BIOFILM FORMATION TO DEFINE RISK FOR COLON CANCER

• US 20160223553A1
• Filed: 09/11/2014
• Published: 08/04/2016
• Est. Priority Date: 09/12/2013
• Status: Active Grant

• Current Assignee: Johns Hopkins University
• Original Assignee: Johns Hopkins University
• Inventors: Dejea, Christine, Wick, Elizabeth, Sears, Cynthia L., Pardoll, Drew M.
• Granted Patent: US 10,203,329 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61K 31/165 having aromatic rings, e.g. colchicine, atenolol, progabide
• CPC Class Codes: A61K 31/407 condensed with other heterocyclic ring systems, e.g. ketorolac, physostigmine
• CPC Class Codes: A61K 31/43 Compounds containing 4-thia-1-azabicyclo [3.2.0] heptane ring systems, i.e. compounds containing a ring system of the formula , e.g. penicillins, penems
• CPC Class Codes: A61K 31/546 containing further heterocyclic rings, e.g. cephalothin
• CPC Class Codes: A61K 31/7048 having oxygen as a ring hetero atom, e.g. leucoglucosan, hesperidin, erythromycin, nystatin , digitoxin or digoxin
• CPC Class Codes: A61K 31/7056 containing five-membered rings with nitrogen as a ring hetero atom
• 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 35/744 Lactic acid bacteria, e.g. enterococci, pediococci, lactococci, streptococci or leuconostocs
• 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: A61P 35/00 Antineoplastic agents
• 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 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: G01N 2800/50 Determining the risk of developing a disease
• CPC Class Codes: G01N 2800/7028 Cancer
• CPC Class Codes: G01N 33/57419 of colon

Abstract

Methods of identifying subjects at increased risk of cancer, based upon detection of biofilms and/or biofilm-associated microbes within a subject, are disclosed. Therapies designed to prevent formation and/or reduce the size of biofilms in a subject identified to be at increased risk of cancer based upon detection of biofilms and/or biofilm-associated microbes are disclosed. In particular embodiments, the invention provides for identification of a subject at elevated risk of developing or having colorectal cancer and/or a colorectal adenoma, based upon detection of a biofilm and/or biofilm-associated bacteria within the gastrointestinal tract of the subject (optionally, within a biopsy specimen and/or stool sample of such subject). Therapies involving administration of an antibiotic agent and/or a probiotic agent to a subject, to prevent or reduce biofilm formation within the gastrointestinal tract of the subject, optionally provided in combination with additional cancer therapy, are also disclosed.

Claims

1. A method for treating or preventing a neoplastic condition in a subject comprising:

(i) detecting a bacterial biofilm within the gastrointestinal tract of a subject; and

(ii) administering an antimicrobial agent or a probiotic agent to said subject in an amount effective to reduce the size of said bacterial biofilm,

thereby treating or preventing a neoplastic condition in said subject.

2. The method of claim 1, wherein said neoplastic condition is selected from the group consisting of a colorectal cancer and a colorectal adenoma.

3. The method of claim 1, wherein said bacterial biofilm is detected within the colon of said subject.

4. The method of claim 1, wherein said bacterial biofilm has invaded the mucus layer of said gastrointestinal tract of said subject.

5. The method of claim 1, wherein said bacterial biofilm occupies a linear distance of at least 200 μ

m of the epithelial surface.

6. The method of claim 1, wherein the density of bacteria in said bacterial biofilm is at least 10⁸ bacteria/ml.

7. The method of claim 1, wherein said bacterial biofilm comprises a bacteria selected from the group consisting of Bacteroidetes, Firmicutes, Gammaproteobacteria, Fusobacteria, and Lachnospiraceae.

8. The method of claim 7, wherein said Lachnospiraceae is selected from the group consisting of Clostridium, Ruminococcus, and Butyrivibrio.

