US20180147221A1 - Glycan therapeutic compositions and related methods thereof - Google Patents

Glycan therapeutic compositions and related methods thereof Download PDF

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US20180147221A1
US20180147221A1 US15/568,243 US201615568243A US2018147221A1 US 20180147221 A1 US20180147221 A1 US 20180147221A1 US 201615568243 A US201615568243 A US 201615568243A US 2018147221 A1 US2018147221 A1 US 2018147221A1
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composition
glycan
glycan therapeutic
therapeutic preparation
cancer
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Geoffrey A. Von Maltzahn
Yvonne J. Yamanaka
Jared Silverman
Jack Milwid
Jacob R. Rubens
John M. GEREMIA
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DSM Nutritional Products LLC
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Kaleido Biosciences Inc
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/715—Polysaccharides, i.e. having more than five saccharide radicals attached to each other by glycosidic linkages; Derivatives thereof, e.g. ethers, esters
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/702—Oligosaccharides, i.e. having three to five saccharide radicals attached to each other by glycosidic linkages
    • A—HUMAN NECESSITIES
    • A23—FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23L—FOODS, FOODSTUFFS, OR NON-ALCOHOLIC BEVERAGES, NOT COVERED BY SUBCLASSES A21D OR A23B-A23J; THEIR PREPARATION OR TREATMENT, e.g. COOKING, MODIFICATION OF NUTRITIVE QUALITIES, PHYSICAL TREATMENT; PRESERVATION OF FOODS OR FOODSTUFFS, IN GENERAL
    • A23L33/00—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof
    • A23L33/10—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof using additives
    • A23L33/125—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof using additives containing carbohydrate syrups; containing sugars; containing sugar alcohols; containing starch hydrolysates
    • A—HUMAN NECESSITIES
    • A23—FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23L—FOODS, FOODSTUFFS, OR NON-ALCOHOLIC BEVERAGES, NOT COVERED BY SUBCLASSES A21D OR A23B-A23J; THEIR PREPARATION OR TREATMENT, e.g. COOKING, MODIFICATION OF NUTRITIVE QUALITIES, PHYSICAL TREATMENT; PRESERVATION OF FOODS OR FOODSTUFFS, IN GENERAL
    • A23L33/00—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof
    • A23L33/10—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof using additives
    • A23L33/135—Bacteria or derivatives thereof, e.g. probiotics
    • A—HUMAN NECESSITIES
    • A23—FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23L—FOODS, FOODSTUFFS, OR NON-ALCOHOLIC BEVERAGES, NOT COVERED BY SUBCLASSES A21D OR A23B-A23J; THEIR PREPARATION OR TREATMENT, e.g. COOKING, MODIFICATION OF NUTRITIVE QUALITIES, PHYSICAL TREATMENT; PRESERVATION OF FOODS OR FOODSTUFFS, IN GENERAL
    • A23L33/00—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof
    • A23L33/20—Reducing nutritive value; Dietetic products with reduced nutritive value
    • A23L33/21—Addition of substantially indigestible substances, e.g. dietary fibres
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
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    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/715—Polysaccharides, i.e. having more than five saccharide radicals attached to each other by glycosidic linkages; Derivatives thereof, e.g. ethers, esters
    • A61K31/716—Glucans
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/715—Polysaccharides, i.e. having more than five saccharide radicals attached to each other by glycosidic linkages; Derivatives thereof, e.g. ethers, esters
    • A61K31/733—Fructosans, e.g. inulin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
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    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P3/00—Drugs for disorders of the metabolism
    • A61P3/02—Nutrients, e.g. vitamins, minerals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/04—Antineoplastic agents specific for metastasis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A23—FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23V—INDEXING SCHEME RELATING TO FOODS, FOODSTUFFS OR NON-ALCOHOLIC BEVERAGES AND LACTIC OR PROPIONIC ACID BACTERIA USED IN FOODSTUFFS OR FOOD PREPARATION
    • A23V2002/00—Food compositions, function of food ingredients or processes for food or foodstuffs
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • compositions for treating diseases, disorders or pathological conditions.
  • glycan therapeutics and pharmaceutical compositions, medical foods and dietary supplements thereof, and related methods, which have been found to be effective to treat a number of diseases, disorders or pathological conditions.
  • the invention relates to methods of treating an immune imbalance in a human subject.
  • a method of treating an immune imbalance in a human subject comprising: administering to the subject a pharmaceutical composition, a medical food or a dietary supplement comprising a glycan therapeutic preparation, in an effective amount to treat the subject.
  • a method of treating an immune imbalance in a human subject comprising: administering to the subject a first agent comprising a glycan therapeutic preparation, optionally in combination with a second agent or therapy.
  • the first agent is a pharmaceutical composition.
  • the first agent is a medical food.
  • the first agent is a dietary supplement.
  • the second agent is an immunomodulatory agent.
  • the second agent or therapy treats a second disease, disorder or pathological condition of the subject.
  • the first agent and the second agent are administered in an effective amount to treat the immune imbalance.
  • the first agent is administered in an effective amount to treat the immune imbalance and the second agent is administered in an effective amount to treat the second disease, disorder or pathological condition of the subject.
  • the second agent is a dietary fiber.
  • the second agent is a probiotic bacterium.
  • the combination is administered to a subject who has been treated for an immune imbalance. In one embodiment, the combination is administered to a subject who has not been treated for an immune imbalance.
  • the first agent is administered to a subject that has been treated with the second agent.
  • the second agent is administered to a subject that has been treated with the first agent.
  • the first agent and the second agent are administered concurrently to a subject.
  • a method for reducing an infection and/or an inflammation in a subject having an immune imbalance comprising administering to the subject a glycan therapeutic preparation in an effective amount to reduce the infection and/or an inflammation.
  • a method of modulating the composition and/or metabolic activity of the intestinal bacterial community of a subject having an immune imbalance comprising administering to the subject a glycan therapeutic composition and, optionally, an anti- or pro-inflammatory agent in an amount effective to modulate the subject's immune system.
  • the methods further comprise administering a probiotic microorganism.
  • a short-chain fatty acid (SCFA) is modulated.
  • the SCFA is one or more of acetate, propionate, butyrate, isovalerate, valerate, hexanoate, heptanoate, and octanoate.
  • the one or more SCFA is reduced.
  • the one or more SCFA is increased.
  • administration of the composition modulates (e.g. stimulates) growth or activity of beneficial gut bacteria, e.g., Bifidobacteria.
  • administration of the glycan therapeutic preparation modulates the growth or function of one or more bacterial taxa, including Bifidobacteria, Bifidobacteriales, Bacteroidales, Clostridiales, Parabacteroides , and Akkermansia .
  • administration of the glycan therapeutic preparation modulates the growth or function of one or more bacterial taxa, including Blautia, Bifidobacterium, Roseburia, Coprococcus, Lachnospiraceae, Faecalibacterium, Parabacteroides , and Ruminococcaceae.
  • one or more host pathways are modulated, including inflammatory responses, complement, apoptosis, antigen presentation, oxidative stress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wnt signaling, and/or one or more of the metabolic pathways listed in Table 19 ((super or sub pathways or level of a metabolite).
  • one or more bile acids are modulated.
  • the bile acid is a primary bile acid. In one embodiment, the bile acid is a secondary bile acid. In one embodiment, the bile acid is one or more of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid. In one embodiment, the bile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid). In one embodiment, the bile acid is increased. In one embodiment, the bile acid is decreased. In one embodiment, administration of the composition results in the modulation of one or more biomarkers including Interleukin 10, Interleukin, 4, Interleukin 13, and Interleukin 35.
  • one or more biomarkers including Interleukin 10, Interleukin, 4, Interleukin 13, and Interleukin 35.
  • administration of the composition results in the modulation of one or more biomarkers including C-reactive protein, interleukin-6, interleukin-8, interleukin-18, insulin, blood glucose, leptin, serum amyloid A, serum amyloid P, and tumor necrosis factor-alpha.
  • one or more cytokine selected from TNF- ⁇ , IL-8, monocyte chemoattracting protein 1 (MCP-1), TGF- ⁇ , IL-12, IFN- ⁇ , IL-4, and IL-10 is modulated.
  • administration of the composition results in a i) a reduced immune response or ii) an enhanced immune response.
  • the production or release of pro-inflammatory cytokines is decreased.
  • the production or release of anti-inflammatory cytokines is increased.
  • the production or release of anti-inflammatory cytokines is decreased.
  • a method of modulating the function and/or activity of a pathway of a subject having an immune imbalance comprising administering to the subject a glycan therapeutic composition and, optionally as second agent.
  • a short-chain fatty acid (SCFA) is modulated.
  • the SCFA is one or more of acetate, propionate, butyrate, isovalerate, valerate, hexanoate, heptanoate, and octanoate.
  • the one or more SCFA is reduced.
  • the one or more SCFA is increased.
  • one or more pathways are modulated, including inflammatory responses, complement, apoptosis, antigen presentation, oxidative stress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wnt signaling, and/or one or more of the metabolic pathways listed in Table 19 ((super or sub pathways or level of a metabolite).
  • one or more bile acids are modulated.
  • the bile acid is a primary bile acid.
  • the bile acid is a secondary bile acid.
  • the bile acid is one or more of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.
  • the bile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid).
  • the bile acid is increased. In one embodiment, the bile acid is decreased.
  • a method of treating a dysbiosis in a subject having an immune imbalance comprising administering to the subject a pharmaceutical composition comprising a glycan therapeutic preparation in an effective amount to treat the dysbiosis.
  • the immune imbalance is a suppression of the subject's immune system. In one embodiment, the subject exhibits a deficient immune-surveillance. In one embodiment, the subject has a pathogenic infection. In one embodiment, the subject has a cancer. In one embodiment, the immune imbalance is an aberrant activation of the subject's immune system. In one embodiment, the subject has a inflammatory disease that increase the risk of developing a cancer. In one embodiment, the subject has graft-versus-host disease. In one embodiment, the subject has an autoimmune disease. In one embodiment, the subject has an inflammatory gastrointestinal disease. In one embodiment, the immune imbalance is acute. In one embodiment, the immune imbalance is chronic. In one embodiment, the immune imbalance is local. In one embodiment, the immune imbalance is systemic. In one embodiment, the immune imbalance is accompanied by aberrant growth of a pathogenic cell. In one embodiment, the pathogenic cell is an intracellular pathogen, an extracellular pathogen, or a cancerous cell.
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the glycan therapeutic preparation has an average degree of branching (DB) of at least 0.01, iv) at least 50% of the glycans in the preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, v) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the preparation overall is between about 1:1 to about 5:1, or vi) any combination of one, two, three, four or five of i), ii), iii), iv) and v).
  • DB average degree of branching
  • DP degree of polymerization
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the branched oligosaccharides comprise glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose glycan units, iv) the average degree of branching (DB) of the branched glycans in the glycan therapeutic preparation is between 0.01 and 0.3, v) at least 50% of the glycans in the glycan therapeutic preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, vi) the average DP of the glycan therapeutic preparation is between about DP6 and about DP10, vii) the ratio of alpha- to beta-glycosidic bonds present in the gly
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise one or more glycan units, iii) the branched glycans comprise at least 1% of branched glycan units, iv) the branched glycans have a degree of polymerization (DP) of between 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycans comprise a mixture of beta and alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeutic preparation comprises a mixture of branched glycans and unbranched glycans, viii) the glycan therapeutic preparation comprises a mixture
  • the invention in a second aspect, relates to methods of treating a nutritional imbalance in a human subject.
  • a method of treating a nutritional imbalance in a human subject comprising: administering to the subject a pharmaceutical composition, a medical food or a dietary supplement comprising a glycan therapeutic preparation, in an effective amount to treat the subject.
  • a method of treating a nutritional imbalance in a human subject comprising: administering to the subject a first agent comprising a glycan therapeutic preparation, optionally in combination with a second agent or therapy.
  • the first agent is a pharmaceutical composition.
  • the first agent is a medical food.
  • the first agent is a dietary supplement.
  • the second agent is metabolism modulating agent.
  • the second agent or therapy treats a second disease, disorder or pathological condition of the subject.
  • the first agent and the second agent are administered in an effective amount to treat the nutritional imbalance.
  • the first agent is administered in an effective amount to treat the nutritional imbalance and the second agent is administered in an effective amount to treat the second disease, disorder or pathological condition of the subject.
  • the second agent is a dietary fiber.
  • the second agent is a probiotic bacterium.
  • the combination is administered to a subject who has been treated for a nutritional imbalance. In one embodiment, the combination is administered to a subject who has not been treated for a nutritional imbalance.
  • the first agent is administered to a subject that has been treated with the second agent.
  • the second agent is administered to a subject that has been treated with the first agent.
  • the first agent and the second agent are administered concurrently to a subject.
  • a method for reducing an inflammation in a subject having a nutritional imbalance comprising administering to the subject a glycan therapeutic preparation in an effective amount to reduce the inflammation.
  • a method of modulating the composition and/or metabolic activity of the intestinal bacterial community of a subject having a nutritional imbalance comprising administering to the subject a glycan therapeutic composition and an anti- or pro-inflammatory agent in an amount effective to modulate the subject's immune system.
  • the methods further comprise administering a probiotic microorganism.
  • a short-chain fatty acid (SCFA) is modulated.
  • the SCFA is one or more of acetate, propionate, butyrate, isovalerate, valerate, hexanoate, heptanoate, and octanoate.
  • the one or more SCFA is reduced.
  • the one or more SCFA is increased.
  • administration of the composition modulates (e.g. stimulates) growth or activity of beneficial gut bacteria, e.g., Bifidobacteria.
  • administration of the glycan therapeutic preparation modulates the growth or function of one or more bacterial taxa, including Bifidobacteria, Bifidobacteriales, Bacteroidales, Clostridiales, Parabacteroides , and Akkermansia .
  • administration of the glycan therapeutic preparation modulates the growth or function of one or more bacterial taxa, including Blautia, Bifidobacterium, Roseburia, Coprococcus, Lachnospiraceae, Faecalibacterium, Parabacteroides , and Ruminococcaceae.
  • one or more host pathways are modulated, including inflammatory responses, complement, apoptosis, antigen presentation, oxidative stress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wnt signaling, and/or one or more of the metabolic pathways listed in Table 19 ((super or sub pathways or level of a metabolite).
  • one or more bile acids are modulated.
  • the bile acid is a primary bile acid. In one embodiment, the bile acid is a secondary bile acid. In one embodiment, the bile acid is one or more of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid. In one embodiment, the bile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid). In one embodiment, the bile acid is increased. In one embodiment, the bile acid is decreased. In one embodiment, administration of the composition results in the modulation of one or more biomarkers including Interleukin 10, Interleukin, 4, Interleukin 13, and Interleukin 35.
  • one or more biomarkers including Interleukin 10, Interleukin, 4, Interleukin 13, and Interleukin 35.
  • administration of the composition results in the modulation of one or more biomarkers including C-reactive protein, interleukin-6, interleukin-8, interleukin-18, insulin, blood glucose, leptin, serum amyloid A, serum amyloid P, and tumor necrosis factor-alpha.
  • one or more cytokine selected from TNF- ⁇ , IL-8, monocyte chemoattracting protein 1 (MCP-1), TGF- ⁇ , IL-12, IFN- ⁇ , IL-4, and IL-10 is modulated.
  • administration of the composition results in a i) a reduced immune response or ii) an enhanced immune response.
  • the production or release of pro-inflammatory cytokines is decreased.
  • the production or release of anti-inflammatory cytokines is increased.
  • the production or release of anti-inflammatory cytokines is decreased.
  • a method of modulating the function and/or activity of a pathway of a subject having an nutritional imbalance comprising administering to the subject a glycan therapeutic composition and, optionally as second agent.
  • a short-chain fatty acid (SCFA) is modulated.
  • the SCFA is one or more of acetate, propionate, butyrate, isovalerate, valerate, hexanoate, heptanoate, and octanoate.
  • the one or more SCFA is reduced.
  • the one or more SCFA is increased.
  • one or more pathways are modulated, including inflammatory responses, complement, apoptosis, antigen presentation, oxidative stress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wnt signaling, and/or one or more of the metabolic pathways listed in Table 19 ((super or sub pathways or level of a metabolite).
  • one or more bile acids are modulated.
  • the bile acid is a primary bile acid.
  • the bile acid is a secondary bile acid.
  • the bile acid is one or more of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.
  • the bile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid).
  • the bile acid is increased. In one embodiment, the bile acid is decreased.
  • a method of treating a dysbiosis in a subject having a nutritional imbalance comprising administering to the subject a pharmaceutical composition comprising a glycan therapeutic preparation in an effective amount to treat the dysbiosis.
  • the nutritional imbalance is acute. In one embodiment, the nutritional imbalance is chronic. In one embodiment, the subject has a metabolic disease or syndrome. In one embodiment, the subject has a wasting syndrome. In one embodiment, the wasting syndrome is cachexia. In one embodiment, the subject has cancer. In one embodiment, the cancer is a gastrointestinal cancer. In one embodiment, the cancer is a non-gastrointestinal cancer.
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the glycan therapeutic preparation has an average degree of branching (DB) of at least 0.01, iv) at least 50% of the glycans in the preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, v) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the preparation overall is between about 1:1 to about 5:1, or vi) any combination of one, two, three, four or five of i), ii), iii), iv) and v).
  • DB average degree of branching
  • DP degree of polymerization
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the branched oligosaccharides comprise glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose glycan units, iv) the average degree of branching (DB) of the branched glycans in the glycan therapeutic preparation is between 0.01 and 0.3, v) at least 50% of the glycans in the glycan therapeutic preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, vi) the average DP of the glycan therapeutic preparation is between about DP6 and about DP10, vii) the ratio of alpha- to beta-glycosidic bonds present in the gly
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise one or more glycan units, iii) the branched glycans comprise at least 1% of branched glycan units, iv) the branched glycans have a degree of polymerization (DP) of between 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycans comprise a mixture of beta and alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeutic preparation comprises a mixture of branched glycans and unbranched glycans, viii) the glycan therapeutic preparation comprises a mixture
  • the invention relates to methods of treating cancer in a human subject.
  • a method of treating cancer in a human subject comprising: administering to the subject a pharmaceutical composition, a medical food or a dietary supplement comprising a glycan therapeutic preparation, in an effective amount to treat the subject.
  • a method of treating cancer in a human subject comprising: administering to the subject a first agent comprising a glycan therapeutic preparation, optionally in combination with a second agent or therapy.
  • the first agent is a pharmaceutical composition. In one embodiment, the first agent is a medical food. In one embodiment, the first agent is a dietary supplement. In one embodiment, the second agent is a checkpoint modulator, a cancer vaccine, an anti-cancer biologic, or a chemotherapeutic agent. In one embodiment, the immune checkpoint inhibitor is an antibody, a fusion protein, or a small molecule. In one embodiment, the cancer vaccine is a tumor cell vaccine, an antigen vaccine, a dendritic cell vaccine, a DNA vaccine, or a vector based vaccine. In one embodiment, the anti-cancer biologic is a cytokine or an antibody.
  • the chemotherapeutic agent is an alkylating agent, an antimetabolite, a folic acid analog, a pyrimidine analog, a purine analog, a vinca alkaloid, an epipodopyyllo toxin, an antibiotic, L-asparaginase, a topoisomerase inhibitor, an interferon, a platinum coordination complex, anthracenedione substituted urea, a methyl hydrazine derivative, an adrenocortical suppressant, an adrenocorticosteroid, a progestin, an estrogen, an anti-estrogen, an androgen, an anti-androgen, or a gonadotropin-releasing hormone analog.
  • the second therapy is adoptive T cell therapy, NK cell therapy, or a non drug treatment.
  • the non-drug treatment is radiation therapy, cryotherapy, hyperthermia or surgical excision of tumor tissue.
  • the adoptive T cell therapy comprises administering autologous and/or allogeneic T-cells.
  • the second agent is a dietary fiber.
  • the second agent is a probiotic bacterium.
  • the combination is administered to a subject who has been treated with an anti-cancer therapy.
  • the combination is administered to a subject who has not been treated with an anti-cancer therapy.
  • the first agent is administered to a subject that has been treated with the second agent.
  • the second agent is administered to a subject that has been treated with the first agent.
  • the first agent and the second agent are administered concurrently to a subject.
  • a method of modulating the composition and/or metabolic activity of the intestinal bacterial community of a subject having cancer comprising administering to the subject a glycan therapeutic composition and an anti- or pro-inflammatory agent in an amount effective to modulate the subject's immune system.
  • the methods further comprise administering an anti-cancer agent.
  • the methods further comprise administering a probiotic microorganism.
  • a short-chain fatty acid (SCFA) is modulated.
  • the SCFA is one or more of acetate, propionate, butyrate, isovalerate, valerate, hexanoate, heptanoate, and octanoate.
  • the one or more SCFA is reduced. In some embodiments, the one or more SCFA is increased. In one embodiment, administration of the composition results in induction of apoptosis of cancer and precancerous cells in the subject. In one embodiment, administration of the composition modulates (e.g. stimulates) growth or activity of beneficial gut bacteria, e.g., Bifidobacteria. In one embodiment, administration of the glycan therapeutic preparation modulates the growth or function of one or more bacterial taxa, including Bifidobacteria, Bifidobacteriales, Bacteroidales, Clostridiales, Parabacteroides , and Akkermansia .
  • administration of the glycan therapeutic preparation modulates the growth or function of one or more bacterial taxa, including Blautia, Bifidobacterium, Roseburia, Coprococcus, Lachnospiraceae, Faecalibacterium, Parabacteroides , and Ruminococcaceae.
  • one or more host pathways are modulated, including inflammatory responses, complement, apoptosis, antigen presentation, oxidative stress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wnt signaling, and/or one or more of the metabolic pathways listed in Table 19 ((super or sub pathways or level of a metabolite).
  • one or more bile acids are modulated.
  • the bile acid is a primary bile acid. In one embodiment, the bile acid is a secondary bile acid. In one embodiment, the bile acid is one or more of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid. In one embodiment, the bile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid). In one embodiment, the bile acid is increased. In one embodiment, the bile acid is decreased. In one embodiment, administration of the composition results in the modulation of one or more biomarkers including Interleukin 10, Interleukin, 4, Interleukin 13, and Interleukin 35.
  • one or more biomarkers including Interleukin 10, Interleukin, 4, Interleukin 13, and Interleukin 35.
  • administration of the composition results in the modulation of one or more biomarkers including C-reactive protein, interleukin-6, interleukin-8, interleukin-18, insulin, blood glucose, leptin, serum amyloid A, serum amyloid P, and tumor necrosis factor-alpha.
  • one or more cytokine selected from TNF- ⁇ , IL-8, monocyte chemoattracting protein 1 (MCP-1), TGF- ⁇ , IL-12, IFN- ⁇ , IL-4, and IL-10 is modulated.
  • administration of the composition results in a i) a reduction of intestinal cancer, and/or ii) an enhanced immune response.
  • the production or release of pro-inflammatory cytokines is decreased.
  • the production or release of anti-inflammatory cytokines is increased.
  • a method of modulating the function and/or activity of a pathway of a subject having an immune imbalance comprising administering to the subject a glycan therapeutic composition and, optionally as second agent.
  • a short-chain fatty acid (SCFA) is modulated.
  • the SCFA is one or more of acetate, propionate, butyrate, isovalerate, valerate, hexanoate, heptanoate, and octanoate.
  • the one or more SCFA is reduced.
  • the one or more SCFA is increased.
  • one or more pathways are modulated, including inflammatory responses, complement, apoptosis, antigen presentation, oxidative stress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wnt signaling, and/or one or more of the metabolic pathways listed in Table 19 ((super or sub pathways or level of a metabolite).
  • one or more bile acids are modulated.
  • the bile acid is a primary bile acid.
  • the bile acid is a secondary bile acid.
  • the bile acid is one or more of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.
  • the bile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid).
  • the bile acid is increased. In one embodiment, the bile acid is decreased.
  • a method of treating a dysbiosis in a subject having cancer comprising administering to the subject a pharmaceutical composition comprising a glycan therapeutic preparation in an effective amount to treat the dysbiosis.
  • the subject undergoes an anti-cancer therapy.
  • the cancer therapy is a non-drug therapy.
  • the subject undergoes pain management therapy for cancer pain.
  • the pain management therapy comprises administering opioids.
  • the subject exhibits constipation.
  • the constipation is acute.
  • the constipation is chronic.
  • the subject exhibits diarrhea.
  • the diarrhea is acute.
  • the diarrhea is chronic.
  • a method for reducing an infection and/or an inflammation in a subject having cancer comprising administering to the subject a glycan therapeutic preparation in an effective amount to reduce the infection and/or an inflammation.
  • a method for inducing apoptosis of a cancer or a precancerous cell in the subject having cancer comprising administering to the subject a glycan therapeutic preparation in an effective amount to induce apoptosis of the cancer or precancerous cell.
  • the cancer is colon cancer or liver cancer.
  • the glycan therapeutic preparation is administered in combination with another agent or therapy.
  • the other agent or therapy is selected from radiation and chemotherapy and antibiotic therapy.
  • the other agent is selected from a probiotic, a prebiotic dietary fiber, an antibacterial agent, an anti-inflammatory agent, or an anti-cancer agent.
  • one or more genes or gene products selected from Jun, Myc, Fos, Adamts1, ATF3, DDit4, Egr1, Sox9, IL1a, Gadd45b, and Gadd45g are modulated.
  • a method of reducing the risk of cancer in a subject comprising administering to the subject a glycan therapeutic preparation in an effective amount to promote a healthy microbiota in the subject, thereby reducing the cancer risk in the subject.
  • the cancer is selected from breast cancer, ovarian cancer, osteosarcoma, cervical cancer, lung cancer, bladder cancer, pancreatic cancer, prostate cancer, or melanoma.
  • the glycan therapeutic preparation is administered in combination with another agent or therapy.
  • the other agent or therapy is selected from radiation and chemotherapy and antibiotic therapy.
  • the other agent is selected from a probiotic, a prebiotic dietary fiber, an antibacterial agent, an anti-inflammatory agent, or an anti-cancer agent.
  • the healthy microbiota comprises microbial strains selected from Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenella minuta , or a Christensenellaceae species, Streptococcus thermophilus, Enterococcus and Bacillus species, E. coli , and Sacharomyces boulardii.
  • Bacteroides Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenella minuta , or
  • a method of modulating the composition of the intestinal bacterial community of a subject having cancer comprising administering to the subject a glycan therapeutic preparation and an anti-cancer agent, in an amount effective to stimulate the growth of beneficial bacteria in the digestive system.
  • a method of modulating the metabolic activity of the intestinal bacterial community of a subject having cancer comprising administering to the subject a glycan therapeutic composition and an anti-cancer agent, in an amount effective to modulate the metabolic activity of beneficial bacteria in the digestive system.
  • the metabolic activity is one or more of those listed in Table 19 ((super or sub pathways or level of a metabolite).
  • the methods further comprise administering an anti-inflammatory agent.
  • the methods further comprise administering a probiotic microorganism.
  • the beneficial bacteria are selected from one or more of: Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenella minuta , and Christensenellaceae.
  • the beneficial bacteria include bifidobacterium .
  • a beneficial gut bacterial microbiota is disturbed.
  • the cancer is colon or liver cancer.
  • the expression of an oncogene is repressed.
  • the oncogene is one of: jun, myc and fos.
  • the glycan therapeutic composition is labeled as a medical food.
  • the method further comprises changes in the diet of the subject.
  • the change is one or more of: i) increasing dietary fiber intake, ii) eliminating gastrointestinal stimulants, iii) administering anticholinergic medications before meals.
  • the method further comprises one or more of: i) taking anxiety reducing measures, ii) regular exercise, iii) counseling for anxiety or depression.
  • the method further comprises identifying risk factors for developing a GI-related disease, to diagnose a GI-related disease, to evaluate the prognosis or severity of said disease, to evaluate the success of a treatment regimen, or any combination thereof, and wherein the GI related disease is cancer.
  • identifying the risk factors comprises acquiring the metabolite profile of a subject's tissue sample or microbial culture from the subject's tissue.
  • the metabolite for the purposes of diagnosis, prognostic risk assessment, or treatment assessment includes short chain fatty acids, bile acids, and lactate and those listed in Table 2.
  • the bile acid is a primary bile acid.
  • the bile acid is a secondary bile acid.
  • the bile acid is one or more of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.
  • the bile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid).
  • the bile acid is increased. In one embodiment, the bile acid is decreased.
  • the cancer is a primary or non-metastatic tumor.
  • the cancer is a metastatic or a metastasized tumor.
  • the cancer is a solid cancer.
  • the cancer is a liquid cancer.
  • the cancer is an immunogenic cancer.
  • the immunogenic cancer comprises one or more of the following characteristics: (a) tumor infiltrating lymphocytes (TIL), (b) somatic mutations, (c) neoantigens, (d) tertiary lymphoid structures; (e) high expression of inflammatory gene expression, or (f) immune cells exhibiting immunosuppressive phenotype.
  • the cancer is a gastrointestinal cancer.
  • the gastrointestinal cancer is colorectal cancer, pancreatic cancer, gastric cancer, oesophageal cancer, hepatocellular cancer, cholangiocellular cancer, oral cancer, or lip cancer.
  • the cancer is a non-gastrointestinal cancer.
  • the non-gastrointestinal cancer is a urogenital cancer, a gynecological cancer, a lung cancer, a head and neck cancer, a CNS cancer, a malignant mesothelioma; a breast cancer, a skin cancer, a thyroid cancer; a bone and soft tissue sarcoma; or a hematologic neoplasia.
  • the urogenital cancer is a hormone sensitive prostate cancer, a hormone refractory prostate cancer, a renal cell cancer, a bladder cancer, or a penile cancer.
  • the gynecological cancer is an ovarian cancer, a cervical cancer, an endometrial cancer.
  • the lung cancer is a small-cell lung cancer or a non-small-cell lung cancer.
  • the head and neck cancer is a squamous cell cancer.
  • the CNS cancer is a malignant glioma, an astrocytomas, a retinoblastoma or a brain metastasis.
  • the breast cancer is a hormone refractory metastatic breast cancer.
  • the skin cancer is a malignant melanoma, a basal and squamous cell skin cancer, a Merkel cell carcinoma, a lymphoma of the skin, or Kaposi Sarcoma.
  • the hematologic neoplasia is a multiple myeloma, an acute myelogenous leukemia, a chronic myelogenous leukemia, a myelodysplastic syndrome, an acute lymphoblastic leukemia, or Hodgkin's lymphoma.
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the glycan therapeutic preparation has an average degree of branching (DB) of at least 0.01, iv) at least 50% of the glycans in the preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, v) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the preparation overall is between about 1:1 to about 5:1, or vi) any combination of one, two, three, four or five of i), ii), iii), iv) and v).
  • DB average degree of branching
  • DP degree of polymerization
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the branched oligosaccharides comprise glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose glycan units, iv) the average degree of branching (DB) of the branched glycans in the glycan therapeutic preparation is between 0.01 and 0.3, v) at least 50% of the glycans in the glycan therapeutic preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, vi) the average DP of the glycan therapeutic preparation is between about DP6 and about DP10, vii) the ratio of alpha- to beta-glycosidic bonds present in the gly
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise one or more glycan units, iii) the branched glycans comprise at least 1% of branched glycan units, iv) the branched glycans have a degree of polymerization (DP) of between 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycans comprise a mixture of beta and alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeutic preparation comprises a mixture of branched glycans and unbranched glycans, viii) the glycan therapeutic preparation comprises a mixture
  • the invention relates to methods of treating subjects with a glycan therapeutic preparation that also receive a second treatment or therapy and methods of selecting subjects for treatment.
  • a method of treating a subject comprising: a) administering a pharmaceutical composition comprising a glycan therapeutic preparation to a subject who has been treated with a second treatment or therapy, b) administering a second treatment or therapy to a subject who has been treated with a pharmaceutical composition comprising a glycan therapeutic preparation, or c) administering a pharmaceutical composition comprising a glycan therapeutic preparation and administering a second treatment or therapy to a subject.
  • the treatment or therapy is an anti-cancer treatment or therapy. In one embodiment, the treatment or therapy is a treatment for nutritional imbalance. In one embodiment, the treatment or therapy is a treatment for immune imbalance.
  • a method of selecting a subject for a treatment comprising: (a) identifying a subject who has a disease, disorder or pathological condition, and (b) selecting the identified subject for treatment with a glycan therapeutic preparation.
  • the disease, disorder or pathological condition is cancer. In one embodiment, the disease, disorder or pathological condition is nutritional imbalance. In one embodiment, the disease, disorder or pathological condition is immune imbalance. In one embodiment, the step of selecting is carried out on the basis that the glycan therapeutic preparation will provide therapeutic benefit to the subject. In one embodiment, the step of selecting is carried out on the basis that the subject will or is expected to benefit from administration of the glycan therapeutic preparation. In one embodiment, the subject is treatment na ⁇ ve. In one embodiment, the subject has received anti-cancer treatment or therapy. In one embodiment, the subject has received treatment for nutritional imbalance. In one embodiment, the subject has received treatment for immune imbalance. In one embodiment, the method further comprises assessing the subject's gastrointestinal microbiota.
  • the assessment is carried out before, during and/or after the treatment.
  • treatment with a glycan therapeutic preparation modulates the abundance of a bacterial taxa.
  • the glycan therapeutic preparation is administered in an amount and for a time effective to result in shifted or modulated bacterial taxa in the subject's gastrointestinal microbiota.
  • the taxa are one or more of Bifidobacteria, Bacterioides and Akkermansia .
  • the taxa are of one or more of Bifidobacteria, Bifidobacteriales, Bacteroidales, Clostridiales, Parabacteroides , and Akkermansia .
  • the taxa are one or more of Blautia, Bifidobacterium, Roseburia, Coprococcus, Lachnospiraceae, Faecalibacterium, Parabacteroides , and Ruminococcaceae.
  • the treatment results in increased levels of Th17 or Th1 cells in the subject.
  • the method further comprises identifying risk factors for developing a cancer or second disease or disorder, to diagnose a cancer or second disease or disorder, to evaluate the prognosis or severity of the a cancer or second disease or disorder, to evaluate the success of a treatment regimen, or any combination thereof.
  • identifying the risk factors comprises acquiring the metabolite profile of a subject's tissue sample or microbial culture from the subject's tissue.
  • the metabolite for the purposes of diagnosis, prognostic risk assessment, or treatment assessment includes short chain fatty acids, bile acids, and lactate and the metabolites listed in Table 2.
  • the bile acid is a primary bile acid.
  • the bile acid is a secondary bile acid.
  • the bile acid is one or more of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.
  • the bile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid). In one embodiment, the bile acid is increased.
  • the bile acid is decreased.
  • the method further comprises changes in the diet of the subject.
  • the change is one or more of: i) increasing dietary fiber intake, ii) eliminating gastrointestinal stimulants, iii) administering anticholinergic medications before meals.
  • the method further comprises one or more of: i) taking anxiety reducing measures, ii) regular exercise, iii) counseling for anxiety or depression.
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the glycan therapeutic preparation has an average degree of branching (DB) of at least 0.01, iv) at least 50% of the glycans in the preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, v) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the preparation overall is between about 1:1 to about 5:1, or vi) any combination of one, two, three, four or five of i), ii), iii), iv) and v).
  • DB average degree of branching
  • DP degree of polymerization
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the branched oligosaccharides comprise glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose glycan units, iv) the average degree of branching (DB) of the branched glycans in the glycan therapeutic preparation is between 0.01 and 0.3, v) at least 50% of the glycans in the glycan therapeutic preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, vi) the average DP of the glycan therapeutic preparation is between about DP6 and about DP10, vii) the ratio of alpha- to beta-glycosidic bonds present in the gly
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise one or more glycan units, iii) the branched glycans comprise at least 1% of branched glycan units, iv) the branched glycans have a degree of polymerization (DP) of between 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycans comprise a mixture of beta and alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeutic preparation comprises a mixture of branched glycans and unbranched glycans, viii) the glycan therapeutic preparation comprises a mixture
  • the invention relates to methods of treating symptoms of a treatment or therapy, such as, e.g., toxicity symptoms in a human subject.
  • a method of reducing a symptom of a treatment or therapy, in a subject comprising a) administering a pharmaceutical composition comprising a glycan therapeutic preparation to a subject who has received the treatment or therapy; b) administering the treatment or therapy to a subject who has been treated with a pharmaceutical composition comprising a glycan therapeutic preparation; or c) administering a pharmaceutical composition comprising a glycan therapeutic preparation and administering the treatment or therapy to a subject, thereby reducing a symptom of the treatment or therapy in the subject.
  • the treatment or therapy is an anti-cancer treatment or therapy. In one embodiment, the treatment or therapy is a treatment for nutritional imbalance. In one embodiment, the treatment or therapy is a treatment for immune imbalance. In one embodiment, the symptom is a side-effect of the treatment or therapy. In one embodiment, the onset of the symptom is prior to administration of the glycan therapeutic preparation. In one embodiment, the glycan therapeutic preparation is administered after onset of the symptom. In one embodiment, the symptom of the treatment or therapy is unwanted. In one embodiment, the symptom is a gastrointestinal symptom. In one embodiment, the symptom is a digestive abnormality.
  • the gastrointestinal symptom is one or more of abdominal pain, cramping, nausea, vomiting, upset stomach, gas, bloating, flatulence, diarrhea, constipation, heartburn, mucositis, and weight-gain, weight loss.
  • the symptom is a non-gastrointestinal symptom.
  • the non-gastrointestinal symptom is one or more of anxiety, fear, depression, mental fog, dermatitis, chest pain, shortness of breath.
  • the symptom is concurrent with or the result of an anti-cancer treatment or therapy.
  • the symptom is concurrent with or the result of a treatment for nutritional imbalance.
  • the symptom is concurrent with or the result of a treatment for immune imbalance.
  • the symptom is one or more of radiation injury pain, surgical pain, phantom pain, acute pain, chronic or persistent pain, breakthrough pain, peripheral neuropathy, stomatitis, mucositis, nausea, vomiting, diarrhea, constipation, urinary incontinence, fatigue, anemia, lymphedema, infection, anxiety, fear, depression, fertility defect, and increased risk of developing a second cancer.
  • the symptom is malnutrition or cachexia.
  • the symptom is mucositis.
  • the mucositisis is oral mucositis.
  • the mucositis is associated with chemotherapy treatment or radiation therapy.
  • the symptom is dose-limiting for the drug treatment or therapy, thereby preventing the subject from being treated with the maximal efficacious dose of a drug.
  • a method of reducing toxicity of a drug treatment in a subject in need thereof comprising: a) administering a pharmaceutical composition comprising a glycan therapeutic preparation to a subject who has received the drug treatment; b) administering the drug treatment to a subject who has been treated with a pharmaceutical composition comprising a glycan therapeutic preparation; or c) administering a pharmaceutical composition comprising a glycan therapeutic preparation and administering the drug treatment to a subject, in an effective amount to treat the subject.
  • the drug treatment comprises administering an immunomodulatory drug. In one embodiment, the drug treatment comprises administering a metabolism modulatory drug. In one embodiment, the drug treatment comprises administering an anti-cancer drug. In one embodiment, the anti-cancer drug is irinotecan or 5-fluorouracil. In one embodiment, the toxicity is a dose-limiting toxicity, thereby preventing the subject from being treated with the maximal efficacious dose of a drug. In one embodiment, tolerance of the subject to drug treatment is increased to a dose exceeding a sub-efficacious dose. In one embodiment, tolerance of the subject to drug treatment is increased to a dose equal to or exceeding the maximal efficacious dose of a drug in the subject.
