Patent Application
20220017907
The content of the electronically submitted sequence listing (Name: 4000_041PC01_SL_ST25.txt, Size: 116,344 bytes; and Date of Creation: May 22, 2019) submitted in this application is incorporated herein by reference in its entirety.
The present disclosure provides extracellular vesicles, e.g., exosomes, enriched in a scaffold protein associated with the extracellular vesicle's luminal surface which can be useful as an agent for the prophylaxis or treatment of cancer and other diseases.
Exosomes are important mediators of intercellular communication. They are also important biomarkers in the diagnosis and prognosis of many diseases, such as cancer. As drug delivery vehicles, exosomes offer many advantages over traditional drug delivery methods as a new treatment modality in many therapeutic areas.
A central feature of exosomes is their ability to contain biologically active payload within their interior space, or lumen. It is well known that exosomes contain endogenous payload including mRNA, miRNA, DNA, proteins, carbohydrates, and lipids, but the ability to direct specific loading of desired therapeutic payload is currently limited. Exosomes may be loaded by overexpressing desired therapeutic payloads in a producer cell, but this loading is often of limited efficiency due to stochastic localization of the payload to cellular exosome processing centers. Alternatively, purified exosomes may be loaded ex vivo by, for example, electroporation. These methods may suffer from low efficiency or be limited to small payloads, such as siRNAs. Therefore, suitable methods for generating highly efficient and well-defined loaded exosomes are needed to better enable therapeutic use and other applications of exosome-based technologies.
An aspect of the present disclosure relates to novel methods of loading Extracellular Vesicles (EVs), e.g., exosomes for therapeutic use. Specifically, the methods use protein markers that are newly identified from the luminal surface of exosomes. In particular, a group of proteins (e.g., myristoylated alanine rich Protein Kinase C substrate (MARCKS); myristoylated alanine rich Protein Kinase C substrate like 1 (MARCKSL1); and brain acid soluble protein 1 (BASP1)) were identified to be highly enriched on the luminal surface of exosomes. Furthermore, a short sequence of the amino terminus of BASP1, e.g., at least seven amino acids, was shown to be sufficient to direct high efficiency loading of fluorescent protein molecules to the same extent as the full length BASP1 protein. This fragment, which is at least seven amino acids and less than ten amino acids, presents a significant advance in the field of engineered EV loading, and allows for the efficient, reproducible loading of any biologically active molecule, e.g., a therapeutic protein payload, into the lumen of EVs, e.g., exosomes, with no additional steps of ex vivo manipulation. The loading of EVs, e.g., exosomes, using the fusion proteins described herein produces engineered EVs, e.g, engineered exosomes, with significantly higher payload levels compared to any other genetic engineering method described thus far.
The proteins and peptide sequences newly identified from exosomes are used in various embodiments of the present disclosure. For example, some embodiments relate to generating a fusion protein by conjugating the EV, e.g., exosome protein or protein fragment (i.e., a scaffold protein) and a biologically active molecule (e.g., therapeutically relevant protein) and producing an EV, e.g., an exosome, containing the fusion protein on the luminal surface of the EV. The native full-length protein or a biologically active fragment of the biologically active molecule (e.g., a therapeutically relevant protein) can be transported to the luminal surface of EVs, e.g., exosomes, by being conjugated to the exosome-enriched proteins or protein fragments.
The present disclosure further relates to generation or use of a lumen-engineered EVs, e.g., lumen-engineered exosomes, designed for more efficient loading, or for loading of a biologically active molecule (e.g., a therapeutically relevant protein) in the lumen of an EV, e.g., an exosome. For example, the EVs' luminal surface can be modified to contain a higher concentration of the native full-length EV, e.g., exosome protein and/or a fragment or a modified protein of the native EV, e.g., exosome protein on the luminal surface.
Some embodiments of the present disclosure relate to a producer cell or a method of generating the producer cell for producing such a lumen-engineered EVs. An exogenous polynucleotide can be introduced transiently or stably into a producer cell to generate a lumen-engineered EV, e.g., a lumen-engineered exosome, from the producer cell.
Accordingly, in an aspect, the present disclosure provides an EV, e.g., an exosome, comprising a scaffold protein, wherein at least a part of the scaffold protein is expressed from an exogenous sequence, and the scaffold protein comprises MARCKS, MARCKSL1, BASP1 or a fragment, variant, derivative, or a modification thereof.
In some aspects, the scaffold protein is present in the EV, e.g., an exosome, at a higher density than a different scaffold protein in a different EV, e.g., an exosome, wherein the different scaffold protein comprises a conventional EV, e.g., exosome protein or a variant thereof. In some embodiments, the conventional EV, e.g., exosome protein is selected from the group consisting of CD9, CD63, CD81, PDGFR, GPI anchor proteins, lactadherin, LAMP2, LAMP2B, and a fragment thereof.
In some embodiments, the EV, e.g., an exosome, is produced from a cell genetically modified to comprise the exogenous sequence, optionally wherein the cell is an HEK293 cell.
In some embodiments, the cell comprises a plasmid comprising the exogenous sequence.
In some embodiments, the exogenous sequence is inserted into a genomic site located 3′ or 5′ relative to a genomic sequence encoding MARCKS, MARCKSL1, or BASP1. In some embodiments, the exogenous sequence is inserted into a genomic sequence encoding MARCKS, MARCKSL1, or BASP1.
In some embodiments, the scaffold protein is a fusion protein comprising MARCKS, MARCKSL1, BASP1, or a fragment thereof, and a therapeutic peptide.
In some embodiments, the biologically active molecule comprises a therapeutic peptide selected from the group consisting of a natural peptide, a recombinant peptide, a synthetic peptide, or a linker to a therapeutic compound. In some embodiments, the biologically active molecule (e.g., a therapeutic compound) is selected from the group consisting of nucleotides, amino acids, lipids, carbohydrates, and small molecules. In some embodiments, the biologically active molecule (e.g., a therapeutic peptide) is an antibody or a fragment or a modification thereof. In some embodiments, the therapeutic peptide is an enzyme, a ligand, a receptor, a transcription factor, or a fragment or a modification thereof. In some embodiments, the therapeutic peptide is an antimicrobial peptide or a fragment or a modification thereof.
In some embodiments, the EV, e.g., an exosome, further comprises a second scaffold protein, wherein the second scaffold protein comprises MARCKS, MARCKSL1, BASP1, or a fragment thereof. In some embodiments, the EV, e.g., an exosome, further comprises a second scaffold protein, wherein the second scaffold protein comprises PTGFRN, BSG, IGSF2, IGSF3, IGSF8, ITGB1, ITGA4, SLC3A2, ATP transporter or a fragment thereof.
In some embodiments, the scaffold protein comprises a peptide sequence corresponding to the pattern (M)(G)(G/A/S)(K/Q)(L/F/S/Q)(S/A)(K)(K) (SEQ ID NO: 118) or the said pattern without the N-terminal (M). In some embodiments, the scaffold protein comprises a peptide of (M)(G)(π)(X)(Φ/π)(π)(+)(+), or the peptide without the N-terminal (M), wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), X is any amino acid, Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu). In some embodiments, the scaffold protein comprises a peptide of sequence (M)(G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+), or the peptide without the N-terminal (M), wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), ξ is any amino acid selected from the group consisting of (Asn, Gln, Ser, Thr, Asp, Glu, Lys, His, Arg), Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu). See R. Aasland et al., FEBS Letters 513 (2002): 141-144 for the nomenclature of amino acids.
In some embodiments, the scaffold protein comprises a peptide of any one of SEQ ID NOS: 4-110. In some embodiments, the scaffold protein comprises a peptide of MGXKLSKKK (SEQ ID NO: 116), or the peptide without the N-terminal M, wherein X is any amino acid. In some embodiments, the scaffold protein comprises a peptide of SEQ ID NO: 110, or the corresponding peptide without the N-terminal M. In some embodiments, the scaffold protein comprises the peptide of SEQ ID NO: 13, or the corresponding peptide without the N-terminal (M).
In some embodiments, the scaffold protein further comprises a payload, e.g., a peptide.
In another embodiment, the present disclosure provides a pharmaceutical composition comprising an EV of the present disclosure, e.g., an exosome, and an excipient.
In some embodiments, the pharmaceutical composition is substantially free of macromolecules, wherein the macromolecules are selected from nucleic acids, exogenous proteins, lipids, carbohydrates, metabolites, and a combination thereof.
In yet another embodiment, the present disclosure provides a population of cells for producing the EV, e.g., an exosome, provided herein.
In some embodiments, the population of cells comprises an exogenous sequence encoding the scaffold protein comprising MARCKS, MARCKSL1, BASP1 or a fragment or a modification thereof. In some embodiments, the population of cells further comprise a second exogenous sequence encoding a second scaffold protein, wherein the second scaffold protein comprises MARCKS, MARCKSL1, BASP1 or a fragment or a modification thereof. In some embodiments, the population of cells further comprises a second exogenous sequence encoding a second scaffold protein, wherein the second scaffold protein comprises PTGFRN, BSG, IGSF2, IGSF3, IGSF8, ITGB1, ITGA4, SLC3A2, ATP transporter or a fragment thereof.
In some embodiments, the exogenous sequence is inserted into a genomic sequence encoding MARCKS, MARCKSL1, or BASP1, wherein the exogenous sequence and the genomic sequence encodes the scaffold protein. In some embodiments, the exogenous sequence is in a plasmid.
In some embodiments, the exogenous sequence encodes a biologically active molecule (e.g., a therapeutic peptide). In some embodiments, the therapeutic peptide is selected from a group consisting of a natural peptide, a recombinant peptide, a synthetic peptide, or a linker to a therapeutic compound. In some embodiments, the therapeutic compound is selected from the group consisting of nucleotides, amino acids, lipids, carbohydrates, and small molecules. In some embodiments, the therapeutic peptide is an antibody or a fragment or a modification thereof. In a particular embodiment, the antibody is a nanobody. A person of ordinary skill in the art would understand that the antibody used in an EV of the present disclosure can be any antigen-binding molecule known in the arts, including, e.g., alternative antibody formats, antigen-drug conjugates (ADC) or immunotoxins.
In some embodiments, the therapeutic peptide is an enzyme, a ligand, a receptor, a transcription factor, or a fragment or a modification thereof. In some embodiments, the therapeutic peptide is an antimicrobial peptide or a fragment or a modification thereof.
In some embodiments, the exogenous sequence encodes a targeting moiety. In some embodiments, the targeting moiety is specific to an organ, a tissue, or a cell.
In some embodiments, the second scaffold protein further comprises a targeting moiety. In some embodiments, the targeting moiety is specific to an organ, a tissue, or a cell.
In one embodiment, the present disclosure provides a polypeptide for modifying an EV, e.g., an exosome, comprising a sequence of
In some embodiments, the polypeptide of the scaffold comprises a sequence of any of SEQ ID NO: 4-110, or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide comprises a sequence of SEQ ID NO: 13, or the corresponding sequence without the N-terminal M. In some embodiments, the polypeptide comprises a sequence of SEQ ID NO: 110, or the corresponding sequence without the N-terminal M. In some embodiments, the polypeptide comprises a sequence of MGXKLSKKK (SEQ ID NO: 116), wherein X is any amino acid, or the corresponding sequence without the N-terminal M.
In one aspect, the present disclosure provides a polynucleotide construct comprising a coding sequence encoding the polypeptide provided herein. In some embodiments, the coding sequence is codon optimized.
In another aspect, the present disclosure provides a method of making an engineered EV, e.g., an exosome, comprising the steps of:
a. introducing into a cell a nucleic acid construct encoding a fusion polypeptide comprising
In some embodiments, the first sequence comprises a sequence of
In some embodiments, the polynucleotide comprises a sequence of any of SEQ ID NO: 4-110, or any of the corresponding sequences without the N-terminal M. In some embodiments, the polynucleotide comprises a sequence of SEQ ID NO: 13, or the corresponding sequence without the N-terminal M. In some embodiments, the polynucleotide comprises a sequence of SEQ ID NO: 110, or the corresponding sequence without the N-terminal M. In some embodiments, the polynucleotide comprises a sequence of MGXKLSKKK (SEQ ID NO: 116), or the corresponding sequence without the N-terminal M, wherein X is any amino acid.
In some embodiments, the fusion polypeptide is present on the luminal surface of the engineered EV, e.g., an engineered exosome, at a higher density than a different scaffold protein in a different EV, e.g., an exosome, wherein the different scaffold protein comprises a conventional EV, e.g., exosome protein or a variant thereof. In some embodiments, the fusion polypeptide is present at more than 2 fold higher density than the different scaffold protein in the different EV, e.g., an exosome.
In some embodiments, the fusion polypeptide is present at more than 4 fold, 16 fold, 100 fold, or 10,000 fold higher density than the different scaffold protein in the different EV, e.g., an exosome.
The present disclosure is directed to an isolated extracellular vesicle (EV) comprising a biologically active molecule linked to a scaffold protein, wherein the scaffold protein comprises an N-terminus domain (ND) and an effector domain (ED), wherein the ND and the ED are associated with the luminal surface of the EV by an ionic interaction, wherein the ED comprises at least two contiguous lysines (Lys) in sequence. In some embodiments, the ND is associated with the luminal surface of the EV via myristoylation. In other embodiments, the ND has Gly at the N-terminus.
In some embodiments, the ED comprises at least three Lys, at least four Lys, at least five Lys, at least six Lys, or at least seven Lys. In other embodiments, the ED is linked to the ND by a peptide bond. In some embodiments, the ED comprises (Lys)n, wherein n is an integer between 1 and 10. In other embodiments, the ED comprises KK, KKK, KKKK (SEQ ID NO: 151), KKKKK (SEQ ID NO: 152), or any combination thereof.
In other embodiments, the ND comprises the amino acid sequence as set forth in G:X2:X3:X4:X5:X6, wherein G is a glycine represented as Gly; wherein “:” represents a peptide bond, wherein each of the X2 to the X6 is independently an amino acid; and wherein the X6 comprises a basic amino acid. In some embodiments, the X6 is selected from the group consisting of Lys, Arg, and His.
In other embodiments, the disclosure is an isolated extracellular vesicle (EV) comprising a biologically active molecule linked to a scaffold protein, wherein the scaffold protein comprises an N-terminus domain (ND) and an effector domain (ED), wherein the ND comprises the amino acid sequence as set forth in G:X2:X3:X4:X5:X6, wherein G is a glycine, represented by Gly; wherein “:” represents a peptide bond, wherein each of the X2 to the X6 is independently an amino acid; wherein the X6 comprises a basic amino acid, and wherein the ED is linked to X6 by a peptide bond and comprises at least one lysine at the N-terminus of the ED. In some embodiments, the ED does not comprise a transmembrane domain or a cytoplasmic domain of a virus. In some embodiments, the X2 is selected from the group consisting of Pro, Gly, Ala, and Ser. In other embodiments, the X4 is selected from the group consisting of Pro, Gly, Ala, Ser, Val, Ile, Leu, Phe, Trp, Tyr, Gln, and Met. In some embodiments, the X5 is selected from the group consisting of Pro, Gly, Ala, and Ser.
In some embodiments, the ND of the scaffold protein comprises the amino acid sequence of G:X2:X3:X4:X5:X6, wherein
G represents Gly;
“:” represents a peptide bond;
the X2 is an amino acid selected from the group consisting of Pro, Gly, Ala, and Ser;
the X3 is an amino acid;
the X4 is an amino acid selected from the group consisting of Pro, Gly, Ala, Ser, Val, Ile, Leu, Phe, Trp, Tyr, Gln, and Met;
the X5 is an amino acid selected from the group consisting of Pro, Gly, Ala, and Ser; and
the X6 is an amino acid selected from the group consisting of Lys, Arg, and His.
In some embodiments, the X3 is selected from the group consisting of Asn, Gln, Ser, Thr, Asp, Glu, Lys, His, and Arg.
In some embodiments, the ND and the ED are joined by a linker. In some embodiments, the linker comprises one or more amino acids.
In some embodiments, the disclosure is directed to an isolated extracellular vesicle (EV) comprising a biologically active molecule linked to a scaffold protein, wherein the scaffold protein comprises ND-ED, wherein:
ND comprises G:X2:X3:X4:X5:X6; wherein:
G represents Gly;
“:” represents a peptide bond;
the X2 is an amino acid selected from the group consisting of Pro, Gly, Ala, and Ser;
the X3 is an amino acid;
the X4 is an amino acid selected from the group consisting of Pro, Gly, Ala, Ser, Val, Ile, Leu, Phe, Trp, Tyr, Glu, and Met;
the X5 is an amino acid selected from the group consisting of Pro, Gly, Ala, and Ser;
the X6 is an amino acid selected from the group consisting of Lys, Arg, and His;
“-” is an optional linker comprising one or more amino acids; and
ED is an effector domain comprising (i) at least two contiguous lysines (Lys), which is linked to the X6 by a peptide bond or one or more amino acids or (ii) at least one lysine, which is directly linked to the X6 by a peptide bond.
In other embodiments, the X2 is selected from the group consisting of Gly and Ala. In some embodiments, the X3 is Lys. In some embodiments, the X4 is Leu or Glu. In some embodiments, the X5 is selected from the group consisting of Ser and Ala. In some embodiments, the X6 is Lys. In other embodiments, the X2 is Gly, Ala, or Ser; the X3 is Lys or Glu, the X4 is Leu, Phe, Ser, and Glu, the X5 is Ser or Ala; and the X6 is Lys.
In some embodiments, the ND and the ED are linked by a linker comprising one or more amino acids. In some embodiments, the ED comprises Lys (K), KK, KKK, KKKK (SEQ ID NO: 151), KKKKK (SEQ ID NO: 152), or any combination thereof.
In some embodiments, the scaffold protein comprises an amino acid sequence selected from the group consisting of (i) GGKLSKK (SEQ ID NO: 157), (ii) GAKLSKK (SEQ ID NO: 158), (iii) GGKQSKK (SEQ ID NO: 159), (iv) GGKLAKK (SEQ ID NO: 160), or (v) any combination thereof. In some embodiments, the scaffold protein comprises an amino acid sequence selected from the group consisting of (i) GGKLSKKK (SEQ ID NO: 161), (ii) GGKLSKKS (SEQ ID NO: 162), (iii) GAKLSKKK (SEQ ID NO: 163), (iv) GAKLSKKS (SEQ ID NO: 164), (v) GGKQSKKK (SEQ ID NO: 165), (vi) GGKQSKKS (SEQ ID NO: 166), (vii) GGKLAKKK (SEQ ID NO: 167), (viii) GGKLAKKS (SEQ ID NO: 168), and (ix) any combination thereof. In some embodiments, the scaffold protein is at least about 8, at least about 9, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 120, at least about 130, at least about 140, at least about 150, at least about 160, at least about 170, at least about 180, at least about 190, or at least about 200 amino acids in length.
In some embodiments, the Scaffold protein comprises (i) GGKLSKKKKGYNVN (SEQ ID NO: 169), (ii) GAKLSKKKKGYNVN (SEQ ID NO: 170), (iii) GGKQSKKKKGYNVN (SEQ ID NO: 171), (iv) GGKLAKKKKGYNVN (SEQ ID NO: 172), (v) GGKLSKKKKGYSGG (SEQ ID NO: 173), (vi) GGKLSKKKKGSGGS (SEQ ID NO: 174), (vii) GGKLSKKKKSGGSG (SEQ ID NO: 175), (viii) GGKLSKKKSGGSGG (SEQ ID NO: 176), (ix) GGKLSKKSGGSGGS (SEQ ID NO: 177), (x) GGKLSKSGGSGGSV (SEQ ID NO: 178), or (xi) GAKKSKKRFSFKKS (SEQ ID NO: 179).
In some embodiments, the scaffold protein does not comprise Met at the N-terminus. In some embodiments, the scaffold protein comprises a myristoylated amino acid residue at the N-terminus of the scaffold protein. In some embodiments, the amino acid residue at the N-terminus of the scaffold protein is Gly. In some embodiments, the amino acid residue at the N-terminus of the scaffold protein is synthetic. In some embodiments, the amino acid residue at the N-terminus of the scaffold protein is a glycine analog.
In some embodiments, the scaffold protein comprises an amino acid sequence having at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% sequence identity to SEQ ID NO: 1 (MARKS), SEQ ID NO: 2 (MARCKSL1), or SEQ ID NO: 3 (BASP1).
In some embodiments, the biologically active molecule is on the luminal surface or lumen of the EV. In some embodiments, the scaffold protein further comprises a transmembrane domain. In some embodiments, the transmembrane domain is between the ED domain of the scaffold protein and the biologically active molecule. In some embodiments, the scaffold protein further comprises an extravesicular domain. In some embodiments, the biologically active molecule is linked to the extravesicular domain.
In some embodiments, the scaffold protein is linked to the biologically active molecule by a linker. In some embodiments, the ND domain is linked to the ED domain by a linker. In some embodiments, the linker comprises one or more amino acids. In some embodiments, the linker comprises a cleavable linker. In some embodiments, the linker comprises a flexible linker.
In other embodiments, the biologically active molecule comprises a protein, a polypeptide, a peptide, a polynucleotide (DNA and/or RNA), a chemical compound, a virus, an ionophore, a carrier for an ionophore, a moiety that forms a channel or a pore, or any combination thereof. In some embodiments, the protein comprises a recombinant peptide, a natural peptide, a synthetic peptide, an antibody, a fusion protein, or any combination thereof. In some embodiments, the protein comprises an enzyme, a cytokine, a ligand, a receptor, a transcription factor, or a combination thereof. In some embodiments, the virus comprises an adeno-associated virus, a parvovirus, a retrovirus, an adenovirus, or any combination thereof.
In other embodiments, the EV further comprises a second scaffold protein. In some embodiments, the second scaffold protein comprises a PTGFRN polypeptide, a BSG polypeptide, an IGSF2 polypeptide, an IGSF3 polypeptide, an IGSF8 polypeptide, an ITGB1 polypeptide, an ITGA4 polypeptide, a SLC3A2 polypeptide, an ATP transporter polypeptide, an aminopeptidase N (ANPEP) polypeptide, an ectonucleotide pyrophosphatase/phosphodiesterase family member 1 (ENPP1) polypeptide, a neprilysin (MME) polypeptide, a neuropilin-1 (NRP1) polypeptide, or a fragment thereof. In some embodiments, the biologically active molecule is an inhibitor for a negative checkpoint regulator or an inhibitor for a binding partner of a negative checkpoint regulator. In some embodiments, the negative checkpoint regulator is selected from the group consisting of: cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), programmed cell death protein 1 (PD-1), lymphocyte-activated gene 3 (LAG-3), T-cell immunoglobulin mucin-containing protein 3 (TIM-3), B and T lymphocyte attenuator (BTLA), T cell immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig suppressor of T cell activation (VISTA), adenosine A2a receptor (A2aR), killer cell immunoglobulin like receptor (KIR), indoleamine 2,3-dioxygenase (IDO), CD20, CD39, and CD73. In some embodiments, the biologically active molecule is an immunogenic protein.
In other embodiments, the biologically active molecule is a toxin, toxoid, or a non-toxic mutant of a toxin. In some embodiments, the toxin is a diphtheria toxin. In some embodiments, the toxoid is a tetanus toxoid. In some embodiments, the biologically active molecule is a non-toxic mutant of diphtheria toxin.
In some embodiments, the biologically active molecule is an activator for a positive co-stimulatory molecule or an activator for a binding partner of a positive co-stimulatory molecule. In some embodiments, the positive co-stimulatory molecule is a TNF receptor superfamily member. In some embodiments, the TNF receptor superfamily member is selected from the group consisting of: CD120a, CD120b, CD18, OX40, CD40, Fas receptor, M68, CD27, CD30, 4-1BB, TRAILR1, TRAILR2, TRAILR3, TRAILR4, RANK, OCIF, TWEAK receptor, TACI, BAFF receptor, ATAR, CD271, CD269, AITR, TROY, CD358, TRAMP, and XEDAR. In some embodiments, the activator for a positive co-stimulatory molecule is a TNF superfamily member. In some embodiments, the TNF superfamily member is selected from the group consisting of: TNFα, TNF-C, OX40L, CD40L, FasL, LIGHT, TL1A, CD27L, Siva, CD153, 4-1BB ligand, TRAIL, RANKL, TWEAK, APRIL, BAFF, CAMLG, NGF, BDNF, NT-3, NT-4, GITR ligand, and EDA-2. In some embodiments, the positive co-stimulatory molecule is a CD28-superfamily co-stimulatory molecule. In some embodiments, the CD28-superfamily co-stimulatory molecule is ICOS or CD28. In some embodiments, the activator for a positive co-stimulatory molecule is ICOSL, CD80, or CD86.
