Novel nucleus targeting signal peptides and uses thereof
Novel signal peptides are developed to address the lack of targeted protein localization in mRNA technologies, enhancing the expression and delivery of therapeutic proteins to specific cellular compartments like the nucleus.
Patent Information
- Application Number
- PCT/US2024/049070
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2023-11-28
- Filing Date
- 2024-09-27
- Publication Date
- 2025-04-03
AI Technical Summary
Current mRNA technologies focus primarily on amplifying intracellular expression of encoded polypeptides, with less attention given to post-translational control and targeted localization of proteins within the body.
Development of novel signal peptides that can direct encoded proteins to specific cellular compartments, such as the nucleus, by incorporating specific amino acid sequences that promote targeted localization and secretion.
The novel signal peptides enhance the expression and localization of therapeutic proteins to the nucleus, offering improved delivery and clearance of therapeutic mRNA.
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Figure US2024049070_03042025_PF_FP_ABST
Abstract
Description
Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT NOVEL NUCLEUS TARGETING SIGNAL PEPTIDES AND USES THEREOF Related Applications
[0001] This application claims the benefit of U.S. Provisional Application Ser. No. 63 / 586,847 filed September 29, 2023, and of U.S. Provisional Application Ser. No. 63 / 603,603 filed November 28, 2023, each of which is hereby incorporated by reference in its entirety. Sequence Listing
[0002] This application contains references to amino acid sequences and / or nucleic acid sequences which have been submitted concurrently herewith as the sequence listing xml file entitled “824623_sequencelisting.xml”, file size 16,384 bytes, created on September 27, 2024. The aforementioned sequence listing is hereby incorporated by reference in its entirety pursuant to 37 C.F.R. §1.52(e)(5).
[0003] Field
[0004] The present disclosure relates generally to novel signal peptides and more particularly to novel signal peptides for targeting an encoded protein to the nucleus of a cell. Background
[0005] Recent scientific discoveries have highlighted the innumerable therapeutic applications of mRNA due to its modular nature and ability to provide customizable “instructions” to create functional proteins. Clinical studies continue to confirm its favorable efficacy, further underscoring its potential as a next-generation genetic medicine wherein scientists have only begun to scratch the surface of potential applications. Most of the research focus so far has been on amplifying intracellular expression of the encoded polypeptide. However, less focus has been placed on post-translational control of encoded proteins and targeted localization and / or secretion of the protein within the body.
[0006] Within the cell, a variety of unique avenues and processes exist that allow for the shuttling of proteins to various organelles as well as the export of proteins into the extracellular space via excretion pathways. However, in order to take advantage of these transport systems, the mRNA 1 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT encoding each protein must also contain a metaphorical shipping label upstream from the protein sequence known as a signal peptide (SP). Design of novel SP for therapeutic mRNA could greatly benefit delivery, localization, and clearance of an encoded therapeutic protein. The present disclosure addresses these needs and others. Summary
[0007] In some embodiments, a signal peptide is provided. In some embodiments, the signal peptide comprises an amino acid sequence selected from the group consisting of Formula I, II, III, IV, V, VI, VII, and VIII; wherein Formula I is represented as: A1-A2-A3-A4-A5-A6-A7-A8-A9-A10-A11-A12-A13-A14-A15-A16(Formula I) and the identities of A1-A16 are as provided in Table 2; wherein Formula II is represented as: B1-B2-B3-B4-B5-B6-B7-B8-B9-B10-B11-B12-B13-B14-B15-B16-B17-B18(Formula II) and the identities of B1-B18 are as provided in Table 3; wherein Formula III is represented as: C1-C2-C3-C4-C5-C6-C7-C8-C9-C10-C11-C12-C13-C14-C15-C16-C17-C18-C19(Formula III) and the identities of C1-C19are as provided in Table 4; wherein Formula IV is represented as: D1-D2-D3-D4-D5-D6-D7-D8-D9-D10-D11-D12-D13-D14-D15-D16-D17-D18-D19-D20 (Formula IV) and the identities of D1-D20are as provided in Table 5; wherein Formula V is represented as: E1-E2-E3-E4-E5-E6-E7-E8-E9-E10-E11-E12-E13-E14-E15-E16-E17-E18-E19-E20-E21-E22 (Formula V) and the identities of E1-E22are as provided in Table 6; wherein Formula VI is represented as: F1-F2-F3-F4-F5-F6-F7-F8-F9-F10-F11-F12-F13-F14-F15-F16-F17-F18-F19-F20-F21-F22-F23 (Formula VI) and the identities of F1-F23are as provided in Table 7; wherein Formula VII is represented as: G1-G2-G3-G4-G5-G6-G7-G8-G9-G10-G11-G12-G13-G14-G15-G16-G17-G18-G19-G20-G21-G22-G23-G24- G25-G26 (Formula VII) and the identities of G1-G26are as provided in Table 8; and 2 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT wherein Formula VIII is represented as: H1-H2-H3-H4-H5-H6-H7-H8-H9-H10-H11-H12-H13-H14-H15-H16-H17-H18-H19-H20-H21-H22-H23-H24- H25-H26-H27-H28-H29-H30 (Formula VIII) and the identities of H1-H30are as provided in Table 9.
[0008] In some embodiments, the signal peptide comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9.
[0009] In some embodiments, a signal peptide is provided, the signal peptide comprising an amino acid sequence having at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9.
[0010] In some embodiments, a signal peptide as provided for herein is a novel signal peptide.
[0011] In some embodiments, a recombinant polypeptide is provided. In some embodiments, the recombinant polypeptide comprises a formula of X1-(Y1)a-Z1, wherein X1 is a signal peptide, Y1 is a peptide linker, and Z1 is a payload protein, wherein a is an integer selected from 0 and 1.
[0012] In some embodiments, the signal peptide X1comprises an amino acid sequence selected from the group consisting of Formula I, II, III, IV, V, VI, VII, and VIII; wherein Formula I is represented as: A1-A2-A3-A4-A5-A6-A7-A8-A9-A10-A11-A12-A13-A14-A15-A16(Formula I) and the identities of A1-A16are as provided in Table 2; wherein Formula II is represented as: B1-B2-B3-B4-B5-B6-B7-B8-B9-B10-B11-B12-B13-B14-B15-B16-B17-B18 (Formula II) and the identities of B1-B18are as provided in Table 3; wherein Formula III is represented as: C1-C2-C3-C4-C5-C6-C7-C8-C9-C10-C11-C12-C13-C14-C15-C16-C17-C18-C19 (Formula III) and the identities of C1-C19are as provided in Table 4; wherein Formula IV is represented as: D1-D2-D3-D4-D5-D6-D7-D8-D9-D10-D11-D12-D13-D14-D15-D16-D17-D18-D19-D20 (Formula IV) and the identities of D1-D20are as provided in Table 5; wherein Formula V is represented as: 3 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT E1-E2-E3-E4-E5-E6-E7-E8-E9-E10-E11-E12-E13-E14-E15-E16-E17-E18-E19-E20-E21-E22(Formula V) and the identities of E1-E22 are as provided in Table 6; wherein Formula VI is represented as: F1-F2-F3-F4-F5-F6-F7-F8-F9-F10-F11-F12-F13-F14-F15-F16-F17-F18-F19-F20-F21-F22-F23(Formula VI) and the identities of F1-F23 are as provided in Table 7; wherein Formula VII is represented as: G1-G2-G3-G4-G5-G6-G7-G8-G9-G10-G11-G12-G13-G14-G15-G16-G17-G18-G19-G20-G21-G22-G23-G24- G25-G26 (Formula VII) and the identities of G1-G26 are as provided in Table 8; and wherein Formula VIII is represented as: H1-H2-H3-H4-H5-H6-H7-H8-H9-H10-H11-H12-H13-H14-H15-H16-H17-H18-H19-H20-H21-H22-H23-H24- H25-H26-H27-H28-H29-H30 (Formula VIII) and the identities of H1-H30 are as provided in Table 9.
[0013] In some embodiments, the signal peptide X1comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9.
[0014] In some embodiments, the payload protein is a therapeutic peptide or protein.
[0015] In some embodiments, a nucleic acid molecule is provided. In some embodiments, the nucleic acid molecule encodes for a signal peptide as provided for herein.
[0016] In some embodiments, a nucleic acid molecule is provided. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide as provided for herein.
[0017] In some embodiments, a vector is provided. In some embodiments, the vector comprises a nucleic acid molecule as provided for herein. In some embodiments, the nucleic acid molecule encodes for a signal peptide as provided for herein. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide as provided for herein.
[0018] In some embodiments, a cell is provided. In some embodiments, the cell comprises a nucleic acid molecule as provided for herein. In some embodiments, the cell comprises a vector as provided for herein. In some embodiments, the nucleic acid molecule encodes for a signal peptide as provided for herein. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide as provided for herein. 4 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT
[0019] In some embodiments, a composition is provided. In some embodiments, the composition comprises a nucleic acid molecule as provided for herein. In some embodiments, the composition comprises a vector as provided for herein. In some embodiments, the nucleic acid molecule encodes for a signal peptide as provided for herein. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide as provided for herein.
[0020] In some embodiments, a method for treating a disease or disorder in a subject in need thereof is provided. In some embodiments, the method comprises administering to the subject an effective among of a nucleic acid molecule as provided for herein to the subject, thereby treating the disease or disorder. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide as provided for herein. In some embodiments, the disease or disorder is a disease or disorder associated with the nucleus of a cell. In some embodiments, the payload protein is a protein useful for gene editing and the disease or disorder is any disease or disorder for which gene editing is useful.
[0021] In some embodiments, a method for treating a disease or disorder associated with the nucleus of a cell in a subject in need thereof is provided. In some embodiments, the method comprises administering to the subject a vector comprising a nucleic acid molecule encoding for a signal peptide fused or linked to a payload protein, wherein the signal peptide is a signal peptide as provided for herein and the payload protein is a therapeutic peptide or protein useful for the treatment of the disease or disorder.
[0022] In some embodiments, a method for treating a disease or disorder in a subject in need thereof is provided. In some embodiments, the method comprises administering to the subject a vector comprising a nucleic acid molecule encoding for: i) a signal peptide fused or linked to a payload protein, wherein the signal peptide is a signal peptide as provided for herein and wherein the payload protein is a protein useful for gene editing; and ii) at least one nucleic acid molecule that targets the payload protein to a gene of interest; wherein the signal peptide promotes translocation of the protein useful for gene editing to the nucleus, wherein the payload protein edits the gene of interest thereby treating the disease or disorder.
[0023] In some embodiments, a method for editing a target nucleic acid in a cell is provided. In some embodiments, the method comprises administering a nucleic acid molecule encoding for: i) a signal peptide fused or linked to a payload protein, wherein the signal peptide is a signal peptide as provided for herein and wherein the payload protein is a protein useful for gene editing; and ii) 5 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT at least one nucleic acid molecule that targets the payload protein to a gene of interest; wherein the signal peptide promotes translocation of the protein useful for gene editing to the nucleus, wherein the payload protein edits the gene of interest thereby editing the target nucleic acid. Brief Description of the Drawings
[0024] FIG.1A provides a schematic of the construct comprising mCherry with the signal peptide at the N-terminus and its use for signal peptide screening by pDNA transfection in vitro.
[0025] FIG. 1B illustrates representative images of signal peptide tagged mCherry colocalized with Hoechst 33342 dye. Top: SP is Nov-Nuc-16-1 (SEQ ID NO: 1). Bottom: SP is Nov-Nuc- 22-1 (SEQ ID NO: 5).
[0026] FIG. 1C illustrates representative images of signal peptide tagged mCherry colocalized with Hoechst 33342 dye. Top: SP is Nov-Nuc-18-1 (SEQ ID NO: 9). Bottom: SP is Nov-Nuc- 26-1 (SEQ ID NO: 7).
[0027] FIG. 1D illustrates representative images of signal peptide tagged mCherry colocalized with Hoechst 33342 dye. Top: SP is Nov-Nuc-19-1 (SEQ ID NO: 3). Bottom: No SP control.
[0028] FIG. 1E illustrates the quantification of the experiments corresponding to the representative images of FIGs.1B, 1C, and 1D.
[0029] FIG. 1F illustrates the quantification of the experiments corresponding to the representative images of FIGs.1B, 1C, and 1D.
[0030] FIG.2A provides quantification of mCherry fluorescence in Hela cell lysates and medium at different time points. mCherry with no signal peptide was used as a control (“WT-mCherry”). gLuc, Gaussia luciferase.