  • the methods further comprise administering a pharmaceutical composition comprising a glycan therapeutic preparation to a subject who has received a first treatment, and optionally, providing a second treatment, e.g., wherein the second treatment comprises administration of the drug or therapy at a higher dosage, at more frequent intervals, at a higher total of individual administrations, providing a higher Cmax, providing a higher trough level, etc., than the prior treatment.
  • the methods further comprise providing a subsequent treatment to a subject who has received a pharmaceutical composition comprising a glycan therapeutic preparation and received the first treatment, wherein the second treatment comprises administration of the drug or therapy at a higher dosage, at more frequent intervals, at a higher total of individual administrations, providing a higher Cmax, providing a higher trough level, etc., than the prior treatment.
  • the methods further comprise evaluating one or more of: the suitability of the subject for glycan treatment, the responsiveness of the subject to glycan treatment, and/or the progression of the glycan treatment in the subject, comprising: a) acquiring a value for a parameter related to the level of a biomarker modulated by a glycan therapeutic preparation, and b) responsive to the value, classifying the subject, selecting a treatment for the subject, or administering the treatment to the subject, thereby evaluating the subject.
  • one or more biomarkers selected from: i) changes in gastrointestinal microbiota, ii) changes in metabolites of the gastric environment, iii) production of organic acids, iv) modulation of the immune system, v) modulation of inflammatory biomarkers, vi) modulation of immunoglobulins vii) increased absorption of minerals in the colon, viii) modulation of lipid metabolism, ix) lowering of cholesterol, x) modulation of host homeostasis.
  • the modulation is of one or more metabolic pathways listed in Table 19 ((super or sub pathways or level of a metabolite).
  • a method of treating symptoms associated with gastrointestinal distress comprising administering to a subject undergoing an anti-cancer therapy a glycan therapeutic composition comprising a mixture of branched glycans in an effective amount to treat one or more symptom associated with gastrointestinal distress.
  • the methods further comprise administering an anti-inflammatory agent. In one embodiment, the methods further comprise administering a probiotic microorganism. In one embodiment, a beneficial gut bacterial microbiota is disturbed. In one embodiment, the anti-cancer therapy is radiation or chemotherapy. In one embodiment, the symptom is constipation or diarrhea. In one embodiment, the symptom is gas, heartburn, stomach upset, bloating, flatulence, diarrhea, abdominal pain, cramping, nausea, or vomiting. In one embodiment, administration of the composition results in a decrease in i) diarrhea, ii) a decrease in constipation, iii) a reduction in toxic catabolites. In one embodiment, a reduction or elimination of symptoms persists after treatment of the condition has concluded.
  • administration of the composition results in an improvement of bowel regularity.
  • the reduction in the at least one of the one or more symptoms of the gastrointestinal disorder following treatment is about a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 100% decrease in a subject reported severity of the at least one of the one or more symptoms of the gastrointestinal disorder.
  • the reduction in at least one of the one or more symptoms of the gastrointestinal disorder persists for at least about a day, a week, a month, 3 months, 6 months, 9 months, or a year after treatment.
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the glycan therapeutic preparation has an average degree of branching (DB) of at least 0.01, iv) at least 50% of the glycans in the preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, v) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the preparation overall is between about 1:1 to about 5:1, or vi) any combination of one, two, three, four or five of i), ii), iii), iv) and v).
  • DB average degree of branching
  • DP degree of polymerization
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the branched oligosaccharides comprise glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose glycan units, iv) the average degree of branching (DB) of the branched glycans in the glycan therapeutic preparation is between 0.01 and 0.3, v) at least 50% of the glycans in the glycan therapeutic preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, vi) the average DP of the glycan therapeutic preparation is between about DP6 and about DP10, vii) the ratio of alpha- to beta-glycosidic bonds present in the gly
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise one or more glycan units, iii) the branched glycans comprise at least 1% of branched glycan units, iv) the branched glycans have a degree of polymerization (DP) of between 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycans comprise a mixture of beta and alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeutic preparation comprises a mixture of branched glycans and unbranched glycans, viii) the glycan therapeutic preparation comprises a mixture
  • the glycan therapeutic preparation may comprise one or more homo-glycans selected from xyl100, rha100, ara100, gal100, glu100, fuc100, fru100, and man100.
  • the glycan therapeutic preparation may comprise one or more hetero-glycans selected from ara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10 and glu90gly10.
  • the glycan therapeutic preparation may comprise one or more hetero-glycans selected from xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, and glu33gal33neu33.
  • the glycan therapeutic preparation may comprise one or more homo or hetero-glycans selected from xyl100, rha100, ara100, gal100, glu100, man100, fuc100, fru100, ara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10 and glu90gly10, xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, and glu33gal33neu33.
  • the glycan therapeutic preparation may comprise one or more homo or hetero-glycans selected from ara50gal50, glu33gal33fuc33, glu50gal50, gal100, glu100, xyl100, ara100, ara60xyl40, glu80man20, glu60man40, man52glu29gal19, man100.
  • the glycan therapeutic preparation may comprise one or more homo-glycans selected from man100, xyl100, or glu100.
  • the glycan therapeutic preparation may comprise man100.
  • the glycan therapeutic preparation may comprise xyl100.
  • the glycan therapeutic preparation may comprise glu100.
  • the glycan therapeutic preparation may comprise one or more hetero-glycans selected from glu50gal50, glu80man20, glu33gal33fuc33, man52glu29gal19.
  • the glycan therapeutic preparation may comprise comprise glu50gal50.
  • the glycan therapeutic preparation may comprise glu80man20.
  • the glycan therapeutic preparation may comprise glu33gal33fuc33.
  • the glycan therapeutic preparation may comprise man52glu29gal19.
  • the beneficial bacteria include bacteria of the genus Akkermansia, Anaerofilum, Bacteroides, Blautia, Bifidobacterium, Butyrivibrio, Clostridium, Coprococcus, Dialister, Dorea, Fusobacterium, Eubacterium, Faecalibacterium, Lachnospira, Lactobacillus, Phascolarctobacterium, Peptococcus, Peptostreptococcus, Prevotella, Roseburia, Ruminococcus , and Streptococcus , and/or one or more of the species Akkermansia municiphilia, minuta, Clostridium coccoides, Clostridium leptum, Clostridium scindens, Dialister invisus, Eubacterium rectal, Eubacterium eligens, Faecalibacterium prausnitzii, Strept
  • kits for treating cancer in a human subject, comprising: a package comprising (i) a first pharmaceutical composition comprising a glycan therapeutic preparation, (ii) optionally, a second anti-neoplastic or anti-cancer pharmaceutical composition, and (iii) instructions for using the first and/or the second pharmaceutical compositions for treating cancer in a human patient.
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the glycan therapeutic preparation has an average degree of branching (DB) of at least 0.01, iv) at least 50% of the glycans in the preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, v) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the preparation overall is between about 1:1 to about 5:1, or vi) any combination of one, two, three, four or five of i), ii), iii), iv) and v).
  • DB average degree of branching
  • DP degree of polymerization
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the branched oligosaccharides comprise glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose glycan units, iv) the average degree of branching (DB) of the branched glycans in the glycan therapeutic preparation is between 0.01 and 0.3, v) at least 50% of the glycans in the glycan therapeutic preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, vi) the average DP of the glycan therapeutic preparation is between about DP6 and about DP10, vii) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the glycan therapeutic preparation is
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise one or more glycan units, iii) the branched glycans comprise at least 1% of branched glycan units, iv) the branched glycans have a degree of polymerization (DP) of between 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycans comprise a mixture of beta and alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeutic preparation comprises a mixture of branched glycans and unbranched glycans, viii) the glycan therapeutic preparation comprises a mixture of digestible and non-digestible g
  • the invention relates to dosage forms for the treatment of a disease, disorder or condition.
  • a unit dosage form effective to treat a disease, disorder, or pathological condition comprising a glycan therapeutic preparation formulated for oral, enteral, rectal, intravenous, or intratumoral administration.
  • the disease, disorder, or pathological condition is cancer. In one embodiment, the disease, disorder, or pathological condition is a nutritional imbalance. In one embodiment, the disease, disorder, or pathological condition is an immune imbalance. In one embodiment, the unit dosage form is formulated as a pharmaceutical composition. In one embodiment, the unit dosage form is formulated as a medical food. In one embodiment, the unit dosage form is formulated as a dietary supplement. In one embodiment, the dosage form is formulated for oral consumption by a subject. In one embodiment, the dosage form is formulated to dissolve in an aqueous solution and is orally administered as a beverage, syrup, solution, or suspension. In one embodiment, the dosage form is formulated for enteral administration.
  • the administration is nasogastric, nasojejunal, oral gastric, or oral jejuna.
  • the dosage form is formulated for rectal administration.
  • the administration is enema, suppository, or colonoscopy.
  • the dosage form is formulated as a delayed release or time controlled system.
  • the dosage form is formulated to release the therapeutic glycan preparation in a specific region of the GI tract.
  • the specific region of the GI tract comprises the stomach, small intestine, large intestine, or colon.
  • the composition modulates the abundance of a bacterial genus present in the GI tract.
  • the bacterial taxa is bifidobacteria, bacterioides, akkamensia . In one embodiment, the bacterial taxa is Bifidobacteria, Bifidobacteriales, Bacteroidales, Clostridiales, Parabacteroides , and Akkermansia . In one embodiment, the bacterial taxa is Blautia, Bifidobacterium, Roseburia, Coprococcus, Lachnospiraceae, Faecalibacterium, Parabacteroides , and Ruminococcaceae. In one embodiment, the composition modulates the abundance of a bacterial genus present in one or both of the small intestine or large intestine.
  • the composition modulates the abundance of a bacterial genus predominant in the small intestine selected from the group of genus Achromobacter, Agrobacterium, Blautia, Burkholderia, Coprococcus, Cryocola, Enterococcus, Eubacterium, Holdemania, Lactococcus, Mycobacterium, Pseudoramibacter, Ralstonia, Sphingomonas, Streptococcus , and Turicibacter .
  • the composition modulates the abundance of a bacterial genus predominant in the large intestine selected from the group of genus Anaerotruncus, Akkermansia, Bacteroides, Bilophila, Butyricimonas, Odoribacter, Parabacteroides, Phascolarctobacterium, Prevotella , and Ruminococcus.
  • a bacterial genus predominant in the large intestine selected from the group of genus Anaerotruncus, Akkermansia, Bacteroides, Bilophila, Butyricimonas, Odoribacter, Parabacteroides, Phascolarctobacterium, Prevotella , and Ruminococcus.
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the glycan therapeutic preparation has an average degree of branching (DB) of at least 0.01, iv) at least 50% of the glycans in the preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, v) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the preparation overall is between about 1:1 to about 5:1, or vi) any combination of one, two, three, four or five of i), ii), iii), iv) and v).
  • DB average degree of branching
  • DP degree of polymerization
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the branched oligosaccharides comprise glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose glycan units, iv) the average degree of branching (DB) of the branched glycans in the glycan therapeutic preparation is between 0.01 and 0.3, v) at least 50% of the glycans in the glycan therapeutic preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, vi) the average DP of the glycan therapeutic preparation is between about DP6 and about DP10, vii) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the glycan therapeutic preparation is
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise one or more glycan units, iii) the branched glycans comprise at least 1% of branched glycan units, iv) the branched glycans have a degree of polymerization (DP) of between 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycans comprise a mixture of beta and alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeutic preparation comprises a mixture of branched glycans and unbranched glycans, viii) the glycan therapeutic preparation comprises a mixture of digestible and non-digestible g
  • the invention relates to a composition comprising glycan therapeutic preparations.
  • a composition comprising: a) a digestible glycan therapeutic preparation and a substantially non-digestible saccharide or dietary fiber, b) a substantially non-digestible glycan therapeutic preparation and a digestible saccharide or dietary fiber, c) a substantially non-digestible glycan therapeutic preparation and a substantially non-digestible saccharide or dietary fiber, or d) a digestible glycan therapeutic preparation and a digestible saccharide or dietary fiber, and any one of (a), (b), (c), (d) optionally comprising a probiotic bacterium.
  • the composition is formulated as a pharmaceutical composition. In one embodiment, the composition further comprises a pharmaceutically acceptable excipient or carrier. In one embodiment, the composition is formulated as a medical food. In one embodiment, the composition is labeled a medical food. In one embodiment, the composition is formulated as a dietary supplement. In one embodiment, the composition is labeled a dietary supplement. In one embodiment, the composition further comprises an essential nutrient. In one embodiment, the composition is effective to treat an immune imbalance. In one embodiment, the composition is effective to treat a nutritional imbalance. In one embodiment, the composition is effective to treat a cancer. In one embodiment, the glycan therapeutic preparation is selectively digested by gut microbiota constituents.
  • selective digestion results in modulation of the composition and/or activity of the gut microbiota.
  • the growth of one or more of Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenella minuta , and Christensenellaceae is selectively stimulated.
  • the glycan therapeutic preparation is substantially non-digestible by humans in the absence of specific bacteria in the gut, wherein the specific bacteria are capable of utilizing the glycan therapeutic as a carbon source.
  • the glycan therapeutic is resistant to gastric acidity.
  • the glycan therapeutic is resistant to hydrolysis by a mammalian enzyme.
  • the mammalian enzyme is human amylase.
  • the glycan therapeutic is resistant to gastrointestinal absorption.
  • composition for use in any of the methods described herein.
  • a dosage form comprising the composition.
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the glycan therapeutic preparation has an average degree of branching (DB) of at least 0.01, iv) at least 50% of the glycans in the preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, v) the ratio of alpha- to beta-glycosidic bonds present in the glycans of the preparation overall is between about 1:1 to about 5:1, or vi) any combination of one, two, three, four or five of i), ii), iii), iv) and v).
  • DB average degree of branching
  • DP degree of polymerization
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise branched oligosaccharides, iii) the branched oligosaccharides comprise glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose glycan units, iv) the average degree of branching (DB) of the branched glycans in the glycan therapeutic preparation is between 0.01 and 0.3, v) at least 50% of the glycans in the glycan therapeutic preparation have a degree of polymerization (DP) of at least 3 and less than 30 glycan units, vi) the average DP of the glycan therapeutic preparation is between about DP6 and about DP10, vii) the ratio of alpha- to beta-glycosidic bonds present in the glycan
  • the glycan therapeutic preparation i) comprises branched glycans, ii) the branched glycans comprise one or more glycan units, iii) the branched glycans comprise at least 1% of branched glycan units, iv) the branched glycans have a degree of polymerization (DP) of between 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycans comprise a mixture of beta and alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeutic preparation comprises a mixture of branched glycans and unbranched glycans, viii) the glycan therapeutic preparation comprises a mixture of
  • the glycan therapeutic preparation may comprise one or more homo-glycans selected from xyl100, rha100, ara100, gal100, glu100, fuc100, fru100, and man100.
  • the glycan therapeutic preparation may comprise one or more hetero-glycans selected from ara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10 and glu90gly10.
  • the glycan therapeutic preparation may comprise one or more hetero-glycans selected from xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, and glu33gal33neu33.
  • the glycan therapeutic preparation may comprise one or more homo or hetero-glycans selected from xyl100, rha100, ara100, gal100, glu100, man100, fuc100, fru100, ara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10 and glu90gly10, xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, and glu33gal33neu33.
  • the glycan therapeutic preparation may comprise one or more homo or hetero-glycans selected from ara50gal50, glu33gal33fuc33, glu50gal50, gal100, glu100, xyl100, ara100, ara60xyl40, glu80man20, glu60man40, man52glu29gal19, man100.
  • the glycan therapeutic preparation may comprise one or more homo-glycans selected from man100, xyl100, or glu100.
  • the glycan therapeutic preparation may comprise man100.
  • the glycan therapeutic preparation may comprise xyl100.
  • the glycan therapeutic preparation may comprise glu100.
  • the glycan therapeutic preparation may comprise one or more hetero-glycans selected from glu50gal50, glu80man20, glu33gal33fuc33, man52glu29gal19.
  • the glycan therapeutic preparation may comprise glu50gal50.
  • the glycan therapeutic preparation may comprise glu80man20.
  • the glycan therapeutic preparation may comprise glu33gal33fuc33.
  • the glycan therapeutic preparation may comprise man52glu29gal19.
  • the a probiotic bacteria may comprise bacteria of the genus Akkermansia, Anaerofilum, Bacteroides, Blautia, Bifidobacterium, Butyrivibrio, Clostridium, Coprococcus, Dialister, Dorea, Fusobacterium, Eubacterium, Faecalibacterium, Lachnospira, Lactobacillus, Phascolarctobacterium, Peptococcus, Peptostreptococcus, Prevotella, Roseburia, Ruminococcus , and Streptococcus , and/or one or more of the species Akkermansia municiphilia, minuta, Clostridium coccoides, Clostridium leptum, Clostridium scindens, Dialister in
  • the cancer agent may comprise, e.g., checkpoint inhibitors (such as, e.g., anti-PD-1, anti-PD-L1, anti-CTLA4, anti-TIM-3, anti-LAG-3); vaccines (such as, e.g., autologous cancer vaccines, allogeneic cancer vaccines, neoantigen cancer vaccines, shared antigen cancer vaccines (e.g.
  • the anti-cancer agent is PD-L1.
  • the anti-cancer is 5-FU and/or irinotecan.
  • the immunomodulatory agent may comprise, e.g., pro-inflammatory agents (e.g. pro-inflammatory cytokines), anti-inflammatory agents (e.g. anti-inflammatory cytokines, NSAIDs, anti-allergy agents), steroids, hormones, interleukins, vaccines/antigens, anti-microbial agents (e.g. anti-virals) and anti-neoplastic agents.
  • pro-inflammatory agents e.g. pro-inflammatory cytokines
  • anti-inflammatory agents e.g. anti-inflammatory cytokines, NSAIDs, anti-allergy agents
  • steroids e.g. anti-inflammatory agents, steroids, hormones, interleukins, vaccines/antigens
  • anti-microbial agents e.g. anti-virals
  • anti-neoplastic agents e.g., anti-neoplastic agents.
  • the metabolism modulating agent may comprise, e.g., insulin, metformin, lorcaserin, somatropin, miglitol, sitagliptin, simvastatin, progestagens, corticosteroids, hormones, and interleukins.
  • the invention features compounds and compositions (e.g., pharmaceutical compositions, medical foods, or dietary supplements) for use in, e.g., treating an immune imbalance in a subject; reducing an infection and/or an inflammation in a subject having an immune imbalance; modulating the composition and/or metabolic activity of the intestinal bacterial community of a subject having an immune imbalance; treating a dysbiosis in a subject having an immune imbalance; treating a nutritional imbalance in a subject; modulating the composition and/or metabolic activity of the intestinal bacterial community of a subject having a nutritional imbalance; treating a dysbiosis in a subject having a nutritional imbalance; treating cancer in a subject; modulating the composition and/or metabolic activity of the intestinal bacterial community of a subject having cancer; treating a dysbiosis in a subject having cancer; reducing an infection and/or an inflammation in a subject having cancer; inducing apoptosis of a cancer or a precancerous cell in a subject having
  • FIG. 1 A representative SEC curve between 16 and 20.5 minutes of a glu100 sample showing the average MW and the MW at 10% of maximum absorption on both the leading and trailing edges of the curve.
  • FIG. 2 A representative anomeric region of an 1 H- 13 C HSQC spectrum of a glu100 sample showing the signal distribution of alpha- and beta-glycosidic bonds
  • FIG. 3 A representative anomeric region of an 1 H- 13 C HSQC spectrum of glu100 ( FIG. 3A ), glu50gal50 ( FIG. 3B ), and gal100 ( FIG. 3C ) samples, demonstrating the additive effect of the fingerprint peaks.
  • FIG. 4 Representative GC chromatograms of three representative permethylated and hydrolyzed glycans showing distribution of regiochemistry as assigned by comparison to known standards.
  • FIG. 5 A representative partial assignment of the peaks in the anomeric region of a glu100 sample 1 H- 13 C HSQC spectrum showing the separation between alpha and beta isomers in the 1 H axis, with alpha isomers downfield ( 1 H>4.8 ppm in this case) and beta isomers upfield ( 1 H ⁇ 4.8 ppm in this case).
  • terminal and internal sugars can be distinguished in the 13 C axis with terminal sugars upfield ( 13 C ⁇ 94 ppm for alpha and 13 C ⁇ 100 ppm for beta in this case) and internal sugars downfield ( 13 C>94 ppm for alpha and 13 C>100 ppm for beta in this case).
  • FIG. 6 A portion of an exemplary catalyst with a polymeric backbone and side chains is illustrated in FIG. 6A .
  • a portion of an exemplary catalyst, in which a side chain with the acidic group is connected to the polymeric backbone by a linker and in which a side chain with the cationic group is connected directly to the polymeric backbone is illustrated in FIG. 6B .
  • FIG. 7 a Anomeric region of the 1H-13C HSQC spectrum of man100.
  • FIG. 7 b Anomeric region of the 1H-13C HSQC spectrum of xyl100.
  • FIG. 8 Taxa shifts in human fecal slurry grown with selected glycan therapeutics.
  • FIG. 8 a Bacterial phyla, percent (%) relative abundance in 1% fecal slurry exposed to no added carbon, xyl100, man52glu29gal19, glu100, and FOS;
  • FIG. 8 b Bifidobacteriales % relative abundance in 1% fecal slurry exposed to no added carbon, xyl100, man52glu29gal19, glu100, and FOS;
  • FIG. 8 a Bacterial phyla, percent (%) relative abundance in 1% fecal slurry exposed to no added carbon, xyl100, man52glu29gal19, glu100, and FOS
  • FIG. 8 b Bifidobacteriales % relative abundance in 1% fecal slurry exposed to no added carbon, xyl100, man52glu29gal19, glu100, and FOS;
  • FIG. 8 c Bifidobacteria % relative abundance in 1% fecal slurry exposed to no added carbon, xyl100, man52glu29gal19, glu100, and FOS;
  • FIG. 8 d Bacteroidales % relative abundance in 1% fecal slurry exposed to no added carbon, xyl100, man52glu29gal19, glu100, and FOS;
  • FIG. 8 e Clostridiales % relative abundance in 1% fecal slurry exposed to no added carbon, xyl100, man52glu29gal19, glu100, and FOS.
  • FIG. 9 Relative abundance of OTU 51 in individuals treated with glu50gal50. Dashed vertical lines represent treatment doses. 62% of individuals did not have this OTU in their gut microbiota prior to treatment.
  • FIG. 10 Distances were calculated for each mouse between microbiota sampled at 1 day before and 5 days after glycan or water administrated. The larger the distance, the bigger change in microbial composition is observed.
  • FIG. 11 Shannon diversity index. Paired Wilcoxon test was used to calculate the significance of observed differences.
  • FIG. 12 Relative abundance of sequences assigned to genus Akkermansia , phylum Verrucomicrobia is shown in FIG. 12 a Relative abundance of sequences assigned to genus Blautia , phylum Firmicutes is shown in FIG. 12 b.
  • FIG. 13 SCFA concentrations in supernatants of BUN.80 and DLO.76 grown with either FOS or glycan glu80man20
  • FIG. 14 Most abundant SCFA in the cecal contents of mice fed either a normal mouse chow, high fat diet, or high fat diet+glycans. (*P ⁇ 0.05,**P ⁇ 0.01, Wilcox, FDR corrected).
  • FIG. 15 PCoA of metabolomic profile.
  • FIG. 16 PCoA of bile acid composition of mouse cecal contents on Normal Chow and High Fat Diet+/ ⁇ glycan treatment.
  • FIG. 17 Glycan treatment resulting in a reduction of (A) DCA (deoxycholic acid) and (B) LCA (lithocholic acid) compared to high fat control.
  • FIG. 18 White blood cell count on Day 5; bars represent mean and standard deviation. Significance was determined by using one-way ANOVA with Dunnett's multiple comparisons test. *p ⁇ 0.05.
  • FIG. 19 Effect of commercial fibers and novel glycans on colonic propulsion in morphine-treated mice. Significance was determined by using one-way ANOVA with Dunnett's multiple comparisons test. *p ⁇ 0.05, **p ⁇ 0.01.
  • FIG. 20 Colonic propulsion in treatment responder ( FIG. 20 a ) and treatment non-responder ( FIG. 20 b ) groups. Average time to bead expulsion, an indicator of colonic propulsion, was similar in animals that responded to naloxone, xyl100 and XOS Likewise, average time to bead expulsion in responders was similar in PDX and ara100. Time to bead expulsion was similar across all non-responder groups regardless of treatment.
  • FIG. 21 Tumor growth curves: Group 1 received vehicle treatment (gray long-dashed line), Group 2 mice received man100 (black solid line), Group 3 mice received anti-PD-L1 (gray shortest-dashed line), and Group 4 mice received the bifidobacteria mix (gray medium-dashed line). Based on one-way ANOVA, the difference between Group 1 and Group 2 was significant with a p ⁇ 0.05 on days 21, 24, 28, and 31. Values shown are mean+/ ⁇ standard deviation across the groups.
  • FIG. 22 Spider plots of vehicle control (Group 1, thin gray dotted lines), anti-PD-L1 (Group 3, thick gray solid lines), and man100 (Group 2, thick black solid lines) show tumor growth curves for each mouse from days 7-31.
  • glycan therapeutics and pharmaceutical compositions, medical foods and dietary supplements thereof, and related methods, which have been found to be effective to treat a number of diseases, disorders or pathological conditions.
  • the term “abundance” as it relates to a microbial taxa refers to the presence of one microbial taxa as compared to another microbial taxa in a defined microbial niche, such as the GI tract, or in the entire host organism (e.g. a human or a laboratory animal model of disease).
  • “Directly acquiring” means performing a process (e.g., performing a synthetic or analytical method or protocol) to obtain the value or physical entity.
  • “Indirectly acquiring” refers to receiving the value or physical entity from another party or source (e.g., a third party laboratory that directly acquired the physical entity or value).
  • Directly acquiring a value or physical entity includes performing a process that includes a physical change in a physical substance or the use of a machine or device. Examples of directly acquiring a value include obtaining a sample from a human subject.
  • Directly acquiring a value includes performing a process that uses a machine or device, e.g., an NMR spectrometer to obtain an N
  • antibody is used in the broadest sense and includes monoclonal antibodies (including full length or intact monoclonal antibodies), polyclonal antibodies, multivalent antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired activity.
  • cancer refers to a cell (or cells) that has an aberrant capacity for autonomous growth or replication and an abnormal state or condition (e.g. of a tissue or organ) characterized by proliferative cell growth.
  • cancer includes any solid or liquid, benign or malignant, non-invasive or invasive cancer or tumor, including hyperplasias, neoplasms, carcinoma, sarcoma, or a hematopoietic neoplastic disorder (e.g., a leukemia) and pre-cancerous or premalignant lesions.
  • colonization of a host organism refers to the non-transitory residence of a bacterium or other microbial organism in a niche.
  • a “combination therapy” or “administered in combination” means that two (or more) different agents or treatments are administered to a subject as part of a defined treatment regimen for a particular disease or condition.
  • the treatment regimen defines the doses and periodicity of administration of each agent such that the effects of the separate agents on the subject overlap.
  • the delivery of the two or more agents is simultaneous or concurrent and the agents may be co-formulated.
  • the two or more agents are not co-formulated and are administered in a sequential manner as part of a prescribed regimen.
  • administration of two or more agents or treatments in combination is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with one agent or treatment delivered alone or in the absence of the other.
  • the effect of the two treatments can be partially additive, wholly additive, or greater than additive (e.g., synergistic).
  • Sequential or substantially simultaneous administration of each therapeutic agent can be effected by any appropriate route including oral routes, intravenous routes, intramuscular routes, and direct absorption through mucous membrane tissues.
  • the therapeutic agents can be administered by the same route or by different routes. For example, a first therapeutic agent of the combination may be administered by intravenous injection while a second therapeutic agent of the combination may be administered orally.
  • Diversity of a microbial community refers to the diversity found in the microbiota of a within a given niche or host subject. Diversity can relate to the number of distinct microbial taxa and/or richness of the microbial taxa within the niche or host and can be expressed, e.g. using the Shannon Diversity index (Shannon entropy), alpha-beta diversity, total number of observed OTUs, or Chao1 index, as described herein. In some embodiments, a microbiome regulator described herein modulates diversity within a microbial community, which may be expressed using Shannon entropy as a measure.
  • a “dosage regimen”, “dosing regimen”, or “treatment regimen” is a modality of drug administration that achieves a therapeutic objective.
  • a dosage regimen includes definition of one, two, three, or four of: a route of administration, a unit dose, a frequency of dosage, or a length of treatment.
  • dysbiosis refers to the state of the microbiota under conditions of host disease, predisposition to host disease, or other unwanted condition or symptom of the host.
  • dysbiosis refers to the state of the microbiota under conditions of disease.
  • Dysbiosis can be contrasted with eubiosis, which refers to the state of the microbiota under healthy conditions of the host.
  • the state of the microbiota may include the characteristics relating to either the structure or function of the microbiota.
  • a dysbiosis includes an imbalance in the state of the microbiota, wherein the normal diversity or relative abundance of a microbial taxa is affected, e.g., relative to a second bacterial taxa or relative to the abundance of said taxa under conditions of health.
  • a dysbiosis comprises an imbalance in the function of the microbiota, e.g., a change in level of gene expression, level of a gene product, or metabolic output (e.g., an immune function such as immune surveillance it the inflammation response).
  • a dysbiosis is an an undesired, e.g., unhealthy, state associated with unwanted symptoms in the host and that no longer promotes health.
  • a “dysbiosis of the gastrointestinal microbiota” refers to an imbalanced state of the microbiota of the GI tract (e.g., in the stomach, small intestine, or large intestine).
  • niche refers to the ecological space in which an organism or group of organisms occupies (such as the GI tract or one or more subsection of the GI-tract, such as, e.g., the stomach, the large and small intestine, the rectum, etc.). In some embodiments, niche specifically refers to a space that microorganisms occupy.
  • Niche may describe how an organism or population of organisms responds to the distribution of resources, physical parameters (e.g., host tissue space) and competitors (e.g., by growing when resources are abundant, and when predators, parasites and pathogens are scarce) and how it in turn alters those same factors (e.g., limiting access to resources by other organisms, acting as a food source for predators and a consumer of prey).
  • physical parameters e.g., host tissue space
  • competitors e.g., by growing when resources are abundant, and when predators, parasites and pathogens are scarce
  • an “effective amount” and “therapeutically effective amount” as used herein refers to an amount of a pharmaceutical composition or a drug agent that is sufficient to provide a desired effect. In some embodiments, a physician or other health professional decides the appropriate amount and dosage regimen. An effective amount also refers to an amount of a pharmaceutical composition or a drug agent that prevents the development or relapse of a medical condition.
  • a “glycan therapeutic preparation” (also referred to as a “preparation of glycan therapeutics”, “glycan preparation” or “glycan therapeutic”) is a preparation comprising glycans (sometimes referred to as glycan species) that exhibits a therapeutic effect.
  • a glycan therapeutic comprises a synthetic mixture of a plurality of mono-, di-, oligomeric and/or polymeric glycan species (e.g. oligo- and/or polysaccharides, referred to as “oligosaccharides”), wherein the oligomeric and/or polymeric glycan species comprise glycan units that are linked by glycosidic bonds.
  • a glycan therapeutic may be formulated into a pharmaceutical composition, a medical food or dietary supplement for human use.
  • a glycan therapeutic may be formulated in any suitable dosage form including a kit.
  • preparations of glycan therapeutics do not contain one or more naturally occurring oligo- or polysaccharide, including: glucooligosaccharide, mannanoligosaccharide, inulin, lychnose, maltotretraose, nigerotetraose, nystose, sesemose, stachyose, isomaltotriose, nigerotriose, maltotriose, melezitose, maltotriulose, raffinose, kestose, fructooligosaccharide, 2′-fucosyllactose, galactooligosaccharide, glycosyl, idraparinux, isomaltooligo
  • a “glycan unit” as used herein refers to the individual unit of a glycan species disclosed herein, e.g., the building blocks from which the glycan species is made.
  • a glycan unit is a monomer.
  • a glycan unit is a dimer.
  • a glycan unit is a monosaccharide.
  • a glycan unit is a disaccharide.
  • the glycan unit is a carbohydrate and may be selected from a sugar alcohol, a short-chain fatty acid, a sugar acid, an imino sugar, a deoxy sugar, and an amino sugar.
  • the glycan unit is erythrose, threose, erythulose, arabinose, lyxose, ribose, xylose, ribulose, xylulose, allose, altrose, galactose, glucose, gulose, idose, mannose, talose, fructose, psicose, sorbose, tagatose, fucose, fuculose, rhamnose, mannoheptulose, sedoheptulose, and the like.
  • the glycan unit is glucose, galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnose.
  • a glycan comprises distinct glycan units, e.g., a first and a second monosaccharide, or a first and a second disaccharide, or a monosaccaride and a disaccharide.
  • a glycan comprises distinct glycan units, e.g., a first, a second, a third, a fourth, and/or a fifth distinct glycan unit.
  • an “isolated” or “purified” glycan therapeutic preparation is substantially pure and free of contaminants, e.g. pathogens or otherwise unwanted biological material, or toxic or otherwise unwanted organic or inorganic compounds.
  • pure or isolated compounds, compositions or preparations may contain traces of solvents and/or salts (such as less than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, less than 0.5% or 0.1% by w/w, w/v, v/v or molar %).
  • Purified compounds are or preparations contain at least about 60% (by w/w, w/v, v/v or molar %), at least about 75%, at least about 90%, at least about 95%, at least about 97%, at least about 98%, or at least about 99% by w/w, w/v, v/v or molar % the compound(s) of interest.
  • a purified (substantially pure) or isolated preparation of glycan therapeutics is one that is at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 98%, 99%, 99.5%, 99.8%, 99.9% or 100% of the glycan therapeutic by w/w, w/v, v/v or molar % (i.e. not including any solvent, such as e.g. water, in which the glycan therapeutic preparation may be dissolved) and separated from the components that accompany it, e.g. during manufacture, extraction/purification and/or processing (e.g. such that the glycan therapeutic is substantially free from undesired compounds).
  • Purity may be measured by any appropriate standard method, for example, by column chromatography (e.g., size-exclusion chromatography (SEC)), thin layer chromatography (TLC), gas chromatography (GC), high-performance liquid chromatography (HPLC) or nuclear magnatic resonance (NMR) spectroscopy.
  • SEC size-exclusion chromatography
  • TLC thin layer chromatography
  • GC gas chromatography
  • HPLC high-performance liquid chromatography
  • NMR nuclear magnatic resonance
  • microbiome refers to the genetic content of the communities of microbes that live in and on a subject (e.g. a human subject), both sustainably and transiently, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses (e.g., phage)), wherein “genetic content” includes genomic DNA, RNA such as ribosomal RNA and messenger RNA, the epigenome, plasmids, and all other types of genetic information.
  • microbiome specifically refers to genetic content of the communities of microorganisms in a niche.
  • Microbiota refers to the community of microorganisms that occur (sustainably or transiently) in and on a subject (e.g. a human subject), including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses, e.g. phage). In some embodiments, microbiota specifically refers to the microbial community in a niche.
  • Modulate the microbiota” or “modulating the microbiota” as used herein refers to changing the state of the microbiota.
  • Changing the state of the microbiota may include changing the structure and/or function of the microbiota.
  • a change in the structure of the microbiota is, e.g., a change in the relative composition of a taxa, e.g., in one or more region of the GI tract such as the cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and/or rectum.
  • a change in the structure of the microbiota comprises a change in the abundance of a taxa, e.g., relative to another taxa or relative to what would be observed in the absence of the modulation.
  • Modulation of the microbiota may also, or in addition, include a change in a function of the microbiota, such as a change in microbiota gene expression, level of a gene product (e.g., RNA or protein), or metabolic output of the microbiota.
  • Functions of the microbiota may also include host pathogen protection, host nutrition, host metabolism and host immune modulation.
  • Modulation of the structure or function of the microbiota may additionally induce a change in one or more functional pathway of the host (e.g., a change in gene expression, level of a gene product, and/or metabolic output of a host cell or host process) as a result of a change in the microbiota or its function.
  • a change in one or more functional pathway of the host e.g., a change in gene expression, level of a gene product, and/or metabolic output of a host cell or host process
  • oligosaccharide refers to a molecule consisting of multiple (i.e., two or more) individual glycan units linked covalently. Each glycan unit may be linked through a glycosidic bond (e.g., a 1->2 glycosidic bond, a 1->3 glycosidic bond, a 1->4 glycosidic bond, a 1->5 glycosidic bond or a 1->6 glycosidic bond) present in either the alpha or beta configuration.
  • a glycosidic bond e.g., a 1->2 glycosidic bond, a 1->3 glycosidic bond, a 1->4 glycosidic bond, a 1->5 glycosidic bond or a 1->6 glycosidic bond
  • pathogenic refers to a substance, microorganism or condition that has the capability to cause a disease.
  • pathogens also include microbes (e.g. bacteria) that are associated with a disease or condition but for which a causative relationship (e.g., a direct causative relationship) has not been established or has yet to be established.
  • a “pharmaceutical composition” or “pharmaceutical preparation” is a composition or preparation having pharmacological activity or other direct effect in the mitigation, treatment, or prevention of disease, and/or a finished dosage form or formulation thereof and is for human use.
  • a pharmaceutical composition or pharmaceutical preparation is typically produced under good manufacturing practices (GMP) conditions.
  • GMP good manufacturing practices
  • Pharmaceutical compositions or preparations may be sterile or non-sterile. If non-sterile, such pharmaceutical compositions meet the microbiological specifications and criteria for non-sterile pharmaceutical products as described in the U.S. Pharmacopeia (USP) or European Pharmacopoeia (EP).
  • Pharmaceutical compositions may further comprise or may be co-administered with additional active agents, such as, e.g. additional therapeutic agents.
  • Pharmaceutical compositions may also comprise pharmaceutically acceptable excipients, solvents, carriers, fillers, or any combination thereof.
  • phenotype refers to a set of observable characteristics of an individual entity.
  • an individual subject may have a phenotype of “healthy” or “diseased.”
  • a phenotype may describe the state of an entity, wherein all entities within a phenotype share the same set of characteristics that describe the phenotype.
  • the phenotype of an individual results in part, or in whole, from the interaction of the entities genome and/or microbiome with the environment.
  • polysaccharide refers to a polymeric molecule consisting of multiple individual glycan units linked covalently.
  • a polysaccharide comprises at least 10 or more glycan units (e.g., at least 10, at least 15, at least 20, at least 25, or at least 50, at least 100, at least 250, at least 500, or at least 1000 glycan units).
  • Each glycan unit may be linked through a glycosidic bond (e.g., a 1->2 glycosidic bond, a 1->3 glycosidic bond, a 1->4 glycosidic bond, a 1->5 glycosidic bond and a 1->6 glycosidic bond) present in either the alpha or beta configuration.
  • a polysaccharide is a homogenous polymer comprising identical repeating units.
  • a polysaccharide is a heterogenous polymer comprised of varied repeating units.
  • Polysaccharides may further be characterized by a degree of branching (DB, branching points per residue) or a degree of polymerization (DP).
  • subject or “patient” generally refers to any human subject.
  • the term does not denote a particular age or gender.
  • Subjects may include pregnant women.
  • Subjects may include a newborn (a preterm newborn, a full term newborn), an infant up to one year of age, young children (e.g., 1 yr to 12 yrs), teenagers, (e.g., 13-19 yrs), adults (e.g., 20-64 yrs), and elderly adults (65 yrs and older).
