5, 726-737; incorporated herein by reference.
  • the therapeutic agent comprises one of the following CRISPR-Cas proteins or a nucleic acid (e.g., mRNA) encoding one of the following CRISPR-Cas proteins: Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas5d, Cas5t, Cas5h, Cas5a, Cas6, Cas7, Cas8, Cas8a, Cas8b, Cas8c, Cas9 (e.g., Csnl or Csxl2), CaslO, CaslOd, Casl2a/Cpfl, Casl2b/C2cl, Casl2c/C2c3, Casl2d/CasY, Casl2e/CasX, Casl2g, Casl2h, Casl2i, Csyl , Csy2, Csy3, Csy4, Csel, Cse2, Cse3, Cse4,
  • the Cas9 comprises one or more substitutions, e.g., selected from H840A, D10A, P475A, W476A, N477A, DI 125A, W1126A, and DI 127A.
  • the Cas9 comprises one or more mutations at positions selected from: DIO, G12, G17, E762, H840, N854, N863, H982, H983, A984, D986, and/or A987, e.g., one or more substitutions selected from D10A, G12A, G17A, E762A, H840A, N854A, N863A, H982A, H983 A, A984A, and/or D986A.
  • the therapeutic agent comprises a Cas (e.g., Cas9) or a nucleic acid encoding a Cas from Cory neb acterium ulcerans, Corynebacterium diphtheria, Spiroplasma syrphidicola, Prevotella intermedia, Spiroplasma taiwanense, Streptococcus iniae, Belliella baltica, Psychroflexus torquis, Streptococcus thermophilus, Listeria innocua, Campylobacter jejuni, Neisseria meningitidis, Streptococcus pyogenes, or Staphylococcus aureus, or a fragment or variant thereof.
  • Cas e.g., Cas9
  • a nucleic acid encoding a Cas from Cory neb acterium ulcerans, Corynebacterium diphtheria, Spiroplasma syrphidicola, Prevotell
  • the therapeutic agent comprises a Cpfl domain, e.g., comprising one or more substitutions, e.g., at position D917, E1006A, D1255 or any combination thereof, e.g., selected from D917A, E1006A, D1255A, D917A/E1006A, D917A/D1255A, E1006A/D1255A, and D917A/E1006A/D1255A, or a nucleic acid encoding the same.
  • the therapeutic agent comprises an spCas9, spCas9-VRQR, spCas9- VRER, xCas9, saCas9, saCas9-KKH, spCas9-MQKSER, spCas9-LRKIQK, or spCas9- LRVSQL, or a nucleic acid encoding the same.
  • the therapeutic agent comprises a Cas9 nickase (nCas9), such as an S. pyogenes nCas9, e.g., wherein the Cas9 comprises an amino acid substitution at position DIO or H840, e.g., D10A or H840A, or a nucleic acid (e.g., mRNA) encoding the Cas9 nickase (nCas9).
  • the therapeutic agent comprises a catalytically inactive or “dead” Cas9 (dCas9), such as an S.
  • Cas9 pyogenes Cas9, e.g., wherein the Cas9 comprises an amino acid substitution at positions DIO and H840, e.g., D10A and H840A, or a nucleic acid (e.g., an mRNA) encoding the catalytically inactive Cas9 (dCas9).
  • DIO and H840 e.g., D10A and H840A
  • a nucleic acid e.g., an mRNA
  • the therapeutic agent comprises a deaminase, such as a cytidine deaminase or an adenine deaminase, or a nucleic acid (e.g., mRNA) encoding a deaminase.
  • conjugates (targeted LNPs) described herein deliver the deaminase to a target cell to generate a substitution mutation in the DNA, e.g., genomic DNA, of the cell.
  • the therapeutic agent is a base editor, as described in the art, e.g., a cytidine base editor (CBE) or an adenine nucleobase editor (ABE).
  • Examples of therapeutic agents comprising a deaminase or nucleic acids encoding deaminases can be found in PCT Application Nos. PCT/US2014/038359, PCT/US2017/045381, PCT/US2018/024208, PCT/US2018/056146, and PCT/US2019/050112 incorporated herein by reference in their entirety, including the sequence listing and sequences therein.
  • the therapeutic agent can be used for epigenome editing.
  • the therapeutic agent comprises a methylase and/or a demethylase, or one or more nucleic acids (e.g., one or more mRNA) encoding a demethylase and/or a methylase.
  • the therapeutic agent demethylates DNA (e.g., genomic DNA) and/or histones.
  • the therapeutic agent methylates DNA (e.g., genomic DNA) and/or histones.
  • the therapeutic agent can be useful in altering the transcription of a gene (e.g., via gene silencing or gene activation using CRISPRoff and/or CRISPRon).
  • the therapeutic agent can comprise a DNA methyltransferase domain or a nucleic acid encoding a DNA methyltransferase domain.
  • the therapeutic agent can comprise a KRAB domain, DNMT3 A domain, DNMT3B domain, DNMT1 domain, DNMMT3L domain, or SETDB1 domain, or can comprise a nucleic acid encoding a KRAB domain, DNMT3A domain, DNMT3B domain, DNMT1 domain, DNMMT3L domain, SETDB1 domain, VP64 domain, p65 domain, TET1 domain, TET2 domain, or TET3 domain.
  • Examples of therapeutic agents comprising a methylase and//or demethylase or nucleic acids encoding methylases and. or demethylases can be found in PCT Application Nos. PCT/IB2015/058202, PCT/US2021/035244, and PCT/US2021/035937 incorporated herein by reference in their entirety, including the sequence listing and sequences therein.
  • the therapeutic agent can be used to alter or modify a nucleic acid sequence, e.g., to introduce an indel or a substitution into DNA (e.g., genomic DNA) by inducing target-primed reverse transcription (TPRT) to insert a heterologous sequence into the DNA.
  • the therapeutic agent i.e., payload
  • the therapeutic agent can be a gene modifying protein, a nucleic acid encoding a gene modifying protein, or a gene modifying system, as described herein.
  • the therapeutic agent can be a gene modifying polypeptide or nucleic acid encoding a gene modifying polypeptide.
  • the therapeutic agent can be a template RNA for use with the gene modifying polypeptide.
  • the therapeutic agent delivered by a conjugate (targeted LNP) described herein is one or more components of a gene modifying system, e.g., a gene modifying polypeptide (or nucleic acid encoding the gene modifying polypeptide) and/or a template RNA for use with the gene modifying polypeptide.
  • the therapeutic agent comprises or is derived from a retrotransposon or mobile genetic element (MGE).
  • MGE retrotransposon or mobile genetic element
  • the therapeutic agent can be a heterologous gene modifying polypeptide or nucleic acid encoding a heterologous gene modifying polypeptide, as described herein.
  • the therapeutic agent can be an RNA for use with the heterologous gene modifying polypeptide.
  • the therapeutic agent delivered by a conjugate (targeted LNP) described herein is one or more components of a heterologous gene modifying system, e.g., a heterologous gene modifying polypeptide (or nucleic acid encoding the heterologous gene modifying polypeptide) and/or an RNA for use with the heterologous gene modifying polypeptide.
  • the therapeutic agent is a fusion protein, e.g., an endonuclease protein fused to a reverse transcriptase, e.g., an endonuclease nickase fused to a reverse transcriptase.
  • the therapeutic agent is a fusion protein, e.g., an endonuclease protein fused to a polymerase, e.g., an endonuclease nickase fused to a polymerase.
  • the mRNA component of a gene modifying system comprises a recombinant nuclease, or a nucleic acid encoding the nuclease, for example a CRISPR-Cas nuclease (such as a nickase), restriction endonuclease, meganuclease, homing endonuclease, zinc finger nuclease (ZFN), or a transcription activator-like effector nuclease (TALEN).
  • CRISPR-Cas nuclease such as a nickase
  • restriction endonuclease such as a nickase
  • meganuclease homing endonuclease
  • ZFN zinc finger nuclease
  • TALEN transcription activator-like effector nuclease
  • the therapeutic agent can be a small molecule.
  • the therapeutic agent can be an siRNA or miRNA.
  • the conjugates (targeted LNPs) described herein can be formulated to comprise one or more components of a gene modifying system or one or more nucleic acids encoding said components.
  • the payload comprises a gene modifying system, or one or more nucleic acids encoding the components of the gene modifying system.
  • the payload comprises a template RNA and an mRNA encoding the gene modifying polypeptide. .
  • conjugates prepared in accordance with this disclosure are used to deliver to target cells systems that are capable of inserting a heterologous object sequence (e.g., a sequence encoding a CAR) into the genome of the cell, e.g., an immune cell, such as a T cell.
  • a heterologous object sequence e.g., a sequence encoding a CAR
  • the system comprises: (A) a gene modifying polypeptide or a nucleic acid encoding the gene modifying polypeptide, wherein the gene modifying polypeptide comprises: (i) an endonuclease and/or DNA binding domain; and (ii) a reverse transcriptase (RT) domain, where (i) and (ii) are both derived from a retrotransposon (e.g., from the same retrotransposon or different retrotransposons); and (B) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.
  • A a gene modifying polypeptide or a nucleic acid encoding the gene modifying polypeptide
  • the gene modifying polypeptide comprises: (i) an endonuclease and/or DNA binding domain; and (ii) a reverse transcriptase (RT) domain, where (i) and (ii) are both derived
  • a gene modifying polypeptide acts as a substantially autonomous protein machine capable of integrating a template nucleic acid sequence into a target DNA molecule (e.g., in a mammalian host cell, such as a genomic DNA molecule in the host cell), substantially without relying on host machinery.
  • the heterologous object sequence may include, e.g., a coding sequence, a regulatory sequence, a gene expression unit.
  • systems described herein can have a number of advantages relative to various earlier systems.
  • the disclosure describes retrotransposases capable of inserting long sequences of heterologous nucleic acid into a genome.
  • retrotransposases described herein can insert heterologous nucleic acid in an endogenous site in the genome, such as the rDNA locus. This is in contrast to Cre/loxP systems, which require a first step of inserting an exogenous loxP site before a second step of inserting a sequence of interest into the loxP site.
  • Non-long terminal repeat (LTR) retrotransposons are a type of mobile genetic elements that are widespread in eukaryotic genomes. They include, for example, the apurinic/apyrimidinic endonuclease (APE)-type, the restriction enzyme-like endonuclease (RLE)-type, and the Penelope-like element (PLE)-type.
  • APE apurinic/apyrimidinic endonuclease
  • RLE restriction enzyme-like endonuclease
  • PLE Penelope-like element
  • the APE class retrotransposons are comprised of two functional domains: an endonuclease/DNA binding domain, and a reverse transcriptase domain.
  • Examples of APE- class retrotransposons can be found, for example, in Table 1 of PCT Application No. PCT/US2019/048607, US 2023/0235358, US 2023/0242899, and US 2020/0109398, the disclosures of which are incorporated herein by reference in their entireties, including the sequence listing and sequences referred to in Table 1 in PCT/US2019/048607 and US 2020/0109398.
  • the RLE class are comprised of three functional domains: a DNA binding domain, a reverse transcription domain, and an endonuclease domain.
  • RLE-class retrotransposons can be found, for example, in Table 2 of PCT Application No. PCT/US2019/048607, US 2023/0235358, US 2023/0242899, and US 2020/0109398, the disclosures of which are incorporated herein by reference in their entireties, including the sequence listing and sequences referred to in Table 2 in in PCT/US2019/048607 and US 2020/0109398.
  • the reverse transcriptase domain of non-LTR retrotransposon functions by binding an RNA sequence template and reverse transcribing it into the host genome’s target DNA.
  • the RNA sequence template has a 3’ untranslated region which is specifically bound to the retrotransposase, and a variable 5’ region generally having Open Reading Frame(s) (“ORF”) encoding retrotransposase proteins.
  • the RNA sequence template may also comprise a 5’ untranslated region which specifically binds the retrotransposase.
  • Penelope-like elements are distinct from both LTR and non-LTR retrotransposons. PLEs generally comprise a reverse transcriptase domain distinct from that of APE and RLE elements, but similar to that of telomerases and Group II introns, and an optional GIY-YIG endonuclease domain.
  • RTE e.g., RTE-1 MD, RTE-3 BF, and RTE-25_LMi
  • CR1 e.g, CR1-1 PH
  • Crack e.g, Crack- 28_RF
  • L2 e.g., L2-2_Dre and L2-5_GA
  • Vingi e.g., Vingi-l_Acar
  • the elements of such retrotransposons can be functionally modularized and/or modified to target, edit, modify or manipulate a target DNA sequence, e.g., to insert an object (e.g., heterologous) nucleic acid sequence into a target genome, e.g., a mammalian genome, by reverse transcription.
  • a target DNA sequence e.g., to insert an object (e.g., heterologous) nucleic acid sequence into a target genome, e.g., a mammalian genome, by reverse transcription.
  • a gene modifying system comprises: (A) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a retrotransposase reverse transcriptase domain, and (ii) a retrotransposase endonuclease domain that contains DNA binding functionality; and (B) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.
  • the RNA template element of a gene modifying system is typically heterologous to the polypeptide element and provides an object sequence to be inserted (reverse transcribed) into the host genome.
  • the gene modifying system comprises a retrotransposase sequence of an element listed in any one of Table 10, Table 11, Table X, Table Z1 Table 3 A, or 3B of PCT Pub. No.: WO/2021/178717, US 2023/0235358, and US 2023/0242899, which are incorporated herein by reference as they relate to domains from retrotransposons.
  • an amino acid sequence encoded by an element of Table 7 is an amino acid sequence encoded by the full length sequence of an element listed in Table 7, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.
  • the full-length sequence of an element listed in Table 7 may comprise one or more (e.g., all of) of a 5’ UTR, polypeptide-encoding sequence, or 3’ UTR of a retrotransposon as described herein.
  • an amino acid sequence of Table 7 is an amino acid sequence encoded by the full length sequence of an element listed in Table 7, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.
  • a 5’ UTR of an element of Table 7 comprises a 5’ UTR of the full length sequence of an element listed in Table 7, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.
  • a 3’ UTR of an element of Table 7 comprises a 3’ UTR of the full length sequence of an element listed in Table 7, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.
  • Table 7 Also indicated in Table 7 are the host organisms from which the nucleic acid sequences were obtained and a listing of domains present within the polypeptide encoded by the open reading frame of the nucleic acid sequence.
  • the gene modifying polypeptide further comprises a heterologous protein domain.
  • Table 7 provides gene modifying polypeptides comprising retrotransposon elements, altered for improved efficiency of integration into the human genome. Retrotransposase polypeptides were improved through consensus mapping to re-derive the optimal amino acid sequence. Template molecules for use with cognate retrotransposase enzymes were mapped back to their host genomes and flanking genomic DNA used to elucidate target site motifs.
