Patent Application
20130121966
The invention relates to treatments B. fragilis. More particularly this invention relates to the generation of PSA only producing mutant strains of B. fragilis.
Bacteroides fragilis produces at least 8 different capsular polysaccharides. In order to facilitate purification of PSA from the other 7 capsular polysaccharides. Others have engineered a PSA producing strain employed mutation of a regulatory gene that controls the transcription of polysaccharide production genes, but left the actual genes that are required for all capsular polysaccharide synthesis intact. However, subsequent to the creation of this strain, it was shown that secondary mutations could cause reversion to polysaccharide production (1).
We created a novel bacterial strain for the production of Polysaccharide A (PSA). In order to facilitate purification of PSA from the other 7 capsular polysaccharides, we devised a strategy to mutate the genes required for production of all known polysaccharides except PSA. This was accomplished by DNA recombination (as described below) to delete the genes that encode for proteins that synthesize all non-PSA polysaccharides, ensuring that additional mutations would not restore production of other polysaccharides. The previous strategy to engineer a PSA producing strain employed mutation of a regulatory gene that controls the transcription of polysaccharide production genes, but left the actual genes that are required for all capsular polysaccharide synthesis intact.
However, subsequent to the creation of this previous strain, it was shown that secondary mutations could cause reversion to polysaccharide production (1). The current approach of deleting the genes that are required for polysaccharide production would overcome this potential shortcoming, and ensure a strain that is stable in this genotype and phenotype.
In an embodiment an isolated B. fragilis bacterial cell producing a native capsular polysaccharide A (PSA) is provided, wherein the cell is incapable of producing capsular polysaccharides PSB, PSC, PSD, PSE, PSF, PSG, and PSH.
In an aspect of any embodiments described herein, the cell's biosynthetic genes for native capsular polysaccharides PSB, PSC, PSD, PSE, PSF, PSG, and PSH have been deleted from the cell's genome.
In yet another aspect of any embodiments described herein, a promoter that controls expression of PSA has not been modified.
In an aspect of any embodiments described herein, the PSA promoter has one or more repeat flanking regions surrounding the promoter, and wherein said flanking regions have not been modified.
In yet another aspect of any embodiments described herein, the cell is administered, as part of a pharmaceutical, to individuals suffering from an inflammatory disease or condition.
In an aspect of any embodiments described herein a composition is provided comprising a bacterial extract or cellular fraction obtained from a B. fragilis bacterial cell that produces a native capsular polysaccharide A (PSA) wherein the cell is incapable of producing capsular polysaccharides PSB, PSC, PSD, PSE, PSF, PSG, and PSH, wherein the cell's biosynthetic genes for native capsular polysaccharides PSB, PSC, PSD, PSE, PSF, PSG, and PSH have been deleted from the cell's genome.
In yet another aspect of any embodiments described herein, a method to treat an individual with inflammation is provided comprising administering to said individual an effective amount of a pharmaceutical comprising an isolated B. fragilis bacterial cell, or an extract or cellular fraction of said cell, wherein the cell produces a native capsular polysaccharide A (PSA); and wherein the cell's biosynthetic genes for native capsular polysaccharides PSB, PSC, PSD, PSE, PSF, PSG, and PSH have been deleted from the cell's genome.
In yet another aspect of any embodiments described herein, the cellular fraction is an outer membrane vesicular fraction.
A “promoter controlling expression of a capsular polysaccharide” as used herein refers to a nontranscribed genetic element associated with and controlling the transcription of a capsular polysaccharide biosynthesis gene. The capsular polysaccharide biosynthesis gene can occur as part of a polycistronic capsular polysaccharide biosynthesis locus. A given promoter can regulate transcription of one or more capsular polysaccharide biosynthesis genes within the associated capsular polysaccharide biosynthesis gene locus. The promoter can include inverted repeat regions separated by intervening sequence. In one embodiment the promoter is contained between inverted repeat regions in the intervening sequence and is subject to inversion such that in one orientation the promoter is transcriptionally active (“on”) with respect to the capsular polysaccharide biosynthesis gene, while in the opposite or flipped orientation the promoter is transcriptionally inactive (“off”) with respect to the capsular polysaccharide biosynthesis gene.
The term “native” when used in connection with biological materials such as nucleic acid molecules, polypeptides, host cells, bacterial cells/strains and the like, refers to materials as they are found in nature and not manipulated by man.
