WO2025064923A1 - Endogenous secretory signal peptides and uses thereof - Google Patents

Abstract

Provided for herein are novel recombinant polypeptides comprising endogenous secretory signal peptides and a payload protein, nucleic acid molecules encoding the same, pharmaceutical compositions comprising the same, and methods of use thereof.

Description

ENDOGENOUS SECRETORY SIGNAL PEPTIDES AND USES THEREOF

Related Applications

[0001] This application claims the benefit of U.S. Provisional Application Ser. No. 63/584,728 filed September 22. 2023, and of U.S. Provisional Application Ser. No. 63/603.598 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 “XX.xml”, file size XX bytes, created on XXX. The aforementioned sequence listing is hereby incorporated by reference in its entirety pursuant to 37 C.F.R. §1.52(e)(5).

Field

[0003] The present disclosure relates generally to endogenous signal peptides and more particularly to endogenous signal peptides for targeting an encoded protein to be exported from the cell.

Background

[0004] 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.

[0005] 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 encoding each protein must also contain a metaphorical shipping label upstream from the protein sequence known as a signal peptide (SP). Incorporation of known endogenous SP into therapeutic mRNA could greatly benefit delivery, localization, and clearance of an encoded therapeutic protein. The present disclosure addresses these needs and others. Summary

[0006] In some embodiments, a recombinant polypeptide is provided. In some embodiments, the recombinant polypeptide comprises a formula of Xi-(Y i)_a-Zi, wherein Xi is an endogenous signal peptide, Yi is a peptide linker, and Zi is a payload protein, wherein a is an integer selected from 0 and 1.

[0007] In some embodiments, Xi comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence as recited in Table 1.

[0008] In some embodiments, the payload protein is a therapeutic peptide or protein.

[0009] 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.

[0010] In some embodiments, a vector is provided. In some embodiments, the vector comprises a nucleic acid molecule as provided for herein.

[0011] 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.

[0012] 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.

[0013] In some embodiments, a method for treating a disease or disorder in a subject need thereof is provided. In some embodiments, the method comprises administering to the subject an effective amount of a nucleic acid molecule as provided for herein to the subj ect, thereby treating the disease or disorder.

[0014] In some embodiments, the disease or disorder is a cancer.

[0015] In some embodiments, a method for treating a cancer in a subject in need thereof is provided. In some embodiments, the method comprises administering to a 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 an endogenous signal peptide and wherein the payload protein is a therapeutic peptide or protein useful for the treatment of the cancer. In some embodiments, the endogenous signal peptide comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence as recited in Table 1. [0016] In some embodiments, a use of an endogenous signal peptide is provided. In some embodiments, the use comprises directing the secretion of a payload protein out of a cell, wherein the payload protein does not natively comprise an amino acid sequence comprising the amino acid sequence of the endogenous signal peptide. In some embodiments, the endogenous signal peptide comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence as recited in Table 1.

Brief Description of the Drawings

[0017] 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.

[0018] FIG. IB illustrates the quantification of mCherry signal assessment in the media of cells transfected with pDNA encoding mCherry with or without a signal peptide as provided for herein directly upstream of the mCherry sequence.

[0019] FIG. 1C illustrates the quantification of mCherry signal assessment in the media of cells transfected with pDNA encoding mCherry with or without a signal peptide as provided for herein directly upstream of the mCherry sequence.

[0020] FIG. 2A provides quantification of mCherry fluorescence in Hela cell ly sates and medium at different time points. mCherry with no signal peptide was used as a control (“WT- mCherry”). gLuc, Gaussia luciferase.

[0021] FIG. 2B provides quantification of mCherry fluorescence in Hela cell lysate and medium after 72 hours.

[0022] FIG. 2C provides quantification of mCherry fluorescence in Huh7 cell lysates and medium at 72h after transfection.

[0023] 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.

[0024] 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.

Detailed Description

[0025] Before the present compositions and methods are described, it is to be understood that the scope of the invention 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 invention. 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

[0026] 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.

