COMPOSITIONS AND METHODS FOR TREATING DISEASES AND DISORDERS USING OSCILLOSPIRACEAE MICROBIAL EXTRACELLULAR VESICLES
Provided herein are methods and pharmaceutical compositions related to microbial extracellular vesicles (mEVs) obtained from Oscillospiraceae bacteria that can be useful as therapeutic agents.
1 . A pharmaceutical composition comprising isolated pharmaceutical composition microbial extracellular vesicles (mEVs) from Oscillospiraceae bacteria (e.g., a therapeutically effective amount of mEVs from Oscillospiraceae bacteria).
2 . The pharmaceutical composition of claim 1 , wherein at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the pharmaceutical composition is mEVs.
3 . A pharmaceutical composition comprising isolated mEVs or a therapeutically effective amount for the treatment of a cancer.
4 . A pharmaceutical composition comprising isolated mEVs or a therapeutically effective amount for the treatment of a dysbiosis.
5 . A pharmaceutical composition comprising isolated mEVs or a therapeutically effective amount for the treatment of an autoimmune disease.
6 . A pharmaceutical composition comprising isolated mEVs or a therapeutically effective amount for the treatment of an inflammatory disease.
7 . A pharmaceutical composition comprising isolated mEVs or a therapeutically effective amount for the treatment of a metabolic disease.
8 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from a strain of Oscillospiraceae bacteria comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Faecalibacterium prausnitzii Strain A (ATCC Deposit Number PTA-126792).
9 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from the Faecalibacterium prausnitrzii Strain A (ATCC Deposit Number PTA-126792).
10 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from a strain of Oscillospiraceae bacteria comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis Strain A (ATCC Deposit Number PTA-126696).
11 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from the Fournierella massiliensis Strain A (ATCC Deposit Number PTA-126696).
12 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from a strain of Oscillospiraceae bacteria comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora Strain A (ATCC Deposit Number PTA-126694).
13 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from the Harryflintia acetispora Strain A (ATCC Deposit Number PTA-126694).
14 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from a strain of Oscillospiraceae bacteria comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).
15 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).
16 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from a strain of Oscillospiraceae bacteria comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Acutalibacter sp. Strain A (ATCC Deposit Number PTA-127006).
17 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from the Acutalibacter sp. Strain A (ATCC Deposit Number PTA-127006).
18 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from a strain of Oscillospiraceae bacteria comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Anaerotruncus colihominis Strain A (ATCC Deposit Number PTA-127005).
19 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from the Anaerotruncus colihominis Strain A (ATCC Deposit Number PTA-127005).
20 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from a strain of Oscillospiraceae bacteria comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Subdoligranulum variabile Strain A (ATCC Deposit Number PTA-127004).
21 . The pharmaceutical composition of any one of claims 1 to 7 , wherein the composition comprises mEVs from the Subdoligranulum variabile Strain A (ATCC Deposit Number PTA-127004).
22 . The pharmaceutical composition of any one of claims 1 to 21 , wherein the composition activates innate antigen presenting cells.
23 . The pharmaceutical composition of any one of claims 1 to 21 , wherein the composition has one or more beneficial immune effects outside the gastrointestinal tract, e.g., when orally administered.
24 . The pharmaceutical composition of any one of claims 1 to 21 , wherein the composition modulates immune effects outside the gastrointestinal tract in the subject, e.g., when orally administered.
25 . The pharmaceutical composition of any one of claims 1 to 24 , wherein the mEVs are produced from a high yield strain.
26 . The pharmaceutical composition of claim 25 , wherein the high yield strain produces at least 3×10 13 mEVs per liter from a bioreactor-grown culture.
27 . The pharmaceutical composition of any one of claims 1 to 26 , wherein the mEVs comprise pmEVs and the pmEVs are produced from bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated or oxygen sparged.
28 . The pharmaceutical composition of any one of claims 1 to 26 , wherein the mEVs comprise pmEVs and the pmEVs are produced from live bacteria.
29 . The pharmaceutical composition of any one of claims 1 to 28 , wherein the composition comprises secreted mEVs (smEVs).
30 . The pharmaceutical composition of any one of claims 1 to 28 , wherein the composition comprises processed mEVs (pmEVs).