The term “isolated” when used in connection biological materials such as nucleic acid molecules, polypeptides, bacterial cells, host cells, bacterial cells/strains and the like, refers to the isolated or purified aforementioned materials, where these materials do not occur naturally and/or where they have markedly different or distinctive characteristics compared to those found in the native material.
The wording “polysaccharide A” (or PSA, or PSA ligand) as used herein indicates a molecule produced by the PSA locus of Bacteroides fragilis and derivatives thereof which include but are not limited to polymers of the repeating unit {→3) α-d-AAT Galp(1→4)-[β-d-Galf (1→3)] α-d-GalpNAc(1→3)- [4,6-pyruvate]-β-d-Galp(1→}, where AATGa is acetamido-amino-2,4,6-trideoxygalactose, and the galactopyranosyl residue is modified by a pyruvate substituent spanning O-4 and O-6. The term “derivative” as used herein with reference to a first polysaccharide (e.g., PSA), indicates a second polysaccharide that is structurally related to the first polysaccharide and is derivable from the first polysaccharide by a modification that introduces a feature that is not present in the first polysaccharide while retaining functional properties of the first polysaccharide. Accordingly, a derivative polysaccharide of PSA, usually differs from the original polysaccharide by modification of the repeating units or of the saccharidic component of one or more of the repeating units that might or might not be associated with an additional function not present in the original polysaccharide. A derivative polysaccharide of PSA retains however one or more functional activities that are herein described in connection with PSA in association with the anti-inflammatory activity of PSA.
In one embodiment, low molecular weight PSA (L-PSA), as used herein, refers to PSA molecule with a molecular weight from 70 kDa to 200 kDa; and high molecular weight PSA (H-PSA), as used herein, refers to PSA molecule whose molecular weight is above 200 kDa.
In particular, in embodiments where the isolated bacterial strain/cell disclosed in this application, or OMV or PSA obtained from said strain, is used as an anti-inflammatory compound, the condition can be any condition associated to an inflammation or inflammatory response; or a condition described as an inflammatory disease itself. The wording “associated to” as used herein with reference to two items indicates a relation between the two items such that the occurrence of a first item is accompanied by the occurrence of the second item, which includes but is not limited to a cause-effect relation and sign/symptoms-disease relation.
Conditions associated with an inflammation (or inflammatory diseases) in humans include but are not limited to inflammatory bowel disease, including but not limited to Crohn's disease and ulcerative colitis, asthma, dermatitis, arthritis, myasthenia gravis, Grave's disease, multiple sclerosis (MS), type I diabetes, type 2 diabetes, food allergy, and psoriasis. A person of skill in the art would be able to identify such subjects suffering from the aforementioned diseases using the appropriate clinical criteria.
In one embodiment, compositions, extracts, or pharmaceutical composition comprising the isolated bacterial strain/cell disclosed in this application or OMVs, extracts, or PSA obtained from said strain, can be used to treat or prevent inflammatory diseases, such as, but not limited to, inflammatory bowel disease (including Crohn's disease and ulcerative colitis), asthma, dermatitis, arthritis, myasthenia gravis, Grave's disease, multiple sclerosis, and psoriasis.
The term “treatment” or “treated” as used herein indicates any activity whether part of a medical care, or not, for or deals with a condition medically or surgically in animals or humans. Such treatments can be administered by either medical or non-medical personnel.
In some embodiments, where the composition is to be administered to an individual with another compound/drug, and/or a pharmaceutically acceptable or appropriate carrier/vehicle or excipient.
The term “excipient” as used herein indicates an inactive substance used as a pharmaceutically acceptable or appropriate carrier for the active ingredients of a medication. Suitable excipients for the pharmaceutical compositions herein disclosed include any substance that enhances the ability of the body of an individual to absorb vesicles herein described. Suitable excipients also include any substance that can be used to bulk up formulations with vesicles herein described to allow for convenient and accurate dosage. In addition to their use in the single-dosage quantity, excipients can be used in the manufacturing process to aid in the handling of vesicles herein described. Depending on the route of administration, and form of medication, different excipients may be used. Exemplary excipients include but are not limited to antiadherents, binders, coatings disintegrants, fillers, flavors (such as sweeteners) and colors, glidants, lubricants, preservatives, sorbents.