In other embodiments, the cytokine is selected from the group consisting of: IL-2, IL-7, IL-10, IL-12, and IL-15. In some embodiments, the protein comprises a T-cell receptor (TCR), a T-cell co-receptor, a major histocompatibility complex (MHC), a human leukocyte antigen (HLA), or a derivative thereof. In some embodiments, the protein comprises a tumor antigen. In some embodiments, the tumor antigen is selected from the group consisting of: alpha-fetoprotein (AFP), carcinoembryonic antigen (CEA), epithelial tumor antigen (ETA), mucin 1 (MUC1), Tn-MUC1, mucin 16 (MUC16), tyrosinase, melanoma-associated antigen (MAGE), tumor protein p53 (p53), CD4, CD8, CD45, CD80, CD86, programmed death ligand 1 (PD-L1), programmed death ligand 2 (PD-L2), NY-ESO-1, PSMA, TAG-72, HER2, GD2, cMET, EGFR, Mesothelin, VEGFR, alpha-folate receptor, CE7R, IL-3, Cancer-testis antigen, MART-1 gp100, and TNF-related apoptosis-inducing ligand.
In other embodiments, the EV is an exosome.
In some embodiments, the disclosure is directed to a pharmaceutical composition comprising the EV of the present disclosure and a pharmaceutically acceptable carrier. In some embodiments, the disclosure is directed to a cell that produces the EV of the present disclosure. In some embodiments, the disclosure is directed to a kit comprising the EV of the present disclosure and instructions for use.
In other embodiments, the disclosure is directed to a method of making EVs comprising culturing the cell of the present disclosure under a suitable condition and obtaining the EVs. In some embodiments, the disclosure is directed to a method of anchoring a biologically active molecule to an extracellular vesicle comprising linking the biologically active molecule to the scaffold protein of disclosed herein.
In other embodiments, the disclosure is directed to a method of preventing or treating a disease in a subject in need thereof, comprising administering the EV of the present disclosure, wherein the disease is associated with the antigen. In some embodiments, the EV is administered parenterally, orally, intravenously, intramuscularly, intra-tumorally, intranasally, subcutaneously, or intraperitoneally.
E1. An EV, e.g., an exosome, comprising a scaffold protein, wherein at least a part of the scaffold protein is expressed from an exogenous sequence, and the scaffold protein comprises MARCKS, MARCKSL1, BASP1 or a fragment or a modification thereof.
E2. The EV, e.g., exosome, of embodiment E1, wherein the scaffold protein is present in the EV, e.g., exosome, at a higher density than a different scaffold protein in a different EV, e.g., exosome, wherein the different scaffold protein comprises a conventional EV, e.g., exosome, protein or a variant thereof.
E3. The EV, e.g., exosome, of embodiment E2, wherein the conventional EV, e.g., exosome, protein is selected from the group consisting of CD9, CD63, CD81, PDGFR, GPI anchor proteins, lactadherin, LAMP2, LAMP2B, and a fragment thereof.
E4. The EV, e.g., exosome, of any of embodiments E1 to E3, wherein the EV, e.g., exosome, is produced from a cell genetically modified to comprise the exogenous sequence, optionally wherein the cell is an HEK293 cell.
E5. The EV, e.g., exosome, of embodiments E1 to E4, wherein the cell comprises a plasmid comprising the exogenous sequence.
E6. The EV, e.g., exosome, of embodiments E1 to E5, wherein the cell comprises the exogenous sequence inserted into a genome of the cell.
E7. The EV, e.g., exosome, of embodiments E1 to E6, wherein the exogenous sequence is inserted into a genomic site located 3′ or 5′ relative to a genomic sequence encoding MARCKS, MARCKSL1, or BASP1.
E8. The EV, e.g., exosome, of embodiments E1 to E7, wherein the exogenous sequence is inserted into a genomic sequence encoding MARCKS, MARCKSL1, or BASP1.
E9. The EV, e.g., exosome, of any of embodiments E1 to E8, wherein the scaffold protein is a fusion protein comprising MARCKS, MARCKSL1, BASP1, or a fragment thereof, and a therapeutic peptide.
E10. The EV, e.g., exosome, of embodiment E9, wherein the therapeutic peptide is selected from the group consisting of a natural peptide, a recombinant peptide, a synthetic peptide, or a linker to a therapeutic compound.
E11. The EV, e.g., exosome, of embodiment E9, wherein the therapeutic compound is selected from the group consisting of nucleotides, amino acids, lipids, carbohydrates, and small molecules.
E12. The EV, e.g., exosome, of embodiment E9, wherein the therapeutic peptide is an antibody or a fragment or a modification thereof.
E13. The EV, e.g., exosome, of embodiment E9, wherein the therapeutic peptide is an enzyme, a ligand, a receptor, a transcription factor, or a fragment or a modification thereof.
E14. The EV, e.g., exosome, of embodiment E9, wherein the therapeutic peptide is an antimicrobial peptide or a fragment or a modification thereof.
E15. The EV, e.g., exosome, of any of embodiments E1 to E14, further comprising a second scaffold protein, wherein the second scaffold protein comprises MARCKS, MARCKSL1, BASP1, or a fragment thereof.
E16. The EV, e.g., exosome, of any of embodiments E1 to E14, further comprising a second scaffold protein, wherein the second scaffold protein comprises PTGFRN, BSG, IGSF2, IGSF3, IGSF8, ITGB1, ITGA4, SLC3A2, ATP transporter or a fragment thereof.
E17. The EV, e.g., exosome, of any of embodiments E1 to E16, wherein the scaffold protein comprises a peptide of sequence (M)(G)(G/A/S)(K/Q)(L/F/S/Q)(S/A)(K)(K) (SEQ ID NO: 118), or the corresponding sequence without the N-terminal (M).
E18. The EV, e.g., exosome, of any of embodiments E1 to E17, wherein the scaffold protein comprises a peptide of sequence (M)(G)(π)(X)(Φ/π)(π)(+)(+), or the corresponding sequence without the N-terminal (M), wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), X is any amino acid, Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu).
E19. The EV, e.g., exosome, of any of embodiments E1 to E18, wherein the scaffold protein comprises a peptide of sequence (M)(G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+), or the corresponding sequence without the N-terminal (M), wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), ξ is any amino acid selected from the group consisting of (Asn, Gln, Ser, Thr, Asp, Glu, Lys, His, Arg), Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu).
E20. The EV, e.g., exosome, of any of embodiments E18 or E19, wherein the scaffold protein comprises a peptide of any one of SEQ ID NO: 4-110, or any of the corresponding sequences without the N-terminal M.
E21. The EV, e.g., exosome, of any of embodiments E18 or E19, wherein the scaffold protein comprises a peptide of MGXKLSKKK (SEQ ID NO: 116), or the corresponding sequence without the N-terminal M, wherein X is any amino acid.
E22. The EV, e.g., exosome, of embodiment E20, wherein the scaffold protein comprises a peptide of SEQ ID NO: 110, or the corresponding sequence without the N-terminal M.
E23. The EV, e.g., exosome, of embodiment E20, wherein the scaffold protein comprises the peptide of SEQ ID NO: 13, or the corresponding sequence without the N-terminal M.
E24. The EV, e.g., exosome, of any of embodiments E1 to E24, wherein the scaffold protein further comprises a payload, e.g., a biologically active molecule such as a peptide.
E25. A pharmaceutical composition comprising the EV, e.g., exosome, of any of embodiments E1 to E24 and an excipient.
E26. The pharmaceutical composition of embodiment E25, substantially free of macromolecules, wherein the macromolecules are selected from nucleic acids, exogenous proteins, lipids, carbohydrates, metabolites, and a combination thereof.
E27. A population of cells for producing the EV, e.g., exosome, of any of embodiments E1 to E24.
E28. The population of cells of embodiment E27, comprising an exogenous sequence encoding the scaffold protein comprising MARCKS, MARCKSL1, BASP1 or a fragment or a modification thereof.
E29. The population of cells of embodiment E28, further comprising a second exogenous sequence encoding a second scaffold protein, wherein the second scaffold protein comprises MARCKS, MARCKSL1, BASP1 or a fragment or a modification thereof.
E30. The population of cells of embodiment E28, further comprising a second exogenous sequence encoding a second scaffold protein, wherein the second scaffold protein comprises PTGFRN, BSG, IGSF2, IGSF3, IGSF8, ITGB1, ITGA4, SLC3A2, ATP transporter or a fragment thereof.
E31. The population of cells of any of embodiments E27 to E30, wherein the exogenous sequence is inserted into a genomic sequence encoding MARCKS, MARCKSL1, or BASP1, wherein the exogenous sequence and the genomic sequence encodes the scaffold protein.
E32. The population of cells of any of embodiments E27 to E30, wherein the exogenous sequence is in a plasmid.
E33. The population of cells of any of embodiments E27 to E32, wherein the exogenous sequence encodes a biologically active molecule, e.g., a therapeutic peptide.
E34. The population of cells of embodiment E33, wherein the therapeutic peptide is selected from a group consisting of a natural peptide, a recombinant peptide, a synthetic peptide, or a linker to a therapeutic compound.
E35. The population of cells of embodiment E33, wherein the therapeutic compound is selected from the group consisting of nucleotides, amino acids, lipids, carbohydrates, and small molecules.
E36. The population of cells of embodiment E33, wherein the therapeutic peptide is an antibody or a fragment or a modification thereof.
E37. The population of cells of embodiment E33, wherein the therapeutic peptide is an enzyme, a ligand, a receptor, a transcription factor, or a fragment or a modification thereof.
E38. The population of cells of embodiment E33, wherein the therapeutic peptide is an antimicrobial peptide or a fragment or a modification thereof.
E39. The population of cells of embodiment E28, wherein the exogenous sequence encodes a targeting moiety.
E40. The population of cells of embodiment E39, wherein the targeting moiety is specific to an organ, a tissue, or a cell.
E41. The population of cells of embodiments E29 or E30, wherein the second scaffold protein further comprises a targeting moiety.
E42. The population of cells of embodiment E41, wherein the targeting moiety is specific to an organ, a tissue, or a cell.
E43. A polypeptide for modifying an EV, e.g., exosome, comprising a sequence of
E44. The polypeptide of embodiment E43, comprising a sequence of any of SEQ ID NO: 4-110, or any of the corresponding sequences without the N-terminal M.
E45. The polypeptide of embodiment E43, comprising a sequence of SEQ ID NO: 13, or the corresponding sequence without the N-terminal M.
E46. The polypeptide of embodiment E43, comprising a sequence of SEQ ID NO: 110, or the corresponding sequence without the N-terminal M.
E47. The polypeptide of embodiment E43, comprising a sequence of MGXKLSKKK (SEQ ID NO: 116), or the corresponding sequence without the N-terminal M, wherein X is any amino acid.
E48. The polypeptide of any of embodiments E43 to E47, wherein the polypeptide is fused to a payload, e.g., a biologically active molecule such as a peptide.
E49. The polypeptide of embodiment E48, wherein the polypeptide is fused to the N-terminus of the peptide.
E50. A polynucleotide construct comprising a coding sequence encoding the polypeptide of any of embodiments E43 to E49.
E51. The polynucleotide construct of embodiment E50, wherein the coding sequence is codon optimized.
E52. A method of making an engineered EV, e.g., exosome, comprising the steps of:
E53. The method of embodiment E52, wherein the first sequence comprises a sequence of
E54. The method of any of embodiments E52 or E53, wherein the first sequence comprises any of SEQ ID NO: 4-110, or any of the corresponding sequences without the N-terminal M.
E55. The method of embodiment E54, wherein the first sequence comprises SEQ ID NO: 13, or the corresponding sequence without the N-terminal M.
E56. The method of embodiment E55, wherein the first sequence comprises SEQ ID NO: 110, or the corresponding sequence without the N-terminal M.
E57. The method of embodiment E53, wherein the first sequence comprises MGXKLSKKK (SEQ ID NO: 116), or the corresponding sequence without the N-terminal M, wherein X is any amino acid.
E58. The method of any of embodiments E52 to E57, wherein the fusion polypeptide is present on the luminal surface of the engineered EV, e.g., exosome, at a higher density than a different scaffold protein in a different EV, e.g., exosome, wherein the different scaffold protein comprises a conventional EV, e.g., exosome protein or a variant thereof.
E59. The method of embodiment E58, wherein the fusion polypeptide is present at more than 2 fold higher density than the different scaffold protein in the different EV, e.g., exosome.
E60. The method of embodiment E59, wherein the fusion polypeptide is present at more than 4 fold, 16 fold, 100 fold, or 10,000 fold higher density than the different scaffold protein in the different EV, e.g., exosome.
The figures depict various aspects of the present disclosure for purposes of illustration only. One skilled in the art will readily recognize from the following discussion that alternative aspects of the structures and methods illustrated herein may be employed without departing from the principles of the disclosure described herein.
The present disclosure is directed to extracellular vesicles (EVs), e.g., exosomes, comprising at least one biologically active molecule linked to the EV, e.g., exosome, via a scaffold protein, wherein the scaffold protein comprises an N-terminus domain (ND) and an effector domain (ED), wherein the ND and/or the ED are associated with the luminal surface of the EV, e.g., an exosome, wherein the ED comprises (i) a lysine repeat in the ED or (ii) a lysine repeat when combined with the ND, e.g., K at the C-terminus in the ND and K at the N-terminus in the ED, wherein the ND and ED are linked directly, i.e., by a peptide bond. The present disclosure also provides the minimum number of amino acids that are capable of anchoring a payload, e.g., a biologically active molecule, to the luminal surface of the EV, e.g., exosome, e.g., seven to 15, seven to 14, seven to 13, seven to 12, seven to 11, seven to 10, seven to 9, or seven to 8 amino acid fragments. The ND can be associated with the luminal surface of the EV, e.g., an exosome, via myristoylation, whereas the ED can be associated with the luminal surface of the EV, e.g., an exosome, by an ionic interaction, e.g., via attractive electrostatic interaction. Non-limiting examples of the various aspects are shown in the present disclosure.
Before the present disclosure is described in greater detail, it is to be understood that this disclosure is not limited to the particular compositions or process steps described, as such can, of course, vary. As will be apparent to those of skill in the art upon reading this disclosure, each of the individual aspects described and illustrated herein has discrete components and features which can be readily separated from or combined with the features of any of the other several aspects without departing from the scope or spirit of the present disclosure. Any recited method can be carried out in the order of events recited or in any other order which is logically possible.
The headings provided herein are not limitations of the various aspects of the disclosure, which can be defined by reference to the specification as a whole. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only, and is not intended to be limiting, since the scope of the present disclosure will be limited only by the appended claims.
Accordingly, the terms defined immediately below are more fully defined by reference to the specification in its entirety.
Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this disclosure belongs. For example, the Concise Dictionary of Biomedicine and Molecular Biology, Juo, Pei-Show, 2nd ed., 2002, CRC Press; The Dictionary of Cell and Molecular Biology, 3rd ed., 1999, Academic Press; and the Oxford Dictionary Of Biochemistry And Molecular Biology, Revised, 2000, Oxford University Press, provide one of skill with a general dictionary of many of the terms used in this disclosure. As used herein, the following terms have the meanings ascribed to them below.
It is to be noted that the term “a” or “an” entity refers to one or more of that entity; for example, “a nucleotide sequence,” is understood to represent one or more nucleotide sequences. As such, the terms “a” (or “an”), “one or more,” and “at least one” can be used interchangeably herein. It is further noted that the claims can be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a negative limitation.
Furthermore, “and/or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. Thus, the term “and/or” as used in a phrase such as “A and/or B” herein is intended to include “A and B,” “A or B,” “A” (alone), and “B” (alone). Likewise, the term “and/or” as used in a phrase such as “A, B, and/or C” is intended to encompass each of the following aspects: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).
It is understood that wherever aspects are described herein with the language “comprising,” otherwise analogous aspects described in terms of “consisting of” and/or “consisting essentially of” are also provided.
Units, prefixes, and symbols are denoted in their Système International de Unites (SI) accepted form.
Numeric ranges are inclusive of the numbers defining the range. Where a range of values is recited, it is to be understood that each intervening integer value, and each fraction thereof, between the recited upper and lower limits of that range is also specifically disclosed, along with each subrange between such values. The upper and lower limits of any range can independently be included in or excluded from the range, and each range where either, neither or both limits are included is also encompassed within the disclosure.
Thus, ranges recited herein are understood to be shorthand for all of the values within the range, inclusive of the recited endpoints. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50.
Unless otherwise indicated, reference to a compound that has one or more stereocenters intends each stereoisomer, and all combinations of stereoisomers, thereof.
Where a value is explicitly recited, it is to be understood that values which are about the same quantity or amount as the recited value are also within the scope of the disclosure. Where a combination is disclosed, each subcombination of the elements of that combination is also specifically disclosed and is within the scope of the disclosure. Conversely, where different elements or groups of elements are individually disclosed, combinations thereof are also disclosed. Where any element of a disclosure is disclosed as having a plurality of alternatives, examples of that disclosure in which each alternative is excluded singly or in any combination with the other alternatives are also hereby disclosed; more than one element of a disclosure can have such exclusions, and all combinations of elements having such exclusions are hereby disclosed.
Nucleotides are referred to by their commonly accepted single-letter codes. Unless otherwise indicated, nucleotide sequences are written left to right in 5′ to 3′ orientation. Nucleotides are referred to herein by their commonly known one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Accordingly, A represents adenine, C represents cytosine, G represents guanine, T represents thymine, U represents uracil.
Amino acid sequences are written left to right in amino to carboxy orientation. Amino acids are referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.
The term “about” is used herein to mean approximately, roughly, around, or in the regions of. When the term “about” is used in conjunction with a numerical range, it modifies that range by extending the boundaries above and below the numerical values set forth. In general, the term “about” can modify a numerical value above and below the stated value by a variance of, e.g., 10 percent, up or down (higher or lower).
As used herein, the term “approximately,” as applied to one or more values of interest, refers to a value that is similar to a stated reference value. In certain aspects, the term “approximately” refers to a range of values that fall within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value).
The terms “administration,” “administering,” and grammatical variants thereof refer to introducing a composition, such as an EV (e.g., exosome) of the present disclosure, into a subject via a pharmaceutically acceptable route. The introduction of a composition, such as an EV (e.g., exosome) of the present disclosure, into a subject is by any suitable route, including intratumorally, orally, pulmonarily, intranasally, parenterally (intravenously, intra-arterially, intramuscularly, intraperitoneally, or subcutaneously), rectally, intralymphatically, intrathecally, periocularly or topically. Administration includes self-administration and the administration by another. A suitable route of administration allows the composition or the agent to perform its intended function. For example, if a suitable route is intravenous, the composition is administered by introducing the composition or agent into a vein of the subject.
As used herein, the term “agonist” refers to a molecule that binds to a receptor and activates the receptor to produce a biological response. Receptors can be activated by either an endogenous or an exogenous agonist. Non-limiting examples of endogenous agonist include hormones, neurotransmitters, and cyclic dinucleotides. Non-limiting examples of exogenous agonist include drugs, small molecules, and cyclic dinucleotides. The agonist can be a full, partial, or inverse agonist.
As used herein, the term “antagonist” refers to a molecule that blocks or dampens an agonist mediated response rather than provoking a biological response itself upon bind to a receptor. Many antagonists achieve their potency by competing with endogenous ligands or substrates at structurally defined binding sites on the receptors. Non-limiting examples of antagonists include alpha blockers, beta-blocker, and calcium channel blockers. The antagonist can be a competitive, non-competitive, or uncompetitive antagonist.
As used herein, the term “extracellular vesicle” or “EV” refers to a cell-derived vesicle comprising a membrane that encloses an internal space (lumen). Extracellular vesicles comprise all membrane-bound vesicles that have a smaller diameter than the cell from which they are derived. Generally extracellular vesicles range in diameter from 20 nm to 1000 nm, and can comprise various payloads either within the internal space (i.e., the lumen), displayed on the external surface or luminal surface of the extracellular vesicle, and/or spanning the membrane. The payload can comprise, e.g., nucleic acids, proteins, carbohydrates, lipids, small molecules, and/or combinations thereof. By way of example and without limitation, extracellular vesicles include apoptotic bodies, fragments of cells, vesicles derived from cells by direct or indirect manipulation (e.g., by serial extrusion or treatment with alkaline solutions), vesiculated organelles, and vesicles produced by living cells (e.g., by direct plasma membrane budding or fusion of the late endosome with the plasma membrane). Extracellular vesicles can be derived from a living or dead organism, explanted tissues or organs, and/or cultured cells. In some aspects, the EV comprises a scaffold protein disclosed herein.
As used herein the term “exosome” refers to a cell-derived small (between 20-300 nm in diameter, more preferably 40-200 nm in diameter) extracellular vesicle (EV) comprising a membrane that encloses an internal space (lumen), and which, in some aspects, is generated from a cell (e.g., a producer cell), for example, by direct plasma membrane budding or by fusion of the late endosome with the plasma membrane. The exosome is a species of extracellular vesicle (EV). In some aspects, the exosome comprises lipid or fatty acid and polypeptide and optionally comprises a payload (e.g., a biologically active molecule such as a therapeutic agent), a receiver (e.g., a targeting moiety), a polynucleotide (e.g., a nucleic acid, RNA, or DNA), a sugar (e.g., a simple sugar, polysaccharide, or glycan), or other molecules. The exosome can be derived from a producer cell, and isolated from the producer cell based on its size, density, biochemical parameters, or a combination thereof. In some aspects, the exosome comprises a scaffold protein of the present disclosure. In some aspects, the exosomes of the present disclosure are produced by cells that express one or more transgene products.
As used herein, the term “exosome lumen protein” refers to a scaffold protein, i.e., a protein attached or associated to the luminal surface of EV, e.g., exosome, such as MARCKS, MARKSL1, BASP1, or any functional fragment thereof, any variant thereof, any derivative thereof, or any combination thereof, and which is suitable for use as a scaffold to target a payload, e.g., a biologically active molecule (e.g., therapeutics proteins) to the luminal surface of EVs, e.g., exosomes.
As used herein, the term “nanovesicle” refers to a cell-derived small (between 20-250 nm in diameter, e.g., 30-150 nm in diameter) vesicle comprising a membrane that encloses an internal space, and which is generated from a cell (e.g., producer cell) by direct or indirect manipulation such that the nanovesicle would not be produced by the producer cell without such manipulation. Appropriate manipulations of the producer cell to produce the nanovesicles include but are not limited to serial extrusion, treatment with alkaline solutions, sonication, or combinations thereof. The production of nanovesicles can, in some instances, result in the destruction of the producer cell. In some aspects, populations of nanovesicles described herein are substantially free of vesicles that are derived from producer cells by way of direct budding from the plasma membrane or fusion of the late endosome with the plasma membrane. In some aspects, the nanovesicle comprises lipid or fatty acid and polypeptide, and optionally comprises a payload (e.g., a therapeutic agent), a receiver (e.g., a targeting moiety), a polynucleotide (e.g., a nucleic acid, RNA, or DNA), a sugar (e.g., a simple sugar, polysaccharide, or glycan) or other molecules. The nanovesicle, once it is derived from a producer cell according to the manipulation, may be isolated from the producer cell based on its size, density, biochemical parameters, or a combination thereof. In some aspects, the nanovesicle can comprise a scaffold protein disclosed herein.
As used herein the term “lumen-engineered EV” refers to an EV, e.g., an exosome with the luminal surface of the membrane or the lumen of the EV, e.g., exosome, modified in its composition so that the luminal surface or the lumen of the engineered EV, e.g., exosome, is different from that of the EV, e.g., exosome, prior to the modification or of the naturally occurring EV, e.g., exosome.
The engineering can be directly in the lumen (i.e., the void within the EV) or in the membrane of the EV (e.g., exosome) in particular the luminal surface of the EV, so that the lumen and/or the luminal surface of the EV, e.g., exosome, is changed. For example, the membrane is modified in its composition of a protein, a lipid, a small molecule, a carbohydrate, etc. so that the luminal surface of the EV, e.g., exosome, is modified. Similarly, the contents of the lumen can be modified. The composition can be changed by a chemical, a physical, or a biological method or by being produced from a cell previously modified by a chemical, a physical, or a biological method. Specifically, the composition can be changed by genetic engineering or by being produced from a cell previously modified by genetic engineering. In some aspects, a lumen-engineered EV, e.g., lumen-engineered exosome, comprises an exogenous protein (i.e., a protein that the EV, e.g., exosome, does not naturally express) or a fragment or variant thereof that can be exposed in the luminal surface or lumen of the EV, e.g., exosome, or can be an anchoring point (attachment) for a moiety exposed on the inner layer of the EV, e.g., exosome. In other aspects, a lumen-engineered EV, e.g., a lumen-engineered exosome, comprises a higher expression of a natural EV, e.g., exosome, protein (e.g., a scaffold protein) or a fragment or variant thereof that can be exposed to the lumen of the EV, e.g., exosome, or can be an anchoring point (attachment) for a moiety exposed on the luminal surface of the EV, e.g., exosome.
As used herein the term “surface-engineered EV” refers to an EV with the external surface of the EV modified in its composition so that the external surface of the engineered EV is different from that of the EV prior to the modification or of the naturally occurring EV.