[0027] 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 w ell 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.

[0028] 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 +/- 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. [0029] 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.

[0030] Methods and materials of non-viral delivery of nucleic acids to cells further include biolistics, virosomes, liposomes, lipid nanoparticles, immunoliposomes, polycation or lipidnucleic 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.

[0031] 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.

[0032] As used herein, “payload protein” or “protein of interest” refers to the protein that will be generated by the host cell and subsequently exported from the cell due to the presence of the secretory⁷ signal peptide. 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 enz me, enzyme inhibitor, growth factor, hormone, antibody, antigen, vaccine, a therapeutic agent, or any combination thereof. More specific examples follow herein below. [0033] 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.

[0034] “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.

[0035] By “substantially identical” is meant a polypeptide or nucleic acid molecule exhibiting at least 50% identity⁷ 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 for comparison. Other percentages of identity in reference to specific sequences are described herein.

[0036] Sequence identity can be measured/determined using sequence analy sis 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 homology⁷ 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 el 00 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.

[0037] 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.

[0038] 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, try ptophan; and (4) uncharged polar i.e. glycine, asparagine, glutamine, cysteine, serine, 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.

[0039] '‘Encoding’’ refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to sen e 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.

[0040] 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.

[0041] 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).

[0042] 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 44^ *5

[0043] 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” 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 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.

[0044] 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. [0045] 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; singlechain antibody molecules, e.g., sc-Fv; nanobodies (single domain antibody) and multispecific antibodies formed from antibody fragments.

[0046] As used here, the term “endogenous” when used in reference to a nucleic acid molecule or a polypeptide refers to a nucleic acid molecule or a protein that is natively found in the host organism or cell or natively found in an organism or cell of the same species as the host organism.

[0047] A “Fab fragment” is comprised of one light chain and the Cnl and variable regions of one heavy chain. The heavy chain of a Fab molecule cannot form a disulfide bond with another heavy chain molecule.

[0048] 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.

[0049] A “Fab¹ fragment” contains one light chain and a portion or fragment of one heavy chain that contains the VH domain and the Cnl domain and also the region between the Cnl 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.

[0050] A “F(ab')2 fragment” contains two light chains and two heavy chains containing a portion of the constant region between the CHI and CH2 domains, such that an interchain disulfide bond is formed between the two heavy chains. A F(ab')2 fragment thus is composed of two Fab' fragments that are held together by a disulfide bond between the two heavy chains. [0051] The “Fv region” comprises the variable regions from both the heavy and light chains, but lacks the constant regions.

[0052] 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 VH and VL domains which enables the scFv to form the desired structure for antigen binding. For a review of scFv, see Pluckthun (1994) THE PHARMACOLOGY OF MONOCLONAL ANTIBODIES, 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.

[0053] 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.

[0054] 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."

[0055] 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.

[0056] 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, 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.

[0057] 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 delivery⁷ 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). [0058] 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.

[0059] “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.

[0060] 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 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.

Endogenous Signal Peptides

[0061] Without being bound to any particular theory, the embodiments provided for herein have been found to show that by providing an endogenous signal peptide on the front of a desired payload protein, the payload protein may be properly directed to be secreted by the cell. The pay load proteins may or may not natively contain a signal peptide directing localization of said protein to the desired location, e.g.. secreted from the cell. Accordingly, the provided endogenous signal peptides can direct enhanced expression and secretion of a protein that natively contains a secretory signal peptide, or can direct secretion of a payload protein that does not natively contain a secretory signal peptide, e.g., a therapeutic protein, from the cell.

[0062] 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 Endogenous Signal Peptides

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 90% (e.g., 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%, 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 of MA. In some embodiments, the signal peptide comprises an amino acid sequence that is at least 90% (e.g., 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%, at least 99%, or 100%) identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 1 - SEQ ID NO: 1622.

Recombinant Polypeptides

[0063] In some embodiments, a recombinant polypeptide is provided, the recombinant polypeptide comprising a formula of Xi-Zi, wherein Xi is a signal peptide as provided for herein and Zi is a pay load protein.