Pharmaceutically acceptable or appropriate carriers can be, but not limited to, organic or inorganic, solid or liquid excipient which is suitable for the selected mode of application such as oral application or injection, and administered in the form of a conventional pharmaceutical preparation. Such preparation includes solid such as tablets, granules, powders, capsules, and liquid such as solution, emulsion, suspension and the like. Said carrier includes starch, lactose, glucose, sucrose, dextrine, cellulose, paraffin, fatty acid glyceride, water, alcohol, gum arabic and the like. If necessary, auxiliary, stabilizer, emulsifier, lubricant, binder, pH adjustor controller, isotonic agent and other conventional additives may be added.
The pharmaceutically acceptable or appropriate carrier may well include other compounds known to be beneficial to an impaired situation of the gut, (e.g., antioxidants, such as Vitamin C, Vitamin E, Selenium or Zinc); or a food composition. The food composition can be, but is not limited to, milk, yoghurt, curd, cheese, fermented milks, milk based fermented products, ice-creams, fermented cereal based products, milk based powders, infant formulae, tablets, liquid bacterial suspensions, dried oral supplement, or wet oral supplement.
An “extract” as used herein indicates either the insoluble material or soluble material obtained from the B. fragilis bacterial cell using various chemical, immunological, biochemical or physical procedures known to those of skill in the art, including but not limited to, precipitation, centrifugation, filtering, column chromatography, and detergent lysis. Extract can also cover PSA, the outer membrane vesicular and/or the supernatant fraction obtained from culturing the said B. fragilis.
The term “diluent” as used herein indicates a diluting agent which is issued to dilute or carry an active ingredient of a composition. Suitable diluent include any substance that can decrease the viscosity of a medicinal preparation.
In certain embodiments, compositions, compounds, and, in particular, pharmaceutical/extract/cell compositions can be formulated for enteral administration including, but not limited to, i) by mouth (orally) as tablets, capsules, or drops; ii) by gastric feeding tube, duodenal feeding tube, or gastrostomy; and enteral nutrition; and iii) rectally as a suppository.
In certain embodiments, the wild type B. fragilis cell, or extracts or PSA derived from the wild type, can be used as pharmaceuticals or food for the above enteral administration to treat or prevent inflammatory diseases, such as, but not limited to, inflammatory bowel disease (including Crohn's disease and ulcerative colitis), asthma, dermatitis, arthritis, myasthenia gravis, Grave's disease, multiple sclerosis, and psoriasis.
In some embodiments, the disclosed bacterial strain/cell, or OMVs derived from either the isolated (as disclosed) or wild type B. fragilis, can be used in a method of treating or preventing a condition in an individual.
The method comprises administering to the individual an effective amount of the composition or pharmaceutical/extract/cell/PSA composition comprising or derived from either the isolated B. fragilis strain (as disclosed here) or wild type B. fragilis; or a combination thereof. The term “individual” as used herein includes a single biological organism wherein inflammation can occur including but not limited to animals and in particular higher animals and in particular vertebrates such as mammals and in particular human beings.
The wild type B. fragilis or the isolated B. fragilis cell, or extracts, OMVs, or PSA derived from wild type or the isolated B. fragilis can be administered as part of or in the form of a nutritional composition, such as but not limited to a beverage, a drink, a bar, a snack, an ice cream, a dairy product, for example a chilled or a shelf-stable dairy product, a confectionery product, a cereal product such as a breakfast cereal, a frozen product intended for consumption after heating in a micro-wave or an oven, a ready-to-eat product, a fast food or a nutritional formula (which encompasses any nutritionally complete or supplementary formulation).
In alternative embodiments, the wild type B. fragilis or the isolated B. fragilis cell, or extracts, OMVs, or PSA derived from wild type B. fragilis or the isolated B. fragilis, can be administered as or part of a neutraceutical; a probiotic alone (or in combination with other probiotics); a pharmaceutical; a medicinal formulation, a cream, or a lotion.
The term neutraceutical, as used in this application, refers to a food, food product, fortified food or a dietary supplement that provides health and medical benefits, including the prevention and treatment of disease.
The “effective amount”, “amount effective to,” or “amount of X effective to” refers to an amount of the compound, composition or pharmaceutical/extract/cell composition that is effective to treat, relieve, reduce, or improve to some extent one or more of the symptoms of the disease in need of treatment, or to retard initiation of clinical markers or symptoms of a disease in need of prevention, when the compound is administered. Thus, for example an effective amount refers to an amount of the compound/composition/pharmaceutical ingredient which exhibits the ‘improved’ effects, as noted below.