  • a subject does not include an agricultural animal, e.g., farm animals or livestock, e.g., cattle, horses, sheep, swine, chickens, etc.
  • a subject comprises a host and its corresponding microbiota.
  • a “substantial decrease” as used herein is a decrease of 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.9%, or 100%.
  • a “substantial increase” as used herein is an increase of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, 550%, 600%, 650%, 700%, 750%, 800%, 850%, 900%, 950%, 1000%, or more than 1000%.
  • Synthetic refers to a man-made compound or preparation, such as a glycan therapeutic preparation, that is not naturally occurring.
  • the polymeric catalyst described herein is used to synthesize the glycans of the preparation under suitable reaction conditions, e.g. by a polymerization reaction that creates oligomers and polymers from individual glycan units that are added to the reaction.
  • the polymeric catalyst acts as a hydrolysis agent and can break glycosidic bonds.
  • the polymer catalyst can form glycosidic bonds.
  • Synthetic glycan therapeutic preparations may also include glycan therapeutics that are not isolated from a natural oligo- or polysaccharide source.
  • the glycan therapeutic preparation is not isolated from a natural oligo- or polysaccharide source
  • the glycan units making up the glycan therapeutic can be and often are isolated from natural oligo- or polysaccharide sources, including those listed herein, or are synthesized de novo.
  • treating and “treatment” as used herein refer to the administration of an agent or composition to a subject (e.g., a symptomatic subject afflicted with an adverse condition, disorder, or disease) so as to affect a reduction in severity and/or frequency of a symptom, eliminate a symptom and/or its underlying cause, and/or facilitate improvement or remediation of damage, and/or preventing an adverse condition, disorder, or disease in an asymptomatic subject who is susceptible to a particular adverse condition, disorder, or disease, or who is suspected of developing or at risk of developing the condition, disorder, or disease.
  • a subject e.g., a symptomatic subject afflicted with an adverse condition, disorder, or disease
  • Preparations comprising a plurality of glycans such as, e.g., oligosaccharide mixtures can be generated using a non-enzymatic catalyst, e.g., the polymeric catalyst described in U.S. Pat. No. 8,466,242, “POLYMERIC ACID CATALYSTS AND USES THEREOF” or by other suitable methods.
  • a non-enzymatic catalyst e.g., the polymeric catalyst described in U.S. Pat. No. 8,466,242, “POLYMERIC ACID CATALYSTS AND USES THEREOF” or by other suitable methods.
  • glycans e.g. oligosaccharides
  • a suitable solvent such as, e.g. water or a non-aqueous solvent
  • preparations of glycans are polymolecular.
  • preparations of glycans are polymolecular and polydisperse.
  • the glycan therapeutic preparations comprise a mixture of distinct oligosaccharide species (e.g. of different degree of polymerization and degree of branching and different alpha-to-beta glycosidic bond ratios).
  • the glycan therapeutic preparations comprise a plurality of distinct species (e.g.
  • oligosaccharides may consist of 1 ⁇ 10 3 , 1 ⁇ 10 4 , 1 ⁇ 10 5 , 1 ⁇ 10 6 , 1 ⁇ 10 7 , 1 ⁇ 10 8 , 1 ⁇ 10 9 , 1 ⁇ 10 10 , 1 ⁇ 10 11 , 1 ⁇ 10 12 , 1 ⁇ 10 13 , 1 ⁇ 10 14 , or more species in various proportions to each other.
  • the average properties of the glycan therapeutic preparations such as degree of polymerization, degree of branching, alpha- and beta-glycosidic bond ratios, etc.
  • the starting material (comprising the glycan units) is contacted with a polymer catalyst under conditions that promote the formation of one or more glycosidic bond between glycan units, thereby producing a preparation of glycans.
  • the glycan unit is a monosaccharide.
  • the glycan unit is a disaccharide.
  • Suitable polymer catalysts comprise acidic monomers and ionic monomers that are connected to form a polymeric backbone, wherein each acidic monomer has at least one Bronsted-Lowry acid, and each ionic monomer independently has at least one nitrogen-containing cationic group or phosphorous-containing cationic group.
  • each acidic monomer of the polymer catalyst may have one Bronsted-Lowry acid, and optionally the Bronsted-Lowry acids are distinct.
  • each ionic monomer of the polymer catalyst has one nitrogen-containing cationic group or phosphorous-containing cationic group.
  • at least one ionic monomer of the polymer catalyst has two nitrogen-containing cationic groups or phosphorous-containing cationic groups. A schematic outlining the general functional groups is shown in FIGS. 6 a and 6 b.
  • the polymeric catalyst and the glycan units are introduced into an interior chamber of a reactor, either concurrently or sequentially.
  • Glycan (e.g. oligosaccharides) synthesis can be performed in a batch process or a continuous process.
  • glycan synthesis is performed in a batch process, where the contents of the reactor are continuously mixed or blended, and all or a substantial amount of the products of the reaction are removed (e.g. isolated and/or recovered).
  • glycan synthesis is performed in a batch process, where the contents of the reactor are initially intermingled or mixed but no further physical mixing is performed.
  • glycan synthesis is performed in a batch process, wherein once further mixing of the contents, or periodic mixing of the contents of the reactor, is performed (e.g., at one or more times per hour), all or a substantial amount of the products of the reaction are removed (e.g. isolated and/or recovered) after a certain period of time.
  • glycan (e.g. oligosaccharide) synthesis is performed in a continuous process, where the contents flow through the reactor with an average continuous flow rate but with no explicit mixing. After introduction of the polymeric catalyst and glycan units into the reactor, the contents of the reactor are continuously or periodically mixed or blended, and after a period of time, less than all of the products of the reaction are removed (e.g. isolated and/or recovered).
  • glycan synthesis is performed in a continuous process, where the mixture containing the catalyst and glycan units is not actively mixed. Additionally, mixing of catalyst and the glycan units may occur as a result of the redistribution of polymeric catalysts settling by gravity, or the non-active mixing that occurs as the material flows through a continuous reactor.
  • the starting material for the polymerization reaction is one or more glycan unit selected from one or more monosaccharides, one or more disaccharides, or a combination thereof. In some embodiments of the method, the starting material for the polymerization reaction is one or more glycan unit selected from a furanose sugar and a pyranose sugar. In some embodiments of the method, the starting material for the polymerization reaction is one or more glycan unit selected from a tetrose, a pentose, a hexose, or a heptose.
  • the starting material for the polymerization reaction is one or more glycan unit selected from a glucose, a galactose, an arabinose, a mannose, a fructose, a xylose, a fucose, and a rhamnose, all optionally in either their L- or D-form, in alpha or beta configuration (for dimers), and/or a deoxy-form, where applicable, and any combination thereof.
  • the glycan units are substituted or derivatized with one or more of an acetate ester, sulfate half-ester, phosphate ester, or a pyruvyl cyclic acetal group, or have been otherwise derivatized at, e.g., at one or more hydroxyl groups.
  • the glycan units used in the methods described herein may include one or more sugars.
  • the one or more sugars are selected from monosaccharides, disaccharides, and trisaccharides, or any mixtures thereof.
  • the one or more sugars are monosaccharides, such as one or more C5 or C6 monosaccharides.
  • the one or more sugars are C5 monosaccharides. In other embodiments, the one or more sugars are C6 monosaccharides.
  • the starting material for the polymerization reaction is one or more glycan unit selected from monosaccharides and other carbohydrates including glycolaldehyde, glyceraldehyde, dihydroxyacetone, erythrose, threose, erythulose, arabinose, lyxose, ribose, xylose, ribulose, xylulose, allose, altrose, galactose, glucose, gulose, idose, mannose, talose, fructose, psicose, sorbose, tagatose, fucose, fuculose, rhamnose, mannoheptulose, sedoheptulose, neuraminic acid, N-acetylneuraminic acid, N-acetylgalactosamine, N-acetylglucosamine, fructosamine, galactosamine, glucosamine, sorbito
  • the starting material for the polymerization reaction is one or more glycan unit selected from a monosaccharide.
  • the monosaccharide is glucose, galactose, fructose, fucose, mannose, arabinose, rhamnose, and xylose.
  • the glycan unit is not glucose.
  • the glycan unit is not galactose.
  • the glycan unit is not fructose.
  • the glycan unit is not fucose.
  • the glycan unit is not mannose.
  • the glycan unit is not arabinose.
  • the glycan unit is not rhamnose.
  • the glycan unit is not xylose.
  • the starting material for the polymerization reaction is one or more glycan unit selected from disaccharides and other carbohydrates including acarviosin, N-acetyllactosamine, allolactose, cellobiose, chitobiose, glactose-alpha-1,3-galactose, gentiobiose, isomalt, isomaltose, isomaltulose, kojibiose, lactitol, lactobionic acid, lactose, lactulose, laminaribiose, maltitol, maltose, mannobiose, melibiose, melibiulose, neohesperidose, nigerose, robinose, rutinose, sambubiose, sophorose, sucralose, sucrose, sucrose acetate isobutyrate, sucrose octaacetate, trehalose, sucralose, suc
  • the starting material for the polymerization reaction is one or more glycan unit selected from an amino sugar, a deoxy sugar, an imino sugar, a sugar acid, a short-chain fatty acid, and a sugar alcohol.
  • Suitable glycan units include amino sugars, such as, e.g. acarbose, N-acetylemannosamine, N-acetylmuramic acid, N-acetylneuraminic acid, N-acetyletalosaminuronic acid, arabinopyranosyl-N-methyl-N-nitrosourea, D-fructose-L-histidine, N-glycolyneuraminic acid, ketosamine, kidamycin, mannosamine, 1B-methylseleno-N-acetyl-D-galactosamine, muramic acid, muramyl dipeptide, phosphoribosylamine, PUGNAc, sialyl-Lewis A, sialyl-Lewis X, validamycin, voglibose, N-acetylgalactosamine, N-acetylglucosamine, aspartylglucosamine, bacillithi
  • Suitable glycan units include deoxy sugars, such as, e.g. 1-5-ahydroglucitol, cladinose, colitose, 2-deoxy-D-glucose, 3-deoxyglucasone, deoxyribose, dideoxynucleotide, digitalose, fludeooxyglucose, sarmentose, and sulfoquinovose.
  • deoxy sugars such as, e.g. 1-5-ahydroglucitol, cladinose, colitose, 2-deoxy-D-glucose, 3-deoxyglucasone, deoxyribose, dideoxynucleotide, digitalose, fludeooxyglucose, sarmentose, and sulfoquinovose.
  • Suitable glycan units include imino sugars, such as, e.g. castanospermine, 1-deoxynojirimycin, iminosugar, miglitol, miglustat, and swainsonine.
  • Suitable glycan units include sugar acids, such as, e.g. N-acetylneuraminic acid, N-acetyltalosamnuronic acid, aldaric acid, aldonic acid, 3-deoxy-D-manno-oct-2-ulosonic acid, glucuronic acid, glucosaminuronic acid, glyceric acid, N-glycolylneuraminic acid, iduronic acid, isosaccharinic acid, pangamic acid, sialic acid, threonic acid, ulosonic acid, uronic acid, xylonic acid, gluconic acid, ascorbic acid, ketodeoxyoctulosonic acid, galacturonic acid, galactosaminuronic acid, mannuronic acid, mannosaminuronic acid, tartaric acid, mucic acid, saccharic acid, lactic acid, oxalic acid, succinic acid, hexanoic acid, fumaric acid
  • Suitable glycan units include short-chain fatty acids, such as, e.g., formic acid, acetic acid, propionic acid, butryic acid, isobutyric acid, valeric acid, and isovaleric acid.
  • Suitable glycan units include sugar alcohols, such as, e.g., methanol, ethylene glycol, glycerol, erythritol, threitol, arabitol, ribitol, xylitol, mannitol, sorbitol, galactitol, iditol, volemitol, fucitol, inositol, maltotritol, maltotetraitol, and polyglycitol.
  • sugar alcohols such as, e.g., methanol, ethylene glycol, glycerol, erythritol, threitol, arabitol, ribitol, xylitol, mannitol, sorbitol, galactitol, iditol, volemitol, fucitol, inositol, maltotritol, maltote
  • the glycan unit may exist as a salt (e.g., a pharmaceutically acceptable salt), such as, e.g., a hydrochlorate, hydroiodate, hydrobromate, phosphate, sulfate, methanesulfate, acetate, formate, tartrate, malate, citrate, succinate, lactate, gluconate, pyruvate, fumarate, propionate, aspartate, glutamate, benzoate, ascorbate salt.
  • a salt e.g., a pharmaceutically acceptable salt
  • the glycan units used in the methods described herein may be obtained from any commercially known sources, or produced according to any methods known in the art.
  • the glycan units and catalyst are allowed to react for at least 1 hour, at least 2 hours, at least 3 hours, at least 4 hours, at least 6 hours, at least 8 hours, at least 16 hours, at least 24 hours, at least 36 hours, or at least 48 hours; or between 1-24 hours, between 2-12 hours, between 3-6 hours, between 1-96 hours, between 12-72 hours, or between 12-48 hours.
  • the degree of polymerization (DP) of the glycan preparation produced according to the methods described herein can be regulated by the reaction time.
  • the degree of polymerization of the glycan preparation is increased by increasing the reaction time, while in other embodiments, the degree of polymerization of the glycan preparation is decreased by decreasing the reaction time.
  • the reaction temperature is maintained in the range of about 25° C. to about 150° C. In certain embodiments, the temperature is from about 30° C. to about 125° C., about 60° C. to about 120° C., about 80° C. to about 115° C., about 90° C. to about 110° C., about 95° C. to about 105° C., or about 100° C. to 110° C.
  • the amount of the glycan unit used in the methods described herein relative to the amount solvent used may affect the rate of reaction and yield.
  • the amount of the glycan unit used may be characterized by the dry solids content.
  • dry solids content refers to the total solids of a slurry as a percentage on a dry weight basis.
  • the dry solids content of the glycan unit is between about 5 wt % to about 95 wt %, between about 10 wt % to about 80 wt %, between about 15 wt %, to about 75 wt %, or between about 15 wt %, to about 50 wt %.
  • the amount of the catalyst used in the methods described herein may depend on several factors including, for example, the selection of the type(s) of glycan unit, the concentration of the glycan unit, and the reaction conditions (e.g., temperature, time, and pH).
  • the weight ratio of the catalyst to the glycan unit(s) is about 0.01 g/g to about 50 g/g, about 0.01 g/g to about 5 g/g, about 0.05 g/g to about 1.0 g/g, about 0.05 g/g to about 0.5 g/g, about 0.05 g/g to about 0.2 g/g, or about 0.1 g/g to about 0.2 g/g.
  • synthesis of the glycans (e.g. oligosaccharides) using the polymeric catalyst is carried out in an aqueous environment.
  • aqueous solvent is water.
  • ionic species e.g., salts of sodium, phosphorous, ammonium, magnesium.
  • the water has a resistivity of at least 0.1 megaohm-centimeters, of at least 1 megaohm-centimeters, of at least 2 megaohm-centimeters, of at least 5 megaohm-centimeters, or of at least 10 megaohm-centimeters.
  • water is produced with each glycosidic bond formed between the one or more glycan units (dehydration reaction).
  • the methods described herein may further include monitoring the amount of water present in the reaction mixture and/or the ratio of water to glycan unit or catalyst over a period of time.
  • the method further includes removing at least a portion of water produced in the reaction mixture (e.g., by removing at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 99%, or 100%, such as by vacuum filtration). It should be understood, however, that the amount of water to glycan unit may be adjusted based on the reaction conditions and specific catalyst used.
  • any method known in the art may be used to remove water in the reaction mixture, including, for example, by vacuum filtration, vacuum distillation, heating, and/or evaporation.
  • the method comprises including water in the reaction mixture.
  • a glycan preparation by: combining a glycan unit and a catalyst having acidic and ionic moieties to form a reaction mixture, wherein water is produced in the reaction mixture; and removing at least a portion of the water produced in the reaction mixture.
  • at least a portion of water is removed to maintain a water content in the reaction mixture of less than 99%, less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, less than 5%, or less than 1% by weight.
  • the degree of polymerization of the glycan preparation produced can be regulated by adjusting or controlling the concentration of water present in the reaction mixture. For example, in some embodiments, the degree of polymerization of the glycan preparation is increased by decreasing the water concentration, while in other embodiments, the degree of polymerization of the glycan preparation is decreased by increasing the water concentration. In some embodiments, the water content of the reaction is adjusted during the reaction to regulate the degree of polymerization of the glycan preparation produced.
  • a majority, e.g. about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of between 2 and 25, between 3 and 25, between 4 and 25, between 5 and 25, between 6 and 25, between 7 and 25, between 8 and 25, between 9 and 25, between 10 and 25, between 2 and 30, between 3 and 30, between 4 and 30, between 5 and 30, between 6 and 30, between 7 and 30, between 8 and 30, between 9 and 30, or between 10 and 30.
  • one or more glycan units may be added along with 1-50% (1-10%, 1-20%, 1-30%, 1-40%, 1-60%, 1-70%) by dry weight of one or more of the catalysts described herein.
  • Water or another compatible solvent 0.1-5 equiv, 1-5 equiv, 1-4 equiv, 0.1-4 equiv
  • the slurry can be combined at slow speed (e.g. 10-100 rpm, 50-200 rpm, 100-200 rpm) using a paddle sized to match the contours of the selected round bottom flask as closely as possible.
  • the mixture is heated to 70-180° C. (70-160° C., 75-165° C., 80-160° C.) under 10-1000 mbar vacuum pressure.
  • the reaction may be stirred for 30 minutes to 6 hours, constantly removing water from the reaction. Reaction progress can be monitored by HPLC.
  • the yield of conversion for the one or more glycan units in the methods described herein can be determined by any suitable method known in the art, including, for example, high performance liquid chromatography (HPLC).
  • HPLC high performance liquid chromatography
  • the yield of conversion to a glycan therapeutic preparation with DP>1 after combining the one or more glycan units with the catalyst is greater than about 50% (e.g., greater than about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%).
  • the yield of conversion to a glycan therapeutic preparation with >DP2 after combining the one or more glycan units with the catalyst is greater than 30% (e.g., greater than 35%, 40%, 45%, 50%, 55%. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%).
  • the yield of conversion to a glycan therapeutic preparation with >DP3 after combining the one or more glycan units with the catalyst is greater than 30% (e.g., greater than 35%, 40%, 45%, 50%, 55%. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%).
  • DP2 0%-40%, such as less than 40%, less than 30%, less than 20%, less than 10%, less than 5%, or less than 2%; or 10%-30% or 15%-25%
  • DP3 0%-20%, such as less than 15%, less than 10%, less than 5%
  • the solid mass obtained by the process can be dissolved in a volume of water sufficient to create a solution of approximately 50 Brix (grams sugar per 100 g solution). Once dissolution is complete, the solid catalyst can be removed by filtration.
  • the solution comprising therapeutic glycans can be concentrated to about 50-75 Brix, e.g., by rotary evaporation. In some embodiments, the solution comprising therapeutic glycans can be concentrated to about 50-60 Brix, 60-70 Brix, 70-80 Brix, 55-65 Brix, 65-75 Brix, or 75-85 Brix. In some embodiments, the solution comprising therapeutic glycans can be concentrated to about 50, 55, 60, 65, 70, 75, 80, or about 85 Brix.
  • an organic solvent can be used and water immiscible solvents can be removed by biphasic extraction and water miscible solvents can be removed, e.g., by rotary evaporation concomitant to the concentration step.
  • the glycan preparation produced may undergo additional processing steps.
  • Additional processing steps may include, for example, purification steps.
  • Purification steps may include, for example, separation, dilution, concentration, filtration, desalting or ion-exchange, chromatographic separation, or decolorization, or any combination thereof.
  • the methods described herein further include a decolorization step.
  • the glycan preparation produced may undergo a decolorization step using any method known in the art, including, for example, treatment with an absorbent, activated carbon, chromatography (e.g., using ion exchange resin), hydrogenation, and/or filtration (e.g., microfiltration).
  • the glycan preparations produced are contacted with a color-absorbing material at a particular temperature, at a particular concentration, and/or for a particular duration of time.
  • the mass of the color absorbing species contacted with the glycan preparation is less than 50% of the mass of the glycan preparation, less than 35% of the mass of the glycan preparation, less than 20% of the mass of the glycan preparation, less than 10% of the mass of the glycan preparation, less than 5% of the mass of the glycan preparation, less than 2% of the mass of the glycan preparation, or less than 1% of the mass of the glycan preparation.
  • the glycan preparations are contacted with a color absorbing material. In certain embodiments, the glycan preparations are contacted with a color absorbing material for less than 10 hours, less than 5 hours, less than 1 hour, or less than 30 minutes. In a particular embodiment, the glycan preparations are contacted with a color absorbing material for 1 hour.
  • the glycan preparations are contacted with a color absorbing material at a temperature from about 20 to 100 degrees Celsius, about 30 to 80 degrees Celsius, about 40 to 80 degrees Celsius, or about 40 to 65 degrees Celsius. In a particular embodiment, the glycan preparations are contacted with a color absorbing material at a temperature of about 50 degrees Celsius.
  • the color absorbing material is activated carbon. In one embodiment, the color absorbing material is powdered activated carbon. In other embodiments, the color absorbing material is an ion exchange resin. In one embodiment, the color absorbing material is a strong base cationic exchange resin in a chloride form. In another embodiment, the color absorbing material is cross-linked polystyrene. In yet another embodiment, the color absorbing material is cross-linked polyacrylate. In certain embodiments, the color absorbing material is Amberlite FPA91, Amberlite FPA98, Dowex 22, Dowex Marathon MSA, or Dowex Optipore SD-2.
  • the glycan preparations are contacted with a material to remove salts, minerals, and/or other ionic species.
  • the glycan preparations are flowed through an anionic/cationic exchange column pair.
  • the anionic exchange column contains a weak base exchange resin in a hydroxide form and the cationic exchange column contains a strong acid exchange resin in a protonated form.
  • the methods described herein further include isolating the glycan preparation produced.
  • isolating the glycan preparation comprises separating at least a portion of the glycan preparation from at least a portion of the catalyst, using any method known in the art, including, for example, centrifugation, filtration (e.g., vacuum filtration, membrane filtration), and gravity settling.
  • isolating the glycan preparation comprises separating at least a portion of the glycan preparation from at least a portion of any unreacted glycan units, using any method known in the art, including, for example, filtration (e.g., membrane filtration), chromatography (e.g., chromatographic fractionation), differential solubility, and centrifugation (e.g., differential centrifugation).
  • filtration e.g., membrane filtration
  • chromatography e.g., chromatographic fractionation
  • differential solubility e.g., differential centrifugation
  • the methods further include a concentration step.
  • the isolated glycan preparations undergo evaporation (e.g., vacuum evaporation) to produce a concentrated glycan preparation.
  • the isolated glycan preparations undergo a spray drying step to produce a powdered glycan preparation.
  • the isolated glycan preparations undergo both an evaporation step and a spray drying step.
  • glycan therapeutic preparations e.g. oligosaccharides
  • the methods described herein further include a fractionation step.
  • Glycan species e.g., oligosaccharides
  • glycan species are separated into pools representing 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or greater than 98% short (about DP1-2), medium (about DP3-10), long (about DP11-18), or very long (about DP>18) species.
  • glycan species are fractionated by adsorption onto a carbonaceous material and subsequent desorption of fractions by washing the material with mixtures of an organic solvent in water at a concentration of 1%, 5%, 10%, 20%, 50%, or 100%.
  • the adsorption material is activated charcoal.
  • the adsorption material is a mixture of activated charcoal and a bulking agent such as diatomaceous earth or Celite 545 in 5%, 10%, 20%, 30%, 40%, or 50% portion by volume or weight.
  • glycan species are separated by passage through a high-performance liquid chromatography system.
  • glycan species are separated by ion-affinity chromatography, hydrophilic interaction chromatography, or size-exclusion chromatography including gel-permeation and gel-filtration.
  • low molecular weight materials are removed by filtration methods.
  • low molecular weight materials may be removed by dialysis, ultrafiltration, diafiltration, or tangential flow filtration.
  • the filtration is performed in static dialysis tube apparatus.
  • the filtration is performed in a dynamic flow filtration system.
  • the filtration is performed in centrifugal force-driven filtration cartridges.
  • the glycan therapeutics described herein may comprise oligosaccharides and/or polysaccharides (referred to herein as “oligosaccharides”).
  • the glycan therapeutics comprise homo-oligo- or polymers (e.g., homoglycans), wherein all the glycan units in the oligomer or polymer are of the same type.
  • Glycan therapeutics comprising homopolymers can include monosaccharides bonded together via a single or multiple glycosidic bond types.
  • the glycan therapeutics comprise hetero-oligo- or polymers (e.g., heteroglycans), wherein more than one type of glycan unit is present.
  • Glycan therapeutics comprising heteropolymers can include distinct types of monosaccharides bonded together via a single or multiple glycosidic bond types.
  • hydrolysis may be used to generate the constituent glycan units that are suitable to produce the glycans described herein.
  • the glycan unit is a monosaccharide.
  • Monosaccharides may exist in many different forms, for example, conformers, cyclic forms, acyclic forms, stereoisomers, tautomers, anomers, and isomers.
  • about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of at least 5 and less than 30 glycan units. In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of at least 3 and less than 30 glycan units. In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of at least 3 and less than 25 glycan units.
  • about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of at least 8 and less than 30 glycan units. In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of at least 10 and less than 30 glycan units.
  • about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of between 3, 4, 5, 6, 7, 8 and 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 glycan units. In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of between 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 and 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 glycan units.
  • about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of between 3, 4, 5, 6, 7, 8, 9, 10 and 20, 21, 22, 23, 24, 25, 26, 27, 28 glycan units.
  • the glycan therapeutic preparation has a degree of polymerization (DP) of at least 3 and less than 30 glycan units. In one embodiment, the glycan therapeutic preparation has a degree of polymerization (DP) of at least 5 and less than 30 glycan units. In one embodiment, the glycan therapeutic preparation has a degree of polymerization (DP) of at least 3 and less than 25 glycan units.
  • about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of at least 2. In one embodiment, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has a DP of at least 3.
  • glycan therapeutic preparations are provided, wherein at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, 99.8%, or at least 99.9% or even 100% of the glycan therapeutic preparation has a degree of polymerization (DP) of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or at least 12 glycan units and less than 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 25, 20, 19, 18, 17, 16, or less than 15 glycan units.
  • DP degree of polymerization
  • glycan therapeutic preparations are provided, wherein at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, 99.8%, or at least 99.9% or even 100% of the glycan therapeutic preparation has a degree of polymerization (DP) of at least 3 and less than 30 glycan units, at least 5 and less than 30 glycan units, or at least 8 and less than 30 glycan units.
  • DP degree of polymerization
  • about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has an average degree of polymerization (DP) of about DP5, DP6, DP7, DP8, DP9, DP10, DP11, DP12, DP13, DP14, or DP15.
  • DP average degree of polymerization
  • glycan therapeutic preparations are provided wherein at least 50%, 60%, 70%, or 80% of the glycan therapeutic preparation has a degree of polymerization of at least 3 and less than 30 glycan units, or of at least 5 and less than 25 glycan units.
  • the average DP of the glycan therapeutic preparation is between about DP7 and DP9 or between about DP6 and DP10.
  • these glycan therapeutic preparations comprise an alpha- to beta-glycosidic bond ratio from 0.8:1 to 5:1 or from 1:1 to 4:1.
  • the fractionated preparations have an average degree of branching of between about 0.01 and about 0.2 or between about 0.05 and 0.1.
  • a polydisperse, fractionated glycan therapeutic preparation comprising at least 85%, 90%, or at least 95% medium-length species with a DP of about 3-10. In one embodiment, a polydisperse, fractionated glycan therapeutic preparation is provided comprising at least 85%, 90%, or at least 95% long-length species with a DP of about 11-18. In one embodiment, a polydisperse, fractionated glycan therapeutic preparation is provided comprising at least 85%, 90%, or at least 95% very long-length species with a DP of about 18-30.
  • the medium, long and very long fractionated preparations comprise an alpha- to beta-glycosidic bond ratio from 0.8:1 to 5:1 or from 1:1 to 4:1. In some embodiments, the fractionated preparations have an average degree of branching of between about 0.01 and about 0.2 or between about 0.05 and 0.1.
  • about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycan therapeutic preparation has an average molecular weight of about 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800 g/mol and less than 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, and 5000 g/mol.
  • the glycan preparations range in structure from linear to highly branched.
  • Unbranched glycans may contain only alpha linkages or only beta linkages.
  • Unbranched glycans may contain at least one alpha and at least one beta linkage.
  • Branched glycans may contain at least one glycan unit being linked via an alpha or a beta glycosidic bond so as to form a branch.
  • the branching rate or degree of branching may vary, such that about every 2 nd , 3 rd , 4 th , 5 th , 6 th , 7 th , 8 th , 9 th , 10 th , 15 th , 20 th , 25 th , 30 th , 35 th , 40 th , 45 th , 50 th , 60 th , or 70 th unit comprises at least one branching point.
  • animal glycogen contains a branching point approximately every 10 units.
  • preparations of glycan therapeutics are provided, wherein the preparation comprises a mixture of branched glycans, wherein the average degree of branching (DB, branching points per residue) is 0, 0.01. 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99, 1, or 2.
  • preparations of glycan therapeutics are provided, wherein the average degree of branching is at least 0.01, 0.05, 0.1, 0.2, 0.3, or at least 0.4.
  • preparations of glycan therapeutics are provided, wherein the average degree of branching is between about 0.01 and 0.1, 0.01 and 0.2, 0.01 and 0.3, 0.01 and 0.4, or 0.01 and 0.5. In some embodiments, preparations of glycan therapeutics are provided, wherein the average degree of branching is between about 0.05 and 0.1, 0.05 and 0.2, 0.05 and 0.3, 0.05 and 0.4, or 0.05 and 0.5. In some embodiments, preparations of glycan therapeutics are provided, wherein the average degree of branching is between about 0.1 and 0.2, 0.1 and 0.3, 0.1 and 0.4, or 0.1 and 0.5.
  • preparations of glycan therapeutics are provided, wherein the average degree of branching is not 0. In some embodiments, preparations of glycan therapeutics are provided, wherein the average degree of branching is not between at least 0.1 and less than 0.4 or at least 0.2 and less than 0.4. In some embodiments, the preparations of glycan therapeutics comprise linear glycans. In some embodiments, the preparations of glycan therapeutics comprise glycans that exhibit a branched or branch-on-branch structure, e.g., branched glycans (such as, e.g., branched oligosaccharides and/or branched polysaccharides).
  • branched glycans such as, e.g., branched oligosaccharides and/or branched polysaccharides.
  • preparations of glycan therapeutics are provided wherein the average degree of branching (DB) is not 0, but is at least 0.01, 0.05, 0.1, or at least 0.2, or ranges between about 0.01 and about 0.2 or between about 0.05 and 0.1.
  • DB average degree of branching
  • linkage or bonds between two glycan units can be expressed, for example, as 1,4, 1->4, or (1-4), used interchangeably and are referred to herein as glycosidic linkages or bonds for compounds comprising one or more sugars (e.g. monosaccharides, disaccharides and the like).
  • Monosaccharides can be in the cyclic form (e.g. pyranose or furanose form).
  • lactose is a disaccharide composed of cyclic forms of galactose and glucose joined by a beta (1-4) linkage where the acetal oxygen bridge is in the beta orientation.
  • Linkages or bonds between the individual glycan units found in preparations of glycan therapeutics may include one or more (e.g., two or more, three or more, four or more, five or more, six or more, etc.) of alpha 1->2, alpha 1->3, alpha 1->4, alpha 1->6, alpha 2->1, alpha 2->3, alpha 2->4, alpha 2->6, beta 1->2, beta 1->3, beta 1->4, beta 1->6, beta 2->1, beta 2->3, beta 2->4, and beta 2->6.
  • the glycan therapeutic preparation comprises both alpha- and beta-glycosidic bonds selected from the group consisting of 1->2 glycosidic bond, a 1->3 glycosidic bond, a 1->4 glycosidic bond, a 1->5 glycosidic bond and a 1->6 glycosidic bond.
  • the glycan therapeutic preparation comprises at least two or at least three alpha and beta 1->2 glycosidic bonds, alpha and beta 1->3 glycosidic bonds, alpha and beta 1->4 glycosidic bonds, alpha and beta 1->5 glycosidic bonds, and/or alpha and beta 1->6 glycosidic bonds.
  • the glycan therapeutic preparations comprise only alpha linkages. In some embodiments, the glycan therapeutics comprise only beta linkages. In some embodiments, the glycan therapeutics comprise mixtures of alpha and beta linkages.
  • the alpha:beta glycosidic bond ratio in a preparation is about 0.1:1, 0.2:1, 0.3:1, 0.4:1, 0.5:1, 0.6:1, 0.7:1, 0.8:1, 0.9:1, 1:1, 1.2:1, 1.5:1, 1.7:1, 2:1, 2.2:1, 2.5:1, 2.7:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, or about 10:1.
  • the glycan therapeutic preparations comprise and alpha:beta glycosidic bond ratio in a preparation of about 0.8:1, 1:1, 2:1, 3:1, 4:1 or 5:1, or it ranges from about 0.8:1 to about 5:1 or from about 1:1 to about 4:1.
  • the preparations of glycan therapeutics comprises substantially all alpha- or beta configured glycan units, optionally comprising about 1%, 2%, 3%, 4% 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or 20% of the respective other configuration.
  • the preparations of glycan therapeutics comprise at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, at least 99.9% or even 100% glycans with alpha glycosidic bonds.
  • the preparations of glycan therapeutics comprise at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, at least 99.9% or even 100% glycans with beta glycosidic bonds.
  • preparations of glycan therapeutics are provided, wherein at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, or at least 85% of glycans with glycosidic bonds that are alpha glycosidic bonds, at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, or at least 85% of glycans with glycosidic bonds that are beta glycosidic bonds, and wherein the percentage of alpha and beta glycosidic bonds does not exceed 100%.
  • preparations of glycan therapeutics are provided, wherein at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, at least 99.9% or even 100% of glycan glycosidic bonds are one or more of: 1->2 glycosidic bonds, 1->3 glycosidic bonds, 1->4 glycosidic bonds, and 1->6 glycosidic bonds.
  • preparations of glycan therapeutics are provided, wherein at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, at least 20%, or 25% each of glycan glycosidic bonds are 1->2, 1->3, 1->4, and 1->6 glycosidic bonds.
  • the preparations of glycan therapeutics further comprise at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, or at least 85% of glycan glycosidic bonds that are selected from the group consisting of: alpha 2->1, alpha 2->3, alpha 2->4, alpha 2->6, beta 2->1, beta 2->3, beta 2->4, and beta 2->6, glycosidic bonds.
  • the preparations of glycan therapeutics comprise glycans with at least two glycosidic bonds selected from the group consisting of alpha 1->2 and alpha 1->3, alpha 1->2 and alpha 1->4, alpha 1->2 and alpha 1->6, alpha 1->2 and beta 1->2, alpha 1->2 and beta 1->3, alpha 1->2 and beta 1->4, alpha 1->2 and beta 1->6, alpha 1->3 and alpha 1->4, alpha 1->3 and alpha 1->6, alpha 1->3 and beta 1->2, alpha 1->3 and beta 1->3, alpha 1->3 and beta 1->4, alpha 1->3 and beta 1->6, alpha 1->4 and alpha 1->6, alpha 1->4 and beta 1->2, alpha 1->4 and beta 1->3, alpha 1->4 and beta 1->4, alpha 1->4 and beta 1->6, alpha 1->6 and beta 1->2, alpha 1->6 and beta 1->3, alpha 1->6 and beta 1->4, alpha 1->4 and
  • branched glycan therapeutics e.g. those with a DB of 0.01. 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99, 1, or 2) comprising a side chain, which can be the same or a different side chain, the side chain may be attached via one or more beta and alpha linkages, such as (1-2), (1-3), (1-4), (1-6), (2-3), (2-6) or other suitable linkages to the main chain.
  • beta and alpha linkages such as (1-2), (1-3), (1-4), (1-6), (2-3), (2-6) or other suitable linkages to the main chain.
  • preparations of glycan therapeutics are provided, wherein at least one glycan unit is a sugar in L-form. In some embodiments, preparations of glycans are provided, wherein at least one glycan unit is a sugar in D-form. In some embodiments, preparations of glycans are provided, wherein the glycan units are sugars in L- or D-form as they naturally occur or are more common (e.g. D-glucose, D-xylose, L-arabinose).
  • the preparation of glycan therapeutics comprises a desired mixture of L- and D-forms of glycan units, e.g. of a desired ratio, such as: 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 1:12, 1:14, 1:16, 1:18, 1:20, 1:25, 1:30, 1:35, 1:40, 1:45, 1:50, 1:55, 1:60, 1:65, 1:70, 1:75, 1:80, 1:85, 1:90, 1:100, 1:150 L- to D-forms or D- to L-forms.
  • a desired ratio such as: 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 1:12, 1:14, 1:16, 1:18, 1:20, 1:25, 1:30, 1:35, 1:40, 1:45, 1:50, 1:55, 1:60, 1:65, 1:70, 1:75, 1:80
  • the preparation of glycan therapeutics comprises glycans with substantially all L- or D-forms of glycan units, optionally comprising about 1%, 2%, 3%, 4% 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% of the respective other form.
  • preparations of glycan therapeutics are provided, wherein at least one glycan unit is a diose, triose, tetrose, a pentose, a hexose, or a heptose.
  • the glycan units involved in the formation of the glycans are varied.
  • monosaccharide glycan units include hexoses, such as glucose, galactose, and fructose, and pentoses, such as xylose.
  • the monosaccharide glycan units may exist in an acyclic (open-chain) form. Open-chain monosaccharides with same molecular graph may exist as two or more stereoisomers.
  • the monosaccharides may also exist in a cyclic form through a nucleophilic addition reaction between the carbonyl group and one of the hydroxyls of the same molecule.
  • the reaction creates a ring of carbon atoms closed by one bridging oxygen atom.
  • the ring usually has 5 (furanoses) or 6 atoms (pyranoses).
  • the preparation of glycan therapeutics comprises a desired mixture of different monosaccharide glycan units, such as a mixture of a diose, a triose, tetrose, pentose, hexose, or heptose, including any mixtures of two or more pentoses (e.g., arabinose and xylose) and mixtures of two or more hexoses (e.g., glucose and galactose), in any desired ratio, e.g.
  • pentoses e.g., arabinose and xylose
  • hexoses e.g., glucose and galactose
  • the preparation of glycan therapeutics comprises a desired mixture of two, three, four or five different glycan units, such as a mixture of, e.g., i) one or more glycan units selected from monosaccharides, selected from glucose, galactose, arabinose, mannose, fructose, xylose, fucose, and rhamnose; ii) one or more glycan units selected from disaccharides selected from acarviosin, n-acetyllactosamine, allolactose, cellobiose, chitobiose, galactose-alpha-1,3-galactose, gentiobiose, isomalt, isomaltose, isomaltulose, kojibiose, lactitol, lactobionic acid, lactose, lactulose, laminaribiose, maltitol, maltose
  • the preparation of glycan therapeutics comprises a glycan unit or plurality of glycan units present in a salt form (e.g., a pharmaceutically acceptable salt form), such as, e.g., a hydrochlorate, hydroiodate, hydrobromate, phosphate, sulfate, methanesulfate, acetate, formate, tartrate, malate, citrate, succinate, lactate, gluconate, pyruvate, fumarate, propionate, aspartate, glutamate, benzoate, ascorbate salt.
  • a salt form e.g., a pharmaceutically acceptable salt form
  • Exemplary glycans are described by a three-letter code representing the monomeric sugar component followed by a number out of one hundred reflecting the percentage of the material that monomer constitutes.