[0064] In some embodiments, Xi comprises an amino acid sequence having at least 90% (e.g., 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 as recited in Table 1. In some embodiments, Xi comprises an amino acid sequence of MA. In some embodiments, Xi comprises an amino acid sequence that is at least 90% (e.g., 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%. at least 99%. or 100%) identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 1 - SEQ ID NO: 1622.

[0065] In some embodiments, the payload protein, Zi, may be any peptide or protein. In some embodiments, the payload protein, Zi, is any peptide or protein that is useful in the treatment of a disease or disorder. In some embodiments, the payload protein, Zi, is any peptide or protein that, once secreted from the cell, is useful in the treatment of a disease or disorder. In some embodiments, the payload protein, Zi, is any peptide or protein that is useful in the treatment of cancer. [0066] In some embodiments, Xi is linked directly to Zi. In some embodiments, Xi is linked indirectly to Zi through, 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 Xi-(Y i)_a-Zi, wherein Xi is a signal peptide as provided for herein, Yi is a linker, such as but not limited to a polypeptide linker, Zi is a payload protein as provided for herein, and a is an integer selected from 0 or 1. In some embodiments, Xi is a novel signal peptide as provided for herein.

Nucleic Acid Molecules

[0067] 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).

[0068] In some embodiments, the nucleic acid molecule encodes for a signal peptide comprising an amino acid sequence having at least 90% (e.g., 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 as recited in Table 1. In some embodiments, the nucleic acid molecule encodes for a signal peptide comprising an amino acid sequence of MA. In some embodiments, the nucleic acid molecule encodes for a signal peptide comprising an amino acid sequence having at least 90% (e.g., 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 - SEQ ID NO: 1622.

[0069] 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 Xi-Zi, wherein Xi is a signal peptide as provided for herein and Zi is a payload protein as provided for herein. In some embodiments, the nucleic acid molecule encodes for a recombinant polypeptide comprising a formula of Xi-(Y i)_a-Zi, wherein Xi is a signal peptide as provided for herein, Yi is a linker, such as but not limited to a polypeptide linker, Zi is a payload protein as provided for herein, and a is an integer selected from 0 or 1. [0070] 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.

[0071] 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. 5’ UTR may comprise a first polynucleotide fragment and a second polynucleotide fragment from the same and/or different genes.

[0072] 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.

[0073] 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 alky l or cycloalkyl intersugar linkages or short chain heteroatomic or heterocyclic inter sugar linkages.

[0074] 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 — C 1-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 sugars comprise more than one nonbridging sugar substituent, for example, T-F-5’-methyl sugar moieties.

[0075] 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. orN(Rm)-alkyl; O, S, orN(Rm)-alkenyl; O, S orN(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, benzy l, phenyl, nitro (NO2), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

[0076] 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 Cl -CIO 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.

[0077] 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., W02008/150729); 4’- CH₂ — O — N(CH₃)-2’ (see, e.g., US2004/0I71570, published Sep. 2, 2004); 4’-CH₂— O— N(R)-2’, and 4-CH₂— N(R)— 0-2’-, wherein each R is, independently, 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)(CH_?)-2’ (see, e.g., Chattopadhyaya et al., J. Org. Chem., 2009, 74, 1 18-134); and 4-CH₂ — C(=CH₂)-2’ and analogs thereof (see, PCT International Application WO 2008/154401).

[0078] 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, S JI, N3, C00J1, acyl (C(=O) — H), substituted acyl, CN, sulfonyl (S(=0)2-Jl), or sulfoxyl (S(=O)-J1); and each JI 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 ary l, acyl (C(=O) — H), substituted acyl, a heterocycle radical, a substituted heterocycle radical, 01-012 aminoalkyl, substituted Cl- C12 aminoalkyl, or a protecting group. [0079] Nucleosides comprising bicyclic sugar moieties are referred to as bicyclic nucleosides or BNAs. Bicyclic nucleosides include, but are not limited to, (A) a-L-Methyleneoxy (4- CH2 — O- 2’) BNA, (B) (3-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.