The “effective amount” may be empirically determined by experimenting with the compounds concerned in known in vivo and in vitro model systems for a disease in need of treatment. An effective amount will vary according to the weight, sex, age and medical history of the individual, as well as the severity of the patient's condition(s), the type of disease(s), mode of administration, and the like. An effective amount may be readily determined using routine experimentation, e.g., by titration (administration of increasing dosages until an effective dosage is found) and/or by reference to amounts that were effective for prior patients. Generally, the effective amount of the present invention will be administered in dosages ranging between about 0.1 mg/kg and about 20 mg/kg of the patient's body-weight.
As used herein, the phrase “prophylactically effective amount” includes the amount of the compound/composition/pharmaceutical/extract/cell composition which is sufficient to result in the prevention or reduction of the development, recurrence or onset of one or more symptoms associated with a disorder (or to enhance or improve the prophylactic effect(s) of another therapy (e.g., another prophylactic agent).
It is further contemplated that the compound/composition/pharmaceutical/extract/cell composition of the present invention can be used with one or more known medicaments known to be useful in the treatment or prevention of inflammatory diseases, either separately or in combination.
For example the compound/composition/pharmaceutical/extract/cell composition of the present invention can be combined with one or a combination of medicaments/treatments known to be useful in the treatment of IBD such as, but not limited to, sulfasalazine (Azulfadine), mesalamine (Asacol, Pentasa), immunosuppressants (Imuran, 6-MP, cyclosporine); methotrexate, TNF-alpha inhibitors (Remicade and Humira); and corticosteroids (Entocort and prednisone). Other treatments (experimental) for ulcerative colitis, include aloe vera, butyrate, boswellia, probiotics, antibiotics, immunosuppressive therapy, and nicotine.
For example the compound/composition/pharmaceutical/extract/cell/PSA of the present invention can be combined with one or a combination of medicaments/treatments known to be useful in the treatment of MS such as, but not limited to, Avonex®, Betaseron®, and Copaxone®. Rebif®; Extavia® Novantrone® (mitoxantrone); Tysabri® (natalizumab), and Gilenya® (fingolimod). Other drugs include intravenous immunoglobulin (IVIg) therapy, methotrexate, azathioprine (Imuran®), and cyclophosphamide (Cytoxan®); corticosteroids; cytoxan® (cyclophosphamide); Imuran® (azathioprine); methotrexate; plasma exchange; pulse solu-medrol® (IV methylprednisolone); prednisone; Decadron® (dexamethasone); Medrol® (oral methylprednisolone); Plasmapheresis (plasma exchange); intravenous immunoglobulin (IVIg) therapy.
Generation of PSA-only Producing Mutant Strain (“Isolated B. Fragilis”)
To create the B. fragilis mutant that produces PSA only from the repertoire of capsular polysaccharides (CPS), the B. fragilis NCTC9343ΔPSB mutant (2) was used as a parent strain from which every CPS biosynthesis locus (PSC-PSH) except for that of PSA was deleted one at a time. DNA segments upstream and downstream of the region to be deleted were PCR amplified by using primers listed in Table 1. A second round of PCR using primers 1 (forward primer of the left flank) and 4 (reverse primer of the right flank) with the 1:1 mix of the two PCR products as templates was performed to fuse the left and right flanking DNA fragments using the 18 bp overlapping region engineered into primers 2 (reverse primer of the left flank) and 3 (forward primer of the right flank). The fused PCR product was digested with BamHI and cloned into the BamHI site of the Bacteroides conjugal suicide vector pNJR6. The plasmid was introduce into Escherichia coli (E. coli.) and subsequently conjugally transferred into B. fragilis NCTC9343 and the cointegrates were selected by resistance to erythromycin encoded by pNJR6. The cointegrate strain was passaged in nonselective medium for 5-8 days and then plated on nonselective medium (BHIS). The resulting colonies were replica plated to BHIS containing erythromycin and the erythromycin-sensitive colonies were screened by PCR to distinguish wild-type revertants from strains with desired mutation (Table 2).