As used herein the term “surface-engineered exosome” refers to an exosome with the external surface of the exosome modified in its composition so that the external surface of the engineered exosome is different from that of the exosome prior to the modification or of the naturally occurring exosome.
The term “modified,” when used in the context of EVs, e.g., exosomes, described herein, refers to an alteration or engineering of an EV, e.g., exosome and/or its producer cell, such that the modified EV, e.g., exosome, is different from a naturally-occurring EV, e.g., exosome. In some aspects, a modified EV, e.g., exosome, described herein comprises a membrane that differs in composition of a protein, a lipid, a small molecular, a carbohydrate, etc. compared to the membrane of a naturally-occurring EV, e.g., exosome. E.g., the membrane comprises higher density or number of natural EV, e.g., exosome, proteins and/or membrane comprises proteins that are not naturally found in EV, e.g., exosomes. In certain aspects, such modifications to the membrane change the exterior surface of the EV, e.g., exosome (e.g., surface-engineered EVs and exosomes described herein). In certain aspects, such modifications to the membrane change the luminal surface of the EV, .e.g., exosome (e.g., lumen-engineered EV and exosomes described herein).
For example, the lumen is modified in its composition of a protein, a lipid, a small molecule, a carbohydrate, etc. The composition can be changed by a chemical, a physical, or a biological method or by being produced from a cell previously modified by a chemical, a physical, or a biological method. Specifically, the composition can be changed by a genetic engineering or by being produced from a cell previously modified by genetic engineering.
As used herein the term “modification” of a protein, e.g., as in “modified protein” or “protein modification” or grammatical variants thereof, refers to a protein having at least 15% identity to the non-mutant amino acid sequence of the protein. A modification of a protein includes a fragment or a variant of the protein. A modification of a protein can further include chemical, or physical modification to a fragment or a variant of the protein. In some aspects, a modified protein retains at least one physiological function of the non-modified protein.
As used herein the term “a fragment” of a protein (e.g., a biologically active molecule such as a therapeutic protein, or a scaffold protein disclosed herein) refers to a protein that is shorter than the naturally-occurring sequence, e.g., N- and/or C-terminally deleted in comparison to the naturally occurring protein.
As used herein, the term “functional fragment” refers to a protein fragment that retains protein function. Accordingly, in some aspects, a functional fragment of a scaffold protein disclosed herein such as MARCKS, MARCKSL1, or BASP1 retains the ability to anchor a biologically active molecule on the luminal surface of the EV, e.g., exosome.
Whether a fragment is a functional fragment in that sense can be assessed by any art known methods to determine the protein content of EVs, e.g., exosomes including Western Blots, FACS analysis and fusions of the fragments with autofluorescent proteins like, e.g., GFP. In a particular aspect, the fragment of MARCKS, MARCKSL1, or BASP1 retains, e.g., at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100% of the ability of the naturally occurring MARCKS, MARCKSL1, or BASP1 to anchor a payload, e.g., a biologically active molecule, on the luminal or on the external surface of the EV, e.g., exosome. In a particular aspect, the ability of a variant of MARCKS, MARCKSL1, BASP1 or of a fragment of MARCKS, MARCKSL1, or BASP1 is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100% of the ability of MARCKS, MARCKSL1, and BASP1, respectively, to anchor a payload, e.g., biologically active molecule, on the luminal or on the external surface of the EV, e.g., exosome. This ability can be assessed, e.g. by fluorescently labeled variants, in the assays described in the experimental section.
The term “derivative” as used herein refers to an EV, e.g., exosome, component (e.g., a protein or a lipid), a scaffold protein of the present disclosure, or to a payload, e.g., a biologically active molecule (e.g., a polypeptide, polynucleotide, lipid, carbohydrate, antibody or fragment thereof) that has been chemically or enzymatically modified.
As used herein the term “variant” of a protein refers to a protein that shares a certain structural (e.g., amino acid sequence identity) and functional identities with another protein upon comparison (e.g., by sequence alignment) by a method known in the art. For example, a variant of a protein can include a substitution, insertion, deletion, frameshift or rearrangement in another protein. In some aspects, a variant of a protein retains at least one physiological function of the non-variant protein.
In a particular aspect, the variant is a variant protein having at least 70% identity to the full length, mature MARCKS, MARCKSL1, BASP1 or a fragment of MARCKS, MARCKSL1, or BASP1.
In some aspects, variants or variants of fragments of MARCKS share at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99% sequence identity with MARCKS according to SEQ ID NO: 1 or with a functional fragment thereof, as determined, e.g., by pairwise alignment using the Needleman-Wunsch algorithm.
In some aspects, variants or variants of fragments of MARCKSL1 share at least 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99% sequence identity with MARCKSL1 according to SEQ ID NO: 2 or with a functional fragment thereof, as determined, e.g., by pairwise alignment using the Needleman-Wunsch algorithm.
In some aspects, variants or variants of fragments of BASP1 share at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99% sequence identity with BASP1 according to SEQ ID NO: 3 or with a functional fragment thereof, as determined, e.g., by pairwise alignment using the Needleman-Wunsch algorithm.
In some aspects, a variant of a scaffold protein (e.g., MARCKS, MARCKSL1, or BASP1), a functional fragment of a scaffold protein, or a variant of a functional fragment of a scaffold protein, is a derivative.
In each of above cases, the variant or variant of a fragment of a scaffold protein (e.g., a variant of MARCKS, MARCKSL1, BASP1 or a fragment of MARCKS, MARCKSL1, or BASP1) retains the ability to anchor payload, e.g., a biologically active molecule, on the luminal or on the external surface of the EV, e.g., exosome.
Recitation of any protein provided herein encompasses a functional variant of the protein. The term “functional variant” of a protein refers to a variant of the protein that retains the ability to anchor a biologically active molecule on the luminal or on the external surface of the EV, e.g., exosome. In a particular aspect the ability of the functional variant of MARCKS, MARCKSL1, BASP1 or of a fragment of MARCKS, MARCKSL1, or BASP1 is at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95% or at least about 99% of the ability of MARCKS, MARCKSL1, and BASP1, respectively, to anchor a payload, e.g., a biologically active molecule, on the luminal or on the external surface of the EV, e.g., exosome.
Naturally occurring variants are called “allelic variants,” and refer to one of several alternate forms of a gene occupying a given locus on a chromosome of an organism (Genes II, Lewin, B., ed., John Wiley & Sons, New York (1985)). These allelic variants can vary at either the polynucleotide and/or polypeptide level and are included in the present disclosure. Alternatively, non-naturally occurring variants can be produced by mutagenesis techniques or by direct synthesis.
Using known methods of protein engineering and recombinant DNA technology, variants can be generated to improve or alter the characteristics of the polypeptides. For instance, one or more amino acids can be deleted from the N-terminus or C-terminus of the secreted protein without substantial loss of biological function. Ron et al., J. Biol. Chem. 268: 2984-2988 (1993), incorporated herein by reference in its entirety, reported variant KGF proteins having heparin binding activity even after deleting 3, 8, or 27 amino-terminal amino acid residues. Similarly, interferon gamma exhibited up to ten times higher activity after deleting 8-10 amino acid residues from the carboxy terminus of this protein. (Dobeli et al., J. Biotechnology 7:199-216 (1988), incorporated herein by reference in its entirety.)
Moreover, ample evidence demonstrates that variants often retain a biological activity similar to that of the naturally occurring protein. For example, Gayle and coworkers (J. Biol. Chem 268:22105-22111 (1993), incorporated herein by reference in its entirety) conducted extensive mutational analysis of human cytokine IL-1a. They used random mutagenesis to generate over 3,500 individual IL-1a mutants that averaged 2.5 amino acid changes per variant over the entire length of the molecule. Multiple mutations were examined at every possible amino acid position. The investigators found that “[m]ost of the molecule could be altered with little effect on either [binding or biological activity].” (See Abstract.) In fact, only 23 unique amino acid sequences, out of more than 3,500 nucleotide sequences examined, produced a protein that significantly differed in activity from wild-type.
As stated above, variants or derivatives include, e.g., modified polypeptides. In some aspects, variants or derivatives of, e.g., polypeptides, polynucleotides, lipids, glycoproteins, are the result of chemical modification and/or endogenous modification. In some aspects, variants or derivatives are the result of in vivo modification. In some aspects, variants or derivatives are the result of in vitro modification. In yet other aspects, variant or derivatives are the result of intracellular modification in producer cells.
Modifications present in variants and derivatives include, e.g., acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation (Mei et al., Blood 116:270-79 (2010), which is incorporated herein by reference in its entirety), proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.
The term “amino acid substitution” refers to replacing an amino acid residue present in a parent or reference sequence (e.g., a wild type sequence) with another amino acid residue. An amino acid can be substituted in a parent or reference sequence (e.g., a wild type polypeptide sequence), for example, via chemical peptide synthesis or through recombinant methods known in the art. Accordingly, a reference to a “substitution at position X” refers to the substitution of an amino acid present at position X with an alternative amino acid residue. In some aspects, substitution patterns can be described according to the schema AnY, wherein A is the single letter code corresponding to the amino acid naturally or originally present at position n, and Y is the substituting amino acid residue. In other aspects, substitution patterns can be described according to the schema An(YZ), wherein A is the single letter code corresponding to the amino acid residue substituting the amino acid naturally or originally present at position n, and Y and Z are alternative substituting amino acid residues that can replace A.
As used herein, the term “antibody” encompasses an immunoglobulin whether natural or partly or wholly synthetically produced, and fragments thereof. The term also covers any protein having a binding domain that is homologous to an immunoglobulin binding domain. “Antibody” further includes a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen. Use of the term antibody is meant to include whole antibodies, polyclonal, monoclonal and recombinant antibodies, fragments thereof, and further includes single-chain antibodies, humanized antibodies, murine antibodies, chimeric, mouse-human, mouse-primate, primate-human monoclonal antibodies, anti-idiotype antibodies, antibody fragments, such as, e.g., scFv, (scFv)2, Fab, Fab′, and F(ab′)2, F(abl)2, Fv, dAb, and Fd fragments, diabodies, and antibody-related polypeptides. Antibody includes bispecific antibodies and multispecific antibodies so long as they exhibit the desired biological activity or function. In some aspects of the present disclosure, the payload is a biologically active molecule comprising an antibody or an antigen binding fragment thereof. In some aspects, the antibody (e.g., a biologically active molecule of the present disclosure) is a nanobody.
The terms “antibody-drug conjugate” and “ADC” are used interchangeably and refer to an antibody linked, e.g., covalently, to a therapeutic agent (sometimes referred to herein as agent, drug, or active pharmaceutical ingredient) or agents. In some aspects of the present disclosure, the payload is a biologically active molecule comprising an antibody-drug conjugate.
A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art, including basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, if an amino acid in a polypeptide is replaced with another amino acid from the same side chain family, the substitution is considered to be conservative. In another aspect, a string of amino acids can be conservatively replaced with a structurally similar string that differs in order and/or composition of side chain family members.
As used herein, the term “conserved” refers to nucleotides or amino acid residues of a polynucleotide sequence or polypeptide sequence, respectively, that are those that occur unaltered in the same position of two or more sequences being compared. Nucleotides or amino acids that are relatively conserved are those that are conserved amongst more related sequences than nucleotides or amino acids appearing elsewhere in the sequences.
In some aspects, two or more sequences are said to be “completely conserved” or “identical” if they are 100% identical to one another. In some aspects, two or more sequences are said to be “highly conserved” if they are at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to one another.
In some aspects, two or more sequences are said to be “highly conserved” if they are about 70% identical, about 80% identical, about 90% identical, about 95%, about 98%, or about 99% identical to one another. In some aspects, two or more sequences are said to be “conserved” if they are at least 30% identical, at least 40% identical, at least 50% identical, at least 60% identical, at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to one another. In some aspects, two or more sequences are said to be “conserved” if they are about 30% identical, about 40% identical, about 50% identical, about 60% identical, about 70% identical, about 80% identical, about 90% identical, about 95% identical, about 98% identical, or about 99% identical to one another. Conservation of sequence may apply to the entire length of a polynucleotide or polypeptide or may apply to a portion, region or feature thereof.
As used herein, the term “homology” refers to the overall relatedness between polymeric molecules, e.g. between nucleic acid molecules (e.g. DNA molecules and/or RNA molecules) and/or between polypeptide molecules. Generally, the term “homology” implies an evolutionary relationship between two molecules. Thus, two molecules that are homologous will have a common evolutionary ancestor. In the context of the present disclosure, the term homology encompasses both to identity and similarity.
In some aspects, polymeric molecules are considered to be “homologous” to one another if at least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% of the monomers in the molecule are identical (exactly the same monomer) or are similar (conservative substitutions). The term “homologous” necessarily refers to a comparison between at least two sequences (polynucleotide or polypeptide sequences).
In the context of the present disclosure, substitutions (even when they are referred to as amino acid substitution) are conducted at the nucleic acid level, i.e., substituting an amino acid residue with an alternative amino acid residue is conducted by substituting the codon encoding the first amino acid with a codon encoding the second amino acid.
As used herein, the term “identity” refers to the overall monomer conservation between polymeric molecules, e.g., between polypeptide molecules or polynucleotide molecules (e.g. DNA molecules and/or RNA molecules). The term “identical” without any additional qualifiers, e.g., protein A is identical to protein B, implies the sequences are 100% identical (100% sequence identity). Describing two sequences as, e.g., “70% identical,” is equivalent to describing them as having, e.g., “70% sequence identity.”
Calculation of the percent identity of two polypeptide sequences, for example, can be performed by aligning the two sequences for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second polypeptide sequences for optimal alignment and non-identical sequences can be disregarded for comparison purposes). In certain aspects, the length of a sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or 100% of the length of the reference sequence. The amino acids at corresponding amino acid positions are then compared.
When a position in the first sequence is occupied by the same amino acid as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which needs to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
Methods of alignment of sequences for comparison are well-known in the art. Various programs and alignment algorithms are described in: Smith and Waterman, Adv. Appl. Math. 2: 482 (1981); Needleman and Wunsch, J. Mol. Bio. 48: 443 (1970); Pearson and Lipman, Methods in Mol. Biol. 24: 307-31 (1988); Higgins and Sharp, Gene 73: 15 237-44 (1988); Higgins and Sharp, CABIOS 5: 151-3 (1989) Corpet et al., Nuc. Acids Res. 16: 10881-90 (1988); Huang et al., Comp. Appl. BioSci. 8: 155-65 (1992); and Pearson et al., Meth. Mol. Biol. 24: 307-31 (1994). The NCBI Basic Local Alignment Search Tool (BLAST) [Altschul 20 et al., J. Mol. Biol. 215: 403-10 (1990) J is available from several sources, including the National Center for Biological Information (NBCl, Bethesda, Md.) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. BLAST and a description of how to determine sequence identify using the program can be accessed at the official website of NCBI (National Center for Biotechnology Information) under NIH (National Institute of Health).
Other suitable programs are, e.g., Needle, Stretcher, Water, or Matcher, part of the EMBOSS suite of bioinformatics programs and also available from the European Bioinformatics Institute (EBI) at www.ebi.ac.uk/Tools/psa. Sequence alignments can be conducted using methods known in the art such as MAFFT, Clustal (ClustalW, Clustal X or Clustal Omega), MUSCLE, etc.
Different regions within a single polynucleotide or polypeptide target sequence that aligns with a polynucleotide or polypeptide reference sequence can each have their own percent sequence identity. It is noted that the percent sequence identity value is rounded to the nearest tenth. For example, 80.11, 80.12, 80.13, and 80.14 are rounded down to 80.1, while 80.15, 80.16, 80.17, 80.18, and 80.19 are rounded up to 80.2. It also is noted that the length value will always be an integer.
In certain aspects, the percentage identity (% ID) or of a first amino acid sequence (or nucleic acid sequence) to a second amino acid sequence (or nucleic acid sequence) is calculated as % ID=100×(Y/Z), where Y is the number of amino acid residues (or nucleobases) scored as identical matches in the alignment of the first and second sequences (as aligned by visual inspection or a particular sequence alignment program) and Z is the total number of residues in the second sequence. If the length of a first sequence is longer than the second sequence, the percent identity of the first sequence to the second sequence will be higher than the percent identity of the second sequence to the first sequence.
One skilled in the art will appreciate that the generation of a sequence alignment for the calculation of a percent sequence identity is not limited to binary sequence-sequence comparisons exclusively driven by primary sequence data. It will also be appreciated that sequence alignments can be generated by integrating sequence data with data from heterogeneous sources such as structural data (e.g., crystallographic protein structures), functional data (e.g., location of mutations), or phylogenetic data. A suitable program that integrates heterogeneous data to generate a multiple sequence alignment is T-Coffee, available at www.tcoffee.org, and alternatively available, e.g., from the EBI. It will also be appreciated that the final alignment used to calculate percent sequence identity can be curated either automatically or manually.
As used herein, the term “similarity” refers to the overall relatedness between polymeric molecules, e.g. between polynucleotide molecules (e.g. DNA molecules and/or RNA molecules) and/or between polypeptide molecules. Calculation of percent similarity of polymeric molecules to one another can be performed in the same manner as a calculation of percent identity, except that calculation of percent similarity takes into account conservative substitutions as is understood in the art. It is understood that percentage of similarity is contingent on the comparison scale used, i.e., whether the amino acids are compared, e.g., according to their evolutionary proximity, charge, volume, flexibility, polarity, hydrophobicity, aromaticity, isoelectric point, antigenicity, or combinations thereof.
As used herein the term “producer cell” refers to a cell used for generating an EV, e.g., an exosome. A producer cell can be a cell cultured in vitro, or a cell in vivo. A producer cell includes, but not limited to, a cell known to be effective in generating EVs, e.g., exosomes, e.g., HEK293 cells, Chinese hamster ovary (CHO) cells, and mesenchymal stem cells (MSCs), BJ human foreskin fibroblast cells, fHDF fibroblast cells, AGE.HN® neuronal precursor cells, CAP® amniocyte cells, adipose mesenchymal stem cells, RPTEC/TERT1 cells. In certain aspects, a producer cell is not an antigen-presenting cell. In some aspects, a producer cell is not a dendritic cell, a B cell, a mast cell, a macrophage, a neutrophil, Kupffer-Browicz cell, cell derived from any of these cells, or any combination thereof.
As used herein, the terms “isolate,” “isolated,” and “isolating” or “purify,” “purified,” and “purifying” as well as “extracted” and “extracting” and grammatical variants thereof are used interchangeably and refer to the state of a preparation (e.g., a plurality of known or unknown amount and/or concentration) of desired EVs, e.g., exosomes, that have undergone one or more processes of purification, e.g., a selection or an enrichment of the desired EV, e.g., exosome, preparation. In some embodiments, isolating or purifying as used herein is the process of removing, partially removing (e.g., a fraction) of the EVs, e.g., exosomes, from a sample containing producer cells. In some embodiment, an isolated EV, e.g., exosome, composition has no detectable undesired activity or, alternatively, the level or amount of the undesired activity is at or below an acceptable level or amount.
In other embodiments, an isolated EV, e.g., exosome, composition has an amount and/or concentration of desired EVs, e.g., exosomes, at or above an acceptable amount and/or concentration. In other aspects, the isolated EV, e.g., exosome, composition is enriched as compared to the starting material (e.g., producer cell preparations) from which the composition is obtained. This enrichment can be by at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, or greater than about 99.9999% as compared to the starting material.
In some aspects, isolated EV, e.g., exosome, preparations are substantially free of residual biological products (e.g., contaminants). In some aspects, the isolated EV, e.g., exosome, preparations are about 100% free, at least about 99% free, at least about 98% free, at least about 97% free, at least about 96% free, at least about 95% free, at least about 94% free, at least about 93% free, at least about 92% free, at least about 91% free, or at least about 90% free of any contaminating biological matter. Residual biological products can include abiotic materials (including chemicals) or unwanted nucleic acids, proteins, lipids, or metabolites. In certain aspects, the isolated EV, e.g., exosome, preparations are about 100% free, at least about 99% free, at least about 98% free, at least about 97% free, at least about 96% free, at least about 95% free, at least about 94% free, at least about 93% free, at least about 92% free, at least about 91% free, or at least about 90% free of any macromolecules, e.g., of any nucleic acids, proteins, lipids, and/or carbohydrates. Substantially free of residual biological products can also mean that the EV, e.g., exosome, composition contains no detectable producer cells and that only EVs, e.g., exosomes, are detectable.
The term “excipient” or “carrier” refers to an inert substance added to a pharmaceutical composition to further facilitate administration of a compound. The terms “pharmaceutically-acceptable carrier,” “pharmaceutically-acceptable excipient,” and grammatical variants thereof encompass any of the agents approved by a regulatory agency of the U.S. Federal government or listed in the U.S. Pharmacopeia for use in animals, including humans, as well as any carrier or diluent that does not cause significant irritation to a subject and does not abrogate the biological activity and properties of the administered compound. Included are excipients and carriers that are useful in preparing a pharmaceutical composition and are generally safe, non-toxic, and desirable.
As used herein, the term “payload” refers to any molecule that can be attached to a scaffold of the present disclosure and subsequently anchored to the membrane of an EV, e.g., an exosome, of the present disclosure. In some embodiments, the payload is attached to the luminal surface of the EV, e.g., exosome, membrane. The term payload encompasses biologically active molecules, e.g., molecules that can have a therapeutic and/or prophylactic effect, as well as diagnostic molecules. Accordingly, the term payload also encompasses detectable moieties such as radionuclides, fluorescent molecules, contrast agents, tags, or molecular entities that can be recognized by a detectable moiety, e.g., ligands or tags.
As used herein, the term payload is equivalent to and interchangeable with the term “cargo.” Accordingly “cargo protein” or “cargo peptide” refer to specific types of payload molecules (protein and peptides, respectively) attached to a scaffold of the present disclosure.
The term “biologically active molecule” as use herein refers to any molecule that can be attached to an EV, e.g., exosome, via a scaffold of the present disclosure wherein the molecule can have a therapeutic or prophylactic effect in a subject in need thereof, or affect the homeostasis of a cell or tissue in a subject. Non-limiting examples of biologically active molecules that can be introduced into an EV, e.g., exosome, and/or a producer cell include, e.g., therapeutic agents such as nucleotides (e.g., nucleotides comprising a detectable moiety or a toxin or that disrupt transcription), nucleic acids (e.g., DNA or mRNA molecules that encode a polypeptide such as an enzyme, or RNA molecules that have regulatory function such as miRNA, dsDNA, lncRNA, and siRNA), amino acids (e.g., amino acids comprising a detectable moiety or a toxin or that disrupt translation), polypeptides (e.g., enzymes or antibodies), lipids, carbohydrates, viruses and viral particles (e.g., adeno-associated viruses and viral particles, retroviruses, adenoviruses, etc.) and small molecules (e.g., small molecule drugs and toxins), including small molecule STING agonists including cyclic dinucleotides such as ML-RR S2 and 3′-3′ cAIMPdFSH). In certain aspects, a payload comprises an antigen. In certain aspects, the biologically active molecule, e.g., the therapeutic agent, e.g., therapeutic agent to human, retains a biological function, e.g., a therapeutic function, when fused to a scaffold protein disclosed herein. In some aspects, the biologically active molecule can have at least 5 amino acids, at least 6 amino acids, at least 7 amino acids, at least 8 amino acids, at least 9 amino acids, at least 10 amino acids, at least 15 amino acids, at least 20 amino acids, at least 25 amino acids, at least 30 amino acids, at least 35 amino acids, at least 40 amino acids, at least 45 amino acids, at least 50 amino acids, at least 55 amino acids, at least 60 amino acids, at least 65 amino acids, at least 70 amino acids, at least 75 amino acids, at least 100 amino acids, at least 150 amino acids, at least 200 amino acids, at least 250 amino acids, at least 300 amino acids, at least 350 amino acids, at least 400 amino acids, or at least 500 amino acids. In some aspects, the biologically active molecule can have at least 5 amino acids. In some aspects, the biologically active molecule can have at least 10 amino acids. In some aspects, the biologically active molecule can have at least 50 amino acids. In some aspects, the biologically active molecule can have at least 100 amino acids. In some aspects, the biologically active molecule can have at least 5 amino acids, e.g., 5-500, 5-450, 5-400, 5-350, 5-300, 5-250, 5-200, 5-150, 5-100, 5-90, 5-80, 5-70, 5-60, 5-50, 5-40, 5-30, 5-20, 5-15, or 5-10 amino acids. In some aspects, the biologically active molecule can have at least 10 amino acids, e.g., 10-500, 10-450, 10-400, 10-350, 10-300, 10-250, 10-200, 10-150, 10-100, 10-90, 10-80, 10-70, 10-60, 10-50, 10-40, 10-30, 10-20, or 10-15 amino acids. In some aspects, the biologically active molecule can have at least 50 amino acids, e.g., 50-500, 50-450, 50-400, 50-350, 50-300, 50-250, 50-200, 50-150, 50-100, 50-90, 50-80, 50-50, or 50-60 amino acids. In some aspects, the biologically active molecule can have at least 100 amino acids, e.g., 100-500, 100-450, 100-400, 100-350, 100-300, 100-250, 100-200, or 100-150 amino acids. In other aspects, the biologically active molecule has at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least 11, at least 12, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 110, at least 120, at least 130, at least 140, at least 150, at least 160, at least 170, at least 180, at least 190, at least 200, at least 300, at least 400, or at least 500 nucleotides. In other aspects, the biologically active molecule has at least two nucleotides, e.g., 2-1000, 2-900, 2-500, 2-300, or 2-50. In other aspects, the biologically active molecule has at least 10 nucleotides, e.g., 10-1000, 10-900, 10-500, 10-300, or 10-50. In other aspects, the biologically active molecule has at least 15 nucleotides, e.g., 15-1000, 15-900, 15-500, 15-300, or 15-50. In other aspects, the biologically active molecule has at least 20 nucleotides, e.g., 20-1000, 20-900, 20-500, 20-300, or 20-50. In other aspects, the biologically active molecule has at least 50 nucleotides, e.g., 50-1000, 50-900, 50-500, 50-300, or 50-100. In other aspects, the biologically active molecule has at least 100 nucleotides, e.g., 100-10000, 100-9000, 100-5005, 100-3000, or 100-500. In other aspects, the biologically active molecule has at least 200 nucleotides, e.g., 200-10000, 200-9000, 200-5000, 200-3000, or 200-500. In other aspects, the biologically active molecule has at least 500 nucleotides, e.g., 500-10000, 500-9000, 500-5000, or 500-3000. As used herein, the term “antigen” refers to any agent that when introduced into a subject elicits an immune response (cellular or humoral) to itself. In some aspects, the payload molecules are covalently linked to the EV, e.g., exosome. In other aspects, a payload comprises an adjuvant.