[0031] FIG.2B provides quantification of mCherry fluorescence in Hela cell lysate and medium after 72 hours.
[0032] FIG.2C provides quantification of mCherry fluorescence in Huh7 cell lysates and medium at 72h after transfection.
[0033] FIG. 3A provides quantification of time-dependent (100 ng mRNA per well) and dose dependent (at 72h) mCherry secretion in Huh7 cells, medium, and cell lysate.
[0034] FIG. 3B shows quantification of mCherry signal in different cell lines. Cells in 96-well plate were treated with mDLNPs-mRNA, at given time-points. 6 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Detailed Description
[0035] Before the present compositions and methods are described, it is to be understood that the scope of the disclosure is not limited to the particular processes, compositions, or methodologies described herein, as these may vary. It is also to be understood that the terminology used in the description is for the purpose of describing the particular versions or embodiments only, and is not intended to limit the scope of the present disclosure. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art. It is further to be understood that any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the methods and systems disclosed herein, and such equivalents are within the scope of the present disclosure. Definitions
[0036] The following explanations of terms and methods are provided to better describe the present disclosure and to guide those of ordinary skill in the art in the practice of the present disclosure.
[0037] As used herein, “comprising” means “including” and the singular forms “a” or “an” or “the” include plural references unless the context clearly dictates otherwise. For example, reference to “comprising a therapeutic agent” includes one or a plurality of such therapeutic agents. The term “or” refers to a single element of stated alternative elements, unless the context clearly indicates otherwise. For example, the phrase “A or B” refers to A alone or B alone. The phrase “A, B, or a combination thereof” refers to A alone, B alone, or a combination of A and B. Similarly, “one or more of A and B” refers to A, B, or a combination of both A and B. The phrase “A and B” refers to a combination of A and B. Furthermore, the various elements, features and steps discussed herein, as well as other known equivalents for each such element, feature or step, can be mixed and matched by one of ordinary skill in this art to perform methods in accordance with principles described herein. Among the various elements, features, and steps some will be specifically included and others specifically excluded in particular examples.
[0038] In some examples, the numbers expressing quantities of ingredients, properties such as molecular weight, reaction conditions, and so forth, used to describe and claim certain embodiments are to be understood as being modified in some instances by the term "about" or "approximately." For example, "about" or "approximately" can indicate + / - 10%, + / - 5%, or + / - 7 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT 1% variation of the value it describes. Accordingly, in some embodiments, the numerical parameters set forth herein are approximations that can vary depending upon the desired properties for a particular embodiment. Additionally, where a phrase recites “about x to y,” the term “about” modifies both x and y and can be used interchangeably with the phrase “about x to about y” unless context dictates differently.
[0039] As used herein, the terms “transformation” and “transfection” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection (e.g., using commercially available reagents such as, for example, LIPOFECTIN® (Invitrogen Corp., San Diego, CA), LIPOFECTAMINE® (Invitrogen), FUGENE® (Roche Applied Science, Basel, Switzerland), JETPEI™ (Polyplus-transfection Inc., New York, NY), EFFECTENE® (Qiagen, Valencia, CA), DREAMFECT™ (OZ Biosciences, France) and the like), or electroporation (e.g., in vivo electroporation). Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual.2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), and other laboratory manuals.
[0040] Methods and materials of non-viral delivery of nucleic acids to cells further include biolistics, virosomes, liposomes, lipid nanoparticles, immunoliposomes, polycation or lipid- nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in U.S. Pat. Nos. 5,049,386, 4,946,787; and 4,897,355 and lipofection reagents are sold commercially (e.g., TRANSFECTAM™ and LIPOFECTIN™). Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those disclosed in WO91 / 17424 and WO 91 / 16024.
[0041] The chemical makeup of a peptide will be described herein by a series of amino acid single letter abbreviations or an “amino acid sequence / s” or “sequence / s,” which are conventional and known to those in the art. While reference sequences will be explicitly disclosed, in any aspect and embodiment, a reference sequence may be modified to include conservative amino acid substitutions, as well as variants and fragments, while maintaining the characteristics and functionality of the reference sequence.
[0042] As used herein, “payload protein” or “protein of interest” refers to the protein that will be generated by the host cell and chaperoned to the desired intracellular location, e.g., chaperoned to 8 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT the nucleus of a cell. Upon translocation to the proper intracellular space, all, some, or none of the novel signal peptide may be fused to the payload protein. Optionally, a payload protein still being attached partially or fully to the novel signal peptide may be further processed, for example, to remove the remaining novel signal peptide. A payload protein may be any protein known or yet to be known, for example, an enzyme, enzyme inhibitor, growth factor, hormone, antibody, antigen, vaccine, a therapeutic agent, or any combination thereof. More specific examples follow herein below.
[0043] As used herein, the term “fused” or “linked” when used in reference to a protein having different domains or heterologous sequences means that the protein domains are part of the same peptide chain that are connected to one another with either peptide bonds or other covalent bonding. The domains or section can be linked or fused directly to one another or another domain or peptide sequence can be between the two domains or sequences and such sequences would still be considered to be fused or linked to one another. In some embodiments, the various domains or proteins provided for herein are linked or fused directly to one another or a linker sequences, such as the glycine / serine sequences described herein link the two domains together.
[0044] “Identity” as used herein refers to the subunit sequence identity between two polymeric molecules such as between two nucleic acid or amino acid molecules, such as, between two polynucleotide or polypeptide molecules. When two amino acid sequences have the same residues at the same positions; e.g., if a position in each of two polypeptide molecules is occupied by an Arginine, then they are identical at that position. The identity or extent to which two amino acid or two nucleic acid sequences have the same residues at the same positions in an alignment is often expressed as a percentage. The identity between two amino acid or two nucleic acid sequences is a direct function of the number of matching or identical positions; e.g., if half of the positions in two sequences are identical, the two sequences are 50% identical; if 90% of the positions (e.g., 9 of 10), are matched or identical, the two amino acids sequences are 90% identical.
[0045] By “substantially identical” is meant a polypeptide or nucleic acid molecule exhibiting at least 50% identity to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein). In some embodiments, such a sequence is at least 60%, 80% or 85%, or 90%, 95% or even 99% identical at the amino acid level or nucleic acid to the sequence used 9 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT for comparison. Other percentages of identity in reference to specific sequences are described herein.
[0046] Sequence identity can be measured / determined using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, BLAST-2, ALIGN, MEGALIGN (DNASTAR), CLUSTALW, CLUSTAL OMEGA, MUSCLE or PILEUP / PRETTYBOX programs). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and / or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. In an exemplary approach to determining the degree of identity, a BLAST program may be used, with a probability score between e3 and e100 indicating a closely related sequence. In some embodiments, sequence identity is determined by using BLAST with the default settings. In some embodiments, sequence identity is determined using Clustal Omega.
[0047] To the extent embodiments provided for herein, includes composition comprising various proteins, these proteins may, in some instances, comprise amino acid sequences that have sequence identity to the amino acid sequences disclosed herein. Therefore, in certain embodiments, depending on the particular sequence, the degree of sequence identity is preferably greater than 50% (e.g., 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more) to the SEQ ID NOs disclosed herein. In addition to these percentages, other percentages of identity are provided for herein. Identity between polypeptides can be determined by the Smith- Waterman homology search algorithm as implemented in the MPSRCH program (Oxford Molecular), using an affine gap search with parameters gap open penalty – 12 and gap extension penalty = 1.
[0048] These proteins may, compared to the disclosed proteins, include one or more (e.g., 1, 2, 3,4, 5, 6, 7, 8, 9, 10, etc.) conservative amino acid replacements i.e., replacements of one amino acid with another which has a related side chain. Genetically-encoded amino acids are generally divided into four families: (1) acidic i.e., aspartate, glutamate; (2) basic i.e., lysine, arginine, histidine; (3) non polar i.e., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar i.e., glycine, asparagine, glutamine, cysteine, serine, 10 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. In general, substitution of single amino acids within these families does not have a major effect on the biological activity. The proteins may have one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) single amino acid deletions relative to the disclosed protein sequences. The proteins may also include one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) insertions (e.g., each of 1, 2, 3, 4 or 5 amino acids) relative to the disclosed protein sequences.
[0049] “Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.
[0050] As used herein, the following abbreviations for the commonly occurring nucleic acid bases are used: “A” refers to adenosine, “C” refers to cytosine, “G” refers to guanosine, “T” refers to thymidine, and “U” refers to uridine.
[0051] Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some versions contain an intron(s).
[0052] The term “oligonucleotide” typically refers to short polynucleotides. It will be understood that when a nucleotide sequence is represented by a DNA sequence (i.e., A, T, C, G), this also provides the corresponding RNA sequence (i.e., A, U, C, G) in which “U” replaces “T.”
[0053] The term “polynucleotide” as used herein is defined as a chain of nucleotides. Furthermore, nucleic acids are polymers of nucleotides. Thus, the terms “nucleic acids” or “nucleic acid molecules” and “polynucleotides” as used herein are interchangeable. As used herein polynucleotides include, but are not limited to, all nucleic acid sequences which are obtained by 11 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT any methods available in the art, including, without limitation, recombinant methods, i.e., the cloning of nucleic acid sequences from a recombinant library or a cell genome, using cloning technology and PCR, and the like, and by synthetic means.
[0054] As used herein, the terms “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprised of a plurality of amino acid residues covalently linked by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. The polypeptides include natural peptides, recombinant peptides, synthetic peptides, or a combination thereof.
[0055] As used herein, unless otherwise indicated, “antibody fragment” or “antigen binding fragment” refers to antigen binding fragments of antibodies, i.e., antibody fragments that retain the ability to bind specifically to the antigen bound by the full-length antibody, e.g., fragments that retain one or more CDR regions. Examples of antibody binding fragments include, but are not limited to, Fab, Fab', F(ab')2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules, e.g., sc-Fv; nanobodies (single domain antibody) and multispecific antibodies formed from antibody fragments.
[0056] A “Fab fragment” is comprised of one light chain and the CH1 and variable regions of one heavy chain. The heavy chain of a Fab molecule cannot form a disulfide bond with another heavy chain molecule.
[0057] An “Fc” region contains two heavy chain fragments comprising the CH2 and CH3 domains of an antibody. The two heavy chain fragments are held together by two or more disulfide bonds and by hydrophobic interactions of the CH3 domains.
[0058] A “Fab' fragment” contains one light chain and a portion or fragment of one heavy chain that contains the VHdomain and the CH1 domain and also the region between the CH1 and CH2 domains, such that an interchain disulfide bond can be formed between the two heavy chains of two Fab' fragments to form a F(ab') 2 molecule.
[0059] A “F(ab')2fragment” contains two light chains and two heavy chains containing a portion of the constant region between the CH1 and CH2 domains, such that an interchain disulfide bond is 12 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT formed between the two heavy chains. A F(ab')2fragment thus is composed of two Fab' fragments that are held together by a disulfide bond between the two heavy chains.
[0060] The “Fv region” comprises the variable regions from both the heavy and light chains, but lacks the constant regions.
[0061] The term “single-chain Fv” or “scFv” antibody refers to antibody fragments comprising the VH and VL domains of an antibody, wherein these domains are present in a single polypeptide chain. Generally, the Fv polypeptide further comprises a polypeptide linker between the VHand VL domains which enables the scFv to form the desired structure for antigen binding. For a review of scFv, see Pluckthun (1994) THEPHARMACOLOGY OFMONOCLONALANTIBODIES, vol. 113, Rosenburg and Moore eds. Springer-Verlag, New York, pp. 269-315. See also, International Patent Application Publication No. WO 88 / 01649 and U.S. Pat. Nos.4,946, 778 and 5,260,203.
[0062] Antibody molecules can be monospecific (e.g., monovalent or bivalent), bispecific (e.g., bivalent, trivalent, tetravalent, pentavalent, or hexavalent), trispecific (e.g., trivalent, tetravalent, pentavalent, or hexavalent), or with higher orders of specificity (e.g, tetraspecific) and / or higher orders of valency beyond hexavalency. An antibody molecule can comprise a functional fragment of a light chain variable region and a functional fragment of a heavy chain variable region, or heavy and light chains may be fused together into a single polypeptide.
[0063] As used herein, the terms “comprising” (and any form of comprising, such as “comprise”, “comprises”, and “comprised”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”), or “containing” (and any form of containing, such as “contains” and “contain”), are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. Any step or composition that uses the transitional phrase of “comprise” or “comprising” can also be said to describe the same with the transitional phase of “consisting of” or “consists.”
