BACTERIA ENGINEERED TO TREAT DISEASES THAT BENEFIT FROM REDUCED GUT INFLAMMATION AND/OR TIGHTENED GUT MUCOSAL BARRIER

• US 20170067065A1
• Filed: 09/08/2016
• Published: 03/09/2017
• Est. Priority Date: 12/22/2014
• Status: Active Grant

• Current Assignee: Synlogic Operating Company, Inc. (Synlogic, Inc.)
• Original Assignee: Synlogic, Inc.
• Inventors: Isabella, Vincent M., Millet, Yves, Fisher, Adam, Falb, Dean, Kotula, Jonathan W., Miller, Paul F.
• Granted Patent: US 11,384,359 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61K 2035/115 Probiotics
• CPC Class Codes: A61K 31/19 Carboxylic acids, e.g. valproic acid salicylic acid A61K31/60
• CPC Class Codes: A61K 31/198 Alpha-amino acids, e.g. alanine or edetic acid [EDTA] betaine A61K31/205; proline A61K31/401; tryptophan A61K31/405; histidine A61K31/4172; peptides not degraded to individual amino acids A61K38/00
• CPC Class Codes: A61K 35/741 Probiotics probiotic yeast, e.g. saccharomyces A61K36/06
• CPC Class Codes: A61K 38/20 Interleukins [IL]
• CPC Class Codes: A61K 38/2013 IL-2
• CPC Class Codes: A61K 38/2066 IL-10
• CPC Class Codes: A61K 38/26 Glucagons
• CPC Class Codes: A61K 38/446 Superoxide dismutase (1.15)
• CPC Class Codes: C12N 15/70 Vectors or expression systems specially adapted for E. coli
• CPC Class Codes: C12N 9/001 acting on the CH-CH group of donors (1.3)
• CPC Class Codes: C12N 9/1217 Phosphotransferases with a carboxyl group as acceptor (2.7.2)
• CPC Class Codes: C12Y 103/08001 Butyryl-CoA dehydrogenase (1.3.8.1), i.e. short chain acyl-CoA dehydrogenase
• CPC Class Codes: C12Y 115/01001 Superoxide dismutase (1.15.1.1)
• CPC Class Codes: C12Y 207/02007 Butyrate kinase (2.7.2.7)
• CPC Class Codes: Y02A 50/30 Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

Genetically engineered bacteria, pharmaceutical compositions thereof, and methods of treating or preventing autoimmune disorders, inhibiting inflammatory mechanisms in the gut, and/or tightening gut mucosal barrier function are disclosed.

Claims

1. A bacterium comprising a non-native gene cassette for producing butyrate, wherein the gene cassette is operably linked to a directly or indirectly inducible promoter that is induced by exogenous environmental conditions found in a mammalian gut.

2. The bacterium of claim 1, wherein the promoter is induced under low-oxygen or anaerobic conditions.

3. The bacterium of claim 2, wherein the promoter is a FNR-responsive promoter, an ANR-responsive promoter, or a DNR-responsive promoter.

4. The bacterium of claim 3, wherein the promoter is a FNR-responsive promoter.

5. The bacterium of claim 1, wherein the promoter is induced by the presence of reactive nitrogen species.

6. The bacterium of claim 5, wherein the promoter is a NsrR-responsive promoter, NorR-responsive promoter, or a DNR-responsive promoter.

7. The bacterium of claim 1, wherein the promoter is induced by the presence of reactive oxygen species.

8. The bacterium of claim 7, wherein the promoter is a OxyR-responsive promoter, PerR-responsive promoter, OhrR-responsive promoter, SoxR-responsive promoter, or a RosR-responsive promoter.

9. The bacterium of claim 1, wherein the non-native gene cassette for producing butyrate is located on a chromosome in the bacterium.

10. The bacterium of claim 1, wherein the non-native gene cassette for producing butyrate is located on a plasmid in the bacterium.

11. The bacterium of claim 1, wherein the bacterium is a probiotic bacterium.

12. The bacterium of claim 11, wherein the bacterium is selected from the group consisting of Bacteroides, Bifidobacterium, Clostridium, Escherichia, Lactobacillus, and Lactococcus.

13. The bacterium of claim 12, wherein the bacterium is Escherichia coli strain Nissle.

14. The bacterium of claim 1, wherein the bacterium is an auxotroph in a gene that is complemented when the bacterium is present in a mammalian gut.

15. The bacterium of claim 14, wherein the bacterium is an auxotroph in diaminopimelic acid or an enzyme in the thymidine biosynthetic pathway.

16. The bacterium of claim 1, further comprising one or more non-native gene(s) or gene cassette(s) for producing an anti-inflammation and/or gut barrier enhancer molecule selected from propionate, acetate, IL-10, IL-22, and GLP-2, wherein the gene(s) or gene cassette(s) is operably linked to a directly or indirectly inducible promoter that is induced by exogenous environmental conditions found in a mammalian gut.

17. The bacterium of claim 16, wherein the bacterium is an auxotroph in a gene that is complemented when the bacterium is present in a mammalian gut.

18. A pharmaceutically acceptable composition comprising the bacterium of claim 1;

and a pharmaceutically acceptable carrier.

19. A method of treating a disease or condition associated with gut inflammation and/or compromised gut barrier function comprising the step of administering to a patient in need thereof, the composition of claim 18.

20. The method of claim 19, wherein the disease or condition is selected from an inflammatory bowel disease, including Crohn'"'"'s disease and ulcerative colitis, and a diarrheal disease.