[0080] 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 configuration. a-L-methyleneoxy (4-CH2 — O-2’) bicyclic nucleosides have previously been incorporated into antisense polynucleotides that showed antisense activity.

[0081] In some embodiments, substituted sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent.

[0082] 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.

[0083] 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).

[0084] 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.

[0085] 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.

[0086] 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.

[0087] 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.

[0088] 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-azapyrimi dines and N-2, N-6 and 0-6 substituted purines, including 2- aminopropyl adenine, 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][l,4]benzoxazin-2(3H)- one), phenothiazine cytidine (1H- pyrimido[5,4-b][l,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g.. 9-(2-aminoethoxy)-H-pyrimido[5,4- 13][l,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.

[0089] In some embodiments, the present disclosure provides nucleic acid molecules comprising linked nucleosides. In some embodiments, the nucleosides may be linked together using any intemucleoside linkage. The two main classes of intemucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus containing intemucleoside linkages include, but are not limited to, phosphodiesters (P=O), phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates (P=S). Representative non-phosphorus containing intemucleoside linking groups include, but are not limited to, 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, intemucleoside 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 intemucleoside linkages are well known to those skilled in the art.

[0090] 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.

[0091] Neutral intemucleoside linkages include without limitation, phosphotriesters, methylphosphonates, MMI (3-CH2 — N(CHs) — O-5’), amide-3 (3-CH2 — C(=O) — N(H)-5’), amide- 4 (3'-CH2 — N(H) — C(=O)-5’), formacetal (3’-0 — CH2 — O-5’), and thioformacetal (3’-5-CH2 — 0-5'). Further neutral intemucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides. Further neutral intemucleoside linkages include nonionic linkages comprising mixed N. O, S and CH2 component parts.

[0092] 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 l,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecyl amine or hexyl amino-carbonyl-oxy cholesterol moiety⁷.

[0093] 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.

Cells

[0094] 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

[0095] 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. [0096] 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.

[0097] In some embodiments, the delivery' system is anon-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 (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.

[0098] The above exemplary delivery⁷ systems are not to be construed to be limiting in any way. Appropriate delivery' systems are known in the art and any⁷ such delivery⁷ system is within the scope of the present disclosure.

Methods

[0099] Also contemplated herein are methods of using the endogenous signal peptides and recombinant polypeptides provided for herein.

[0100] 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. Non-limiting examples of diseases or disorders, or therapeutic fields for which the recombinant polypeptides disclosed herein may be useful include, but are not limited to, oncology, inflammatory diseases or disorders, autoimmune disease or disorders, immunotherapeutics, enzyme replacement therapeutics, protein replacement therapeutics, biologies manufacturing, diabetes, blood disorders (e.g, hemophilia), hormone replacement therapies, or peptide-based drugs (e.g., GLP-1 for obesity). In some embodiments, the disease or disorder is cancer. In some embodiments, the disease or disorder is an inflammatory disease or disorder. In some embodiments, the disease or disorder is an autoimmune disease or disorder. In some embodiments, the disease or disorder is diabetes. In some embodiments, the disease or disorder is a blood disorder. In some embodiments, the disease or disorder is any disease or disorder for which immunotherapies would be beneficial. In some embodiments, the disease or disorder is any disease or disorder for which enzyme replacement therapies would be beneficial. In some embodiments, the disease or disorder is any disease or disorder for which protein replacement therapies would be beneficial. In some embodiments, the disease or disorder is any disease or disorder for which hormone replacement therapies would be beneficial. In some embodiments, the disease or disorder is any disease or disorder for which a peptide based drug would be beneficial.