9. The method of claim 1, wherein said bacterial biofilm comprises a Fusobacteria-dominant microbiota membership.

10. The method of claim 1, wherein said detecting step comprises colonoscopy or administering a bacteria visualizing agent or biofilm visualizing agent to said subject or a sample of said subject.

14. The method of claim 1, wherein said detecting step comprises administering a FISH probe or other bacteria labeling agent or label of the polymeric biofilm matrix to the colon mucosa of said subject, optionally during colonoscopy.

15. The method of claim 1, wherein said antimicrobial agent is an antibiotic, wherein said antibiotic is selected from the group consisting of clindamycin, beta lactams (including but not limited to carbenicillin, cefoperazone, cefamandole, penicillin), macrolides (including but not limited to erythromycin), chloramphenicol, aminoglycosides, fluoroquinolones, carbapenems and sulbactam.

17. The method of claim 1, wherein said probiotic agent comprises one or more species of selected from the group consisting of Bacteroides, Prevotella, Porphyromonas, Fusobacterium, Sutterella, Bilophila, Campylobacter, Wolinella, Butyrovibrio, Megamonas, Desulfomonas, Desulfovibrio, Bifidobacterium, Lactobacillus, Eubacterium, Actinomyces, Eggerthella, Coriobacterium, Propionibacterium, other genera of non-sporeforming anaeroibic gram-positive bacilli, Bacillus, Peptostreptococcus (and newly created genera originally in Peptostreptococcus), Peptococcus, Acidaminococcus, Ruminococcus, Megasphaera, Gaffkya, Coprococcus, Veillonella, Sarcina, certain of the species of Clostridium, Aerococcus, Streptococcus, Enterococcus, Pediococcus, Micrococcus, Staphylococcus, Corynebacterium, and species of the genera comprising the Enterobacteriaceae and Pseudomonadaceae.

18. The method of claim 1, wherein said detecting step comprises identification of bacterial species or polymeric biofilm matrix within a sample of said subject, wherein said sample of said subject is a colonic biopsy sample or a stool sample, wherein said identification comprises detection of bacterial DNA or RNA sequences or polymeric biofilm matrix.

21. The method of claim 1, wherein said antimicrobial agent reduces colon epithelial proliferation or increases apoptosis in the colon cells of said subject, optionally in colon tumor cells of said subject.

22. The method of claim 1, wherein said detecting step comprises identification of an aggregated association of Bacterioidetes, Firmicutes, Proteobacteria, Lahnospiracae, Fusobacteria, Lactococcus, Leuconostoc, Comamonas or other Burkholderiales in said subject.

23. The method of claim 1, wherein said detecting step comprises identification of a reduced level of a candidate Ruminococcaceae member, Bacilli or Bacteroidetes in said subject.

24. The method of claim 1, further comprising administering a chemotherapeutic agent to said subject.

11. (canceled)

12. The method of claim 11, wherein said bacteria visualizing agent or biofilm visualizing agent is a FISH probe or other bacteria labeling agent or labeling agent taken up by polymeric matrix of the biofilm, wherein said FISH probe or other bacteria labeling agent or labeling agent taken up by polymeric matrix of the biofilm is selected from FIG. 11.

13. (canceled)

16. (canceled)

19. (canceled)

20. (canceled)

25. A method for identifying a subject at increased risk of developing cancer comprising detecting a bacterial biofilm within the gastrointestinal tract of a subject, thereby identifying a subject at increased risk of developing cancer;

or

A method for treating or preventing cancer in a subject comprising administering an antimicrobial agent or a probiotic agent to a subject harboring a bacterial biofilm within the gastrointestinal tract of said subject, wherein said antimicrobial agent or probiotic agent reduces or eliminates the presence of a said biofilm, thereby treating or preventing cancer in said subject;

or

A kit for identifying the presence of a biofilm within the gastrointestinal tract of a subject comprising a bacteria visualizing agent or a biofilm visualizing agent, and instructions for its use.

26. (canceled)

27. (canceled)