  • ‘glu100’ is ascribed to a glycan generated from a 100% D-glucose (glycan unit) input
  • ‘glu50gal50’ is ascribed to a glycan generated from 50% D-glucose and 50% D-galactose (glycan units) input or, alternatively from a lactose dimer (glycan unit) input.
  • the preparation of glycan therapeutics comprises one glycan unit A selected from i) to vii) above, wherein glycan unit A comprises 100% of the glycan unit input.
  • the glycan therapeutic preparation is selected from the homo-glycans xyl100, rha100, ara100, gal100, glu100, and man100.
  • the glycan therapeutic preparation is selected from the homo-glycans fuc100 and fru100.
  • the glycan therapeutic preparation comprises man100.
  • the preparation of glycan therapeutics comprises a mixture of two glycan units A and B selected independently from i) to vii) above, wherein A and B may be selected from the same or a different group i) to vii) and wherein A and B may be selected in any desired ratio (e.g. anywhere from 1-99% A and 99-1% B, not exceeding 100%).
  • the glycan therapeutic preparation is selected from the hetero-glycans ara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10 and glu90gly10.
  • the preparation of glycan therapeutics comprises a mixture of three glycan units A, B and C selected independently from i) to vii) above, wherein A, B and C may be selected from the same or a different group i) to vii) and wherein A, B and C may be selected in any desired ratio (e.g. anywhere from 1-99% A, 1-99% B, 1-99% C, not exceeding 100%).
  • the glycan therapeutic preparation is selected from the hetero-glycans xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, and the hybrid glycan glu33gal33neu33.
  • the preparation of glycan therapeutics comprises a mixture of four glycan units A, B, C and D selected independently from i) to vii) above, wherein A, B, C and D may be selected from the same or a different group i) to vii) and wherein A, B, C and D may be selected in any desired ratio (e.g. anywhere from 1-99% A, 1-99% B, 1-99% C, 1-99% D, not exceeding 100%).
  • the preparation of glycan therapeutics comprises a mixture of five glycan units A, B, C, D and E selected independently from i) to vii) above, wherein A, B, C, D and E may be selected from the same or a different group i) to vii) and wherein A, B, C, D and E may be selected in any desired ratio (e.g. anywhere from 1-99% A, 1-99% B, 1-99% C, 1-99% D, 1-99% E, not exceeding 100%).
  • preparations of glycan therapeutics are provided, wherein at least one glycan unit is selected from the group consisting of a glucose, a galactose, an arabinose, a mannose, a fructose, a xylose, a fucose, and a rhamnose.
  • the glycan unit is not glucose.
  • the glycan unit is not galactose.
  • the glycan unit is not fructose.
  • the glycan unit is not fucose.
  • the glycan unit is not mannose.
  • the glycan unit is not arabinose.
  • the glycan unit is not rhamnose.
  • the glycan unit is not xylose.
  • the preparation of glycan therapeutics comprises a desired mixture of two different monosaccharide glycan units, such as a mixture of, e.g., glucose and galactose, glucose and arabinose, glucose and mannose, glucose and fructose, glucose and xylose, glucose and fucose, glucose and rhamnose, galactose and arabinose, galactose and mannose, galactose and fructose, galactose and xylose, galactose and fucose, and galactose and rhamnose, arabinose and mannose, arabinose and fructose, arabinose and xylose, arabinose and fucose, and arabinose and rhamnose, mannose and fructose, mannose and xylose, mannose and fucose, and mannose and rhamnose, fructose and xylose, fructose and fucose, and
  • the preparation of glycan therapeutics comprises a desired mixture of three different monosaccharide glycan units, such as a mixture of, e.g. for glucose-containing glycan-therapeutic preparations, glucose, galactose and arabinose; glucose, galactose and mannose; glucose, galactose and fructose; glucose, galactose and xylose; glucose, galactose and fucose, glucose, galactose and rhamnose; glucose, arabinose, and mannose; glucose, arabinose and fructose; glucose, arabinose and xylose; glucose, arabinose and fucose; glucose, arabinose and rhamnose; glucose, mannose and fructose; glucose, mannose and xylose; glucose, mannose and fucose; glucose, mannose rhamnose; glucose, mannose and fructose; glucose, mannose and xylose; glucose, mannose and fucose; glucose,
  • preparations of glycan therapeutics are provided, wherein at least one glycan unit is a furanose sugar. In some embodiments, preparations of glycans are provided, wherein at least one glycan unit is a pyranose sugar. In some embodiments, glycan therapeutics comprise mixtures of furanose and pyranose sugars.
  • the furanose: pyranose sugar ratio in a preparation is about 0.1:1, 0.2:1, 0.3:1, 0.4:1, 0.5:1, 0.6:1, 0.7:1, 0.8:1, 0.9:1, 1:1, 1.2:1, 1.5:1, 1.7:1, 2:1, 2.2:1, 2.5:1, 2.7:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, or about 10:1.
  • the preparation of glycan therapeutics comprises a desired mixture of furanose and pyranose sugars, e.g. of a desired ratio, such as: 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 1:12, 1:14, 1:16, 1:18, 1:20, 1:25, 1:30, 1:35, 1:40, 1:45, 1:50, 1:55, 1:60, 1:65, 1:70, 1:75, 1:80, 1:85, 1:90, 1:100, 1:150 furanose to and pyranose or pyranose to furanose.
  • a desired ratio such as: 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 1:12, 1:14, 1:16, 1:18, 1:20, 1:25, 1:30, 1:35, 1:40, 1:45, 1:50, 1:55, 1:60, 1:65, 1:70, 1:75, 1:80
  • the preparation of glycan therapeutics comprises substantially all furanose or pyranose sugar, optionally comprising 1%, 2%, 3%, 4% 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or 20% of the respective other sugar.
  • the preparation of glycan therapeutics comprises substantially all pyranose sugar and no more than about 0.1%, 02%, 0.5%, 1%, 2%, 3%, 4%, or no more than 5% of monomeric glycan units in the preparation in furanose form. In some embodiments, no more than 3%, 2% or no more than 1% of monomeric glycan units in the preparation are in furanose form.
  • the preparation of glycan therapeutics does not comprise N-acetylgalactosamine or N-acetylglucosamine. In some embodiments, the preparation of glycans does not comprise sialic acid. In some embodiments, the preparation of glycan therapeutics does not comprise a lipid and fatty acid. In some embodiments, the preparation of glycan therapeutics does not comprise an amino acid.
  • the preparation of glycan therapeutics does not comprise a detectable repeating unit. In some embodiments, the preparation of glycan therapeutics does not comprise a statistically significant amount of a repeating unit. In some embodiments, the repeating unit has a DP of at least 2, 3, 4, 5, or at least 6 glycan units.
  • hyaluronan is a glycosaminoglycan with a repeating disaccharide unit consisting of two glucose derivatives, glucuronate (glucuronic acid) and N-acetylglucosamine. The glycosidic linkages are beta (1->3) and beta (1->4).
  • Cellulose is a polymer made with repeated glucose units linked together by beta-linkages.
  • the presence and amount of repeating units can be determined, e.g. using by total hydrolysis (e.g. to determine the proportion of glycan units), methylation analysis (e.g. to determine the distribution of bond types), and HSQC (e.g. to determine the distribution of alpha- and beta-glycosides). Statistical methods to determine significance are known by one of skill in the art.
  • the monosaccharide or oligosaccharide glycan units of the glycans are further substituted or derivatized, e.g., hydroxyl groups can be etherified or esterified.
  • the glycans e.g. oligosaccharide
  • the degree of substitution can be 1, 2, or 3, or another suitable DS.
  • the degree of substitution varies between subunits, e.g., a certain percentage is not derivatized, exhibits a DS of 1, exhibits a DS of 2, or exhibits a DS of 3. Any desired mixture can be generated, e.g. 0-99% of subunits are not derivatized, 0-99% of subunits exhibit a DS of 1, 0-99% of subunits exhibit a DS of 2, and 0-99% of subunits exhibit a DS of 3, with the total making up 100%.
  • the degree of substitution can be controlled by adjusting the average number of moles of substituent added to a glycosyl moiety (molar substitution (MS)).
  • the distribution of substituents along the length of the glycan oligo- and polysaccharide chain can be controlled by adjusting the reaction conditions, reagent type, and extent of substitution.
  • the monomeric subunits are substituted with one or more of an acetate ester, sulfate half-ester, phosphate ester, or a pyruvyl cyclic acetal group.
  • the glycan therapeutic preparations are highly branched, e.g. have an average DB of at least 0.01, 0.05, or 0.1. In some embodiments, the glycan therapeutic preparations have an average DB of about 0.01 to about 0.05, 0.01 to 0.1, 0.05 to 0.1, or about 0.1 to about 0.2. In some embodiments, the glycan therapeutic preparations comprising branched oligosaccharide are highly soluble. In some embodiments, glycan therapeutic preparations can be concentrated to at least to 55 Brix, 65 Brix, 60 Brix, 65 Brix, 70 Brix, 75 Brix, 80 Brix, or at least 85 Brix without obvious solidification or crystallization at 23° C.
  • glycan therapeutic preparations can be concentrated to about 50-60 Brix, 60-70 Brix, 70-80 Brix, 55-65 Brix, 65-75 Brix, or to about 75-85 Brix. In some embodiments, glycan therapeutic preparations can be concentrated to about 50, 55, 60, 65, 70, 75, 80, or about 85 Brix without obvious solidification or crystallization at 23° C. (final solubility limit).
  • glycan therapeutic preparations are concentrated to at least about 0.5 g/ml, 1 g/ml, 1.5 g/ml, 2 g/ml, 2.5 g/ml, 3 g/ml, 3.5 g/ml or at least 4 g/ml without obvious solidification or crystallization at 23° C. (final solubility limit).
  • the glycan therapeutic preparations are branched, e.g. have an average DB of at least 0.01, 0.05, or 0.1 and has a final solubility limit in water of at least about 70 Brix, 75 Brix, 80 Brix, or at least about 85 Brix at 23° C. or is at least about 1 g/ml, 2 g/ml or at least about 3 g/ml.
  • the preparation of glycan therapeutics has a final solubility limit of at least 0.001 g/L, 0.005 g/L, 0.01 g/L, 0.05 g/L, 0.1 g/L, 0.2 g/L, 0.3 g/L, 0.4 g/L, 0.5 g/L, 0.6 g/L, 0.7 g/L, 0.8 g/L, 0.9 g/L, 1 g/L, 5 g/L, 10 g/L, 20 g/L, 30 g/L, 40 g/L, 50 g/L, 100 g/L, 200 g/L, 300 g/L, 400 g/L, 500 g/L, 600 g/L, 700 g/L, 800 g/L, 900 g/L, 1000 g/L in deionized water, or in a suitable buffer such as, e.g., phosphate-buffered saline, pH
  • the preparation of glycan therapeutics is greater than 50%, greater than 60%, greater than 70%, greater than 80%, greater than 90%, greater than 95%, greater than 96%, greater than 97%, greater than 98%, greater than 99%, or greater than 99.5% soluble with no precipitation observed at a concentration of greater than 0.001 g/L, 0.005 g/L, 0.01 g/L, 0.05 g/L, 0.1 g/L, 0.2 g/L, 0.3 g/L, 0.4 g/L, 0.5 g/L, 0.6 g/L, 0.7 g/L, 0.8 g/L, 0.9 g/L, 1 g/L, 5 g/L, 10 g/L, 20 g/L, 30 g/L, 40 g/L, 50 g/L, 100 g/L, 200 g/L, 300 g/L, 400 g/L, 500 g/L, 600 g/L, 700 g
  • the preparation of glycan therapeutics has a desired degree of sweetness.
  • sucrose table sugar
  • Sucrose in solution has a sweetness perception rating of 1, and other substances are rated relative to this (e.g., fructose, is rated at 1.7 times the sweetness of sucrose).
  • the sweetness of the preparation of glycan therapeutics ranges from 0.1 to 500,000 relative to sucrose.
  • the relative sweetness is 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 25000, 50000, 75000, 100000, 150000, 200000, 250000, 300000, 350000, 40000, 450000, 500000, or more than 500,000 relative to sucrose (with sucrose scored as one).
  • the preparation of glycan therapeutics is mildly sweet, or both sweet and bitter.
  • the preparation of glycan therapeutics e.g. a preparation that is substantially DP2+ or DP3+ (e.g. at least 80%, 90%, or at least 95%, or a fractionated preparation of DP2+ or DP3+), is substantially imperceptible as sweet and the relative sweetness is about 0, 0.0001, 0.001, 0.005, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, or about 0.9 relative to sucrose (with sucrose scored as one).
  • the glycan therapeutic preparations can be characterized by any method known in the art and by the methods described herein.
  • DP(n) degree of polymerization
  • HPLC high performance liquid chromatography
  • RI refractive index
  • the columns are selected from chemistries including HILIC, metal coordination, and aqueous size-exclusion chromatography that best isolate the species of interest.
  • Molar % DP(n) is determined by the formula:
  • % DP ( n ) 100*AUC[ DP ( n )]/AUC[ DP (total)],
  • AUC is defined as the area under the curve for the species of interest as determined by calibration to known standards.
  • the molar percentage of glycosidic bond isomers (% alpha and beta) are determined by nuclear magnetic resonance (NMR) spectroscopy using a variety of 2D techniques familiar to those skilled in the art.
  • NMR nuclear magnetic resonance
  • Alpha- and beta-isomers may be distinguished, e.g., by their distinct shift on the NMR spectrum and the molar percentage is determined by the formula:
  • glycosidic bonds 100*AUC[shift(isomer n )]/AUC[shift(isomer alpha+isomer beta)],
  • AUC is defined as the area under the curve at a specific shift value known to represent the desired isomer n.
  • the molar percentage of regiochemical isomers is determined in an analogous fashion using the formula:
  • % (regioisomer n ) of regioisomers 100*AUC[shift (regioisomer n )]/AUC[shift (all regioisomers)].
  • the relative percentage of monomeric sugars making up the oligomeric population is determined, e.g., by total acidic digestion of the oligomeric sample followed by conversion to the alditol acetate followed by gas chromatographic (GC) analysis of the resultant monomeric solutions compared against GC of known standards.
  • GC gas chromatographic
  • % (sugar n ) 100*AUC[sugar n ]/AUC[total of all monomeric sugars].
  • the solubility of the preparation of glycan therapeutics can be controlled, e.g. by selecting the charge, structure (e.g. DP, degree of branching), and/or derivatization of the glycan units.
  • the monomeric building blocks e.g. the monosaccharide or glycan unit composition
  • the anomeric configuration of side chains e.g. the anomeric configuration of side chains
  • the presence and location of substituent groups e.g. the amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids,
  • the crystal structure can be solved using, e.g., solid-state NMR, FT-IR (Fourier transform infrared spectroscopy), and WAXS (wide-angle X-ray scattering).
  • the DP, DP distribution, and polydispersity can be determined by, e.g., viscosimetry and SEC (SEC-HPLC, high performance size-exclusion chromatography).
  • Alien groups, end groups and substituents can be identified, e.g., using SEC with labeling, aqueous analytics, MALDI-MS, FT-IR, and NMR.
  • To identify the monomeric components of the glycans methods such as, e.g.
  • HPLC high performance liquid chromatography
  • GLC gas-liquid chromatography
  • the polysaccharide is methylated with methyl iodide and strong base in DMSO
  • hydrolysis is performed, a reduction to partially methylated alditols is achieved, an acetylation to methylated alditol acetates is performed, and the analysis is carried out by GLC/MS (gas-liquid chromatography coupled with mass spectrometry).
  • a partial depolymerization is carried out using an acid or enzymes to determine the structures. Possible structures of the polysaccharide are compared to those of the hydrolytic oligomers, and it is determined which one of the possible structures could produce the oligomers.
  • the intact polysaccharide or a preparation of oligosaccharides are subjected to enzymatic analysis, e.g. they are contacted with an enzyme that is specific for a particular type of linkage, e.g., ⁇ -galactosidase, or ⁇ -glucosidase, etc., and NMR may be used to analyze the products.
  • the distribution of (or average) degree of polymerization (DP) of a glycan therapeutic preparation may be measured by injecting a sample with a concentration of, e.g., 10-100 mg/mL onto an Agilent 1260 BioPure HPLC (or similar) equipped with a 7.8 ⁇ 300 mm BioRad Aminex HPX-42A column (or similar) and RI detector as described, e.g., in Gomez et al. (Purification, Characterization, and Prebiotic Properties of Pectic Oligosaccharides from Orange Peel Wastes, J Agric Food Chem, 2014, 62:9769).
  • a sample with a concentration may be injected into a Dionex ICS5000 HPLC (or similar) equipped with a 4 ⁇ 250 mm Dionex CarboPac PA1 column (or similar) and PAD detector as described, e.g., in Holck et al., (Feruloylated and nonferuloylated arabino-oligosaccharides from sugar beet pectin selectively stimulate the growth of bifidobacterium spp. in human fecal in vitro fermentations, Journal of Agricultural and Food Chemistry, 2011, 59(12), 6511-6519). Integration of the resulting spectrum compared against a standard solution of oligomers allows determination of the average DP.
  • Distribution of molecular weights can be measured, e.g, by MALDI mass spectrometry.
  • Oligosaccharide concentration can be measured with a Mettler-Toledo sugar refractometer (or similar) with the final value adjusted against a standardized curve to account for refractive differences between monomers and oligomers.
  • Distribution of glycoside regiochemistry can be characterized, e.g., by a variety of 2D-NMR techniques including COSY, HMBC, HSQC, DEPT, and TOCSY analysis using standard pulse sequences and a Bruker 500 MHz spectrometer. Peaks can be assigned by correlation to the spectra of naturally occurring polysaccharides with known regiochemistry.
  • the relative peak assignment of a sample is dependent on a number of factors including the concentration and purity of the sample, the identity and quality of the solvent (e.g., the isotopically labeled solvent), and the pulse sequence utilized.
  • the relative peak assignment of, for example, a glycan comprising glucose may vary (e.g., by about 0.01 ppm, about 0.02 ppm, or about 0.05 ppm) when the NMR spectrum is obtained in similar conditions due to said factors.
  • corresponding peak or “corresponding peaks” refer to NMR peaks associated with the same sample but that vary (e.g., by about 0.01 ppm, about 0.02 ppm, or about 0.05 ppm) due to factors including, for example, the concentration and purity of the sample, the identity and quality of the isotopically labeled solvent, and the pulse sequence utilized.
  • Monomeric compositions of oligomers may be measured, e.g., by the complete hydrolysis method in which a known amount of oligomer is dissolved into a strong acid at elevated temperature and allowed sufficient time for total hydrolysis to occur. The concentration of individual monomers may then be measured by the HPLC or GC methods described herein and known in the art to achieve relative abundance measurements as in Holck et al. Absolute amounts can be measured by spiking the HPLC sample with a known amount of detector active standard selected to prevent overlap with any of the critical signals.
  • the degree of branching in any given population may be measured by the methylation analysis method established, e.g, by Hakomori (J. Biochem. (Tokyo), 1964, 55, 205). With these data, identification of potential repeat units may be established by combining data from the total hydrolysis, average DP, and methylation analysis and comparing them against the DEPT NMR spectrum. Correlation of the number of anomeric carbon signals to these data indicates if a regular repeat unit is required to satisfy the collected data as demonstrated, e.g., in Harding, et al. (Carbohydr. Res. 2005, 340, 1107).
  • glycan therapeutics e.g. those comprising monosaccharide or disaccharide glycan units such as glucose, galactose, fucose, xylose, arabinose, rhamnose, and mannose
  • glycan therapeutics may be identified using one, two, three, or four of the following parameters: a) the presence of 2, 3, 4, 5, 6, 7 or more (e.g. at least 4 or 5) diagnostic anomeric NMR peaks each representing a different glycosidic bond type, b) an alpha- to beta-bond ratio between about 0.8 to 1 and about 5 to 1 (e.g.
  • glycan therapeutic preparations have average properties (e.g., DP, DB, alpha:beta glycosidic bond ratio) that are distinct from naturally occurring preparations of oligosaccharides. These structural features may be analyzed and optionally quantified by any suitable method known in the art and those described herein.
  • the glycan therapeutic preparations described herein have at least one, two, three, four, or at least five of the following characteristics:
  • compositions comprising glycan therapeutic preparations.
  • medical foods comprising glycan therapeutic preparations.
  • dietary supplements comprising glycan therapeutic preparations.
  • the pharmaceutical compositions, medical foods and dietary supplements comprising glycan therapeutic preparations further comprise a second (or third, fourth, etc.) therapeutic agent or active compound.
  • the agent or compound is a prebiotic substance, such as a dietary fiber.
  • the agent or compound is a probiotic bacterium.
  • the agent or compound is a micronutrient, such as a vitamin, mineral or polyphenol compound.
  • the agent or compound is a therapeutic drug, such as, e.g., an anti-cancer drug, a pain management drug, a drug that manages treatment side-effects, a drug that manages metabolism, an anti-inflammatory drug, or an anti-microbial agent.
  • a therapeutic drug such as, e.g., an anti-cancer drug, a pain management drug, a drug that manages treatment side-effects, a drug that manages metabolism, an anti-inflammatory drug, or an anti-microbial agent.
  • the pharmaceutical compositions and medical foods and dietary supplements comprising glycan therapeutic preparations do not contain a prebiotic substance. In some embodiments, the pharmaceutical compositions and medical foods and dietary supplements comprising glycan therapeutic preparations do not contain a probiotic bacterium.
  • the pharmaceutical compositions or medical foods and dietary supplements comprise a glycan therapeutic preparation of xyl100, rha100, ara100, gal100, glu100, fuc100, fru100 or man100.
  • the pharmaceutical compositions or medical foods and dietary supplements comprise a glycan therapeutic preparation of ara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10 or glu90gly10.
  • the pharmaceutical compositions or medical foods and dietary supplements comprise a glycan therapeutic preparation of xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, and the hybrid glycan glu33gal33neu33.
  • the pharmaceutical compositions or medical foods and dietary supplements comprise a glycan therapeutic preparation of glu100, ara100, xyl100, glu50gal50, man52glu29gal19, or glu33gal33fuc33.
  • the pharmaceutical compositions or medical foods and dietary supplements comprise a glycan therapeutic preparation of glu100 and man52glu29gal19.
  • the pharmaceutical compositions or medical foods and dietary supplements comprise a glycan therapeutic preparation of man100.
  • the pharmaceutical compositions or medical foods and dietary supplements comprise a glycan therapeutic preparation of xyl100.
  • compositions and medical foods and dietary supplements comprising glycan therapeutic preparations comprise one or more micronutrient.
  • the micronutrient is selected from the group consisting of a trace mineral, choline, a vitamin, and a polyphenol.
  • the micronutrient is a trace metal.
  • Trace minerals suitable as a micronutrient include boron, cobalt, chromium, calcium, copper, fluoride, iodine, iron, magnesium, manganese, molybdenum, selenium, and zinc.
  • the micronutrient is a vitamin.
  • Vitamins suitable as a micronutrient include Vitamin B complex, Vitamin B1 (thiamin), Vitamin B2 (riboflavin), Vitamin B3 (niacin), Vitamin B5 (pantothenic acid), Vitamin B6 group (pyridoxine, pyridoxal, pyridoxamine), Vitamin B7 (biotin), Vitamin B8 (ergadenylic acid), Vitamin B9 (folic acid), Vitamin B12 (cyanocobalamin), Choline, Vitamin A (retinol), Vitamin C (ascorbic acid), Vitamin D, Vitamin E (tocopherol), Vitamin K, carotenoids (alpha carotene, beta carotene, cryptoxanthin, lutein, lycopene) and zeaxanthin.
  • the micronutrient is a polyphenol.
  • Polyphenols are chemical compounds or molecules that are characterized by having at least one aromatic ring with one or more hydroxyl groups.
  • the polyphenol is a synthetic polyphenol or a naturally occurring polyphenol.
  • the polyphenol is a naturally occurring polyphenol and is derived from plant source material.
  • the polyphenol is a flavonoid or catechin.
  • the flavonoid or catechin is selected from anthocyanins, chalcones, dihydrochalcones, dihydroflavonols, flavanols, flavanones, flavones, flavonols and isoflavonoids.
  • the polyphenol is a lignan.
  • the polyphenol is selected from alkylmethoxyphenols, alkylphenols, curcuminoids, furanocoumarins, hydroxybenzaldehydes, hydroxybenzoketones, hydroxycinnamaldehydes, hydroxycoumarins, hydroxyphenylpropenes, methoxyphenols, naphtoquinones, phenolic terpenes, and tyrosols.
  • the polyphenol is a tannin or tannic acid.
  • the polyphenol is selected from hydroxybenzoic acids, hydroxycinnamic acids, hydroxyphenylacetic acids, hydroxyphenylpropanoic acids, and hydroxyphenylpentanoic acids. In some embodiments, the polyphenol is a stilbene.
  • compositions and medical foods and dietary supplements comprising glycan therapeutic preparations described herein further comprise a prebiotic substance or preparation thereof.
  • Prebiotics include various galactans and carbohydrate based gums, such as psyllium, guar, carrageen, gellan, lactulose, and konjac.
  • the prebiotic is one or more of galactooligosaccharides (GOS), lactulose, raffinose, stachyose, lactosucrose, fructo-oligosaccharides (FOS, e.g.
  • oligofructose or oligofructan inulin, isomalto-oligosaccharide, xylo-oligosaccharides (XOS), paratinose oligosaccharide, isomaltose oligosaccharides (IMOS), transgalactosylated oligosaccharides (e.g. transgalacto-oligosaccharides), transgalactosylate disaccharides, soybean oligosaccharides (e.g.
  • soyoligosaccharides chitosan oligosaccharide (chioses), gentiooligosaccharides, soy- and pectin-oligosaccharides, glucooligosaccharides, pecticoligosaccharides, palatinose polycondensates, difructose anhydride III, sorbitol, maltitol, lactitol, polyols, polydextrose, linear and branched dextrans, pullalan, hemicelluloses, reduced paratinose, cellulose, beta-glucose, beta-galactose, beta-fructose, verbascose, galactinol, xylan, inulin, chitosan, beta-glucan, guar gum, gum arabic, pectin, high sodium alginate, and lambda carrageenan, or mixtures thereof.
  • the pharmaceutical compositions and medical foods and dietary supplements comprising glycan therapeutic preparations further comprise a probiotic bacterium or preparation thereof, e.g., derived from bacterial cultures that are generally recognized as safe (GRAS) or known commensal or probiotic microbes.
  • a probiotic bacterium or preparation thereof e.g., derived from bacterial cultures that are generally recognized as safe (GRAS) or known commensal or probiotic microbes.
  • probiotics examples include organisms classified as genera Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacillus, Bacillus, Enterococcus, Escherichia, Streptococcus, Saccharomyces, Streptomyces , and family Christensenellaceae.
  • probiotic bacteria that can be used in the methods and compositions described herein include L. acidophilus, Lactobacillus species, such as L. crispatus, L. casei, L.
  • yogurt is a product which already contains bacteria species, such as Lactobacillus bulgaricus and Streptococcus thermophilus.
  • Beneficial bacteria may include one or more of the genus Akkermansia, Anaerofilum, Bacteroides, Blautia, Bifidobacterium, Butyrivibrio, Clostridium, Coprococcus, Dialister, Dorea, Fusobacterium, Eubacterium, Faecalibacterium, Lachnospira, Lactobacillus, Phascolarctobacterium, Peptococcus, Peptostreptococcus, Prevotella, Roseburia, Ruminococcus , and Streptococcus , and/or one or more of the species Akkermansia municiphilia, minuta, Clostridium coccoides, Clostridium leptum, Clostridium scindens, Dialister invisus, Eubacterium rectal, Eubacterium eligens, Faecalibacterium prausnitzii, Streptococcus salivarius , and Streptococcus thermophilus
  • Beneficial bacteria for the modulation of the gastrointestinal microbiota may include bacteria that produce organic acids (e.g. SCFAs) or that produce cytotoxic or cytostatic agents (to inhibit pathogenic growth), such as, e.g., hydrogen peroxide (H 2 O 2 ) and bacteriocins.
  • SCFAs organic acids
  • cytotoxic or cytostatic agents to inhibit pathogenic growth
  • Bacteriocins are small antimicrobial peptides which can kill both closely-related bacteria, or exhibit a broader spectrum of activity (e.g., nisin).
  • the prebiotic substances and probiotic strains that may be combined with glycan therapeutics described herein to produce a composition may be isolated at any level of purity by standard methods and purification can be achieved by conventional means known to those skilled in the art, such as distillation, recrystallization and chromatography.
  • the cultivated bacteria may be used in the composition.
  • the bacteria may be separated from the culture broth by any method including, without limitations, centrifugation, filtration or decantation.
  • the cells separated from the fermentation broth are optionally washed by water, saline (0.9% NaCl) or with any suitable buffer.
  • the wet cell mass obtained may be dried by any suitable method, e.g., by lyophilization.
  • the probiotic bacteria are lyophilized vegetative cells. In some embodiments, preparations of spores from sporulating probiotic bacteria are used.
  • the pharmaceutical compositions, medical foods, or dietary supplements comprise a glycan therapeutic preparation and probiotics whose viability has been partially attenuated (e.g. a mixture comprising 10%, 20%, 30%, 40%, 50% or more non-viable bacteria), or probiotics consisting primarily of non-viable microbes (e.g. 95%, 96%, 97%, 98%, 99%, 99.9% or 100%).
  • the compositions may further comprise microbial membranes and/or cell walls that have been isolated and purified from microbes or microbial vesicles.
  • the probiotic organism(s) can be incorporated into the pharmaceutical glycan therapeutic composition as a culture in water or another liquid or semisolid medium in which the probiotic remains viable.
  • a freeze-dried powder containing the probiotic organism may be incorporated into a particulate material or liquid or semisolid material comprising the glycan preparation by mixing or blending.
  • the pharmaceutical compositions and medical foods and dietary supplements comprising glycan therapeutic preparations further comprise a second therapeutic agent or preparation thereof, such as a drug.
  • the second therapeutic agent is an anti-cancer drug.
  • anti-cancer drugs include: checkpoint inhibitors (such as, e.g., anti-PD-1, anti-PD-L1, anti-CTLA4, anti-TIM-3, anti-LAG-3); vaccines (such as, e.g., autologous cancer vaccines, allogeneic cancer vaccines, neoantigen cancer vaccines, shared antigen cancer vaccines (e.g.
  • targeted kinase inhibitors such as, e.g., Imatinib mesylate, Ibrutinib, Neratinib, Palpociclib, Erlotinib, Lapatinib
  • antibodies such as, e.g., Bevacizumab, Trastuzumab, Rituximab, Cetuximab
  • chemotherapeutics such as, e.g., irinotecan, 5-flurouracil, lenalidomide, capecitabine, docetaxel
  • antibody-drug conjugates e.g. ado-trastuzumab emtansine
  • the second therapeutic agent is a pain-management drug.
  • the pain-management drug is an opioid, such as, e.g., codeine, fentanyl, hydrocodone, hydrocodone/acetaminophen, hydromorphone, meperidine, methadone, morphine, oxycodone, oxycodone and acetaminophen, or oxycodone and naloxone.
  • the pain-management drug is a non-opioid, such as, e.g., acetaminophen or nonsteroidal anti-inflammatory drugs (NSAIDs), such as aspirin and ibuprofen.
  • NSAIDs nonsteroidal anti-inflammatory drugs
  • the second therapeutic agent is an antidepressant, such as, e.g., amitriptyline, imipramine, doxepin and trazodone.
  • an antidepressant such as, e.g., amitriptyline, imipramine, doxepin and trazodone.
  • the second therapeutic agent is an antiepileptic, such as, e.g., gabapentin.
  • the second therapeutic agent is a steroid, such as, e.g. prednisone or dexamethasone.
  • the second therapeutic agent is a drug for managing a GI tract motility disorder, such as, e.g., acute diarrhea, chronic diarrhea, acute constipation, or chronic constipation.
  • Drugs for GI motility disorders include opioids, antibiotics, bile acid sequestrants and heavy metal containing compounds (bismuth subsalicylate).
  • Drugs to manage diarrhea include, but are not limited to liperamide, diphenoxylate with atropine, Cholestyramine, and bismuth subsalicylate.
  • Drugs to manage constipation include, but are not limited to magnesium citrate, magnesium hydroxide, magnesium sulfate/potassium sulfate/sodium sulfate, sodium biphosphate/sodium phosphate, lactulose, sennosides, bisacodyl, polyethylene glycol (e.g., PEG3350), docusate, polycarbophil, psyllium, methylcellulose, and mineral oil.
  • the therapeutic agent is an anti-inflammatory agent, such as, e.g., an NSAID, including ibuprofen, naproxen sodium, aspirin, celecoxib, sulindac, oxaprozin, salsalate, diflunisal, piroxicam, indomethacin, etodolac, meloxicam, nabumetone, ketorolac tromethamine, naproxen/esomeprazole, or diclofenac.
  • an NSAID including ibuprofen, naproxen sodium, aspirin, celecoxib, sulindac, oxaprozin, salsalate, diflunisal, piroxicam, indomethacin, etodolac, meloxicam, nabumetone, ketorolac tromethamine, naproxen/esomeprazole, or diclofenac.
  • an NSAID including ibuprofen, naproxen sodium, aspirin
  • the second therapeutic agent is an antimicrobial agent, such as an antibiotic, an antifungal agent, or an antiviral.
  • Antibiotics include aminoglycosides, such as amikacin, gentamicin, kanamycin, neomycin, streptomycin, and tobramycin; cephalosporins, such as cefamandole, cefazolin, cephalexin, cephaloglycin, cephaloridine, cephalothin, cephapirin, and cephradine; macrolides, such as erythromycin and troleandomycin; penicillins, such as penicillin G, amoxicillin, ampicillin, carbenicillin, cloxacillin, dicloxacillin, methicillin, nafcillin, oxacillin, phenethicillin, and ticarcillin; polypeptide antibiotics, such as bacitracin, colistimethate, colistin, polymyxin B; tetracyclines
  • glycan therapeutic preparations described herein and the therapeutic agent or active compound may be comingled or mixed in a single pharmaceutical composition or medical food or dietary supplement. In other embodiments, they may be contained in separate containers (and/or in various suitable unit dosage forms) but packaged together in one or more kits. In some embodiments, the preparations or compositions are not packaged or placed together.
  • a pharmaceutical composition comprises between 0.1% and 100% glycan therapeutic preparation by w/w, w/v, v/v or molar %.
  • a pharmaceutical composition comprises about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 7
  • a pharmaceutical composition comprises about 1-90%, about 10-90%, about 20-90%, about 30-90%, about 40-90%, about 40-80%, about 40-70%, about 40-60%, about 40-50%, about 50-90%, about 50-80%, about 50-70%, about 50-60%, about 60-90%, about 60-80%, about 60-70%, about 70-90%, about 70-80%, about 70-90%, about 70-80%, about 80-90%, about 90-96%, about 93-96%, about 93-95%, about 94-98%, about 93-99%, or about 90-100% of glycan therapeutic preparation by w/w, w/v, v/v or molar %.
  • the pharmaceutical compositions and medical foods and dietary supplements comprising glycan therapeutic preparations comprise one or more excipients or carriers, including diluents, binders, disintegrants, dispersants, lubricants, glidants, stabilizers, surfactants, flavoring agents, and colorants.
  • the pharmaceutical composition can comprise from about 1% to about 90% of the one or more excipients or carriers by w/w, w/v, v/v or molar %.
  • the pharmaceutical composition can comprise about 1-90%, 1-75%, 1-60%, 1-55%, 1-50%, 1-45%, 1-40%, 1-25%, 1-15%, 1-10%, 10-90%, 10-75%, 10-60%, 10-55%, 10-50%, 10-45%, 10-40%, 10-25%, 10-15%, 15-90%, 15-75%, 15-60%, 15-55%, 15-50%, 15-45%, 15-40%, 15-25%, 25-90%, 25-75%, 25-60%, 25-55%, 25-50%, 25-45%, 25-40%, 40-90%, 40-75%, 40-60%, 40-55%, 40-50%, 40-45%, 45-90%, 45-75%, 45-60%, 45-55%, 45-50%, 50-90%, 50-75%, 50-60%, 50-55%, 55-90%, 55-75%, 55-60%, 60-90%, 60-75%, 75-90% of the one or more excipients or carriers by w/w, w/v, v/v or molar
  • compositions suitable for administration of the pharmaceutical glycan therapeutic compositions provided herein include all such carriers known to those skilled in the art to be suitable for the particular mode of administration.
  • the compositions can one or more components that do not impair the desired action, or with components that supplement the desired action, or have another action.
  • the glycan therapeutic preparations described herein may be formulated into any suitable dosage form, e.g. for oral or enteral administration or formulated for injection.
  • the dosage forms described herein can be manufactured using processes that are known to those of skill in the art.
  • the dosage form may be suitable for any route of administration, including orally or parenterally, such as intravenously, intramuscularly, subcutaneously, intraorbitally, intracapsularly, intraperitoneally, intrarectally, intracisternally, intratumorally, intravasally, intradermally or by passive or facilitated absorption through the skin.
  • the dosage form may be a packet, such as any individual container that contains a pharmaceutical glycan therapeutic composition in the form of, e.g., a liquid (wash/rinse), a gel, a cream, an ointment, a powder, a tablet, a pill, a capsule, a depository, a single-use applicator or medical device (e.g. a syringe).
  • a pharmaceutical glycan therapeutic composition in the form of, e.g., a liquid (wash/rinse), a gel, a cream, an ointment, a powder, a tablet, a pill, a capsule, a depository, a single-use applicator or medical device (e.g. a syringe).
  • a container comprising a unit dosage form of the pharmaceutical glycan therapeutic composition, and a label containing instructions for use of such glycan therapeutic.
  • compositions that can be used orally include tablets, push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. Tablets can be made by compression or molding, optionally with one or more accessory ingredients.
  • Compressed tablets can be prepared by compressing in a suitable machine the active ingredient in a free-flowing form such as a powder or granules, optionally mixed with binders (e.g., povidone, gelatin, hydroxypropylmethyl cellulose), inert diluents, preservative, antioxidant, disintegrant (e.g., sodium starch glycolate, cross-linked povidone, cross-linked sodium carboxymethyl cellulose) or lubricating, surface active or dispersing agents.
  • binders e.g., povidone, gelatin, hydroxypropylmethyl cellulose
  • inert diluents preservative, antioxidant
  • disintegrant e.g., sodium starch glycolate, cross-linked povidone, cross-linked sodium carboxymethyl cellulose
  • Molded tablets can be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.
  • the tablets can optionally be coated or scored and can be formulated so as to provide slow or controlled release of the active ingredient therein. Tablets can optionally be provided with an enteric coating, to provide release in parts of the gut (e.g., colon, lower intestine) other than the stomach. All formulations for oral administration can be in dosages suitable for such administration.
  • the push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers.
  • the active compounds and/or other agents can be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols.
  • suitable liquids such as fatty oils, liquid paraffin, or liquid polyethylene glycols.
  • stabilizers can be added.
  • Dragee cores are provided with suitable coatings.
  • suitable coatings for this purpose, concentrated sugar solutions can be used, which can optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • Dyestuffs or pigments can be added to the tablets or Dragee coatings for identification or to characterize different combinations of active compound doses.
  • Formulations for oral use can also be presented as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent, for example, calcium carbonate, calcium phosphate or kaolin, or as soft gelatin capsules wherein the active ingredient is mixed with water soluble carrier such as polyethylene glycol or an oil medium, for example peanut oil, liquid paraffin, or olive oil.
