HUMAN-DERIVED BACTERIA THAT INDUCE PROLIFERATION OR ACCUMULATION OF REGULATORY T CELLS

• US 20140341921A1
• Filed: 11/29/2012
• Published: 11/20/2014
• Est. Priority Date: 12/01/2011
• Status: Active Grant

• Current Assignee: School Corporation Azabu Veterinary Medicine Educational Institution, University of Tokyo
• Original Assignee: School Corporation Azabu Veterinary Medicine Educational Institution, University of Tokyo
• Inventors: Honda, Kenya, Atarashi, Koji, Tanoue, Takeshi, Hattori, Masahira, Morita, Hidetoshi
• Granted Patent: US 10,238,694 B2
• Time in Patent Office: Days
• US Class Current: 424/141.1
• CPC Class Codes: A61K 2035/11 Medicinal preparations comprising living procariotic cells
• CPC Class Codes: A61K 35/74 Bacteria therapeutic use of a bacterial protein A61K38/00
• CPC Class Codes: A61K 35/741 Probiotics probiotic yeast, e.g. saccharomyces A61K36/06
• CPC Class Codes: A61K 35/742 Spore-forming bacteria, e.g. Bacillus coagulans, Bacillus subtilis, clostridium or Lactobacillus sporogenes
• CPC Class Codes: A61K 35/745 Bifidobacteria
• CPC Class Codes: A61K 35/747 Lactobacilli, e.g. L. acidophilus or L. brevis
• CPC Class Codes: A61K 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61K 9/0053 Mouth and digestive tract, i.e. intraoral and peroral administration rectal administration A61K9/0031
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 33/00 Antiparasitic agents
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 37/08 Antiallergic agents antiasthmatic agents A61P11/06; ophthalmic antiallergics A61P27/14
• CPC Class Codes: C12N 1/20 Bacteria; Culture media therefor
• CPC Class Codes: C12N 1/205 Bacterial isolates
• CPC Class Codes: C12Q 1/04 Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor C12Q1/6897 takes precedence
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12R 2001/145 Clostridium
• 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

Species of human-derived bacteria belonging to the Clostridia class have been shown to induce accumulation of regulatory T cells (Treg cells) in the colon and suppress immune functions. Pharmaceutical compositions containing these bacteria can be used to prevent and treat immune-mediated diseases such as autoimmune diseases.

Claims

1. A composition that induces proliferation and/or accumulation of regulatory T cells, the composition comprising:

(a) one or more bacteria of the Clostridia class;

(b) a culture supernatant of one or more bacteria of (a);

(c) one or more physiologically active substance derived from (a) or (b);

or

(d) a combination of any 2 or 3 of (a), (b) and (c).

2. The composition of claim 1, wherein the one or more bacteria of (a) are human-derived commensal bacteria (species) belonging to Clostridium Cluster IV and Clostridium Cluster XIVa.

3. The composition of claim 1, wherein the one or more bacteria of (a) is one or more human-derived commensal bacteria (species) belonging to Clostridium Cluster XIVa

4. The composition of claim 1, wherein (a) is selected from the group consisting of:

Clostridium saccharogumia, Clostridium ramosum JCM1298, Clostridium ramosum, Flavonifractor plautii, Pseudoflavonifractor capillosus ATCC 29799, Clostridium hathewayi, Clostridium saccharolyticum WM1, Bacteroides sp. MANG, Clostridium saccharolyticum, Clostridium scindens, Lachnospiraceae bacterium 5_—

1_—

57 FAA, Lachnospiraceae bacterium 6_—

1_—

63 FAA, Clostridium sp. 14616, Clostridium bolteae ATCC BAA-613, cf. Clostridium sp. MLG055, Erysipelotrichaceae bacterium 2_—

2_—

44A, Clostridium indolis, Anaerostipes caccae, Clostridium bolteae, Lachnospiraceae bacterium DJF_VP30, Lachnospiraceae bacterium 3_—