A “recombinant” polypeptide or protein refers to a polypeptide or protein produced via recombinant DNA technology. Recombinantly produced polypeptides and proteins expressed in engineered host cells are considered isolated for the purpose of the disclosure, as are native or recombinant polypeptides which have been separated, fractionated, or partially or substantially purified by any suitable technique. The polypeptides disclosed herein can be recombinantly produced using methods known in the art. Alternatively, the proteins and peptides disclosed herein can be chemically synthesized. In some aspects of the present disclosure, scaffold proteins present in EVs, e.g., exosomes, are recombinantly produced by overexpressing the scaffold proteins in the producer cells, so that levels of scaffold proteins in the resulting EVs, e.g., exosomes are significantly increased with respect to the levels of scaffold proteins present in EVs, e.g., exosomes, of producer cells not overexpressing such scaffold proteins.
As used herein the terms “anchor” or “anchoring” a biologically active molecule on the luminal or external surface of an EV (e.g., exosome) of the present disclosure via a scaffold protein refers to attaching covalently the biologically active molecule to the portion of the scaffold molecule located on the luminal or external surface of the EV (e.g., exosome), respectively.
The terms “associated,” “association,” and grammatical variants thereof are used interchangeably and refer to a first moiety, e.g., a first amino acid sequence or nucleotide sequence, covalently or non-covalently joined to a second moiety, e.g., a second amino acid sequence or nucleotide sequence, respectively. The first moiety can be directly joined or juxtaposed to the second moiety or alternatively an intervening moiety can covalently join the first moiety to the second moiety. In some embodiments, the term “associated” includes myristoylation, ionic interaction, or any combination thereof.
The term “linked” or “fused” as used herein refers to a fusion of a first moiety to a second moiety at the C-terminus or the N-terminus by a peptide bond or by a linker of one or more amino acids. The term “linked” or “fused” also includes insertion of the whole first moiety (or the second moiety) into, e.g., between, any two points, e.g., amino acids, in the second moiety (or the first moiety, respectively). In one aspect, the first moiety is linked to a second moiety by a peptide bond or a linker. The first moiety can be linked to a second moiety by a phosphodiester bond or a linker. The linker can be a peptide or a polypeptide (for polypeptide chains) or a nucleotide or a nucleotide chain (for nucleotide chains) or any chemical moiety (for polypeptide or polynucleotide chains or any chemical molecules). The term “linked” can also be indicated by a hyphen (−). In some aspects, a scaffold protein on an EV, e.g., exosome, can be linked or fused to a payload, e.g., a biologically active molecule.
As used herein, “a mammalian subject” includes all mammals, including without limitation, humans, domestic animals (e.g., dogs, cats and the like), farm animals (e.g., cows, sheep, pigs, horses and the like) and laboratory animals (e.g., monkey, rats, mice, rabbits, guinea pigs and the like).
The terms “individual,” “subject,” “host,” and “patient,” and variants thereof, are used interchangeably herein and refer to any mammalian subject for whom diagnosis, treatment, or therapy is desired, particularly humans. The methods described herein are applicable to both human therapy and veterinary applications. In some aspects, the subject is a mammal, and in other aspects the subject is a human.
As used herein, the term “substantially free” means that the sample comprising EVs, e.g., exosomes comprise less than 10% of macromolecules, e.g., contaminants, by mass/volume (m/v) percentage concentration. Some fractions may contain less than about 0.001%, less than about 0.01%, less than about 0.05%, less than about 0.1%, less than about 0.2%, less than about 0.3%, less than about 0.4%, less than about 0.5%, less than about 0.6%, less than about 0.7%, less than about 0.8%, less than about 0.9%, less than about 1%, less than about 2%, less than about 3%, less than about 4%, less than about 5%, less than about 6%, less than about 7%, less than about 8%, less than about 9%, or less than about 10% (m/v) of macromolecules.
As used herein, the term “macromolecule” means nucleic acids, exogenous proteins, lipids, carbohydrates, metabolites (e.g., polymeric metabolites), or a combination thereof.
As used herein, the term “conventional EV protein” means a protein previously known to be enriched in EVs.
As used herein, the term “conventional EV, e.g., exosome protein” means a protein previously known to be enriched in exosomes, including but not limited to CD9, CD63, CD81, PDGFR, GPI anchor proteins, lactadherin LAMP2, and LAMP2B, a fragment thereof, or a peptide that binds thereto. For the avoidance of doubt, PTGFRN, BSG, IGSF2, IGSF3, IGSF8, ITGB1, ITGA4, SLC3A2, ATP transporter or a fragment or a variant thereof are not conventional EV, e.g., exosome proteins.
As used herein, the term “pharmaceutical composition” refers to one or more of the compounds described herein, such as, e.g., an EV, such as exosome of the present disclosure, mixed or intermingled with, or suspended in one or more other chemical components, such as pharmaceutically-acceptable carriers and excipients. One purpose of a pharmaceutical composition is to facilitate administration of preparations of EVs, e.g., exosomes, to a subject.
The term “polynucleotide” as used herein refers to polymers of nucleotides of any length, including ribonucleotides, deoxyribonucleotides, analogs thereof, or mixtures thereof. This term refers to the primary structure of the molecule. Thus, the term includes triple-, double- and single-stranded deoxyribonucleic acid (“DNA”), as well as triple-, double- and single-stranded ribonucleic acid (“RNA”). It also includes modified, for example by alkylation, and/or by capping, and unmodified forms of the polynucleotide. More particularly, the term “polynucleotide” includes polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), including tRNA, rRNA, hRNA, siRNA and mRNA, whether spliced or unspliced, any other type of polynucleotide which is an N- or C-glycoside of a purine or pyrimidine base, and other polymers containing normucleotidic backbones, for example, polyamide (e.g., peptide nucleic acids “PNAs”) and polymorpholino polymers, and other synthetic sequence-specific nucleic acid polymers providing that the polymers contain nucleobases in a configuration which allows for base pairing and base stacking, such as is found in DNA and RNA. In particular aspects, the polynucleotide comprises an mRNA. In other aspect, the mRNA is a synthetic mRNA. In some aspects, the synthetic mRNA comprises at least one unnatural nucleobase. In some aspects, all nucleobases of a certain class have been replaced with unnatural nucleobases (e.g., all uridines in a polynucleotide disclosed herein can be replaced with an unnatural nucleobase, e.g., 5-methoxyuridine). In some aspects of the present disclosure, the biologically active molecule is a polynucleotide.
The terms “polypeptide,” “peptide,” and “protein” are used interchangeably herein to refer to polymers of amino acids of any length. The polymer can comprise modified amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids such as homocysteine, ornithine, p-acetylphenylalanine, D-amino acids, and creatine), as well as other modifications known in the art. In some aspects of the present disclosure, the payload, e.g., a biologically active molecule, attached to the EV, e.g., exosome, is a polypeptide, e.g., an antibody or a derivative thereof such as an ADC, a PROTAC, a toxin, a fusion protein, or an enzyme.
The term “polypeptide,” as used herein, refers to proteins, polypeptides, and peptides of any size, structure, or function. Polypeptides include gene products, naturally occurring polypeptides, synthetic polypeptides, homologs, orthologs, paralogs, fragments and other equivalents, variants, and analogs of the foregoing. A polypeptide can be a single polypeptide or can be a multi-molecular complex such as a dimer, trimer or tetramer. They can also comprise single chain or multichain polypeptides. Most commonly disulfide linkages are found in multichain polypeptides. The term polypeptide can also apply to amino acid polymers in which one or more amino acid residues are an artificial chemical analogue of a corresponding naturally occurring amino acid. In some aspects, a “peptide” can be less than or equal to 50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long. In some aspects, a “peptide” can be at least about 2 to about 50, at least about 3 to about 50, at least about 4 to about 50, at least about 5 to about 50, at least about 10 to about 50, at least about 15 to about 50, at least about 20 to about 50, at least about 25 to about 50, at least about 30 to about 50, at least about 35 to about 50, at least about 40 to about 50, or at least about 45 to about 50 amino acids long.
As used herein, the term “scaffold protein of the present disclosure,” or grammatical variants, refers to
As used herein, the term “EV, e.g., exosome, of the present disclosure,” or grammatical variants, refers to an EV, e.g., an exosome, that comprises at least one scaffold protein of the present disclosure.
As used herein, the term “producer cell of the present disclosure,” or grammatical variants, refers to a cell that can produce an EV, e.g., exosome, of the present disclosure.
Some aspects of the present disclosure relate to identification, use and modification of EV, e.g., exosome proteins (scaffold proteins), which are highly enriched in EV, e.g., exosome, luminal surfaces. Such EV proteins or exosome proteins (scaffold proteins) can be identified by analyzing highly purified EV, e.g., exosomes, with mass spectrometry or other methods known in the art.
The scaffold proteins of the present disclosure include various luminal proteins or membrane proteins, such as transmembrane proteins (i.e., proteins spanning the EV membrane through one or more transmembrane helices), integral proteins, and peripheral proteins (i.e., proteins on the luminal surface interacting with the surface via electrostatic interactions and/or anchoring moieties), enriched on the EV, e.g., exosome, membranes. Specifically, the scaffold proteins of the present disclosure include, but not limited to,
(1) myristoylated alanine rich Protein Kinase C substrate (MARCKS);
(2) myristoylated alanine rich Protein Kinase C substrate like 1 (MARCKSL1); and
(3) brain acid soluble protein 1 (BASP1).
One or more EV, e.g., exosome, proteins identified herein (scaffold proteins) can be selectively used depending on a producer cell, production condition, purification methods, or intended application of the exosomes.
EV, e.g., exosome, proteins enriched in the lumen (e.g., on the luminal surface of the EV membrane) of certain EVs, e.g., exosomes, with a specific size range, a targeting moiety, a charge density, a payload, etc. can be identified and used in some aspects of the present disclosure.
In some aspects, more than one EV, e.g., exosome, protein disclosed herein (e.g., scaffold proteins such as MARCKS, MARKSL1, BASP1, any functional fragment, variant, or derivative thereof, or any combination thereof) can be used concurrently or subsequently for generation and isolation of therapeutic EV, e.g., exosomes, of the present disclosure.
Extracellular vesicles (EVs), e.g., exosomes, typically have 20 nm to 1000 nm in diameter. Exosomes, which are small extracellular vesicles, have typically 100-200 nm in diameter. EVs, e.g., exosomes, are composed of a limiting lipid bilayer and a diverse set of proteins and nucleic acids (Maas, S. L. N., et al., Trends. Cell Biol. 27(3):172-188 (2017)). EVs, e.g., exosomes, exhibit preferential uptake in discrete cell types and tissues, and their tropism can be directed by adding proteins to their surface that interact with receptors on the surface of target cells (Alvarez-Erviti, L., et al., Nat. Biotechnol. 29(4):341-345 (2011)).
Unlike antibodies, EVs, e.g., exosomes, can accommodate large numbers of molecules attached to their surface, on the order of thousands to tens of thousands of molecules per EV, e.g., exosome. Conjugates or complexes comprising EVs, e.g., exosomes, and payloads, e.g., biologically active molecules (e.g., therapeutic molecules), thus represent a platform to deliver a high concentration of therapeutic or diagnostic compound to discrete cell types, while at the same time limiting overall systemic exposure to the compound, which in turn reduces off-target toxicity. Furthermore, EVs, e.g., exosomes, offer the possibility of accommodating multiple payloads, e.g., biologically active molecules, in different compartments. For example, the EV, e.g., exosome, can comprise, e.g., targeting moieties attached to the EV's external surface which would direct the EV to a certain target cell (e.g., a cancer cell) or target tissue (e.g., liver or brain), one or more therapeutics moieties (e.g., drugs), and/or one or more detectable moieties (e.g., contrast reagents or radionuclides).
The EV, e.g., exosome, can also comprise different payloads, e.g., therapeutics moieties (e.g., drugs) and/or detectable moieties (e.g., contrast reagents or radionuclides) attached to the EV's luminal surface. In addition, the EV, e.g., exosome, can also comprise one or more payloads, e.g., biologically active molecules (e.g., therapeutics agents, diagnostic reagents, adjuvants, etc.), in the lumen of the EV, e.g., an exosome.
Thus, EVs, e.g., exosomes, provide a delivery format that combine multiple payloads, e.g., biologically active molecules, with the same or different roles in a single delivery vehicle, and at a very high density.
EVs, e.g., exosomes, described herein are extracellular vesicles with a diameter between about 20-300 nm. In certain embodiments, an EV, e.g., exosome, of the present disclosure has a diameter between about 20-290 nm, 20-280 nm, 20-270 nm, 20-260 nm, 20-250 nm, 20-240 nm, 20-230 nm, 20-220 nm, 20-210 nm, 20-200 nm, 20-190 nm, 20-180 nm, 20-170 nm, 20-160 nm, 20-150 nm, 20-140 nm, 20-130 nm, 20-120 nm, 20-110 nm, 20-100 nm, 20-90 nm, 20-80 nm, 20-70 nm, 20-60 nm, 20-50 nm, 20-40 nm, 20-30 nm, 30-300 nm, 30-290 nm, 30-280 nm, 30-270 nm, 30-260 nm, 30-250 nm, 30-240 nm, 30-230 nm, 30-220 nm, 30-210 nm, 30-200 nm, 30-190 nm, 30-180 nm, 30-170 nm, 30-160 nm, 30-150 nm, 30-140 nm, 30-130 nm, 30-120 nm, 30-110 nm, 30-100 nm, 30-90 nm, 30-80 nm, 30-70 nm, 30-60 nm, 30-50 nm, 30-40 nm, 40-300 nm, 40-290 nm, 40-280 nm, 40-270 nm, 40-260 nm, 40-250 nm, 40-240 nm, 40-230 nm, 40-220 nm, 40-210 nm, 40-200 nm, 40-190 nm, 40-180 nm, 40-170 nm, 40-160 nm, 40-150 nm, 40-140 nm, 40-130 nm, 40-120 nm, 40-110 nm, 40-100 nm, 40-90 nm, 40-80 nm, 40-70 nm, 40-60 nm, 40-50 nm, 50-300 nm, 50-290 nm, 50-280 nm, 50-270 nm, 50-260 nm, 50-250 nm, 50-240 nm, 50-230 nm, 50-220 nm, 50-210 nm, 50-200 nm, 50-190 nm, 50-180 nm, 50-170 nm, 50-160 nm, 50-150 nm, 50-140 nm, 50-130 nm, 50-120 nm, 50-110 nm, 50-100 nm, 50-90 nm, 50-80 nm, 50-70 nm, 50-60 nm, 60-300 nm, 60-290 nm, 60-280 nm, 60-270 nm, 60-260 nm, 60-250 nm, 60-240 nm, 60-230 nm, 60-220 nm, 60-210 nm, 60-200 nm, 60-190 nm, 60-180 nm, 60-170 nm, 60-160 nm, 60-150 nm, 60-140 nm, 60-130 nm, 60-120 nm, 60-110 nm, 60-100 nm, 60-90 nm, 60-80 nm, 60-70 nm, 70-300 nm, 70-290 nm, 70-280 nm, 70-270 nm, 70-260 nm, 70-250 nm, 70-240 nm, 70-230 nm, 70-220 nm, 70-210 nm, 70-200 nm, 70-190 nm, 70-180 nm, 70-170 nm, 70-160 nm, 70-150 nm, 70-140 nm, 70-130 nm, 70-120 nm, 70-110 nm, 70-100 nm, 70-90 nm, 70-80 nm, 80-300 nm, 80-290 nm, 80-280 nm, 80-270 nm, 80-260 nm, 80-250 nm, 80-240 nm, 80-230 nm, 80-220 nm, 80-210 nm, 80-200 nm, 80-190 nm, 80-180 nm, 80-170 nm, 80-160 nm, 80-150 nm, 80-140 nm, 80-130 nm, 80-120 nm, 80-110 nm, 80-100 nm, 80-90 nm, 90-300 nm, 90-290 nm, 90-280 nm, 90-270 nm, 90-260 nm, 90-250 nm, 90-240 nm, 90-230 nm, 90-220 nm, 90-210 nm, 90-200 nm, 90-190 nm, 90-180 nm, 90-170 nm, 90-160 nm, 90-150 nm, 90-140 nm, 90-130 nm, 90-120 nm, 90-110 nm, 90-100 nm, 100-300 nm, 110-290 nm, 120-280 nm, 130-270 nm, 140-260 nm, 150-250 nm, 160-240 nm, 170-230 nm, 180-220 nm, or 190-210 nm. The size of the EV, e.g., exosome, described herein can be measured according to methods described, infra.
In some aspects, an EV, e.g., exosome, of the present disclosure comprises a bi-lipid membrane (“EV, e.g., exosome, membrane”), comprising an interior surface and an exterior surface. In certain embodiments, the interior surface faces the inner core (i.e., lumen) of the EV, e.g., exosome. In certain aspects, the exterior surface can be in contact with the endosome, the multivesicular bodies, or the membrane/cytoplasm of a producer cell or a target cell.
In some aspects, the EV, e.g., exosome, membrane comprises lipids and fatty acids. In some aspects, the EV, e.g., exosome, membrane comprises phospholipids, glycolipids, fatty acids, sphingolipids, phosphoglycerides, sterols, cholesterols, and phosphatidylserines.
In some aspects, the EV, e.g., exosome, membrane comprises an inner leaflet and an outer leaflet. The composition of the inner and outer leaflet can be determined by transbilayer distribution assays known in the art, see, e.g., Kuypers et al., Biohim Biophys Acta 1985 819:170. In some aspects, the composition of the outer leaflet is between approximately 70-90% choline phospholipids, between approximately 0-15% acidic phospholipids, and between approximately 5-30% phosphatidylethanolamine. In some aspects, the composition of the inner leaflet is between approximately 15-40% choline phospholipids, between approximately 10-50% acidic phospholipids, and between approximately 30-60% phosphatidylethanolamine.
In one aspect, the present disclosure relates to generation and use of lumen-engineered EVs, e.g., exosomes. Lumen-engineered exosomes have an internal space (the EV's luminal surface) modified in its compositions, e.g., modified with respect to the compositions of exosomes found in nature. For example, the composition of the luminal surface can be modified by changing the protein, lipid or glycan content of the components of the luminal side of the EV, e.g., exosome, membrane. In some aspects, the luminal surface of the EVs, e.g., exosomes, can comprise one or more recombinantly expressed proteins, e.g., scaffold proteins of the present disclosure, e.g., exosome lumen protein, that are not natural to the EVs, e.g., exosomes. Accordingly, the present disclosure provides compositions that allow the anchoring of a payload, e.g., a biologically active molecule, to an EV, e.g., an exosome, comprising linking the payload, e.g., a biologically active molecule, to a scaffold protein, e.g., exosome lumen protein, of the present disclosure. The present disclosure also provides a method of anchoring a payload, e.g., a biologically active molecule, to an EV, e.g., an exosome, comprising linking the biologically active molecule to a scaffold protein, e.g., exosome lumen protein, of the present disclosure.
In some aspects, the scaffold proteins, e.g., exosome lumen protein, of the present disclosure are attached to the luminal surface of the EV, e.g., exosome, via lipidation. In some aspects, the scaffold protein of the present disclosure is fatty acylated. In some aspects, the scaffold protein is myristoylated.
Myristoylation is a lipidation modification where a myristoyl group, derived from myristic acid, is covalently attached by an amide bond to the alpha-amino group of an N-terminal glycine. Myristic acid is a 14-carbon saturated fatty acid (14:4) with the systematic name of n-tetradecanoic acid. This modification can be added either co-translationally or post-translationally. During co-translational addition of the myristoyl group, the N-terminal glycine is modified following cleavage of the N-terminal methionine residue in the newly forming, growing polypeptide. This occurs in approximately 80% of myristoylated proteins. Post-translational myristoylation typically occurs following a caspase cleavage event resulting in the exposure of an internal glycine residue, which would then be available for myristic acid addition. In addition to co-translational or post-translational myristoylation (conduct either in vivo or in vitro, e.g., enzymatically), the myristoylation of the scaffold proteins, e.g., exosome lumen proteins, of the present disclosure can also occur via chemical synthesis, e.g., by appending, as a synthetic step, the myristic acid to a scaffold protein during chemical synthesis.
In some embodiments, the lipidic anchoring to biological membranes is not palmitoylation (i.e., attachment of palmitic acid, generally to cysteine and less frequently to serine or threonine). In other embodiments, the lipidic anchoring to biological membranes is prenylation (attachment of prenyl groups) or glycosylphosphatidylinositol-linking (GPI-linking). Prenylated proteins are proteins with covalently attached hydrophobic isoprene polymers (i.e., branched five-carbon hydrocarbon) at cysteine residues of the protein. GPI-linked proteins are attached to a GPI complex molecular group via an amide linkage to the protein's C-terminal carboxyl group. The GPI attachment occurs through the action of GPI-transamidase complex. The fatty acid chains of the phosphatidylinositol are inserted into the membrane and thus are what anchor the protein to the membrane.
In some embodiments, the lumen-engineered EVs, e.g., exosomes, are generated by chemical and/or physical methods, such as PEG-induced fusion and/or ultrasonic fusion.
In other embodiments, the lumen-engineered EVs, e.g., exosomes, are generated by genetic engineering. Exosomes produced from a genetically-modified producer cell or a progeny of the genetically-modified cell can contain modified lumen compositions. In some embodiments, lumen-engineered EVs, e.g., exosomes, have the EV, e.g., exosome, protein (e.g., a scaffold protein, e.g., exosome lumen protein, such as MARCKS, MARKSL1, BASP1, or a combination thereof) at a higher or lower density or include a modification or a fragment of the EV, e.g., exosome, protein (e.g., any functional fragment, variant, or derivative thereof, or any combination thereof).
For example, lumen-engineered EVs, e.g., exosomes, can be produced from a cell transformed with an exogenous sequence encoding the EV, e.g., exosome, protein or a modification or a fragment of the EV, e.g., exosome, protein (e.g., a scaffold protein, e.g., exosome lumen protein, such as MARCKS, MARKSL1, BASP1, any functional fragment, variant, or derivative thereof, or any combination thereof). EVs, e.g., exosomes, including proteins expressed from the exogenous sequence can include modified luminal surface protein (scaffold protein) compositions.
Various modifications or fragments of the EV protein, e.g., exosome protein (e.g., a scaffold protein, e.g., exosome lumen protein, such as MARCKS, MARKSL1, BASP1, any functional fragment, variant, or derivative thereof, or any combination thereof), can be used for the embodiments of the present disclosure. For example, proteins modified to be more effectively targeted to EV, e.g., exosome, luminal surfaces can be used. Proteins modified to comprise a minimal fragment required for specific and effective targeting to EV, e.g., exosome, luminal surfaces can be also used.
In some aspects, the scaffold protein, e.g., exosome lumen protein, of the present disclosure comprises the MARCKS protein, or a fragment, variant, or derivative thereof. The MARCKS protein (Uniprot accession no. P29966) is also known as protein kinase C substrate, 80 kDa protein, light chain. The full-length human MARCKS protein is 332 amino acids in length and comprises a calmodulin-binding domain at amino acid residues 152-176. In some embodiments, the scaffold protein of the present disclosure comprises a mature MARCKS protein (i.e., without N-terminal methionine). In some aspects, the scaffold protein of the present disclosure is derived from a mature MARCKS protein, i.e., it is a fragment, variant, or derivate of a mature MARCKS protein and therefore it lacks the N-terminal methionine present in the non-mature protein.