  • a template RNA described herein comprises one or both of a first homology domain comprising a sequence of a 5' Human Homology Arm of Table 7 (or a sequence having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto) and a second homology domain comprising a sequence of a 3' Human Homology Arm of Table 7 (or a sequence having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto).
  • transposable elements in genomic DNA often exist as tandem or interspersed repeats (Jurka Curr Opin Struct Biol 8, 333-337 (1998)).
  • Tools capable of recognizing such repeats can be used to identify new elements from genomic DNA and for populating databases, e.g., Repbase (Jurka et al Cytogenet Genome Res 110, 462-467 (2005)).
  • Repbase Jurka et al Cytogenet Genome Res 110, 462-467 (2005).
  • One such tool for identifying repeats that may comprise transposable elements is RepeatFinder (Volfovsky et al Genome Biol 2 (2001)), which analyzes the repetitive structure of genomic sequences.
  • Repeats can further be collected and analyzed using additional tools, e.g., Censor (Kohany et al BMC Bioinformatics 7, 474 (2006)).
  • Censor Kelhany et al BMC Bioinformatics 7, 474 (2006).
  • the Censor package takes genomic repeats and annotates them using various BLAST approaches against known transposable elements.
  • An all-frames translation can be used to generate the ORF(s) for comparison.
  • transposable elements include RepeatModeler2, which automates the discovery and annotation of transposable elements in genome sequences (Flynn et al bioRxiv (2019)).
  • RepeatModeler2 automates the discovery and annotation of transposable elements in genome sequences
  • Retrotransposons can be further classified according to the reverse transcriptase domain using a tool such as RTclassl (Kapitonov et al Gene 448, 207-213 (2009)).
  • the reverse transcriptase domain of the gene modifying system is based on a reverse transcriptase domain of an APE-type or RLE-type non-LTR retrotransposon, or of a PLE-type retrotransposon.
  • a wild-type reverse transcriptase domain of an APE-type, RLE-type, or PLE-type retrotransposon can be used in a gene modifying system or can be modified (e.g., by insertion, deletion, or substitution of one or more residues) to alter the reverse transcriptase activity for target DNA sequences.
  • the reverse transcriptase is altered from its natural sequence to have altered codon usage, e.g. improved for human cells.
  • the reverse transcriptase domain is a heterologous reverse transcriptase from a different LTR-retrotransposon, non-LTR retrotransposon, or other source.
  • a gene modifying system includes a polypeptide that comprises a reverse transcriptase domain of a RTE (e.g., RTE-1 MD, RTE-3 BF, and RTE-25_LMi), CR1 (e.g., CR1-1 PH), Crack (e.g., Crack-28_RF), L2 (e.g., L2-2_Dre and L2-5 GA), and Vingi (e.g., Vingi-l_Acar) retrotransposon.
  • RTE e.g., RTE-1 MD, RTE-3 BF, and RTE-25_LMi
  • CR1 e.g., CR1-1 PH
  • Crack e.g., Crack-28_RF
  • L2 e.g., L2-2_Dre and L2-5 GA
  • Vingi
  • a gene modifying system includes a polypeptide that comprises a reverse transcriptase domain of a retrotransposon listed in Table 10, Table 11, Table X, Table Zl, Table Z2, or Table 3A or 3B of PCT Pub. No.: WO/2021/178717.
  • a gene modifying system includes a polypeptide that comprises a reverse transcriptase domain of a retrotransposon listed in Table 7.
  • the amino acid sequence of the reverse transcriptase domain of a gene modifying system is at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identical to the amino acid sequence of a reverse transcriptase domain of a retrotransposon whose DNA sequence is referenced in Table 7.
  • Reverse transcriptase domains can be identified, for example, based upon homology to other known reverse transcription domains using routine tools as Basic Local Alignment Search Tool (BLAST).
  • BLAST Basic Local Alignment Search Tool
  • reverse transcriptase domains are modified, for example by site-specific mutation.
  • the reverse transcriptase domain is engineered to bind a heterologous template RNA.
  • a polypeptide (e.g., RT domain) comprises an RNA-binding domain, e.g., that specifically binds to an RNA sequence.
  • a template RNA comprises an RNA sequence that is specifically bound by the RNA-binding domain.
  • the RT domain forms a dimer (e.g., a heterodimer or homodimer).
  • the RT domain is monomeric.
  • an RT domain naturally functions as a monomer or as a dimer (e.g., heterodimer or homodimer).
  • an RT domain naturally functions as a monomer.
  • Naturally heterodimeric RT domains may, in some embodiments, also be functional as homodimers.
  • dimeric RT domains are expressed as fusion proteins, e.g., as homodimeric fusion proteins or heterodimeric fusion proteins.
  • the RT function of the system is fulfilled by multiple RT domains (e.g., as described herein).
  • the multiple RT domains are fused or separate, e.g., may be on the same polypeptide or on different polypeptides.
  • a gene modifying polypeptide described herein comprises an RNase H domain, e.g., wherein the RNase H domain may be part of the RT domain.
  • an RT domain e.g., as described herein
  • comprises an RNase H domain e.g., an endogenous RNAse H domain or a heterologous RNase H domain.
  • an RT domain e.g., as described herein
  • an RT domain (e.g., as described herein) comprises an RNase H domain that has been added, deleted, mutated, or swapped for a heterologous RNase H domain.
  • mutation of an RNase H domain yields a polypeptide exhibiting lower RNase activity, e.g., as determined by the methods described in Kotewicz et al. Nucleic Acids Res 16(l):265-277 (1988), e.g., lower by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared to an otherwise similar domain without the mutation.
  • RNase H activity is abolished.
  • an RT domain is mutated to increase fidelity compared to an otherwise similar domain without the mutation.
  • a YADD (SEQ ID NO: 69) or YMDD (SEQ ID NO: 70) motif in an RT domain e.g., in a reverse transcriptase
  • YVDD e.g., in a reverse transcriptase
  • replacement of the YADD (SEQ ID NO: 69) or YMDD (SEQ ID NO: 70) or YVDD (SEQ ID NO: 71) results in higher fidelity in retroviral reverse transcriptase activity (e.g., as described in Jamburuthugoda and Eickbush J Mol Biol 2011).
  • the polypeptide comprises an endonuclease domain (e.g., a heterologous endonuclease domain).
  • the endonuclease/DNA binding domain of an APE-type retrotransposon, the endonuclease domain of an RLE-type retrotransposon, or the endonuclease domain of a PLE-type retrotransposon can be used or can be modified (e.g., by insertion, deletion, or substitution of one or more residues) in a gene modifying system described herein.
  • the endonuclease domain or endonuclease/DNA binding domain is altered from its natural sequence to have altered codon usage, e.g. improved for human cells.
  • the endonuclease element is a heterologous endonuclease element.
  • amino acid sequence of an endonuclease domain of a gene modifying system described herein may be at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identical to the amino acid sequence of an endonuclease domain of a retrotransposon whose DNA sequence is referenced in Table X, Zl, Z2, 3A, or 3B of PCT Pub. No: WO/2021/178717.
  • a gene modifying system includes a polypeptide that comprises an endonuclease domain of a retrotransposon listed in Table 7.
  • the amino acid sequence of the endonuclease domain of a gene modifying system is at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identical to the amino acid sequence of a endonuclease domain of a retrotransposon whose DNA sequence is referenced in Table 7.
  • Endonuclease domains can be identified, for example, based upon homology to other known endonuclease domains using tools as Basic Local Alignment Search Tool (BLAST).
  • BLAST Basic Local Alignment Search Tool
  • a gene modifying polypeptide possesses the function of DNA target site cleavage via an endonuclease domain.
  • the endonuclease domain is also a DNA-binding domain.
  • the endonuclease domain is also a template nucleic acid (e.g., template RNA) binding domain.
  • the endonuclease/DNA binding domain of an APE-type retrotransposon or the endonuclease domain of an RLE-type retrotransposon can be used or can be modified (e.g., by insertion, deletion, or substitution of one or more residues) in a gene modifying system described herein.
  • a gene modifying polypeptide typically contains regions capable of associating with the template nucleic acid (e.g., template RNA).
  • the template nucleic acid binding domain is an RNA binding domain.
  • the RNA binding domain is a modular domain that can associate with RNA molecules containing specific signatures, e.g., structural motifs, e.g., secondary structures present in the 3’ UTR in non-LTR retrotransposons.
  • the template nucleic acid binding domain (e.g., RNA binding domain) RNA binding domain is contained within the reverse transcription domain, e.g., the reverse transcriptase-derived component has a known signature for RNA preference, e.g., secondary structures present in the 3’ UTR in non-LTR retrotransposons.
  • the DNA-binding domain of a gene modifying polypeptide described herein is selected, designed, or constructed for binding to a desired host DNA target sequence.
  • the DNA-binding domain of the engineered retrotransposon is a heterologous DNA-binding protein or domain relative to a native retrotransposon sequence.
  • the heterologous DNA-binding domain is a DNA binding domain of a retrotransposon described in Table 7 herein or in Table X, Table Zl, Table Z2, or Table 3A or 3B of PCT Pub. No.: WO/2021/178717.
  • DNA binding domains can be identified based upon homology to other known DNA binding domains using tools as Basic Local Alignment Search Tool (BLAST).
  • BLAST Basic Local Alignment Search Tool
  • DNA-binding domains are modified, for example by site-specific mutation.
  • the DNA binding domain is altered from its natural sequence to have altered codon usage, e.g. improved for human cells.
  • the DNA binding domain comprises one or more modifications relative to a wild-type DNA binding domain, e.g., a modification via directed evolution, e.g., phage-assisted continuous evolution (PACE).
  • PACE phage-assisted continuous evolution
  • the host DNA-binding site integrated into by the gene modifying system can be in a gene, in an intron, in an exon, an ORF, outside of a coding region of any gene, in a regulatory region of a gene, or outside of a regulatory region of a gene.
  • the engineered retrotransposon may bind to one or more than one host DNA sequence.
  • the engineered retrotransposon may have low sequence specificity, e.g., bind to multiple sequences or lack sequence preference.
  • a gene modifying system is used to edit a target locus in multiple alleles.
  • a gene modifying system is designed to edit a specific allele.
  • a gene modifying polypeptide may be directed to a specific sequence that is only present on one allele, e.g., comprises a template RNA with homology to a target allele, e.g., an annealing domain, but not to a second cognate allele.
  • a gene modifying system can alter a haplotype-specific allele.
  • a gene modifying system that targets a specific allele preferentially targets that allele, e.g., has at least a 2, 4, 6, 8, or 10-fold preference for a target allele.
  • a gene modifying system RNA further comprises an intracellular localization sequence, e.g., a nuclear localization sequence.
  • the nuclear localization sequence may be an RNA sequence that promotes the import of the RNA into the nucleus.
  • the nuclear localization signal is located on the template RNA.
  • the retrotransposase polypeptide is encoded on a first RNA, and the template RNA is a second, separate, RNA, and the nuclear localization signal is located on the template RNA and not on an RNA encoding the retrotransposase polypeptide.
  • the RNA encoding the retrotransposase is targeted primarily to the cytoplasm to promote its translation, while the template RNA is targeted primarily to the nucleus to promote its retrotransposition into the genome.
  • the nuclear localization signal is at the 3’ end, 5’ end, or in an internal region of the template RNA. In some embodiments the nuclear localization signal is 3’ of the heterologous sequence (e.g., is directly 3’ of the heterologous sequence) or is 5’ of the heterologous sequence (e.g., is directly 5’ of the heterologous sequence). In some embodiments, the nuclear localization signal is placed outside of the 5’ UTR or outside of the 3’ UTR of the template RNA.
  • the nuclear localization signal is placed between the 5’ UTR and the 3’ UTR, wherein optionally the nuclear localization signal is not transcribed with the transgene (e.g., the nuclear localization signal is an anti-sense orientation or is downstream of a transcriptional termination signal or polyadenylation signal).
  • the nuclear localization sequence is situated inside of an intron.
  • a plurality of the same or different nuclear localization signals are in the RNA, e.g., in the template RNA.
  • the nuclear localization signal is less than 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 bp in legnth.
  • RNA nuclear localization sequences can be used.
  • Lubelsky and Ulitsky, Nature 555 (107-111), 2018 describe RNA sequences, which drive RNA localization into the nucleus.
  • the nuclear localization signal is a SINE-derived nuclear RNA localization (SIRLOIN) signal.
  • the nuclear localization signal binds a nuclear-enriched protein.
  • the nuclear localization signal binds the HNRNPK protein.
  • the nuclear localization signal is rich in pyrimidines, e.g., is a C/T rich, C/U rich, C rich, T rich, or U rich region.
  • the nuclear localization signal is derived from a long non-coding RNA.
  • the nuclear localization signal is derived from MALAT1 long non-coding RNA or is the 600 nucleotide M region of MALAT1 (described in Miyagawa et al., RNA 18, (738-751), 2012).
  • the nuclear localization signal is derived from BORG long non-coding RNA or is a AGCCC motif (described in Zhang et al., Molecular and Cellular Biology 34, 2318-2329 (2014).
  • the nuclear localization sequence is described in Shukla et al., The EMBO Journal e98452 (2016).
  • the nuclear localization signal is derived from a non-LTR retrotransposon, an LTR retrotransposon, retrovirus, or an endogenous retrovirus.
  • a polypeptide described herein comprises one or more (e.g., 2, 3, 4, 5) nuclear targeting sequences, for example, a nuclear localization sequence (NLS), e.g., as described herein.
  • the NLS is a bipartite NLS.
  • an NLS facilitates the import of a protein comprising an NLS into the cell nucleus.
  • the NLS is fused to the N-terminus of a gene modifying polypeptide described herein.
  • the NLS is fused to the C-terminus of the gene modifying polypeptide.
  • a linker sequence is disposed between the NLS and the neighboring domain of the gene modifying polypeptide.
  • an NLS comprises the amino acid sequence of an NLS described herein.
  • a nucleic acid described herein (e.g., an RNA encoding a gene modifying polypeptide, or a DNA encoding the RNA) comprises a microRNA binding site.
  • the microRNA binding site is used to increase the target-cell specificity of a gene modifying system.
  • the microRNA binding site can be chosen on the basis that is recognized by a miRNA that is present in a non-target cell type, but that is not present (or is present at a reduced level relative to the non-target cell) in a target cell type.
  • RNA encoding the gene modifying polypeptide when the RNA encoding the gene modifying polypeptide is present in a non-target cell, it would be bound by the miRNA, and when the RNA encoding the gene modifying polypeptide is present in a target cell, it would not be bound by the miRNA (or bound but at reduced levels relative to the non-target cell). While not wishing to be bound by theory, binding of the miRNA to the RNA encoding the gene modifying polypeptide may reduce production of the gene modifying polypeptide, e.g., by degrading the mRNA encoding the polypeptide or by interfering with translation. Accordingly, the heterologous object sequence would be inserted into the genome of target cells more efficiently than into the genome of non-target cells.