1_—

57 FAA_CT1, Anaerotruncus colihominis, Anaerotruncus colihominis DSM 17241, Ruminococcus sp. ID8, Lachnospiraceae bacterium 2_—

1_—

46 FAA, Clostridium lavalense, Clostridium asparagiforme DSM 15981, Clostridium symbiosum, Clostridium symbiosum WAL-14163, Eubacterium contortum, Clostridium sp. D5, Oscillospiraceae bacterium NML 061048, Oscillibacter valericigenes, Lachnospiraceae bacterium A4, Clostridium sp. 316002/08, Clostridiales bacterium 1_—

7_—

47 FAA, Blautia cocoides, and Anaerostipes caccae DSM 14662.

5. The composition of claim 1, wherein (a) is selected from the group consisting of:

Clostridium saccharogumia, Clostridium ramosum JCM1298, Flavonifractor plautii, Pseudoflavonifractor capillosus ATCC 29799, Clostridium hathewayi, Clostridium saccharolyticum WM1, Bliautia coccoides, Lachnospiraceae bacterium 6_—

1_—

63 FAA, Clostridium sp. Clostridium bolteae ATCC BAA-613, cf. Clostridium sp. MLG055, Erysipelotrichaceae bacterium 2_—

2_—

44A, Clostridium indolis, Anaerostipes caccae DSM 14662, Anaerotruncus colihominis, Anaerotruncus colihominis DSM 17241, Ruminococcus sp. ID8, Lachnospiraceae bacterium 2_—

1_—

46 FAA, Clostridium lavalense, Clostridium asparagiforme DSM 15981, Clostridium symbiosum, Clostridium symbiosum WAL-14163, Clostridium ramosum, Eubacterium contortum, Clostridium sp. D5, Clostridium scindens, Lachnospiraceae bacterium 5_—

1_—

57 FAA, Lachnospiraceae bacterium A4, Lachnospiraceae bacterium 3_—

1_—

57 FAA_CT1, Clostridium sp. 316002/08, and Clostridiales bacterium 1_—

7_—

47FAA.

10. The composition according to claim 1, wherein the regulatory T cells are transcription factor Foxp3-positive regulatory T cells, IL-10-producing regulatory T cells, or Helios-negative Foxp3-positive regulatory T cell.

11. The composition according to claim 1, wherein the composition has an immunosuppressive effect.

12. A pharmaceutical composition comprising a composition according to claim 1 and a pharmaceutically acceptable component.

13. A method of inducing proliferation, accumulation or both proliferation and accumulation of regulatory T cells in an individual in need thereof, comprising administering, to the individual, a composition of claim 1.

16. A method of increasing the levels of regulatory T cells in an individual undergoing a course of Gram+ antibiotics, comprising administering a composition of claim 1 to the individual.

17. The method according to claim 13, further comprising measuring the induction of proliferation or accumulation of regulatory T cells in the individual using a measurement selected from the group consisting of expression of Fop3 Tregs, promotion of IL-10 expression, promotion of CTLA4 expression, promotion of IDO expression, and suppression of IL-4 expression.

18. A method of treating, aiding in treating, reducing the severity of, or preventing at least one disease selected from an autoimmune disease, an inflammatory disease, an allergic disease, and an infectious disease in an individual in need thereof, the method comprising administering the composition of claim 1 to the individual.

19. A method of selecting an individual for treatment with a composition according to claim 1, comprising:

(a) obtaining a (at least one) sample, such as a fecal sample or a colonic biopsy from an individual;

(b) measuring in the individual'"'"'s sample the percentages or absolute counts of bacterial species that belong to Clostridium Clusters IV and XIVa, thereby obtaining a measurement for the individual;

(c) comparing the measurement of (b) with a corresponding measurement obtained from a sample from a healthy individual; and

(d) selecting the individual for treatment with the composition according to claim 1 if the measurement obtained in (b) is smaller than the measurement obtained from a sample from a healthy individual.