In some aspects, the scaffold protein, e.g., exosome lumen protein, of the present disclosure comprises the MARCKSL1 protein (Uniprot accession no. P49006), also known as MARCKS-like protein 1, and macrophage myristoylated alanine-rich C kinase substrate. The full-length human MARCKSL1 protein is 195 amino acids in length. The MARCKSL1 protein has an effector domain involved in lipid-binding and calmodulin-binding at amino acid residues 87-110. In some embodiments, the scaffold protein of the present disclosure comprises a mature MARCKSL1 protein (i.e., without N-terminal methionine). In some aspects, the scaffold protein of the present disclosure is derived from a mature MARCKSL1 protein, i.e., it is a fragment, variant, or derivate of a mature MARCKSL1 protein and therefore it lacks the N-terminal methionine present in the non-mature protein.
In some aspects, the scaffold of the present disclosure comprises the BASP1 protein (Uniprot accession number P80723), also known as 22 kDa neuronal tissue-enriched acidic protein or neuronal axonal membrane protein NAP-22. The full-length human BASP1 protein sequence (isomer 1) is 227 amino acids in length. An isomer produced by an alternative splicing is missing amino acids 88 to 141 from isomer 1. In some embodiments, the scaffold protein, e.g., exosome lumen protein, of the present disclosure comprises a mature BASP1 protein (i.e., without N-terminal methionine). In some aspects, the scaffold protein of the present disclosure is derived from a mature BASP1 protein, i.e., it is a fragment, variant, or derivate of a mature BASP1 protein and therefore it lacks the N-terminal methionine present in the non-mature protein.
In some aspects, the scaffold protein, e.g., exosome lumen protein, of the present disclosure comprises an “N-terminus domain” (ND) and an “effector domain,” wherein the ND and/or the ED are associated with the luminal surface of the EV, e.g., an exosome. As used herein the term “associated with” refers to the interaction between a scaffold protein of the present disclosure with the luminal surface of the EV, e.g., an exosome, that does not involve covalent linking to a membrane component. For example, the scaffolds of the present disclosure can be associated with the luminal surface of the EV, e.g., via a lipid anchor (e.g., myristic acid), and/or a polybasic domain that interacts electrostatically with the negatively charged head of membrane phospholipids. In other aspects, the scaffold protein comprises an N-terminus domain (ND) and an effector domain (ED), wherein the ND is associated with the luminal surface of the EV and the ED are associated with the luminal surface of the EV by an ionic interaction, wherein the ED comprises at least two, at least three, at least four, at least five, at least six, or at least seven contiguous lysines (Lys) in sequence.
In other aspects, the ED further comprises one or more low complexity regions, e.g., a PEST motif. A PEST sequence is a peptide sequence that is rich in proline (P), glutamic acid (E), serine (S), and threonine (T). In some aspects, the ED further comprises negatively charged residues (for example, Glu) and many Ser and Thr that undergo transient phosphorylation (thus, both adding negative charges to the areas out of ED).
In some aspects, the ND is associated with the luminal surface of the EV, e.g., an exosome, via lipidation, e.g., via myristoylation. In some embodiments, the ND has Gly at the N-terminus. In some embodiments, the N-terminal Gly is myristoylated. In some aspects, the ND does not comprise Met at the N-terminus. In other embodiments, the ND comprises Gly, which is myristoylated, and does not comprise Met at the N-terminus.
In some aspects, the ED is associated with the luminal surface of the EV, e.g., an exosome, by an ionic interaction. In some embodiments, the ED is associated with the luminal surface of the EV, e.g., an exosome, by an electrostatic interaction, in particular, an attractive electrostatic interaction.
In some aspects, the ED comprises (i) a basic amino acid (e.g., lysine), or (ii) two or more basic amino acids (e.g., lysine) next to each other in a polypeptide sequence. In some aspects, the basic amino acid is lysine (Lys; K), arginine (Arg, R), or Histidine (His, H). In some embodiments, the basic amino acid is (Lys)n, wherein n is an integer between 1 and 10.
In other aspects, the ED comprises at least a lysine and the ND comprises a lysine at the C-terminus if the N-terminus of the ED is directly linked to lysine at the C-terminus of the ND, i.e., the lysine is in the N-terminus of the ED and is fused to the lysine in the C-terminus of the ND. In other embodiments, the ED comprises at least two lysines, at least three lysines, at least four lysines, at least five lysines, at least six lysines, or at least seven lysines when the N-terminus of the ED is linked to the C-terminus of the ND by a linker, e.g., one or more amino acids.
In some aspects, the ED comprises K, KK, KKK, KKKK (SEQ ID NO: 151), KKKKK (SEQ ID NO: 152), or any combination thereof. The present disclosure also provides that in some aspects, the lysine repeats can be replaced with arginines. In other aspects, the arginine repeats in the ED or in the scaffold proteins provide lower loading efficacy compared to the lysine efficacy.
In some aspects, the scaffold protein, e.g., exosome lumen protein, useful for the present disclosure requires at least two lysines or at least three lysines, repeated in sequence in the ED or in the ED together with the ND, i.e., lysine at the C-terminus of the ND and K in the N-terminus of the ED. In some embodiments, the ED comprises K, KK, KKK, KKKK (SEQ ID NO: 151), KKKKK (SEQ ID NO: 152), or any combination thereof. In some aspects, the ND comprises the amino acid sequence as set forth in G:X2:X3:X4:X5:X6, wherein G represents Gly; wherein “:” represents a peptide bond, wherein each of the X2 to the X6 independently represents an amino acid; and wherein the X6 represents a basic amino acid. In some aspects, the X6 amino acid is selected is selected from the group consisting of Lys, Arg, and His. In some aspects, the X5 amino acid is selected from the group consisting of Pro, Gly, Ala, and Ser. In some embodiments, the X2 amino acid is selected from the group consisting of Pro, Gly, Ala, and Ser. In some aspects, the X4 is selected from the group consisting of Pro, Gly, Ala, Ser, Val, Ile, Leu, Phe, Trp, Tyr, Gln, and Met. In some aspects, the scaffold protein does not comprise Met at the N-terminus, e.g., myristoylated.
In some aspects, the scaffold protein, e.g., exosome lumen protein, comprises an ND and an ED, wherein ND comprises the amino acid sequence as set forth in G:X2:X3:X4:X5:X6, wherein G represents Gly; wherein “:” represents a peptide bond, wherein each of the X2 to the X6 independently represents an amino acid; wherein the X6 represents a basic amino acid, the X5 amino acid is selected from the group consisting of Pro, Gly, Ala, and Ser, the X4 is selected from the group consisting of Pro, Gly, Ala, Ser, Val, Ile, Leu, Phe, Trp, Tyr, Gln, and Met, the X3 represents an amino acid, and the X2 amino acid is selected from the group consisting of Pro, Gly, Ala, and Ser, wherein the ED comprises at least one amino acid, e.g., at least one Lys, and wherein the scaffold protein is not (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, 122-150, or 180-190 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121.
In some aspects, the scaffold protein, e.g., exosome lumen protein, comprises an N-terminus domain (ND) and an effector domain (ED), wherein the ND comprises the amino acid sequence as set forth in G:X2:X3:X4:X5:X6, wherein G is a glycine, represented as Gly; wherein “:” represents a peptide bond, wherein each of the X2 to the X6 is independently an amino acid; wherein the X6 comprises a basic amino acid, and wherein the ED is linked to X6 by a peptide bond and comprises at least one lysine at the N-terminus of the ED. In some aspects, the scaffold protein does not comprise Met at the N-terminus, e.g., myristoylated. In other aspects, the scaffold protein does not comprise or does not consist of (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, 122 to 150, or 180 to 190 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121.
In some embodiments, the ND of the scaffold protein, e.g., exosome lumen protein, comprises the amino acid sequence of G:X2:X3:X4:X5:X6, wherein
In some aspects, the scaffold protein, e.g., exosome lumen protein, does not comprise Met at the N-terminus, e.g., myristoylated. In other aspects, the scaffold protein does not comprise or consist of (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121. In some aspects, the X3 amino acid is selected from the group consisting of Asn, Gln, Ser, Thr, Asp, Glu, Lys, His, and Arg.
In some aspects, the ND and ED are joined by a linker. In some embodiments, the linker comprises one or more amino acids. In some aspects, the term “linker” refers to a peptide or polypeptide sequence (e.g., a synthetic peptide or polypeptide sequence) or to a non-polypeptide, e.g., an alkyl chain. In some aspects, two or more linkers can be linked in tandem. Generally, linkers provide flexibility or prevent/ameliorate steric hindrances. Linkers are not typically cleaved; however, in certain aspects, such cleavage can be desirable. Accordingly, in some embodiments a linker can comprise one or more protease-cleavable sites, which can be located within the sequence of the linker or flanking the linker at either end of the linker sequence. When the ND and ED are joined by a linker, the ED comprise at least two lysines, at least three lysines, at least four lysines, at least five lysines, at least six lysines, or at least seven lysines.
In some aspects, the linker is a peptide linker. In some aspects, the peptide linker can comprise at least about two, at least about three, at least about four, at least about five, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, or at least about 100 amino acids.
In some aspects, the linker is a glycine/serine linker. In some embodiments, the peptide linker is glycine/serine linker according to the formula [(Gly)n-Ser]m where n is any integer from 1 to 100 and m is any integer from 1 to 100. In other aspects, the glycine/serine linker is according to the formula [(Gly)x-Sery]z wherein x in an integer from 1 to 4, y is 0 or 1, and z is an integers from 1 to 50. In some aspects, the peptide linker comprises the sequence Gn, where n can be an integer from 1 to 100. In some aspects, the peptide linker can comprise the sequence (GlyAla)n, wherein n is an integer between 1 and 100. In other aspects, the peptide linker can comprise the sequence (GlyGlySer)n, wherein n is an integer between 1 and 100.
In some aspects, the peptide linker is synthetic, i.e., non-naturally occurring. In one embodiment, a peptide linker includes peptides (or polypeptides) (e.g., natural or non-naturally occurring peptides) which comprise an amino acid sequence that links or genetically fuses a first linear sequence of amino acids to a second linear sequence of amino acids to which it is not naturally linked or genetically fused in nature. For example, in one aspect the peptide linker can comprise non-naturally occurring polypeptides which are modified forms of naturally occurring polypeptides (e.g., comprising a mutation such as an addition, substitution or deletion).
In other aspects, the peptide linker can comprise non-naturally occurring amino acids. In yet other aspects, the peptide linker can comprise naturally occurring amino acids occurring in a linear sequence that does not occur in nature. In still other aspects, the peptide linker can comprise a naturally occurring polypeptide sequence.
The present disclosure also provides an isolated extracellular vesicle (EV), e.g., an exosome, comprising a biologically active molecule linked to a scaffold protein, e.g., exosome lumen protein, wherein the scaffold protein comprises ND-ED, wherein:
In some aspects, the X2 amino acid is selected from the group consisting of Gly and Ala. In some aspects, the X3 amino acid is Lys. In some aspects, the X4 amino acid is Leu or Glu. In some aspects, the X5 amino acid is selected from the group consisting of Ser and Ala. In some aspects, the X6 amino acid is Lys. In some aspects, the X2 amino acid is Gly, Ala, or Ser; the X3 amino acid is Lys or Glu; the X4 amino acid is Leu, Phe, Ser, or Glu; the X5 amino acid is Ser or Ala; and X6 amino acid is Lys. In some aspects, the - linker comprises a peptide bond or one or more amino acids.
In some aspects, the ED in the scaffold protein, e.g., exosome lumen protein, comprises Lys (K), KK, KKK, KKKK (SEQ ID NO: 151), KKKKK (SEQ ID NO: 152), Arg (R), RR, RRR, RRRR (SEQ ID NO: 153); RRRRR (SEQ ID NO: 154), KR, RK, KKR, KRK, RKK, KRR, RRK, (K/R)(K/R)(K/R)(K/R) (SEQ ID NO: 155), (K/R)(K/R)(K/R)(K/R)(K/R) (SEQ ID NO: 156), or any combination thereof.
In some aspects, the scaffold protein, e.g., exosome lumen protein, comprises an amino acid sequence as set forth in (i) GGKLSKK (SEQ ID NO: 157), (ii) GAKLSKK (SEQ ID NO: 158), (iii) GGKQSKK (SEQ ID NO: 159), (iv) GGKLAKK (SEQ ID NO: 160), or (v) any combination thereof. In some aspects, the scaffold protein does not comprise the amino acid sequence having Met at the N-terminus of the sequence in (i) to (v). In other aspects, the scaffold protein does not comprise or consist of (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, or 122-150 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121.
In some aspects, the ND in the scaffold protein, e.g., exosome lumen protein, comprises an amino acid sequence of (i) GGKLSK (SEQ ID NO: 203), (ii) GAKLSK (SEQ ID NO: 204), (iii) GGKQSK (SEQ ID NO: 205), (iv) GGKLAK (SEQ ID NO: 206), or (v) any combination thereof and the ED in the scaffold protein comprises (a) K, (b) KK, (c) KKK, (d) KKKG (SEQ ID NO: 207), (e) KKKGY (SEQ ID NO: 208), (f) KKKGYN (SEQ ID NO: 209), (g) KKKGYNV (SEQ ID NO: 210), (h) KKKGYNVN (SEQ ID NO: 211), (i) KKKGYS (SEQ ID NO: 212), (k) KKKGYG (SEQ ID NO: 213), (1) KKKGYGG (SEQ ID NO: 214), (m) KKKGS (SEQ ID NO: 215), (n) KKKGSG (SEQ ID NO: 216), (o) KKKGSG (SEQ ID NO: 217), (p) KKKGSGS (SEQ ID NO: 218), (q) KKKS (SEQ ID NO: 219), (r) KKKSG (SEQ ID NO: 220), (s) KKKSGG (SEQ ID NO: 221), (t) KKKSGGS (SEQ ID NO: 222), (u) KKKSGGSG (SEQ ID NO: 223), (v) KKSGGSGG (SEQ ID NO: 224), (w) KKKSGGSGGS (SEQ ID NO: 225), (x) KRFSFKKS (SEQ ID NO: 226), or any combination thereof. In some aspects, the scaffold protein does not comprise the amino acid sequence having Met at the N-terminus of the sequence in (i) to (v). In some aspects, the scaffold protein does not comprise or consist of (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121.
In some aspects, the polypeptide sequence of a scaffold protein, e.g., exosome lumen protein, of the present disclosure consists of an amino acid sequence selected from the group consisting of (i) GGKLSKK (SEQ ID NO: 157), (ii) GAKLSKK (SEQ ID NO: 158), (iii) GGKQSKK (SEQ ID NO: 159), (iv) GGKLAKK (SEQ ID NO: 160), or (v) any combination thereof.
In some aspects, the scaffold protein, e.g., exosome lumen protein, comprises an amino acid sequence of (i) GGKLSKKK (SEQ ID NO: 161), (ii) GGKLSKKS (SEQ ID NO: 162), (iii) GAKLSKKK (SEQ ID NO: 163), (iv) GAKLSKKS (SEQ ID NO: 164), (v) GGKQSKKK (SEQ ID NO: 165), (vi) GGKQSKKS (SEQ ID NO: 166), (vii) GGKLAKKK (SEQ ID NO: 167), (viii) GGKLAKKS (SEQ ID NO: 168), or (ix) any combination thereof. In some aspects, the scaffold protein does not comprise the amino acid sequence having Met at the N-terminus of the sequence in (i) to (ix). In some aspects, the scaffold protein does not comprise or consist of (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121.
In some aspects, the polypeptide sequence of a scaffold protein, e.g., exosome lumen protein, of the present disclosure consists of an amino acid sequence selected from the group consisting of (i) GGKLSKKK (SEQ ID NO: 161), (ii) GGKLSKKS (SEQ ID NO: 162), (iii) GAKLSKKK (SEQ ID NO: 163), (iv) GAKLSKKS (SEQ ID NO: 164), (v) GGKQSKKK (SEQ ID NO: 165), (vi) GGKQSKKS (SEQ ID NO: 166), (vii) GGKLAKKK (SEQ ID NO: 167), (viii) GGKLAKKS (SEQ ID NO: 168), and (ix) any combination thereof.
In some aspects, the scaffold protein, e.g., exosome lumen protein, is at least about 8, at least about 9, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 26, at least about 27, at least about 28, at least about 29, at least about 30, at least 31, at least about 32, at least about 33, at least about 34, at least about 35, at least about 36, at least about 37, at least about 38, at least about 39, at least about 39, at least about 40, at least about 41, at least about 42, at least about 43, at least about 44, at least about 50, at least about 46, at least about 47, at least about 48, at least about 49, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, at least about 195, at least about 200, at least about 205, at least about 210, at least about 215, at least about 220, at least about 225, at least about 230, at least about 235, at least about 240, at least about 245, at least about 250, at least about 255, at least about 260, at least about 265, at least about 270, at least about 275, at least about 280, at least about 285, at least about 290, at least about 295, at least about 300, at least about 305, at least about 310, at least about 315, at least about 320, at least about 325, at least about 330, at least about 335, at least about 340, at least about 345, or at least about 350 amino acids in length.
In some aspects, the scaffold protein, e.g., exosome lumen protein, is between about 5 and about 10, between about 10 and about 20, between about 20 and about 30, between about 30 and about 40, between about 40 and about 50, between about 50 and about 60, between about 60 and about 70, between about 70 and about 80, between about 80 and about 90, between about 90 and about 100, between about 100 and about 110, between about 110 and about 120, between about 120 and about 130, between about 130 and about 140, between about 140 and about 150, between about 150 and about 160, between about 160 and about 170, between about 170 and about 180, between about 180 and about 190, between about 190 and about 200, between about 200 and about 210, between about 210 and about 220, between about 220 and about 230, between about 230 and about 240, between about 240 and about 250, between about 250 and about 260, between about 260 and about 270, between about 270 and about 280, between about 280 and about 290, between about 290 and about 300, between about 300 and about 310, between about 310 and about 320, between about 320 and about 330, between about 330 and about 340, or between about 340 and about 250 amino acids in length.
In some aspects, the scaffold protein, e.g., exosome lumen protein, comprises (i) GGKLSKKKKGYNVN (SEQ ID NO: 169), (ii) GAKLSKKKKGYNVN (SEQ ID NO: 170), (iii) GGKQSKKKKGYNVN (SEQ ID NO: 171), (iv) GGKLAKKKKGYNVN (SEQ ID NO: 172), (v) GGKLSKKKKGYSGG (SEQ ID NO: 173), (vi) GGKLSKKKKGSGGS (SEQ ID NO: 174), (vii) GGKLSKKKKSGGSG (SEQ ID NO: 175), (viii) GGKLSKKKSGGSGG (SEQ ID NO: 176), (ix) GGKLSKKSGGSGGS (SEQ ID NO: 177), (x) GGKLSKSGGSGGSV (SEQ ID NO: 178), or (xi) GAKKSKKRFSFKKS (SEQ ID NO: 179). In some aspects, the scaffold protein does not comprise the amino acid sequence having Met at the N-terminus of the sequence in (i) to (xi). In some aspects, the scaffold protein does not comprise or consist of (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121.
In some aspects, the polypeptide sequence of a scaffold protein, e.g., exosome lumen protein, of the present disclosure consists of (i) GGKLSKKKKGYNVN (SEQ ID NO: 169), (ii) GAKLSKKKKGYNVN (SEQ ID NO: 170), (iii) GGKQSKKKKGYNVN (SEQ ID NO: 171), (iv) GGKLAKKKKGYNVN (SEQ ID NO: 172), (v) GGKLSKKKKGYSGG (SEQ ID NO: 173), (vi) GGKLSKKKKGSGGS (SEQ ID NO: 174), (vii) GGKLSKKKKSGGSG (SEQ ID NO: 175), (viii) GGKLSKKKSGGSGG (SEQ ID NO: 176), (ix) GGKLSKKSGGSGGS (SEQ ID NO: 177), (x) GGKLSKSGGSGGSV (SEQ ID NO: 178), or (xi) GAKKSKKRFSFKKS (SEQ ID NO: 179). In some aspects, the scaffold protein does not comprise the amino acid sequence having Met at the N-terminus of the sequence in (i) to (xi). In some aspects, the scaffold protein does not comprise or consist of (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121.
In other aspects, the scaffold protein, e.g., exosome lumen protein, comprises any one of the sequences disclosed herein, but does not comprise the corresponding sequence having Met at the N-terminus, e.g., SEQ ID NO: 4 to 109. In some aspects, the scaffold protein comprises any one of the sequences in TABLE 1, but does not comprise or consist of (i) the amino acid sequence comprising SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190 or (ii) the amino acid sequence encoded by SEQ ID NO: 115 or 118 to 121.
Non-limiting examples of the scaffold proteins, e.g., exosome lumen proteins, useful for the present disclosure is listed below.
In some aspects, the scaffold protein, e.g., exosome lumen protein, of the present disclosure consists or consists essentially of any of the sequences in the present disclosure. In some aspects, the scaffold of the present disclosure consists of a sequence disclosed in TABLE 1. In some aspects, the scaffold of the present disclosure consists of a sequence disclosed herein, e.g., a sequence disclosed in TABLE 1, covalently attached to a membrane anchor (e.g., a myristic acid). In some aspects, membrane anchoring can be conducted via lipidation. In some embodiments, the lipidation can be, e.g., fatty acylation. In some aspects, the fatty aceylation can be, e.g., myristoylation. In some aspects, the membrane anchor is covalently attached to the N-terminal amino acid of a sequence disclosed herein, e.g., a sequence disclosed in TABLE 1. In some aspects, the membrane anchor is covalently attached to N-terminal glycine of a sequence disclosed herein, e.g., a sequence disclosed in TABLE 1. Accordingly, in some aspects, the scaffold of the present disclosure consists of a sequence disclosed, e.g., a sequence disclosed in TABLE 1, that has been N-myristoylated.
In some aspects, the scaffold protein, e.g., exosome lumen protein, of the present disclosure does not contain an N-terminal Met. In some aspects, the scaffold protein comprises a lipidated amino acid, e.g., a myristoylated amino acid, at the N-terminus of the scaffold protein, which functions as a lipid anchor. In some aspects, the amino acid residue at the N-terminus of the scaffold protein in Gly. The presence of an N-terminal Gly is a requirement for N-myristoylation. In some aspects, the amino acid residue at the N-terminus of the scaffold protein is synthetic. In some aspects, the amino acid residue at the N-terminus of the scaffold protein is a glycine analog, e.g., allylglycine, butylglycine, or propargylglycine.
In some aspects, a lipid anchor can be attached by chemical synthesis or enzymatically to any N-terminal amino acid of a scaffold protein of the present disclosure.
In other aspects, the lipid anchor can be any lipid anchor known in the art, e.g., palmitic acid or glycosylphosphatidylinositols. Under unusual circumstances, e.g., by using a culture medium where myristic acid is limiting, some other fatty acids including shorter-chain and unsaturated, can be attached to the N-terminal glycine. For example, in BK channels, myristate has been reported to be attached posttranslationally to internal serine/threonine or tyrosine residues via a hydroxyester linkage. Membrane anchors known in the art are presented in the following table.
In some embodiments, the scaffold protein, e.g., exosome lumen protein, comprises an amino acid sequence having at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% sequence identity to the mature form of SEQ ID NO: 1 (MARCKS), SEQ ID NO: 2 (MARCKSL1), or SEQ ID NO: 3 (BASP1), i.e., without the N-terminal methionine amino acid present in SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
In some embodiments, the scaffold protein, e.g., exosome lumen protein, comprises an amino acid sequence having at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% sequence identity to a functional fragment of the mature form of SEQ ID NO: 1 (MARCKS), SEQ ID NO: 2 (MARCKSL1), or SEQ ID NO: 3 (BASP1), i.e., without the N-terminal methionine amino acid present in SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
In some aspects, a biologically active molecule attached to the scaffold protein of the present disclosure is on the luminal side of the EV (e.g., an exosome).
In some aspects, the scaffold protein, e.g., exosome lumen protein, further comprises a transmembrane domain. In some aspects, the transmembrane domain is interposed between the ED domain of the scaffold protein, which is located on the luminal side of the EV (e.g., an exosome) and the payload, e.g., a biologically active molecule. Thus, the payload, e.g., a biologically active molecule, is anchored to the external surface of the EV (e.g., an exosome).
In some aspects, the scaffold protein, e.g., exosome lumen protein, further comprises an extravesicular domain. In some embodiments, the extravesicular domain is interposed between the transmembrane domain and the biologically active molecule.