  • a system having a microRNA binding site in the RNA encoding the gene modifying polypeptide (or encoded in the DNA encoding the RNA) may also be used in combination with a template RNA that is regulated by a second microRNA
  • a polypeptide for use in any of the systems described herein can be a molecular reconstruction or ancestral reconstruction based upon the aligned polypeptide sequence of multiple retrotransposons.
  • a 5’ or 3’ untranslated region for use in any of the systems described herein can be a molecular reconstruction based upon the aligned 5’ or 3’ untranslated region of multiple retrotransposons.
  • polypeptides or nucleic acid sequences can be aligned, e.g., by using routine sequence analysis tools as Basic Local Alignment Search Tool (BLAST) or CD-Search for conserved domain analysis.
  • BLAST Basic Local Alignment Search Tool
  • CD-Search conserved domain analysis.
  • the retrotransposon from which the 5’ or 3 ’ untranslated region or polypeptide is derived is a young or a recently active mobile element, as assessed via phylogenetic methods such as those described in Boissinot et al., Molecular Biology and Evolution 2000, 915-928.
  • the gene modifying system comprises an intein.
  • an intein comprises a polypeptide that has the capacity to join two polypeptides or polypepide fragments together via a peptide bond.
  • the intein is a trans-splicing intein that can join two polypeptide fragments, e.g., to form the polypeptide component of a system as described herein. Promoters
  • one or more promoter or enhancer elements are operably linked to a nucleic acid encoding a gene modifying protein or a template nucleic acid, e.g., that controls expression of the heterologous object sequence.
  • the one or more promoter or enhancer elements comprise cell-type or tissue specific elements.
  • the promoter or enhancer is the same or derived from the promoter or enhancer that naturally controls expression of the heterologous object sequence.
  • a gene modifying system is capable of producing a substitution into the target site of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100 or more nucleotides.
  • the substitution is a transition mutation. In some embodiments, the substitution is a transversion mutation.
  • the substitution converts an adenine to a thymine, an adenine to a guanine, an adenine to a cytosine, a guanine to a thymine, a guanine to a cytosine, a guanine to an adenine, a thymine to a cytosine, a thymine to an adenine, a thymine to a guanine, a cytosine to an adenine, a cytosine to a guanine, or a cytosine to a thymine.
  • a gene modifying system is capable of producing an insertion into the target site of at least 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides (and optionally no more than 500, 400, 300, 200, or 100 nucleotides). In some embodiments, a gene modifying system is capable of producing an insertion into the target site of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides (and optionally no more than 500, 400, 300, 200, or 100 nucleotides).
  • a gene modifying system is capable of producing an insertion into the target site of at least 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 kilobases (and optionally no more than 1, 5, 10, or 20 kilobases).
  • a gene modifying system is capable of producing a deletion of at least 81, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides).
  • a gene modifying system is capable of producing a deletion of at least 81, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides). In some embodiments, a gene modifying system is capable of producing a deletion of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides).
  • a gene modifying system is capable of producing a deletion of at least 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 kilobases (and optionally no more than 1, 5, 10, or 20 kilobases).
  • an insertion, deletion, substitution, or combination thereof increases or decreases expression (e.g. transcription or translation) of a gene.
  • an insertion, deletion, substitution, or combination thereof increases or decreases expression (e.g. transcription or translation) of a gene by altering, adding, or deleting sequences in a promoter or enhancer, e.g. sequences that bind transcription factors.
  • an insertion, deletion, substitution, or combination thereof alters translation of a gene (e.g. alters an amino acid sequence), inserts or deletes a start or stop codon, alters or fixes the translation frame of a gene.
  • an insertion, deletion, substitution, or combination thereof alters splicing of a gene, e.g. by inserting, deleting, or altering a splice acceptor or donor site. In some embodiments, an insertion, deletion, substitution, or combination thereof alters transcript or protein half-life. In some embodiments, an insertion, deletion, substitution, or combination thereof alters protein localization in the cell (e.g. from the cytoplasm to a mitochondria, from the cytoplasm into the extracellular space (e.g. adds a secretion tag)). In some embodiments, an insertion, deletion, substitution, or combination thereof alters (e.g. improves) protein folding (e.g. to prevent accumulation of misfolded proteins). In some embodiments, an insertion, deletion, substitution, or combination thereof, alters, increases, decreases the activity of a gene, e.g. a protein encoded by the gene.
  • a system or method described herein results in “scarless” insertion of the heterologous object sequence, while in some embodiments, the target site can show deletions or duplications of endogenous DNA as a result of insertion of the heterologous sequence.
  • the mechanisms of different retrotransposons could result in different patterns of duplications or deletions in the host genome occurring during retrotransposition at the target site.
  • the system results in a scarless insertion, with no duplications or deletions in the surrounding genomic DNA.
  • the system results in a deletion of less than 1, 2, 3, 4, 5, 10, 50, or 100 bp of genomic DNA upstream of the insertion.
  • the system results in a deletion of less than 1, 2, 3, 4, 5, 10, 50, or 100 bp of genomic DNA downstream of the insertion. In some embodiments, the system results in a duplication of less than 1, 2, 3, 4, 5, 10, 50, or 100 bp of genomic DNA upstream of the insertion. In some embodiments, the system results in a duplication of less than 1, 2, 3, 4, 5, 10, 50, or 100 bp of genomic DNA downstream of the insertion.
  • a gene modifying system described herein, or a DNA-binding domain thereof binds to its target site specifically, e.g., as measured using an assay of Example 21 of PCT Application No. PCT/US2019/048607.
  • the gene modifying polypeptide or DNA-binding domain thereof binds to its target site more strongly than to any other binding site in the human genome.
  • the target site represents more than 50%, 60%, 70%, 80%, 90%, or 95% of binding events of the gene modifying polypeptide or DNA-binding domain thereof to human genomic DNA.
  • the DNA binding domain of the gene modifying polypeptide is heterologous to the remainder of the gene modifying polypeptide, e.g., such that the gene modifying polypeptide targets a different target site that the endogenous DNA binding domain associated with the remainder of the gene modifying polypeptide.
  • a retrotransposase described herein comprises two connected subunits as a single polypeptide.
  • two wild-type retrotransposases could be joined with a linker to form a covalently “dimerized” protein.
  • the nucleic acid coding for the retrotransposase codes for two retrotransposase subunits to be expressed as a single polypeptide.
  • the subunits are connected by a peptide linker. Based on mechanism, not all functions are required from both retrotransposase subunits.
  • the fusion protein may consist of a fully functional subunit and a second subunit lacking one or more functional domains.
  • one subunit may lack reverse transcriptase functionality.
  • one subunit may lack the reverse transcriptase domain.
  • one subunit may possess only endonuclease activity.
  • one subunit may possess only an endonuclease domain.
  • the two subunits comprising the single polypeptide may provide complimentary functions.
  • one subunit may lack endonuclease functionality. In some embodiments, one subunit may lack the endonuclease domain. In some embodiments, one subunit may possess only reverse transcriptase activity. In some embodiments, one subunit may possess only a reverse transcriptase domain. In some embodiments, one subunit may possess only DNA-dependent DNA synthesis functionality. Evolved Variants o f Gene Modifying Polypeptides
  • the invention provides evolved variants of gene modifying polypeptides. Evolved variants are described, e.g., at p. 1179-1 182 of PCT application WO/2021/178720.
  • the gene modifying systems described herein can transcribe an RNA sequence template into host target DNA sites by target-primed reverse transcription.
  • the gene modifying system can insert an object sequence into a target genome without the need for exogenous DNA sequences to be introduced into the host cell (unlike, for example, CRISPR systems), as well as eliminate an exogenous DNA insertion step. Therefore, the gene modifying system provides a platform for the use of customized RNA sequence templates containing object sequences, e.g., sequences comprising heterologous gene coding and/or function information.
  • the template RNA encodes a gene modifying protein in cis with a heterologous object sequence.
  • a gene modifying protein e.g., a protein comprising (i) a reverse transcriptase domain and (ii) an endonuclease domain, e.g., as described herein
  • a 5’ untranslated region e.g., as described herein
  • a 3’ untranslated region e.g., as described herein
  • the gene modifying protein and heterologous object sequence are encoded in different directions (sense vs. anti-sense), e.g., using an arrangement shown in Figure 3 A of Kuroki -Kami et al, Id.
  • the gene modifying protein and heterologous object sequence are encoded in the same direction.
  • the nucleic acid encoding the polypeptide and the template RNA or the nucleic acid encoding the template RNA are covalently linked, e.g., are part of a fusion nucleic acid, and/or are part of the same transcript.
  • the fusion nucleic acid comprises RNA or DNA.
  • the nucleic acid encoding the gene modifying polypeptide may, in some instances, be 5’ of the heterologous object sequence.
  • the template RNA comprises, from 5’ to 3’, a 5’ untranslated region, a sense-encoded gene modifying polypeptide, a sense-encoded heterologous object sequence, and 3’ untranslated region.
  • the template RNA comprises, from 5’ to 3’, a 5’ untranslated region, a sense-encoded gene modifying polypeptide, anti-sense-encoded heterologous object sequence, and 3’ untranslated region.
  • RNA when a template RNA is described as comprising an open reading frame or the reverse complement thereof, in some embodiments the template RNA must be converted into double stranded DNA (e.g., through reverse transcription) before the open reading frame can be transcribed and translated.
  • customized RNA sequence template can be identified, designed, engineered and constructed to contain sequences altering or specifying host genome function, for example by introducing a heterologous coding region into a genome; affecting or causing exon structure/al ternative splicing; causing disruption of an endogenous gene; causing transcriptional activation of an endogenous gene; causing epigenetic regulation of an endogenous DNA; causing up- or down-regulation of operably liked genes, etc.
  • a customized RNA sequence template can be engineered to contain sequences coding for exons and/or transgenes, provide for binding sites to transcription factor activators, repressors, enhancers, etc., and combinations of thereof.
  • the coding sequence can be further customized with splice acceptor sites, poly-A tails.
  • the RNA sequence can contain sequences coding for an RNA sequence template homologous to the retrotransposase, be engineered to contain heterologous coding sequences, or combinations thereof.
  • the template RNA may have some homology to the target DNA.
  • the template RNA has at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 175, 200 or more bases of exact homology to the target DNA at the 3’ end of the RNA.
  • the template RNA has at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 175, 180, or 200 or more bases of at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% homology to the target DNA, e.g., at the 5’ end of the template RNA.
  • the template RNA has a 3’ untranslated region derived from a retrotransposon, e.g. a retrotransposons described herein.
  • the template RNA has a 3’ region of at least 10, 15, 20, 25, 30, 40, 50, 60, 80, 100, 120, 140, 160, 180, 200 or more bases of at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% homology to the 3’ sequence of a retrotransposon, e.g., a retrotransposon described herein, e.g. a retrotransposon in Table 7.
  • the template RNA has a 5’ untranslated region derived from a retrotransposon, e.g. a retrotransposons described herein.
  • the template RNA has a 5’ region of at least 10, 15, 20, 25, 30, 40, 50, 60, 80, 100, 120, 140, 160, 180, or 200 or more bases of at least 40%, 50%, 60%, 70%, 80%, 90%, 95% or greater homology to the 5’ sequence of a retrotransposon, e.g., a retrotransposon described herein, e.g. a retrotransposon described in Table 7.
  • a retrotransposon e.g., a retrotransposon described herein, e.g. a retrotransposon described in Table 7.
  • the template RNA component of a gene modifying system described herein typically is able to bind the gene modifying protein of the system.
  • the template RNA has a 3’ region that is capable of binding a gene modifying genome editing protein.
  • the binding region e.g., 3’ region, may be a structured RNA region, e.g., having at least 1, 2 or 3 hairpin loops, capable of binding the gene modifying protein of the system.
  • the template RNA component of a gene modifying system described herein typically is able to bind the gene modifying protein of the system.
  • the template RNA has a 5’ region that is capable of binding a gene modifying protein.
  • the binding region e.g., 5’ region, may be a structured RNA region, e.g., having at least 1, 2 or 3 hairpin loops, capable of binding the gene modifying protein of the system.
  • the 5’ untranslated region comprises a pseudoknot, e.g., a pseudoknot that is capable of binding to the gene modifying protein.
  • the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 5’ untranslated region) comprises a stem-loop sequence.
  • the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 5’ untranslated region) comprises a hairpin.
  • the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 5’ untranslated region) comprises a helix.
  • the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 5’ untranslated region) comprises a psuedoknot.
  • the template RNA comprises a ribozyme.
  • the ribozyme is similar to a hepatitis delta virus (HDV) ribozyme, e.g., has a secondary structure like that of the HDV ribozyme and/or has one or more activities of the HDV ribozyme, e.g., a self-cleavage activity. See, e.g., Eickbush et al., Molecular and Cellular Biology, 2010, 3142-3150.
  • HDV hepatitis delta virus
  • the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 3’ untranslated region) comprises one or more stem-loops or helices.
  • Exemplary structures of R2 3’ UTRs are shown, for example, in Ruschak et al. “Secondary structure models of the 3' untranslated regions of diverse R2 RNAs” RNA.
  • a template RNA described herein comprises a sequence that is capable of binding to a gene modifying protein described herein.
  • the template RNA comprises an MS2 RNA sequence capable of binding to an MS2 coat protein sequence in the gene modifying protein.
  • the template RNA comprises an RNA sequence capable of binding to a B-box sequence.
  • the template RNA in addition to or in place of a UTR, is linked (e.g., covalently) to a non-RNA UTR, e.g., a protein or small molecule.
  • the template RNA has a poly-A tail at the 3’ end. In some embodiments, the template RNA does not have a poly-A tail at the 3’ end.
  • the template RNA has a 5’ region of at least 10, 15, 20, 25, 30, 40, 50, 60, 80, 100, 120, 140, 160, 180, 200 or more bases of at least 40%, 50%, 60%, 70%, 80%, 90%, 95% or greater homology to the 5’ sequence of a retrotransposon, e.g., a retrotransposon described herein.
  • the template RNA of the system typically comprises an object sequence for insertion into a target DNA.
  • the object sequence may be coding or non-coding.
  • a system or method described herein comprises a single template RNA. In some embodiments, a system or method described herein comprises a plurality of template RNAs.
  • the object sequence may contain an open reading frame.
  • the template RNA has a Kozak sequence.
  • the template RNA has an internal ribosome entry site.
  • the template RNA has a self-cleaving peptide such as a T2A or P2A site.
  • the template RNA has a start codon.
  • the template RNA has a splice acceptor site.
  • the template RNA has a splice donor site.
  • Exemplary splice acceptor and splice donor sites are described in US10435677, incorporated herein by reference in its entirety.
  • Exemplary splice acceptor site sequences are known to those of skill in the art and include, by way of example only, CTGACCCTTCTCTCTCTCCCCCAGAG (SEQ ID NO: 72) (from human HBB gene) and TTTCTCTCCCACAAG (SEQ ID NO: 73) (from human immunoglobulin-gamma gene).