[0101] In some embodiments, a method of treating a cancer is provided, the method comprising administering to a subj ect in need thereof a vector comprising a nucleic acid molecule encoding for a recombinant polypeptide as provided for herein, thereby treating the cancer. In some embodiments, the payload protein of the recombinant polypeptide is a peptide or protein useful for the treatment of the cancer. In some embodiments, the signal peptide directs the payload protein to be secreted by the cell, providing the payload protein into circulation whereby it is useful in treating the cancer. 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.

[0102] 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. Non-limiting examples of diseases or disorders, or therapeutic fields for which the recombinant polypeptides disclosed herein may be useful include, but are not limited to, oncology', inflammatory' diseases or disorders, autoimmune disease or disorders, immunotherapeutics, enzyme replacement therapeutics, protein replacement therapeutics, biologies manufacturing, diabetes, blood disorders (e.g., hemophilia), hormone replacement therapies, or peptide-based drugs (e.g, GLP-1 for obesity). In some embodiments, the disease or disorder is cancer. In some embodiments, the disease or disorder is an inflammatory disease or disorder. In some embodiments, the disease or disorder is an autoimmune disease or disorder. In some embodiments, the disease or disorder is diabetes. In some embodiments, the disease or disorder is a blood disorder. In some embodiments, the disease or disorder is any disease or disorder for which immunotherapies would be beneficial. In some embodiments, the disease or disorder is any disease or disorder for which enzyme replacement therapies would be beneficial. In some embodiments, the disease or disorder is any disease or disorder for which protein replacement therapies would be beneficial. In some embodiments, the disease or disorder is any disease or disorder for which hormone replacement therapies would be beneficial. In some embodiments, the disease or disorder is any disease or disorder for which a peptide based drug would be beneficial.

[0103] In some embodiments, a method of treating a cancer 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 cancer. In some embodiments, the payload protein of the recombinant polypeptide is a peptide or protein useful for the treatment of the cancer. In some embodiments, the signal peptide directs the payload protein to be secreted by the cell, providing the payload protein into circulation whereby it is useful in treating the cancer. 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.

[0104] 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.

[0105] 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.

[0106] The present disclosure is directed, in part, toward novel recombinant polypeptides comprising an endogenous signal peptide and a payload protein. Without being bound to any particular theory, the novel recombinant polypeptides of the disclosure are useful in the treatment of a cancer by using the subj ect’ s own cells to produce and secrete the pay load protein that is useful for the treatment of cancer. This will allow the subject to produce and circulate the pay load protein, thereby treating the cancer. Furthermore, by utilizing the subject’s own cells to produce the payload protein, the present methods avoid the need of timely and inefficient recombinant protein infusions. Furthermore, by having the patient’s own cells produce the payload proteins, adverse immune responses to the payload proteins due to post translational modifications during production may be reduced.

[0107] The present disclosure is also directed, in part, toward methods of producing or manufacturing a payload protein using the endogenous signal peptides as provided for herein. Without being bound to any particular theory, the endogenous signal peptides as provided for herein direct the payload protein to a particular cellular or extracellular location, such as but not limited to, secreting the payload protein from the cell. Use of the endogenous 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.

EXAMPLES

[0108] The following examples illustrative of the compounds, compositions, particles, polypeptides, and methods described herein and should not be construed to be limiting in any wav. SP-mCherry plasmid (pDNA) construction

[0109] 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 entirety⁷. 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 2 below:

Table 2

Enzyme digested SP-mCherry products were cloned into pCS2-MT vector based on standard protocols. After validation by sequencing, SP-mCherry plasmids were ready for in vitro screening.

In vitro SP screening by pDNA transfection

[0110] To perform SPs screening, pDNA transfection was executed in cells. pDNAs were encapsulated in Lipfectamine2000 and administered to HeLa cells at 50 ng/well in 96 well plates and allowed to incubate for 24 hours. Cell lysates and media were collected an mCherry signal was quantified via plate reader.

Example 1: Use of endogenous signal peptides to drive export of mCherry.