  • an inert solid diluent for example, calcium carbonate, calcium phosphate or kaolin
  • water soluble carrier such as polyethylene glycol or an oil medium, for example peanut oil, liquid paraffin, or olive oil.
  • a provided glycan therapeutic composition includes a softgel formulation.
  • a softgel can contain a gelatin based shell that surrounds a liquid fill.
  • the shell can be made of gelatin, plasticizer (e.g., glycerin and/or sorbitol), modifier, water, color, antioxidant, or flavor.
  • the shell can be made with starch or carrageenan.
  • the outer layer can be enteric coated.
  • a softgel formulation can include a water or oil soluble fill solution, or suspension of a composition covered by a layer of gelatin.
  • Formulations for oral use may also be presented in a liquid dosage from.
  • Liquid preparations can be in the form of, for example, aqueous or oily suspensions, solutions, emulsions syrups or elixirs, or can be presented as a dry product for reconstitution with water or other suitable vehicle before use.
  • Such liquid preparations can contain conventional additives, such as suspending agents, for example sorbitol, methyl cellulose, glucose syrup, gelatin, hydroxyethyl cellulose, carboxymethyl cellulose, aluminum stearate gel or hydrogenated edible fats, emulsifying agents, for example lecithin, sorbitan monooleate, acacia; nonaqueous vehicles (which can include edible oils), for example almond oil, oily esters such as glycerine, propylene glycol, or ethyl alcohol; preservatives, for example methyl or propyl p-hydoxybenzoate or sorbic acid, and, if desired, conventional flavoring or coloring agents.
  • suspending agents for example sorbitol, methyl cellulose, glucose syrup, gelatin, hydroxyethyl cellulose, carboxymethyl cellulose, aluminum stearate gel or hydrogenated edible fats, emulsifying agents, for example lecithin, sorbitan monooleate, aca
  • liquid formulations can comprise, for example, an agent in water-in-solution and/or suspension form; and a vehicle comprising polyethoxylated castor oil, alcohol, and/or a polyoxyethylated sorbitan mono-oleate with or without flavoring.
  • Each dosage form may comprise an effective amount of a glycan therapeutic and can optionally comprise pharmaceutically inert agents, such as conventional excipients, vehicles, fillers, binders, disintegrants, pH adjusting substances, buffer, solvents, solubilizing agents, sweeteners, coloring agents, and any other inactive agents that can be included in pharmaceutical dosage forms for administration. Examples of such vehicles and additives can be found in Remington's Pharmaceutical Sciences, 22nd edition (2012).
  • compositions provided herein can be in unit-dosage forms or multiple-dosage forms.
  • a unit-dosage form refers to physically discrete unit suitable for administration to human in need thereof.
  • the unit-dosage form is provided in a package.
  • Each unit-dose can contain a predetermined quantity of an active ingredient(s) sufficient to produce the desired therapeutic effect, in association with other pharmaceutical carriers or excipients.
  • Examples of unit-dosage forms include ampoules, syringes, and individually packaged tablets and capsules.
  • Unit-dosage forms can be administered in fractions or multiples thereof.
  • a multiple-dosage form is a plurality of identical unit-dosage forms packaged in a single container, which can be administered in segregated unit-dosage form.
  • multiple-dosage forms include vials, bottles of tablets or capsules, or bottles of pints or gallons.
  • the multiple dosage forms comprise different pharmaceutically active agents.
  • a multiple dosage form can be provided which comprises a first dosage element comprising a composition comprising a glycan therapeutic and a second dosage element comprising a second active compound or therapeutic agent (e.g. an anti-cancer drug).
  • the dosage elements can be in a modified release form.
  • a pair of dosage elements can make a single unit dosage.
  • kits comprising multiple unit dosages, wherein each unit comprises a first dosage element comprising a composition comprising a glycan therapeutic and a second dosage element comprising a second active compound or therapeutic agent (e.g., a pharmaceutical agent, a probiotic, a prebiotic, a micronutrient, etc. or a combination thereof).
  • a second active compound or therapeutic agent e.g., a pharmaceutical agent, a probiotic, a prebiotic, a micronutrient, etc. or a combination thereof.
  • the unit-dosage form comprises between about 0.001 mg to about 10 g of the glycan therapeutic.
  • the unit-dosage form may comprise about 0.001 mg to about 9.5 g, about 0.005 mg to about 9 g, about 0.01 mg to about 8.5 g, about 0.05 mg to about 8 g, about 0.075 mg to about 7.5 g, about 0.1 mg to about 7 g, about 0.25 mg to about 6.5 g, about 0.5 mg to about 6 g, about 0.75 mg to about 5.5 g, about 1 mg to about 5 g, about 2.5 mg to about 4.5 g, about 5 mg to about 4 g, about 7.5 mg to about 3.5 g, about 10 mg to about 3 g, about 12.5 mg to about 2.5 g, about 15 mg to about 2 g, about 17.5 mg to about 1.5 g, about 20 mg to about 1 g, about 25 mg to about 750 mg, about 50 mg to about 500 g, or about 75 mg to about 250
  • the unit-dosage form may comprise about 1 g to about 5 g, about 1 g to about 10 g, about 1 g to about 15 g, about 1 g to about 20 g, about 1 g to about 25 g, about 1 g to about 30 g, about 5 g to about 10 g, about 5 g to about 15 g, about 5 g to about 20 g, about 5 g to about 25 g, about 5 g to about 30 g, about 10 g to about 20 g, or about 10 g to about 30 g of the glycan therapeutic.
  • the unit-dosage form comprises about 0.001 mg to about 100 mg, about 0.005 mg to about 75 mg, about 0.01 mg to about 50 mg, about 0.05 mg to about 25 mg, about 0.1 mg to about 10 mg, about 0.5 mg to about 7.5 mg, or about 1 mg to about 5 mg of the glycan therapeutic. In other embodiments, the unit-dosage form comprises about 1 mg to about 100 mg, about 2.5 mg to about 75 mg, about 5 mg to about 50 mg, or about 10 mg to about 25 mg of the glycan therapeutic.
  • the unit-dosage form comprises about 100 mg to about 10 g, about 250 mg to about 7.5 g, about 500 mg to about 5 g, about 750 mg to about 2.5 g, or about 1 g to about 2 g of the glycan therapeutic.
  • the unit-dosage form comprises between about 0.001 mL to about 1000 mL of the glycan therapeutic.
  • the unit-dosage form may comprise about 0.001 mL to about 950 mL, about 0.005 mL to about 900 mL, about 0.01 mL to about 850 mL, about 0.05 mL to about 800 mL, about 0.075 mL to about 750 mL, about 0.1 mL to about 700 mL, about 0.25 mL to about 650 mL, about 0.5 mL to about 600 mL, about 0.75 mL to about 550 mL, about 1 mL to about 500 mL, about 2.5 mL to about 450 mL, about 5 mL to about 400 mL, about 7.5 mL to about 350 mL, about 10 mL to about 300 mL, about 12.5 mL to about 250 mL, about 15 mL
  • the unit-dosage form comprises about 0.001 mL to about 10 mL, about 0.005 mL to about 7.5 mL, about 0.01 mL to about 5 mL, about 0.05 mL to about 2.5 mL, about 0.1 mL to about 1 mL, about 0.25 mL to about 1 mL, or about 0.5 mL to about 1 mL of the glycan therapeutic.
  • the unit-dosage form comprises about 0.01 mL to about 10 mL, about 0.025 mL to about 7.5 mL, about 0.05 mL to about 5 mL, or about 0.1 mL to about 2.5 mL of the glycan therapeutic.
  • the unit-dosage form comprises about 0.1 mL to about 10 mL, about 0.25 mL to about 7.5 mL, about 0.5 mL to about 5 mL, about 0.5 mL to about 2.5 mL, or about 0.5 mL to about 1 mL of the glycan therapeutic.
  • the unit-dosage form e.g., a tablet, capsule (e.g., a hard capsule, push-fit capsule, or soft capsule), or softgel, has a body length of between about 0.1 inches to about 1.5 inches (e.g., about 0.5 inches and about 1 inch), or about 5 mm to about 50 mm (e.g., about 10 mm to about 25 mm). In some embodiments, the unit-dosage form.
  • a tablet, capsule e.g., a hard capsule, push-fit capsule, or soft capsule
  • softgel has an external diameter of about 0.05 inches to about 1 inch (e.g., about 0.1 inches to about 0.5 inches), or about 1 mm to about 25 mm (e.g., about 5 mm to about 10 mm).
  • Each unit-dosage form of the glycan therapeutic may have a caloric value of between about 0.01 kcal and about 1000 kcal.
  • the unit-dosage form may have a caloric value of about 0.01 kcal to about 900 kcal, about 0.05 kcal to about 800 kcal, about 0.1 kcal to about 700 kcal, about 0.25 kcal to about 600 kcal, about 0.5 kcal to about 500 kcal, about 0.75 kcal to about 400 kcal, about 1 kcal to 300 kcal, about 5 kcal to about 200 kcal, or about 10 kcal to about 100 kcal.
  • the unit-dosage form of the glycan therapeutic has a caloric value of between 10 kcal to about 500 kcal. In other embodiments, the unit-dosage form of the glycan therapeutic has a caloric value of between 50 kcal to about 500 kcal.
  • the unit-dosage form may have a caloric value of about 0.001 kcal to about 100 kcal, about 0.005 kcal to about 90 kcal, about 0.01 kcal to about 80 kcal, about 0.025 kcal to about 70 kcal, about 0.05 kcal to about 60 kcal, about 0.075 kcal to about 50 kcal, about 0.1 kcal to 40 kcal, about 0.25 kcal to about 30 kcal, about 0.5 kcal to about 25 kcal, about 0.25 kcal to about 20 kcal, or about 0.1 kcal to about 10 kcal.
  • the unit-dosage form of the glycan therapeutic may be formulated to dissolve in an aqueous solution (e.g., water, milk, juice, and the like) and is orally administered as a beverage, syrup, solution, or suspension.
  • an aqueous solution e.g., water, milk, juice, and the like
  • the unit-form dosage of the glycan therapeutic may comprise a cube, packet, lozenge, pill, tablet, capsule, candy, powder, elixir, or concentrated syrup formulated for dissolving into an aqueous solution prior to oral administration.
  • the unit-dosage form of the glycan therapeutic may comprise a cube, packet, lozenge, pill, tablet, capsule, candy, powder, elixir, or concentrated syrup formulated to dissolve in vivo, e.g., in the mouth, stomach, intestine, or colon of the subject upon oral administration.
  • an effective amount of a glycan therapeutic preparation can be dispersed uniformly in one or more excipients or additives, for example, using high shear granulation, low shear granulation, fluid bed granulation, or by blending for direct compression.
  • Excipients and additives include diluents, binders, disintegrants, dispersants, lubricants, glidants, stabilizers, surfactants, antiadherents, sorbents, sweeteners, and colorants, or a combination thereof.
  • Diluents or fillers can be used to increase the bulk of a tablet so that a practical size is provided for compression.
  • Non-limiting examples of diluents include lactose, cellulose, microcrystalline cellulose, mannitol, dry starch, hydrolyzed starches, powdered sugar, talc, sodium chloride, silicon dioxide, titanium oxide, dicalcium phosphate dihydrate, calcium sulfate, calcium carbonate, alumina and kaolin.
  • Binders can impart cohesive qualities to a tablet formulation and can be used to help a tablet remain intact after compression.
  • binders include starch (including corn starch and pregelatinized starch), gelatin, sugars (e.g., glucose, dextrose, sucrose, lactose and sorbitol), celluloses, polyethylene glycol, alginic acid, dextrin, casein, methyl cellulose, waxes, natural and synthetic gums, e.g., acacia, tragacanth, sodium alginate, gum arabic, xantan gum, and synthetic polymers such as polymethacrylates, polyvinyl alcohols, hydroxypropylcellulose, and polyvinylpyrrolidone.
  • starch including corn starch and pregelatinized starch
  • gelatin e.g., glucose, dextrose, sucrose, lactose and sorbitol
  • sugars e.g., glucose, dextrose, sucrose, lactose and sorbitol
  • celluloses polyethylene glycol
  • alginic acid e.g.
  • Lubricants can also facilitate tablet manufacture; non-limiting examples thereof include magnesium stearate, calcium stearate, stearic acid, glyceryl behenate, and polyethylene glycol.
  • Disintegrants can facilitate tablet disintegration after administration, and non-limiting examples thereof include starches, alginic acid, crosslinked polymers such as, e.g., crosslinked polyvinylpyrrolidone, croscarmellose sodium, potassium or sodium starch glycolate, clays, celluloses (e.g., carboxymethylcelluloses (e.g., carboxymethylcellulose (CMC), CMC-Na, CMC-Ca)), starches, gums and the like.
  • suitable glidants include silicon dioxide, talc, and the like.
  • Stabilizers can inhibit or retard drug decomposition reactions, including oxidative reactions.
  • Surfactants can also include and can be anionic, cationic, amphoteric or nonionic.
  • Exemplary sweeteners may include stevia extract, aspartame, sucrose, alitame, saccharin, and the like.
  • the tablets can also comprise nontoxic auxiliary substances such as pH buffering agents, preservatives, e.g., antioxidants, wetting or emulsifying agents, solubilizing agents, coating agents, flavoring agents (e.g., mint, cherry, anise, peach, apricot, licorice, raspberry, vanilla), and the like.
  • Additional excipients and additives may include aluminum acetate, benzyl alcohol, butyl paraben, butylated hydroxy toluene, calcium disodium EDTA, calcium hydrogen phosphate dihydrate, dibasic calcium phosphate, tribasic calcium phosphate, candelilla wax, carnuba wax, castor oil hydrogenated, cetylpyridine chloride, citric acid, colloidal silicone dioxide, copolyvidone, corn starch, cysteine HCl, dimethicone, disodium hydrogen phosphate, erythrosine sodium, ethyl cellulose, gelatin, glycerin, glyceryl monooleate, glyceryl monostearate, glycine, HPMC pthalate, hydroxypropylcellulose, hydroxyl propyl methyl cellulose, hypromellose, iron oxide red or ferric oxide, iron oxide yellow, iron oxide or ferric oxide, magnesium carbonate, magnesium oxide, magnesium stearate, methionine,
  • Immediate-release formulations of an effective amount of a glycan therapeutic composition can comprise one or more combinations of excipients that allow for a rapid release of a pharmaceutically active agent (such as from 1 minute to 1 hour after administration).
  • Controlled-release formulations also referred to as sustained release (SR), extended-release (ER, XR, or XL), time-release or timed-release, controlled-release (CR), or continuous-release refer to the release of a glycan therapeutic composition from a dosage form at a particular desired point in time after the dosage form is administered to a subject.
  • a controlled release dosage form begins its release and continues that release over an extended period of time. Release can occur beginning almost immediately or can be sustained. Release can be constant, can increase or decrease over time, can be pulsed, can be continuous or intermittent, and the like.
  • a controlled release dosage refers to the release of an agent from a composition or dosage form in which the agent is released according to a desired profile over an extended period of time.
  • controlled-release refers to delayed release of an agent from a composition or dosage form in which the agent is released according to a desired profile in which the release occurs after a period of time.
  • the dosage form can be an effervescent dosage form.
  • Effervescent means that the dosage form, when mixed with liquid, including water and saliva, evolves a gas.
  • Some effervescent agents (or effervescent couple) evolve gas by means of a chemical reaction which takes place upon exposure of the effervescent disintegration agent to water or to saliva in the mouth. This reaction can be the result of the reaction of a soluble acid source and an alkali monocarbonate or carbonate source. The reaction of these two general compounds produces carbon dioxide gas upon contact with water or saliva.
  • An effervescent couple (or the individual acid and base separately) can be coated with a solvent protective or enteric coating to prevent premature reaction.
  • the acid sources can be any which are safe for human consumption and can generally include food acids, acid and hydrite antacids such as, for example: citric, tartaric, amalic, fumeric, adipic, and succinics.
  • Carbonate sources include dry solid carbonate and bicarbonate salt such as sodium bicarbonate, sodium carbonate, potassium bicarbonate and potassium carbonate, magnesium carbonate and the like. Reactants which evolve oxygen or other gasses and which are safe for human consumption are also included. In one embodiment citric acid and sodium bicarbonate are used.
  • the dosage form can be in a candy form (e.g., matrix), such as a lollipop or lozenge.
  • a candy form e.g., matrix
  • an effective amount of a glycan therapeutic is dispersed within a candy matrix.
  • the candy matrix comprises one or more sugars (such as dextrose or sucrose).
  • the candy matrix is a sugar-free matrix.
  • Conventional sweeteners e.g., sucrose
  • sugar alcohols suitable for use with diabetic patients e.g., sorbitol or mannitol
  • other sweeteners e.g., sweeteners described herein
  • the candy base can be very soft and fast dissolving, or can be hard and slower dissolving.
  • Various forms will have advantages in different situations.
  • a candy mass composition comprising an effective amount of the glycan therapeutic can be orally administered to a subject in need thereof so that an effective amount of the glycan therapeutic will be released into the subject's mouth as the candy mass dissolves and is swallowed.
  • a subject in need thereof includes a human adult or child.
  • the dosage forms described herein can also take the form of pharmaceutical particles manufactured by a variety of methods, including high-pressure homogenization, wet or dry ball milling, or small particle precipitation.
  • Other methods useful to make a suitable powder formulation are the preparation of a solution of active ingredients and excipients, followed by precipitation, filtration, and pulverization, or followed by removal of the solvent by freeze-drying, followed by pulverization of the powder to the desired particle size.
  • the pharmaceutical particles have a final size of 3-1000 microns, such as at most 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 microns.
  • the pharmaceutical particles have a final size of 10-500 microns.
  • the pharmaceutical particles have a final size of 50-600 microns.
  • the pharmaceutical particles have a final size of 100-800 microns.
  • an oral dosage form comprising a glycan therapeutic composition, wherein the oral dosage form is a syrup.
  • the syrup can comprise about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, or 85% solid.
  • the syrup can comprise about 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% liquid, for example, water.
  • the solid can comprise a glycan therapeutic composition.
  • the solid can be, for example, about 1-96%, 10-96%, 20-96%, 30-96%, 40-96%, 50-96%, 60-96%, 70-96%, 80-96%, or 90-96% glycan therapeutic composition.
  • a glycan therapeutic composition is formulated as a viscous fluid.
  • the composition comprises a foaming component, a neutralizing component, or a water-insoluble dietary fiber.
  • a foaming component can be at least one member selected from the group consisting of sodium hydrogencarbonate, sodium carbonate, and calcium carbonate.
  • a neutralizing component can be at least one member selected from the group consisting of citric acid, L-tartaric acid, fumaric acid, L-ascorbic acid, DL-malic acid, acetic acid, lactic acid, and anhydrous citric acid.
  • a water-insoluble dietary fiber can be at least one member selected from the group consisting of crystalline cellulose, wheat bran, oat bran, cone fiber, soy fiber, and beet fiber.
  • the formulation can contain a sucrose fatty acid ester, powder sugar, fruit juice powder, and/or flavoring material.
  • the dosage forms are formulated to release the pharmaceutical compositions comprising glycan therapeutic preparations in a specific region(s) of the GI tract, such as the small or the large intestine. In some embodiments, the dosage forms are formulated to release the pharmaceutical compositions comprising therapeutic glycan preparations in a specific region(s) of the GI tract, such as the cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and/or rectum.
  • Solid formulations for oral use may comprise an enteric coating, which may control the location at which a glycan therapeutic composition is absorbed in the digestive system.
  • an enteric coating can be designed such that a glycan therapeutic composition does not dissolve in the stomach but rather travels to the small or the large intestine, cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and/or rectum, where it dissolves.
  • An enteric coating can be stable at low pH (such as in the stomach) and can dissolve at higher pH (for example, in the small or large intestine or colon).
  • Material that can be used in enteric coatings includes, for example, alginic acid, cellulose acetate phthalate, plastics, waxes, shellac, and fatty acids (e.g., stearic acid, palmitic acid).
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is an enzyme-responsive delivery system.
  • trypsin responsive polymers can be made using hydrogels that are crosslinked by peptides that are degraded by trypsin. Trypsin is active in the small intestine. Trypsin-responsive delivery systems can be used to target delivery of the pharmaceutical glycan therapeutic compositions to the small intestine.
  • enzyme-digestible hydrogels consisting of poly(vinyl pyrrolidone) crosslinked with albumin are degraded in the presence of pepsin.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is a delivery device that enables prolonged retention at a specific site in the GI tract.
  • a gastroretentive delivery system enables prolonged release of the pharmaceutical glycan therapeutic compositions to the stomach.
  • Gastroretentive delivery may be used for the pharmaceutical glycan therapeutic compositions that modulate bacteria in the stomach or in the upper small intestine.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is a mucoadhesive delivery system that adheres to the mucosal surfaces of the stomach. They are typically composed of polymers with numerous hydrogen-bonding groups, e.g., cross-linked polyacrylic acids, sodium carboxymethyl cellulose, sodium alginate, carrageenan, Carbopol 934P, or thiolated polycarbophil.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is an expanding delivery system that rapidly increases in size in the stomach, which slows its passage through the pylorus.
  • Such systems include systems that unfold in the stomach. For example, geometric shapes such as tetrahedrons, rings, disks, etc. can be packed into a gelatin capsule. When the capsule dissolves, the shape unfolds.
  • the systems can be composed of one or more erodible polymer (e.g., hydroxypropyl cellulose), one or more nonerodible polymer (e.g., polyolefins, polyamides, polyurethanes).
  • the glycan therapeutic may then be dispersed within the polymer matrix.
  • the retention times can be fine-tuned by the polymer blend.
  • devices made out of elastic polymers that are stable in the acidic pH of the stomach but dissolve in the neutral/alkaline conditions further along the GI tract can be used.
  • Such polymer formulations can prevent intestinal obstruction when the device exits the stomach.
  • Supramolecular polymer gels crosslinked by hydrogen bonds between carboxyl groups may also be used, e.g. composed of poly(acryloyl 6-aminocaproic acid) (PA6ACA) and poly(methacrylic acid-co-ethyl acrylate) (EUDRAGIT L 100-55).
  • PA6ACA poly(acryloyl 6-aminocaproic acid)
  • EUDRAGIT L 100-55 poly(methacrylic acid-co-ethyl acrylate)
  • Other systems include swellable excipients, such as collagen sponges.
  • a hydrogel matrix e.g.
  • a swellable core polyvinyl pyrrolidone XL, Carbopol 934P, calcium carbonate
  • swells 2-50 times in the stomach superporous hydrogel composites swell to hundreds of times their original volume in a few minutes.
  • Some systems exploit gas generation to achieve expansion, e.g. carbon dioxide-generating, expandable systems that are surrounded by a hydrophilic membrane.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is a density-controlled delivery system.
  • These systems are designed to either float or sink in gastric fluids which delays their emptying from the stomach.
  • high-density systems enable the device to settle to the bottom of the stomach, below the pylorus, and thus avoid stomach emptying.
  • Other systems are low-density/floating systems.
  • Such devices may, e.g., comprise entrapped air in hollow chambers or may incorporate low-density materials like fats, oils, or foam powder.
  • Low density may be achieved through swelling, e.g. hydrocolloid containing capsules dissolve upon contacting gastric fluid and the hydrocolloids swell to form a mucous body.
  • Alternative polymers include: chitosans, sodium alginate, and glycerol monooleate matrix. Low density may be achieved through gas generation. For example, tablets loaded with carbonate and optionally citric acid generate carbon dioxide after contact with acidic aqueous media. The carbon dioxide generated is entrapped within the gelling hydrocolloid causing the system to float. Hydrocolloids include hydroxypropyl methylcellulose and Carbopol 934P.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein employs a design to retain a device in the small or large intestine.
  • the location-specific nature of the device is provided by a specific triggering method, e.g. pH, enzyme, etc.
  • a specific triggering method e.g. pH, enzyme, etc.
  • microneedle pills comprise a drug reservoir spiked with microneedles that is encapsulated in a pH-responsive coating. When the pill reaches the desired location in the GI tract and the coating dissolves, the microneedles enable the pill to become stuck to the lining of the GI tract.
  • the microneedle pills comprise a capsule that consists of two chemical compartments filled with citric acid and sodium bicarbonate, respectively. As the pill dissolves in the digestive system, barriers between the two substances erode, allowing them to mix and create a chemical reaction that pushes micro-needles of saccharides through the outer layer of the capsule and into the lining of the small intestine.
  • the saccharide needles can be filled with drugs that are delivered into nearby blood vessels as the saccharide is absorbed.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein employs a pH sensitive polymer coating.
  • pH-dependent polymers can be insoluble at low pH levels (e.g. acid resistance in the stomach, pH 1-2) and become increasingly soluble as pH rises, e.g. to about 5.5-6.2 in the duodenum, to about pH 5.7 in the ascending colon, to about pH 6.4 in the cecum, to about pH 6.6 in the transverse colon, to about pH 7.0 in the descending colon, to about 7.2-7.5 in the ileum, or to about pH 7.5 in the distal small intestine.
  • TARGITTM technology may be used for site-specific delivery of the pharmaceutical glycan therapeutic compositions in the gastrointestinal (GI) tract.
  • GI gastrointestinal
  • the system employs pH-sensitive coatings onto injection-moulded starch capsules to target the terminal ileum and colon.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is a delayed release system or time controlled release system.
  • Such systems usually employ enteric coatings that may be combined with pH sensitive and time release functions.
  • ETP enteric coated time-release press coated
  • tablets may be used that are composed of three components: a glycan therapeutic-containing core tablet (rapid release function), a press-coated, swellable hydrophobic polymer layer (e.g. hydroxypropyl cellulose layer (HPC), and a time release function.
  • the duration of lag phase can be controlled either by weight or composition of polymer layer and an enteric coating layer (acid resistance function).
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein employs Eudragit® enteric coatings of tablets and capsules.
  • suitable synthetic polymers include: Shellac, ethyl cellulose, cellulose acetate phthalate, hydroxypropylmethyl cellulose, polyvinyl acetate phthalate and poly glutamic acid coatings, such as poly- ⁇ -glutamic acid ( ⁇ -PGA). These coatings combine both mucoadhesive and pH-dependent release strategies.
  • Eudragits® are methacrylic co-polymers with varying side group compositions that alter the pH at which they are soluble. For example, for Eudragit®-coated systems no significant drug release occurs in the stomach (e.g. at pH 1.4) and in the small intestine (e.g. at pH 6.3), while significant drug release can be seen at pH 7.8 in the ileocaecal region.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is a microbial-triggered system, such as a polysaccharide based delivery system.
  • Polysaccharide based delivery systems contain biodegradable and mucoadhesive polymer coatings, including coatings of chitosan and pectin.
  • Other suitable natural polymers include, e.g., guar gum, inulin, cyclodextrin, dextran, amylase, chondrotin sulphate, and locust bean gum. These delivery systems can be used to target the glycan therapeutic to the small or the large intestine, cecum, ascending colon, transverse colon, descending colon, sigmoid colon.
  • Coatings with naturally occurring polysaccharides like guar gum, xanthan gum, chitosan, alginates, etc. are degraded by resident gut microbes, e.g. microbes comprising enzymes such as, xylosidase, arabinosidase, galactosidase, glucosidases, etc.
  • the microbes and associated enzyme activities are predominatly located in a specific region of the GI tract (e.g., Jain A. et al., Perspectives of Biodegradable Natural Polysaccharides for Site-Specific Drug Delivery to the Colon, J Pharm Pharmaceut Sci 10(1):86-128, 2007).
  • CODESTM technology may be used to deliver the pharmaceutical glycan therapeutic compositions.
  • This system combines the polysaccharide coating with a pH-sensitive coating.
  • the system consists of a core tablet coated with three layers of polymer coatings:
  • the outer coating is composed of Eudragit L.
  • This coating gets dissolved in the duodenum and exposes the next coating.
  • the next coating is composed of Eudragit E.
  • This layer allows the release of lactulose present in the inner core.
  • the lactulose gets metabolized into short chain fatty acids that lower the surrounding pH where the Eudragit E layer dissolves.
  • the dissolving of Eudragit E results in the exposure of the glycan therapeutic.
  • the bacteria present in the colon are responsible for the degradation of polysaccharides that are released from the core tablet.
  • the degradation of polysaccharides may result in organic acids formation that lowers the pH of the contents surrounding the tablet.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is a pressure-controlled delivery system.
  • the system employs the fact that higher pressures are encountered in the colon than in the small intestine.
  • the release of glycan therapeutics occurs following disintegration of a water-insoluble polymer capsule as a result of pressure in the lumen of the colon.
  • the release profile may be adjusted by varying the thickness of the ethylcellulose, the capsule size and/or density of the capsule.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is a pulsatile colon targeted delivery system.
  • the system can be a pulsincap system.
  • the capsule which is employed comprises a plug that is placed in the capsule that controls the release of the glycan therapeutic.
  • a swellable hydrogel e.g. hydroxyl propyl methyl cellulose (HPMC), poly methyl methacrylate or polyvinyl acetate
  • HPMC hydroxyl propyl methyl cellulose
  • the release profile can be controlled by varying the length and/or point of intersection of the plug with the capsule body.
  • Another system is a port system.
  • the capsule body is enclosed in a semi-permeable membrane.
  • the insoluble plug consists of an osmotically active agent and the glycan therapeutic.
  • the semi-permeable membrane permits inflow of the fluid which increases pressure in the capsule body. This leads to an expelling of the plug and release of the glycan therapeutic.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is an osmotically controlled colon targeted delivery system.
  • An exemplary system, OROS-CT consists of osmotic units (up to 5 or 6 push pull units) encapsulated in a hard gelatin capsule.
  • the push pull units are bilayered with outer enteric impermeable membrane and inner semi-permeable membrane.
  • the internal, central part of the push pull consists of the drug layer and push layer.
  • the glycan therapeutic is released through the semi-permeable membrane.
  • the capsule body enclosing the push pull units is dissolved immediately after administration. In the GI tract the enteric impermeable membrane prevents water absorption.
  • the enteric coating is dissolved in small intestine (higher pH, >7), water enters the unit through the semi-permeable membrane causing push layer to swell and force out the glycan therapeutic.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is “smart pill” which can be used to release the glycan therapeutic just before reaching the ileocecal valve.
  • the dosage form for the pharmaceutical glycan therapeutic compositions described herein is a rectally administered formulation.
  • enemas introduce a pharmaceutical glycan therapeutic composition in liquid formulation into the rectum.
  • the volume administered is typically less than 10 mL.
  • Suppositories introduce a pharmaceutical glycan therapeutic composition into the rectum.
  • Suppositories are solid dosage forms that melt or dissolve when inserted into the rectum, releasing the glycan therapeutics.
  • Typical excipients for suppository formulations include cocoa butter, polyethylene glycols, and agar.
  • a unit-dosage form described herein comprising providing a glycan therapeutic; formulating the glycan therapeutic into a unit-dosage form, packaging the unit-dosage form, labelling the packaged unit-dosage form, and/or selling or offering for sale the packaged and labeled unit-dosage form.
  • the unit-dosage forms described herein may also be processed.
  • the processing comprises one or more of: processing the dosage form into a pharmaceutical composition, e.g., formulating, combining with a second component, e.g., an excipient or buffer or a second active compound or therapeutic agent; portioning into smaller or larger aliquots; disposing into a container, e.g., a gas or liquid tight container; packaging; associating with a label; shipping or moving to a different location.
  • the processing comprises one or more of: classifying, selecting, accepting or discarding, releasing or withholding, processing into a pharmaceutical composition, shipping, moving to a different location, formulating, labeling, packaging, releasing into commerce, or selling or offering for sale, depending on whether the predetermined threshold is met.
  • the processed dosage forms comprise a glycan therapeutic described herein.
  • Any glycan therapeutic preparation described herein may be formulated as a medical food.
  • a medical food is defined in section 5(b)(3) of the Orphan Drug Act (21 U.S.C. 360ee(b)(3)).
  • Medical food is formulated to be consumed (oral intake) or administered enterally (e.g. feeding/nasogastric tube) under medical supervision, e.g. by a physician. It is intended for the specific dietary management of a disease or condition, such as, e.g. cancer.
  • Medical foods as used herein do not include food that is merely recommended by a physician as part of an overall diet to manage the symptoms or reduce the risk of a disease or condition.
  • Medical foods comprising a preparation of glycan therapeutics are administered to a subject who has a cancer or tumor under medical supervision (which may be active and ongoing) and usually, the subject receives instructions on the use of the medical food.
  • Medical foods may comprise, in addition to a glycan therapeutic described herein, one or more food additives, color additives, GRAS excipients and other agents or substances suitable for medical foods.
  • Medical food preparations may be nutritionally complete or incomplete formulas.
  • glycan therapeutic preparation described herein may be formulated as a dietary supplement.
  • Dietary supplements are regulated under the Dietary Supplement Health and Education Act (DSHEA) of 1994.
  • a dietary supplement is a product taken by mouth that contains a “dietary ingredient” intended to supplement the diet.
  • the “dietary ingredients” in these products may include, in addition to a glycan therapeutic described herein, one or more of: vitamins, minerals, herbs or other botanicals, amino acids, and substances such as enzymes, organ tissues, glandulars, and metabolites.
  • Dietary supplements can also be extracts or concentrates, and may be found in many forms such as tablets, capsules, softgels, gelcaps, liquids, or powders.
  • DSHEA requires that every supplement be labeled a dietary supplement and not as a general food.
  • kits are also contemplated.
  • a kit can comprise unit dosage forms of the pharmaceutical glycan therapeutic composition, and a package insert containing instructions for use of the glycan therapeutic in treatment of a disease, disorder or pathological condition, such as, e.g., cancer.
  • the kits include a pharmaceutical glycan therapeutic composition in suitable packaging for use by a subject in need thereof. Any of the compositions described herein can be packaged in the form of a kit.
  • a kit can contain an amount of a pharmaceutical glycan therapeutic composition (optionally additionally comprising a prebiotic substance, a probiotic bacterium, a micronutrient, and/or a second therapeutic agent, such as a drug) sufficient for an entire course of treatment, or for a portion of a course of treatment.
  • Doses of a pharmaceutical glycan therapeutic composition can be individually packaged, or the pharmaceutical glycan therapeutic composition can be provided in bulk, or combinations thereof.
  • a kit provides, in suitable packaging, individual doses of a glycan therapeutic composition that correspond to dosing points in a treatment regimen, wherein the doses are packaged in one or more packets.
  • the pharmaceutical glycan therapeutic composition can be provided in bulk in a single container, or in two, three, four, five, or more than five containers.
  • each container may contain enough of a pharmaceutical glycan therapeutic composition for a particular week of a treatment program that runs for a month.
  • the bulk containers can be suitably packaged together to provide sufficient pharmaceutical glycan therapeutic composition for all or a portion of a treatment period.
  • the container or containers can be labeled with a label indicating information useful to the subject in need thereof or the physician performing the treatment protocol, such as, e.g. dosing schedules.
  • kits include a dosage form containing all the ingredients intended to be used in a course of treatment or a portion of a course of treatment, e.g., a pharmaceutical glycan therapeutic composition and optionally a second active compound or therapeutic agent or a buffer/carrier.
  • a pharmaceutical glycan therapeutic composition is packaged in one package or set of packages, and additional components, such as probiotic bacteria, prebiotics, and therapeutic agents (e.g., drugs, such as anti-cancer drugs) are packaged separately from the pharmaceutical glycan therapeutic composition.
  • additional components such as probiotic bacteria, prebiotics, and therapeutic agents (e.g., drugs, such as anti-cancer drugs) are packaged separately from the pharmaceutical glycan therapeutic composition.
  • kits for treating cancer in a patient comprising a package comprising (a) a pharmaceutical composition or medical food or dietary supplement comprising a glycan therapeutic preparation described herein, and (b) instructions for using the pharmaceutical composition for treating cancer (e.g., a cancer described herein) in a patient.
  • the kit also includes a second agent which is a pharmaceutical composition, e.g., a chemotherapeutic drug or other anti-cancer drug described herein.
  • the kit also contains a probiotic.
  • Kits can further include written materials, such as instructions, expected results, testimonials, explanations, warnings, clinical data, information for health professionals, and the like.
  • the kits contain a label or other information indicating that the kit is only for use under the direction of a health professional.
  • the container can further include scoops, syringes, bottles, cups, applicators or other measuring or serving devices.
  • the glycan therapeutic preparations, pharmaceutical compositions and therapeutic agents described herein can be administered to a subject in need thereof by various routes (e.g., systemically or locally) including, for example, orally or parenterally, such as intravenously, intramuscularly, subcutaneously, intraorbitally, intracapsularly, intraperitoneally, intrarectally, intracisternally, intratumorally, intravasally, intradermally or by passive or facilitated absorption through the skin.
  • the therapeutic agents can be administered locally to the site of a pathologic condition, for example, intravenously or intra-arterially into a blood vessel supplying a tumor.
  • the glycan therapeutic composition is administered enterically.
  • administration includes oral administration, or by an oral or nasal tube (including nasogastric, nasojejunal, oral gastric, or oral jejunal).
  • administration includes rectal administration (including enema, suppository, or colonoscopy).
  • Active compounds and pharmaceutical agents may be administered separately, e.g., prior to, concurrent with or after administration of the glycan therapeutics and not as a part of the pharmaceutical composition or medical food or dietary supplement (e.g. as a co-formulation) of glycan therapeutics.
  • pharmaceutical compositions or medical foods comprising preparations of glycan therapeutics are administered in combination with a recommended or prescribed diet, e.g. a diet that is rich in probiotic and/or prebiotic-containing foods, such as it may be determined by a physician or other healthcare professional.
  • a recommended or prescribed diet e.g. a diet that is rich in probiotic and/or prebiotic-containing foods, such as it may be determined by a physician or other healthcare professional.
  • Suitable sources of soluble and insoluble fibers are commercially available. Prebiotics can be found in certain foods, e.g.
  • the composition and metabolic activity of the intestinal bacterial community may be modified. Modification of the composition and metabolic activity of the intestinal bacterial community may be performed through the administration of i) a glycan therapeutic alone (such as in the absence of exogenously administered bacteria), ii) a glycan therapeutic and one or more beneficial microorganisms (probiotics), or iii) a combination of a glycan therapeutic, a probiotics, and another agent, such as, e.g. a prebiotic (e.g. a dietary fiber), or a therapeutic agent, such as, e.g. an antibacterial agent (e.g. antibiotic), an anti-inflammatory agent, an anti-cancer agent, and the like.
  • a glycan therapeutic alone such as in the absence of exogenously administered bacteria
  • a glycan therapeutic and one or more beneficial microorganisms probiotics
  • a combination of a glycan therapeutic, a probiotics, and another agent such as, e.g.
  • glycan therapeutics e.g. oligosaccharides
  • oligosaccharides have a desired degree of digestibility
  • Digestibility depends on many factors, including, e.g. the degree of polymerization, the degree of branching, the type of glycosidic linkages, position of the linkages, anomeric configuration (e.g. L- or D-configuration, alpha/beta configuration) of the glycan unit.
  • furanosides are generally more susceptible to hydrolysis than pyranosides.
  • Deoxy sugars are generally more acid labile than non-deoxy sugars.
  • Uronic acids are generally less susceptible to hydrolysis than non-uronic monosaccharides.
  • Digestibility is a parameter that can be ascertained for the glycan therapeutics described herein.
  • glycan therapeutics disclosed herein are screened to assess their digestibility.
  • Digestibility of glycan therapeutics can be assessed by any suitable method known in the art (e.g. by simulated gastric digestion half-life).
  • digestibility is assessed by a physiologically relevant in vitro digestion reaction, e.g. simulated gastric digestion and simulated intestinal digestion.