  • the template RNA has a microRNA binding site downstream of the stop codon.
  • the template RNA has a polyA tail downstream of the stop codon of an open reading frame.
  • the template RNA comprises one or more exons.
  • the template RNA comprises one or more introns. In some embodiments, the template RNA comprises a eukaryotic transcriptional terminator. In some embodiments, the template RNA comprises an enhanced translation element or a translation enhancing element. In some embodiments, the RNA comprises the human T-cell leukemia virus (HTLV-1) R region. In some embodiments, the RNA comprises a posttranscriptional regulatory element that enhances nuclear export, such as that of Hepatitis B Virus (HPRE) or Woodchuck Hepatitis Virus (WPRE). In some embodiments, in the template RNA, the heterologous object sequence encodes a polypeptide and is coded in an antisense direction with respect to the 5’ and 3 ’ UTR. In some embodiments, in the template RNA, the heterologous object sequence encodes a polypeptide and is coded in a sense direction with respect to the 5’ and 3’ UTR.
  • HPRE Hepatitis B Virus
  • WPRE Woodchuck Hepatitis Virus
  • a nucleic acid described herein (e.g., a template RNA or a DNA encoding a template RNA) comprises a microRNA binding site.
  • the microRNA binding site is used to increase the target-cell specificity of a gene modifying system.
  • the microRNA binding site can be chosen on the basis that is recognized by a miRNA that is present in a non-target cell type, but that is not present (or is present at a reduced level relative to the non-target cell) in a target cell type.
  • the template RNA when the template RNA is present in a non-target cell, it would be bound by the miRNA, and when the template RNA is present in a target cell, it would not be bound by the miRNA (or bound but at reduced levels relative to the non-target cell). While not wishing to be bound by theory, binding of the miRNA to the template RNA may interfere with insertion of the heterologous object sequence into the genome. Accordingly, the heterologous object sequence would be inserted into the genome of target cells more efficiently than into the genome of non-target cells.
  • a system having a microRNA binding site in the template RNA (or DNA encoding it) may also be used in combination with a nucleic acid encoding a gene modifying polypeptide, wherein expression of the gene modifying polypeptide is regulated by a second microRNA binding site, e.g., as described herein, e.g., in the section entitled “Polypeptide component of gene modifying system.”
  • the object sequence may contain a non-coding sequence.
  • the template RNA may comprise a promoter or enhancer sequence.
  • the template RNA comprises a tissue specific promoter or enhancer, each of which may be unidirectional or bidirectional.
  • the promoter is an RNA polymerase I promoter, RNA polymerase II promoter, or RNA polymerase III promoter.
  • the promoter comprises a TATA element.
  • the promoter comprises a B recognition element.
  • the promoter has one or more binding sites for transcription factors.
  • the non-coding sequence is transcribed in an antisense-direction with respect to the 5’ and 3’ UTR. In some embodiments, the non-coding sequence is transcribed in a sense direction with respect to the 5’ and 3’ UTR.
  • a nucleic acid described herein comprises a promoter sequence, e.g., a tissue specific promoter sequence.
  • the tissue-specific promoter is used to increase the target-cell specificity of a gene modifying system.
  • the promoter can be chosen on the basis that it is active in a target cell type but not active in (or active at a lower level in) a non-target cell type. Thus, even if the promoter integrated into the genome of a non-target cell, it would not drive expression (or only drive low-level expression) of an integrated gene.
  • a system having a tissue-specific promoter sequence in the template RNA may also be used in combination with a microRNA binding site, e.g., in the template RNA or a nucleic acid encoding a gene modifying protein, e.g., as described herein.
  • a system having a tissue-specific promoter sequence in the template RNA may also be used in combination with a DNA encoding a gene modifying polypeptide, driven by a tissue-specific promoter, e.g., to achieve higher levels of gene modifying protein in target cells than in non-target cells.
  • a heterologous object sequence comprised by a template RNA (or DNA encoding the template RNA) is operably linked to at least one regulatory sequence.
  • the heterologous object sequence is operably linked to a tissue-specific promoter, such that expression of the heterologous object sequence, e.g., a therapeutic protein, is upregulated in target cells, as above.
  • the heterologous object sequence is operably linked to a miRNA binding site, such that expression of the heterologous object sequence, e.g., a therapeutic protein, is downregulated in cells with higher levels of the corresponding miRNA, e.g., non-target cells, as above.
  • the template RNA comprises a microRNA sequence, a siRNA sequence, a guide RNA sequence, a piwi RNA sequence.
  • the template RNA comprises a non-coding heterologous object sequence, e.g., a regulatory sequence.
  • integration of the heterologous object sequence thus alters the expression of an endogenous gene.
  • integration of the heterologous object sequence upregulates expression of an endogenous gene.
  • integration of the heterologous object sequence downregulated expression of an endogenous gene.
  • the template RNA comprises a site that coordinates epigenetic modification.
  • the template RNA comprises an element that inhibits, e.g., prevents, epigenetic silencing.
  • the template RNA comprises a chromatin insulator.
  • the template RNA comprises a CTCF site or a site targeted for DNA methylation.
  • the template RNA may include features that prevent or inhibit gene silencing. In some embodiments, these features prevent or inhibit DNA methylation. In some embodiments, these features promote DNA demethylation. In some embodiments, these features prevent or inhibit histone deacetylation. In some embodiments, these features prevent or inhibit histone methylation. In some embodiments, these features promote histone acetylation. In some embodiments, these features promote histone demethylation. In some embodiments, multiple features may be incorporated into the template RNA to promote one or more of these modifications. CpG dinculeotides are subject to methylation by host methyl transferases.
  • the template RNA is depleted of CpG dinucleotides, e.g., does not comprise CpG nucleotides or comprises a reduced number of CpG dinucleotides compared to a corresponding unaltered sequence.
  • the promoter driving transgene expression from integrated DNA is depleted of CpG dinucleotides.
  • the template RNA comprises a gene expression unit composed of at least one regulatory region operably linked to an effector sequence.
  • the effector sequence may be a sequence that is transcribed into RNA (e.g., a coding sequence or a non-coding sequence such as a sequence encoding a micro RNA).
  • the object sequence of the template RNA is inserted into a target genome in an endogenous intron. In some embodiments, the object sequence of the template RNA is inserted into a target genome and thereby acts as a new exon. In some embodiments, the insertion of the object sequence into the target genome results in replacement of a natural exon or the skipping of a natural exon.
  • the object sequence of the template RNA is inserted into the target genome in a genomic safe harbor site, such as AAVS1, CCR5, or ROSA26. In some embodiments, the object sequence of the template RNA is inserted into the albumin locus. In some embodiments, the object sequence of the template RNA is inserted into the TRAC locus. In some embodiments, the object sequence of the template RNA is added to the genome in an intergenic or intragenic region.
  • the object sequence of the template RNA is added to the genome 5’ or 3’ within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb of an endogenous active gene.
  • the object sequence of the template RNA is added to the genome 5’ or 3’ within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb of an endogenous promoter or enhancer.
  • the object sequence of the template RNA can be, e.g., 50-50,000 base pairs (e.g., between 50- 40,000 bp, between 500-30,000 bp between 500-20,000 bp, between 100-15,000 bp, between 500-10,000 bp, between 50-10,000 bp, between 50-5,000 bp.
  • the heterologous object sequence is less than 1,000, 1,300, 1500, 2,000, 3,000, 4,000, 5,000, or 7,500 nucleotides in length.
  • the template nucleic acid (e.g., template RNA) component of a gene modifying system described herein typically is able to bind the gene modifying protein of the system.
  • the template nucleic acid (e.g., template RNA) has a 3’ region that is capable of binding a gene modifying protein.
  • the binding region e.g., 3’ region, may be a structured RNA region, e.g., having at least 1, 2 or 3 hairpin loops, capable of binding the gene modifying protein of the system.
  • the binding region may associate the template nucleic acid (e.g., template RNA) with any of the polypeptide modules.
  • the binding region of the template nucleic acid may associate with an RNA-binding domain in the polypeptide.
  • the binding region of the template nucleic acid may associate with the reverse transcription domain of the polypeptide (e.g., specifically bind to the RT domain).
  • the template nucleic acid e.g., template RNA
  • the template nucleic acid may contain a binding region derived from a non-LTR retrotransposon, e.g., a 3’ UTR from a non-LTR retrotransposon.
  • a system or method described herein comprises a single template nucleic acid (e.g., template RNA). In some embodiments a system or method described herein comprises a plurality of template nucleic acids (e.g., template RNAs). In some embodiments, when the system comprises a plurality of nucleic acids, each nucleic acid comprises a conjugating domain. In some embodiments, a conjugating domain enables association of nucleic acid molecules, e.g., by hybridization of complementary sequences.
  • the template nucleic acid may comprise one or more UTRs (e.g., a 5’ UTR or a 3’ UTR, e.g., from an R2-type retrotransposon).
  • the UTR facilitates interaction of the template with the reverse transcriptase domain of the polypeptide.
  • the template possesses one or more sequences aiding in association of the template with the gene modifying polypeptide. In some embodiments, these sequences may be derived from retrotransposon UTRs.
  • the UTRs may be located flanking the desired insertion sequence. In some embodiments, a sequence with target site homology may be located outside of one or both UTRs.
  • the sequence with target site homology can anneal to the target sequence to prime reverse transcription.
  • the 5’ and/or 3’ UTR may be located terminal to the target site homology sequence.
  • the gene modifying system may result in the insertion of a desired payload without any additional sequence (e.g., a gene expression unit without UTRs used to bind the gene modifying protein).
  • the template nucleic acid (e.g., template RNA) can be designed to result in insertions, mutations, or deletions at the target DNA locus.
  • the template nucleic acid (e.g., template RNA) may be designed to cause an insertion in the target DNA.
  • the template nucleic acid e.g., template RNA
  • the RNA template may be designed to write a deletion into the target DNA.
  • the template nucleic acid may match the target DNA upstream and downstream of the desired deletion, wherein the reverse transcription will result in the copying of the upstream and downstream sequences from the template nucleic acid (e.g., template RNA) without the intervening sequence, e.g., causing deletion of the intervening sequence.
  • the template nucleic acid e.g., template RNA
  • the template nucleic acid may be designed to write an edit into the target DNA.
  • the template RNA may match the target DNA sequence with the exception of one or more nucleotides, wherein the reverse transcription will result in the copying of these edits into the target DNA, e.g., resulting in mutations, e.g., transition or transversion mutations.
  • a gene modifying system is capable of producing an insertion into the target site of at least 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides (and optionally no more than 500, 400, 300, 200, or 100 nucleotides). In some embodiments, a gene modifying system is capable of producing an insertion into the target site of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides (and optionally no more than 500, 400, 300, 200, or 100 nucleotides).
  • a gene modifying system is capable of producing an insertion into the target site of at least 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 kilobases (and optionally no more than 1, 5, 10, or 20 kilobases).
  • a gene modifying system is capable of producing a deletion of at least 81, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides).
  • a gene modifying system is capable of producing a deletion of at least 81, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides). In some embodiments, a gene modifying system is capable of producing a deletion of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides).
  • a gene modifying system is capable of producing a deletion of at least 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 kilobases (and optionally no more than 1, 5, 10, or 20 kilobases).
  • RNA e.g., template RNA
  • an RNA component of the system (e.g., a template RNA, as described herein) comprises one or more nucleotide modifications.
  • the modification pattern of the template RNA can significantly affect in vivo activity compared to unmodified or end-modified guides. Without wishing to be bound by theory, this process may be due, at least in part, to a stabilization of the RNA conferred by the modifications.
  • Nonlimiting examples of such modifications may include 2'-O-methyl (2'-O-Me), 2'-O-(2- methoxy ethyl) (2'-0-M0E), 2'- fluoro (2'-F), phosphorothioate (PS) bond between nucleotides, G-C substitutions, and inverted abasic linkages between nucleotides and equivalents thereof.
  • the template RNA (e.g., at the portion thereof that binds a target site) comprises a 5' terminus region. In some embodiments, the template RNA does not comprise a 5' terminus region. In some embodiments, the 5' terminus region comprises a 5' end modification. In some embodiments, the template RNA comprises a 2'-O-methyl (2'-0-Me) modified nucleotide. In some embodiments, the template RNA comprises a 2'-O-(2 -methoxy ethyl) (2'-O-moe) modified nucleotide. In some embodiments, the template RNA comprises a 2'-fluoro (2'- F) modified nucleotide.
  • the template RNA comprises a phosphorothioate (PS) bond between nucleotides.
  • the template RNA comprises a 5' end modification, a 3' end modification, or 5' and 3' end modifications.
  • the 5' end modification comprises a phosphorothioate (PS) bond between nucleotides.
  • the 5' end modification comprises a 2'-O-methyl (2'-O- Me), 2'-O-(2 -methoxy ethyl) (2'-0-M0E), and/or 2'-fluoro (2'-F) modified nucleotide.
  • the 5' end modification comprises at least one phosphorothioate (PS) bond and one or more of a 2'-O-methyl (2'-O- Me), 2'-O-(2-methoxy ethyl) (2'-0-M0E), and/or 2'-fluoro (2'-F) modified nucleotide.
  • the end modification may comprise a phosphorothioate (PS), 2'- O-methyl (2'-O-Me) , 2'-O-(2- methoxyethyl) (2'-0-M0E), and/or 2'-fluoro (2'-F) modification.
  • Equivalent end modifications are also encompassed by embodiments described herein.
  • the template RNA comprises an end modification in combination with a modification of one or more regions of the template RNA.
  • structure-guided and systematic approaches are used to introduce modifications (e.g., 2'-OMe-RNA, 2'-F-RNA, and PS modifications) to a template RNA, for example, as described in Mir et al. Nat Commun 9:2641 (2016) (incorporated by reference herein in its entirety).
  • the incorporation of 2'-F-RNAs increases thermal and nuclease stability of RNA:RNA or RNA:DNA duplexes, e.g., while minimally interfering with C3'-endo sugar puckering.
  • 2'-F may be better tolerated than 2'-0Me at positions where the 2'-OH is important for RNA:DNA duplex stability.
  • structure-guided and systematic approaches e.g., as described in Mir et al. Nat Commun 9:2641 (2016); incorporated herein by reference in its entirety
  • a structure of polypeptide bound to template RNA is used to determine non-protein-contacted nucleotides of the RNA that may then be selected for modifications, e.g., with lower risk of disrupting the association of the RNA with the polypeptide.
  • Secondary structures in a template RNA can also be predicted in silico by software tools, e.g., the RNAstructure tool available at ma.urmc.rochester.edu/RNAstructureWeb (Bellaousov et al. Nucleic Acids Res 4LW471- W474 (2013); incorporated by reference herein in its entirety), e.g., to determine secondary structures for selecting modifications, e.g., hairpins, stems, and/or bulges.
