Targeted extracellular vesicles comprising membrane proteins with engineered glycosylation sites
Disclosed are extracellular vesicles comprising an engineered targeting protein for targeting the extracellular vesicles to target cells. The targeting protein is a fusion protein that includes a ligand, an engineered glycosylation site, and an exosome-targeting domain. Exemplary extracellular vesicles may include but are not limited to exosomes.
1. An extracellular vesicle comprising a targeting protein, wherein the targeting protein is a fusion protein comprising as components:
(i) a ligand that is expressed on the surface of the extracellular vesicles and targets the extracellular vesicles to target cells;
(ii) an engineered glycosylation site; and
(iii) an exosome-targeting domain;
wherein the engineered glycosylation site comprises an amino acid sequence that is not naturally present in the fusion protein or any of the components of the fusion protein.
2. The extracellular vesicle of claim 1 , wherein the extracellular vesicle is an exosome.
3. The extracellular vesicle of claim 1 , wherein the exosome-targeting domain is a domain of a lysosome-associated protein.
4. The extracellular vesicle of claim 3 , wherein the lysosome-associated protein is a lysosome membrane protein.
5. The extracellular vesicle of claim 4 , wherein the lysosome membrane protein comprises a luminal N-terminus and a cytoplasmic C-terminus and the fusion protein comprises from N-terminus to C-terminus: the ligand, the engineered glycosylation site, and the exosome-targeting domain.
6. The extracellular vesicle of claim 1 , wherein the exosome-targeting domain comprises a sequence selected from a group consisting of SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:31, and SEQ ID NO:34, SEQ ID NO:35, and SEQ ID NO:36, or a variant thereof having at least 80% amino acid sequence identity to SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:31, and SEQ ID NO:34, SEQ ID NO:35, and SEQ ID NO:36, respectively.
7. The extracellular vesicle of claim 1 , wherein the extracellular vesicles further comprise a therapeutic agent selected from the group consisting of a small molecule therapeutic, a therapeutic RNA, and a therapeutic protein.
8. The extracellular vesicle of claim 7 , wherein the therapeutic RNA is a cargo RNA and the fusion protein further comprises an RNA-binding domain for the cargo RNA.
9. The extracellular vesicle of claim 8 , wherein the RNA-binding domain is present at the C-terminus of the fusion protein.
10. The extracellular vesicle of claim 9 , wherein the cargo RNA comprises an RNA-motif and the RNA-binding domain of the fusion protein binds specifically to the RNA-motif of the cargo RNA.
11. The extracellular vesicle of claim 10 , wherein the RNA-binding domain is an RNA-binding domain of a bacteriophage, and wherein the RNA-motif comprises one or more high affinity binding loops of RNA of the bacteriophage.
12. The extracellular vesicle of claim 11 , wherein the RNA-binding domain is the RNA-binding domain of MS2 bacteriophage comprising SEQ ID NO:2 or a variant thereof having at least 80% amino acid sequence identity to SEQ ID NO:2, and wherein the RNA-motif comprises one or more high affinity binding loops comprising a sequence and structure selected from the group consisting of:
where N—N is any two base-paired RNA nucleotides.
13. A method for preparing the extracellular vesicle of claim 10 , the method comprising: (a) expressing in a eukaryotic cell an mRNA that encodes the fusion protein and (b) expressing in a eukaryotic cell the cargo RNA or transducing the eukaryotic cell with the cargo RNA.
14. A kit for preparing the extracellular vesicle of claim 10 , the kit comprising: (a) a vector for expressing the fusion protein, and (b) a vector for expressing the cargo RNA.
15. The kit of claim 14 , wherein the vectors are separate vectors.
16. A method for preparing the extracellular vesicle of claim 1 , the method comprising expressing in a eukaryotic cell an mRNA that encodes the fusion protein.
17. An extracellular vesicle comprising a targeting protein, wherein the targeting protein is a fusion protein comprising as components:
(i) a ligand that is expressed on the surface of the extracellular vesicles and targets the extracellular vesicles to target cells;
(ii) an engineered glycosylation site; and
(iii) an exosome-targeting domain of a lysosome transmembrane protein that comprises a luminal N-terminus and a cytoplasmic C-terminus, and the exosome-targeting domain is present in the cytoplasmic C-terminus of the lysosome transmembrane protein and the targeting protein does not comprise the luminal N-terminus of the lysosome transmembrane protein;
wherein the engineered glycosylation site comprises an amino acid sequence that is not naturally present in the fusion protein or any of the components of the fusion protein.
18. The extracellular vesicle of claim 17 , wherein the extracellular vesicle is an exosome vesicles are exosomes.
19. An extracellular vesicle comprising a targeting protein, wherein the targeting protein is a fusion protein comprising as components:
(i) a ligand that is expressed on the surface of the extracellular vesicles and targets the extracellular vesicles to target cells;
(ii) an engineered glycosylation site; and
(iii) an exosome-targeting domain;
wherein the engineered glycosylation site comprises an amino acid sequence that is not naturally present in the fusion protein or any of the components of the fusion protein, and the engineered glycosylation site comprises an amino acid sequence selected from the amino acid sequence of SEQ ID NO:37 and the amino acid sequence of SEQ ID NO:38.
20. The extracellular vesicle of claim 19 , wherein the extracellular vesicles are exosomes.
21. The extracellular vesicle of claim 19 , wherein the fusion protein has a luminal N-terminus and a cytosolic C-terminus and the fusion protein comprises from N-terminus to C-terminus: the ligand, the glycosylation site, and the exosome-targeting domain.