  • SGF simulated gastric fluid
  • Samples at different stages of the digestion can be analyzed by standard glycan techniques known in the art and described herein.
  • glycan techniques known in the art and described herein.
  • the half-life of digestion can be calculated. Suitable assays can be used to assess comparative digestibility (i.e., against a benchmark glycan such as, e.g. a prebiotic) or to assess absolute digestibility.
  • the digestibility (expressed as half-life) is 30 minutes or less, 20 minutes or less, 15 minutes or less, 10 minutes or less, 5 minutes or less, 4 minutes or less, 3 minutes or less, 2 minutes or less or 1 minute or less. In some embodiments, the digestibility (expressed as half-life) is 30 minutes or more, 45 minutes or more, 1 hour or more, 2 hours or more, 3 hours or more, 4 hours or more, 5 hours or more, or 10 hours or more.
  • the glycan therapeutic is digested at a constant rate and/or at a controlled rate.
  • the rate of digestion of the glycan therapeutic may not be optimized for the highest possible rate of digestion.
  • the rate of absorption of the glycan therapeutic following ingestion by a mammal may be slower and the total time period over which absorption occurs following ingestion may be longer than for glycan therapeutic of similar glycan unit composition that are digested at a faster initial rate.
  • the glycan therapeutic is completely or substantially completely digested. In some embodiments the glycan therapeutic is substantially not digested or not digested.
  • the glycan therapeutic composition comprises non-digestible oligo- or polysaccharides.
  • the glycan therapeutic is indigestible or incompletely digestible by human digestive systems.
  • Glycan therapeutics are, in some embodiments, selectively digested by gut microbiota constituents that allows specific changes, both in the composition and/or activity in the commensal gut microbiota.
  • provided herein are glycan therapeutics that are non-digestible or incompletely digestible by humans in the absence of specific microbes in the gut. In these embodiments, only specific bacteria are capable of utilizing the glycan therapeutic as a carbon source.
  • glycan therapeutics that are non-digestible and stimulate the growth or activity of bacteria in the digestive system that are beneficial to the health of the body.
  • the glycan therapeutic is resistant to gastric acidity.
  • the glycan therapeutic is resistant to hydrolysis by mammalian enzymes.
  • the glycan therapeutic is resistant to gastrointestinal absorption.
  • the glycan therapeutic is a substrate for fermentation by the intestinal microbiota.
  • the glycan therapeutic is a selective substrate for one or a limited number of potentially beneficial bacteria in the colon, stimulating their growth and/or metabolic activity.
  • the glycan therapeutic is capable of altering the composition of intestinal microbiota to a composition richer in specific bacteria. In some embodiments, the glycan therapeutic selectively stimulates the growth and/or selective activity of intestinal bacteria associated with health and well-being.
  • the glycan therapeutic capable of selectively stimulating the growth of beneficial bacteria including Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenella minuta , or a Christensenellaceae in the large intestine.
  • the glycan therapeutic is digested by the gut microbiota, resulting, e.g., in the release of hydrogen and carbon dioxide gas and short-chain fatty acids such as butyrate, if desired.
  • a glycan therapeutic preparation in some embodiments, promotes the selective growth of beneficial colonic bacteria, including multiple species and strains of Bifidobacteria and Lactobacilli .
  • Bifidobacteria carry out non hydrogen-producing lactose fermentation reactions in addition to inhibiting hydrogen producing bacteria, such as Escherichia coli.
  • glycan therapeutics that affect the composition and/or activity of the intestinal microbiota.
  • administration of the glycan therapeutic to a subject may result in an increased prebiotic index.
  • the prebiotic index (PI) relates to the sum of: (Bifidobacteria/total bacteria)+( Lactobacilli /total bacteria) ⁇ ( Bacteroides /total bacteria) ⁇ ( Clostridia /total bacteria), (see Palframan et al, 2003, Lett Appl Microbiol 37:281-284).
  • Administration of a glycan therapeutic to a subject may result in an increase in: Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenella minuta, or a Christensenellaceae.
  • glycan therapeutics are provided that comprise beta glycosidic linkages.
  • the beta glycosidic linkages make the glycans substantially non-digestible and/or unabsorbable to a human host in the stomach and small intestine.
  • certain probiotic and commensal microbes are able to metabolize the glycans.
  • glycan therapeutics are provided that comprise alpha glycosidic linkages.
  • the alpha glycosidic linkages are not hydrolyzed by human salivary amylase, but can be metabolized by Bifidobacterium bifidum and Clostridium butyricum.
  • the therapeutic glycan is indigestible. Digestibility may differ between different enzymes or sets of enzymes, e.g. a therapeutic glycan may be digestible for certain microbes expressing certain enzymes, but may be indigestible to a mammal lacking the required enzyme(s) in the absence of hosting the microbes.
  • the glycan therapeutic is an oligosaccharide that is optionally non-digestible by a human digestive system, contains at least one beta-glycosidic bond and/or at least one alpha-glycosidic bond that can be digested by a bacterium.
  • the bacterium is a probiotic or an endogenous commensal bacterium such as, e.g. a Lactobacilli or a Bifidobacteria.
  • the glycan therapeutics pass through the small intestine and into the large intestine (colon) mostly intact.
  • the glycan therapeutic comprises less than 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 14%, 16%, 18%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or less than 99% of bonds that are hydrolyzable by a mammalian amylase enzyme.
  • bonds that are hydrolyzable bonds that are hydrolyzable by a mammalian amylase enzyme.
  • hydrolyzable bonds are recognized by a mammalian amylase enzyme.
  • Other types of hydrolyzable bonds e.g. alpha 1,4; alpha 1,6, alpha 1,2; and alpha 1,6 glycosidic linkages
  • specific microbial enzymes e.g.
  • bonds may also be hydrolyzable by hydrolases (e.g. Amylases, Cellulases, Mannanases, Pectinases, Pullulanases, Xylanases and the like), oxireductases (Catalases, Glucose oxidases, and the like), transferases (Fructosyltransferases, Glucosyltransferases), lyases, isomerases (Glucose isomerases), ligases, and the like.
  • hydrolases e.g. Amylases, Cellulases, Mannanases, Pectinases, Pullulanases, Xylanases and the like
  • oxireductases Catalases, Glucose oxidases, and the like
  • transferases Fructosyltransferases, Glucosyltransferases
  • lyases isomerases (Glucose isomerases), ligases, and the like
  • the glycan therapeutic exhibits a slow rate of fermentability by the microbiota.
  • the glycan therapeutic has a high degree of branching to resist digestion.
  • the glycan therapeutic has a DP of 10 or more, 12 or more, 14 or more, 16 or more, 18 or more, 20 or more, 25 or more, 30 or more to slow its digestibility.
  • the branching of the glycan therapeutic protects against digestion by human enzymes.
  • the size of the glycan therapeutic lessens the fermentation speed (digestibility speed by bacteria), e.g., in the colon.
  • the glycan therapeutic characteristics promote indigestibility by human glycosidases and promote selective digestion by the microbiota.
  • glycan therapeutics that can be digested by the microbiota (e.g. by carbohydrate fermentation) without certain side effects or with a substantial reduction of symptoms of fermentation, such as increased gas formation that may cause flatulence, discomfort, and/or bloating.
  • the glycan therapeutic composition comprises one or more mono-, oligo-, and/or polysaccharides which are non-digestible by a human digestive system. In another embodiment, the glycan therapeutic composition consists essentially of a mono-, oligo-, and/or polysaccharide which is non-digestible by a human digestive system.
  • the glycan therapeutic composition comprises a mixture of non-digestible oligosaccharides. In another embodiment, the glycan therapeutic composition comprises one or more digestible saccharides and one or more non-digestible oligosaccharides. In some embodiments, the glycan therapeutic composition comprises at least one non-digestible saccharide and optionally contains one or more digestible mono-saccharides, oligo- or polysaccharides. In one embodiment the glycan therapeutic composition comprises a mixture of one or more non-digestible oligosaccharides, non-digestible polysaccharides, free monosaccharides, non-digestible saccharides, starch, or non-starch polysaccharides.
  • Exemplary natural non-digestible saccharides are fructo-oligosaccharides, galacto-oligosaccharides, gluco-oligosaccharides, arabino-oligosaccharides, mannan-oligosaccharides, xylo-oligosaccharides, fuco-oligosaccharides, arabinogalacto-oligosaccharides, glucomanno-oligosaccharides, galactomanno-oligosaccharides, sialic acid comprising oligosaccharides and uronic acid oligosaccharides.
  • Natural saccharides that are not digestible by humans include transgalactooligosaccharides, galacto-oligosaccharides, lactulose, raffinose, stachyose, lactosucrose, fructo-oligosaccharides, isomalto-oligosaccharides, xylo-oligosaccharides, paratinose oligosaccharides, difructose anhydride III, sorbitol, maltitol, lactitol, reduced paratinose, cellulose, beta-glucose, beta-galactose, beta-fructose, verbascose, galactinol, and beta-glucan, guar gum, pectin, high sodium alginate, and lambda carrageenan.
  • Other natural saccharides include inulin, fructo-oligosaccharide (FOS), lactulose, galacto-oligosaccharide (GOS
  • Digestible monosaccharides or oligosaccharides are carbohydrates that can be digested by the human digestive system, and include, e.g., lactose, galactose, or glucose.
  • a glycan therapeutic composition is a mixture of non-digestible oligosaccharides and lactose, glucose or galactose.
  • a prebiotic composition comprises a glycan therapeutic composition wherein the glycan therapeutic composition comprises about 1-90%, about 1-80%, about 1-70%, about 1-60%, about 1-50%, about 1-40%, about 40-90%, about 40-80%, about 40-70%, about 40-60%, about 40-50%, about 50-90%, about 50-80%, about 50-70%, about 50-60%, about 60-90%, about 60-80%, about 60-70%, about 70-90%, about 70-80%, about 70-90%, about 70-80%, about 80-90%, about 92-100%, about 93-99%, about 94-98%, about 92-96%, about 93-96%, or about 93-95% glycan therapeutic by weight with the remainder comprising digestible saccharides.
  • the digestible saccharides are less than about 10% (such as about 9, 8, 7, 6, 5, 4, 3, 2, or less than 1%).
  • a glycan therapeutic composition can comprise about 1-5% digestible saccharides, such as lactose, glucose or galactose.
  • the digestible saccharides are byproducts of the glycan therapeutic synthesis process.
  • a glycan therapeutic composition comprises about 1-90%, about 1-80%, about 1-70%, about 1-60%, about 1-50%, about 1-40%, about 40-90%, about 40-80%, about 40-70%, about 40-60%, about 40-50%, about 50-90%, about 50-80%, about 50-70%, about 50-60%, about 60-90%, about 60-80%, about 60-70%, about 70-90%, about 70-80%, about 70-90%, about 70-80%, about 80-90%, about 90-96%, about 93-96%, about 93-95%, about 94-98%, about 93-99%, or about 92-100% glycan therapeutic by weight and no digestible saccharides.
  • the glycan therapeutic composition comprises one or more non-digestible or essentially non-digestible (by a human) prebiotics.
  • This non-digestibility is because humans lack the enzymes to break down some or all of the prebiotic oligosaccharide as it travels through the digestive tract.
  • bacteria e.g., Bifidobacteria and Lactobacilli
  • Suitable prebiotics can include one or more of a carbohydrate, carbohydrate monomer, carbohydrate oligomer, or carbohydrate polymer.
  • the prebiotics are non-digestible saccharides, which include non-digestible monosaccharides, non-digestible oligosaccharides, or non-digestible polysaccharides.
  • the glycan therapeutic composition comprises one or more of GOS, lactulose, raffinose, stachyose, lactosucrose, FOS (e.g. oligofructose or oligofructan), inulin, isomalto-oligosaccharide, xylo-oligosaccharide, paratinose oligosaccharide, transgalactosylated oligosaccharides (e.g.
  • transgalacto-oligosaccharides transgalacto-oligosaccharides
  • transgalactosylate disaccharides soybean oligosaccharides (e.g. soyoligosaccharides), gentiooligosaccharides, glucooligosaccharides, pecticoligosaccharides, palatinose polycondensates, difructose anhydride III, sorbitol, maltitol, lactitol, polyols, polydextrose, reduced paratinose, cellulose, beta-glucose, beta-galactose, beta-fructose, verbascose, galactinol, and beta-glucan, guar gum, pectin, high, sodium alginate, and lambda carrageenan, or mixtures thereof.
  • soybean oligosaccharides e.g. soyoligosaccharides
  • gentiooligosaccharides
  • prebiotics include fructo-oligosaccharides (FOS), galactooligosaccharides (GOS), Xylo-oligosaccharides (XOS), chitosan oligosaccharide (chioses), isomaltose oligosaccharides (IMOS), gum arabic, soy- and pectin-oligosaccharides, pectin, xylan, inulin, chitosan, and/or beta-glucan.
  • Other prebiotics include various galactans and carbohydrate based gums, such as psyllium, guar, carrageen, gellan, and konjac.
  • dietary fibers such as, for example, resistant maltodextrin, fiber dextrin, polydextrose, inulin, IMOS, the linear and branched dextrans, pullalan, hemicellulose, and combinations thereof.
  • Dietary fiber may consist of non-starch polysaccharides such as cellulose and many other plant components such as dextrins, inulin, lignin, chitins, pectins, beta-glucans, fructo-oligosaccharides, resistant starches, soluble corn (gluco) fiber, polydextrose, and gums such as guar, locust bean, xanthan or pullulan gum.
  • Fiber sources include oligo- or polysaccharides, selected from the group consisting of resistant maltodextrin, polydextrose, soluble corn (gluco) fiber, fiber dextrin, pullulan, resistant starch, inulin, fructo-oligosaccharides, galacto-oligosaccharides, hemicellulose and fructose oligomer syrup or lactulose or any other prebiotic compounds (including prebiotic disaccharides such as lactulose and tagatose among others).
  • both soluble and insoluble fibers are used.
  • the weight ratio of soluble fiber to insoluble fiber may be about 1:4 to about 4:1; or about 1:1 to about 2:1.
  • Additional substances can be given in conjunction with a glycan therapeutic composition. These substances can enhance the action of the increasing doses of glycan therapeutic by, e.g., encouraging the growth of bacteria in the gut that alleviate symptoms of GI diseases, increasing adhesion of probiotic or beneficial commensal bacteria, or allowing doses of probiotic bacteria to more readily pass through the stomach without being destroyed. These substances can be given prior to treatment with glycan therapeutic, during treatment with glycan therapeutic, after treatment with glycan therapeutic, or any combination thereof. If administered during glycan therapeutic treatment, they can be administered with the dose of glycan therapeutic being given, or before or after the dose of glycan therapeutic, or any combination thereof.
  • a disease, disorder or pathological condition comprising administering to a subject in need thereof a glycan therapeutic preparation.
  • methods of treating cancer with a pharmaceutical composition comprising a glycan therapeutic preparation described herein are also provided herein.
  • the method includes identifying a human subject in need of treatment for a tumor or cancer, and administering to the subject a pharmaceutical composition or medical food or dietary supplement comprising a glycan therapeutic preparation described herein.
  • the glycan therapeutic preparation is formulated as a pharmaceutical composition. In other embodiments, the glycan therapeutic preparation is formulated as a medical food. In other embodiments, the glycan therapeutic preparation is formulated as a dietary supplement.
  • the cancer may be any solid or liquid cancer and includes benign or malignant, non-invasive or invasive tumors, hyperplasias, and premalignant lesions, including gastrointestinal cancer (such as non-metastatic or metastatic colorectal cancer, pancreatic cancer, gastric cancer, oesophageal cancer, hepatocellular cancer, cholangiocellular cancer, oral cancer, lip cancer); urogenital cancer (such as hormone sensitive or hormone refractory prostate cancer, renal cell cancer, bladder cancer, penile cancer); gynecological cancer (such as ovarian cancer, cervical cancer, endometrial cancer); lung cancer (such as small-cell lung cancer and non-small-cell lung cancer); head and neck cancer (e.g.
  • gastrointestinal cancer such as non-metastatic or metastatic colorectal cancer, pancreatic cancer, gastric cancer, oesophageal cancer, hepatocellular cancer, cholangiocellular cancer, oral cancer, lip cancer
  • urogenital cancer such as hormone sensitive or hormone refrac
  • CNS cancer including malignant glioma, astrocytomas, retinoblastomas and brain metastases; malignant mesothelioma; non-metastatic or metastatic breast cancer (e.g.
  • skin cancer such as malignant melanoma, basal and squamous cell skin cancers, Merkel Cell Carcinoma, lymphoma of the skin, Kaposi Sarcoma); thyroid cancer; bone and soft tissue sarcoma; and haematologic neoplasias (such as multiple myeloma, acute myelogenous leukemia, chronic myelogenous leukemia, myelodysplastic syndrome, acute lymphoblastic leukemia, Hodgkin's lymphoma).
  • skin cancer such as malignant melanoma, basal and squamous cell skin cancers, Merkel Cell Carcinoma, lymphoma of the skin, Kaposi Sarcoma
  • thyroid cancer bone and soft tissue sarcoma
  • haematologic neoplasias such as multiple myeloma, acute myelogenous leukemia, chronic myelogenous leukemia, myelodysplastic syndrome, acute lymphoblastic leukemia, Hod
  • the cancer is acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast); brain cancer (e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma; chord
  • liver cancer e.g., hepatocellular cancer (HCC), malignant hepatoma
  • lung cancer e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung
  • leiomyosarcoma LMS
  • mastocytosis e.g., systemic mastocytosis
  • muscle cancer myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a.
  • myelofibrosis MF
  • chronic idiopathic myelofibrosis chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)
  • neuroblastoma e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis
  • neuroendocrine cancer e.g., gastroenteropancreatic neuroendocrine tumor (GEP-NET), carcinoid tumor
  • osteosarcoma e.g., bone cancer
  • ovarian cancer e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma
  • papillary adenocarcinoma pancreatic cancer
  • pancreatic cancer e.g., pancreatic adenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors
  • the subject has metastatic cancer. In other embodiments, the subject has non-metastatic cancer. In some embodiments, the subject has a benign tumor. In some embodiments, the subject has a premalignant lesion or a pre-cancerous condition. Examples of premalignant lesions or pre-cancerous conditions include: actinic keratosis, Barrett's esophagus, atrophic gastritis, ductal carcinoma in situ, dyskeratosis congenital, sideropenic dysphagia, lichen planus, oral submucous fibrosis, solar elastosis, cervical dysplasia, leukoplakia, and erythroplakia.
  • the cancer is a highly immunogenic cancer, e.g., the cancer has (e.g., as determined by analysis of a cancer biopsy) one or more of the following characteristics: (a) tumor infiltrating lymphocytes (TIL), e.g., 1 TIL per 1000 tumor cells; (b) mutations, e.g., 0.1 or more somatic mutations per megabase of tumor genomic DNA; (c) neoantigens, e.g., 1 or more neoantigen with one or more endogenous T cell receptor and/or one or more idiotype clone that recognizes a processed and presented moiety of the neoantigen; (d) tertiary lymphoid structures; (e) high expression of inflammatory gene expression, e.g., 2-fold increased expression of cytokines above baseline expression in non-cancerous tissue; and (f) immune cells exhibiting immunosuppressive phenotype, e.g.
  • TIL tumor infiltrating lymphocytes
  • the cancer is melanoma, lung cancer, bladder cancer, colorectal cancer, esophageal cancer, cervical cancer, head and neck cancer, stomach cancer, uterine cancer, liver cancer, kidney cancer, ovarian cancer, prostate cancer, myeloma, B cell lymphoma, or glioma.
  • Methods of assessing these characteristics of the cancer are known (see, e.g., Clin Cancer Res. 2000 May; 6(5):1875-81; Nature. 2013 Aug. 22; 500(7463):415-21. doi: 10.1038/nature12477. Epub 2013 Aug. 14; Nature. 2014 Nov. 27; 515(7528):577-81.
  • the cancer is a primary tumor, in some embodiments, the cancer is a metastasized tumor. In some embodiments, the cancer patient has: had one or more tumors resected, received chemotherapy or other pharmacological treatment for the cancer, received radiation therapy, and/or received other therapy for the cancer.
  • the method of treating a cancer in a subject includes a) administering a pharmaceutical composition comprising a glycan therapeutic preparation to a subject who has been treated with an anti-cancer therapy, b) administering an anti-cancer therapy to a subject who has been treated with a pharmaceutical composition comprising a glycan therapeutic preparation; or c) administering a pharmaceutical composition comprising a glycan therapeutic preparation and administering an anti-cancer therapy to a subject.
  • the method includes administering pharmaceutical composition comprising a glycan therapeutic preparation to a subject who has been treated with an anti-cancer therapy and the treatment with the anti-cancer therapy was initiated, or completed, within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 21, 28 days of initiation, or completion, of the glycan therapeutic administration.
  • the method includes administering an anti-cancer therapy to a subject who has been treated with a pharmaceutical composition comprising a glycan therapeutic preparation and the treatment with the glycan therapeutic preparation was initiated, or completed, within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 21, 28 days of initiation, or completion, of the administration of the anti-cancer therapy.
  • the method includes administering a pharmaceutical composition comprising a glycan therapeutic preparation and administering an anti-cancer therapy to a subject and the glycan therapeutic preparation and the anti-cancer therapy are provided within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 minutes, hours, days, weeks of one another.
  • the first and second therapeutic agents e.g. a pharmaceutical glycan therapeutic preparation and a second active compound or pharmaceutical agent
  • the first therapeutic agent may be administered immediately, up to 1 hour, up to 2 hours, up to 3 hours, up to 4 hours, up to 5 hours, up to 6 hours, up to 7 hours, up to, 8 hours, up to 9 hours, up to 10 hours, up to 11 hours, up to 12 hours, up to 13 hours, 14 hours, up to hours 16, up to 17 hours, up 18 hours, up to 19 hours up to 20 hours, up to 21 hours, up to 22 hours, up to 23 hours up to 24 hours or up to 1-7, 1-14, 1-21 or 1-30 days before or after the second therapeutic agent.
  • the pharmaceutical composition is administered in an amount and for a time effective to result in one of (or more, e.g., 2 or more, 3 or more, 4 or more of): (a) reduced tumor size, (b) reduced rate of tumor growth, (c) increased tumor cell death (d) reduced tumor progression, (e) reduced number of metastases, (f) reduced rate of metastasis, (g) decreased tumor recurrence (h) increased survival of subject, (i) increased cancer progression free survival of subject.
  • the method of treatment optionally results in one or more of: i) enhancement of the subject's immune function, ii) improvement of the subject's gut health, iii) induction of production of epithelial enzymes, iv) induction of the synthesis of vitamins in the intestines of the subject, v) reduction in the levels of toxins in the subject's GI tract, vi) induction of apoptosis of cancer and precancerous cells in the subject, vii) improvement of the overall gastrointestinal and colonic health of the subject, viii) reduction in bloating, abdominal distention or gas production, and/or ix) improvement of bowel regularity.
  • methods are provided to modulate GI fluid turnover. In some embodiments, methods are provided to balance (or rebalance) GI fluid homeostasis. In some embodiments, methods are provided to modulate electrolyte balance. Fluid loss can lead to electrolyte loss (Na, K, Mg, Cl).
  • the methods include administering to a subject in need to GI fluid modulation a glycan therapeutic described herein in an amount effective to substantially (re-)balance the fluid turnover. For example, diarrhea and constipation are conditions associated with a fluid imbalance. Osmotic diarrhea can be caused, e.g., by laxatives and sugar intolerance.
  • Secretory diarrhea can be caused, e.g, by malabsorption syndromes, drugs (e.g., quinidine, quinine, colchicine, anthraquinone cathartics, castor oil, prostaglandins), and endocrine tumors that produce substances that increase secretion, e.g., vipomas (vasoactive intestinal peptide), gastrinomas (gastrin), mastocytosis (histamine), medullary carcinoma of the thyroid (calcitonin and prostaglandins), and carcinoid tumors (histamine, serotonin, and polypeptides).
  • drugs e.g., quinidine, quinine, colchicine, anthraquinone cathartics, castor oil, prostaglandins
  • endocrine tumors that produce substances that increase secretion, e.g., vipomas (vasoactive intestinal peptide), gastrinomas (gastrin), mastocytosis (histamine
  • the pharmaceutical glycan therapeutic composition is administered in an amount and for a time effective to result in shifted or modulated state of the subject's gastrointestinal microbiota. In one embodiment, the the pharmaceutical glycan therapeutic composition is administered in an amount and for a time effective to result in shifted or modulated bacterial taxa (one or more, two or more, three or more, etc.). In one embodiment, the pharmaceutical glycan therapeutic composition is administered in an amount and for a time effective to result in shifted or modulated microbial function (e.g., a metabolic function). In one embodiment, the pharmaceutical glycan therapeutic composition is administered in an amount and for a time effective to result in a shift or modulation of the microbiome (genome), transcriptome, metabolome, or proteome of the microbiota.
  • administration of the pharmaceutical glycan therapeutic compositions improves the overall health of the host and/or the health of a specific niche, such as the GI tract, e.g. by modulating (e.g. increasing or decreasing) the growth or abundance of one or more members of the microbial community in the niche (such as resident commensal bacteria and/or acquired pathogens or pathobionts).
  • administration of the glycan therapeutics described herein improves the overall health of the gastrointestinal tract by influencing members of the microbial community.
  • the glycan therapeutics described herein e.g., activate signaling pathways within the intestinal mucosa, inhibit pathogen binding to mucosal surfaces, and/or attenuate inflammation of the intestinal mucosa.
  • administration of the glycan therapeutics results in the treatment or prevention of an inflammatory disease, including intestinal inflammation.
  • the treatment results in increased levels of bacteria adherent to gastrointestinal epithelial cells.
  • the treatment results in increased levels of Citrobacter rodentium , EHEC O157:H7, Candida albicans, Clostridium bolteae 90B3 Clostridium cf. saccharolyticum K10, Clostridium symbiosum WAL-14673, Clostridium hathewayi 12489931 , Ruminococcus obeum A2-162 , Ruminococcus gnavus AGR2154, Butyrate-producing bacterium SSC/2, Clostridium sp. ASF356 , Coprobacillus sp. D6 cont1.1, Eubacterium sp.
  • the glycan therapeutics described herein promote the metabolism and growth of beneficial components of the gut microbiota, such as, e.g., Bacteroides, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli , or Christensenella .
  • beneficial components of the gut microbiota such as, e.g., Bacteroides, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli , or Christensenella .
  • the glycan therapeutics may be beneficial in the treatment of diseases associated with disturbed gut
  • the glycan therapeutics described herein increase the levels of Bifidobacteria. In one embodiment, the glycan therapeutics described herein increase the levels of Bacteroides . In one embodiment, the glycan therapeutics described herein increase the levels of Akkermansia . In one embodiment, the treatment results in an increase in the proportion of Bifidobacteria, Bacteroides , and/or Akkermansia relative to another bacterial species.
  • methods to protect against pathogenic infection comprising administering to a subject a glycan therapeutic preparation described herein.
  • pathogenic species are capable of causing disease by producing infection or increasing cancer risk for the host.
  • a healthy human microbiota reduces the risk of disease upon ingestion and may comprise Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenella minuta , or a Christensenellaceae species, Streptococcus thermophilus, Enterococcus and Bacillus species, E.
  • a healthy bacterial community protects the host, e.g., by providing an increased barrier to translocation of bacteria across the gut mucosa, by competitive exclusion of potential pathogens, and by growth inhibition of bacterial pathogens.
  • the treatment with a glycan therapeutic described herein results in an increase in the concentration of one or more microbial metabolite in the GI tract (which may be measured, e.g., in the stool). In one embodiment, the treatment with a glycan therapeutic described herein results in a change (e.g., an improvement) in gut permeability.
  • the glycan therapeutics described herein when administered to a subject in an effective amount may modulate the production of one or more microbial metabolites.
  • the glycan therapeutics when administered to a subject in an effective amount may modulate the production of one or more microbial metabolites listed in Table 2.
  • glycan therapeutics when administered to a subject in an effective amount may modulate (e.g. increase or decrease) one or more of the following microbial metabolites: formic acid, acetic acid, propionic acid, butryic acid, isobutyric acid, valeric acid, isovaleric acid, ascorbic acid, lactic acid, tryptophan, serotonin, and/or indole.
  • glycan therapeutics when administered to a subject in an effective amount may modulate (e.g. increase or decrease) one or more of the following microbial metabolites: succinic acid, trimethylamine (TMA), TMAO (trimethylamine N-oxide), deoxy cholic acid, ethyphenyl sulfate, acetylaldehyde, hydrogen peroxide, and/or butanedione.
  • TMA trimethylamine
  • TMAO trimethylamine N-oxide
  • deoxy cholic acid ethyphenyl sulfate
  • acetylaldehyde acetylaldehyde
  • hydrogen peroxide and/or butanedione.
  • a substantial increase or decrease in a metabolite may be detected.
  • glycan therapeutics described herein when administered to a subject in an effective amount may modulate (e.g. increase) one or more of the following microbial metabolites: formic acid, acetic acid, propionic acid, butryic acid, isobutyric acid, valeric acid, isovaleric acid, acorbic acid, tryptophan, serotonin, and/or indole.
  • glycan therapeutics described herein when administered to a subject in an effective amount may modulate (e.g. increase) one or more of the following microbial metabolites: formic acid, acetic acid, propionic acid, butryic acid, isobutyric acid, valeric acid, isovaleric acid, acorbic acid, tryptophan, serotonin, and/or indole.
  • glycan therapeutics described herein when administered to a subject in an effective amount may modulate (e.g.
  • glycan therapeutics described herein when administered to a subject in an effective amount may modulate (e.g. decrease) one or more of the following microbial metabolites: formic acid, acetic acid, propionic acid, butryic acid, isobutyric acid, valeric acid, isovaleric acid, acorbic acid, tryptophan, serotonin, and/or indole.
  • glycan therapeutics described herein when administered to a subject in an effective amount may modulate (e.g. increase) one or more of the following microbial metabolites: Succinic acid, TMAO, deoxy cholic acid, ethyphenyl sulfate, acetylaldehyde, and/or butanedione.
  • the glycan therapeutic is digested by the gut microbiota resulting, e.g., in the release of short-chain fatty acids such as butyrate, acetate, and propionate, which may act immunomodulatory (e.g. anti-inflammatory) and other metabolites (e.g. bile acids, and lactate) that may confer beneficial health effects on the host.
  • short-chain fatty acids such as butyrate, acetate, and propionate
  • immunomodulatory e.g. anti-inflammatory
  • other metabolites e.g. bile acids, and lactate
  • Some methods described herein include the administration of glycan therapeutics to modulate the host's immune functions and/or intestinal epithelial cell functions.
  • the glycan therapeutics may upregulate the immune function, e.g. to improve the ability of the host to fight cancers, while downregulation of immune function may treat inflammation (such as, e.g., intestinal inflammation).
  • Modulated beneficial bacteria may stimulate intestinal epithelial cell responses, including restitution of damaged epithelial barrier, production of antibacterial substances and cell-protective proteins, and blocking of cytokine-induced intestinal epithelial cell apoptosis.
  • method of modulating a functional pathway of the microbiota of the gastrointestinal tract include administering to the human subject a pharmaceutical composition comprising a glycan therapeutic preparation in an amount effective to modulate the functional pathway.
  • the functional pathway modulates the production of anti-microbial agent, a secondary bile acid, a short-chain fatty acid, a siderophore or a metabolite listed in Table 2 by the microbiota.
  • Bacteria can elicit both pro- and anti-inflammatory responses from host (mammalian) cells.
  • glycan therapeutics are used to alter the bacterial population or its function to elicit a desired host response.
  • the host response may be modulated a) via secreted or shed bacterial products (e.g., short-chain fatty acids), b) stimulation of the production of antimicrobial peptides (AMPs), c) modulation (increasing or decreasing the production of) inflammatory and immunomodulatory cytokines including: interleukin-1 ⁇ (IL-1 ⁇ ), IL-1 ⁇ , IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-17A, IL-17F, IL-22, IL-23, tumor necrosis factor (TNF), chemokine (C-C motif) ligand 5 (CCL5, also known as RANTES), transforming growth factor beta (TGF- ⁇ ), interferon gamma (IF
  • the glycan therapeutics when administered to a subject in an effective amount may modulate one or more host pathways.
  • an inflammatory state e.g. of the GI tract is modulated by administration of a glycan therapeutic.
  • production of short-chain fatty acids may be modulated.
  • SCFAs produced by the gut microbiota may serve as energy sources for colonic epithelial cells and in some embodiments contribute to the maintenance of gut barrier function.
  • gut barrier function limits plasma endotoxin levels and prevents systemic inflammation (Cani et al., Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability, Gut, 2009, 58:1091).
  • SCFAs promote gut barrier function by affecting mucin production and gastrointestinal peptide LL-37.
  • SCFAs modulate a number of human immunological factors.
  • SCFAs modulate inflammation by suppressing NF-kB and the production of inflammatory cytokines such as IL-6 and TNF- ⁇ (Kim C H et al. 2014.
  • treatment with a glycan therapeutic described herein modulates (e.g., increases) that SCFA propionate.
  • propionate increases expression of Foxp3, a T cell regulatory factor, and/or IL-10, an anti-inflammatory cytokine, in colonic regulatory T cells.
  • SCFAs promote the generation of (e.g., colonic) regulatory T (Treg) cells and/or CD4+ T cells thereby limiting inflammatory responses (Arpaia et al., Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation, Nature, 2013, 504:451; Smith P M et al. 2013. The microbial metabolites, short chain fatty acids, regulate colonic Treg cell homeostasis. Science; 341(6145)).
  • Treg colonic regulatory T
  • glycan therapeutics are administered to modulate short chain fatty acid (SCFA) production of commensal bacteria including members of the families Ruminocaccaceae and Lachnospiraceae (Vital M, Howe A C, Tiedje J M. 2014. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. mBio 5(2):e00889-14. doi:10.1128/mBio.00889-14).
  • SCFA short chain fatty acid
  • glycan therapeutics when administered in an effective amount modulate bacterial species that produce SCFAs, such as, e.g., those of the Ruminocacceae family and/or Lachnospiraceae family.
  • the glycan therapeutics modulate host immunity and inflammation.
  • glycan therapeutics are administered to induce systemic effects, e.g. of SCFAs and other microbially produced immunomodulatory molecules or metabolites to modulate the inflammatory state of distal sites.
  • the treatment with the glycan therapeutics described herein results in increased levels of Th17 or Th1 cells in the subject. In some embodiments, the treatment with the glycan therapeutics described herein results in increased levels of cytotoxic T-cells or natural killer cells in the subject. In some embodiments, the treatment with the glycan therapeutics described herein promote the growth of immune cells of the subject. In some embodiments, the treatment with the glycan therapeutics described herein promotes the differentiation of immune cells of the subject. In some embodiments, the treatment with the glycan therapeutics described herein results in increased tumor surveillance. In some embodiments, the treatment with the glycan therapeutics described herein results in increased anti-tumor activity of the host's immune system.
  • the glycan therapeutics promote the growth of beneficial taxa (e.g., Bacteroides and Bifidobacteria). In some embodiments, promoting growth of certain taxa modulates (e.g. upregulates) the immune response of the host.
  • beneficial taxa e.g., Bacteroides and Bifidobacteria
  • promoting growth of certain taxa modulates (e.g. upregulates) the immune response of the host.
  • the treatment with the glycan therapeutics described herein results an increase in tumor-infiltrating bacteria, e.g., in the GI tract that may infiltrate gastrointestinal tumors.
  • the treatment with the glycan therapeutics described herein results an increase of bacteria that produce toxins and/or small-molecules that decrease the growth of cancers or increase cell death of cancer cells, e.g., that of gastrointestinal cancers.
  • the treatment with the glycan therapeutics described herein results in the production of microbial metabolites that are toxic to the tumor or repress oncogene expression or oncogenic metabolism.
  • methods of selecting a subject for a treatment are provided.
  • the methods include: (a) identifying a subject who has a tumor or cancer (e.g., a tumor or cancer described herein), and (b) selecting the identified subject for treatment with a glycan therapeutic preparation described herein.
  • the subject is further selected for treatment with a second anti-cancer drug or therapy (e.g., a second anti-cancer drug or therapy described herein).
  • methods of selecting a subject for a treatment include selecting a subject that is treatment na ⁇ ve.
  • the subject is treatment na ⁇ ve with respect to an anti-cancer therapy, such as, e.g., chemotherapy, radiation therapy or surgical removal of the tumor.
  • the subject is treatment na ⁇ ve with respect to an immune suppressive therapy.
  • the subject is treatment na ⁇ ve with respect to an antimicrobial therapy.
  • methods of selecting a subject for a treatment include selecting the glycan therapeutic preparation on the basis that it will provide therapeutic benefit to the subject. In some embodiments, methods of selecting a subject for a treatment include selecting the subject on the basis that the subject will or is expected to benefit from administration of the glycan therapeutic preparation.
  • the selection methods include assessing the subject's gastrointestinal microbiota, e.g., before, during and/or after the treatment. In one embodiment, the subject's gastrointestinal microbiota is assessed before starting treatment. In some embodiments, the results of the assessment are used to select the subject for treatment. Alternatively or in addition, assessment is used to identify a dosage or dosage regimen for the treatment.
  • subjects are identified and selected that respond to a glycan therapeutic for initial and/or continued treatment.
  • Responders may be identified using one or more suitable parameter as determined by a physician or other healthcare provider.
  • the parameters include one or more of: a) a physiological treatment effect (e.g. reduction of a fever, increased well-being, increased energy, etc.), b) a desired change in a (host) biomarker (e.g. a cancer marker, an inflammatory marker, etc.), c) a microbial taxa shift (e.g., in relative abundance, change in diversity, etc.), d) a functional shift of the microbiota (e.g.
  • non-responders are identified and selected.
  • treatment methods include rendering the non-responder responsive to the treatment. In some embodiments, this may include administering to the non-responder one or more bacterial taxa (e.g. one or more commensals) that are responsive to glycan (and/or second agent) treatment.
  • methods of evaluating a subject e.g., to evaluate suitability for glycan treatment, responsiveness to glycan treatment, or glycan treatment progression, are provided.
  • the glycan treatment is in combination with another treatment or therapy (e.g., a drug treatment, such as an anti-cancer drug).
  • Changes in a variety of suitable biomarkers may be assessed.
  • changes in the microbiota are assessed or corresponding values are acquired.
  • changes in microbial metabolism e.g. metabolite input and/or output
  • changes in the microbiome e.g. changes on the genome or transcriptome level
  • are assessed or corresponding values are acquired.
  • changes in the microbial proteome are assessed or corresponding values are acquired.
  • changes in the host e.g., metabolic, inflammatory, cardio-vascular, etc.
  • changes in the host proteome e.g. protein synthesis
  • metabolome e.g. gene transcription/expression
  • cell signaling e.g., cell signaling, etc.
  • the methods include a) acquiring a value for a parameter related to the level of a biomarker modulated by a glycan therapeutic preparation (and/or the drug or therapy in a combination treatment); b) responsive to the value, classifying the subject, selecting a treatment for the subject, or administering the treatment to the subject, thereby evaluating a subject.
  • Treatment responsiveness and/or progression may be assessed or evaluated using one or more biomarker.
  • Suitable biomarkers may be determined by a physician and may include: i) changes in gastrointestinal microbiota and the overall metabolism of the gastric environment, such as the production of organic acids (e.g., SCFAs), ii) modulation of the immune system, assessing inflammatory and immune globulins iii) increase the absorption of minerals in the colon, such as calcium, zinc or magnesium iv) regulation of lipid metabolism, lowering cholesterol, v) induction of other important processes for host homeostasis (see, reviews by Pool-Zobel B L. Inulin-type fructans and reduction in colon cancer risk: review of experimental and human data. 2005.