  • software tools e.g., the RNAstructure tool available at ma.urmc.rochester.edu/RNAstructureWeb (Bellaousov et al. Nucleic Acids Res 4LW471- W474 (2013); incorporated by reference herein in its entirety), e.g., to determine secondary structures for selecting modifications, e.g., hairpins, stems, and/or bulges.
  • a gene modifying system comprises one or more circular RNAs (circRNAs).
  • a gene modifying system comprises one or more linear RNAs.
  • a nucleic acid as described herein e.g., a template nucleic acid, a nucleic acid molecule encoding a gene modifying polypeptide, or both
  • a circular RNA molecule encodes the gene modifying polypeptide.
  • the circRNA molecule encoding the gene modifying polypeptide is delivered to a host cell.
  • the circRNA molecule encoding the gene modifying polypeptide is linearized (e.g., in the host cell, e.g., in the nucleus of the host cell) prior to translation. Circular RNAs are described, e.g., at p. 1215-1218 of PCT Pub. No. WO/2021/178720.
  • compositions and methods for the assembly of full or partial template RNA molecules are described, e.g., at p. 1 ISO- 1155 of PCT Pub. No. WO/2021/178720. Additional Template Features
  • the template (e.g., template RNA) comprises certain structural features, e.g., determined in silico.
  • the template RNA is predicted to have minimal energy structures between -280 and -480 kcal/mol (e.g., between -280 to -300, -300 to -350, -350 to -400, -400 to -450, or -450 to -480 kcal/mol), e.g., as measured by RNAstructure, e.g., as described in Turner and Mathews Nucleic Acids Res 38:D280-282 (2009) (incorporated herein by reference in its entirety).
  • the template (e.g., template RNA) comprises certain structural features, e.g., determined in vitro.
  • the template RNA is sequence optimized, e.g., to reduce secondary structure as determined in vitro, for example, by SHAPE-MaP (e.g., as described in Siegfried et al. Nat Methods 11 :959-965 (2014); incorporated herein by reference in its entirety).
  • the template (e.g., template RNA) comprises certain structural features, e.g., determined in cells.
  • the template RNA is sequence optimized, e.g., to reduce secondary structure as measured in cells, for example, by DMS-MaPseq (e.g., as described in Zubradt et al. Nat Methods 14:75-82 (2017); incorporated by reference herein in its entirety).
  • a gene modifying system as described herein may, in some instances, be characterized by one or more functional measurements or characteristics.
  • the DNA binding domain has one or more of the functional characteristics described below.
  • the RNA binding domain has one or more of the functional characteristics described below.
  • the endonuclease domain has one or more of the functional characteristics described below.
  • the reverse transcriptase domain has one or more of the functional characteristics described below.
  • the template e.g., template RNA
  • the target site bound by the gene modifying polypeptide has one or more of the functional characteristics described below.
  • the DNA binding domain is capable of binding to a target sequence (e.g., a dsDNA target sequence) with greater affinity than a reference DNA binding domain.
  • the reference DNA binding domain is a DNA binding domain from R2 BM of B. mori.
  • the DNA binding domain is capable of binding to a target sequence (e.g., a dsDNA target sequence) with an affinity between 100 pM - 10 nM (e.g., between 100 pM-1 nM or 1 nM - 10 nM).
  • the affinity of a DNA binding domain for its target sequence is measured in vitro, e.g., by thermophoresis, e.g., as described in Asmari et al. Methods 146: 107-119 (2016) (incorporated by reference herein in its entirety).
  • the DNA binding domain is capable of binding to its target sequence (e.g., dsDNA target sequence), e.g, with an affinity between 100 pM - 10 nM (e.g., between 100 pM-1 nM or 1 nM - 10 nM) in the presence of a molar excess of scrambled sequence competitor dsDNA, e.g., of about 100-fold molar excess.
  • target sequence e.g., dsDNA target sequence
  • the DNA binding domain is found associated with its target sequence (e.g., dsDNA target sequence) more frequently than any other sequence in the genome of a target cell, e.g., human target cell, e.g., as measured by ChlP-seq (e.g., in HEK293T cells), e.g., as described in He and Pu (2010) Curr. Protoc Mol Biol Chapter 21 (incorporated herein by reference in its entirety).
  • target sequence e.g., dsDNA target sequence
  • human target cell e.g., as measured by ChlP-seq (e.g., in HEK293T cells), e.g., as described in He and Pu (2010) Curr. Protoc Mol Biol Chapter 21 (incorporated herein by reference in its entirety).
  • the DNA binding domain is found associated with its target sequence (e.g., dsDNA target sequence) at least about 5-fold or 10-fold, more frequently than any other sequence in the genome of a target cell, e.g., as measured by ChlP-seq (e.g., in HEK293T cells), e.g., as described in He and Pu (2010), supra.
  • target sequence e.g., dsDNA target sequence
  • ChlP-seq e.g., in HEK293T cells
  • a gene modifying polypeptide comprises a modification to a DNA-binding domain, e.g., relative to the wild-type polypeptide.
  • the DNA-binding domain comprises an addition, deletion, replacement, or modification to the amino acid sequence of the original DNA-binding domain.
  • the DNA- binding domain is modified to include a heterologous functional domain that binds specifically to a target nucleic acid (e.g., DNA) sequence of interest.
  • the functional domain replaces at least a portion (e.g., the entirety of) the prior DNA-binding domain of the polypeptide.
  • a gene modifying polypeptide comprises a modification to an endonuclease domain, e.g., relative to the wild-type polypeptide.
  • the endonuclease domain comprises an addition, deletion, replacement, or modification to the amino acid sequence of the original endonuclease domain.
  • the endonuclease domain is modified to include a heterologous functional domain that binds specifically to and/or induces endonuclease cleavage of a target nucleic acid (e.g., DNA) sequence of interest.
  • the RNA binding domain is capable of binding to a template RNA with greater affinity than a reference RNA binding domain.
  • the reference RNA binding domain is an RNA binding domain from R2 BM of B. mori.
  • the RNA binding domain is capable of binding to a template RNA with an affinity between 100 pM - 10 nM (e.g., between 100 pM-1 nM or 1 nM - 10 nM).
  • the affinity of a RNA binding domain for its template RNA is measured in vitro, e.g., by thermophoresis, e.g., as described in Asmari et al. Methods 146: 107-119 (2016) (incorporated by reference herein in its entirety).
  • the affinity of a RNA binding domain for its template RNA is measured in cells (e.g., by FRET or CLIP-Seq).
  • the RNA binding domain is associated with the template RNA in vitro at a frequency at least about 5-fold or 10-fold higher than with a scrambled RNA.
  • the frequency of association between the RNA binding domain and the template RNA or scrambled RNA is measured by CLIP-seq, e.g., as described in Lin and Miles (2019) Nucleic Acids Res 47(11):5490-5501 (incorporated by reference herein in its entirety).
  • the RNA binding domain is associated with the template RNA in cells (e.g., in HEK293T cells) at a frequency at least about 5-fold or 10-fold higher than with a scrambled RNA.
  • the frequency of association between the RNA binding domain and the template RNA or scrambled RNA is measured by CLIP-seq, e.g., as described in Lin and Miles (2019), supra.
  • the endonuclease domain is associated with the target dsDNA in vitro at a frequency at least about 5-fold or 10-fold higher than with a scrambled dsDNA. In some embodiments, the endonuclease domain is associated with the target dsDNA in vitro at a frequency at least about 5-fold or 10-fold higher than with a scrambled dsDNA, e.g., in a cell (e.g., a HEK293T cell). In some embodiments, the frequency of association between the endonuclease domain and the target DNA or scrambled DNA is measured by ChlP-seq, e.g., as described in He and Pu (2010) Curr. ProtocMol Biol Chapter 21 (incorporated by reference herein in its entirety).
  • the endonuclease domain can catalyze the formation of a nick at a target sequence, e.g., to an increase of at least about 5-fold or 10-fold relative to a nontarget sequence (e.g., relative to any other genomic sequence in the genome of the target cell).
  • the level of nick formation is determined using NickSeq, e.g., as described in Elacqua et al. (2019) bioRxiv doi.org/10.1101/867937 (incorporated herein by reference in its entirety).
  • the endonuclease domain is capable of nicking DNA in vitro.
  • the nick results in an exposed base.
  • the exposed base can be detected using a nuclease sensitivity assay, e.g., as described in Chaudhry and Weinfeld (1995) Nucleic Acids Res 23(19):3805-3809 (incorporated by reference herein in its entirety).
  • the level of exposed bases e.g., detected by the nuclease sensitivity assay
  • the reference endonuclease domain is an endonuclease domain from R2 BM of B. mori.
  • the endonuclease domain is capable of nicking DNA in a cell. In embodiments, the endonuclease domain is capable of nicking DNA in a HEK293T cell.
  • an unrepaired nick that undergoes replication in the absence of Rad51 results in increased NHEJ rates at the site of the nick, which can be detected, e.g., by using a Rad51 inhibition assay, e.g., as described in Bothmer et al. (2017) Nat Commun 8: 13905 (incorporated by reference herein in its entirety).
  • NHEJ rates are increased above 0-5%. In embodiments, NHEJ rates are increased to 20-70% (e.g., between 30%-60% or 40-50%), e.g., upon Rad51 inhibition.
  • the endonuclease domain releases the target after cleavage.
  • release of the target is indicated indirectly by assessing for multiple turnovers by the enzyme, e.g., as described in Yourik at al. RNA 25(l):35-44 (2019) (incorporated herein by reference in its entirety) and shown in Figure 2.
  • the kexp of an endonuclease domain is 1 x 10' 3 - 1 x 10'5 min-1 as measured by such methods.
  • the endonuclease domain has a catalytic efficiency (& C at/Am) greater than about 1 x 10 8 s' 1 M' 1 in vitro. In embodiments, the endonuclease domain has a catalytic efficiency greater than about 1 x 10 5 , 1 x 10 6 , 1 x 10 7 , or 1 x 10 8 , s' 1 M' 1 in vitro. In embodiments, catalytic efficiency is determined as described in Chen et al. (2016) Science 360(6387):436-439 (incorporated herein by reference in its entirety).
  • the endonuclease domain has a catalytic efficiency (& C at/Am) greater than about 1 x 10 8 s' 1 M' 1 in cells. In embodiments, the endonuclease domain has a catalytic efficiency greater than about 1 x 10 5 , 1 x 10 6 , 1 x 10 7 , or 1 x 10 8 s' 1 M' 1 in cells.
  • the reverse transcriptase domain has a lower probability of premature termination rate (Poff) in vitro relative to a reference reverse transcriptase domain.
  • the reference reverse transcriptase domain is a reverse transcriptase domain from R2 BM of B. mori or a viral reverse transcriptase domain, e.g., the RT domain from M-MLV.
  • the reverse transcriptase domain has a lower probability of premature termination rate ( off) in vitro of less than about 5 x 10' 3 /nt, 5 x 10' 4 /nt, or 5 x 10" 6 /nt, e.g., as measured on a 1094 nt RNA.
  • the in vitro premature termination rate is determined as described in Bibillo and Eickbush (2002) J Biol Chem 277(38):34836- 34845 (incorporated by reference herein its entirety).
  • the reverse transcriptase domain is able to complete at least about 30% or 50% of integrations in cells.
  • the percent of complete integrations can be measured by dividing the number of substantially full-length integration events (e.g., genomic sites that comprise at least 98% of the expected integrated sequence) by the number of total (including substantially full-length and partial) integration events in a population of cells.
  • the integrations in cells is determined (e.g., across the integration site) using long-read amplicon sequencing, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety).
  • quantifying integrations in cells comprises counting the fraction of integrations that contain at least about 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of the DNA sequence corresponding to the template RNA (e.g., a template RNA having a length of at least 0.05, 0.1, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 3, 4, or 5 kb, e.g., a length between 0.5-0.6, 0.6-0.7, 0.7-0.8, 0.8-0.9, 1.0-1.2, 1.2-1.4, 1.4-1.6, 1.6-1.8, 1.8-2.0, 2-3, 3-4, or 4-5 kb).
  • the template RNA e.g., a template RNA having a length of at least 0.05, 0.1, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 3, 4, or 5 kb, e.g., a length between 0.5-0.6, 0.6-0.7, 0.7
  • the reverse transcriptase domain is capable of polymerizing dNTPs in vitro.
  • the reverse transcriptase domain is capable of polymerizing dNTPs in vitro at a rate between 0.1 - 50 nt/sec (e.g., between 0.1-1, 1-10, or 10-50 nt/sec).
  • polymerization of dNTPs by the reverse transcriptase domain is measured by a single-molecule assay, e.g., as described in Schwartz and Quake (2009) PNAS 106(48):20294- 20299 (incorporated by reference in its entirety).
  • the reverse transcriptase domain has an in vitro error rate (e.g., misincorporation of nucleotides) of between 1 x 10' 3 - 1 x 10' 4 or 1 x 10' 4 - 1 x 10' 5 substitutions/nt , e.g., as described in Yasukawa et al. (2017) Biochem Biophys Res Commun 492(2): 147-153 (incorporated herein by reference in its entirety).
  • in vitro error rate e.g., misincorporation of nucleotides
  • the reverse transcriptase domain has an error rate (e.g., misincorporation of nucleotides) in cells (e.g., HEK293T cells) of between 1 x 10' 3 - l x 10' 4 or 1 x 10' 4 - l x 10' 5 substitutions/nt, e.g., by long-read amplicon sequencing, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety).
  • error rate e.g., misincorporation of nucleotides
  • the reverse transcriptase domain is capable of performing reverse transcription of a target RNA in vitro.
  • the reverse transcriptase requires a primer of at least 3 nt to initiate reverse transcription of a template.
  • reverse transcription of the target RNA is determined by detection of cDNA from the target RNA (e.g., when provided with a ssDNA primer, e.g., which anneals to the target with at least 3, 4, 5, 6, 7, 8, 9, or 10 nt at the 3’ end), e.g., as described in Bibillo and Eickbush (2002) J Biol Chem 277(38):34836-34845 (incorporated herein by reference in its entirety).
  • the reverse transcriptase domain performs reverse transcription at least 5 or 10 times more efficiently (e.g., by cDNA production), e.g., when converting its RNA template to cDNA, for example, as compared to an RNA template lacking the protein binding motif (e.g., a 3’ UTR).
  • efficiency of reverse transcription is measured as described in Yasukawa et al. (2017) Biochem Biophys Res Commun 492(2): 147- 153 (incorporated by reference herein in its entirety).
  • the reverse transcriptase domain specifically binds a specific RNA template with higher frequency (e.g., about 5 or 10-fold higher frequency) than any endogenous cellular RNA, e.g., when expressed in cells (e.g., HEK293T cells).