We determined whether PSA could be detected in the outer membrane vesicles (OMV) extracts of our strain. For this purpose outer membrane vesicles (OMV) extracts were prepared based on a modification of a previously described protocol for the preparation of OMVs from E. coli (Amanda L. Horstman and Meta J. Kuehn. (2000) Enterotoxigenic Escherichia coli secretes active heat-labile enterotoxin via outer membrane vesicles. J Biol Chem. 275: 12489-12496. ) Briefly, electron dense layer (EDL)-enriched B. fragilis was grown in customized MM. OMVs were recovered from the bacteria-free supernatant of the culture by centrifugation at 40,000 g for 2hrs at 4 C and further washed twice with PBS and filtered through 0.45 μm spin columns (Millipore #20-218). Total protein concentration of the purified OMVs was determined by Bradford assay (Biorad #500-0205). FITC-labeled OMVs were prepared as previously described (Nicole C. Kesty and Meta J. Keuhn. (2004) Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles. J Biol Chem. 279: 2069-2076). Briefly, OMVs were incubated in the staining buffer (1 mg/ml FITC (Thermo Scientific #46424), 100 mM NaCl, 50 mM Na2CO3, pH 9.2) for 1 hr at RT. Labeled OMVs were collected by centrifugation at 40,000 g for 30 min at 4 C and washed twice with PBS+200 mM NaCl.
The disclosed bacterial strain/cell can be used to treat or prevent a variety of diseases, such as but not limited to, inflammatory bowel disease, Crohn's disease and ulcerative colitis, asthma, dermatitis, arthritis, myasthenia gravis, Grave's disease, multiple sclerosis (MS), type I diabetes, type 2 diabetes, food allergy, and psoriasis. Thus, either the live, viable or lyophilized embodiments of the bacteria cell disclosed expresses only PSA can be administered alone or part of a pharmaceutical; or in conjunction with any other therapeutic agent useful in the treatment the aforementioned diseases. In another embodiments, the OMVs from the disclosed bacterial strain/cell can be can be administered alone or part of a pharmaceutical; or in conjunction with any other therapeutic agent useful in the treatment the aforementioned diseases.
It should be mentioned that prior investigators have described an isolated Bacteroides fragilis bacterial cell producing a native capsular polysaccharide A (PSA), having a native promoter that controls expression of native biosynthetic genes of PSA and native promoters that control expression of native biosynthetic genes of native capsular polysaccharides PSB, PSD, PSE, PSF, PSG and PSH, wherein the promoter that controls expression of the native biosynthetic genes of PSA is locked on, wherein at least one of the promoters that controls expression of the native biosynthetic genes of the native capsular polysaccharides selected from the group consisting of: PSB, PSD, PSE, PSF, PSG, and PSH is locked off, wherein the promoter controlling expression of the native biosynthetic genes of PSA is locked on by deletion of the gene that encodes for a DNA recombinase that inverts promoters. Upon deletion of this gene, named multiple promoter invertase (mpi), bacterial isolates were screened for a strain that has the PSA promoter in the locked on orientation, but all other promoters in the locked off orientation. In that study, the promoter controlling expression of a capsular polysaccharide is “locked on” when the invertible promoter is in its transcriptionally active orientation and it cannot invert to the transcriptionally inactive orientation. The promoter can be locked on because a sequence-specific enzyme that normally inverts the promoter is not present or is otherwise disabled. Alternatively, the promoter can be locked on because at least one inverted repeat flanking the invertible region of the promoter is altered, e.g., deleted, so that the inversion is not possible. Alternatively, the promoter controlling expression of a capsular polysaccharide is “locked off” when the invertible promoter is in its transcriptionally inactive orientation and it cannot invert to the transcriptionally active orientation. The promoter can be locked off because a sequence-specific enzyme that normally inverts the promoter is not present or is otherwise disabled. Alternatively, the promoter can be locked off because at least one inverted repeat flanking the invertible region of the promoter is altered, e.g., deleted, so that the inversion is not possible.
References (which are all incorporated by reference in their entirety).
1. Liu C H, Lee S M, Vanlare J M, Kasper D L, Mazmanian S K. 2008. Regulation of surface architecture by symbiotic bacteria mediates host colonization. Proc Natl Acad Sci USA 105: 3951-6
2. Coyne M J, Kalka-Moll W, Tzianabos A O, Kasper D L, Comstock L E. 2000. Bacteroides fragilis NCTC9343 produces at least three distinct capsular polysaccharides: cloning, characterization, and reassignment of polysaccharide B and C biosynthesis loci. Infect Immun 68: 6176-81
This application claims the benefit of Provisional Patent Application 61/542,549 filed on Oct. 3, 2011, which is incorporated by reference herein in its entirety.
This invention was made with government support under R21DK083633 and RO1DK078938A awarded by the National Institutes of Health. The U.S. Government has certain rights in this invention.
| Number | Date | Country | |
|---|---|---|---|
| 61542549 | Oct 2011 | US |