31 . The pharmaceutical composition of any one of claims 1 to 30 , wherein the mEVs are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient).
32 . The pharmaceutical composition of any one of claims 1 to 31 , wherein the mEVs are gamma irradiated.
33 . The pharmaceutical composition of any one of claims 1 to 31 , wherein the mEVs are UV irradiated.
34 . The pharmaceutical composition of any one of claims 1 to 31 , wherein the mEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).
35 . The pharmaceutical composition of any one of claims 1 to 31 , wherein the mEVs are acid treated.
36 . The pharmaceutical composition of any one of claims 1 to 31 , wherein the mEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).
37 . The pharmaceutical composition of any one of claims 1 to 36 , wherein the dose of mEVs is about 2×10 6 to about 2×10 16 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)).
38 . The pharmaceutical composition of any one of claims 1 to 36 , wherein the dose of mEVs is about 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA assay).
39 . The pharmaceutical composition of any one of claims 1 to 38 , wherein the pharmaceutical composition comprises a solid dose form.
40 . The pharmaceutical composition of claim 39 , wherein the solid dose form comprises a tablet, a minitablet, a capsule, a pill, or a powder, or a combination of the foregoing.
41 . The pharmaceutical composition of claim 39 or 40 , wherein the solid dose form further comprises a pharmaceutically acceptable excipient.
42 . The pharmaceutical composition of any one of claims 39 to 41 , wherein the solid dose form comprises an enteric coating.
43 . The pharmaceutical composition of any one of claims 39 to 42 , wherein the solid dose form is for oral administration.
44 . The pharmaceutical composition of any one of claims 1 to 38 , wherein the pharmaceutical composition comprises a suspension.
45 . The pharmaceutical composition of claim 44 , wherein the suspension is for oral administration (e.g., the suspension comprises PBS, and optionally, sucrose or glucose).
46 . The pharmaceutical composition of claim 44 , wherein the suspension is for intravenous administration (e.g., the suspension comprises PBS).
47 . The pharmaceutical composition of claim 44 , wherein the suspension is for intraperitoneal administration (e.g., the suspension comprises PBS).
48 . The pharmaceutical composition of claim 44 , wherein the suspension is for intratumoral administration (e.g., the suspension comprises PBS).
49 . The pharmaceutical composition of any one of claims 44 to 48 , wherein the suspension further comprises a pharmaceutically acceptable excipient.
50 . The pharmaceutical composition of any one of claims 44 to 49 , wherein the suspension further comprises a buffer (e.g., PBS).
51 . The pharmaceutical composition of any one of claims 1 to 50 , wherein the composition comprises a bacterial strain listed in Table 2.
52 . The pharmaceutical composition of any one of claims 1 to 50 , wherein the composition further comprises one or more additional therapeutic agents.
53 . The pharmaceutical composition of any one of claims 1 to 52 for use in treating a disease (e.g., a cancer, an autoimmune disease, an inflammatory disease, a dysbiosis, and/or a metabolic disease).
54 . Use of a pharmaceutical composition of any one of claims 1 to 52 for the preparation of a medicament for the treatment of a disease (e.g., a cancer, an autoimmune disease, an inflammatory disease, a dysbiosis, and/or a metabolic disease).
55 . A method of treating a subject (e.g., human), comprising administering to the subject a pharmaceutical composition of any one of claims 1 - 52 .
56 . The method of claim 55 , wherein the subject is in need of treatment for a cancer.
57 . The method of claim 55 , wherein the subject is in need of treatment for an inflammatory disease.
58 . The method of claim 55 , wherein the subject is in need of treatment for a dysbiosis.
59 . The method of claim 55 , wherein the subject is in need of treatment for an autoimmune disease.
60 . The method of claim 55 , wherein the subject is in need of treatment for a metabolic disease.
61 . The method of any one of claims 55 to 60 , wherein the pharmaceutical composition is administered in combination with an additional therapeutic agent.
62 . The method of any one of claims 55 to 61 , wherein the pharmaceutical composition is administered intravenously.
63 . The method of any one of claims 55 to 61 , wherein the pharmaceutical composition is administered intratumorally.
64 . The method of any one of claims 55 to 61 , wherein the pharmaceutical composition is administered subtumorally.