  • frequency of specific binding between the reverse transcriptase domain and the template RNA are measured by CLIP-seq, e.g., as described in Lin and Miles (2019) Nucleic Acids Res 47(11):5490-5501 (incorporated herein by reference in its entirety).
  • the target site surrounding the integrated sequence contains a limited number of insertions or deletions, for example, in less than about 50% or 10% of integration events, e.g., as determined by long-read amplicon sequencing of the target site, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety).
  • the target site does not show multiple insertion events, e.g., head-to-tail or head-to-head duplications, e.g., as determined by long-read amplicon sequencing of the target site, e.g., as described in Karst et al.
  • the target site contains an integrated sequence corresponding to the template RNA.
  • the target site does not contain insertions resulting from endogenous RNA in more than about 1% or 10% of events, e.g., as determined by long-read amplicon sequencing of the target site, e.g., as described in Karst et al. bioRxiv doi.org/10.1101/645903 (2020) (incorporated herein by reference in its entirety).
  • the target site contains the integrated sequence corresponding to the template RNA.
  • the target site contains an integrated sequence corresponding to the template RNA.
  • the target site does not comprise sequence outside of the template, e.g., as determined by long-read amplicon sequencing of the target site (for example, as described in Karst et al. bioRxiv doi.org/10.1101/645903 (2020); incorporated herein by reference in its entirety).
  • DNA Damage Response for example, as described in Karst et al. bioRxiv doi.org/10.1101/645903 (2020); incorporated herein by reference in its entirety.
  • modifying a genome of a cell does not result in activation of the endogenous DNA damage response (DDR) pathway.
  • modifying a genome of a cell (e.g., a primary cell) using a gene modifying system results in activation of the cell’s endogenous DDR pathway less than in an otherwise similar cell treated with Cas9.
  • modifying a genome of a cell does not result in activation of the endogenous interferon response.
  • modifying a genome of a cell using a gene modifying system results in activation of the cell’s interferon response less than in an otherwise similar cell treated with a gene modifying system comprising elements from a LINE-1 retrotransposase.
  • the gene modifying polypeptide systems described herein includes a self-inactivating module.
  • the self-inactivating module leads to a decrease of expression of the gene modifying polypeptide, the gene modifying template, or both.
  • Selfinactivating modules are described, e.g., at p. 1200-1201 of PCT Pub. No. WO/2021/178720.
  • a polypeptide described herein e.g., a gene modifying polypeptide
  • the polypeptide is dimerized via a small molecule.
  • Polypeptides of this type are described, e.g., at p. 1201-1203 of WO/2021/178720.
  • the conjugates (targeted LNPs) described herein can be formulated to comprise one or more components of a heterologous gene modifying system, or one or more nucleic acids encoding said components.
  • the payload comprises a heterologous gene modifying system, or one or more nucleic acids encoding the components of the heterologous gene modifying polypeptide.
  • the payload comprises a template RNA and an mRNA encoding the heterologous gene modifying polypeptide.
  • a heterologous gene modifying system may comprise a heterologous gene modifying polypeptide and a template RNA.
  • the heterologous gene modifying polypeptide may comprise an endonuclease domain, a DNA binding domain, a linker, and a reverse transcriptase domain derived from a retrovirus.
  • the heterologous gene modifying polypeptide may comprise a Cas domain, a linker, and a reverse transcriptase domain derived from a retrovirus.
  • the template RNA compatible with the heterologous gene modifying polypeptide may comprise (e.g., from 5' to 3') (i) a gRNA spacer that binds a target site, (ii) a gRNA scaffold that binds the heterologous gene modifying polypeptide, e.g., the Cas domain of the heterologous gene modifying polypeptide, (iii) a heterologous object sequence, and (iv) a primer binding site (PBS) sequence.
  • a gRNA spacer that binds a target site
  • a gRNA scaffold that binds the heterologous gene modifying polypeptide, e.g., the Cas domain of the heterologous gene modifying polypeptide
  • PBS primer binding site
  • a heterologous gene modifying polypeptide described herein comprises (e.g., a system described herein comprises a gene modifying polypeptide that comprises): 1) a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); 2) a reverse transcriptase (RT) domain, wherein the RT domain is C-terminal of the Cas domain; and a linker disposed between the RT domain and the Cas domain.
  • a Cas domain e.g., a Cas nickase domain, e.g., a Cas9 nickase domain
  • RT reverse transcriptase
  • the heterologous gene modifying polypeptide comprises a sequence of SEQ ID NO: 4000 which comprises the first NLS and the Cas domain, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.
  • the heterologous gene modifying polypeptide comprises a sequence of SEQ ID NO: 4001 which comprises the second NLS, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.
  • a heterologous gene modifying polypeptide described herein comprises an RT domain having an amino acid sequence according to Table 6 of International Application WO/2023/039440 (which Table is incorporated herein by reference in its entirety), or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.
  • a heterologous gene modifying polypeptide comprises: (i) a linker comprising a linker sequence as listed in a row of Table 11, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto; and (ii) an RT domain comprising an RT domain sequence as listed in the same row of Table 11, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.
  • a heterologous gene modifying polypeptide comprises an amino acid sequence according to Table 12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. Table 11. Selection of exemplary gene modifying polypeptides Table 12. Full length amino acid sequence corresponding to Table 11
  • the heterologous gene modifying polypeptide has a sequence disclosed in International Application WO/2023/039424 (which is incorporated by reference herein in its entirety), or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.
  • the heterologous gene modifying polypeptide has an RT domain as described in Table 6 of International Application WO/2023/039424 (which table is incorporated by reference herein in its entirety), or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.
  • a heterologous gene modifying polypeptide may comprise a linker, e.g., a peptide linker, e.g., a linker as described in Table 10 of International Application WO/2023/039424 (which Table is incorporated herein by reference in its entirety).
  • the heterologous gene modifying polypeptide has a sequence according to Table T2 of International Application WO/2023/039424 (which table is incorporated by reference herein in its entirety), or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.
  • the heterologous gene modifying polypeptide has a sequence according to Table Al of International Application WO/2023/039424 (which table is incorporated by reference herein in its entirety), or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.
  • a gene modifying polypeptide comprises the RT domain from a retroviral reverse transcriptase, e.g., an M-MLV RT, e.g., comprising the following sequence:
  • an M-MLV RT domain comprises, relative to the M-MLV (WT) sequence above, one or more mutations, e.g., selected from D200N, L603W, T330P, T306K, W313F, D524G, E562Q, D583N, P51L, S67R, E67K, T197A, H204R, E302K, F309N, L435G, N454K, H594Q, D653N, R110S, K103L, e.g., a combination of mutations, such as D200N, L603W, and T330P, optionally further including T306K and W313F.
  • an M-MLV RT used herein comprises the mutations D200N, L603W, T330P, T306K and W313F.
  • the mutant M-MLV RT comprises the following amino acid sequence:
  • Exemplary gene modifying system comprises mutant M-MLV RT region:
  • the heterologous gene modifying polypeptide comprises an amino acid sequence according to SEQ ID NO: 4002, or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.
  • a template RNA molecule for use in the system comprises, from 5' to 3' (1) a gRNA spacer; (2) a gRNA scaffold; (3) heterologous object sequence (4) a primer binding site (PBS) sequence.
  • PBS primer binding site
  • the gRNA scaffold comprises one or more hairpin loops, e.g., 1, 2, of 3 loops for associating the template with a Cas domain, e.g., a nickase Cas9 domain.
  • the gRNA scaffold comprises the sequence, from 5' to 3', GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC TTGAAAAAGTGGGACCGAGTCGGTCC (SEQ ID NO: 88).
  • the heterologous object sequence is, e.g., 7-74, e.g., 10-20, 20- 30, 30-40, 40-50, 50-60, 60-70, or 70-80 nt or, 80-90 nt in length.
  • the PBS sequence that binds the target priming sequence after nicking occurs is e.g., 3-20 nt, e.g., 7-15 nt, e.g., 12-14 nt. In some embodiments, the PBS sequence has 40-60% GC content.
  • Lipid nanoparticles that are conjugated targeting moieties in a site-specific manner through specific enzyme-recognized linkers, as disclosed herein.
  • Lipid nanoparticles in some embodiments, comprise one or more ionic lipids, such as non-cationic lipids (e.g., neutral or anionic, or zwitterionic lipids); one or more conjugated lipids (such as PEG-conjugated lipids or lipids conjugated to polymers described in Table 5 of WO2019217941; incorporated herein by reference in its entirety); one or more sterols (e.g., cholesterol); or combinations of the foregoing.
  • ionic lipids such as non-cationic lipids (e.g., neutral or anionic, or zwitterionic lipids)
  • conjugated lipids such as PEG-conjugated lipids or lipids conjugated to polymers described in Table 5 of WO2019217941; incorporated herein by reference in its entirety
  • Lipids that can be used in nanoparticle formations include, for example those described in Table 4 of US20210371858, which is incorporated by reference — e.g., a lipid-containing nanoparticle can comprise one or more of the lipids in Table 4 of US20210371858.
  • Lipid nanoparticles can include additional elements, such as polymers, such as the polymers described in Table 5 of US20210371858, incorporated by reference.
  • conjugated lipids when present, can include one or more of PEG-diacylglycerol (DAG) (such as l-(m onom ethoxy-poly ethyleneglycol)-2, 3- dimyristoylglycerol (PEG-DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG- ceramide (Cer), a pegylated phosphatidylethanoloamine (PEG-PE), PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0-(2',3'-di(tetradecanoyloxy)propyl-l-0-(w- methoxy(polyethoxy)ethyl) butanedioate (PEG-S-DMG)), PEG dialkoxypropylcarbam, N- (carbonyl-methoxypoly ethylene glycol 2000)- 1 ,2-
  • DAG PEG-di
  • sterols that can be incorporated into lipid nanoparticles include one or more of cholesterol or cholesterol derivatives, such as those in US11141378 or US2010/0130588, which are incorporated by reference. Additional exemplary sterols include phytosterols, including those described in Eygeris et al (2020), dx.doi.org/10.1021/acs.nanolett.0c01386, incorporated herein by reference.
  • the lipid particle comprises an ionizable lipid, a non-cationic lipid, a conjugated lipid that inhibits aggregation of particles, and a sterol.
  • the amounts of these components can be varied independently and to achieve desired properties.
  • the lipid nanoparticle comprises an ionizable lipid is in an amount from about 20 mol % to about 90 mol % of the total lipids (in other embodiments it may be 20-70% (mol), 30-60% (mol) or 40-50% (mol); about 50 mol % to about 90 mol % of the total lipid present in the lipid nanoparticle), a non-cationic lipid in an amount from about 5 mol % to about 30 mol % of the total lipids, a conjugated lipid in an amount from about 0.5 mol % to about 20 mol % of the total lipids, and a sterol in an amount from about 20 mol % to about 50 mol % of the total lipids.
  • the ratio of total lipid to nucleic acid can be varied as desired.
  • the total lipid to nucleic acid (mass or weight) ratio can be from about 10: 1 to about 30: 1.
  • the lipid to nucleic acid ratio (mass/mass ratio; w/w ratio) can be in the range of from about 1 : 1 to about 25: 1, from about 10: 1 to about 14: 1, from about 3 : 1 to about 15: 1, from about 4: 1 to about 10: 1, from about 5: 1 to about 9: 1, or about 6: 1 to about 9: 1.
  • the amounts of lipids and nucleic acid can be adjusted to provide a desired N/P ratio, for example, N/P ratio of 3, 4, 5, 6, 7, 8, 9, 10 or higher.
  • the lipid nanoparticle formulation’s overall lipid content can range from about 5 mg/ml to about 30 mg/mL.
  • lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the conjugates described herein, include a lipid of any one of formulas (i)-(ix).
  • lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the conjugates described herein, include a lipid of formula (x): wherein
  • X 1 is O, NR 1 , or a direct bond
  • X 2 is C2-5 alkylene
  • R 1 is H or Me
  • R 3 is Cl -3 alkyl
  • R 2 is Cl -3 alkyl
  • R 2 is taken together with the nitrogen atom to which it is attached and 1-3 carbon atoms of X 2 to form a 4-, 5-, or 6-membered ring
  • X 1 is NR 1
  • R 1 and R 2 are taken together with the nitrogen atoms to which they are attached form a 5- or 6-membered ring
  • R 2 is taken together with R 3 and the nitrogen atom to which they are attached form a 5-, 6-, or 7-membered ring
  • Y 1 is C2-12 alkylene
  • Y 2 is selected from
  • R 4 is Cl-15 alkyl
  • Z 1 is Cl-6 alkylene or a direct bond
  • R 5 is C5-9 alkyl or C6-10 alkoxy
  • R 6 is C5-9 alkyl or C6-10 alkoxy
  • W is methylene or a direct bond
  • R 4 is linear C5 alkyl
  • Z 1 is C2 alkylene
  • Z 2 is absent
  • W is methylene
  • R 7 is H
  • R 5 and R 6 are not Cx alkoxy.
  • lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the conjugates described herein, include a lipid of any one of the formulas (xii)-(xiv):
  • lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the conjugates described herein, include a lipid of formula (xv):
  • lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the conjugates described herein, include a lipid of formula (xvi):
  • lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the conjugates described herein, include a lipid of any one of the formulas (xvii)-(xix):
  • lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the conjugates described herein, include a lipid of any one of the formulas (xx)(a) or (xx)(b):
  • a conjugate described herein comprises an LNP that comprises an ionizable lipid.
  • the ionizable lipid is heptadecan-9-yl 8-((2- hydroxyethyl)(6-oxo-6-(undecyloxy)hexyl)amino)octanoate (SM-102); e.g., as described in Example 1 of US9,867,888 (incorporated by reference herein in its entirety).
  • the ionizable lipid is 9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3- (diethylamino)propoxy)carbonyl)oxy)methyl)propyl octadeca-9,12-di enoate (LP01), e.g., as synthesized in Example 13 of US 11420933 (incorporated by reference herein in its entirety).
  • the ionizable lipid is Di((Z)-non-2-en-l-yl) 9-((4- dimethylamino)butanoyl)oxy)heptadecanedioate (L319), e.g. as synthesized in Example 7, 8, or 9 of US2012/0027803 (incorporated by reference herein in its entirety).
  • the ionizable lipid is l,l'-((2-(4-(2-((2-(Bis(2-hydroxydodecyl)amino)ethyl)(2- hydroxy dodecyl) amino)ethyl)piperazin-l-yl)ethyl)azanediyl)bis(dodecan-2-ol) (Cl 2-200), e.g., as synthesized in Examples 14 and 16 of US8450298 (incorporated by reference herein in its entirety).
  • the ionizable lipid is Imidazole cholesterol ester (ICE) lipid (3S, 10R, 13R, 17R)-10, 13 -dimethyl -17- ((R)-6-methylheptan-2-yl)-2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17-tetradecahydro-lH- cyclopenta[a]phenanthren-3-yl 3-(lH-imidazol-4- yl)propanoate, e.g., Structure (I) from US 2022/0324926 (incorporated by reference herein in its entirety).