In some aspects, the scaffold protein is linked to the biologically active molecule via at least one linker, e.g., a peptide linker. In some aspects, the ND is linked to the ED by a linker directly interposed between both domains. In some aspects, the linker comprises, e.g., a peptide bond or one of more amino acids. In some aspects, the linker comprises a cleavable linker. In some aspects, the linker comprises a flexible linker. In some aspects, the linker comprises a self-immolative linker.
Fusions between a scaffold protein of the present disclosure and biologically active molecule (e.g., a molecule having a therapeutic activity) can be also used. For example, the fusion protein can comprise a scaffold protein such as MARCKS, MARCKSL1, BASP1, or a modification thereof, in particular a fragment or variant thereof, and a payload, e.g., a biologically active molecule (e.g., a therapeutic peptide). In some aspects, the fusion protein comprises a scaffold protein comprising a fragment of the amino terminus of BASP1. In some aspects, the biologically active molecule comprises a protein, a polypeptide, a peptide, a polynucleotide (DNA and/or RNA), a chemical compound, a virus, an ionophore, a carrier for an ionophore, a moiety that forms a channel or a pore, or any combination thereof.
The biologically active molecule (e.g., a therapeutic peptide) can be selected from a group consisting of a natural peptide, a recombinant peptide, a synthetic peptide, fusion protein, or a linker to a therapeutic compound. The biologically active molecule (e.g., a therapeutic compounds) can also be a nucleotide, amino acid, lipid, carbohydrate, or a small molecule. The biologically active molecule (e.g., a therapeutic peptide) can be an antibody, an enzyme, a ligand, an antigen (e.g., a tumor antigen or an antigen from an infectious agent such as a bacteria, virus, fungus, or protozoa), a receptor, an antimicrobial peptide, a transcription factor, or a fragment or a modification thereof.
The fusion protein comprising the scaffold of the present disclosure fused or conjugated to a payload, e.g., a biologically active molecule, can be attached to the luminal surface of the EV, e.g., an exosomes, and provide, e.g., a therapeutic activity to the EV, e.g., exosome.
In some embodiments, the biologically active molecule (e.g., a therapeutic peptide) is a component of a genome editing complex. In some embodiments, said genome editing complex is a transcription activator-like effector nuclease (TAL-effector nuclease or TALEN); a zinc finger nuclease (ZFN); a recombinase; a CRISPR/Cas9 complex, a CRISPR/Cpf1 complex, a CRISPR/C2c1, C2c2, or C2c3 complex, a CRISPR/CasY or CasX complex, or any other appropriate CRISPR complex known in the art; or any other appropriate genome editing complex known in the art or any combination thereof.
In some embodiments, the biologically active molecule (e.g., a therapeutic peptide) is a transmembrane peptide. The transmembrane peptides described herein may be expressed as fusion proteins to any of the sequences described herein or any fragments or variants thereof. In some embodiments, the transmembrane protein has a first end fused to the luminal sequence in the lumen of the EV, e.g., exosome, and a second end expressed on the surface of the EV, e.g., exosome.
In some embodiments, an EV, e.g., of the present disclosure can comprise a second scaffold protein. In some embodiments, the second scaffold protein comprises a transmembrane protein comprising a PTGFRN polypeptide, a BSG polypeptide, an IGSF2 polypeptide, an IGSF3 polypeptide, an IGSF8 polypeptide, an ITGB1 polypeptide, an ITGA4 polypeptide, a SLC3A2 polypeptide, an ATP transporter polypeptide, an aminopeptidase N (ANPEP) polypeptide, an ectonucleotide pyrophosphatase/phosphodiesterase family 1 (ENPP1) polypeptide, a neprilysin (MME) polypeptide, a neuropilin-1 (NRP1) polypeptide, or a fragment, variant, or derivative thereof. Non limiting examples of the second scaffold protein can be found at U.S. Pat. No. 10,195,290 and PCT Publication No. WO 2019/040920, which is incorporated herein by reference in its entirety.
In some embodiments, the biologically active molecule (e.g., a therapeutic peptide) is a nucleic acid binding protein. In some embodiments, the nucleic acid binding protein is Dicer, an Argonaute protein, TRBP, MS2 bacteriophage coat protein. In some embodiments, the nucleic acid binding protein additionally comprises one or more RNA or DNA molecules. In some embodiments, the one or more RNA is a miRNA, siRNA, guide RNA, lincRNA, mRNA, antisense RNA, dsRNA, or combinations thereof.
In some embodiments, the biologically active molecule (e.g., a therapeutic peptide) is a part of a protein-protein interaction system. In some embodiments, the protein-protein interaction system comprises an FRB-FKBP interaction system, e.g., the FRB-FKBP interaction system as described in Banaszynski et al., J Am Chem Soc. 2005 Apr. 6; 127(13):4715-21.
The fusion proteins can be targeted to the luminal surface of EVs, e.g., exosomes and provide a therapeutic activity to the EV, e.g., exosome.
In some embodiments, fusion proteins having a targeting moiety are used. For example, fusion proteins can comprise (i) a scaffold protein such as MARCKS, MARCKSL1, BASP1, or a fragment, variant, or a modification thereof, and (ii) a targeting moiety. The targeting moiety can be used for targeting the EV, e.g., exosome, to a specific organ, tissue, or cell for a treatment using the EV, e.g., exosome. In some embodiments, the targeting moiety is an antibody or antigen-binding fragment thereof.
Antibodies and antigen-binding fragments thereof include whole antibodies, polyclonal, monoclonal and recombinant antibodies, fragments thereof, and further includes single-chain antibodies, humanized antibodies, murine antibodies, chimeric, mouse-human, mouse-primate, primate-human monoclonal antibodies, anti-idiotype antibodies, antibody fragments, such as, e.g., scFv, (scFv)2, Fab, Fab′, and F(ab′)2, F(abl)2, Fv, dAb, and Fd fragments, diabodies, minibodies, camelid antibodies, and antibody-related polypeptides.
Antibodies and antigen-binding fragments thereof also includes bispecific antibodies and multispecific antibodies so long as they exhibit the desired biological activity or function. The modular architecture of antibodies has been exploited to create more than 60 different bispecific antibody formats. See Spiess et al. (2015) Molecular Immunology 67:95-106, which is herein incorporated by reference in its entirety. Accordingly, in some embodiments, the bispecific antibody format is selected from crossMab, DAF (Dual Action Fab) (two-in-one), DAF (four-in-one), DutaMab, DT-IgG, Knobs-in-holes common LC, Knobs-in-holes assembly, Charge pair, Fab-arm exchange, SEEDbody, Triomab, LUZ-Y (bispecific antibody with a leucize zipper inducing heterodimerization of two HCs), Fcab, Kλ-body, Orthogonal Fab, DVD-IgG (dual variable domain IgG), IgG(H)-scFv, scFv-(H)IgG, IgG(L)-scFv, scFv-(L)IgG, IgG(L,H)-Fv, IgG(H)-V, V(H)-IgG, IgG(L)-V, V(L)-IgG, KIH IgG-scFab, 2scFv-IgG, IgG-2scFv, scFv4-Ig, Zybody, DVI-IgG (four-in-one), Nanobody, Nanobody-HSA, BiTE (bispecific T cell engager), Diabody, DART (dual-affinity-retargeting), TandAb (tandem antibody), scDiabody, scDiabody-CH3, Triple Body, Miniantibody, Minibody, TriBi minibody, scFv-CH3 KIH, Fab-scFv, scFv-CH-CL-scFv, F(ab′)2, F(ab′)2-ScFv2, scFv-KIH, Fab-scFv-Fc, Tetravalent HC Ab, scDiabody-Fc, Diabody-Fc, Tandem scFv-Fc, Intrabody, Dock and Locck, ImmTAC, HSAbody, scDiabody-HSA, Tandem scFv-Toxin, IgG-IgG, Cov-X-Body, and scFv1-PEG-scFV2. Bispecific antibodies can be monospecific antibodies engineered for bispecificity by appending either the amino or carboxy termini of either the light or heavy chains with additional antigen-binding units. Alternatives for these additional antigen-binding units include single domain antibodies (unpaired VL or VH), paired antibody variable domains (e.g., Fv or scFv) or engineered protein scaffolds. Numerous bispecific fragment forms lacking some or all of the bispecific antibody constant domains are known in the art.
In some embodiments, the biologically active molecule (e.g., a therapeutic peptide) is a fusion protein comprising a scaffold protein of the present disclosure and a viral protein. In some embodiments, the viral protein comprises a viral capsid, an envelope protein, or a combination thereof. In some embodiments, the fusion proteins allow for the assembly of intact viruses that are retained on the luminal surface of an EV, e.g., an exosome.
In some embodiments, the biologically active molecule is an inhibitor a negative checkpoint regulator or an inhibitor for a binding partner of a negative checkpoint regulator. In some embodiments, the negative checkpoint regulator is selected from the group consisting of: cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), programmed cell death protein 1 (PD-1), lymphocyte-activated gene 3 (LAG-3), T-cell immunoglobulin mucin-containing protein 3 (TIM-3), B and T lymphocyte attenuator (BTLA), T cell immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig suppressor of T cell activation (VISTA), adenosine A2a receptor (A2aR), killer cell immunoglobulin like receptor (KIR), indoleamine 2,3-dioxygenase (IDO), CD20, CD39, and CD73.
In some embodiments, the biologically active molecule is an immunogenic protein. In some embodiments, the biologically active molecule is a toxin, toxoid, or a non-toxic mutant of a toxin. In some embodiments, the toxin is diphtheria toxin. In some embodiments, the toxoid is a tetanus toxoid. In some embodiments, the diphtheria toxin is a non-toxic mutant of diphtheria toxin.
In some embodiments, the biologically active molecule is an activator for a positive co-stimulatory molecule or an activator for a binding partner of a positive co-stimulatory molecule. In some embodiments, the positive co-stimulatory molecule is a TNF receptor superfamily member selected from the group consisting of: CD120a, CD120b, CD18, OX40, CD40, Fas receptor, M68, CD27, CD30, 4-1BB, TRAILR1, TRAILR2, TRAILR3, TRAILR4, RANK, OCIF, TWEAK receptor, TACI, BAFF receptor, ATAR, CD271, CD269, AITR, TROY, CD358, TRAMP, and XEDAR. In some embodiments the activator for a positive co-stimulatory molecule is a TNF superfamily member selected from the group consisting of: TNFα, TNF-C, OX40L, CD40L, FasL, LIGHT, TL1A, CD27L, Siva, CD153, 4-1BB ligand, TRAIL, RANKL, TWEAK, APRIL, BAFF, CAMLG, NGF, BDNF, NT-3, NT-4, GITR ligand, and EDA-2. In some embodiments, the positive co-stimulatory molecule is a CD28-superfamily co-stimulatory molecule. In some embodiments, the CD28-superfamily co-stimulatory molecule is ICOS or CD28. In some embodiments, the activator for a positive co-stimulatory molecule is ICOSL, CD80, or CD86.
In some embodiments, the biologically active molecule is a cytokine selected from the group consisting of: IL-2, IL-7, IL-10, IL-12, and IL-15. In some embodiments, the biologically active molecule is a protein comprising a T-cell receptor (TCR), a T-cell co-receptor, a major histocompatibility complex (MHC), a human leukocyte antigen (HLA), or a derivative thereof. In some embodiments, the biologically active molecule is a protein comprising a tumor antigen. In some embodiments, the tumor antigen is selected from the group consisting of: alpha-fetoprotein (AFP), carcinoembryonic antigen (CEA), epithelial tumor antigen (ETA), mucin 1 (MUC1), Tn-MUC1, mucin 16 (MUC16), tyrosinase, melanoma-associated antigen (MAGE), tumor protein p53 (p53), CD4, CD8, CD45, CD80, CD86, programmed death ligand 1 (PD-L1), programmed death ligand 2 (PD-L2), NY-ESO-1, PSMA, TAG-72, HER2, GD2, cMET, EGFR, Mesothelin, VEGFR, alpha-folate receptor, CE7R, IL-3, Cancer-testis antigen, MART-1 gp100, and TNF-related apoptosis-inducing ligand.
In some aspects, fusion proteins that comprise a biologically active molecule and a scaffold protein of the present disclosure (e.g., MARCKS, MARCKSL1, BASP1, any of SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any scaffold protein sequences disclosed herein (e.g., Table 1), or a modification thereof, in particular a fragment or variant thereof), result in enrichment of the biologically active molecule in EVs, e.g., exosomes, compared to expression of the biologically active molecule lacking the scaffold protein. In some aspects, fusion proteins that comprises a biologically active molecule and a scaffold protein of the present disclosure (e.g., MARCKS, MARCKSL1, BASP1 without the N-terminal M, the amino acid sequence of SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190 without the N-terminal M, the amino acid sequence encoded by SEQ ID NO: 115, or 118 to 121, or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M) result in enrichment of the biologically active molecule in EVs, e.g., exosomes, compared to expression of the biologically active molecule lacking the scaffold protein.
In some embodiments, the scaffold protein useful for the present disclosure comprises any of SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any sequences disclosed in TABLE 1. In some aspects, the scaffold protein useful for the present disclosure comprises any of SEQ ID NO: 4-109, wherein the scaffold protein does not comprise an N-terminal Met. In some aspects, the scaffold protein comprises a sequence disclosed in Table 1, wherein the scaffold protein does not comprise an N-terminal Met. In some aspects, the scaffold protein useful for the present disclosure comprises MARCKS, MARCKSL1, BASP1 without the N-terminal M, the amino acid sequence of SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190 without the N-terminal M, the amino acid sequence encoded by SEQ ID NO: 115, or 118 to 121, or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M. In some aspects, the scaffold protein useful for the present disclosure comprises MARCKS, MARCKSL1, or BASP1, wherein the scaffold protein does not comprise an N-terminal Met. In some aspects, the scaffold protein comprises the amino acid sequence of SEQ ID NO: 4 to 114, 116 to 118, 122 to 150 or 180 to 190, wherein the scaffold protein does not comprise an N-terminal Met. In some aspects, the scaffold protein comprises the amino acid sequence encoded by SEQ ID NO: 115, or 118 to 121, wherein the scaffold protein does not comprise an N-terminal Met. In other embodiments, the scaffold protein useful for the present disclosure comprises any sequence disclosed herein, but is not any one of SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any sequences disclosed in TABLE 1 without the N-terminal M. In other embodiments, the scaffold protein useful for the present disclosure comprises any sequence disclosed herein, but does not comprise any one of SEQ ID NO: 4-109.
In some embodiments, the fusion proteins comprise a scaffold protein comprising a peptide with the sequence MGXKLSKKK, where X is alanine or any other amino acid (SEQ ID NO: 117); or a peptide with sequence of (M)(G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+), wherein the N-terminal M is cleaved, such that the resulting fusion protein comprises GXKLSKKK (SEQ ID NO: 425) or (G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+) joined to the biologically active molecule, wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), ξ is any amino acid selected from the group consisting of (Asn, Gln, Ser, Thr, Asp, Glu, Lys, His, Arg), Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu). In some embodiments, the scaffold protein useful for the present disclosure is not MGXKLSKKK, where X is alanine or any other amino acid (SEQ ID NO: 117) or is not a peptide with sequence of (M)(G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+). In some embodiments, the scaffold protein useful for the present disclosure does not comprise MGXKLSKKK, where X is alanine or any other amino acid (SEQ ID NO: 117) or does not comprise a peptide with sequence of (M)(G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+).
In some embodiments, the fusion protein comprises a scaffold protein comprising a peptide with sequence of (M)(G)(π)(X)(Φ/π)(π)(+)(+) or (G)(π)(X)(Φ/π)(π)(+)(+), wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), X is any amino acid, Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu). In some embodiments, the fusion protein comprises a scaffold protein comprising a peptide with sequence of (G)(it)(X)(Φ/π)(π)(+)(+), wherein the scaffold protein does not comprise an N-terminal M (e.g., an N-terminal methionine).
In some aspects, the fusion protein comprises a scaffold protein comprising a peptide with sequence of (G)(π)(X)(Φ/π)(π)(+)(+), wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), X is any amino acid, Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu), wherein the sequence is not (M)(G)(π)(X)(Φ/π)(π)(+)(+). In some aspects, the scaffold protein comprises the peptide with sequence of (G)(π)(X)(Φ/π)(π)(+)(+), wherein the scaffold protein does not comprise an N-terminal Met.
In some embodiments, the conventional EV, e.g., exosome, protein is selected from the list consisting of CD9, CD63, CD81, PDGFR, GPI anchor proteins, LAMP2, LAMP2B, and a fragment, variant, or derivative thereof.
In some embodiments, the enrichment of the fusion protein comprising MARCKS, MARCKSL1, BASP1, or any of SEQ ID NO: 4-109 in exosomes is >2-fold, >4-fold, >8-fold, >16-fold, >25-fold, >50-fold, >100-fold, >200-fold, >500-fold, >750-fold, >1,000-fold, >2,000-fold, >5,000-fold, >7,500-fold, >10,000-fold higher than the fusion protein lacking MARCKS, MARCKSL1, BASP1, any of SEQ ID NO: 4-109 or compared to fusion proteins that comprise conventional EV, e.g., exosome, proteins. In some aspects, the enrichment of the fusion protein comprising MARCKS, MARCKSL1, BASP1 without the N-terminal M, any of SEQ ID NO: 4-109 without the N-terminal M or any sequences disclosed herein, e.g., TABLE 1, without the N-terminal M in exosomes is >2-fold, >4-fold, >8-fold, >16-fold, >25-fold, >50-fold, >100-fold, >200-fold, >500-fold, >750-fold, >1,000-fold, >2,000-fold, >5,000-fold, >7,500-fold, >10,000-fold higher than the fusion protein lacking MARCKS, MARCKSL1, BASP1 without the N-terminal M, any of SEQ ID NO: 4-109 without the N-terminal M or any sequences disclosed herein, e.g., TABLE 1, without the N-terminal M or compared to fusion proteins that comprise conventional EV, e.g., exosome, proteins.
In some embodiments, the enrichment of the fusion protein comprising MARCKS, MARCKSL1, BASP1, any of SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M in exosomes is at least about 2-fold, at least about 4-fold, at least about 6-fold, at least about 8-fold, at least about 10-fold, at least about 12-fold, at least about 14-fold, at least about 16-fold, at least about 18-fold, at least about 20-fold, at least about 25-fold, at least about 30-fold, at least about 35-fold, at least about 40-fold, at least about 45-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, at least about 100-fold, at least about 200-fold, at least about 300-fold, at least about 400-fold, at least about 500-fold, at least about 750-fold, at least about 1,000-fold, at least about 1,500-fold, at least about 2,000-fold, at least about 2,500-fold, at least about 3,000-fold, at least about 3,500-fold, at least about 4,000-fold, at least about 4,500-fold, at least about 5,000-fold, at least about 5,500-fold, at least about 6,000-fold, at least about 6,500-fold, at least about 7,000-fold, at least about 7,500-fold, at least about 8,000-fold, at least about 8,500-fold, at least about 9,000-fold, at least about 9,500-fold or at least about 10,000-fold higher than the fusion protein lacking MARCKS, MARCKSL1, BASP1, any of SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M, or compared to fusion proteins that comprise conventional EV, e.g., exosome, proteins.
In some embodiments, the protein sequence of any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M, or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is sufficient to load the EVs, e.g., exosomes, with the fusion protein.
In some embodiments, the lumen-engineered EV, e.g., exosome, comprising a fusion protein containing an exogenous sequence (e.g., a biologically active molecule) and an EV, e.g., exosome, lumen protein (scaffold protein) newly-identified herein has a higher density of the fusion protein than similarly engineered EVs, e.g., exosomes, comprising an exogenous sequence conjugated to a conventional EV, e.g., exosome, protein known in the art (e.g., CD9, CD63, CD81, PDGFR, GPI anchor proteins, lactadherin, LAMP2, and LAMP2B, a fragment thereof, or a peptide that binds thereto).
In some embodiments, the fusion protein containing an EV, e.g., exosome, lumen protein (scaffold protein) newly-identified herein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density in the EV, e.g., exosome, luminal surface than fusion proteins in other EV, e.g., exosome, luminal surfaces similarly modified using a conventional EV, e.g., exosome, protein.
In some embodiments, the fusion protein containing an EV, e.g., exosome, lumen protein (scaffold protein) newly-identified herein is present at 2 to 4-fold, 4 to 8-fold, 8 to 16-fold, 16 to 32-fold, 32 to 64-fold, 64 to 100-fold, 100 to 200-fold, 200 to 400-fold, 400 to 800-fold, 800 to 1,000-fold or to a higher density in the EV, e.g., exosome, luminal surface than fusion proteins in other EV, e.g., exosome, luminal surfaces similarly modified using a conventional EV, e.g., exosome, protein.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD9.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD63.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD81.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using PDGFR.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using GPI anchor proteins.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using lactadherin.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2B.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using an conventional protein.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKS, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes similarly modified using a variant of a conventional EV, e.g., exosome, protein.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD9.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD63.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD81.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using PDGFR.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher, density than at EVs, e.g., exosomes, similarly modified using GPI anchor proteins.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using lactadherin.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2B.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using an conventional protein.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., MARCKSL1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes similarly modified using a variant of a conventional EV, e.g., exosome, protein.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD9.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD63.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD81.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using PDGFR.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using GPI anchor proteins.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using lactadherin.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2B.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using an conventional protein.
In some embodiments, a fusion protein comprising a scaffold protein, e.g., exosome lumen protein, of the present disclosure (e.g., BASP1, a variant, a fragment, a variant of a fragment, or a modification thereof) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using a variant of a conventional EV, e.g., exosome protein.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD9. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD9.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD63. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD63.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD81. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using CD81.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using PDGFR. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using PDGFR.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using GPI anchor proteins. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using GPI anchor proteins.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using lactadherin. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using lactadherin.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2B. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using LAMP2Bt.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using a conventional protein. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using a conventional protein.
In some embodiments, a fusion protein comprising any of SEQ ID NO: 1-109, the corresponding sequence without the N-terminal M or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using a variant of a conventional EV protein, e.g., exosome protein. In some aspects, the EV, e.g., exosome, comprises a fusion protein comprising any of SEQ ID NO: 1-109, wherein the fusion protein does not comprise an N-terminal Met, and wherein the fusion protein is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or a higher density than at EVs, e.g., exosomes, similarly modified using a conventional EV protein, e.g., exosome protein
In some embodiments, the lumen-engineered EVs, e.g., exosomes, described herein demonstrate superior characteristics compared to lumen-engineered EVs, e.g., exosomes known in the art. For example, lumen-engineered EVs, e.g., exosomes, produced by using the newly-identified EV, e.g., exosome, proteins provided herein contain modified proteins more highly enriched on their luminal surface compared to EVs, e.g., exosomes in prior art, e.g., those produced using conventional EV, e.g., exosome, proteins.
Moreover, the lumen-engineered EVs, e.g., exosomes, of the present disclosure can have greater, more specific, or more controlled biological activity compared to lumen-engineered EVs, e.g., exosomes, known in the art. For example, a lumen-engineered EV, e.g., exosome, comprising a payload, e.g., a therapeutic or biologically relevant exogenous sequence fused to an EV, e.g., exosome, protein or a fragment thereof described herein (e.g., a scaffold of the present disclosure such as BASP1 or a fragment, variant, or derivative thereof) can have more of the desired engineered characteristics than fusion to scaffolds known in the art.
Scaffold proteins known in the art include tetraspanin molecules (e.g., CD63, CD81, CD9 and others), lysosome-associated membrane protein 2 (LAMP2 and LAMP2B), platelet-derived growth factor receptor (PDGFR), GPI anchor proteins, lactadherin and fragments thereof, and peptides that have affinity to any of these proteins or fragments thereof. For the avoidance of doubt, PTGFRN, BSG, IGSF2, IGSF3, IGSF8, ITGB1, ITGA4, SLC3A2, ATP transporter or a fragment or a variant thereof are not conventional EV, e.g., exosome, proteins. Previously, overexpression of exogenous proteins relied on stochastic or random disposition of the exogenous proteins into the exosome for producing lumen-engineered exosomes. This resulted in low-level, unpredictable density of the exogenous proteins in exosomes. Thus, the EV, e.g., exosome proteins and fragments thereof described herein provide important advancements in novel EV, e.g., exosome compositions and methods of making the same.
Fusion proteins provided herein can comprise a scaffold protein, e.g., exosome lumen protein, of the present disclosure such as MARCKS, MARCKSL1, BASP1, or a fragment, a variant, or a derivative thereof, and an additional peptide. The additional peptide can be attached to either the N-terminus or the C-terminus of the EV, e.g., exosome, protein (scaffold protein) or a fragment, a variant, or a derivative thereof.
In some embodiments, fusion proteins provided herein comprise a scaffold protein of the present disclosure such as MARCKS, MARCKSL1, BASP1, or a fragment, a variant, or a derivative thereof, and two additional peptides. Both of the two additional peptides can be attached to either the N-terminus or the C-terminus of the EV, e.g., exosome, protein (scaffold protein) or a fragment, a variant, or derivative thereof. In some embodiments, one of the two additional peptides is attached to the N-terminus and the other of the two additional peptides is attached to the C-terminus of the EV, e.g., exosome, protein (scaffold protein) or a fragment, a variant, or a derivative thereof.