6. A composition that induces proliferation and/or accumulation of regulatory T cells, the composition comprising, as an active component:

(a) bacteria that contain DNA comprising a nucleotide sequence that has at least 90% homology with a DNA sequence designated herein as OTU136;

OTU46;

OTU221;

OTU9;

OTU296;

OTU21;

OTU166;

OTU73;

OTU174;

OTU14;

OTU55;

OTU337;

OTU314;

OTU195;

OTU306;

OTU87;

OTU86;

OTU152;

OTU253;

OTU259;

OTU281;

OTU288;

OTU334;

OTU359;

OTU362;

or OTU367; and

DNA comprising a nucleotide sequence that has a percent homology of at least 90% with DNA of one or more of the following;

Clostridium saccharogumia, Clostridium ramosum JCM1298, Clostridium ramosum, Flavonifractor plautii, Pseudoflavonifractor capillosus ATCC 29799, Clostridium hathewayi, Clostridium saccharolyticum WM1, Bacteroides sp. MANG, Clostridium saccharolyticum, Clostridium scindens, Lachnospiraceae bacterium 5_—

1_—

57 FAA, Lachnospiraceae bacterium 6_—

1_—

63FAA, Clostridium sp. 14616, Clostridium bolteae ATCC BAA-613, cf. Clostridium sp. MLG055, Erysipelotrichaceae bacterium 2_—

2_—

44A, Clostridium indolis, Anaerostipes caccae, Clostridium bolteae, Lachnospiraceae bacterium DJF_VP30, Lachnospiraceae bacterium 3_—

1_—

57 FAA_CT1, Anaerotruncus colihominis, Anaerotruncus colihominis DSM 17241, Ruminococcus sp. ID8, Lachnospiraceae bacterium 2_—

1_—

46 FAA, Clostridium lavalense, Clostridium asparagiforme DSM 15981, Clostridium symbiosum, Clostridium symbiosum WAL-14163, Eubacterium contortum, Clostridium sp. D5, Oscillospiraceae bacterium NML 061048, Oscillibacter valericigenes, Lachnospiraceae bacterium A4, Clostridium sp. 316002/08, Clostridiales bacterium 1_—

7_—

47 FAA, Blautia cocoides, or Anaerostipes caccae DSM 14662;

(b) a culture supernatant of one or more bacteria of (a);

(c) one or more physiologically active substance derived from (a) or (b);

or

(d) a combination of any 2 or 3 of (a), (b) and (c).

7. The composition of claim 6, wherein the percent homology is at least 97%.

8. A composition that induces proliferation and/or accumulation of regulatory T cells, the composition comprising at least two organisms and/or substances selected from the group consisting of:

(a) Clostridium saccharogumia, Clostridium ramosum JCM1298, Clostridium ramosum, Flavonifractor plautii, Pseudoflavonifractor capillosus ATCC 29799, Clostridium hathewayi, Clostridium saccharolyticum WM1, Bacteroides sp. MANG, Clostridium saccharolyticum, Clostridium scindens, Lachnospiraceae bacterium 5_—

1_—

57 FAA, Lachnospiraceae bacterium 6_—

1_—

63FAA, Clostridium sp. 14616, Clostridium bolteae ATCC BAA-613, cf. Clostridium sp. MLG055, Erysipelotrichaceae bacterium 2_—

2_—

44A, Clostridium indolis, Anaerostipes caccae, Clostridium bolteae, Lachnospiraceae bacterium DJFVP30, Lachnospiraceae bacterium 3_—

1_—

57 FAA_CT1, Anaerotruncus colihominis, Anaerotruncus colihominis DSM 17241, Ruminococcus sp. ID8, Lachnospiraceae bacterium 2_—

1_—

46 FAA, Clostridium lavalense, Clostridium asparagiforme DSM 15981, Clostridium symbiosum, Clostridium symbiosum WAL-14163, Eubacterium contortum, Clostridium sp. D5, Oscillospiraceae bacterium NML 061048, Oscillibacter valericigenes, Lachnospiraceae bacterium A4, Clostridium sp. 316002/08, Clostridiales bacterium 1_—

7_—

47 FAA, Blautia cocoides, and Anaerostipes caccae DSM 14662;

(b) a culture supernatant of one or more bacteria of (a);

(c) one or more physiologically active substances derived from (a) or (b);

or

(d) a combination of any 2 or 3 of (a), (b) and (c).