  • ICE Imidazole cholesterol ester
  • an ionizable lipid may be a cationic lipid, an ionizable cationic lipid, e.g., a cationic lipid that can exist in a positively charged or neutral form depending on pH, or an amine-containing lipid that can be readily protonated.
  • the cationic lipid is a lipid capable of being positively charged, e.g., under physiological conditions.
  • Exemplary cationic lipids include one or more amine group(s) which bear the positive charge.
  • the lipid particle comprises a cationic lipid in formulation with one or more of neutral lipids, ionizable amine-containing lipids, biodegradable alkyn lipids, steroids, phospholipids including polyunsaturated lipids, structural lipids (e.g., sterols), PEG, cholesterol and polymer conjugated lipids.
  • the cationic lipid may be an ionizable cationic lipid.
  • An exemplary cationic lipid as disclosed herein may have an effective pKa over 6.0.
  • a lipid nanoparticle may comprise a second cationic lipid having a different effective pKa (e.g., greater than the first effective pKa), than the first cationic lipid.
  • a lipid nanoparticle may comprise between 40 and 60 mol percent of a cationic lipid, a neutral lipid, a steroid, a polymer conjugated lipid, and a therapeutic agent, e.g., a nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a desired polypeptide), encapsulated within or associated with the lipid nanoparticle.
  • a nucleic acid e.g., RNA
  • the nucleic acid is co-formulated with the cationic lipid.
  • the nucleic acid may be adsorbed to the surface of an LNP, e.g., an LNP comprising a cationic lipid.
  • the nucleic acid may be encapsulated in an LNP, e.g., an LNP comprising a cationic lipid.
  • the lipid nanoparticle may comprise a targeting moiety, e.g., coated with a targeting agent.
  • the LNP formulation is biodegradable.
  • a lipid nanoparticle comprising one or more lipid described herein, e.g., Formula (i), (ii), (ii), (vii) and/or (ix) encapsulates at least 1%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98% or 100% of an RNA molecule, e.g., template RNA and/or a mRNA encoding a desired polypeptide.
  • RNA molecule e.g., template RNA and/or a mRNA encoding a desired polypeptide.
  • Exemplary ionizable lipids that can be used in the disclosed conjugates include, without limitation, those listed in Table 1 of US20210059953, incorporated herein by reference. Additional exemplary lipids include, without limitation, one or more of the following formulae: X of US2016/0311759; I of US20150376115 or in US2016/0376224; I, II or III of US20160151284; I, IA, II, or IIA of US20170210967; I-c of US20150140070; A of US2013/0178541; I of US2013/0303587 or US2013/0123338; I of US2015/0141678; II, III, IV, or V of US2015/0239926; I of US2017/0119904; I or II of WO2017/117528; A of US2012/0149894; A of US2015/0057373; A of WO2013/116126; A of US2013/0090372; A of US2013/0274523;
  • the ionizable lipid is MC3 (6Z,9Z,28Z,3 lZ)-heptatriaconta- 6,9,28,3 l-tetraen-19-yl-4-(dimethylamino) butanoate (DLin-MC3-DMA or MC3), e.g., as described in Example 9 of US2021/0059953 (incorporated by reference herein in its entirety).
  • the ionizable lipid is the lipid ATX-002, e.g., as described in Example 10 of US2021/0059953 (incorporated by reference herein in its entirety).
  • the ionizable lipid is (13Z,16Z)-A,A-dimethyl-3- nonyldocosa-13, 16-dien-l- amine (Compound 32), e.g., as described in Example 11 of US2021/0059953 (incorporated by reference herein in its entirety).
  • the ionizable lipid is Compound 6 or Compound 22, e.g., as described in Example 12 of US2021/0059953 (incorporated by reference herein in its entirety).
  • Exemplary non-cationic lipids include, but are not limited to, di stearoyl -sn-glycero- phosphoethanolamine, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl-phosphatidylethanolamine 4-(N-maleimidomethyl)-cyclohexane- 1 - carboxylate (DOPE-mal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimy
  • acyl groups in these lipids are preferably acyl groups derived from fatty acids having C10-C24 carbon chains, e.g., lauroyl, myristoyl, paimitoyl, stearoyl, or oleoyl.
  • Additional exemplary lipids include, without limitation, those described in Kim et al. (2020) dx.doi.org/10.1021/acs.nanolett.0c01386, incorporated herein by reference.
  • Such lipids include, in some embodiments, plant lipids found to improve liver transfection with mRNA (e g., DGTS).
  • non-cationic lipids suitable for use in the lipid nanoparticles include, without limitation, nonphosphorous lipids such as, e.g., stearylamine, dodeeylamine, hexadecylamine, acetyl palmitate, glycerol ricinoleate, hexadecyl stereate, isopropyl myristate, amphoteric acrylic polymers, triethanolamine-lauryl sulfate, alkyl-aryl sulfate polyethyloxylated fatty acid amides, dioctadecyl dimethyl ammonium bromide, ceramide, sphingomyelin, and the like.
  • non-cationic lipids are described in WO2017/099823 or US patent publication US2018/0028664, the contents of which is incorporated herein by reference in their entirety.
  • the non-cationic lipid is oleic acid or a compound of Formula I, II, or IV of US2018/0028664, incorporated herein by reference in its entirety.
  • the noncationic lipid can comprise, for example, 0-30% (mol) of the total lipid present in the lipid nanoparticle.
  • the non-cationic lipid content is 5-20% (mol) or 10-15% (mol) of the total lipid present in the lipid nanoparticle.
  • the molar ratio of ionizable lipid to the neutral lipid ranges from about 2: 1 to about 8: 1 (e.g., about 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, or 8: 1).
  • the lipid nanoparticles do not comprise any phospholipids.
  • the lipid nanoparticle can further comprise a component, such as a sterol, to provide membrane integrity.
  • a component such as a sterol
  • a sterol that can be used in the lipid nanoparticle is cholesterol and derivatives thereof.
  • cholesterol derivatives include polar analogues such as 5a-choiestanol, 53-coprostanol, cholesteryl-(2 - hydroxy)-ethyl ether, cholesteryl-(4'- hydroxy)-butyl ether, and 6-ketocholestanol; non-polar analogues such as 5a-cholestane, cholestenone, 5a-cholestanone, 5p-cholestanone, and cholesteryl decanoate; and mixtures thereof.
  • the cholesterol derivative is a polar analogue, e.g., dcholesterol-(4 '-hydroxy)-butyl ether.
  • a polar analogue e.g., dcholesterol-(4 '-hydroxy)-butyl ether.
  • Exemplary cholesterol derivatives are described in PCT publication W02009/127060 and US patent publication US2010/0130588, which is incorporated herein by reference in its entirety.
  • the component providing membrane integrity such as a sterol
  • such a component is 20-50% (mol) 30-40% (mol) of the total lipid content of the lipid nanoparticle.
  • the lipid nanoparticle can comprise a polyethylene glycol (PEG) or a conjugated lipid molecule. Generally, these are used to inhibit aggregation of lipid nanoparticles and/or provide steric stabilization.
  • PEG polyethylene glycol
  • exemplary conjugated lipids include, but are not limited to, PEG-lipid conjugates, polyoxazoline (POZ)-lipid conjugates, polyamide-lipid conjugates (such as ATTA-lipid conjugates), cationic-polymer lipid (CPL) conjugates, and mixtures thereof.
  • the conjugated lipid molecule is a PEG-lipid conjugate, for example, a (methoxy polyethylene glycol)-conjugated lipid.
  • Exemplary PEG-lipid conjugates include, but are not limited to, PEG-diacylglycerol (DAG) (such as l-(monomethoxy-polyethyleneglycol)-2,3-dimyristoylglycerol (PEG-DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG-ceramide (Cer), a pegylated phosphatidylethanoloamine (PEG-PE), PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0-(2',3'-di(tetradecanoyloxy)propyl-l-0-(w-methoxy(polyethoxy)ethyl) butanedioate (PEG-
  • DAG PEG-diacylglycerol
  • PEG-DMG PEG-dialkyloxypropyl
  • DAA PEG-phospholipid
  • PEG-ceramide Cer
  • PEG dialkoxypropylcarbam N-(carbonyl-methoxypolyethylene glycol 2000)4,2- distearoyl-sn-glycero-3-phosphoethanolamine sodium salt, or a mixture thereof.
  • Additional exemplary PEG-lipid conjugates are described, for example, in US5,885,613, US6,287,591, US2003/0077829, US2003/0077829, US2005/0175682, US2008/0020058, US2011/0117125, US2010/0130588, US2016/0376224, US2017/0119904, and US/099823, the contents of all of which are incorporated herein by reference in their entirety.
  • a PEG- lipid is a compound of Formula III, III-a-I, III-a-2, III-b-1, III-b-2, or V of US2018/0028664, the content of which is incorporated herein by reference in its entirety.
  • a PEG-lipid is of Formula II of US20150376115 or US2016/0376224, the content of both of which is incorporated herein by reference in its entirety.
  • the PEG-DAA conjugate can be, for example, PEG-dilauryloxypropyl, PEG- dimyristyloxypropyl, PEG-dipalmityloxypropyl, or PEG-distearyloxypropyl.
  • the PEG-lipid can be one or more of PEG-DMG, PEG-dilaurylglycerol, PEG-dipalmitoylglycerol, PEG- disterylglycerol, PEG-dilaurylglycamide, PEG-dimyristylglycamide, PEG- dipalmitoylglycamide, PEG-disterylglycamide, PEG-cholesterol (l-[8'-(Cholest-5-en-3[beta]- oxy)carboxamido-3',6'-dioxaoctanyl] carbamoyl-[omega]-methyl-poly(ethylene glycol), PEG- DMB (3,4-Ditetradecoxylbenzyl- [omega]-methyl-poly(ethylene glycol) ether), and 1,2- dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-
  • lipids conjugated with a molecule other than a PEG can also be used in place of PEG-lipid.
  • PEG-lipid conjugates polyoxazoline (POZ)-lipid conjugates, polyamidelipid conjugates (such as ATTA-lipid conjugates), and cationic-polymer lipid (GPL) conjugates can be used in place of or in addition to the PEG-lipid.
  • POZ polyoxazoline
  • GPL cationic-polymer lipid
  • conjugated lipids i.e., PEG-lipids, (POZ)-lipid conjugates, ATTA-lipid conjugates and cationic polymer-lipids are described in the PCT and LIS patent applications listed in Table 2 of US2021/0059953, the contents of all of which are incorporated herein by reference in its entirety.
  • the PEG or the conjugated lipid can comprise 0-20% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, PEG or the conjugated lipid content is 0.5- 10% or 2-5% (mol) of the total lipid present in the lipid nanoparticle. Molar ratios of the ionizable lipid, non-cationic-lipid, sterol, and PEG/conjugated lipid can be varied as needed.
  • the lipid particle can comprise 30-70% ionizable lipid by mole or by total weight of the composition, 0-60% cholesterol by mole or by total weight of the composition, 0-30% non-cationic-lipid by mole or by total weight of the composition and 1- 10% conjugated lipid by mole or by total weight of the composition.
  • the composition comprises 30-40% ionizable lipid by mole or by total weight of the composition, 40-50% cholesterol by mole or by total weight of the composition, and 10- 20% non-cationic- lipid by mole or by total weight of the composition.
  • the composition is 50-75% ionizable lipid by mole or by total weight of the composition, 20-40% cholesterol by mole or by total weight of the composition, and 5 to 10% non-cationic-lipid, by mole or by total weight of the composition and 1-10% conjugated lipid by mole or by total weight of the composition.
  • the composition may contain 60-70% ionizable lipid by mole or by total weight of the composition, 25-35% cholesterol by mole or by total weight of the composition, and 5-10% non-cationic-lipid by mole or by total weight of the composition.
  • the composition may also contain up to 90% ionizable lipid by mole or by total weight of the composition and 2 to 15% non-cationic lipid by mole or by total weight of the composition.
  • the formulation may also be a lipid nanoparticle formulation, for example comprising 8-30% ionizable lipid by mole or by total weight of the composition, 5-30% non- cationic lipid by mole or by total weight of the composition, and 0-20% cholesterol by mole or by total weight of the composition; 4-25% ionizable lipid by mole or by total weight of the composition, 4- 25% non-cationic lipid by mole or by total weight of the composition, 2 to 25% cholesterol by mole or by total weight of the composition, 10 to 35% conjugate lipid by mole or by total weight of the composition, and 5% cholesterol by mole or by total weight of the composition; or 2-30% ionizable lipid by mole or by total weight of the composition, 2-30% non-cationic lipid by mole or by total weight of the composition, 1 to 15% cholesterol by mole or by total weight of the composition, 2 to 35% conjugate lipid by mole or by total weight of the composition, and 1-20% cholesterol by mole or by total weight of the
  • the lipid particle formulation comprises ionizable lipid, phospholipid, cholesterol and a PEG-ylated lipid in a molar ratio of 50: 10:38.5: 1.5. In some other embodiments, the lipid particle formulation comprises ionizable lipid, cholesterol and a PEG-ylated lipid in a molar ratio of 60:38.5: 1.5.
  • the lipid particle comprises ionizable lipid, non-cationic lipid (e.g. phospholipid), a sterol (e.g., cholesterol) and a PEG-ylated lipid, where the molar ratio of lipids ranges from 20 to 70 mole percent for the ionizable lipid, with a target of 40-60, the mole percent of non-cationic lipid ranges from 0 to 30, with a target of 0 to 15, the mole percent of sterol ranges from 20 to 70, with a target of 30 to 50, and the mole percent of PEG-ylated lipid ranges from 1 to 6, with a target of 2 to 5.
  • non-cationic lipid e.g. phospholipid
  • a sterol e.g., cholesterol
  • PEG-ylated lipid e.g., PEG-ylated lipid
  • the lipid particle comprises ionizable lipid / non-cationic- lipid / sterol / conjugated lipid at a molar ratio of 50: 10:38.5: 1.5.
  • the disclosure provides a lipid nanoparticle formulation comprising phospholipids, lecithin, phosphatidylcholine and phosphatidylethanolamine.
  • LNPs are directed to specific tissues by the addition of targeting domains (other than the targeting moieties of the disclosed conjugates).
  • targeting domains other than the targeting moieties of the disclosed conjugates.
  • biological ligands may be displayed on the surface of LNPs to enhance interaction with cells displaying cognate receptors, thus driving association with and cargo delivery to tissues wherein cells express the receptor.
  • the biological ligand may be a ligand that drives delivery to the liver, e.g., LNPs that display GalNAc result in delivery of nucleic acid cargo to hepatocytes that display asialoglycoprotein receptor (ASGPR).