In some embodiments, the compositions and methods of generating lumen-engineered extracellular vesicles described herein comprise nanovesicles.
EV, e.g., exosomes, of the present disclosure can be produced from a cell grown in vitro or a body fluid of a subject. When EVs, e.g., exosomes, are produced from in vitro cell culture, various producer cells, e.g., HEK293 cells, can be used for the present disclosure. Additional cell types that can be used for the production of the lumen-engineered EVs, e.g., exosomes, described herein include, without limitation, mesenchymal stem cells, T-cells, B-cells, dendritic cells, macrophages, and cancer cell lines.
Accordingly, the present disclosure provides cells that produce the EVs, e.g., exosomes, of the present disclosure. In some embodiments, the comprises one or more vectors, wherein the vectors comprise a nucleic acid sequence encoding the scaffold protein and the payload, e.g., a biologically active molecule. In some embodiments, a nucleic acid sequence encodes the scaffold protein and a second nucleic acid sequence encodes the payload, e.g., a biologically active molecule. In some embodiments, the nucleic acid sequence encoding the scaffold protein and the nucleic acid sequence encoding the payload, e.g., a biologically active molecule, are in a single open reading frame; thus, the expression product would be a fusion protein comprising the scaffold protein fused to the payload, e.g., a biologically active molecule. In some embodiments, the nucleic acid sequence is operably linked to a promoter.
The producer cell can be genetically modified to comprise one or more exogenous sequences to produce lumen-engineered EVs, e.g., exosomes. The genetically-modified producer cell can contain the exogenous sequence by transient or stable transformation. The exogenous sequence can be transformed as a plasmid. The exogenous sequences can be stably integrated into a genomic sequence of the producer cell, at a targeted site or in a random site. In some embodiments, a stable cell line is generated for production of lumen-engineered EVs, e.g., exosomes.
The exogenous sequences can be inserted into a genomic sequence of the producer cell, located within, upstream (5′-end) or downstream (3′-end) of an endogenous sequence encoding the EV, e.g., exosome, protein. Various methods known in the art can be used for the introduction of the exogenous sequences into the producer cell. For example, cells modified using various gene editing methods (e.g., methods using a homologous recombination, transposon-mediated system, loxP-Cre system, CRISPR/Cas9 or TALEN) are within the scope of the present disclosure.
The exogenous sequences can comprise a sequence encoding a scaffold protein of the present disclosure (e.g., an EV, e.g., exosome, protein or a modification or a fragment of the EV, e.g., exosome, protein). An extra copy of the sequence encoding the scaffold protein (e.g., an EV, e.g., exosome, protein) can be introduced to produce a lumen-engineered EV, e.g., exosome, having a higher density of the EV, e.g., exosome, protein. An exogenous sequence encoding a modification or a fragment of the EV, e.g., exosome, protein can be introduced to produce a lumen-engineered EV, e.g., exosome, containing the modification or the fragment of the EV, e.g., exosome, protein. An exogenous sequence encoding an affinity tag can be introduced to produce a lumen-engineered EV, e.g., exosome, containing a fusion protein comprising the affinity tag attached to the EV, e.g., exosome, protein.
In some embodiments, a lumen-engineered EV, e.g., exosome, has a higher density of the EV, e.g., exosome, protein (scaffold protein) than native EVs, e.g., exosomes, isolated from the same or similar producer cell types. In some embodiments, said EV, e.g., exosome, protein (scaffold protein) is present at 2-, 4-, 8-, 16-, 32-, 64-, 100-, 200-, 400-, 800-, 1,000-fold or to a higher density on said lumen-engineered EV, e.g., exosome, than the native EV<e.g., exosome. In some embodiments, the EV, e.g., exosome, protein (scaffold protein) is present at 2 to 4-fold, 4 to 8-fold, 8 to 16-fold, 16 to 32-fold, 32 to 64-fold, 64 to 100-fold, 100 to 200-fold, 200 to 400-fold, 400 to 800-fold, 800 to 1,000-fold or to a higher density on the lumen-engineered EV, e.g., exosome, than the native EV, e.g., exosome. In some embodiments, a fusion protein comprising the EV, e.g., exosome, protein (scaffold protein) is present at 2 to 4-fold, 4 to 8-fold, 8 to 16-fold, 16 to 32-fold, 32 to 64-fold, 64 to 100-fold, 100 to 200-fold, 200 to 400-fold, 400 to 800-fold, 800 to 1,000-fold or to a higher density on said lumen-engineered EV, e.g., exosome, than the unmodified EV, e.g., exosome, protein (scaffold protein) on the native EV, e.g., exosome. In some embodiments, a fragment or a variant of the EV, e.g., exosome, protein (scaffold protein) is present at 2 to 4-fold, 4 to 8-fold, 8 to 16-fold, 16 to 32-fold, 32 to 64-fold, 64 to 100-fold, 100 to 200-fold, 200 to 400-fold, 400 to 800-fold, 800 to 1,000-fold or to a higher density on the lumen-engineered EV, e.g., exosome, than the unmodified EV, e.g., exosome, protein (scaffold protein) on the native EV, e.g., exosome.
In particular embodiments, MARCKS, a fragment or a variant of MARCKS, or a modification thereof is present at 2 to 4-fold, 4 to 8-fold, 8 to 16-fold, 16 to 32-fold, 32 to 64-fold, 64 to 100-fold, 100 to 200-fold, 200 to 400-fold, 400 to 800-fold, 800 to 1,000-fold or to a higher density on said lumen-engineered EV, e.g., exosome, than the unmodified MARCKS on said native EV, e.g., exosome. In some embodiments, MARCKSL1, a fragment or a variant of MARCKSL1, or a modification thereof is present at 2 to 4-fold, 4 to 8-fold, 8 to 16-fold, 16 to 32-fold, 32 to 64-fold, 64 to 100-fold, 100 to 200-fold, 200 to 400-fold, 400 to 800-fold, 800 to 1,000-fold or to a higher density on said lumen-engineered EV, e.g., exosome, than the unmodified MARCKSL1 on said native EV, e.g., exosome. In some embodiments, BASP1, a fragment or a variant of BASP1, or a modification thereof is present at 2 to 4-fold, 4 to 8-fold, 8 to 16-fold, 16 to 32-fold, 32 to 64-fold, 64 to 100-fold, 100 to 200-fold, 200 to 400-fold, 400 to 800-fold, 800 to 1,000-fold or to a higher density on said lumen-engineered EV, e.g., exosome, than the unmodified BASP1 on the native EV, e.g., exosome.
In some embodiments, the producer cell is further modified to comprise an additional exogenous sequence. For example, an additional exogenous sequence can be included to modulate endogenous gene expression, or produce an exosome including a certain polypeptide as a payload. In some embodiments, the producer cell is modified to comprise two exogenous sequences, one encoding the EV, e.g., exosome, protein (scaffold protein) or a modification or a fragment of the EV, e.g., exosome, protein (scaffold protein), and the other encoding a payload.
More specifically, lumen-engineered EVs, e.g., exosomes, can be produced from a cell transformed with a sequence encoding one or more exosome lumen proteins (scaffold proteins) including, but not limited to, (1) myristoylated alanine rich Protein Kinase C substrate (MARCKS); (2) myristoylated alanine rich Protein Kinase C substrate like 1 (MARCKSL1); and (3) brain acid soluble protein 1 (BASP1). Any of the one or more EV, e.g., exosome, lumen proteins (scaffold proteins) described herein can be expressed from a plasmid, an exogenous sequence inserted into the genome or other exogenous nucleic acid such as a synthetic messenger RNA (mRNA).
In some embodiments, the one or more EV, e.g., exosome, lumen protein (scaffold protein) is expressed in a cell transformed with an exogenous sequence encoding its full length, endogenous form. In some embodiments, such an exogenous sequence encodes MARCKS protein of SEQ ID NO: 1 or the corresponding sequence without the N-terminal M. In certain aspects, such an exogenous sequence encodes MARCKS protein of SEQ ID NO: 1. In some embodiments, such an exogenous sequence encodes MARCKS protein of SEQ ID NO: 1, wherein the MARKS protein encoded by the exogenous sequence does not comprise an N-terminal Met. In some embodiments, such an exogenous sequence encodes MARCKSL1 protein of SEQ ID NO: 2 or the corresponding sequence without the N-terminal M. In certain aspects, such an exogenous sequence encodes MARCKSL1 protein of SEQ ID NO: 2. In some embodiments, such an exogenous sequence encodes MARCKSL1 protein of SEQ ID NO: 2, wherein the MARCKSL1 protein encoded by the exogenous sequence does not comprise an N-terminal Met. In some embodiments, such an exogenous sequence encodes BASP1 protein of SEQ ID NO: 3 or the corresponding sequence without the N-terminal M. In certain aspects, such an exogenous sequence encodes BASP1 protein of SEQ ID NO: 3. In some embodiments, such an exogenous sequence encodes BASP1 protein of SEQ ID NO: 3, wherein the BASP1 protein encoded by the exogenous sequence does not comprise an N-terminal Met.
Lumen-engineered EVs, e.g., exosomes, can be produced from a cell transformed with a polynucleotide sequence encoding a fragment of one or more EV, e.g., exosome, lumen proteins (scaffold proteins) including, but not limited to, (1) myristoylated alanine rich Protein Kinase C substrate (MARCKS); (2) myristoylated alanine rich Protein Kinase C substrate like 1 (MARCKSL1); and (3) brain acid soluble protein 1 (BASP1).
In some embodiments, the polynucleotide sequence encodes a fragment of the EV, e.g., exosome, lumen protein (e.g., a scaffold protein such as MARCKS, MARCKSL1, or BASP1) lacking at least 5, 10, 50, 100, 200, or 300 amino acids from the N-terminus of the native protein. In some embodiments, the polynucleotide sequence encodes a fragment of the EV, e.g., exosome, lumen protein (e.g., a scaffold protein such as MARCKS, MARCKSL1, or BASP1) lacking at least 5, 10, 50, 100, 200, or 300 amino acids from the C-terminus of the native protein. In some embodiments, the polynucleotide sequence encodes a fragment of the EV, e.g., exosome, lumen protein (e.g., a scaffold protein such as MARCKS, MARCKSL1, or BASP1) lacking at least 5, 10, 50, 100, 200, or 300 amino acids from both the N-terminus and C-terminus of the native protein. In some embodiments, the polynucleotide sequence encodes a fragment of the EV, e.g., exosome, lumen protein (e.g., a scaffold protein such as MARCKS, MARCKSL1, or BASP1) lacking one or more functional or structural domains of the native protein.
In some embodiments, the fusion protein comprises a peptide of SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any scaffold protein sequences disclosed herein (e.g., Table 1) without the N-terminal M. In some embodiments, the fusion protein comprises a peptide of SEQ ID NO: 4-109 or any scaffold protein sequence disclosed herein (e.g., Table 1), wherein the fusion protein does not comprise an N-terminal Met. In some embodiments, the fusion protein comprises the peptide of SEQ ID NO: 13. In some embodiments, the fusion protein comprises the peptide of SEQ ID NO: 13, wherein the fusion protein does not comprise an N-terminal Met. In some embodiments, the fusion protein comprises a scaffold protein, e.g., exosome lumen protein, comprising a peptide with the sequence MGXKLSKKK (SEQ ID NO: 117) or GXKLSKKK (SEQ ID NO:425), where X is alanine or any other amino acid. In some embodiments, the fusion protein comprises a scaffold protein, e.g., exosome lumen protein, comprising a peptide with the sequence GXKLSKKK (SEQ ID NO:425), where X is alanine or any other amino acid, and wherein the scaffold protein, e.g., exosome lumen protein, does not comprise an N-terminal Met. In some embodiments, the fusion protein comprises a scaffold protein, e.g., exosome lumen protein, comprising a peptide with the sequence GXKLSKKK (SEQ ID NO:425), where X is alanine or any other amino acid, and wherein the fusion protein does not comprise an N-terminal Met. In some embodiments, the fusion protein comprises a scaffold protein comprising the amino acid sequence of GXKLSKKK (SEQ ID NO:425), wherein X is alanine or any other amino acid, wherein the scaffold protein does not have Met at the N-terminus of the amino acid sequence, e.g., comprise MGXKLSKKK (SEQ ID NO: 117). In other embodiments, the fusion protein comprises a scaffold protein, e.g., exosome lumen protein, comprising an amino acid sequence of GXKLSKKK (SEQ ID NO: 425), wherein the fusion protein does not comprise MGXKLSKKK. In some embodiments, the fusion protein comprises a scaffold protein comprising a peptide with sequence of (M)(G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+) or (G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+), wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), ξ is any amino acid selected from the group consisting of (Asn, Gln, Ser, Thr, Asp, Glu, Lys, His, Arg), Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu). In some embodiments, the fusion protein comprises a scaffold protein, e.g., exosome lumen protein, an amino acid sequence of (G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+), wherein the fusion protein does not comprise (M)(G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+). In some embodiments, the fusion protein comprises a scaffold protein, e.g., exosome lumen protein, comprising a peptide with sequence of (M)(G)(π)(X)(Φ/π)(π)(+)(+) or (G)(π)(X)(Φ/π)(π)(+)(+), wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), X is any amino acid, Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu). In other embodiments, the fusion protein comprises a scaffold protein, e.g., exosome lumen protein, comprising an amino acid sequence of (G)(π)(X)(Φ/π)(π)(+)(+), wherein the fusion protein does not comprise (M)(G)(π)(X)(Φ/π)(π)(+)(+).
In some embodiments, lumen-engineered EVs, e.g., exosomes, can be produced from a cell transformed with a sequence encoding an EV, e.g., exosome, protein (e.g., a scaffold protein e.g., exosome lumen protein, such as MARCKS, MARCKSL1, or BASP1) or a fragment or a modification thereof fused to one or more heterologous proteins. In some embodiments, the one or more heterologous proteins are fused to the N-terminus of the EV, e.g., exosome, protein (e.g., a scaffold protein such as MARCKS, MARCKSL1, or BASP1) or a modification thereof, in particular a fragment or variant thereof. In some embodiments, the one or more heterologous proteins are fused to the C-terminus of the EV, e.g., exosome, protein (e.g., a scaffold protein such as MARCKS, MARCKSL1, or BASP1) or a modification thereof, in particular a fragment or variant thereof. In some embodiments, the one or more heterologous proteins are fused to the N-terminus and the C-terminus of the EV, e.g., exosome, protein (e.g., a scaffold protein such as MARCKS, MARCKSL1, or BASP1) or a modification thereof, in particular a fragment or variant thereof. In some embodiments, the one or more heterologous proteins are mammalian proteins. In some embodiments, the one or more heterologous proteins are human proteins.
In some embodiments lumen-engineered EVs, e.g., exosomes, are produced from a cell transformed with a sequence encoding a polypeptide of a sequence identical or similar to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein) including, but not limited to,
(1) myristoylated alanine rich Protein Kinase C substrate (MARCKS);
(2) myristoylated alanine rich Protein Kinase C substrate like 1 (MARCKSL1); and
(3) brain acid soluble protein 1 (BASP1).
In some embodiments, the polypeptide is at least about 50% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., 50% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 55% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 55% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 60% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 60% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 65% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 65% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 70% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 70% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 75% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 75% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, said polypeptide is at least about 80% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 80% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 85% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 85% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, said polypeptide is at least about 90% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 90% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 95% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 95% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 99% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 99% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M. In some embodiments, the polypeptide is at least about 99.9% identical to a full-length or a fragment of a native EV, e.g., exosome, lumen protein (scaffold protein), e.g., at least about 99.9% identical to SEQ ID NO: 1-3 or any of the corresponding sequences without the N-terminal M.
In some embodiments, lumen-engineered EVs, e.g., exosomes, produced from the cell comprise a polypeptide of a sequence identical or similar to a fragment of brain acid soluble protein 1 (BASP1). In some embodiments, the polypeptide is at least about 50% identical to a full-length or a fragment of BASP1, e.g., at least about 50% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 55% identical to a full-length or a fragment of BASP1, e.g., at least about 50% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, said polypeptide is at least about 60% identical to a full-length or a fragment of BASP1, e.g., at least about 60% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 65% identical to a full-length or a fragment of BASP1, e.g., at least about 65% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 70% identical to a full-length or a fragment of BASP1, e.g., at least about 70% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 75% identical to a full-length or a fragment of BASP1, e.g., at least about 75% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 80% identical to a full-length or a fragment of BASP1, e.g., at least about 80% identical to SEQ ID NO4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 85% identical to a full-length or a fragment of BASP1, e.g., at least about 85% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 90% identical to a full-length or a fragment of BASP1, e.g., at least about 90% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 95% identical to a full-length or a fragment of BASP1, e.g., at least about 95% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 99% identical to a full-length or a fragment of BASP1, e.g., at least about 99% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is at least about 99.9% identical to a full-length or a fragment of BASP1, e.g., at least about 99.9% identical to SEQ ID NO: 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M. In some embodiments, the polypeptide is about 100% identical to a fragment of BASP1, e.g., about 100% identical to 4-109, the corresponding sequence without the N-terminal M, or any BASP1 sequences described herein, e.g., TABLE 1, without the N terminal M.
In some embodiments, lumen-engineered EVs, e.g., exosomes, produced from the cell comprise a polypeptide of a sequence identical or similar to a fragment of brain acid soluble protein 1 (BASP1), wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 50% identical to a full-length or a fragment of BASP1, e.g., at least about 50% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 55% identical to a full-length or a fragment of BASP1, e.g., at least about 50% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, said polypeptide is at least about 60% identical to a full-length or a fragment of BASP1, e.g., at least about 60% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 65% identical to a full-length or a fragment of BASP1, e.g., at least about 65% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 70% identical to a full-length or a fragment of BASP1, e.g., at least about 70% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 75% identical to a full-length or a fragment of BASP1, e.g., at least about 75% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 80% identical to a full-length or a fragment of BASP1, e.g., at least about 80% identical to SEQ ID NO4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 85% identical to a full-length or a fragment of BASP1, e.g., at least about 85% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 90% identical to a full-length or a fragment of BASP1, e.g., at least about 90% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 95% identical to a full-length or a fragment of BASP1, e.g., at least about 95% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 99% identical to a full-length or a fragment of BASP1, e.g., at least about 99% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is at least about 99.9% identical to a full-length or a fragment of BASP1, e.g., at least about 99.9% identical to SEQ ID NO: 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met. In some embodiments, the polypeptide is about 100% identical to a fragment of BASP1, e.g., about 100% identical to 4-109 or any BASP1 sequences described herein, e.g., TABLE 1, wherein the polypeptide does not comprise an N-terminal Met.
EVs (e.g., exosomes) of the present disclosure can be produced by chemical synthesis, recombinant DNA technology, biochemical or enzymatic fragmentation of larger molecules, combinations of the foregoing or by any other method. In one embodiment, the present disclosure provides a method of conjugating a biologically active molecule to an EV (e.g., exosome). The method comprises linking a biologically active molecule to an EV (e.g., exosome) as described above.
In some embodiments of the present disclosure, the EVs, e.g., exosomes of the present disclosure can be manufactured using producer cells as described above. Accordingly, the present disclosure provides a method of making EVs, e.g., exosomes, comprising culturing a producer cell disclosed herein under suitable conditions and obtaining the EVs, e.g., exosomes of the present disclosure.
In other embodiments, the scaffold proteins, e.g., exosome lumen proteins, of the present disclosure can be produced recombinantly and subsequently incorporated into an EV, e.g., exosome, of the present disclosure. In other embodiments, only the polypeptide portion of the scaffold protein is produced recombinantly. In some embodiments, the polypeptide portion of the scaffold protein produced recombinantly is subsequently modified, e.g., chemically or enzymatically, to incorporate a membrane anchor (e.g., an N-terminal myristic acid). In some embodiments, the scaffold protein produced semi-recombinantly (i.e., combining recombinant product of the polypeptide portion followed by chemical or enzymatic modification) is subsequently incorporated into an EV, e.g., exosome, of the present disclosure.
In other embodiments, the scaffold proteins, e.g., exosome lumen proteins, of the present disclosure can be produced chemically, e.g., using solid phase peptide synthesis, and subsequently incorporated into an EV, e.g., exosome, of the present disclosure. In other embodiments, only the polypeptide portion of the scaffold protein is produced synthetically. In some embodiments, the polypeptide portion of the scaffold protein produced synthetically is subsequently modified, e.g., chemically or enzymatically, to incorporate a membrane anchor (e.g., an N-terminal myristic acid). In some embodiments, the scaffold protein produced semi-synthetically (i.e., combining synthetic product of the polypeptide portion followed by chemical or enzymatic modification) is subsequently incorporated into an EV, e.g., exosome, of the present disclosure.
In other embodiments, the scaffold proteins, e.g., exosome lumen proteins, of the present disclosure can be produced in vitro, e.g., using a cell-free expression such a reticulocyte system, and subsequently incorporated into an EV, e.g., exosome, of the present disclosure. In other embodiments, only the polypeptide portion of the scaffold protein is produced in vitro, e.g., in a cell-free system. In some embodiments, the polypeptide portion of the scaffold protein produced in vitro, e.g., in a cell-free system is subsequently modified, e.g., chemically or enzymatically, to incorporate a membrane anchor (e.g., an N-terminal myristic acid). In some embodiments, the scaffold protein produced semi-in vitro (i.e., combining in vitro product of the polypeptide portion followed by chemical or enzymatic modification) is subsequently incorporated into an EV, e.g., exosome, of the present disclosure.
In some embodiments, the methods described herein further comprise the step of characterizing EVs, e.g., exosomes, contained in each collected fraction during their production and purification. In some embodiments, contents of the EVs, e.g., exosomes, can be extracted for study and characterization. In some embodiments, EVs, e.g., exosomes, are isolated and characterized by metrics including, but not limited to, size, shape, morphology, or molecular compositions such as nucleic acids, proteins, metabolites, and lipids.
The present disclosure also provides pharmaceutical compositions comprising EVs (e.g., exosomes) described herein that are suitable for administration to a subject. The pharmaceutical compositions generally comprise a plurality of EVs (e.g., exosomes) comprising at least one payload, e.g., a biologically active molecule, covalently or non-covalently linked to the plurality of EVs (e.g., exosomes) and a pharmaceutically-acceptable excipient or carrier in a form suitable for administration to a subject.
Pharmaceutically acceptable excipients or carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions comprising a plurality of EVs (e.g., exosomes). (See, e.g., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. 18th ed. (1990)). The pharmaceutical compositions are generally formulated sterile and in full compliance with all Good Manufacturing Practice (GMP) regulations of the U.S. Food and Drug Administration. In some embodiments, the pharmaceutical composition comprises one or more chemical compounds, such as for example, small molecules covalently linked to an EV (e.g., exosome) described herein.
In some embodiments, a pharmaceutical composition comprises one or more therapeutic or diagnostic agents and an EV (e.g., exosome) described herein. In certain embodiments, the EVs (e.g., exosomes) are co-administered with of one or more additional therapeutic or diagnostic agents, in a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition comprising the EV (e.g., exosome) is administered prior to administration of the additional therapeutic or diagnostic agents. In other embodiments, the pharmaceutical composition comprising the EV (e.g., exosome) is administered after the administration of the additional therapeutic or diagnostic agents. In further embodiments, the pharmaceutical composition comprising the EV (e.g., exosome) is administered concurrently with the additional therapeutic or diagnostic agents.
Provided herein are pharmaceutical compositions comprising an EV (e.g., exosome) of the present disclosure having the desired degree of purity, and a pharmaceutically acceptable carrier or excipient, in a form suitable for administration to a subject. Pharmaceutically acceptable excipients or carriers can be determined in part by the particular composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions comprising a plurality of extracellular vesicles. (See, e.g., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. 21st ed. (2005)). The pharmaceutical compositions are generally formulated sterile and in full compliance with all Good Manufacturing Practice (GMP) regulations of the U.S. Food and Drug Administration.
In some embodiments, a pharmaceutical composition comprises one or more therapeutic or diagnostic agents and an EV (e.g., exosome) described herein. In certain embodiments, the EVs (e.g., exosomes) are co-administered with of one or more additional therapeutic agents or diagnostic agents, in a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition comprising the EV (e.g., exosome) is administered prior to administration of the additional therapeutic or diagnostic agents. In other embodiments, the pharmaceutical composition comprising the EV (e.g., exosome) is administered after the administration of the additional therapeutic or diagnostic agents. In further embodiments, the pharmaceutical composition comprising the EV (e.g., exosome) is administered concurrently with the additional therapeutic or diagnostic agents.
Acceptable carriers, excipients, or stabilizers are nontoxic to recipients (e.g., animals or humans) at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG).