[0064] As used herein, the term “contacting” means bringing together of two elements in an in vitro system or an in vivo system. For example, “contacting” virus or vector described herein with an individual or patient or cell includes the administration of the virus to an individual or patient, such as a human, as well as, for example, introducing a compound into a sample containing a cellular or purified preparation containing the cell.
[0065] As used herein, the term “individual” or “subject,” or “patient” used interchangeably, means any animal, including mammals, such as mice, rats, other rodents, rabbits, dogs, cats, swine, 13 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT cattle, sheep, horses, or primates, such as humans. In some embodiments, the subject is a human. A subject that is “in need thereof” refers to a subject that has been identified as requiring treatment for the condition that is to be treated and is treated with the specific intent of treating such condition. The conditions can be, for example, any of the conditions described herein.
[0066] The compositions disclosed herein may be provided to a subject in a variety of ways through administration of the composition to the subject. As used herein, administer or administration means to provide or the providing of a composition to a subject. Oral administration, as used herein, refers to delivery of an active agent through the mouth. Topical administration, as used herein, refers to the delivery of an active agent to a body surface, such as the skin, a mucosal membrane (e.g., nasal membrane, vaginal membrane, buccal membrane, or the like).
[0067] A “disease” is a state of health of an animal wherein the animal cannot maintain homeostasis, and wherein if the disease is not ameliorated then the animal’s health continues to deteriorate. In contrast, a “disorder” in an animal is a state of health in which the animal is able to maintain homeostasis, but in which the animal’s state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal’s state of health.
[0068] “Effective amount” or “therapeutically effective amount” are used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological result or provides a therapeutic or prophylactic benefit. Such results may include, but are not limited to an amount that when administered to a mammal, causes a detectable level of immune cell activation compared to the immune cell activation detected in the absence of the composition. The immune response can be readily assessed by a plethora of art-recognized methods. The skilled artisan would understand that the amount of the composition administered herein varies and can be readily determined based on a number of factors such as the disease or condition being treated, the age and health and physical condition of the mammal being treated, the severity of the disease, the particular compound being administered, and the like.
[0069] Ranges: throughout this disclosure, various aspects of the embodiments can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation. Accordingly, the 14 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range. Unless otherwise explicitly stated to the contrary, a range that is disclosed also includes the endpoints of the range. Novel Signal Peptides
[0070] Without being bound to any particular theory, the embodiments provided for herein have been found to show that novel signal peptides may direct payload proteins as provided for herein to be expressed in the nucleus of a cell. The novel signal peptides provided for herein may direct the payload protein to any appropriate location on or within the nucleus. The payload proteins may or may not natively contain a signal peptide directing localization of said protein to the specific cellular compartment, e.g., the nucleus of a cell. Accordingly, the provided novel signal peptides can direct enhanced expression of a native nuclear protein in the nucleus, or can direct expression of a payload protein, e.g., a therapeutic protein to the nucleus for expression.
[0071] In some embodiments, a signal peptide is provided. In some embodiments, the signal peptide comprises an amino acid sequence as recited in Table 1 below: Table 1: Exemplary Novel Signal Peptides SEQ ID NO: Amino Acid Sequence15 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT
[0072] In some embodiments, the signal peptide comprises an amino acid sequence that is substantially similar to an amino acid sequence as recited in Table 1. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence as recited in Table 1. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 1. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 2. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 3. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 4. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 5. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 6. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 7. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 16 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 8. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 70% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) identical to an amino acid sequence of SEQ ID NO: 9.
[0073] In some embodiments, the signal peptide is a variant of an amino acid sequence as provided in Table 1. In some embodiments, the signal peptide comprises an amino acid sequence as defined by Formula I-VIII below.
[0074] Variants of SEQ ID NO: 1 (Formula I)
[0075] In some embodiments, the signal peptide comprises an amino acid sequence represented by: A1-A2-A3-A4-A5-A6-A7-A8-A9-A10-A11-A12-A13-A14-A15-A16(Formula I); wherein the identity of each of A1 – A16 are as provided for in Table 2 below. Table 2 Position Suitable Amino Acids17 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Position Suitable Amino Acids A16 A L Gembodiments, A2 is an amino acid selected from the group consisting of K, R, and V. In some embodiments, A3is an amino acid selected from the group consisting of I, W, and T. In some embodiments, A4is an amino acid selected from the group consisting of S, L, and I. In some embodiments, A5 is an amino acid selected from the group consisting of I, W, and A. In some embodiments, A6 is an amino acid selected from the group consisting of L and F. In some embodiments, A7is leucine (L). In some embodiments, A8 is an amino acid selected from the group consisting of M, L, and R. In some embodiments, A9 is an amino acid selected from the group consisting of F and L. In some embodiments, A10is an amino acid selected from the group consisting of L, P, and I. In some embodiments, A11 is an amino acid selected from the group consisting of W, D, and T. In some embodiments, A12 is an amino acid selected from the group consisting of G, S, and T. In some embodiments, A13is an amino acid selected from the group consisting of L and P. In some embodiments, A14is an amino acid selected from the group consisting of V and S. In some embodiments, A15 is an amino acid selected from the group consisting of C, T, and K. In some embodiments, A16 is an amino acid selected from the group consisting of A, L, and G.
[0077] It is to be understood that a variant of SEQ ID NO: 1 is not required to comprise a substitution at each position where a substitution is provided, but rather need only contain one substitution to be within the scope of Formula I. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 2 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 3 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 4 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 5 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 6 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 8 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 9 of 18 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 10 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 11 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 12 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 13 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 14 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 15 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at position 16 of SEQ ID NO: 1. The variant may also comprise any number of substitutions as provided by Formula I. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at at least one position corresponding to position 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, or 16 of SEQ ID NO: 1. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 1 and a substitution at more than one position corresponding to position 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, or 16 of SEQ ID NO: 1.
[0078] Variants of SEQ ID NO: 2 (Formula II)
[0079] In some embodiments, the signal peptide comprises an amino acid sequence represented by: B1-B2-B3-B4-B5-B6-B7-B8-B9-B10-B11-B12-B13-B14-B15-B16-B17-B18(Formula II); wherein the identity of each of B1 – B18 are as provided for in Table 3 below. Table 3 Position Suitable Amino Acids19 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Position Suitable Amino Acids B7 L S
[0080] In some embodiments, B1 is methionine (M). In some embodiments, B2 is an amino acid selected from the group consisting of K and S. In some embodiments, B3 is an amino acid selected from the group consisting of F and I. In some embodiments, B4is an amino acid selected from the group consisting of L and S. In some embodiments, B5is an amino acid selected from the group consisting of H and L. In some embodiments, B6 is an amino acid selected from the group consisting of W and S. In some embodiments, B7is an amino acid selected from the group consisting of L and S. In some embodiments, B8is an amino acid selected from the group consisting of M and L. In some embodiments, B9 is an amino acid selected from the group consisting of S and I. In some embodiments, B10 is an amino acid selected from the group consisting of V and L. In some embodiments, B11is an amino acid selected from the group consisting of Y and L. In some embodiments, B12 is an amino acid selected from the group consisting of V and P. In some embodiments, B13 is an amino acid selected from the group consisting of V and I. In some embodiments, B14is an amino acid selected from the group consisting of E and W. In some embodiments, B15 is an amino acid selected from the group consisting of L and I. In some embodiments, B16 is an amino acid selected from the group consisting of L and N. In some embodiments, B17is an amino acid selected from the group 20 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT consisting of R and M. In some embodiments, B18is an amino acid selected from the group consisting of S and A.
[0081] It is to be understood that a variant of SEQ ID NO: 2 is not required to comprise a substitution at each position where a substitution is provided, but rather need only contain one substitution to be within the scope of Formula II. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 2 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 3 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 4 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 5 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 6 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 7 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 8 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 9 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 10 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 11 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 12 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 13 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 14 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 15 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 16 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 17 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at position 18 of SEQ ID NO: 2. The variant may also comprise any number of substitutions as provided by 21 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Formula II. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at at least one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 of SEQ ID NO: 2. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 2 and a substitution at more than one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 of SEQ ID NO: 2.
[0082] In some non-limiting embodiments, the variant of SEQ ID NO: 2 comprises the amino acid sequence of SEQ ID NO: 9. In some embodiments, the amino acid sequence of SEQ ID NO: 9 is derived from Formula II as follows: B1 is methionine (M), B2 is lysine (K), B3 is phenylalanine (F), B4is leucine (L), B5is histidine (H), B6is tryptophan (W), B7is leucine (L), B8is methionine (M), B9is serine (S), B10is valine (V), B11is tyrosine (Y), B12is valine (V), B13is valine (V), B14is glutamate (E), B15 is leucine (L), B16 is leucine (L), B17 is arginine (R), and B18 is serine (S).
[0083] Variants of SEQ ID NO: 3 (Formula III)
[0084] In some embodiments, the signal peptide comprises an amino acid sequence represented by: C1-C2-C3-C4-C5-C6-C7-C8-C9-C10-C11-C12-C13-C14-C15-C16-C17-C18-C19 (Formula III); wherein the identity of each of C1 – C19 are as provided for in Table 4 below. Table 4 Position Suitable Amino Acids22 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Position Suitable Amino Acids C11 G A Ln some em o men s,1s me on ne . n some embodiments, C2is an amino acid selected from the group consisting of A, R, T, and W. In some embodiments, C3is an amino acid selected from the group consisting of A, M, L, and T. In some embodiments, C4 is an amino acid selected from the group consisting of Q, M, G, and L. In some embodiments, C5is an amino acid selected from the group consisting of A, V, and K. In some embodiments, C6is an amino acid selected from the group consisting of A, V, and S. In some embodiments, C7 is an amino acid selected from the group consisting of S, A, and G. In some embodiments, C8 is an amino acid selected from the group consisting of A and L. In some embodiments, C9is an amino acid selected from the group consisting of V, A, and F. In some embodiments, C10 is an amino acid selected from the group consisting of Q, H, S, and L. In some embodiments, C11 is an amino acid selected from the group consisting of G, A, and L. In some embodiments, C12is an amino acid selected from the group consisting of L, A, and S. In some embodiments, C13is an amino acid selected from the group consisting of A, F, W, and C. In some embodiments, C14 is an amino acid selected from the group consisting of A, T, G, and L. In some embodiments, C15is an amino acid selected from the group consisting of Q, A, G, and T. In some embodiments, C16is an amino acid selected from the group consisting of C, A, and S. In some embodiments, C17 is an amino acid selected from the group consisting of A and S. In some embodiments, C18 is an amino acid selected from the group consisting of Q, A, L, and Y. In some embodiments, C19is an amino acid selected from the group consisting of A and P. 23 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT
[0086] It is to be understood that a variant of SEQ ID NO: 3 is not required to comprise a substitution at each position where a substitution is provided, but rather need only contain one substitution to be within the scope of Formula III. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 2 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 3 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 4 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 5 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 6 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 7 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 8 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 9 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 10 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 11 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 12 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 13 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 14 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 15 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 16 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 17 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 18 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at position 19 of SEQ ID NO: 3. The variant may also comprise any number of substitutions as provided by Formula III. Accordingly, in some 24 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at at least one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO: 3. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 3 and a substitution at more than one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO: 3.
[0087] Variants of SEQ ID NO: 4 (Formula IV)
[0088] In some embodiments, the signal peptide comprises an amino acid sequence represented by: D1-D2-D3-D4-D5-D6-D7-D8-D9-D10-D11-D12-D13-D14-D15-D16-D17-D18-D19-D20(Formula IV); wherein the identity of each of D1 – D20 are as provided for in Table 5 below. Table 5 Position Suitable Amino Acids25 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Position Suitable Amino Acids D17 L S, . embodiments, D2is serine (S). In some embodiments, D3 is an amino acid selected from the group consisting of K and R. In some embodiments, D4 is an amino acid selected from the group consisting of C and E. In some embodiments, D5is leucine (L). In some embodiments, D6is an amino acid selected from the group consisting of P and A. In some embodiments, D7is an amino acid selected from the group consisting of A and P. In some embodiments, D8 is an amino acid selected from the group consisting of V and L. In some embodiments, D9 is an amino acid selected from the group consisting of F and L. In some embodiments, D10is leucine (L). In some embodiments, D11is an amino acid selected from the group consisting of A and L. In some embodiments, D12 is an amino acid selected from the group consisting of H and L. In some embodiments, D13 is an amino acid selected from the group consisting of W and L. In some embodiments, D14is an amino acid selected from the group consisting of V and S. In some embodiments, D15 is an amino acid selected from the group consisting of L and I. In some embodiments, D16 is an amino acid selected from the group consisting of L and H. In some embodiments, D17is an amino acid selected from the group consisting of L and S. In some embodiments, D18is an amino acid selected from the group consisting of V and A. In some embodiments, D19 is leucine (L). In some embodiments, D20 is an amino acid selected from the group consisting of R and A.