  • the glycan therapeutic treatment may result in increases or decreases of one or more biomarkers that can be determined by methods known in the art.
  • An investigator can determine at which point or points during treatment the biomarker(s) should be measured, e.g. prior to treatment, at various intervals during treatment and/or after treatment.
  • Any suitable sample e.g. a gastrointestinal-specific sample such as, e.g. a tissue sample or biopsy, a swab, a gastrointestinal secretion (such as feces/a stool sample), etc. may be drawn from the subject and the sample may be analyzed by suitable methods known in the art.
  • a substantial increase or decrease in a biomarker may be detected to assess treatment progression.
  • treatment with the glycan therapeutic results in the release of short-chain fatty acids such as butyrate, acetate, and propionate and other metabolites (e.g. bile acids, and lactate) by the microbiota that may affect one or more biological pathways of the host subject (e.g. have an immunomodulatory effect on the host).
  • short-chain fatty acids such as butyrate, acetate, and propionate and other metabolites (e.g. bile acids, and lactate)
  • the microbiota may affect one or more biological pathways of the host subject (e.g. have an immunomodulatory effect on the host).
  • SCFA levels particularly acetate, propionate, and butyrate may be quantified.
  • SCFAs, creatines, and hydroxy-SCFAs can be quantified by alkalinizing stool samples, obtaining fingerprints of the metabolic composition of the sample using, e.g., 1D 1H NMR spectrometer, and analyzing with supervised multivariate statistical methods. Inulin may serve as a positive control.
  • microbial metabolite profiles of patient samples or microbes cultures from subject samples are used to identify risk factors for developing a disease, disorder or condition, such as, e.g., cancer.
  • exemplary metabolites for the purposes of diagnosis, prognostic risk assessment, or treatment assessment purposes include those listed in Table 2.
  • microbial metabolite profiles are taken at different time points during a subject's disease and treatment in order to evaluate the subject's disease state including recovery or relapse events, e.g., that of a tumor.
  • metabolite profiles are acquired to inform subsequent treatment.
  • the method includes administering to the human subject a first agent which is a pharmaceutical composition or medical food or dietary supplement comprising a glycan therapeutic preparation described herein in combination with a second agent.
  • a first agent which is a pharmaceutical composition or medical food or dietary supplement comprising a glycan therapeutic preparation described herein in combination with a second agent.
  • the glycan therapeutics described herein may be used in combination with other anti-proliferative, anti-neoplastic or anti-tumor drugs or treatments.
  • drugs or treatments include chemotherapeutic drugs, e.g., cytotoxic drugs (e.g., alkylating agents, antimetabolites, anti-tumor antibiotics, topoisomerase inhibitors, mitotic inhibitors, corticosteroids); cancer growth blockers such as tyrosine kinase inhibitors and proteasome inhibitors; other chemical drugs such as L-asparaginase and bortezomib (Velcade®).
  • Hormone therapies may be used, e.g., for hormone-sensitive cancers.
  • the glycan therapeutics described herein may be used in combination with other anti-proliferative, anti-neoplastic or anti-tumor drugs or treatments that include an anti-cancer drug, such as, e.g., checkpoint inhibitors (such as, e.g., anti-PD-1, anti-PD-L1, anti-CTLA4, anti-TIM-3, anti-LAG-3); vaccines (such as, e.g., autologous cancer vaccines, allogeneic cancer vaccines, neoantigen cancer vaccines, shared antigen cancer vaccines (e.g.
  • an anti-cancer drug such as, e.g., checkpoint inhibitors (such as, e.g., anti-PD-1, anti-PD-L1, anti-CTLA4, anti-TIM-3, anti-LAG-3); vaccines (such as, e.g., autologous cancer vaccines, allogeneic cancer vaccines, neoantigen cancer vaccines, shared antigen cancer vaccines (e.g.
  • targeted kinase inhibitors such as, e.g., Imatinib mesylate, Ibrutinib, Neratinib, Palpociclib, Erlotinib, Lapatinib
  • antibodies such as, e.g., Bevacizumab, Trastuzumab, Rituximab, Cetuximab
  • chemotherapeutics such as, e.g., irinotecan, 5-flurouracil, lenalidomide, capecitabine, docetaxel
  • antibody-drug conjugates e.g. ado-trastuzumab emtansine.
  • Immunotherapies are another class of anti-cancer agent that may be used in the combination with glycan therapeutics.
  • Immunotherapies include checkpoint inhibitors (see, e.g., PMID: 26598056, PMID: 26680224); T cell therapy (e.g., CAR-T cell therapy) (see, e.g., PMID: 26611350), Natural Killer (NK) cell immunomodulation (see, e.g., PMID: 26697006); and cancer vaccines (PMID: 26579225).
  • the glycan therapeutics described herein may be used in combination with non-drug therapies for cancer such as surgery, radiotherapy, or cryotherapy. Treatment methods may include glycan therapeutics described herein in combination with 2 or more other therapies or drugs.
  • breast cancer may be treated with a combination of glycan therapeutics described herein and surgery or radiotherapy and a chemotherapeutic cocktail or biologic (e.g., an anti-HER2 antibody).
  • the glycan therapeutics described herein may be used in combination with one or more of: a pain-management drug an antidepressant, an antiepileptic, a steroid, a drug for managing a GI tract motility disorder, an anti-inflammatory agent, and an antimicrobial agent, described elsewhere herein.
  • the second agent is a therapeutic agent which is an immune checkpoint modulator.
  • the checkpoint modulator may be an inhibitory or agonist form of the following: antibody (e.g., a monospecific antibody such as a monoclonal antibody (mAb), e.g., a humanized or fully human mAb); a fusion protein, e.g., an Fc-receptor fusion protein; or a small molecule.
  • the check point modulator may modulate a checkpoint protein or a ligand of a checkpoint protein.
  • the checkpoint modulator is an inhibitor (e.g., an inhibitory antibody or small molecule inhibitor) of CTLA-4 (e.g., an anti-CTLA4 antibody such as ipilimumab/Yervoy or tremelimumab).
  • CTLA-4 e.g., an anti-CTLA4 antibody such as ipilimumab/Yervoy or tremelimumab
  • the checkpoint modulator is an inhibitor (e.g., an inhibitory antibody or small molecule inhibitor) of PD-1 (e.g., nivolumab/Opdivo®; pembrolizumab/Keytruda®; pidilizumab/CT-011).
  • the checkpoint modulator is an inhibitor (e.g., an inhibitory antibody or small molecule inhibitor) of PDL1 (e.g., MPDL3280A/RG7446; MEDI4736; MSB0010718C; BMS 936559).
  • the checkpoint modulator is an inhibitor (e.g., an inhibitory antibody or Fc fusion or small molecule inhibitor) of PDL2 (e.g., a PDL2/Ig fusion protein such as AMP 224).
  • the checkpoint modulator modulates (e.g., an antibody modulator or small molecule modulator) B7-H3 (e.g., MGA271), B7-H4, BTLA, HVEM, TIM3, GALS, LAG3, VISTA, KIR, 2B4, CD160, CGEN-15049, CHK 1, CHK2, A2aR, B-7 family ligands, or a combination thereof.
  • B7-H3 e.g., MGA271
  • B7-H4 e.g., MGA271
  • HVEM HVEM
  • TIM3 e.g., GALS
  • LAG3, VISTA KIR
  • KIR KIR
  • CD160 CD160
  • CGEN-15049 CHK 1, CHK2, A2aR, B-7 family ligands, or a combination thereof.
  • the second agent is a therapeutic agent which is an adoptive T cell (CAR-T cell) or NK cell for anti-cancer therapy.
  • the adoptive T cell therapy comprises administering to a subject autologous and/or allogeneic T-cells.
  • the autologous and/or allogeneic T-cells are targeted against tumor antigens (e.g., CD19, CD20, CD22, AFP, CEA, CA-125, MUC-1, ETA, MAGE, CA15-3, CA27-29, CA19-9, CD34, CD117, PSA, MART-1 etc.).
  • the adoptive NK cell therapy comprises administering to a subject autologous and/or allogeneic NK cells.
  • the second agent is a therapeutic agent which is a cancer vaccine (e.g., a tumor cell vaccine, an antigen vaccine, a dendritic cell vaccine, a DNA vaccine, or vector based vaccine).
  • the therapeutic cancer vaccine may be a dendritic cell vaccine, e.g., a dendritic cell vaccine composed of autologous dendritic cells and/or allogeneic dendritic cells.
  • the autologous or allogeneic dendritic cells are loaded with cancer antigens prior to administration to the subject.
  • the autologous or allogeneic dendritic cells are loaded with cancer antigens through direct administration to the tumor.
  • the therapeutic cancer vaccine may be a peptide vaccine, e.g.
  • the peptides encode tumor antigens.
  • the tumor antigens encoded by the peptides are neoantigens.
  • the second agent is a therapeutic agent which is a chemotherapeutic agent (e.g., a cytotoxic agent or other chemical compound useful in the treatment of cancer).
  • chemotherapeutic agent e.g., a cytotoxic agent or other chemical compound useful in the treatment of cancer.
  • alkylating agents include alkylating agents, antimetabolites, folic acid analogs, pyrimidine analogs, purine analogs and related inhibitors, vinca alkaloids, epipodopyyllotoxins, antibiotics, L-asparaginase, topoisomerase inhibitors, interferons, platinum coordination complexes, anthracenedione substituted urea, methyl hydrazine derivatives, adrenocortical suppressant, adrenocorticosteroides, progestins, estrogens, antiestrogen, androgens, antiandrogen, and gonadotropin-releasing hormone analog.
  • chemotherapeutic agent e.g.,
  • 5-fluorouracil 5-FU
  • leucovorin LV
  • irenotecan oxaliplatin
  • capecitabine paclitaxel
  • doxetaxel chemotherapeutic agents
  • alkylating agents such as thiotepa and cyclosphosphamide
  • alkyl sulfonates such as busulfan, improsulfan and piposulfan
  • aziridines such as benzodopa, carboquone, meturedopa, and uredopa
  • ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine
  • acetogenins especially bullatacin and bullatacinone
  • a camptothecin including the synthetic analogue topotecan
  • bryostatin callystatin
  • CC-1065 including its
  • dynemicin including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, ADRIAMYCIN® doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin
  • Cremophor-free, albumin-engineered nanoparticle formulation of paclitaxel American Pharmaceutical Partners, Schaumberg, Ill.), and TAXOTERE® doxetaxel (Rhone-Poulenc Rorer, Antony, France); chloranbucil; GEMZAR® gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum coordination complexes such as cisplatin, oxaliplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; NAVELBINE® vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11); topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO);
  • Two or more (e.g., three, four, five, etc.) chemotherapeutic agents can be used in a cocktail to be administered in combination with the first therapeutic agent described herein.
  • Suitable dosing regimens of combination chemotherapies are known in the art and described in, for example, Saltz et al. (1999) Proc ASCO 18:233a and Douillard et al. (2000) Lancet 355:1041-7.
  • the second agent is a therapeutic agent which is a biologic such as a cytokine (e.g., interferon or an interleukin (e.g., IL-2)).
  • a biologic such as a cytokine (e.g., interferon or an interleukin (e.g., IL-2)).
  • the biologic is an immunoglobulin-based biologic, e.g., a monoclonal antibody (e.g., a humanized antibody, a fully human antibody, an Fc fusion protein or a functional fragment thereof) that agonizes a target to stimulate an anti-cancer response, or antagonizes an antigen promoting cancer growth or maintenance.
  • Such agents include Rituxan (Rituximab); Zenapax (Daclizumab); Simulect (Basiliximab); Synagis (Palivizumab); Remicade (Infliximab); Herceptin (Trastuzumab); Mylotarg (Gemtuzumab ozogamicin); Campath (Alemtuzumab); Zevalin (Ibritumomab tiuxetan); Humira (Adalimumab); Xolair (Omalizumab); Bexxar (Tositumomab-I-131); Raptiva (Efalizumab); Erbitux (Cetuximab); Avastin (Bevacizumab); Tysabri (Natalizumab); Actemra (Tocilizumab); Vectibix (Panitumumab); Lucentis (Ranibizumab); Soliris (Eculizumab
  • the second agent is an immunomodulatory drug, e.g., ABREVA (docosanol), Acyclovir, Agenerase (amprenavir), Albenza (albendazole), Aldara (imiquimod), Alinia (nitazoxanide), Allegra-D, Altabax (rumblemulin), Amevive (alefacept), Aphthasol, Aptivus (tipranavir), Aptivus (tipranavir), Arcapta (indacaterol maleate inhalation powder), Astepro (azelastine hydrochloride nasal spray), Avelox I.V.
  • ABREVA docosanol
  • Acyclovir Agenerase (amprenavir), Albenza (albendazole), Aldara (imiquimod), Alinia (nitazoxanide), Allegra-D, Altabax (rumblemulin), Amevive (alefacept), Aphthasol, Aptivus (tipranavir),
  • the second agent is metabolism-modulating or cachexia-modulating drug, e.g. Accretropin (somatropin rDNA Original), ACTOplus met (pioglitazone hydrochloride and metformin hydrochloride), ACTOS, Afrezza (insulin human) Inhalation Powder, Amaryl (Glimepiride), Avandamet (rosiglitazone maleate and metformin HCl), Avandia (rosiglitazone maleate), Belviq (lorcaserin hydrochloride), Bydureon (exenatide extended-release for injectable suspension), Byetta (exenatide), Cernevit, Cycloset, bromocriptine mesylate, Desmopressin Acetate (DDAVP), Farxiga (dapagliflozin) Genotropin (somatropin) injection, Genotropin (somatropin) lyophilized powder, Geref (sermorelin acetate for injection), Glipizide Tablets
  • the second agent is a therapeutic agent which is a non-drug treatment.
  • the second therapeutic agent is radiation therapy, cryotherapy, hyperthermia and/or surgical excision of tumor tissue.
  • the subject is treated with a glycan therapeutic described herein in combination with two or more other pharmaceutical agents, e.g., two or more (e.g., 3 or more, 4 or more) chemotherapeutic agents, or a combination of different classes of therapeutic agents described herein.
  • a cancer subject may be treated with a glycan therapeutic described herein in combination with radiation therapy, a chemotherapeutic cocktail of 2, 3, 4 or more drugs, and optionally also in combination with a checkpoint inhibitor or a cell therapy (e.g., T cell therapy).
  • the pharmaceutical glycan therapeutic compositions described herein can be administered in combination with various other standard of care therapies.
  • the combination of administration of the glycan therapeutic and the standard-of-care therapy agent e.g., an anti-cancer drug
  • the pharmaceutical glycan therapeutic compositions may be administered prior to, concurrent with, or post treatment with standard of care therapies.
  • the therapies e.g., treatment with cytotoxic or anti-microbial drugs disrupt the composition or health of the GI tract's host cells and microbiota or that of non-GI sites.
  • the disruption by the drugs leads to the undesirable proliferation of harmful bacteria or pathogens.
  • the disruption of the host cells and/or microbiota by the drugs causes one or more of the symptoms described herein.
  • administration of the pharmaceutical glycan therapeutic compositions described herein is useful for alleviating those symptoms.
  • administration of the pharmaceutical glycan therapeutic composition improves the composition of the gastrointestinal or non-gut microbial community and host cells (e.g., modulates shifts in the composition or function of the microbiota that decrease the intensity or duration of the symptoms).
  • a method of treating an immune imbalance in a human subject comprising: administering to the subject a pharmaceutical composition, a medical food or a dietary supplement comprising a glycan therapeutic preparation, in an effective amount to treat the subject.
  • a second agent may be administered.
  • the methods also include methods for reducing an infection and/or an inflammation in a subject having an immune imbalance.
  • methods of modulating the composition and/or metabolic activity of the intestinal bacterial community of a subject having an immune imbalance and methods of modulating one or more functional pathways in a subject having an immune imbalance.
  • methods of treating a dysbiosis in a subject having an immune imbalance are provided.
  • the immune imbalance results in or is associated with a cancer.
  • immune suppression and/or insufficient immune inflammatory activation is characterized by the overgrowth of pathogenic cells.
  • pathogenic cells include intracellular pathogens, extracellular pathogens, viruses, and cancerous cells.
  • Immune suppression and/or insufficient immune inflammatory activation in some embodiments, is associated with tolerance, e.g., resulting from an imbalance in the ratio of tolerogenic cell subsets (e.g. regulatory T cells) or activities (e.g. tolerogenic cytokine secretion such IL-10, TGF-beta) to inflammatory cell subsets (e.g. Th1 cells) or activities (e.g.
  • Immune suppression and/or insufficient immune inflammatory activation is associated with the immune system not recognizing the pathogenic cell as a pathogen, which frequently occurs in the case of cancerous cells.
  • Non-pathogenic cells are any cells or cell-structures (including tissues and organs) that are not-targeted by the immune system for attack in a healthy individual.
  • non-pathogenic cells are any cells or cell-structures (including tissues and organs) that are not-targeted by the immune system for attack in a healthy individual.
  • the epithelium of the gastrointestinal tract is not substantially damaged by the immune system in healthy individuals but is damaged by the immune system in individuals with inflammatory diseases such as, e.g., inflammatory bowel disease.
  • the pancreas is not substantially targeted by the inflammatory arm of the immune system in patients who do not have autoimmune diabetes, but is targeted in patients with type-1 diabetes.
  • Aberrant immune inflammatory activation is associated with an imbalance in the ratio of tolerogenic cell subsets (e.g. regulatory T cells) or activities (e.g. tolerogenic cytokine secretion such IL-10, TGF-beta) to inflammatory cell subsets (e.g. Th1 cells) or activities (e.g. inflammatory cytokine secretion such as TNF-alpha, IL-17), with the inflammatory functions displaying higher activity than the tolerogenic functions.
  • tolerogenic cell subsets e.g. regulatory T cells
  • activities e.g. tolerogenic cytokine secretion such IL-10, TGF-beta
  • inflammatory cell subsets e.g. Th1 cells
  • activities e.g. inflammatory cytokine secretion such as TNF-alpha, IL-17
  • immune imbalances include: Clostridium difficile infection (CDI); Vancomycin-resistant enterococci (VRE) infection, infectious colitis, and C. difficile colitis; mycoses, such as, e.g., Candida albicans infection, Campylobacter jejuni infection, Helicobacter pylori infection; diarrhea, such as, e.g., Clostridium difficile associated diarrhea (CDAD), antibiotic-associated diarrhea (AAD), antibiotic-induced diarrhea, travellers' diarrhea (TD), pediatric diarrhea, (acute) infectious diarrhea, colon and liver cancers, ameboma; necrotizing enterocolitis (NEC), and small intestine bacterial overgrowth (SIBO); indigestion or non-ulcer dyspepsia; anal fissures, perianal abscess and anal fistula; diverticulosis or diverticulitis; peptic ulcers; and gastroenteritis.
  • CDAD Clostridium difficile associated diarrhea
  • AAD antibiotic-associated diarrhea
  • TD
  • gastrointestinal cancer such as non-metastatic or metastatic colorectal cancer, pancreatic cancer, gastric cancer, oesophageal cancer, hepatocellular cancer, cholangiocellular cancer, oral cancer, lip cancer
  • urogenital cancer such as hormone sensitive or hormone refractory prostate cancer, renal cell cancer, bladder cancer, penile cancer
  • CNS cancer including malignant glioma, astrocytomas, retinoblastomas and brain metastases; malignant mesothelioma; non-metastatic or metastatic breast cancer (e.g.
  • skin cancer such as malignant melanoma, basal and squamous cell skin cancers, Merkel Cell Carcinoma, lymphoma of the skin, Kaposi Sarcoma); thyroid cancer; bone and soft tissue sarcoma; and haematologic neoplasias (such as multiple myeloma, acute myelogenous leukemia, chronic myelogenous leukemia, myelodysplastic syndrome, acute lymphoblastic leukemia, Hodgkin's lymphoma).
  • skin cancer such as malignant melanoma, basal and squamous cell skin cancers, Merkel Cell Carcinoma, lymphoma of the skin, Kaposi Sarcoma
  • thyroid cancer bone and soft tissue sarcoma
  • haematologic neoplasias such as multiple myeloma, acute myelogenous leukemia, chronic myelogenous leukemia, myelodysplastic syndrome, acute lymphoblastic leukemia, Hod
  • immune imbalances include: Gastrointestinal inflammatory diseases including inflammatory bowel disease (IBD), ulcerative colitis (UC), Crohn's disease (CD), idiopathic inflammation of the small bowel, indeterminatal colitis, pouchitis; irritable bowel syndrome (IBS), colon and liver cancers, necrotizing enterocolitis (NEC), intestinal inflammation, constipation, microscopic colitis, diarrhea; graft versus host disease (GVHD); (food) allergies; pseudomembranous colitis; indigestion or non-ulcer dyspepsia; diverticulosis or diverticulitis, ischemic colitis; radiation colitis or enteritis; collagenous colitis; gastroenteritis; and polyps.atopic dermatitis, asthma, multiple sclerosis, immune-mediated or Type I diabetes mellitus, systemic lupus erythematosus, psoriasis, scleroderma, autoimmune thyroid disease, alopecia greata, Grave'
  • kits for treating a nutritional imbalance in a subject comprising: administering to the subject a pharmaceutical composition, a medical food or a dietary supplement comprising a glycan therapeutic preparation, in an effective amount to treat the subject.
  • a second agent may be administered.
  • the methods also include methods for reducing an infection and/or an inflammation in a subject having a nutritional imbalance.
  • methods of modulating the composition and/or metabolic activity of the intestinal bacterial community of a subject having a nutritional imbalance and methods of modulating one or more functional pathways in a subject having a nutritional imbalance.
  • methods of treating a dysbiosis in a subject having a nutritional imbalance are provided.
  • the nutritional imbalance results in or is associated with a cancer.
  • the nutritional imbalances is associated with an aberrant inflammatory immune activation that alters metabolic homeostasis.
  • the nutritional imbalance is associated with an imbalance in the ratio of tolerogenic cell subsets (e.g. regulatory t cells) or activities (e.g. tolerogenic cytokine secretion such IL-10, TGF-beta) to inflammatory cell subsets (e.g. Th1 cells) or activities (e.g. inflammatory cytokine secretion such as TNF-alpha, IL-17), with the inflammatory functions displaying higher activity than the tolerogenic functions.
  • an increased immune in inflammatory activity affects the mechanisms that metabolic organs and systems utilize for communication.
  • cancer patients who have malnutrition often exhibit a high level of leptin, which is a hormone that induces satiety and thus decreases the patient's hunger.
  • Other diseases that lead to cachexia include, e.g. chronic obstructive pulmonary disease (COPD), rheumatoid arthritis, chronic infection or sepsis, renal failure, heart failure and cancer.
  • COPD chronic obstructive pulmonary disease
  • the condition is characterized by inflammation, anorexia, insulin resistance and increased muscle protein breakdown with or without a loss of fat mass.
  • Examples of nutritional imbalance include: Cachexia, anorexia nervosa, kwashiorkor and marasmus.
  • Diseases that lead to cachexia include, e.g. chronic obstructive pulmonary disease (COPD), rheumatoid arthritis, chronic infection or sepsis, renal failure, heart failure and cancer.
  • COPD chronic obstructive pulmonary disease
  • the condition is characterized by inflammation, anorexia, insulin resistance and increased muscle protein breakdown with or without a loss of fat mass.
  • a human subject e.g. a subject undergoing anti-cancer treatment (being treated with an anti-cancer agent), and subjects in treatment for or having an immune imbalance or a nutritional imbalance.
  • drug- or treatment-induced symptoms include any toxicity, digestive abnormalities or gastrointestinal distress.
  • methods for preventing, treating or alleviating the symptoms of various gastrointestinal ailments by administering the glycan therapeutic compositions described herein.
  • the method include administering to the human subject a pharmaceutical composition comprising a glycan therapeutic preparation in an amount effective to reduce one or more symptoms induced by a drug or treatment.
  • the treatment is radiation treatment, cryotherapy, hyperthermia or surgical excision of tumor tissue.
  • Exemplary toxicities or digestive abnormalies include weight-gain, constipation, heartburn, upset stomach, gas, bloating, flatulence, diarrhea, abdominal pain, cramping, nausea, and vomiting.
  • the digestive abnormality is diarrhea.
  • the digestive abnormality is constipation.
  • Treatment (or toxicity) associated symptoms such as gas, heartburn, stomach upset, bloating, flatulence, diarrhea, abdominal pain, cramping, nausea, or vomiting.
  • Minor digestive problems related to the GI also include occasional bloating, diarrhea, constipation, gas, or stomach upset.
  • the glycan therapeutic compositions described herein can be administered in combination with various therapies that are associated with gastrointestinal distress.
  • Such therapies include, without limitation, radiation and chemotherapy for cancers, and antibiotic therapy for various microbial maladies.
  • the therapies disrupt the composition and health of the intestine's normal microbiota. In some instances, the disruption leads to the undesirable proliferation of harmful bacteria and accompanying symptoms described herein. Administration of the glycan therapeutic compositions described herein is useful for treating those symptoms.
  • the glycan therapeutic compositions described herein are suitable for administration to humans in need thereof.
  • the subject is a human who has one or more symptoms of a disturbed gut microbiota.
  • the disturbance can be rectified by the use of the glycan therapeutics described herein so that normal physiological growth and function of both the commensal microbiota and the host can be achieved.
  • the glycan therapeutics described herein may be used in combination with one or more of: a pain-management drug (e.g., opioids) an antidepressant, an antiepileptic, a steroid, a drug for managing a GI tract motility disorder, an anti-inflammatory agent (e.g., NSAID), and an antimicrobial agent (e.g., antibiotic), described elsewhere herein, to treat any toxicity, digestive abnormalies and other gastrointestinal distress associated with administration of the drugs to a subject.
  • a pain-management drug e.g., opioids
  • an antidepressant e.g., an antidepressant
  • an antiepileptic e.g., an antiepileptic
  • a steroid e.g., a drug for managing a GI tract motility disorder
  • an anti-inflammatory agent e.g., NSAID
  • an antimicrobial agent e.g., antibiotic
  • drugs which often are associated with drug- or treatment-induced (toxicity) symptoms include, a cancer drug, an anti-diabetic, an immune-suppressive drug, an antimicrobial drug, a chemotherapeutic, an anti-psychotic, a proton pump inhibitor, and a non-steroid anti-inflammatory drug (NSAID).
  • NSAID non-steroid anti-inflammatory drug
  • the glycan therapeutics described herein may be used in combination with one or more anti-cancer agents, including, checkpoint modulators, cell therapies, cancer vaccines, chemotherapeutic agents, and biologics, described elsewhere herein, to treat toxicities, digestive abnormalies and other gastrointestinal distress associated with administration of the drugs to a subject.
  • anti-cancer agents including, checkpoint modulators, cell therapies, cancer vaccines, chemotherapeutic agents, and biologics, described elsewhere herein, to treat toxicities, digestive abnormalies and other gastrointestinal distress associated with administration of the drugs to a subject.
  • a treatment or therapy such as, e.g., an anti-cancer treatment or therapy (and treatments or therapies relating to immune imbalances or nutritional imbalances), in a subject, comprising a) administering a pharmaceutical composition comprising a glycan therapeutic preparation described herein to a subject who has received the treatment or therapy; b) administering the treatment or therapy to a subject who has been treated with a pharmaceutical composition comprising a glycan therapeutic preparation; or c) administering a pharmaceutical composition comprising a glycan therapeutic preparation and administering the treatment or therapy, to a subject, thereby decreasing the side effect effect of the treatment or therapy in the subject.
  • the onset of the side effect is prior to administration of the glycan therapeutic preparation. In some embodiments, the glycan therapeutic preparation is administered after onset of the side effect. In some embodiments, the side effect of the treatment or therapy results in an unwanted symptom. In some embodiments, the unwanted side effect is a gastrointestinal side effect, such as a digestive abnormality. In some embodiments, the unwanted side effect is a non-gastrointestinal side effect, such as, e.g., anxiety, fear, depression, mental fog, dermatitis, chest pain, shortness of breath, weight gain, weight loss, etc.
  • the unwanted side effect is one or more of: abdominal pain, cramping, nausea, or vomiting, upset stomach, gas, bloating, flatulence, diarrhea, constipation, heartburn, mucositis, weight loss, and weight-gain.
  • the unwanted side effect is associated with anti-cancer treatment (or treatments for an immune imbalance or a nutritional imbalance).
  • the unwanted side effects related to anti-cancer treatment include one or more of: radiation injury pain, surgical pain, phantom pain, acute pain, chronic or persistent pain, breakthrough pain, peripheral neuropathy, stomatitis, mucositis, nausea, vomiting, diarrhea (acute, chronic), constipation (acute, chronic), urinary incontinence, fatigue (acute or chronic), anemia, lymphedema, infections, anxiety, fear, depression, fertility defects, and risk of developing a second cancer.
  • the unwanted side effects related to anti-cancer treatment include infections, such as bacterial infections, including: Pseudomonas aeruginosa, Klebsiella pneumonia, Escherichia coli, Salmonella, Clostridium difficile, Staphylococcus aureus, Staphylococcus epidemidis, Streptococcus viridians, Pneumococcus, Enterococcus ; viral infections, including: Varicella zoster virus (VZV), Herpes simplex virus (HSV), Cytomegalovirus (CMV), hepatitis viruses, respiratory viruses (e.g., influenza, respiratory syncytial virus (RSV)); protozoal infections, including: Toxoplasma gondii , and Cryptosporidium ; and fungal infections, including: Pneumocystis jirovecii, Candida, Aspergillus, Cryptococcus, Histoplasma, Coccidioides.
  • bacterial infections including: P
  • the unwanted side effects related to anti-cancer treatment include malnutrition and cachexia (wasting syndrome).
  • the unwanted side effect related to anti-cancer treatment is mucositis, including mucosal tissue ulceration and infection.
  • the unwanted side effect related to anti-cancer treatment (such as, e.g., chemotherapy and radiation) is oral mucositis.
  • the one or more unwanted side effects are dose-limiting, e.g., they require a reduction in subsequent therapeutic doses (e.g. for chemotherapy). Dose limiting toxicity prevents subjects from being treated with the maximal efficacious dose of a drug.
  • the methods further comprise administering a pharmaceutical composition comprising a glycan therapeutic preparation to a subject who has received a first treatment (e.g. an anti-cancer drug treatment or anti-cancer therapy), and optionally, providing a second treatment, e.g., wherein the second treatment comprises administration of the drug or therapy at a higher dosage, at more frequent intervals, at a higher total of individual administrations, providing a higher Cmax, providing a higher trough level, etc., than the prior treatment.
  • a first treatment e.g. an anti-cancer drug treatment or anti-cancer therapy
  • a second treatment e.g., wherein the second treatment comprises administration of the drug or therapy at a higher dosage, at more frequent intervals, at a higher total of individual administrations, providing a higher Cmax, providing a higher trough level, etc., than the prior treatment.
  • the methods further comprise providing a subsequent treatment (e.g. an anti-cancer drug treatment or anti-cancer therapy) to a subject who has received a pharmaceutical composition comprising a glycan therapeutic preparation and received the first treatment, wherein the second treatment comprises administration of the drug or therapy at a higher dosage, at more frequent intervals, at a higher total of individual administrations, providing a higher Cmax, providing a higher trough level, etc., than the prior treatment.
  • a subsequent treatment e.g. an anti-cancer drug treatment or anti-cancer therapy
  • the subject being identified to be suitable for treatment with a glycan therapeutic has, is suspected of having or is suspected of developing drug-induced diarrhea (such as, e.g., 5-fluorouracil (5-FU), methotrexate, irinotecan, taxanes, monoclonal antibodies and hormonal agents).
  • drug-induced diarrhea such as, e.g., 5-fluorouracil (5-FU), methotrexate, irinotecan, taxanes, monoclonal antibodies and hormonal agents.
  • the subject being identified to be suitable for treatment with a glycan therapeutic has, is suspected of having or is suspected of developing drug-induced constipation (such as, e.g., vinca alkaloids, platinums (e.g., cisplatin), thalidomide and hormonal agents).
  • the subject being identified to be suitable for treatment with a glycan therapeutic has, is suspected of having or is suspected of developing a drug-induced toxicity. In one embodiment, the subject being identified to be suitable for treatment with a glycan therapeutic has, is suspected of having or is suspected of developing chemotherapy-induced mucositis. In one embodiment, the subject being identified to be suitable for treatment with a glycan therapeutic has, is suspected of having or is suspected of developing a drug-induced intolerance (e.g. to chemotherapies). In one embodiment, the subject being identified to be suitable for treatment with a glycan therapeutic has, is suspected of having or is suspected of developing cachexia (wasting syndrome).
  • wasting syndrome wasting syndrome
  • the subject being identified to be suitable for treatment with a glycan therapeutic has, is suspected of having or is suspected of developing drug-induced microbiome damage, drug-induced microbiome disease, drug-induced gastrointestinal disease, drug-induced enteritis or colitis or similar drug-induced disorder or condition.
  • the pharmaceutical composition comprising a glycan therapeutic preparation is administered prior to, concomitant with or after administration of the (e.g. anti-cancer) drug or non-drug (e.g., anti-cancer) treatment, administration of which induces the symptoms.
  • the (e.g. anti-cancer) drug or non-drug (e.g., anti-cancer) treatment administration of which induces the symptoms.
  • administration of a drug is associated with dysbioses that can, e.g., occur during the treatment regimen.
  • the dysbiosis causes or amplifies the drug- or treatment-induced symptoms, such as toxicities, including digestive abnormalities.
  • administration of the glycan therapeutic modulates the microbiome such that the drug- or treatment-induced symptoms are reduced.
  • the glycan therapeutic promotes the growth of commensal bacteria and/or supports the growth of beneficial microbial communities which would negatively be affected or lost in response to the drug treatment or which can complement commensal bacteria that have been negatively affected or lost in response to the drug treatment.
  • a dysbiosis in a subject comprising administering to the subject a pharmaceutical composition comprising a glycan therapeutic preparation thereby treating the dysbiosis.
  • the dysbiosis in some embodiments, is concurrent with (or the result of) a disease, disorder or condition, such as, e.g., an immune imbalance, a nutritional imbalance and/or cancer.
  • the dysbiosis is concurrent with (or the result of) a treatment or therapy, e.g., anti-cancer therapy, pain management, etc.
  • the unwanted side effects are associated with treatment of the subject with a chemotherapeutic agent.
  • the digestive abnormality is diarrhea.
  • the chemotherapeutic agent is Irinotecan, 5-fluorouracil, leucovorin, or combinations thereof.
  • the chemotherapeutic agent is oxaliplatin, leucovorin, 5-fluorouracil, or combinations thereof.
  • the chemotherapeutic agent is bortezomib, imatinib, lenalidomide, imbruvica, ipilimumab, pertuzumab, capecitabine, docetaxel, lapatinib, erlotinib, or combinations thereof.
  • the chemotherapeutic agent is Carmustine, Etoposide, Aracytine, Melphalan, or combinations thereof.
  • the chemotherapeutic agent is cytarabine, daunorubicine, etoposide, or combinations thereof.
  • the chemotherapeutic agent is amsacrine, cytarabine, etoposide, or combinations thereof.
  • the chemotherapeutic agent is mitoxantrone, cytarabine, or combinations thereof.
  • the unwanted side effects are associated with treatment of the subject with an antibiotic.
  • the digestive abnormality is diarrhea.
  • the antibiotic is ciprofloxacin, clindamycin, amoxicillin-clavulanate, cefixime, ephalosporins, fluoroquinolones, azithromycin, clarithromycin, erythromycin, tetracycline, or azithromycin.
  • the unwanted side effects including toxicities such as digestive abnormalities, are associated with treatment of the subject with an anti-psychotic drug.
  • the digestive abnormality is weight gain.
  • the drug is olanzapine.
  • the unwanted side effects are associated with treatment of the subject with a proton-pump inhibitor drug.
  • the digestive abnormality is diarrhea.
  • the drug is ranitidine, famotidine, cimetidine, omeprazole, sucralfate, or esomeprazole.
  • the unwanted side effects are associated with treatment of the subject with a non-steroidal anti-inflammatory drug (NSAID).
  • NSAID non-steroidal anti-inflammatory drug
  • the digestive abnormality is diarrhea.
  • the drug is naproxen, diclofenac, indomethacin, ibuprofen, ketoprofen, piroxicam, celecoxib, nimesulid, or aspirin.
  • the unwanted side effects are associated with treatment of the subject with metformin, paroxetine, valproic acid, or clozapine.
  • reducing the one or more symptoms increases compliance by the subject to the treatment regimen.
  • reducing one or more symptom enables the physician to prescribe a higher-dose of the drug to be administered.
  • treatment of the underlying disease is more effective (e.g. increased reduction of disease symptoms, shorter period to achieve a disease or symptom-free state, or longer maintenance of a disease or symptom-free state, etc.).
  • a method of lowering toxicity of a drug treatment in a subject.
  • the method includes: a) administering a pharmaceutical composition comprising a glycan therapeutic preparation to a subject who has received the drug treatment; b) administering the drug treatment to a subject who has been treated with a pharmaceutical composition comprising a glycan therapeutic preparation; or c) administering a pharmaceutical composition comprising a glycan therapeutic preparation and administering the drug treatment, to a subject, thereby treating the subject.
  • the toxicity is dose-limiting toxicity.
  • the method increases the tolerance of the subject to drug treatment, e.g. an anti-cancer drug treatment.
  • dose limiting toxicity prevents subjects from being treated with the maximal efficacious dose of a drug.
  • diarrhea can be caused by the chemotherapy drugs irinotecan and 5-fluoruracil.
  • Irinotecan and 5-fluorouracil may damage the intestinal epithelium of subjects.
  • nutrient and fluid absorption and secretion is modulated.
  • the digestive abnormality forces a clinician to reduce the dose of the drug to adjust it to the subject's tolerance level.
  • the lowering may lead to a treatment regimen with a less efficacious dose thereby limiting the treatment effect (or prolonging the treatment interval.
  • glycan therapeutic preparations are administered to treat dose limiting toxicity, e.g., to increase the dose that is tolerated by the subject.
  • tolerability is increased by limiting one or more digestive abnormalities associated with the respective efficacious drug dose.
  • the subject experiences a reduction in at least one symptom of the gastrointestinal disease, disorder or condition following treatment.
  • a reduction in the severity of a symptom following treatment can be determined (e.g. by measuring a known biomarker) and is in the order of about 3%, 5%, 7%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or about 100%.
  • the symptoms, measured as described herein are decreased by an average of about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or about 100% when compared to symptoms prior to the administration of a pharmaceutical glycan therapeutic composition.
  • the reduction in the severity of the symptom persists for at least about a day, two days, three days, four days, five days, a week, two weeks, three weeks, a month, 3 months, 6 months, 9 months, a year, two years, five years, ten years after treatment or the reduction is permanent.
  • a symptom of a gastrointestinal disease, disorder or condition remains partially, substantially, or completely eliminated or decreased in severity in a subject for at least about 1 day, 1 week, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 9 months, one year, 18 months, two years, three years, four years, five years, ten years, or more than ten years after the termination of treatment.
  • a symptom of a gastrointestinal disease, disorder or condition is permanently eliminated or decreased in severity in a subject after the termination of treatment.
  • Preparations of glycan therapeutics may be selected based on their ability to increase the expression of microbial proteins associated with healthy states or to decrease the expression of microbial proteins associated with diseased states.