9. (canceled)

14. A method of inducing proliferation, accumulation or both proliferation and accumulation of regulatory T cells in an individual in need thereof, comprising administering, to the individual, at least one organism or substance selected from the group consisting of:

(a) at least one bacterium containing DNA comprising a nucleotide sequence having at least 97% homology with any of SEQ ID NOs. 19 to 44;

(b) at least one physiologically active substance derived from bacteria containing DNA comprising a nucleotide sequence having at least 90% homology with any of SEQ ID NOs. 19 to 44; and

(c) a culture supernatant of one of the following;

Clostridium saccharogumia, Clostridium ramosum JCM1298, Clostridium ramosum, Flavonifractor plautii, Pseudoflavonifractor capillosus ATCC 29799, Clostridium hathewayi, Clostridium saccharolyticum WM1, Bacteroides sp. MANG, Clostridium saccharolyticum, Clostridium scindens, Lachnospiraceae bacterium 5_—

1_—

57 FAA, Lachnospiraceae bacterium 6_—

1_—

63 FAA, Clostridium sp. 14616, Clostridium bolteae ATCC BAA-613, cf. Clostridium sp. MLG055, Erysipelotrichaceae bacterium 2_—

2_—

44A, Clostridium indolis, Anaerostipes caccae, Clostridium bolteae, Lachnospiraceae bacterium DJF_VP30, Lachnospiraceae bacterium 3_—

1_—

57 FAA_CT1, Anaerotruncus colihominis, Anaerotruncus colihominis DSM 17241, Ruminococcus sp. ID8, Lachnospiraceae bacterium 2_—

1_—

46 FAA, Clostridium lavalense, Clostridium asparagiforme DSM 15981, Clostridium symbiosum, Clostridium symbiosum WAL-14163, Eubacterium contortum, Clostridium sp. D5, Oscillospiraceae bacterium NML 061048, Oscillibacter valericigenes, Lachnospiraceae bacterium A4, Clostridium sp. 316002/08, Clostridiales bacterium 1_—

7_—

47 FAA, Blautia cocoides, and Anaerostipes caccae DSM 14662.

15. The method of claim 14, further comprising administering to the individual a substance selected from the group consisting of almond skin, inulin, oligofructose, raffinose, lactulose, pectin, hemicellulose, amylopectin, acetyl-Co A, biotin, beet molasses, yeast extracts, resistant starch, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, immunosuppressive drugs, cyclosporin A, mercaptopurine, azathiopurine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anti-cholinergic drugs for rhinitis, anti-cholinergic decongestants, mast-cell stabilizers, monoclonal anti-IgE antibodies, vaccines, anti-TNF inhibitors, and combinations thereof.

20. A method of selectin g a bacterium that induces proliferation and/or accumulation of regulatory T cells, comprising

(a) isolating the bacterial spore-forming fraction from a fecal or biopsy sample obtained from a mammal;

(b) plating serial dilutions of the isolated spore-forming fraction, and

(c) picking a single colony from the culture plate.

26. The process of claim 20, wherein the single colony picked in (c) induces proliferation and/or accumulation of regulatory T cells by measuring one or more of:

the expression of Fop3 Tregs, promotion of IL-10 expression, promotion of CTLA4 expression, promotion of IDO expression, and/or suppression of IL-4 expression as an index of the ability to induce proliferation or accumulation of regulatory T cells.

21-25. -25. (canceled)