[0090] It is to be understood that a variant of SEQ ID NO: 4 is not required to comprise a substitution at each position where a substitution is provided, but rather need only contain one substitution to be within the scope of Formula IV. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 3 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 4 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 6 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of 26 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT SEQ ID NO: 4 and a substitution at position 7 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 8 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 9 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 11 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 12 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 13 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 14 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 15 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 16 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 17 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 18 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at position 20 of SEQ ID NO: 4. The variant may also comprise any number of substitutions as provided by Formula IV. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at at least one position corresponding to position 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, or 20 of SEQ ID NO: 4. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 4 and a substitution at more than one position corresponding to position 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, or 20 of SEQ ID NO: 4.
[0091] Variants of SEQ ID NO: 5 (Formula V)
[0092] In some embodiments, the signal peptide comprises an amino acid sequence represented by: E1-E2-E3-E4-E5-E6-E7-E8-E9-E10-E11-E12-E13-E14-E15-E16-E17-E18-E19-E20-E21-E22 (Formula V); wherein the identity of each of E1– E22are as provided for in Table 6 below. Table 6 27 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Position Suitable Amino Acids E1 M
[0093] In some embodiments, E1 is methionine (M). In some embodiments, E2 is an amino acid selected from the group consisting of D, A, F, and P. In some embodiments, E3 is an amino acid selected from the group consisting of L, P, and G. In some embodiments, E4is an amino acid selected from the group consisting of P, L, E, and F. In some embodiments, E5 is an amino acid selected from the group consisting of C, L, and Q. In some embodiments, E6 is an amino acid selected from the group consisting of C, F, A, Y, and L. In some embodiments, E7is an amino acid selected from the group consisting of L, V, and Q. In some embodiments, E8is an amino acid 28 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT selected from the group consisting of W, A, L, N, and T. In some embodiments, E9is an amino acid selected from the group consisting of L, G, F, and C. In some embodiments, E10 is an amino acid selected from the group consisting of V, L, and P. In some embodiments, E11 is an amino acid selected from the group consisting of F, V, A, and L. In some embodiments, E12is an amino acid selected from the group consisting of F, V, L, Y, and I. In some embodiments, E13 is an amino acid selected from the group consisting of F, L, C, and T. In some embodiments, E14 is an amino acid selected from the group consisting of S, L, A, V, and G. In some embodiments, E15is an amino acid selected from the group consisting of C, L, V, F, and T. In some embodiments, E16 is an amino acid selected from the group consisting of L, S, and W. In some embodiments, E17 is an amino acid selected from the group consisting of V, S, G, and L. In some embodiments, E18is an amino acid selected from the group consisting of P, M, D, H, and S. In some embodiments, E19is an amino acid selected from the group consisting of P, A, G, and W. In some embodiments, E20 is an amino acid selected from the group consisting of G, A, R, T, and V. In some embodiments, E21is an amino acid selected from the group consisting of H, T, Q, N, and A. In some embodiments, E22 is an amino acid selected from the group consisting of G, P, C, and L.
[0094] It is to be understood that a variant of SEQ ID NO: 5 is not required to comprise a substitution at each position where a substitution is provided, but rather need only contain one substitution to be within the scope of Formula V. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 2 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 3 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 4 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 5 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 6 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 7 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 8 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 9 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 10 of 29 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 11 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 12 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 13 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 14 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 15 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 16 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 17 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 18 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 19 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 20 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 21 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at position 22 of SEQ ID NO: 5. The variant may also comprise any number of substitutions as provided by Formula V. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at at least one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 of SEQ ID NO: 5. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 5 and a substitution at more than one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 of SEQ ID NO: 5.
[0095] Variants of SEQ ID NO: 6 (Formula VI)
[0096] In some embodiments, the signal peptide comprises an amino acid sequence represented by: F1-F2-F3-F4-F5-F6-F7-F8-F9-F10-F11-F12-F13-F14-F15-F16-F17-F18-F19-F20-F21-F22-F23 (Formula VI); wherein the identity of each of F1– F23are as provided for in Table 7 below. 30 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Table 7 Position Suitable Amino Acids F1 M
[0097] In some embodiments, F1 is methionine (M). In some embodiments, F2 is an amino acid selected from the group consisting of A and P. In some embodiments, F3is an amino acid selected from the group consisting of G and S. In some embodiments, F4is glycine (G). In some embodiments, F5 is an amino acid selected from the group consisting of R and T. In some embodiments, F6 is an amino acid selected from the group consisting of C and G. In some 31 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT embodiments, F7is an amino acid selected from the group consisting of G and K. In some embodiments, F8 is an amino acid selected from the group consisting of P and T. In some embodiments, F9 is an amino acid selected from the group consisting of Q and V. In some embodiments, F10is an amino acid selected from the group consisting of L and S. In some embodiments, F11 is an amino acid selected from the group consisting of T and L. In some embodiments, F12 is an amino acid selected from the group consisting of A and L. In some embodiments, F13is an amino acid selected from the group consisting of L and A. In some embodiments, F14 is leucine (L). In some embodiments, F15 is an amino acid selected from the group consisting of A and I. In some embodiments, F16 is an amino acid selected from the group consisting of A and M. In some embodiments, F17is an amino acid selected from the group consisting of W and A. In some embodiments, F18is an amino acid selected from the group consisting of I and Y. In some embodiments, F19 is an amino acid selected from the group consisting of A and Q. In some embodiments, F20 is an amino acid selected from the group consisting of A and R. In some embodiments, F21is an amino acid selected from the group consisting of V and A. In some embodiments, F22 is an amino acid selected from the group consisting of A and Y. In some embodiments, F23 is an amino acid selected from the group consisting of A and P.
[0098] It is to be understood that a variant of SEQ ID NO: 6 is not required to comprise a substitution at each position where a substitution is provided, but rather need only contain one substitution to be within the scope of Formula VI. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 2 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 3 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 5 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 6 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 7 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 8 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 9 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of 32 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT SEQ ID NO: 6 and a substitution at position 10 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 11 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 12 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 13 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 15 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 16 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 17 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 18 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 19 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 20 of SEQ ID NO: 6. . In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 21 of SEQ ID NO: 6. . In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 22 of SEQ ID NO: 6. . In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at position 23 of SEQ ID NO: 6. The variant may also comprise any number of substitutions as provided by Formula VI. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at at least one position corresponding to position 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, or 23 of SEQ ID NO: 6. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 6 and a substitution at more than one position corresponding to position 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, or 23 of SEQ ID NO: 6.
[0099] Variants of SEQ ID NO: 7 (Formula VII)
[0100] In some embodiments, the signal peptide comprises an amino acid sequence represented by: G1-G2-G3-G4-G5-G6-G7-G8-G9-G10-G11-G12-G13-G14-G15-G16-G17-G18-G19-G20-G21-G22-G23-G24- G25-G26(Formula VII); 33 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT wherein the identity of each of G1 – G26 are as provided for in Table 8 below. Table 8 Position Suitable Amino Acids G1 M34 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT
[0101] In some embodiments, G1 is methionine (M). In some embodiments, G2 is an amino acid selected from the group consisting of A and L. In some embodiments, G3 is an amino acid selected from the group consisting of A, V, and M. In some embodiments, G4is an amino acid selected from the group consisting of R, L, and K. In some embodiments, G5 is an amino acid selected from the group consisting of G, F, and R. In some embodiments, G6 is an amino acid selected from the group consisting of R, P, and L. In some embodiments, G7is an amino acid selected from the group consisting of G, L, and A. In some embodiments, G8 is an amino acid selected from the group consisting of L, S, and A. In some embodiments, G9 is an amino acid selected from the group consisting of L, S, and R. In some embodiments, G10is an amino acid selected from the group consisting of C and L. In some embodiments, G11is an amino acid selected from the group consisting of L, G, and F. In some embodiments, G12 is an amino acid selected from the group consisting of T, W, and A. In some embodiments, G13 is an amino acid selected from the group consisting of L, A, and G. In some embodiments, G14is an amino acid selected from the group consisting of S, A, and L. In some embodiments, G15 is an amino acid selected from the group consisting of V, I, and L. In some embodiments, G16 is an amino acid selected from the group consisting of L, S, and I. In some embodiments, G17is leucine (L). In some embodiments, G18is an amino acid selected from the group consisting of A, F, and S. In some embodiments, G19 is an amino acid selected from the group consisting of A, L, and P. In some embodiments, G20 is an amino acid selected from the group consisting of G, S, and L. In some embodiments, G21is an amino acid selected from the group consisting of P, A, and T. In some embodiments, G22is an amino acid selected from the group consisting of S, Q, and V. In some embodiments, G23 is an amino acid selected from the group consisting of A, S, and I. In some embodiments, G24 is an amino acid selected from the group consisting of A, C, and S. In some embodiments, G25is an amino acid selected from the group consisting of A, Y, and D. In some embodiments, G26 is an amino acid selected from the group consisting of S and A.
[0102] It is to be understood that a variant of SEQ ID NO: 7 is not required to comprise a substitution at each position where a substitution is provided, but rather need only contain one substitution to be within the scope of Formula VII. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 2 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of 35 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT SEQ ID NO: 7 and a substitution at position 3 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 4 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 5 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 6 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 7 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 8 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 9 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 10 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 11 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 12 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 13 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 14 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 15 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 16 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 18 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 19 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 20 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 21 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 22 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 23 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 24 of SEQ ID NO: 7. In some embodiments, the 36 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 25 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at position 26 of SEQ ID NO: 7. The variant may also comprise any number of substitutions as provided by Formula VII. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at at least one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, or 26 of SEQ ID NO: 7. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 7 and a substitution at more than one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, or 26 of SEQ ID NO: 7.
[0103] Variants of SEQ ID NO: 8 (Formula VIII)
[0104] In some embodiments, the signal peptide comprises an amino acid sequence represented by: H1-H2-H3-H4-H5-H6-H7-H8-H9-H10-H11-H12-H13-H14-H15-H16-H17-H18-H19-H20-H21-H22-H23-H24- H25-H26-H27-H28-H29-H30 (Formula VIII); wherein the identity of each of H1– H30are as provided for in Table 9 below. Table 9 Position Suitable Amino Acids37 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Position Suitable Amino Acids H12 L K
[0105] In some embodiments, H1is methionine (M). In some embodiments, H2is an amino acid selected from the group consisting of A and G. In some embodiments, H3 is an amino acid selected from the group consisting of P and A. In some embodiments, H4 is an amino acid selected from the group consisting of H and A. In some embodiments, H5is an amino acid selected from the group consisting of D and G. In some embodiments, H6is an amino acid selected from the group consisting of P and R. In some embodiments, H7 is an amino acid selected from the group consisting of G and Q. In some embodiments, H8 is an amino acid selected from the group consisting of S and D. In some embodiments, H9is an amino acid selected from the group consisting of L and F. In some embodiments, H10 is an amino acid selected from the group consisting of T and L. In some embodiments, H11 is an amino acid selected from the group 38 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT consisting of T and F. In some embodiments, H12is an amino acid selected from the group consisting of L and K. In some embodiments, H13 is an amino acid selected from the group consisting of V and A. In some embodiments, H14 is an amino acid selected from the group consisting of P and M. In some embodiments, H15is an amino acid selected from the group consisting of W and L. In some embodiments, H16 is an amino acid selected from the group consisting of A and T. In some embodiments, H17 is an amino acid selected from the group consisting of A and I. In some embodiments, H18is an amino acid selected from the group consisting of A and S. In some embodiments, H19 is an amino acid selected from the group consisting of L and W. In some embodiments, H20 is leucine (L). In some embodiments, H21 is an amino acid selected from the group consisting of L ad T. In some embodiments, H22is an amino acid selected from the group consisting of A and L. In some embodiments, H23is an amino acid selected from the group consisting of L and T. In some embodiments, H24 is an amino acid selected from the group consisting of G and C. In some embodiments, H25 is an amino acid selected from the group consisting of V and F. In some embodiments, H26is an amino acid selected from the group consisting of E and P. In some embodiments, H27 is an amino acid selected from the group consisting of R and G. In some embodiments, H28 is alanine (A). In some embodiments, H29is an amino acid selected from the group consisting of L and T. In some embodiments, H30is an amino acid selected from the group consisting of A and S.