  • ASGPR asialoglycoprotein receptor
  • the work of Akinc et al. Mol Ther 18(7): 1357-1364 (2010) teaches the conjugation of a trivalent GalNAc ligand to a PEG-lipid (GalNAc-PEG-DSG) to yield LNPs dependent on ASGPR for observable LNP cargo effect (see, e.g., FIG. 6 of Akinc et al. 2010, supra).
  • ligand-displaying LNP formulations e.g., incorporating folate, transferrin, or antibodies
  • WO2017223135 is incorporated herein by reference in its entirety, in addition to the references used therein, namely Kolhatkar et al., Curr Drug Discov Technol. 2011 8: 197-206; Musacchio and Torchilin, Front Biosci. 2011 16: 1388-1412; Yu et al., Mol Membr Biol. 2010 27:286-298; Patil et al., Crit Rev Ther Drug Carrier Syst. 2008 25: 1-61 ; Benoit et al., Biomacromolecules.
  • LNPs are selected for tissue-specific activity by the addition of a Selective ORgan Targeting (SORT) molecule to a formulation comprising traditional components, such as ionizable cationic lipids, amphipathic phospholipids, cholesterol and poly(ethylene glycol) (PEG) lipids.
  • SORT Selective ORgan Targeting
  • traditional components such as ionizable cationic lipids, amphipathic phospholipids, cholesterol and poly(ethylene glycol) (PEG) lipids.
  • PEG poly(ethylene glycol)
  • the LNPs comprise biodegradable, ionizable lipids.
  • the LNPs comprise (9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3- (diethylamino)propoxy)carbonyl)oxy)methyl)propyl octadeca-9,12-di enoate, also called 3- ((4,4-bis(octyloxy)butanoyl)oxy)-2-(((3-(diethylamino)propoxy)carbonyl)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate) or another ionizable lipid.
  • lipids of WO20 19/067992, WO/2017/173054, W02015/095340, and WO2014/136086 as well as references provided therein.
  • the term cationic and ionizable in the context of LNP lipids is interchangeable, e.g., wherein ionizable lipids are cationic depending on the pH.
  • the average LNP diameter of the LNP formulation may be between 10 nm and 150 nm, e.g., measured by dynamic light scattering (DLS). In some embodiments, the average LNP diameter of the LNP formulation may be between 10 nm and 100 nm, e.g., measured by dynamic light scattering (DLS).
  • DLS dynamic light scattering
  • the average LNP diameter of the LNP formulation may be from about 40 nm to about 150 nm, such as about 40 nm, 45 nm, 50 nm, 55 nm, 60 nm, 65 nm, 70 nm, 75 nm, 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 105 nm, 110 nm, 115 nm, 120 nm, 125 nm, 130 nm, 135 nm, 140 nm, 145 nm, or 150 nm.
  • the average LNP diameter of the LNP formulation may be from about 70 nm to about 150 nm, from about 80 nm to about 120 nm, from about 80 nm to about 110 nm, from about 50 nm to about 100 nm, from about 50 nm to about 90 nm, from about 50 nm to about 80 nm, from about 50 nm to about 70 nm, from about 50 nm to about 60 nm, from about 60 nm to about 100 nm, from about 60 nm to about 90 nm, from about 60 nm to about 80 nm, from about 60 nm to about 70 nm, from about 70 nm to about 100 nm, from about 70 nm to about 90 nm, from about 70 nm to about 80 nm, from about 80 nm to about 100 nm, from about 80 nm to about 90 nm, or from about 90 nm to about 100 nm.
  • the average LNP diameter of the LNP formulation may be from about 70 nm to about 100 nm. In a particular embodiment, the average LNP diameter of the LNP formulation may be about 80 nm. In some embodiments, the average LNP diameter of the LNP formulation may be about 100 nm. In some embodiments, the average LNP diameter of the LNP formulation ranges from about 1 mm to about 500 mm, from about 5 mm to about 200 mm, from about 10 mm to about 100 mm, from about 20 mm to about 80 mm, from about 25 mm to about 60 mm, from about 30 mm to about 55 mm, from about 35 mm to about 50 mm, or from about 38 mm to about 42 mm.
  • a LNP may, in some instances, be relatively homogenous.
  • a poly dispersity index may be used to indicate the homogeneity of a LNP, e.g., the particle size distribution of the lipid nanoparticles.
  • a small (e.g., less than 0.3) poly dispersity index generally indicates a narrow particle size distribution.
  • a LNP may have a poly dispersity index from about 0 to about 0.25, such as 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, or 0.25.
  • the poly dispersity index of a LNP may be from about 0.10 to about 0.20.
  • the zeta potential of a LNP may be used to indicate the electrokinetic potential of the composition.
  • the zeta potential may describe the surface charge of a LNP. Lipid nanoparticles with relatively low charges, positive or negative, are generally desirable, as more highly charged species may interact undesirably with cells, tissues, and other elements in the body.
  • the zeta potential of a LNP may be from about - 10 mV to about +20 mV, from about -10 mV to about +15 mV, from about -10 mV to about +10 mV, from about -10 mV to about +5 mV, from about -10 mV to about 0 mV, from about -10 mV to about -5 mV, from about -5 mV to about +20 mV, from about -5 mV to about +15 mV, from about -5 mV to about +10 mV, from about -5 mV to about +5 mV, from about -5 mV to about 0 mV, from about 0 mV to about +20 mV, from about 0 mV to about +15 mV, from about 0 mV to about +10 mV, from about 0 mV to about +5 mV, from about 0 mV to about +20 mV,
  • the efficiency of encapsulation of a protein and/or nucleic acid describes the amount of protein and/or nucleic acid that is encapsulated or otherwise associated with a LNP after preparation, relative to the initial amount provided.
  • the encapsulation efficiency is desirably high (e.g., close to 100%).
  • the encapsulation efficiency may be measured, for example, by comparing the amount of protein or nucleic acid in a solution containing the lipid nanoparticle before and after breaking up the lipid nanoparticle with one or more organic solvents or detergents.
  • an anion exchange resin may be used to measure the amount of free protein or nucleic acid (e.g., RNA) in a solution. Fluorescence may be used to measure the amount of free protein and/or nucleic acid (e.g., RNA) in a solution.
  • the encapsulation efficiency of a protein and/or nucleic acid may be at least 50%, for example 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the encapsulation efficiency may be at least 80%.
  • the encapsulation efficiency may be at least 90%. In some embodiments, the encapsulation efficiency may be at least 95%.
  • a LNP may optionally comprise one or more coatings. In some embodiments, a LNP may be formulated in a capsule, film, or table having a coating. A capsule, film, or tablet including a composition described herein may have any useful size, tensile strength, hardness or density.
  • a lipid nanoparticle (or a formulation comprising lipid nanoparticles) lacks reactive impurities (e.g., aldehydes or ketones), or comprises less than a preselected level of reactive impurities (e.g., aldehydes or ketones).
  • a lipid reagent is used to make a lipid nanoparticle formulation, and the lipid reagent may comprise a contaminating reactive impurity (e.g., an aldehyde or ketone).
  • a lipid regent may be selected for manufacturing based on having less than a preselected level of reactive impurities (e.g., aldehydes or ketones).
  • aldehydes can cause modification and damage of RNA, e.g., cross-linking between bases and/or covalently conjugating lipid to RNA (e.g., forming lipid-RNA adducts). This may, in some instances, lead to failure of a reverse transcriptase reaction and/or incorporation of inappropriate bases, e.g., at the site(s) of lesion(s), e.g., a mutation in a newly synthesized target DNA.
  • a lipid nanoparticle formulation is produced using a lipid reagent comprising less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content.
  • a lipid nanoparticle formulation is produced using a lipid reagent comprising less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.
  • a lipid nanoparticle formulation is produced using a lipid reagent comprising: (i) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content; and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.
  • a lipid reagent comprising: (i) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.
  • the lipid nanoparticle formulation is produced using a plurality of lipid reagents, and each lipid reagent of the plurality independently meets one or more criterion described in this paragraph. In some embodiments, each lipid reagent of the plurality meets the same criterion, e.g., a criterion of this paragraph.
  • the lipid nanoparticle formulation comprises less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content. In some embodiments, the lipid nanoparticle formulation comprises less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.
  • any single reactive impurity e.g., aldehyde
  • the lipid nanoparticle formulation comprises: (i) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content; and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.
  • any single reactive impurity e.g., aldehyde
  • one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a formulation thereof comprise less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content.
  • one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a formulation thereof comprise less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.
  • any single reactive impurity e.g., aldehyde
  • one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a formulation thereof comprise: (i) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content; and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.
  • any single reactive impurity e.g., aldehyde
  • total aldehyde content and/or quantity of any single reactive impurity (e.g., aldehyde) species is determined by liquid chromatography (LC), e.g., coupled with tandem mass spectrometry (MS/MS), e.g., as described herein.
  • LC liquid chromatography
  • MS/MS tandem mass spectrometry
  • reactive impurity (e.g., aldehyde) content and/or quantity of reactive impurity (e.g., aldehyde) species is determined by detecting one or more chemical modifications of a nucleic acid molecule (e.g., an RNA molecule, e.g., as described herein) associated with the presence of reactive impurities (e.g., aldehydes), e.g., in the lipid reagents.
  • a nucleic acid molecule e.g., an RNA molecule, e.g., as described herein
  • reactive impurity (e.g., aldehyde) content and/or quantity of reactive impurity (e.g., aldehyde) species is determined by detecting one or more chemical modifications of a nucleotide or nucleoside (e.g., a ribonucleotide or ribonucleoside, e.g., comprised in or isolated from a template nucleic acid, e.g., as described herein) associated with the presence of reactive impurities (e.g., aldehydes), e.g., in the lipid reagents, e.g., as described herein.
  • a nucleotide or nucleoside e.g., a ribonucleotide or ribonucleoside, e.g., comprised in or isolated from a template nucleic acid, e.g., as described herein
  • reactive impurities e.g., aldehydes
  • chemical modifications of a nucleic acid molecule, nucleotide, or nucleoside are detected by determining the presence of one or more modified nucleotides or nucleosides, e.g., using LC-MS/MS analysis, e.g., as described herein.
  • the lipid nanoparticle are liposomes or other similar vesicles.
  • Liposomes are spherical vesicle structures composed of a uni- or multilamellar lipid bilayer surrounding internal aqueous compartments and a relatively impermeable outer lipophilic phospholipid bilayer. Liposomes may be anionic, neutral or cationic. Liposomes are biocompatible, nontoxic, can deliver both hydrophilic and lipophilic drug molecules, protect their cargo from degradation by plasma enzymes, and transport their load across biological membranes and the blood brain barrier (BBB) (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011. doi: 10.1155/2011/469679 for review).
  • BBB blood brain barrier
  • Vesicles can be made from several different types of lipids; however, phospholipids are most commonly used to generate liposomes as drug carriers.
  • Methods for preparation of multilamellar vesicle lipids are known in the art (see for example U.S. Pat. No. 6,693,086, the teachings of which relating to multilamellar vesicle lipid preparation are incorporated herein by reference).
  • vesicle formation can be spontaneous when a lipid film is mixed with an aqueous solution, it can also be expedited by applying force in the form of shaking by using a homogenizer, sonicator, or an extrusion apparatus (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol.
  • Extruded lipids can be prepared by extruding through filters of decreasing size, as described in Templeton et al., Nature Biotech, 15:647-652, 1997, the teachings of which relating to extruded lipid preparation are incorporated herein by reference.
  • the ratio between the ionizable lipid and the non-pegylated phospholipid is from about 1 : 1 to about 7:1. In some embodiments, the ratio between the ionizable lipid and the non-pegylated phospholipid (e.g., DSPC) is from about 1 : 1 to about 4: 1.
  • the ratio between the ionizable lipid and the non-pegylated phospholipid is from about 1 : 1 to about 3: 1. In some embodiments, the ratio between the ionizable lipid and the non-pegylated phospholipid (e.g., DSPC) is from about 1 : 1 to about 2.5: 1. In some embodiments, the ratio between the ionizable lipid and the non-pegylated phospholipid (e.g., DSPC) is from about 1 : 1 to about 2: 1.
  • the ratio between the ionizable lipid and the non-pegylated phospholipid is from about 1.5: 1 to about 2.5: 1. In some embodiments, the ratio between the ionizable lipid and the non-pegylated phospholipid (e.g., DSPC) is from about 2: 1 to about 2.5: 1.
  • non-pegylated phospholipid e.g., DSPC
  • the ratio between the cholesterol molecule and the non-pegylated phospholipid is from about 6: 1 to about 0.5: 1.
  • the ratio between the cholesterol molecule and the non-pegylated phospholipid is from about 3: 1 to about 0.5: 1.
  • the ratio between the cholesterol molecule and the non-pegylated phospholipid is from about 2: 1 to about 0.5: 1. In some embodiments, the ratio between the cholesterol molecule and the non-pegylated phospholipid (e.g., DSPC) is from about 1.5: 1 to about 0.5: 1. In some embodiments, the ratio between the cholesterol molecule and the non-pegylated phospholipid (e.g., DSPC) is from about 1 : 1 to about 0.5: 1. In some embodiments, the ratio between the cholesterol molecule and the non-pegylated phospholipid (e.g., DSPC) is from about 1 :2 to about 0.8: 1.
  • Anti-CD117 Fab was produced with an additional LplA acceptor peptide (LAP) tag on C terminus of the heavy chain.
  • LAP LplA acceptor peptide
  • a solution containing 20uM anti-CD117 Fab-LAP tag, 2 uM LplA enzyme lipoic acid ligase W37V, 200 pM 10-azidodecanoic acid, 1 mM ATP, and 5 mM magnesium acetate in PBS pH 7.4 was incubated at 37 °C for 1.5 hours with shaking at 800 rpm.
  • the lipoic acid ligase reaction is schematized in FIG. 4.. Excess reagents were removed and buffer was exchanged with PBS containing lOmM EDTA by Amicon centrifugal filter.
  • DOL degree of labeling
  • the lipidated Fab fragment is inserted into a precursor LNP to form a surface-modified LNP.
  • the lipidated Fab fragment can be combined with individual components (e.g., lipids and cholesterol) to form a surface-modified LNP.

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Abstract

La divulgation concerne des conjugués comprenant une fraction de ciblage, par exemple, un anticorps, un fragment Fab ou un fragment variable à chaîne unique (ScFv), et une nanoparticule lipidique (NPL) encapsulant un agent thérapeutique (c'est-à-dire, une charge utile), la fraction de ciblage, par exemple, l'anticorps, le fragment Fab ou le ScFv, étant conjuguée à la nanoparticule lipidique par l'intermédiaire d'une séquence de liaison, et la séquence de liaison comprenant une séquence de reconnaissance d'enzyme telle qu'un motif de reconnaissance de la sortase ou un peptide accepteur d'acide lipoïque. La divulgation concerne en outre des procédés de préparation de tels conjugués.
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