Examples of carriers or diluents include, but are not limited to, water, saline, Ringer's solutions, dextrose solution, and 5% human serum albumin. The use of such media and compounds for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or compound is incompatible with the extracellular vesicles described herein, use thereof in the compositions is contemplated. Supplementary therapeutic agents can also be incorporated into the compositions. Typically, a pharmaceutical composition is formulated to be compatible with its intended route of administration. The EVs (e.g., exosomes) of the present disclosure can be administered by parenteral, topical, intravenous, oral, subcutaneous, intra-arterial, intradermal, transdermal, rectal, intracranial, intraperitoneal, intranasal, intratumoral, intramuscular route or as inhalants. In certain embodiments, the pharmaceutical composition comprising EVs (e.g., exosomes) is administered intravenously, e.g. by injection. The EVs (e.g., exosomes) can optionally be administered in combination with other therapeutic agents that are at least partly effective in treating the disease, disorder or condition for which the EVs (e.g., exosomes) are intended.
Solutions or suspensions can include the following components: a sterile diluent such as water, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial compounds such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfate; chelating compounds such as ethylenediaminetetraacetic acid (EDTA); buffers such as acetates, citrates or phosphates, and compounds for the adjustment of tonicity such as sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (if water soluble) or dispersions and sterile powders. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). The composition is generally sterile and fluid to the extent that easy syringeability exists. The carrier can be a solvent or dispersion medium containing, e.g., water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, e.g., by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal compounds, e.g., parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. If desired, isotonic compounds, e.g., sugars, polyalcohols such as mannitol, sorbitol, and sodium chloride can be added to the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition a compound which delays absorption, e.g., aluminum monostearate and gelatin.
Sterile injectable solutions can be prepared by incorporating the EVs (e.g., exosomes) of the present disclosure in an effective amount and in an appropriate solvent with one or a combination of ingredients enumerated herein, as desired. Generally, dispersions are prepared by incorporating the EVs (e.g., exosomes) into a sterile vehicle that contains a basic dispersion medium and any desired other ingredients. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The EVs (e.g., exosomes) can be administered in the form of a depot injection or implant preparation which can be formulated in such a manner to permit a sustained or pulsatile release of the EVs (e.g., exosomes).
Systemic administration of compositions comprising EVs (e.g., exosomes) of the present disclosure can also be by transmucosal means. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, e.g., for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of, e.g., nasal sprays.
In certain embodiments the pharmaceutical composition comprising EVs (e.g., exosomes) of the present disclosure is administered intravenously into a subject that would benefit from the pharmaceutical composition. In certain other embodiments, the composition is administered to the lymphatic system, e.g., by intralymphatic injection or by intranodal injection (see e.g., Senti et al., PNAS 105(46): 17908 (2008)), or by intramuscular injection, by subcutaneous administration, by intratumoral injection, by direct injection into the thymus, or into the liver.
In certain embodiments, the pharmaceutical composition comprising EVs (e.g., exosomes) of the present disclosure is administered as a liquid suspension. In certain embodiments, the pharmaceutical composition is administered as a formulation that is capable of forming a depot following administration. In certain preferred embodiments, the depot slowly releases the EVs (e.g., exosomes) into circulation, or remains in depot form.
Typically, pharmaceutically-acceptable compositions are highly purified to be free of contaminants, are biocompatible and not toxic, and are suited to administration to a subject. If water is a constituent of the carrier, the water is highly purified and processed to be free of contaminants, e.g., endotoxins.
The pharmaceutically-acceptable carrier can be lactose, dextrose, sucrose, sorbitol, mannitol, starch, gum acacia, calcium phosphate, alginates, gelatin, calcium silicate, micro-crystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup, methyl cellulose, methylhydroxy benzoate, propylhydroxy benzoate, talc, magnesium stearate, and/or mineral oil, but is not limited thereto. The pharmaceutical composition can further include a lubricant, a wetting agent, a sweetener, a flavor enhancer, an emulsifying agent, a suspension agent, and/or a preservative.
The pharmaceutical compositions described herein comprise the EVs (e.g., exosomes) described herein and optionally a pharmaceutically active or therapeutic agent, and/or a diagnostic agent. The therapeutic agent can be a biological agent, a small molecule agent, or a nucleic acid agent. The diagnostic agent can be, e.g., a contrast reagent.
Dosage forms are provided that comprise a pharmaceutical composition comprising the EVs (e.g., exosomes) described herein. In some embodiments, the dosage form is formulated as a liquid suspension for intravenous injection. In some embodiments, the dosage form is formulated as a liquid suspension for intratumoral injection.
In certain embodiments, the preparation of EVs (e.g., exosomes) of the present disclosure is subjected to radiation, e.g., X rays, gamma rays, beta particles, alpha particles, neutrons, protons, elemental nuclei, UV rays in order to damage residual replication-competent nucleic acids.
In certain embodiments, the preparation of EVs (e.g., exosomes) of the present disclosure is subjected to gamma irradiation using an irradiation dose of more than 1, 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, or more than 100 kGy.
In certain embodiments, the preparation of EVs (e.g., exosomes) of the present disclosure is subjected to X-ray irradiation using an irradiation dose of more than 0.1, 0.5, 1, 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, or
The EVs (e.g., exosomes) of the present disclosure may be used concurrently with other drugs. To be specific, the EVs (e.g., exosomes) of the present disclosure may be used together with medicaments such as hormonal therapeutic agents, chemotherapeutic agents, immunotherapeutic agents, medicaments inhibiting the action of cell growth factors or cell growth factor receptors and the like.
The present disclosure provides methods of treating a disease or condition in a subject in need thereof comprising administering a composition comprising EVs (e.g., exosomes) of the present disclosure to the subject. The present disclosure also provides methods of preventing or ameliorating the symptoms of a disease or condition in a subject in need thereof comprising administering a composition comprising EVs (e.g., exosomes) of the present disclosure to the subject. Also provided are methods to diagnose a disease or condition in a subject in need thereof comprising administering a composition comprising EVs (e.g., exosomes) of the present disclosure to the subject. Also provided are EVs (e.g., exosomes) of the present disclosure for use in therapy, for use as a medicament, for use in treating a disease or condition in a subject in need thereof, for use in preventing or ameliorating the symptoms of a disease or condition in a subject in need thereof, or for diagnosing a disease or condition in a subject in need thereof.
In one embodiment, the disease or disorder is a cancer, an inflammatory disease, a neurodegenerative disorder, a central nervous disease or a metabolic disease.
Present disclosure also provides methods of preventing and/or treating a disease or disorder in a subject in need thereof, comprising administering an EV (e.g., exosome) disclosed herein to the subject. In some embodiments, a disease or disorder that can be treated with the present methods comprises a cancer, graft-versus-host disease (GvHD), autoimmune disease, infectious diseases, or fibrotic diseases. In some embodiments, the treatment is prophylactic. In other embodiments, the EVs (e.g., exosomes) for the present disclosure are used to induce an immune response. In other embodiments, the EVs (e.g., exosomes) for the present disclosure are used to vaccinate a subject. In some embodiments, the disease or disorder is a cancer.
In some embodiments, the disease or disorder is an infectious disease. In certain embodiments, the disease or disorder is an oncogenic virus. In some embodiments, infectious diseases that can be treated with the present disclosure includes, but not limited to, Human Gamma herpes virus 4 (Epstein Barr virus), influenza A virus, influenza B virus, cytomegalovirus, Staphylococcus aureus, Mycobacterium tuberculosis, Chlamydia trachomatis, HIV-1, HIV-2, corona viruses (e.g., MERS-CoV and SARS CoV), filoviruses (e.g., Marburg and Ebola), Streptococcus pyogenes, Streptococcus pneumoniae, Plasmodia species (e.g., vivax and falciparum), Chikunga virus, Human Papilloma virus (HPV), Hepatitis B, Hepatitis C, human herpes virus 8, herpes simplex virus 2 (HSV2), Klebsiella sp., Pseudomonas aeruginosa, Enterococcus sp., Proteus sp., Enterobacter sp., Actinobacter sp., coagulase-negative staphylococci (CoNS), Mycoplasma sp., or combinations thereof.
In some embodiments, the EVs (e.g., exosomes) are administered intravenously to the circulatory system of the subject. In some embodiments, the EVs (e.g., exosomes) are infused in suitable liquid and administered into a vein of the subject.
In some embodiments, the EVs (e.g., exosomes) are administered intra-arterialy to the circulatory system of the subject. In some embodiments, the EVs (e.g., exosomes) are infused in suitable liquid and administered into an artery of the subject.
In some embodiments, the EVs (e.g., exosomes) are administered to the subject by intrathecal administration. In some embodiments, the EVs (e.g., exosomes) are administered via an injection into the spinal canal, or into the subarachnoid space so that it reaches the cerebrospinal fluid (CSF).
In some embodiments, the EVs (e.g., exosomes) are administered intratumorally into one or more tumors of the subject.
In some embodiments, the EVs (e.g., exosomes) are administered to the subject by intranasal administration. In some embodiments, the EVs (e.g., exosomes) can be insufflated through the nose in a form of either topical administration or systemic administration. In certain embodiments, the EVs (e.g., exosomes) are administered as nasal spray.
In some embodiments, the EVs (e.g., exosomes) are administered to the subject by intraperitoneal administration. In some embodiments, the EVs (e.g., exosomes) are infused in suitable liquid and injected into the peritoneum of the subject. In some embodiments, the intraperitoneal administration results in distribution of the EVs (e.g., exosomes) to the lymphatics. In some embodiments, the intraperitoneal administration results in distribution of the EVs (e.g., exosomes) to the thymus, spleen, and/or bone marrow. In some embodiments, the intraperitoneal administration results in distribution of the EVs (e.g., exosomes) to one or more lymph nodes. In some embodiments, the intraperitoneal administration results in distribution of the EVs (e.g., exosomes) to one or more of the cervical lymph node, the inguinal lymph node, the mediastinal lymph node, or the sternal lymph node. In some embodiments, the intraperitoneal administration results in distribution of the EVs (e.g., exosomes) to the pancreas.
In some embodiments, the EVs (e.g., exosomes) are administered to the subject by periocular administration. In some embodiments, the EVs (e.g., exosomes) are injected into the periocular tissues. Periocular drug administration includes the routes of subconjunctival, anterior sub-Tenon's, posterior sub-Tenon's, and retrobulbar administration.
The present disclosure also provides kits, or products of manufacture comprising one or more EVs (e.g., exosomes) of the present disclosure and optionally instructions for use. In some embodiments, the kit, or product of manufacture contains a pharmaceutical composition described herein which comprises at least one EV (e.g., exosome) of the present disclosure, and instructions for use.
In some embodiments, the kit, or product of manufacture comprises at least one EV (e.g., exosome) of the present disclosure or a pharmaceutical composition comprising the EVs (e.g., exosomes) in one or more containers. One skilled in the art will readily recognize that the EVs (e.g., exosomes) of the present disclosure, pharmaceutical composition comprising the EVs (e.g., exosomes) of the present disclosure, or combinations thereof can be readily incorporated into one of the established kit formats which are well known in the art.
In some embodiments, the kit, or product of manufacture comprises (i) EVs (e.g., exosomes), (ii) one or more payload, e.g., biologically active molecules, (ii) reagents to covalently attach the one or more payloads, e.g., biologically active molecules, to the EVs (e.g., exosomes), or (iv) any combination thereof, and instructions to conduct the reaction to covalently attach the one or more payloads, e.g., biologically active molecules to the EVs (e.g., exosomes).
In some embodiments, the kit comprises reagents to conjugate a payload, e.g., a biologically active molecule to an EV (e.g., exosome), and instructions to conduct the conjugation.
The practice of the present disclosure will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Sambrook et al., ed. (1989) Molecular Cloning A Laboratory Manual (2nd ed.; Cold Spring Harbor Laboratory Press); Sambrook et al., ed. (1992) Molecular Cloning: A Laboratory Manual, (Cold Springs Harbor Laboratory, NY); D. N. Glover ed., (1985) DNA Cloning, Volumes I and II; Gait, ed. (1984) Oligonucleotide Synthesis; Mullis et al. U.S. Pat. No. 4,683,195; Hames and Higgins, eds. (1984) Nucleic Acid Hybridization; Hames and Higgins, eds. (1984) Transcription And Translation; Freshney (1987) Culture Of Animal Cells (Alan R. Liss, Inc.); Immobilized Cells And Enzymes (IRL Press) (1986); Perbal (1984) A Practical Guide To Molecular Cloning; the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Miller and Calos eds. (1987) Gene Transfer Vectors For Mammalian Cells, (Cold Spring Harbor Laboratory); Wu et al., eds., Methods In Enzymology, Vols. 154 and 155; Mayer and Walker, eds. (1987) Immunochemical Methods In Cell And Molecular Biology (Academic Press, London); Weir and Blackwell, eds., (1986) Handbook Of Experimental Immunology, Volumes I-IV; Manipulating the Mouse Embryo, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., (1986); Crooke, Antisense drug Technology: Principles, Strategies and Applications, 2nd Ed. CRC Press (2007) and in Ausubel et al. (1989) Current Protocols in Molecular Biology (John Wiley and Sons, Baltimore, Md.).
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present disclosure, and are not intended to limit the scope of what the inventors regard as their disclosure nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, etc.) but some experimental errors and deviations should be accounted for.
Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations can be used, e.g., bp, base pair(s); kb, kilobase(s); pl, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); nt, nucleotide(s); and the like.
The practice of the present disclosure will employ, unless otherwise indicated, conventional methods of protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., T.E. Creighton, Proteins: Structures and Molecular Properties (W.H. Freeman and Company, 1993); AL. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.); Remington's Pharmaceutical Sciences, 21th Edition (Easton, Pa.: Mack Publishing Company, 2005); Carey and Sundberg Advanced Organic Chemistry 3rd Ed. (Plenum Press) Vols A and B(1992).
To identify the minimal BASP1 amino acid sequence between the twelve-amino acid truncation that facilitated loading and the six-amino acid truncation that failed to facilitate loading as shown above, individual truncation mutants of the N-terminus of BASP1 fused to a FLAG® tag and GFP were generated and stably expressed in HEK293SF cells (
The serine at position 6 of BASP1 is highly conserved across species and in MARCKS and MARCKSL1. To determine whether this amino acid was required for payload loading into exosomes, HEK293SF cells were stably transfected with expression plasmids encoding BASP1 1-30-FLAG®-GFP or BASP1 1-30-FLAG®-GFP including a point mutant, replacing serine six with aspartic acid (S6D; polar charged substitution) or alanine (S6A; small nonpolar substitution). Additionally, the lysine at position five was mutated to a glutamic acid (L5Q) to test the potential role of this position in modulating myristoylation, palmitoylation, and other membrane functions of several membrane-associated proteins (Gottlieb-Abraham et al., Mol. Biol. Cell. 2016 Dec. 1; 27(24):3926-3936) (
The first thirty amino acids of BASP1 contain the N-terminal leader sequence identified above, followed by a lysine-rich stretch of amino acids. To understand whether MARCKS and MARCKSL1 N-termini can load exosomes similarly to BASP1, HEK293SF cells were stably transfected with MARCKS and MARCKSL1 full-length proteins or amino acids 1-30 fused to FLAG®-GFP. Purified exosomes were analyzed by SDS PAGE and COOMASSIE® staining to determine the extent of loading. Full-length MARCKS and MARCKSL1 were able to load exosomes with GFP, but amino acids 1-30 were inferior to the full-length proteins, suggesting that there are additional structural or sequence features in distal regions of the MARCKS and MARCKSL1 proteins required for loading (
Amino acids 152-173 of MARCKS and 87-110 of MARCKSL1 are lysine-rich with interspersed phenylalanine and serine residues and are predicted to be phosphorylation site domains (PSD) or effector domains (ED) (
The narrowest motif, Motif 1, allows for a protein sequence of (M)(G)(G/A/S)(K/Q)(L/F/S/Q)(S/A)(K)(K) (SEQ ID NO: 118) or (G)(G/A/S)(K/Q)(L/F/S/Q)(S/A)(K)(K) (SEQ ID NO: 202) without the first Met, where each parenthetical letter or group of letters is an amino acid position, and wherein additionally position five cannot be a positively charged amino acid (K/R/H) and position six cannot be a negatively charged amino acid (D/E).
Sub-motifs of Motif 1 include, without being limiting, the protein sequences:
where position five cannot be a positively charged amino acid (K/R/H) and position six cannot be a negatively charged amino acid (D/E).
Motif 2, a broader motif, can be expressed as (M)(G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+) or (G)(π)(ξ)(Φ/π)(S/A/G/N)(+)(+) without the first Met, wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), ξ is any amino acid selected from the group consisting of (Asn, Gln, Ser, Thr, Asp, Glu, Lys, His, Arg), is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu). See R. Aasland et al., FEBS Letters 513 (2002): 141-144 for the nomenclature of amino acids.
Motif 3, the broadest motif, can be expressed as (M)(G)(π)(X)(Φ/π)(π)(+)(+) or (G)(π)(X)(Φ/π)(π)(+)(+) without the first Met, wherein each parenthetical position represents an amino acid, and wherein π is any amino acid selected from the group consisting of (Pro, Gly, Ala, Ser), X is any amino acid, Φ is any amino acid selected from the group consisting of (Val, Ile, Leu, Phe, Trp, Tyr, Met), and (+) is any amino acid selected from the group consisting of (Lys, Arg, His); and wherein position five is not (+) and position six is neither (+) nor (Asp or Glu). In all cases of Motifs 1-3, the sequence may be truncated by one amino acid to be seven total amino acids in length (i.e., consisting of amino acids 1-7 in the order presented in Motifs 1-3). Any of the sequences derived from any of Motifs 1, 2, or 3 (or these motifs lacking amino acid 7), can be used to load a payload into exosomes to the same extent as, or comparable to, full length BASP1 or natural truncation sequences of BASP1. This deep analysis of amino acid sequence-structure-function provides novel insights into the requirements for directing biologically expressed payload into exosomes by producer cells.
The results in Example 1 suggest that the N-terminus of BASP1 may be a useful engineering scaffold for generating luminally loaded exosomes directly from producer cells. To test this hypothesis, stable HEK293SF cells were generated to express full-length Cas9 protein with codon optimization (as described in Zetsche B, Volz S E, Zhang F. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat Biotechnol. 2015 February; 33(2):139-42) fused to amino acids 1-30 or 1-10 of BASP1. Exosomes were purified from cell culture as described above and analyzed by SDS-PAGE and Western blotting using an anti-Cas9 antibody (Abcam; Catalog #ab191468, clone 7A9-3A3). As shown in
As an additional validation of the diversity of payload proteins that can be loaded as a fusion to the N-terminus of BASP1, ovalbumin was stably expressed in HEK293SF cells as a fusion to amino acids 1-10 of BASP1 (“BASP1(1-10)-OVA”). A separate cell line was co-transfected with the same plasmid and a second plasmid encoding trimeric CD40L fused to an exosome-specific surface glycoprotein PTGFRN (“3×CD40L-PTGFRN”) using a second selectable marker. Exosomes were purified from the two transfected cell cultures and analyzed by SDS-PAGE (
Another class of proteins that may be useful in the context of therapeutic exosomes are antibodies and antibody fragments. A single chain camelid nanobody targeting GFP (as described in Caussinus E, Kanca O, Affolter M. Fluorescent fusion protein knockout mediated by anti-GFP nanobody. Nat Struct Mol Biol. 2011 Dec. 11; 19(1):117-21) was stably expressed in HEK293SF cells as a fusion protein to amino acids 1-10 of BASP1 and a FLAG® tag (“BASP1(1-10)-Nanobody”) or a FLAG® tag alone (“Nanobody”) (
Nucleic acids, and in particular RNAs (e.g., mRNAs, siRNAs, miRNAs) are an attractive class of therapeutic payload to be loaded in the lumen of therapeutic exosomes. Exosome loading of RNA may protect the RNA from degradation in the extracellular environment and the loaded exosome can be directed to certain cells and/or tissues through additional levels of exosome engineering, e.g., surface expression of a targeting construct. To understand whether the EV, e.g., exosome proteins (or protein fragments) identified above can be used to generate mRNA-loaded exosomes, combinatorial engineered exosomes were generated. As shown in
The cells stably expressing the BASP1-MCP and Luciferase-MS2 mRNA were isolated and total Luciferase mRNA was quantified by RT-qPCR (FWD Primer: 5′-TGGAGGTGCTCAAAGAGTTG-3′ (SEQ ID NO: 119); REV Primer: 5′-TTGGGCGTGCACTTGAT-3′ (SEQ ID NO: 120); PROBE: 5′-/56-FAM/CAGCTTTCC/ZEN/GGGCATTGGCTTC/3IABkFQ/-3′ (SEQ ID NO: 121)). Untransfected cells expressed lower levels of Luciferase than all of the 811-expressing cells, which expressed comparable levels of Luciferase (
The results in the previous experiments demonstrate that full-length and N-terminal regions of MARCKS, MARCKSL1, and BASP1 can be used to generate luminally loaded exosomes. To further explore the potential of these proteins for exosome engineering, amino acids 1-30 of MARCKS, MARCKSL1 and BASP1, or amino acids 1-10 of BASP1 were fused to the endogenous transmembrane region of CD40L expressed as a homotrimer. Constructs were prepared for both human and mouse sequences of CD40L because the ligands do not cross-react with the cognate receptor on the other species (
Cell lines from different tissues of origin (HEK293, kidney; HT1080, connective tissue; K562, bone marrow; MDA-MB-231, breast; Raji, lymphoblast) were grown to logarithmic phase and transferred to media supplemented with exosome-depleted serum for ˜6 days except for the HEK293 cells, which were grown in chemically-defined media. Bone marrow-derived mesenchymal stem cells (MSC) were grown on 3D microcarriers for five days and supplemented in serum-free media for three days. Supernatant from each cell line culture was isolated, and exosomes were purified using the OPTIPREP™ density-gradient ultracentrifugation method described above. Each of the purified exosome preparations was analyzed by LC-MS/MS as described above, and the number of peptide spectrum matches (PSMs) was quantified for BASP1, MARCKS, and MARCKSL1 and two widely studied EV, e.g., exosome proteins (CD81 and CD9). The tetraspanins CD81 and CD9 were detectable in most purified exosome populations, but were, in some cases, equal to or lower than the luminal EV, e.g., exosome, proteins (e.g., compare CD9 to BASP1 or MARCKSL1) (
The results in Example 5 demonstrate that numerous human-derived cells naturally express BASP1 and the other novel EV. To determine whether BASP1 can be used as a universal exosome scaffold protein, Chinese hamster ovary (CHO) cells were stably transfected with either a plasmid expressing full-length BASP1 fused to a FLAG® tag and GFP (“BASP1-GFP-FLAG”), a plasmid expressing amino acids 1-30 of BASP1 fused to a FLAG® tag and GFP (“BASP1(1-30)-GFP-FLAG”) or a plasmid expressing amino acids 1-8 of BASP1 fused to a FLAG® tag and GFP (“BASP1(1-8)-GFP-FLAG”). Exosomes were purified from wild-type CHO cells and CHO cells transfected with one of the three BASP1 plasmids. As shown in
It is to be appreciated that the Detailed Description section, and not the Summary and Abstract sections, is intended to be used to interpret the claims. The Summary and Abstract sections may set forth one or more but not all exemplary embodiments of the present disclosure as contemplated by the inventor(s), and thus, are not intended to limit the present disclosure and the appended claims in any way.
The present disclosure has been described above with the aid of functional building blocks illustrating the implementation of specified functions and relationships thereof The boundaries of these functional building blocks have been arbitrarily defined herein for the convenience of the description. Alternate boundaries can be defined so long as the specified functions and relationships thereof are appropriately performed.
All publications, patents, patent applications and other documents cited in this application are hereby incorporated by reference in their entireties for all purposes to the same extent as if each individual publication, patent, patent application or other document were individually indicated to be incorporated by reference for all purposes.
The present disclosure provides, inter alia, compositions of EVs, e.g., exosomes containing modified exogenous proteins and peptides for use in enrichment of exogenous proteins in EVs, e.g., exosomes. The present disclosure also provides method of and methods of producing enriched EVs, e.g., exosomes. While various specific embodiments have been illustrated and described, the above specification is not restrictive. The breadth and scope of the present disclosure should not be limited by any of the above-described exemplary embodiments, but should be defined only in accordance with the following claims and their equivalents. It will be appreciated that various changes can be made without departing from the spirit and scope of the disclosure(s). Many variations will become apparent to those skilled in the art upon review of this specification.
This application claims the benefit of International Application No. PCT/US2018/061679, filed Nov. 16, 2018, and U.S. Provisional Application No. 62/835,430, filed Apr. 17, 2019, which are incorporated by reference herein in their entireties.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2019/033629 | 5/22/2019 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62835430 | Apr 2019 | US | |
| 62634750 | Feb 2018 | US | |
| 62587767 | Nov 2017 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US18/61679 | Nov 2018 | US |
| Child | 17293833 | US |