[0106] It is to be understood that a variant of SEQ ID NO: 8 is not required to comprise a substitution at each position where a substitution is provided, but rather need only contain one substitution to be within the scope of Formula VIII. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 2 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 3 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 4 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 5 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 6 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 7 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 8 of 39 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 9 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 10 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 11 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 12 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 13 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 14 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 15 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 16 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 17 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 18 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 19 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 21 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 22 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 23 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 24 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 25 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 26 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 27 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 29 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at position 30 of SEQ ID NO: 8. The variant may also comprise any number of substitutions as provided by 40 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Formula VIII. Accordingly, in some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at at least one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, or 30 of SEQ ID NO: 8. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 8 and a substitution at more than one position corresponding to position 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, or 30 of SEQ ID NO: 8.
[0107] In some embodiments, the signal peptide is a novel signal peptide. In the context of the present disclosure, a “novel” signal peptide is understood to comprise an amino acid sequence not found in nature or not yet known to exist in nature. Accordingly, if an embodiment references a novel signal peptide, it is understood to exclude any corresponding native sequence. For example, in some embodiments, a novel signal peptide is provided, wherein the novel signal peptide comprises an amino acid sequence corresponding to Formula V. In such an embodiment, if a native signal peptide could be construed from the formula of Formula V, the embodiment is understood to exclude said native signal peptide.
[0108] In some embodiments, a novel signal peptide is provided. In some embodiments, the novel signal peptide comprises an amino acid sequence selected from the group consisting of Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII. In some embodiments, the novel signal peptide comprises an amino acid sequence of Formula I. In some embodiments, the novel signal peptide comprises an amino acid sequence of Formula II. In some embodiments, the novel signal peptide comprises an amino acid sequence of Formula III. In some embodiments, the novel signal peptide comprises an amino acid sequence of Formula IV. In some embodiments, the novel signal peptide comprises an amino acid sequence of Formula V. In some embodiments, the novel signal peptide comprises an amino acid sequence of Formula VI. In some embodiments, the novel signal peptide comprises an amino acid sequence of Formula VII. In some embodiments, the novel signal peptide comprises an amino acid sequence of Formula VIII. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% (e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identity to an amino acid sequence selected 41 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, or 8. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 1. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 2. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 3. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 4. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 5. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 6. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 7. In some embodiments, the novel signal peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 8. Recombinant Polypeptides
[0109] In some embodiments, a recombinant polypeptide is provided, the recombinant polypeptide comprising a formula of X1-Z1, wherein X1 is a signal peptide as provided for herein and Z1 is a payload protein. In some embodiments, the recombinant polypeptide comprises a formula of X1-Z1, wherein X1is a novel signal peptide as provided for herein and Z1is a payload protein.
[0110] In some embodiments, X1 comprises an amino acid sequence selected from the group consisting of Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII. In some embodiments, X1comprises an amino acid sequence of Formula I. In some embodiments, X1 comprises an amino acid sequence of Formula II. In some embodiments, X1 comprises an amino acid sequence of Formula III. In some embodiments, X1 comprises an amino acid sequence of Formula IV. In some embodiments, X1comprises an amino acid sequence of Formula V. In some embodiments, X1 comprises an amino acid sequence of Formula VI. In some embodiments, X1 comprises an amino acid sequence of Formula VII. In some embodiments, X1comprises an amino acid sequence of Formula VIII. 42 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT
[0111] In some embodiments, X1comprises an amino acid sequence having at least 70% (e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9. In some embodiments, X1 comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 1. In some embodiments, X1comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 2. In some embodiments, X1 comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 3. In some embodiments, X1comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 4. In some embodiments, X1comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 5. In some embodiments, X1 comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 6. In some embodiments, X1comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 7. In some embodiments, X1 comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 8. In some embodiments, X1comprises an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 9.
[0112] In some embodiments, the payload protein, Z1, may be any peptide or protein. In some embodiments, the payload protein, Z1, is any peptide or protein that is useful in the treatment of a disease or disorder. In some embodiments, the payload protein, Z1, is any peptide or protein that is useful in the treatment of a disease or disorder associated with the nucleus of a cell. In some embodiments, the payload protein, Z1, is any peptide or protein that is useful for gene editing, such as, but not limited to, Cas9, a zinc finger nuclease, a Transcription Activator-Like Effector Nuclease (TALEN), or a meganucleas.
[0113] In some embodiments, X1 is linked directly to Z1. In some embodiments, X1 is linked indirectly to Z1through, for example, a polypeptide linker. Polypeptide linkers are known in the art, and any such linker may be incorporated into the recombinant polypeptide of the present disclosure. Accordingly, in some embodiments, the recombinant polypeptide may be represented by the formula X1-(Y1)a-Z1, wherein X1is a signal peptide as provided for herein, Y1is a linker, such as but not limited to a polypeptide linker, Z1is a payload protein as provided for herein, and 43 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT a is an integer selected from 0 or 1. In some embodiments, X1is a novel signal peptide as provided for herein. Nucleic Acid Molecules
[0114] In some embodiments, a nucleic acid molecule is provided. In some embodiments, the nucleic acid molecule encodes for a signal peptide as provided for herein. In some embodiments, the nucleic acid molecule encodes for a novel signal peptide as provided for herein. In some embodiments, the nucleic acid molecule is a deoxyribonucleotide sequence (DNA). In some embodiments, the nucleic acid molecule is a ribonucleic acid sequence (RNA).
[0115] In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence selected from the group consisting of Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence of Formula I. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence of Formula II. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence of Formula III. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence of Formula IV. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence of Formula V. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence of Formula VI. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence of Formula VII. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence of Formula VIII.
[0116] In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% (e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identity to an amino acid sequence selected from the group consisting 44 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 1. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 2. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 3. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 4. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 5. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 6. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 7. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 8. In some embodiments, the nucleic acid molecule encodes for a signal peptide (e.g., a novel signal peptide) comprising an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO: 9.
[0117] In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide as provided for herein. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide comprising a formula of X1-Z1, wherein X1is a signal peptide as provided for herein and Z1 is a payload protein as provided for herein. In some embodiments, the recombinant polypeptide comprises a formula of X1-Z1, wherein X1 is a novel signal peptide as provided for herein and Z1is a payload protein as provided for herein. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide comprising a formula of X1-(Y1)a-Z1, wherein X1 is a signal peptide (e.g., a novel signal peptide) as provided for herein, Y1 is a linker, such as but not limited to a polypeptide linker, Z1is a payload protein as provided for herein, and a is an integer selected from 0 or 1. 45 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT
[0118] In embodiments wherein Z1is a peptide or protein useful for gene editing, the nucleic acid molecule may further comprise any additional necessary components for gene editing, for example a guide RNA or the like. Alternatively, the additional necessary components for gene editing may be provided in one or more additional nucleic acid molecules.
[0119] The skilled artisan will readily be able to deduce an appropriate DNA or RNA sequence based on the amino acid sequences and variations provided for herein. Further, the skilled artisan will readily recognize that, due to the degenerate nature of codons, multiple nucleic acid molecules are available to encode for the same amino acid sequence. Thus, any nucleic acid sequence capable of encoding for the amino acid sequences provided for herein are within the scope of the present disclosure.
[0120] In some embodiments, a nucleic acid molecule as provided for here disclosed may further comprise one or more elements selected from, but not limited to, a promoter, an enhancer, a leader, a transcription start site (TSS), a linker, 5’ and 3’ untranslated regions (UTRs), Kozak sequence, an intron, a polyadenylation signal, cap sequences, enhancers, viral sequences, IRES sequences or a termination region or any element, that is suitable or necessary for regulating or allowing expression of the recombinant polypeptide as provided for herein in a cell. By definition, wild type untranslated regions (UTRs) of a gene are transcribed but not translated. In mRNA, the 5’ UTR starts at the transcription start site and continues to the start codon but does not include the start codon; whereas, the 3’ UTR starts immediately following the stop codon and continues until the transcriptional termination signal. The regulatory features of a UTR can be incorporated into the polynucleotides of the present disclosure to, for example, enhance the stability of the molecule. The specific features can also be incorporated to ensure controlled down-regulation of the transcript in case they are misdirected to undesired organs sites. In some embodiments, any suitable naturally occurring or synthetic UTR sequence can be incorporated into the nucleic acid molecules disclosed herein. Other non-UTR sequences may also be incorporated within the nucleic acid molecules. For example, introns or portions of intron sequences may be incorporated into regions of the nucleic acid molecules of the disclosure. Incorporation of intronic sequences may increase protein production as well as polynucleotide levels. Combinations of features may be included in flanking regions and may be contained within other features. For example, the ORF may be flanked by a 5’ UTR which may contain a strong Kozak translational initiation signal and / or a 3’ UTR which may include an oligo(dT) sequence for templated addition of a poly-A tail. 46 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT 5’ UTR may comprise a first polynucleotide fragment and a second polynucleotide fragment from the same and / or different genes.
[0121] In some embodiments, the nucleic acid molecules disclosed herein may be assembled inside a cell. In some embodiments, the nucleic acid molecules may be synthesized in vivo. In some embodiments, the nucleic acid molecules may be synthesized in vitro using methods known in the art for example in vitro transcription, DNA, RNA and cDNA synthesis methods. In some embodiments, the nucleic acid molecules disclosed herein may be incorporated into a suitable viral vector, expression cassette, expression vector, transposon, extrachromosomal element, integrated into the chromosome, host cell, delivery systems.
[0122] In some embodiments, the nucleic acid molecule is a chemically modified nucleic acid molecule. In some embodiments, the nucleic acid molecule e may comprise one or more modified nucleosides comprising a modified sugar moiety. Such compounds comprising one or more sugar- modified nucleosides may have desirable properties, such as enhanced nuclease stability relative to an oligonucleotide comprising only nucleosides comprising naturally occurring sugar moieties. In some embodiments, modified sugar moieties are substituted sugar moieties. In some embodiments, modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of substituted sugar moieties. In some embodiments, the modified nucleic acid molecule may comprise a modified backbone, for example, phosphorothioates, phosphotriesters, morpholinos, methyl phosphonates, short chain alkyl or cycloalkyl intersugar linkages or short chain heteroatomic or heterocyclic inter sugar linkages.
[0123] In some embodiments, modified sugar moieties are substituted sugar moieties comprising one or more non-bridging sugar substituent, including but not limited to substituents at the 2’ and / or 5’ positions. Examples of sugar substituents suitable for the 2’-position, include, but are not limited to: 2’-F, 2-OCH3 (“OMe” or “O-methyl”), and 2’-O(CH2)2OCH3 (“MOE”). In certain aspects, sugar substituents at the 2’ position is selected from allyl, amino, azido, thio, O-allyl, O— C1-C10 alkyl, O—C1-C10 substituted alkyl; OCF3, O(CH2)2SCH3, O(CH2)2—O—N(Rm)(Rn), and O—CH2— C(=O)—N(Rm)(Rn), where each Rm and Rn is, independently, H or substituted or unsubstituted C1-C10 alkyl. Examples of sugar substituents at the 5’-position, include, but are not limited to: 5’- methyl (R or S); 5’-vinyl, and 5’-methoxy. In some embodiments, substituted 47 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT sugars comprise more than one non-bridging sugar substituent, for example, T-F-5’-methyl sugar moieties.
[0124] Nucleosides comprising 2’-substituted sugar moieties are referred to as 2’-substituted nucleosides. In some embodiments, a 2’-substituted nucleoside comprises a 2’-substituent group selected from halo, allyl, amino, azido, SH, CN, OCN, CF3, OCF3, O, S, or N(Rm)-alkyl; O, S, or N(Rm)-alkenyl; O, S or N(Rm)-alkynyl; O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O- aralkyl, O(CH2)2SCH3, O(CH2)2—O—N(Rm)(Rn) or O—CH2—C(=O)—N(Rm)(Rn), where each Rm and Rn is, independently, H, an amino protecting group or substituted or unsubstituted CI-C10 alkyl. These 2’-substituent groups can be further substituted with one or more substituent groups independently selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO2), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.