[OHl] The ability of the endogenous signal peptides provided for herein to secrete payload proteins was tested by constructing signal peptide modified mCherry plasmids containing an encoded secretory signal peptide directly upstream of the mCherry sequence. As a control, unmodified mCherry plasmids containing no signal peptide sequence were also used. The general plasmid construction as well as the general method is as provided above and in FIG. 1A. [0112] As shown in FIG. IB and 1C, each of the endogenous signal peptides tested were able to drive export of mCherry protein to the cell media, whereas mCherry protein without the secretory signal peptides was not secreted from the cell. Results for each of Nat-Sec-19-1 (SEQ ID NO: 337), Nat-Sec-20-1 (SEQ ID NO: 527), Nat-Sec-21-1 (SEQ ID NO: 699), Nat- Sec-22-1 (SEQ ID NO: 781), and Nat-Sec-23-1 (SEQ ID NO: 950) exhibited a statistically significant increase of mCherry signal in the cell media as compared to the NO SP control.

[0113] The data for this example demonstrates that secretory signal peptide sequences encoded directly upstream from the mCherry sequence drive export of the mCherry protein from the cell.

Example 2: Use of endogenous signal peptides to secrete antibodies from a cell.

[0114] Example 2 is carried out using similar methods to Example 1, with the exception that the payload protein is an antibody. As a control, plasmids encoding antibodies without the secretory signal peptides are also used. In lieu of mCherry assessment, proper antibody targeting is determined via Western Blot or ELISA analysis using a proper secondary antibody and detection reagent.

Example 3: mRNA synthesis and mRNA-Nanoparticle formulation

[0115] 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 Nl-methylpseudouridine-5’-triphosphate modification. Finally, mRNA was capped (Cap-1) by Vaccinia Capping Enzyme and 2’-O-methyltransferase (NEB).

[0116] 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 room temperature, the mRNA LNPs formulations were added immediately into cells or dialyzed against PBS for 2 h for in vivo experiments.

Example 4: Signal peptide targeted mCherry is properly secreted from cells transfected with pDNA or treated with mRNA loaded LNPs.

[0117] The SPs of the present example are as provided in Table 3 below:

Table 3

[0118] pDNA constructs encoding mCherry immediately downstream of a secretory' signal 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). [0119] 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 FVlI-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).

[0120] 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.

Claims

CLAIMS What is claimed is:

1. A recombinant polypeptide comprising a formula of Xi-(Y i)_a-Zi, wherein:

Xi is an endogenous signal peptide,

Yi is a peptide linker, and

Zi is a payload protein. wherein a is an integer selected from 0 and 1 .

2. The recombinant polypeptide of claim 1 , wherein Xi comprises an amino acid sequence having at least 90%, 91%, 92%. 93%. 94%. 95%. 96%. 97%, 98%, 99%, or 100% identity to an amino acid sequence as recited in Table 1.

3. The recombinant polypeptide of claim 1 or claim 2, wherein the pay load protein is a therapeutic peptide or protein.

4. A nucleic acid molecule encoding for the recombinant polypeptide of any one of claims 1-3.

5. A vector comprising the nucleic acid molecule of claim 4.

6. A cell comprising the nucleic acid molecule of claim 4 or the vector of claim 5.

7. A composition comprising the nucleic acid molecule of claim 4 or the vector of claim 5.

8. 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 4 to the subject, thereby treating the disease or disorder.

9. The method of claim 8, wherein the disease or disorder is a cancer.

10. A method for treating a cancer 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 an endogenous signal peptide and wherein the payload protein is a therapeutic peptide or protein useful for the treatment of the cancer.

11. The method of claim 10, wherein the endogenous signal peptide comprises an amino acid sequence having at least 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%. 99%, or 100% identity to an amino acid sequence as recited in Table 1.

12. Use of an endogenous signal peptide to direct secretion of a payload protein out of a cell, wherein the payload protein does not natively comprise an amino acid sequence comprising the amino acid sequence of the endogenous signal peptide.

13. The use of claim 12, wherein the endogenous signal peptide comprises an amino acid sequence having at least 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an amino acid sequence as recited in Table 1.