65 . The method of any one of claims 55 to 61 , wherein the pharmaceutical composition is administered by injection, e.g., subcutaneous, intradermal, or intraperitoneal injection.
66 . The method of any one of claims 55 to 65 , wherein the composition further comprises one or more additional therapeutic agents.
67 . The method of any one of claims 55 to 66 , wherein the pharmaceutical composition is administered orally.
68 . The method of any one of claims 55 to 67 , wherein the dose of mEVs in the pharmaceutical composition is about 2×10 6 to about 2×10 16 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)).
69 . The method of any one of claims 55 to 67 , wherein the dose of mEVs in the pharmaceutical composition is 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA assay).
70 . The method of any one of claims 55 to 68 , wherein the pharmaceutical composition is administered once a day.
71 . The method of any one of claims 55 to 68 , wherein the pharmaceutical composition is administered twice a day.
72 . The method of any one of claims 55 to 68 , wherein the pharmaceutical composition is formulated for a daily dose.
73 . The method of any one of claims 55 to 68 , wherein the pharmaceutical composition is formulated for twice a day dose, wherein each dose is half of the daily dose.
74 . A method for preparing a pharmaceutical composition comprising mEVs (e.g., a therapeutically effective amount thereof) of any one of claims 1 - 52 in a suspension, the method comprising: combining mEVs with a pharmaceutically acceptable buffer (e.g., PBS); thereby preparing the pharmaceutical composition.
75 . The method of claim 74 , wherein the suspension further comprises sucrose or glucose.
76 . The method of claim 74 or 75 , wherein the suspension is for oral administration.
77 . The method of claim 74 or 75 , wherein the suspension is for intravenous administration.
78 . The method of claim 74 or 75 , wherein the suspension is for intraperitoneal administration.
79 . The method of claim 74 or 75 , wherein the suspension is for intratumoral administration.
80 . The method of any one of claims 74 to 79 , wherein the suspension further comprises a pharmaceutically acceptable excipient.
81 . The method of any one of claims 74 to 80 , wherein the suspension further comprises a buffer (e.g., PBS).
82 . The method of any one of claims 74 to 81 , wherein the composition further comprises one or more additional therapeutic agents.
83 . The method of any one of claims 74 to 82 , wherein the pharmaceutical composition is administered orally.
84 . The method of any one of claims 74 to 82 , wherein the pharmaceutical composition is administered intravenously.
85 . The method of any one of claims 74 to 82 , wherein the pharmaceutical composition is administered intratumorally.
86 . The method of any one of claims 74 to 82 , wherein the pharmaceutical composition is administered subtumorally.
87 . The method of any one of claims 74 to 82 , wherein the pharmaceutical composition is administered by injection, e.g., subcutaneous, intradermal, or intraperitoneal injection.
88 . The method of any one of claims 74 to 87 , wherein the dose of mEVs in the pharmaceutical composition is about 2×10 6 to about 2×10 16 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)).
89 . The method of any one of claims 74 to 87 , wherein the dose of mEVs in the pharmaceutical composition is 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA assay).
90 . A pharmaceutical composition prepared by the method of any one of claims 74 to 89 .
91 . A method for preparing a pharmaceutical composition comprising mEVs (e.g., a therapeutically effective amount thereof) in a solid dose form, the method comprising:
a) combining mEVs of any one of claims 1 - 52 with a pharmaceutically acceptable excipient; and
b) compressing the mEVs and pharmaceutically acceptable excipient; thereby preparing the pharmaceutical composition.
92 . The method of claim 91 , wherein the method further comprises enterically coating the solid dose form.
93 . The method of claim 91 or 92 , wherein the solid dose form comprises a tablet, a minitablet, a capsule, a pill, or a powder, or a combination of the foregoing.
94 . The method of any one of claims 91 to 93 , wherein the composition further comprises one or more additional therapeutic agents.
95 . The method of any one of claims 91 to 94 , wherein the pharmaceutical composition is administered orally.
96 . The method of any one of claims 91 to 95 , wherein the dose of mEVs in the pharmaceutical composition is about 2×10 6 to about 2×10 16 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)).
97 . The method of any one of claims 91 to 95 , wherein the dose of mEVs in the pharmaceutical composition is 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA assay).
98 . A pharmaceutical composition prepared by the method of any one of claims 91 to 97 .