[0125] In some embodiments, a 2’-substituted nucleoside comprises a 2’-substituent group selected from F, NH2, N3 OCF3, O—CH3, O(CH2)3NH2, CH2—CH=CH2, O—CH2—CH=CH2, OCH2CH2OCH3, O(CH2)2SCH3, O—(CH2)2—O—N(Rm)(Rn), O(CH2)2O(CH2)2N(CH3)2, and N- substituted acetamide (O—CH2—C(=O)—N(Rm)(Rn) where each Rm and R. is, independently, H, an amino protecting group or substituted or unsubstituted C1-C10 alkyl. In some embodiments, a 2’- substituted nucleoside comprises a sugar moiety comprising a 2’-substituent group selected from F, OCF3, O—CH3, O2CH2OCH3, O(CH2)2SCH3, O(CH2)2—O—N(CH3)2, — O(CH2)2O(CH2)2N(CH3)2, and O—CH2—C(=O)—N(H)CH3. In some embodiments, a 2’- substituted nucleoside comprises a sugar moiety comprising a 2’-substituent group selected from F, O—CH3, and OCH2CH2OCH3.
[0126] Certain modified sugar moieties comprise a bridging sugar substituent that forms a second ring resulting in a bicyclic sugar moiety. In some such aspects, the bicyclic sugar moiety comprises a bridge between the 4’ and the 2’ furanose ring atoms. Examples of such 4’ to 2’ sugar substituents, include, but are not limited to: —[C(Ra)(Rb)]—, —[C(Ra)(Rb)]n—O—, — C(RaRb)— N(R)—O— or, —C(RaRb)—O—N(R)—; 4’-CH2-2’, 4’-(CH2)2-2’, 4’-(CH2)—0-2’ (LNA); 4’-(CH2)— S-2’; 4’-(CH2)2—0-2’ (ENA); 4’-CH(CH3)—0-2’ (cEt) and 4’- CH(CH2OCH3)—0-2’, and analogs thereof (see, e.g., U.S. Pat. No.7,399,845); 4’-C(CH3)(CH3)— 0-2’ and analogs thereof, (see, e.g., WO 2009 / 006478); 4’-CH2—N(OCH3)-2’ and analogs thereof (see, e.g., WO2008 / 150729); 4’- CH2—O—N(CH3)-2’ (see, e.g., US2004 / 0171570, published Sep.2, 2004); 4’-CH2—O—N(R)-2’, and 4-CH2—N(R)—0-2’-, wherein each R is, independently, 48 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT H, a protecting group, or C1-C12 alkyl; 4-CH2—N(R)—0-2’, wherein R is H, C1-C12 alkyl, or a protecting group (see, U.S. Pat. No. 7,427,672); 4’-CH2—C(H)(CH3)-2’ (see, e.g., Chattopadhyaya et al., J. Org. Chern., 2009, 74, 118-134); and 4-CH2—C(=CH2)-2’ and analogs thereof (see, PCT International Application WO 2008 / 154401).
[0127] In some embodiments, such 4’ to 2’ bridges independently comprise from 1 to 4 linked groups independently selected from —[C(Ra)(Rb)]n—, —C(Ra)=C(Rb)—, —C(Ra)=N—, — C(=NRa)— , —C(=O)—, —C(=S)—, —O—, —Si(Ra)2—S(=O)x—, and —N(Ra)—; wherein: x is 0, 1, or 2; n is 1,2, 3, or 4; each Ra and Rb is, independently, H, a protecting group, hydroxyl, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, heterocycle radical, substituted heterocycle radical, heteroaryl, substituted heteroaryl, C5-C7 alicyclic radical, substituted C5-C7 alicyclic radical, halogen, OJ1, NJ1J2, SJ1, N3, C00J1, acyl (C(=O)—H), substituted acyl, CN, sulfonyl (S(=0)2-J1), or sulfoxyl (S(=0)-J1); and each J1 and J2 is, independently, H, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, acyl (C(=O)—H), substituted acyl, a heterocycle radical, a substituted heterocycle radical, 01-012 aminoalkyl, substituted C1- C12 aminoalkyl, or a protecting group.
[0128] Nucleosides comprising bicyclic sugar moieties are referred to as bicyclic nucleosides or BNAs. Bicyclic nucleosides include, but are not limited to, (A) α-L-Methyleneoxy (4-CH2—O- 2’) BNA, (B) β-D-Methyleneoxy (4-CH2—0-2’) BNA (also referred to as locked nucleic acid or LNA), (C) Ethyleneoxy (4’-(CH2)2—0-2’) BNA, (D) Aminooxy (4’-CH2—O—N(R)-2’) BNA, (E) Oxyamino (4’-CH2—N(R)—0-2’) BNA, (F) Methyl (methyleneoxy) (4’-CH(CH3)—0-2’) BNA (also referred to as constrained ethyl or cEt), (G) methylene-thio (4-CH2—S-2’) BNA, (H) methylene¬amino (4’-CH2—N(R)-2’) BNA, (I) methyl carbocyclic (4’-CH2—CH(CH3)-2’) BNA, (J) propylene carbocyclic (4’-(CH2)3-2’) BNA, and (K) Methoxy(ethyleneoxy) (4’- CH(CH2OMe)-O-2’) BNA (also referred to as constrained MOE or cMOE). Additional bicyclic sugar moieties are known in the art, and any such bicyclic sugar moiety is within the scope of the present disclosure.
[0129] In some embodiments, bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration. For example, a nucleoside comprising a 4’-2’ methylene-oxy bridge, may be in the .alpha.-L configuration or in the .beta.-D 49 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT configuration. α-L-methyleneoxy (4-CH2—O-2’) bicyclic nucleosides have previously been incorporated into antisense polynucleotides that showed antisense activity.
[0130] In some embodiments, substituted sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent.
[0131] In some embodiments, modified sugar moieties are sugar surrogates. In some embodiments, the oxygen atom of the naturally occurring sugar is substituted, e.g., with a sulfur, carbon or nitrogen atom. In some such aspects, such modified sugar moiety also comprises bridging and / or non-bridging substituents as described above. For example, certain sugar surrogates comprise a 4’-sulfur atom and a substitution at the 2’-position and / or the 5’ position. By way of additional example, carbocyclic bicyclic nucleosides having a 4-2’ bridge have been described.
[0132] In some embodiments, sugar surrogates comprise rings having other than 5-atoms. For example, In some embodiments, a sugar surrogate comprises a six-membered tetrahydropyran (THP). Such tetrahydropyrans may be further modified or substituted. Nucleosides comprising such modified tetrahydropyrans include, but are not limited to, hexitol nucleic acid (HNA), anitol nucleic acid (ANA), mannitol nucleic acid (MNA), and fluoro HNA (F-HNA).
[0133] Many other bicyclo and tricyclo sugar surrogate ring systems are also known in the art that can be used to modify nucleosides for incorporation into antisense compounds, and any such sugar surrogate ring system is within the scope of the present disclosure.
[0134] Combinations of modifications are also provided without limitation, such as, but not limited to, 2-F-5’- methyl substituted nucleosides and replacement of the ribosyl ring oxygen atom with S and further substitution at the 2’-position or alternatively 5’-substitution of a bicyclic nucleic acid. The synthesis and preparation of carbocyclic bicyclic nucleosides along with their oligomerization and biochemical studies have also been described.
[0135] In some embodiments, the present disclosure provides nucleic acid molecules comprising modified nucleosides. Those modified nucleotides may include modified sugars, modified nucleobases, and / or modified linkages. The specific modifications are selected such that the resulting polynucleotides possess desirable characteristics. In some embodiments, the nucleic acid molecules comprise one or more RNA-like nucleosides. In some embodiments, the nucleic acid molecules comprise one or more DNA- like nucleotides. 50 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT
[0136] In some embodiments, nucleosides of the present disclosure comprise one or more unmodified nucleobases. In some embodiments, nucleosides of the present disclosure comprise one or more modified nucleobases.
[0137] In some embodiments, modified nucleobases are selected from: universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. 5- substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2- aminopropyladenine, 5-propynyluracil; 5-propynylcytosine; 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2- propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2- thiothymine and 2- thiocytosine, 5-halouracil and cytosine, 5-propynyl CH3, uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4- thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8- substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5- substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 2-F-adenine, 2-amino- adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine, 3-deazaguanine and 3-deazaadenine, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidine([5,4-b][1,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1H- pyrimido[5,4-b][1,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g., 9-(2-aminoethoxy)-H-pyrimido[5,4-13][1,4]benzoxazin-2(3H)-one), carbazole cytidine (2H-pyrimido[4,5-b]indol-2-one), pyridoindole cytidine (H- pyrido[3’,2’:4,5]pyrrolo[2,3- d]pyrimidin-2-one). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza- adenine, 7-deazaguanosine, 2- aminopyridine and 2-pyridone.
[0138] In some embodiments, the present disclosure provides nucleic acid molecules comprising linked nucleosides. In some embodiments, the nucleosides may be linked together using any internucleoside linkage. The two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters (P=O), phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates (P=S). Representative non- phosphorus containing internucleoside linking groups include, but are not limited to, 51 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT methylenemethylimino (—CH2— N(CH3)—O—CH2—), thiodiester (—O—C(O)—S—). thionocarbamate (—O—C(O)(NH)—S—); siloxane (—O—Si(H)2—O—); and N,N’- dimethylhydrazine (—CH2—N(CH3)—N(CH3)—). Modified linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the polynucleotide. In some embodiments, internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers. Representative chiral linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.
[0139] The nucleic acid molecules described herein may comprise one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), such as for sugar anomers, or as (D) or (L) such as for amino acids etc. Included in the antisense compounds provided herein are all such possible isomers, as well as their racemic and optically pure forms.
[0140] Neutral internucleoside linkages include without limitation, phosphotriesters, methylphosphonates, MMI (3-CH2—N(CH3)—O-5’), amide-3 (3-CH2—C(=O)—N(H)-5’), amide- 4 (3’-CH2—N(H)—C(=O)-5’), formacetal (3’-O—CH2—O-5’), and thioformacetal (3’-5- CH2—O-5’). Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides. Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH2 component parts.
[0141] Additional modifications may also be made at other positions on the nucleic acid molecule, particularly the 3’ position of the sugar on the 3’ terminal nucleotide and the 5’ position of 5’ terminal nucleotide. For example, one additional modification of the nucleic acid molecules of the present disclosure involves chemically linking to the polynucleotide one or more additional moieties or conjugates which enhance the activity, cellular distribution or cellular uptake of the polynucleotide. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-5-tritylthiol, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or a 52 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety.
[0142] In some embodiments, a vector is provided. In some embodiments, the vector comprises a nucleic acid molecule as provided for herein. In some embodiments, the nucleic acid molecule encodes for a signal peptide as provided for herein. In some embodiments, the nucleic acid molecule encodes for a novel signal peptide as provided for herein. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide as provided for herein. Cells
[0143] In some embodiments, a cell is provided. In some embodiments, the cell comprises a nucleic acid molecule encoding for a signal peptide as provided for herein. In some embodiments, the cell comprises a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein. In some embodiments, the cell comprises a vector as provided for herein. In some embodiments, the cell is any appropriate cell. In some embodiments, the cell is a mammalian cell. In some embodiments, the cell is a human cell. In some embodiments, the cell is a mammalian cell used in a method of manufacturing a protein product. In some embodiments, the cell is any in vitro cell line. In some embodiments, the cell is any ex vivo cell. In some embodiments, the cell is present in vivo. Compositions
[0144] In some embodiments, a composition is provided. In some embodiments, the composition comprises a vector encoding for a signal peptide as provided for herein and a delivery system. In some embodiments, the composition comprises a vector encoding for a recombinant polypeptide as provided for herein and a delivery system.
[0145] In some embodiments, the delivery system may be a viral vector. In some embodiments, the viral vector is an RNA viral vector. In some embodiments, the viral vector is a DNA viral vector. Non-limiting examples of suitable viral vectors include adenovirus, adeno associated virus (AAV), retrovirus, herpesvirus, lentivirus, poxvirus, or papilloma virus vector.
[0146] In some embodiments, the delivery system is a non-viral delivery system. Non-limiting examples of non-viral delivery systems include polymers, polyplexes, lipids, lipidoids, lipoplexes, liposomes, lipid fusion constructs, polymer nanoparticles, nanoparticles, lipid nanoparticles 53 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT (LNPs), core-shell nanoparticles, solid lipid nanoparticles, metal nanoparticles, self-assembled nucleic acid nanoparticles, hyaluronidase, nanoparticle mimics, ribonucleoproteins, positively charged peptides, small molecule RNA-conjugates, aptamer-RNA chimeras, RNA-fusion protein complexes and any combination thereof.
[0147] The above exemplary delivery systems are not to be construed to be limiting in any way. Appropriate delivery systems are known in the art and any such delivery system is within the scope of the present disclosure. Methods
[0148] Also contemplated herein are methods of using the novel signal peptides and recombinant polypeptides provided for herein.
[0149] In some embodiments, a method of treating a disease or disorder is provided. In some embodiments, the method comprises administering to a subject in need thereof a vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein, thereby treating the disease or disorder. In some embodiments, the payload protein of the recombinant polypeptide is a peptide or protein useful for the treatment of the disease or disorder. In some embodiments, the signal peptide directs the payload protein to be expressed at a particular cellular localization useful for the treatment of the disease or disorder. In some embodiments, the subject in need thereof is administered an effective amount of the vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein. In some embodiments, the subject in need thereof is administered a therapeutically effective amount of the vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein. In some embodiments, the disease or disorder is a disease or disorder associated with the nucleus of a cell. In some embodiments, the disease or disorder is a genetic disease or disorder. In some embodiments, the disease or disorder is any disease or disorder for that would benefit from gene editing or genetic modifications. In some embodiments, the disease or disorder is a DNA associated disease or disorder. In some embodiments, the disease or disorder is any disease or disorder relating to transcription factors, initiation factors, DNA-associated complexes, DNA- associate proteins, or the like.
[0150] In some embodiments, a method of treating a disease or disorder associated with the nucleus of a cell is provided, the method comprising administering to a subject in need thereof a 54 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein, thereby treating the disease or disorder. In some embodiments, the payload protein of the recombinant polypeptide is a peptide or protein useful for the treatment of the disease or disorder associated with the nucleus of a cell. In some embodiments, the signal peptide directs the payload protein to be expressed in the nucleus of a cell, thereby treating the disease or disorder. In some embodiments, the subject in need thereof is administered an effective amount of the vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein. In some embodiments, the subject in need thereof is administered a therapeutically effective amount of the vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein.
[0151] In some embodiments, a method of treating a disease or disorder is provided. In some embodiments, the method comprises administering to a subject in need thereof a composition comprising a vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein, thereby treating the disease or disorder. In some embodiments, the payload protein of the recombinant polypeptide is a peptide or protein useful for the treatment of the disease or disorder. In some embodiments, the signal peptide directs the payload protein to be expressed at a particular cellular localization useful for the treatment of the disease or disorder. In some embodiments, the subject in need thereof is administered an effective amount of the composition. In some embodiments, the subject in need thereof is administered a therapeutically effective amount of the composition. In some embodiments, the disease or disorder is a disease or disorder associated with the nucleus of a cell. In some embodiments, the disease or disorder is a genetic disease or disorder. In some embodiments, the disease or disorder is any disease or disorder for which gene editing may be useful.
[0152] In some embodiments, a method of treating a disease or disorder associated with the nucleus of a cell is provided, the method comprising administering to a subject in need thereof a composition comprising a vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein, thereby treating the disease or disorder. In some embodiments, the payload protein of the recombinant polypeptide is a peptide or protein useful for the treatment of the disease or disorder associated with the nucleus of a cell. In some embodiments, the signal peptide directs the payload protein to be expressed in the nucleus, thereby treating the disease or disorder. In some embodiments, the subject in need thereof is administered an effective amount 55 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT of the composition. In some embodiments, the subject in need thereof is administered a therapeutically effective amount of the composition.
[0153] In some embodiments, a method of producing a payload protein is provided, the method comprising administering to a cell a vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein and culturing the cell under conditions sufficient to produce the payload protein. In some embodiments, the payload protein is secreted from the cell, and the method further comprises collecting a cell supernatant containing the payload protein and purifying the payload protein from the cell supernatant. In some embodiments, the payload protein is not secreted, and the method further comprises collecting the cells comprising the payload protein, lysing the cells, and purifying the payload protein from the cell lysate.
[0154] In some embodiments, a method of manufacturing a payload protein is provided, the method comprising administering to a cell a vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein and culturing the cell under conditions sufficient to produce the payload protein. In some embodiments, the payload protein is secreted from the cell, and the method further comprises collecting a cell supernatant containing the payload protein and purifying the payload protein from the cell supernatant. In some embodiments, the payload protein is not secreted, and the method further comprises collecting the cells comprising the payload protein, lysing the cells, and purifying the payload protein from the cell lysate.
[0155] Without being bound to any particular theory, the novel signal peptides of the present disclosure are useful in the treatment of a disease or disorder associated with the nucleus of a cell through inclusion of the signal peptide in a recombinant polypeptide comprising a payload protein used in the treatment of the disease or disorder. Correct or, in some instances, enhanced targeting of the payload protein to the nucleus is beneficial in the treatment of the disease or disorder. The payload protein is not limited to a particular payload, but rather encompasses any therapeutic (e.g., therapeutic protein) with action in the nucleus of the cell. Furthermore, by utilizing the cells that are afflicted with the disease or disorder associate with the nucleus of a cell to produce the payload protein, the present methods avoid the need of timely and inefficient recombinant protein infusions and instead allow the patient’s own cells to produce the therapeutic molecule.
[0156] The present disclosure is also directed, in part, toward methods of producing or manufacturing a payload protein using the novel signal peptides as provided for herein. Without being bound to any particular theory, the novel signal peptides as provided for herein direct the 56 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT payload protein to a particular cellular or extracellular location, such as but not limited to, the nucleus of the cell. Use of the novel signal peptides to direct a payload protein to a particular cellular or extracellular location can enhance the expression and or production of the payload protein.
[0157] The signal peptides of the present disclosure may also be useful for the delivery of gene editing technologies to the nucleus of a cell. Accordingly, in some embodiments, a method of editing a target nucleic acid molecule in a cell is provided, the method comprising administering a vector comprising a nucleic acid molecule encoding for a recombinant polypeptide having the formula X1-(Y1)a-Z1, wherein X1 is a signal peptide as provided for herein, Y1 is a peptide linker as provided for herein, a is an integer selected from 0 and 1, and Z1is a payload protein useful for gene editing as provided for herein; and at least one nucleic acid molecule that targets the payload protein to the target nucleic acid molecule, thereby editing the target nucleic acid molecule. In some embodiments, the payload protein Z1 is a Cas9, a zinc finger nuclease, a TALEN, or a meganuclease. In some embodiments, the at least one nucleic acid molecule that targets the payload protein to the target nucleic acid molecule is a guide RNA. In some embodiments, the nucleic acid molecule encoding for a recombinant polypeptide having the formula X1-(Y1)a-Z1 and the at least one nucleic acid molecule that targets the payload protein to the target nucleic acid molecule are located in the same vector. In some embodiments, the nucleic acid molecule encoding for a recombinant polypeptide having the formula X1-(Y1)a-Z1 and the at least one nucleic acid molecule that targets the payload protein to the target nucleic acid molecule are located in different vectors.
[0158] In some embodiments, a method of editing a target nucleic acid molecule in a cell in a subject in need thereof is provided, the method comprising administering to the subject a vector comprising a nucleic acid molecule encoding for a recombinant polypeptide having the formula X1-(Y1)a-Z1, wherein X1 is a signal peptide as provided for herein, Y1 is a peptide linker as provided for herein, a is an integer selected from 0 and 1, and Z1 is a payload protein useful for gene editing as provided for herein; and at least one nucleic acid molecule that targets the payload protein to the target nucleic acid molecule, thereby editing the target nucleic acid molecule. In some embodiments, the payload protein Z1 is a Cas9, a zinc finger nuclease, a TALEN, or a meganucleas. In some embodiments, the at least one nucleic acid molecule that targets the payload protein to the target nucleic acid molecule is a guide RNA. In some embodiments, the nucleic acid 57 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT molecule encoding for a recombinant polypeptide having the formula X1-(Y1)a-Z1and the at least one nucleic acid molecule that targets the payload protein to the target nucleic acid molecule are located in the same vector. In some embodiments, the nucleic acid molecule encoding for a recombinant polypeptide having the formula X1-(Y1)a-Z1and the at least one nucleic acid molecule that targets the payload protein to the target nucleic acid molecule are located in different vectors.
[0159] Without being bound to any particular theory, the novel signal peptides of the present disclosure are useful in editing of a target nucleic acid molecule through inclusion of the signal peptide in a recombinant polypeptide comprising a payload protein useful for gene editing, such as Cas9. The novel signal peptides direct the payload protein to the nucleus wherein it can facilitate editing of the target nucleic acid molecule. Accordingly, the novel signal peptides of the present disclosure are also useful in the treatment of any disease or disorder for which gene editing may be useful, as provided for herein. EXAMPLES
[0160] The following examples illustrative of the compounds, compositions, particles, polypeptides, and methods described herein and should not be construed to be limiting in any way. Methods SP-mCherry plasmid (pDNA) construction
[0161] Plasmids were constructed in a similar manner as described in Cheng, Qiang et al. Proceedings of the National Academy of Sciences of the United States of America vol. 120,52 (2023) and International Patent Publication Serial No. WO2024064874A2, each of which is hereby incorporated by reference in their entirety. Briefly, SP-mCherry coding region were obtained directly by PCR with well-designed primers. The SPs of the following examples are as provided in Table 10 below: Table 10 Sequence Reference Sequence SEQ ID NO:58 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Sequence Reference Sequence SEQ ID NO: Nov-Nuc-26-1 MAARGRGLLCLTLSVLLAAGPSAAAS SEQ ID NO: 7ard protocols. After validation by sequencing, SP-mCherry plasmids were ready for in vitro screening. In vitro SP screening by pDNA transfection
[0162] To perform SPs screening, pDNA transfection was executed in cells. pDNAs were encapsulated in Lipfectamine2000 and administered to HeLa cells at 100 ng / well in 6 well plates and allowed to incubate for 24 hours. Following incubation, Hoechst 33342 dye was used to stain DNA in the nucleus of live cells via manufacturer protocols. The cells were then imaged using confocal microscopy for Hoechst 33342 (nucleus) signal with mCherry signal. Fiji software was utilized to assess co-localization of nucleus signal with mCherry signal and quantified. Example 1: Use of novel signal peptides to deliver mCherry to the nucleus of a cell.
[0163] The ability of the novel signal peptides provided for herein to deliver payload protein to the nucleus of a cell was tested by constructing signal peptide modified mCherry pDNA plasmids containing an encoded nucleus targeting signal peptide directly upstream of the mCherry sequence. As a control, unmodified mCherry plasmids containing no signal peptide were also used. The general plasmid construction as well as the general method is as provided above and in FIG.1A.
[0164] As shown in FIG.1B-1F, four of the five novel signal peptides tested were able to drive mCherry protein to the nucleus, whereas mCherry protein without the nucleus targeting signal peptides did not localize to the nucleus. Results for each of Nov-Nuc 18-1 (SEQ ID NO: 9), Nov- Nuc 19-1 (SEQ ID NO: 3), Nov-Nuc 22-1 (SEQ ID NO: 5), and Nov-Nuc 26-1 (SEQ ID NO: 7) exhibited a statistically significant increase in nucleus localized mCherry as compared to the NO SP control, while Nov-Nuc 16-1 (SEQ ID NO: 1) demonstrated a trend toward an increase in nuclear localized mCherry, albeit not a significant increase.
[0165] The data for this example demonstrates that nucleus targeting signal peptide sequences encoded directly upstream from the mCherry sequence drives localization of the mCherry protein to the nucleus. 59 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT Example 2: Use of novel signal peptides to deliver Cas9 to the nucleus.
[0166] Example 2 is carried out using similar methods to Example 1, with the exception that the payload protein is Cas9. As a control, plasmids encoding Cas9 without the nucleus targeting signal peptides are also used. In lieu of mCherry assessment, proper Cas9 targeting is determined via staining for Cas9 with an appropriate antibody and assessment via confocal microscopy. Example 3: Use of novel signal peptides to deliver an antibody to the nucleus.
[0167] Example 3 is carried out using similar methods to Example 1, with the exception that the payload protein is an antibody. As a control, plasmids encoding the payload antibody without the nucleus targeting signal peptides are also used. In lieu of mCherry assessment, proper antibody targeting is determined via staining with an appropriate secondary antibody and assessment via confocal microscopy. Example 4: mRNA synthesis and mRNA-Nanoparticle formulation
[0168] mRNA are produced by in vitro transcription as described in Cheng, Qiang et al. Proceedings of the National Academy of Sciences of the United States of America vol. 120,52 (2023); Cheng, Qiang et al. Nature Nanotechnology 15, 313-320 (2020); and International Patent Publication Serial No. WO2024064874A2, each of which is hereby incorporated by reference in their entirety. Briefly, linear pDNA with optimized 5’(3’)-untranslated regions (UTR) and poly A sequences were obtained first by enzyme digestion, then IVT reactions were prepared with standard protocols with N1-methylpseudouridine-5’-triphosphate modification. Finally, mRNA was capped (Cap-1) by Vaccinia Capping Enzyme and 2’-O-methyltransferase (NEB).
[0169] mRNA-loaded LNP formulations are formed using the ethanol dilution method as described in Cheng, Qiang et al. Proceedings of the National Academy of Sciences of the United States of America vol. 120,52 (2023); Cheng, Qiang et al. Nature Nanotechnology 15, 313-320 (2020); and International Patent Publication Serial No. WO2024064874A2, each of which is hereby incorporated by reference in their entirety. Briefly, all lipids with specified molar ratios were dissolved in ethanol and RNA was dissolved in 10 mM citrate buffer (pH 4.0) first. Then the two solutions were rapidly mixed at an aqueous to ethanol ratio of 3:1 by volume (3:1, aq.:ethanol, vol:vol) to satisfy a final weight ratio of 40:1 (total lipids:mRNA). After incubation for 10 min at 60 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT room temperature, the mRNA LNPs formulations were added immediately into cells or dialyzed against PBS for 2 h for in vivo experiments. Example 5: Signal peptide targeted mCherry is properly secreted from cells transfected with pDNA or treated with mRNA loaded LNPs.
[0170] The SPs of the present example are as provided in Table 11 below: Table 11 Sequence Reference Sequence SEQ ID NO: L MKWVTFISLLFLFSSAYS SE ID NO 10
[0000] p constructs encod ng mC erry mmed ate y downstream o a secretory s gna peptide were generated and tested as detailed in Cheng, Qiang et al. Proceedings of the National Academy of Sciences of the United States of America vol. 120,52 (2023); and International Patent Publication Serial No. WO2024064874A2, each of which is hereby incorporated by reference in their entirety. Briefly, HeLa cells were transfected with wild type (WT) mCherry pDNA containing no SP and gLuc-mCherry pDNA via Lipofectamine2000, and both intracellular and extracellular fluorescence were quantified via fluorescent microscopy at 24-, 48-, and 72-hours post transfection, wherein the gLuc SP induced high levels of mCherry expression into media. Additionally, mCherry protein content present in cell medium and cell lysates were quantified via a fluorescent plate reader individually at 24-, 48-, and 72-hours revealing an increase in mCherry fluorescence in the gLuc SP group (FIG. 2A). The set of SPs was then expanded to include a negative control (scramble sequence), hAlb, hApoB, and hFVII, in addition to gLuc. HeLa cells were again transfected with the pDNA constructs using Lipofectamine2000. Images taken 72h post transfection via fluorescence microscopy and IVIS demonstrated that the SPs hApoB, gLuc, and hFVII all generated high levels of mCherry protein secretion, while the NC and hAlb constructs effectively mediated intracellular mCherry expression but did not promote significant extracellular secretion (FIG.2B). The same set of SPs were evaluate in the liver cancer cell line Huh7 wherein the observed trends of mCherry secretion in HeLa cells persisted (FIG.2C). 61 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT
[0172] Based on the above, it was investigated whether mRNA containing an integrated SP sequence would yield similar observations to what was exhibited with pDNA. hFVII-mCherry mRNA from the FVII-mCherry-pCS2-MT plasmid was generated via in vitro transcription (IVT). A mDLNP lipid nanoparticle was tested for use as an initial carrier for the RNA. Transfection of multiple different cell lines with mDLNPs containing FVII-mCherry mRNA demonstrated that protein export into medium positively correlates with time post-transfection as well as dose, with greater fluorescence signal intensity being observed at longer time intervals and higher dosages across cell lines (FIGs 3A and 3B). The data for this example demonstrates that pDNA can be transcribed into mRNA via IVT, and that transfection of cells with pDNA via lipofectamine or transfection of cells with mRNA generated from the same pDNA via LNPs results in comparable experimental outcomes. Thus, the data in this example supports the conclusion that the constructs tested in Example 1 in pDNA format would be expected to result in similar outcomes in embodiments where the pDNA is first transcribed into mRNA via IVT. 62 ACTIVE / 131811621.1
Claims
Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT CLAIMS What is claimed is:
1. A signal peptide comprising an amino acid sequence selected from the group consisting of Formula I, II, III, IV, V, VI, VII, and VIII; wherein Formula I is represented as: A1-A2-A3-A4-A5-A6-A7-A8-A9-A10-A11-A12-A13-A14-A15-A16(Formula I) and the identities of A1-A16 are as provided in Table 2; wherein Formula II is represented as: B1-B2-B3-B4-B5-B6-B7-B8-B9-B10-B11-B12-B13-B14-B15-B16-B17-B18(Formula II) and the identities of B1-B18are as provided in Table 3; wherein Formula III is represented as: C1-C2-C3-C4-C5-C6-C7-C8-C9-C10-C11-C12-C13-C14-C15-C16-C17-C18-C19 (Formula III) and the identities of C1-C19are as provided in Table 4; wherein Formula IV is represented as: D1-D2-D3-D4-D5-D6-D7-D8-D9-D10-D11-D12-D13-D14-D15-D16-D17-D18-D19-D20 (Formula IV) and the identities of D1-D20are as provided in Table 5; wherein Formula V is represented as: E1-E2-E3-E4-E5-E6-E7-E8-E9-E10-E11-E12-E13-E14-E15-E16-E17-E18-E19-E20-E21-E22 (Formula V) and the identities of E1-E22are as provided in Table 6; wherein Formula VI is represented as: F1-F2-F3-F4-F5-F6-F7-F8-F9-F10-F11-F12-F13-F14-F15-F16-F17-F18-F19-F20-F21-F22-F23 (Formula VI) and the identities of F1-F23 are as provided in Table 7; wherein Formula VII is represented as: G1-G2-G3-G4-G5-G6-G7-G8-G9-G10-G11-G12-G13-G14-G15-G16-G17-G18-G19-G20-G21-G22-G23-G24- G25-G26 (Formula VII) and the identities of G1-G26are as provided in Table 8; and wherein Formula VIII is represented as: H1-H2-H3-H4-H5-H6-H7-H8-H9-H10-H11-H12-H13-H14-H15-H16-H17-H18-H19-H20-H21-H22-H23-H24- H25-H26-H27-H28-H29-H30(Formula VIII) and the identities of H1-H30are as provided in Table 9. 63 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT 2. The signal peptide of claim 1, comprising an amino acid sequence having at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9.
3. A signal peptide comprising an amino acid sequence having at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9.
4. The signal peptide of any one of claims 1-3, wherein the signal peptide is a novel signal peptide.
5. A recombinant polypeptide comprising a formula of X1-(Y1)a-Z1, wherein: X1 is a signal peptide, Y1is a peptide linker, and Z1 is a payload protein, wherein a is an integer selected from 0 and 1.
6. The recombinant polypeptide of claim 5, wherein X1comprises an amino acid sequence selected from the group consisting of Formula I, II, III, IV, V, VI, VII, and VIII; wherein Formula I is represented as: A1-A2-A3-A4-A5-A6-A7-A8-A9-A10-A11-A12-A13-A14-A15-A16(Formula I) and the identities of A1-A16 are as provided in Table 2; wherein Formula II is represented as: B1-B2-B3-B4-B5-B6-B7-B8-B9-B10-B11-B12-B13-B14-B15-B16-B17-B18(Formula II) and the identities of B1-B18 are as provided in Table 3; wherein Formula III is represented as: C1-C2-C3-C4-C5-C6-C7-C8-C9-C10-C11-C12-C13-C14-C15-C16-C17-C18-C19(Formula III) and the identities of C1-C19are as provided in Table 4; 64 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT wherein Formula IV is represented as: D1-D2-D3-D4-D5-D6-D7-D8-D9-D10-D11-D12-D13-D14-D15-D16-D17-D18-D19-D20 (Formula IV) and the identities of D1-D20 are as provided in Table 5; wherein Formula V is represented as: E1-E2-E3-E4-E5-E6-E7-E8-E9-E10-E11-E12-E13-E14-E15-E16-E17-E18-E19-E20-E21-E22 (Formula V) and the identities of E1-E22 are as provided in Table 6; wherein Formula VI is represented as: F1-F2-F3-F4-F5-F6-F7-F8-F9-F10-F11-F12-F13-F14-F15-F16-F17-F18-F19-F20-F21-F22-F23 (Formula VI) and the identities of F1-F23 are as provided in Table 7; wherein Formula VII is represented as: G1-G2-G3-G4-G5-G6-G7-G8-G9-G10-G11-G12-G13-G14-G15-G16-G17-G18-G19-G20-G21-G22-G23-G24- G25-G26 (Formula VII) and the identities of G1-G26 are as provided in Table 8; and wherein Formula VIII is represented as: H1-H2-H3-H4-H5-H6-H7-H8-H9-H10-H11-H12-H13-H14-H15-H16-H17-H18-H19-H20-H21-H22-H23-H24- H25-H26-H27-H28-H29-H30 (Formula VIII) and the identities of H1-H30are as provided in Table 9.
7. The recombinant polypeptide of claim 5 or claim 6, wherein X1 comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, or 9.
8. The recombinant polypeptide of any one of claims 5-7, wherein the payload protein is a therapeutic peptide or protein.
9. A nucleic acid molecule encoding for the signal peptide of any one of claims 1-4.
10. A nucleic acid molecule encoding for the recombinant polypeptide of any one of claims 5- 8. 65 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT 11. A vector comprising the nucleic acid molecule of claim 9 or claim 10.
12. A cell comprising the nucleic acid molecule of claim 9 or claim 10 or the vector of claim 11.
13. A composition comprising the nucleic acid molecule of claim 9 or claim 10 or the vector of claim 11.
14. A method for treating a disease or disorder in a subject in need thereof, the method comprising administering to the subject an effective amount of the nucleic acid molecule of claim 10 to the subject, thereby treating the disease or disorder.
15. The method of claim 14, wherein the payload protein is a protein useful for gene editing and the disease or disorder is any disease or disorder for which gene editing is useful.
16. The method of claim 14, wherein the disease or disorder is a disease or disorder associated with the nucleus of a cell.
17. A method for treating a disease or disorder associated with the nucleus of a cell in a subject in need thereof, the method comprising administering to the subject a vector comprising a nucleic acid molecule encoding for a signal peptide fused or linked to a payload protein, wherein the signal peptide is the signal peptide of any one of claims 1-4 and wherein the payload protein is a therapeutic peptide or protein useful for the treatment of the disease or disorder.
18. A method for treating a disease or disorder in a subject in need thereof, the method comprising administering to the subject a vector comprising a nucleic acid molecule encoding for: i) a signal peptide fused or linked to a payload protein, wherein the signal peptide is the signal peptide of any one of claims 1-4 and wherein the payload protein is a protein useful for gene editing; and ii) at least one nucleic acid molecule that targets the payload protein to a gene of interest; 66 ACTIVE / 131811621.1Attorney Docket No. UTSD 4324 (106546-824623) SIGY-007WO PATENT wherein the signal peptide promotes translocation of the protein useful for gene editing to the nucleus, wherein the payload protein edits the gene of interest thereby treating the disease or disorder.
19. A method for editing a target nucleic acid in a cell, the method comprising administering a nucleic acid molecule encoding for: i) a signal peptide fused or linked to a payload protein, wherein the signal peptide is the signal peptide of any one of claims 1-4 and wherein the payload protein is a protein useful for gene editing; and ii) at least one nucleic acid molecule that targets the payload protein to a gene of interest; wherein the signal peptide promotes translocation of the protein useful for gene editing to the nucleus, wherein the payload protein edits the gene of interest thereby editing the target nucleic acid. 67 ACTIVE / 131811621.1
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