  • Proteomic analysis of microbial populations can be performed following protocols known to one skilled in the art (e.g., Cordwell, Exploring and exploiting bacterial proteomes, Methods in Molecular Biology, 2004, 266:115).
  • proteomic analysis can be performed as described, e.g., in Juste et al. (Bacterial protein signals are associated with Crohn's disease, Gut, 2014, 63:1566).
  • the protein is isolated from the microbial lysates of two samples (for example, an untreated microbial population and a population that has been treated with glycan therapeutics).
  • Each protein sample is labeled (e.g., with a fluorescent dye, e.g., Cy3 or Cy5 CyDye DIGE Fluor minimal dye, GE Healthcare) and analyzed by two-dimensional differential gel electrophoresis (2D-DIGE). Gels are stained and protein spots identified as being significantly different between the two samples are excised, digested, and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS).
  • X!TandemPipeline http://pappso.inra.fr/bioinfo/xtandempipeline/) can be used to identify differentially expressed proteins.
  • Preparations of glycan therapeutics may also be selected for administration to a human subject based on their effect on the presence of microbial fermentation products.
  • preparations of glycan therapeutics can be selected for their ability to induce or promote growth of bacteria that produce short chain fatty acids such as propionate (propionic acid), acetate, and/or butyrate (butyric acid).
  • preparations of glycan therapeutics can be selected for their ability to induce or promote growth of bacteria that produce lactic acid, which can modulate the growth of other bacteria by producing an acidic environment.
  • Such analysis may also be used to pair probiotic bacteria with glycan therapeutics such that the glycan therapeutic is a substrate for the production of the desired fermentation products.
  • metabolites that are present in fresh or spent culture media or in biological samples collected from human subjects may be determined using methods known in the art and described herein. Unbiased methods that may be used to determine the relative concentration of metabolites in a sample and are known to one skilled in the art, such as gas or liquid chromatography combined with mass spectrometry or 1 H-NMR. These measurements may be validated by running metabolite standards through the same analytical systems.
  • polar metabolites and fatty acids can be extracted using monophasic or biphasic systems of organic solvents and an aqueous sample and derivatized
  • GC-MS gas chromatography-mass spectrometry
  • LC-MS liquid-chromatography-mass spectrometry
  • An exemplary protocol for derivatization of polar metabolites involves formation of methoxime-tBDMS derivatives through incubation of the metabolites with 2% methoxylamine hydrochloride in pyridine followed by addition of N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA) with 1% tert-butyldimethylchlorosilane (t-BDMCS).
  • MTBSTFA N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide
  • t-BDMCS 1% tert-butyldimethylchlorosilane
  • Non-polar fractions including triacylglycerides and phospholipids, may be saponified to free fatty acids and esterified to form fatty acid methyl esters, for example, either by incubation with 2% H 2 SO 4 in methanol or by using Methyl-8 reagent (Thermo Scientific). Derivatized samples may then be analyzed by GC-MS using standard LC-MS methods, for example, a DB-35MS column (30 m ⁇ 0.25 mm i.d. ⁇ 0.25 ⁇ m, Agilent J&W Scientific) installed on a gas chromatograph (GC) interfaced with an mass spectrometer (MS).
  • a DB-35MS column (30 m ⁇ 0.25 mm i.d. ⁇ 0.25 ⁇ m, Agilent J&W Scientific) installed on a gas chromatograph (GC) interfaced with an mass spectrometer (MS).
  • Mass isotopomer distributions may be determined by integrating metabolite ion fragments and corrected for natural abundance using standard algorithms, such as those adapted from Fernandez et al. (Fernandez et al., Correction of 13C mass isotopomer distributions for natural stable isotope abundance, J Mass Spectrom, 1996, 31:255).
  • LC-MS liquid chromatography-mass spectrometry
  • polar metabolites may be analyzed using a standard benchtop LC-MS/MS equipped with a column, such as a SeQuant ZIC-pHILIC Polymeric column (2.1 ⁇ 150 mm; EMD Millipore).
  • Exemplary mobile phases used for separation could include buffers and organic solvents adjusted to a specific pH value.
  • extracted samples may be analyzed by 1 H-nuclear magnetic resonance ( 1 H-NMR).
  • Samples may be combined with isotopically enriched solvents such as D2O, optionally in the presence of a buffered solution (e.g., Na 2 HPO 4 , NaH 2 PO 4 in D 2 O, pH 7.4).
  • Samples may also be supplemented with a reference standard for calibration and chemical shift determination (e.g., 5 mM 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS-d 6 , Isotec, USA)).
  • the solution may be filtered or centrifuged to remove any sediment or precipitates, and then transferred to a suitable NMR tube or vessel for analysis (e.g., a 5 mm NMR tube).
  • a suitable NMR tube or vessel for analysis e.g., a 5 mm NMR tube.
  • 1 H-NMR spectra may be acquired on a standard NMR spectrometer, such as an Avance II+500 Bruker spectrometer (500 MHz) (Bruker, DE), equipped with a 5 mm QXI-Z C/N/P probe-head) and analyzed with spectra integration software (such as Chenomx NMR Suite 7.1; Chenomx Inc., Edmonton, AB).
  • 1 H-NMR 1 H-NMR protocol for exometabolome analysis of cultured mammalian cells, Methods Mol Biol, 2014:237-47.
  • 1 H-NMR may be performed following other published protocols known in the art (Chassaing et al., Lack of soluble fiber drives diet-induced adiposity in mice, Am J Physiol Gastrointest Liver Physiol, 2015; Bal et al., Comparison of Storage Conditions for Human Vaginal Microbiome Studies, PLoS ONE, 2012:e36934).
  • the reaction was stirred for 30 minutes to 8 hours, constantly removing water from the reaction. Reaction progress was monitored by HPLC. When sufficient oligomerization had occurred, the stirrer was shut off, the reaction was cooled to room temperature and vented to atmospheric pressure, and the solid mass was dissolved in a volume of water sufficient to create a solution of approximately 50 Brix (grams sugar per 100 g solution). Once dissolution was complete, solid catalyst was removed by filtration and the oligomer solution was concentrated to approximately 50-75 Brix by rotary evaporation. In cases in which an organic solvent has been used, water immiscible solvents can be removed by biphasic extraction and water miscible solvents can be removed by rotary evaporation concomitant to the concentration step.
  • Single glycan unit (homo-glycans): xyl100, rha100, ara100, gal100, glu100, and man100.
  • Two glycan units (hetero-glycans): ara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10 and glu90gly10.
  • glycan units xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, and glu33gal33neu33.
  • Oligosaccharides synthesized as in Example 1 were dissolved in deionized water to a final concentration of 25-50 Brix. The material was then exposed to at least 2 mass equivalents of Dowex Monosphere 88 ion exchange resin. Exposure may occur by swirling in a flask at 120-170 rpm or by filtration through a wet slurry packed column as long as the residence time is sufficient for the solution to achieve a final pH between 3 and 5. The oligomer solution was isolated by filtration (as in the case of swirled reactions) or elution (as in the case of column filtration) and the process was repeated with Dowex Monosphere 77 ion exchange resin in an analogous fashion until the solution pH was above 5.5.
  • Man100 and xyl100 were synthesized as in Example 1 and were purified by ion exchange.
  • the material was purified by elution through three different ion-exchange chromatography columns using deionized water as an eluent at a speed of 2 bed volumes per hour.
  • the columns were arranged serially in the following order: Dowex Monosphere 88 strong cation resin, Dowex Monosphere 77 weak base resin, and Dowex Optipore SD-2 adsorbent decolorizing resin. Each column was 220 mL in bed volume. After passage, the solution was filtered through a 0.20 micron filter to remove residual resin and resin fines.
  • Oligomers prepared and purified as in Examples 1 and 2 were modified so as to remove low molecular weight species. The separation was achieved by osmotic separation. Approximately 45 cm of 1.0 kD MWCO Biotech CE dialysis tubing (31 mm flat width) from Spectrum Labs was placed into deionized water and soaked for 10 minutes, then one end was sealed with a dialysis tubing clip. A 25 Brix solution of 8 grams dry oligosaccharide was sterile filtered and sealed into the tube with a second clip along with a few mL of air to permit the tube to float. The filled tube was then placed in a 3 gallon tank of deionized water which was stirred with sufficient force to induce slow swirling of the sealed tubes.
  • the dilute solution was sterile filtered and concentrated in vacuo to a final concentration of approximately 65 Brix or lyophilized to a solid with a residual moisture between 1 and 10%.
  • the separation was achieved by tangential flow filtration (TFF). In this case, 100 mL of 25 Brix glycan sample dissolved in deionized water and sterile filtered was placed into the feed bottle of a Spectrum Labs KrosFlo Research IIi TFF system that was prepared according to the manufacturer's recommendation.
  • the sample was then diafiltered through a 1 kD mPES MidiKros hollow-fiber filter at a transmembrane pressure of 25 psig.
  • HPLC samples of the feed stock taken every 0.5 diafiltration volumes were used to determine when the material had a DP2+ yield greater than 95% and a DP3+ yield greater than 90% at which point the solution was sterile filtered and concentrated in vacuo to a 65 Brix syrup or lyophilized to a solid with residual water content of 1-10% by mass.
  • Low molecular weight oligomers can also be removed by precipitation with 70% ethanol as in Gras, et al. Food Chem. 2001, 128, 773-777.
  • Glycans can also be fractionated into pools with different average molecular weights by activated charcoal chromatography as in Sanz, et al. Chromatographia 2006, 64, 233-236.
  • This experiment was designed to quantitate the amount of glycan in any given aqueous solution.
  • a Mettler-Toledo Refracto 30GS portable sugar refractometer was calibrated using high-purity reverse-osmosis deionized water.
  • Several drops of the glycan solution were filtered through a 0.2 micron syringe filter directly onto the lens of the refractometer. The measurement was taken at room temperature and reported as Brix.
  • the glycans were routinely concentrated to 75 Brix without obvious solidification or crystallization at 23° C. Brix can then be converted to solubility assuming a specific density of water equal to 1.0 g/mL.
  • 75 Brix 100 grams of solution consisting of 75 grams of glycan and 25 grams of water
  • aqueous solubility of 3.0 g/mL As a comparison, the aqueous solubility of D-glucose is reported to be 0.909 g/mL (48 Brix) at 25° C. by Sigma-Aldrich.
  • This experiment was designed to quantitate the ratio of monomer content within a given oligosaccharide.
  • Glycosyl composition analysis was performed by combined gas chromatography/mass spectrometry (GC/MS) of the per-O-trimethylsilyl (TMS) derivatives of the monosaccharide methyl glycosides produced from the sample by acidic methanolysis as described previously by Santander et al. (2013) Microbiology 159:1471. Between 100 and 200 ⁇ g of sample were lyophilized into a suitable test tube. Inositol (20 ⁇ g) was added to the sample as an internal standard, then the sample was heated to 80° C. in 1M HCl/methanol for 18 hours.
  • GC/MS gas chromatography/mass spectrometry
  • the resulting monosaccharides were then re-acetylated using pyridine and acetic anhydride in MeOH, and per-O-trimethylsilylated with Tri-Sil (Pierce) at 80° C. for 30 minutes.
  • GC/MS analysis of the TMS methyl glycosides was performed on an Agilent 7890A GC interfaced to a 5975C MSD, using a Supelco Equity-1 fused silica capillary column (30 m ⁇ 0.25 mm ID). Each peak was assigned to a component sugar based upon comparison to known standards and integration of the respective peaks allowed clean calculation of the relative percentage of monomers within an exemplified glycan. In all tested cases, the monomer composition of a given oligosaccharide matched the input ratio within experimental error and the output composition matched the input composition within the precision of the measurement.
  • This experiment was designed to quantitate the distribution of molecular weights within a given oligosaccharide.
  • the measurement was made by HPLC using the method described in Monograph of United States Pharmacopeia, 38(6) In-Process Revision: Heparin Sodium (USP37-NF32). Separations were achieved on an Agilent 1100 HPLC system via dual Shodex OHpak SB-802.5 HQ columns using pure HPLC grade water as the eluent at 1.0 mL/min flow rate and an RI detector held at 40° C. The column temperature was set at 40° C.
  • FIG. 1 shows the curve generated during the SEC evaluation of a glu100 sample in which the average molecular weight was determined to be 1212 g/mol or approximately DP7.
  • the upper end of molecular weight of the material as defined by the point of the curve at 10% of maximum absorption leading the curve was determined to be 4559 g/mol or approximately DP28.
  • the lower end of molecular weight of the material as defined by 10% of the maximum absorption trailing the curve was determined to be 200 g/mol or approximately DP1.
  • Similar analysis of a glu50gal50 sample showed a MW, high mass, and low mass of 1195 g/mol ( ⁇ DP7), 4331 g/mol ( ⁇ DP27), and 221 g/mol ( ⁇ DP1) respectively.
  • the proportion of glycan with DP greater than or equal to 2 (DP2+) and 3 (DP3+) may be measured by ion-affinity chromatography.
  • a sample of glycan was diluted out to 50-100 mg/mL and 10 ⁇ L of this solution was injected onto an Agilent 1260 BioPure HPLC equipped with a 7.8 ⁇ 300 mm BioRad Aminex HPX-42A column and RI detector. Using pure HPLC-grade water as an eluent, the sample was eluted at 0.6 mL/min through an 80° C. column and an RI detector maintained at 50° C. The peaks representing DP1-6 are assigned by comparison to reference standards and integrated using the Agilent ChemStation software.
  • Peaks are typically integrated as DP1, DP2, DP3, DP4-7, and DP8+.
  • the DP that is achievable by the reaction described in Example 1 varies from monomer to monomer although it is consistent across batches if the procedure is followed correctly, e.g. glucose reliably achieves higher DP values than arabinose.
  • DP2+ values ranged from 85-93% and DP3+ values ranged from 80-90%.
  • DP2+ values ranged from 63-78% and DP3+ values ranged from 48-71%.
  • Mixtures of monomers behaved as averages of the individual components. For man100 and xyl100 the DP2+ yield was 91.9% and 89.6, respectively, and the DP3+ yield was 85.5 and 85.5, respectively.
  • This experiment was designed to quantitate the ratio of alpha- and beta-glycosidic bonds within a given sample by two-dimensional NMR.
  • Approximately 150 mg of 65 Brix oligosaccharide solution was dried to stable mass in a vacuum oven at 45-95° C. under 400 mbar pressure.
  • the sample was subjected to two cycles of dissolution in D 2 O and drying to remove residual H 2 O.
  • Once dried, the sample was dissolved in 750 ⁇ L D 2 O with 0.1% acetone, placed into a 3 mm NMR tube, and analyzed in a Bruker Avance-III operating at 500.13 MHz 1H (125.77 MHz 13C) equipped with a Bruker BBFO probe operating at 21.1° C.
  • HSQC heteroatomic single quantum coherence pulse sequence
  • Anomeric protons between 4-6 ppm (1H) and 80-120 ppm (13C) were assigned by analogy to glucose as reported in Roslund, et al. (2008) Carbohydrate Res. 343:101-112. Spectra were referenced to the internal acetone signal: 1H—2.22 ppm; 13C—30.8 ppm. Isomers were quantitated by integration of their respective peaks using the MNova software package from Mestrelab Research (Santiago de Compostela, Spain).
  • FIG. 2 shows the anomeric region of a representative spectrum.
  • Table 6 lists the distribution across 13 distinct combinations of monomers showing the alpha-/beta-ratio to be as high as 4:1 as in the case of rha100 and as low as 1:1 as in the case of glu50gal50.
  • This experiment was designed to identify the composition of a glycan by 2D-NMR identification of the constituent monomers. Approximately 150 mg of 65 Brix oligosaccharide solution was dried to stable mass in a vacuum oven at 45° C. under 300 mbar pressure, typically requiring 4-8 hours. Once dried, the sample was dissolved in 1.0 mL D 2 O with 0.1% acetone, placed into a 3 mm NMR tube, and analyzed in a Bruker Avance-III using the spectral parameters listed in Table 7. The sample was analyzed using a 13C-1H heteroatomic single quantum coherence pulse sequence (HSQC) using the standard Bruker pulse sequence.
  • HSQC heteroatomic single quantum coherence pulse sequence
  • Spectra were manually phased then referenced in both dimensions to the internal acetone signal: 1H—2.22 ppm; 13C—30.89 ppm.
  • the anomeric region of each glycan spectra derived from a single sugar monomer was then examined for peaks representing specific glycosidic bonds characteristic to that monomer.
  • Tables 7 and 8 list the diagnostic HSQC peaks for man100 and xyl100, respectively.
  • FIGS. 7 a and 7 b show the HSQC spectra for man100 and xyl100, respectively.
  • the HSQC spectrum of a glycan with more than one monomer is predicted to be represented by the sum of the HSQC peaks of each of its constituent sugars. Therefore, each constituent monomer has unique HSQC peaks that will appear in any glycan that contains that monomer irrespective of other constituent monomers and furthermore, the monomers used to synthesize a glycan can be determined by identifying the fingerprint peaks unique to each constituent monomer. For example, FIG. 3 shows that the HSQC spectra of glu50gal50 is a hybrid of the spectra of glu100 and gal100. Table 10 lists the fingerprint peaks for selected glycan units.
  • HSQC spectra of glycan therapeutics containing 4 or more distinct glycan units have at least 4 peaks for each constituent glycan unit.
  • This experiment was designed to quantitate the distribution of glycosidic regioisomers (branching) within a given oligosaccharide.
  • the samples were permethylated, depolymerized, reduced, and acetylated; and the resultant partially methylated alditol acetates (PMAAs) analyzed by gas chromatography-mass spectrometry (GC-MS) as described by Heiss et al (2009) Carbohydr. Res. 344:915.
  • the samples were suspended in 200 ⁇ l of dimethyl sulfoxide and left to stir for 1 day. Permethylation was effected by two rounds of treatment with sodium hydroxide (15 min) and methyl iodide (45 min).
  • the aqueous solution was hydrolyzed by addition of 2M trifluoroacetic acid and heating to 121° C. for 2 hours. Solids were isolated in vacuo and acetylated in acetic acid/trifluoroacetic acid.
  • the resulting PMAAs were analyzed on an Agilent 7890A GC interfaced to a 5975C MSD (mass selective detector, electron impact ionization mode); separation was performed on a 30 m Supelco SP-2331 bonded phase fused silica capillary column.
  • FIG. 4 shows three representative GC spectra from this analysis.
  • the glycans had at least 0.1-10% of each of the 1,2-; 1,3-; 1,4-, and 1,6-glycoside bond types.
  • the materials also contained at least 5% of the branched bond types (including but not limited to 1,3,6-; 1,4,6-; or 1,2,4-glycosides) and at least 3% of the monomeric units existed in the furanose form.
  • a glycan originating from a single monomer consisted of at least 12 distinct non-terminal substitution patterns.
  • a glycan originating from two monomers consisted of at least 18 distinct non-terminal substitution patterns.
  • a glycan originating from three or more monomers consisted of at least 24 distinct non-terminal substitution patterns.
  • bacterial cultures are grown in the presence of candidate glycans and assayed for their growth, community composition (e.g., by 16S rRNA gene sequencing), production of metabolites, and phenotypic or transcriptomic properties. Desired glycans are selected based on their ability to elicit desired properties within the bacterial culture.
  • Bacterial cultures include monocultures, mixed cultures, cultures isolated from humans or laboratory animal models, cultures isolated from a human or laboratory animal model and spiked with an isolate or collection of isolates, or cultures isolated from a human or laboratory animal model and depleted of a collection of species (for example, by application of an antibiotic).
  • This assay can be performed in the presence of antibiotics or other test compounds. The results obtained from the in vitro assays are compared with those obtained after treating humans with glycans or administering the glycans to a laboratory animal establishing the in vitro-in vivo correlation of results.
  • An in vitro assay was performed to assess the ability of various bacterial strains, including commensals of the gastrointestinal tract, to utilize different glycans as growth substrates. This assay was designed to assess the ability of selected glycans to promote the growth of microbiota associated with effects on cancer progression, including protective effects.
  • Bacterial strains were handled at all steps in an anaerobic chamber (AS-580, Anaerobe Systems) featuring a palladium catalyst. The chamber was initially made anaerobic by purging with an anaerobic gas mixture of 5% hydrogen, 5% carbon dioxide and 90% nitrogen and subsequently maintained in an anaerobic state using this same anaerobic gas mixture.
  • Anaerobicity of the chamber was confirmed daily using Oxoid anaerobic indicator strips that change color in the presence of oxygen. All culture media, assay plates, other reagents and plastic consumables were pre-reduced in the anaerobic chamber for 24-48 hours prior to contact with bacteria.
  • FOS France Foods
  • Bacterial isolates were obtained from the American Type Culture Collection (ATCC) and Leibniz Institute DSMZ-German Institute of Microorganisms and Cell Cultures (DSMZ). Cultures of the Bacteroidetes Bacteroides caccae ATCC 43185 “BCA.26”, Bacteroides thetaiotaomicron ATCC 29741 “BTH.8”, Bacteroides cellulosilyticus DSM 14838 “BCE.71 ”, Parabacteroides distasonis ATCC 8503 “PDI.6”, Bacteroides vulgatus ATCC 8482 “BVU.10” and Prevotella copri DSM 18205 “PCO.72”; the Clostridiales Clostridium scindens ATCC 35704 “CSC.32 ”, Dorea formicigenerans ATCC 27755 “DFO.36 ”, Dorea longicatena DSM 13814 “DLO.76 ”, Ruminococcus obeum ATCC 29714
  • Inocula were prepared by determining the optical density of each culture at 600 nM (OD 600 ) in a Costar 3370 polystyrene 96-well flat-bottom assay plate using a Biotek Synergy 2 plate reader with Gen5 2.0 All-In-One Microplate Reader Software according to manufacturer's protocol, and diluting the cells to OD 600 0.01 final in defined and semi-defined media that were prepared without sugars.
  • longicatena isolates were tested in 900 mg/L sodium chloride, 26 mg/L calcium chloride dihydrate, 20 mg/L magnesium chloride hexahydrate, 10 mg/L manganese chloride tetrahydrate, 40 mg/L ammonium sulfate, 4 mg/L iron sulfate heptahydrate, 1 mg/L cobalt chloride hexahydrate, 300 mg/L potassium phosphate dibasic, 1.5 g/L sodium phosphate dibasic, 5 g/L soidum bicarbonate, 0.125 mg/L biotin, 1 mg/L pyridoxine, 1 m/L pantothenate, 75 mg/L histidine, 75 mg/L glycine, 75 mg/L tryptophan, 150 mg/L arginine, 150 mg/L methionine, 150 mg/L threonine, 225 mg/L valine, 225 mg/L isoleucine, 300 mg/L leucine, 400 mg/L cyst
  • B. thetaiotaomicron, B. caccae and B. cellulosyliticus were tested in 100 mM potassium phosphate buffer (pH 7.2), 15 mM sodium chloride, 8.5 mM ammonium sulfate, 4 mM L-cysteine, 1.9 ⁇ M hematin, 200 ⁇ M L-histidine, 100 ⁇ M magnesium chloride, 1.4 ⁇ M iron sulfate heptahydrate, 50 ⁇ M calcium chloride, 1 ⁇ g/mL vitamin K3 and 5 ng/mL vitamin B12 (Martens E C et al.
  • C. scindens, P. copri and R. obeum were tested in 10 g/L tryptone peptone, 5 g/L yeast extract, 0.5 g/L L-cysteine hydrochloride, 0.1 M potassium phosphate buffer pH 7.2, 1 ⁇ g/mL vitamin K3, 0.08% w/v calcium chloride, 0.4 ⁇ g/mL iron sulfate heptahydrate, 1 ⁇ g/mL resazurin, 1.2 ⁇ g/mL hematin, 0.2 mM histidine, 0.05% Tween 80, 0.5% meat extract (Sigma), 1% trace mineral supplement (ATCC), 1% vitamin supplement (ATCC), 0.017% v/v acetic acid, 0.001% v/v isovaleric acid, 0.2% v/v propionic acid and 0.2% v/v N-butyric acid (Romano K A et al)
  • OD 600 measurements for each isolate at the end of the incubation period were obtained using a Biotek Synergy2 reader with Gen5 2.0 software according to manufacturer's specifications. Measurements were normalized by dividing the OD 600 readings of the isolate on test glycans by the average OD 600 of the isolate in medium supplemented with 0.5% w/v dextrose to facilitate comparison of glycan utilization by strains that grow within significantly different OD 600 ranges. Table 11 provides a key to Tables 12-14.
  • glycans supported growth of most of the commensal strains tested in the assay, with Average Normalized Growth values of at least 0.2. Glycans varied in the number and diversity of strains they supported (see Table 12) in the assay. In the assay, glu50gal50, ara50gal50, glu100, gal100, glu80man20, glu60man40, glu33gal33fuc33 and ara100 supported growth of a combination of Bacteroidales; Clostridiales, including the Lachnospiraceae DFO.36, DLO.76, CSC.32 and BHA.20; and Bifidobacteria.
  • man52glu29gal19, ara60xyl40 and man80glu20 supported growth of a combination of Bacteroidales and Lachnospiraceae, and xyl100 and man100 supported growth of members of Bacteroidales.
  • Glycans may increase the concentration of microbial proteins that are sufficiently similar to tumor antigens to elicit immune cell activity via antigenic mimicry or cross-reactivity.
  • Antigen mimicry may drive anti-tumor effects via two mechanisms. First, if microbes remain confined in the intestinal lumen, microbes or microbial antigens are locally captured by CD103+ CD11b+ dendritic cells that migrate to the draining lymph node to present relevant antigen to T cells.
  • T cells can traffic to the tumor to drive an anti-tumor immune response.
  • a second mechanism is that microbial antigens, rather than T cells, can travel through the body to a tumor site. Translocation of microbial proteins and even entire microorganisms from the intestine to mesenteric lymph nodes, the spleen, and other sites has been documented (Abt et al. (2012). Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity 37, 158-170; Wheeler et al. (2014). The biology of bacterial peptidoglycans and their impact on host immunity and physiology. Cell. Microbiol.
  • antigenic mimicry determines the long-range effects of the microbiome on immunosurveillance. Additionally, such antigenic mimicry may aid the immune systems recognition of pathogenic microorgnaisms that share antigens with microbial molecules that are exposed to the immune system.
  • CTLA4 blockade lost its therapeutic activity against fibrosarcomas in mice that were either raised in a germ-free environment or that had been raised in specific pathogen-free conditions and then treated with multiple broad-spectrum antibiotics to sterilize the gut (Vetizou, et al. (2015). Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 350, 1079-1084). This defect was overcome by gavage with Bacteroides fragilis , by immunization with B. fragilis polysaccharides, or by adoptive transfer of B.
  • T cell receptor TCR
  • B. fragilis and B. thetaiotaomicron T cell receptor specific for distinct Bacteroides species
  • CTLA-4 blockade efficacy of CTLA-4 blockade.
  • the microbiome also affects the therapeutic efficacy of PD-L1 blockade. Injection of a blocking antibody against PD-L1 was much more efficient in reducing the growth of melanomas in mice containing a high abundance of Bifidobacterium in their gut than in mice lacking this genus.
  • Bifidobacterium -treated mice exhibited significantly improved tumor control compared with their untreated littermates, and this effect was mediated by CD8+ T cells.
  • DCs purified from mice that had been treated with Bifidobacterium were particularly active in presenting a melanoma-derived peptide antigen to T cells for stimulation of their proliferation and IFN-g production, suggesting that Bifidobacterium improves the anticancer immune response through an effect on DCs (Sivan et al. (2015) Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350, 1084-9), which may increase the presentation of a microbiome-derived antigen. By shifting the concentration of microbes present in the microbiome, the antigens may also be shifted and the prevalence of antigens that mimic tumor-associated antigens may be increased.
  • Clostridiales include the Lachnospiraceae DFO.36, DLO.76, CSC.32 and BHA.20.
  • Fecal samples were collected by providing subjects with the Fisherbrand Commode Specimen Collection System (Fisher Scientific) and associated instructions for use. Collected samples were stored with ice packs or at ⁇ 80° C. until processing (McInnes & Cutting, Manual of Procedures for Human Microbiome Project: Core Microbiome Sampling Protocol A, v12.0, 2010, hmpdacc.org/doc/HMP_MOP_Version12_0_072910.pdf). Alternative collection devices may also be used. For example, samples may be collected into the Globe Scientific Screw Cap Container with Spoon (Fisher Scientific) or the OMNIgene-GUT collection system (DNA Genotek, Inc.), which stabilizes microbial DNA for downstream nucleic acid extraction and analysis. Aliquots of fecal samples were stored at ⁇ 20° C. and ⁇ 80° C. following standard protocols known to one skilled in the art.
  • Example 8 Determining the Titer of Microbial Samples Collected from Feces and Culturing Samples
  • fecal samples were collected as described in Example 7 and prepared as a 10% weight/volume suspensions in sterile phosphate buffered saline (PBS).
  • PBS sterile phosphate buffered saline
  • Ten-fold serial dilutions were prepared in sterile PBS and plated (100 ⁇ L per dilution) to Brucella Blood Agar (Anaerobe Systems; incubated anaerobically to non-selectively titer common member of the gut microbiota, including Bacteroides , or incubated aerobically to non-selectively titer facultative anaerobes such as Proteobacteria).
  • Bile Esculin Agar (Anaerobe Systems; cultured anaerobically to titer Bacteroides fragilis group), Cycloserine-Cefoxitin Fructose Agar (Anaerobe Systems; cultured anaerobically to titer Clostridium difficile ), Lactobacillus -MRS Agar (Anaerobe Systems; cultured anaerobically to titer Lactobacillus ), Eosin Methylene Blue Agar (Teknova; cultured aerobically to titer Escherichia coli and other Gram-negative enteric bacteria), Bile Esculin Agar (BD; cultured aerobically to titer Enterococcus species), Bifidobacterium Selective Agar (Anaerobe Systems; to titer Bifidobacterium species), or MacConkey Agar (Fisher Scientific; to titer E.
  • coli and other Gram-negative enteric bacteria may also be used. Plates were incubated at 37° C. under aerobic or anaerobic conditions as appropriate for the target species. After 24-48 hours, colonies were counted and used to back-calculate the concentration of viable cells in the original sample.
  • agar such as Brucella Blood Agar (Anaerobe Systems), Brain Heart Infusion Broth (Teknova), or Chopped Meat Glucose Broth (Anaerobe Systems) were used.
  • a minimal media formulation such as M9 (Life Technologies) supplemented with amino acids, carbon sources, or other nutrients as needed were used to non-selectively culture bacteria during in vitro assays testing the effects of glycans or other compounds on bacterial populations.
  • M9 Life Technologies
  • other minimal media formulations known to one skilled in the art were used, for example, as reported in Martens et al.
  • fecal slurries at a concentration of 0.1%-10% weight/volume in PBS were used in the presence or absence of additional media elements for in vitro assays testing the effects of glycans or other compounds on bacterial populations.
  • the ex vivo assay was designed to determine if glycans can modulate a complex human fecal microbial community. Modulation of the community may induce functional and/or taxa shifts that may affect various host responses that may relate to the protection against or treatment of diseases, including cancer.
  • Fecal samples and slurries were handled in an anaerobic chamber (AS-580, Anaerobe Systems) featuring a palladium catalyst.
  • FOS Flutraflora FOS
  • a human fecal sample donation was stored at ⁇ 80° C. To prepare working stocks the fecal sample was transferred into the anaerobic chamber and allowed to thaw. The fecal sample was prepared to 20% w/v in phosphate buffered saline (PBS) pH 7.4 (P0261, Teknova Inc., Hollister, Calif.), 15% glycerol, centrifuged at 2,000 ⁇ g, the supernatant was removed, and the pellet was suspended in PBS pH 7.4 to 1% w/v fecal slurry. Prepared 1% w/v fecal slurry were contacted with glycans to 500 ⁇ L final volume per well, at 37° C.
  • PBS phosphate buffered saline
  • Genomic DNA was extracted from the fecal samples and variable region 4 of the 16S rRNA gene was amplified and sequenced (Earth Microbiome Project protocolwww.earthmicrobiome.org/emp-standard-protocols/16s/and Caporaso J G et al. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J.). Operational Taxonomic Units (OTUs) were generated by aligning 16S rRNA sequences at 97% identity. Microbial communities were compared to each other using UniFrac distance metric (Lozupone C. et al., Appl. Environ. Microbiol. December 2005 vol. 71 no. 12 8228-8235).
  • FIG. 8 a Actinobacteria relative abundance is increased while Bacteroidetes and Firmicutes relative abundance is decreased in 1% w/v fecal slurry in FOS control and glu100, compared to control fecal slurry lacking added carbon source.
  • FIG. 8 b - e glu100 and FOS control significantly increased the relative abundance of Bifidobacteriales ( FIG. 8 b ) and Bifidobacteria ( FIG. 8 e ) compared to control fecal slurry lacking added carbon source.
  • Glu100 and FOS also significantly reduced the relative abundance of Bacteroidales ( FIG. 8 c ) and Clostridiales ( FIG. 8 d ).
  • Xyl100 and man52glu29gal19 did not have a statistically significant effect in this assay. Modulation of Bifidobacterium and Bacteroides species is thought to play a role in controlling and treating tumors (see Example 6).
  • Therapeutic glycans modulated a larger number of OTU than the commercial FOS control: two in FOS and four each in glu100 and glu50gal50. The glycans showed overlapping (OTU 11 and OTU 51) and differential modulation of OTUs (see, Table 15).
  • OTUs that respond to glycan treatments in humans Percentages represent the approximate number of individuals in which the indicated taxa responded to the treatment. Percentages in the parentheses represent the number of individuals Taxa FOS glu100 glu50gal50 OTU 11 Blautia species 64% (79%) 29% (100%) OTU 10 Bifidobacterium species 57% (93%) OTU 2 Roseburia species 45% (93%) OTU 14 Coprococcus species 64% (100%) OTU 5 Lachnospiraceae (family) 50% (93%) OTU 50 Faecalibacterium prausnitzii 36% (93%) OTU 20 Parabacteroides species 62% (69%) OTU 51 Ruminococcaceae species 43% (43%) 38% (38%)
  • OTUs 11, 10, 2, 14, 5, 50, and 20 are present in most subjects tested (in about 70% or more of subjects).
  • growth modulation varies between subjects, some of which show modulation while others don't exhibit a shift in the taxa.
  • OTU 51 all subjects hosting the OTU showed a modulation.
  • the microbial community in the subjects was stable during the course of the study. Bacteria that were absent at the beginning of the study did not appear during the course of the study (see FIG. 9 ). As shown in FIG.
  • subjects that host the OTU show growth of the OTU in the GI tract in response to the glycan treatment, often shortly after the begin of consumption of the glycan. Others that do not host the OTU do not show any changes in abundance for OTU upon administration of the glycan.
  • Subjects may be classified as responders and non-responders to glycans and may further be selected for glycan treatment, e.g. on the basis of the presence or absence of particular taxa.
  • Genus that respond to glycan treatments in humans. Percentages represent the approximate number of individuals in which the indicated genera responded to the treatment. Genus FOS glu50gal50 Bifidobacterium 57% (100%) Parabacteroides 85% (100%)
  • mice In a study two groups of mice are used. The control group of mice are fed with standard chow, and the different treatment groups of mice are fed with standard chow supplemented with glycans. After 1-30 days, blood samples are drawn from the mice, the mice are sacrificed, and tissues from the intestine, liver, skin, and other sites of interest are collected and stored at ⁇ 80° C. RNA is isolated from the tissues and converted to cDNA. The GeneChip Mouse Genome 430 2.0 Array (Affymetrix) is used to analyze the differential expression between the untreated and glycan-treated animals of approximately 14,000 murine genes. The experimental protocol and raw data analysis are performed according to the manufacturer's instructions and standard protocols.
  • the biological function of the differentially expressed genes and their involvement in various processes are obtained from the following databases: RefGene (Reference for genes, proteins and antibodies: refgene.com/), CTD (Comparative Toxicogenomics Database: ctd.mdibl.org/), MGI (Mouse Genomics Informatics: www.informatics.jax.org/), KEGG (Kyoto Encyclopedia of Genes and Genomes: www.genome.jp/kegg/genes.html). This procedure is used to identify the differential expression of genes encoding inflammatory cytokines, immunomodulatory cytokines, antimicrobial peptides, and other relevant effector molecules.
  • mice normal mice are administered glycans in their drinking water over a period of 6 days with fecal samples taken from each mouse for 16S rRNA analysis.
  • mice C57Bl/6 (B6N Tac), mouse pathogen free (MPF; Taconic Biosciences, Germantown, N.Y.) aged 8-10 weeks were housed singly in cages, with 6 animals per dose group. Animals were fed PicoLab Rodent Diet 20 (“5053”; LabDiet, St. Louis, Mo.) or zero fiber diet (“ZFD”; Modified rodent diet AIN-93G: D15091701, Research Diets, New Brunswick, N.J.) ad libitum throughout the course of the study and had free access to water. Mice were maintained on a 12 h light/dark cycle. Mice were acclimated for 7 days (days ⁇ 7 to ⁇ 1) prior to glycan administration.
  • PicoLab Rodent Diet 20 (“5053”; LabDiet, St. Louis, Mo.) or zero fiber diet (“ZFD”; Modified rodent diet AIN-93G: D15091701, Research Diets, New Brunswick, N.J.
  • Glycans were administered to the mice by inclusion in their drinking water at 1% weight/volume (w/v) from day 0 through day 5. Control mice received water containing no glycan. Fresh fecal collections were performed for each mouse from days ⁇ 2 to 5. Mouse weights were monitored on days ⁇ 1, 1, 3 and 4. Body weights of the mice did not change significantly throughout the course of the study.
  • Akkermansia muciniphila The most prominent Akkermansia species in the mammalian gut is Akkermansia muciniphila . Its preferred energy source is host intestinal mucin. Consumption of a low fiber diet and high intake of simple sugars and fat results in decreased mucus production (British Journal of Nutrition/Volume 102/Issue 01/July 2009, pp 117-125, Quantitative Imaging of Gut Microbiota Spatial Organization, Earle K A et al, Cell Host Microbe. 2015 Oct. 14; 18(4):478-88). Thinning of intestinal mucus may result in increased gut permeability and translocation of microorganisms or their components, such as lipopolysaccharide (LPS), which induce inflammation. LPS levels are increased upon consumption of high fat diet in rodents which then develop metabolic syndrome (Metabolic endotoxemia initiates obesity and insulin resistance, Cani P D et al, Diabetes. 2007 July; 56(7):1761
  • Bacteroidetes may induce the growth of Akkermansia .
  • colonization of germ free mice with Bacteroides thetaiotaomicron induces mucus production by intestinal goblet cells (Wrzosek et al. BMC Biology 2013 11:).
  • This may create a favorable environment for Akkermansia growth.
  • Consumption of mucus by Akkermansia may stimulate increased mucus production and play a role in the restoration of the gut barrier that prevents leaking of microbial endotoxin LPS.
  • Decreased endotoxemia reduces inflammation. Inflammation precedes most cancers.
  • Bronchitis, colitis, cervicitis, gastritis, and hepatitis reflect inflammation of the bronchus, colon, cervix, stomach, and liver, respectively.
  • Many cancers, especially solid tumors appear to be preceded by inflammation of a given organ. For instance, people who smoke cigarette develop bronchitis, and 15% to 20% of these people develop lung cancer (Wingo et al. Annual report to the nation on the status of cancer, 1973-1996, with a special section on lung cancer and tobacco smoking. J Natl Cancer Inst 1999; 91:675-90).
  • people who have colitis are at high risk of developing colon cancer (Itzkowitz, Inflammation and cancer IV.
  • Akkermansia muciniphila metabolites include the SCFA propionate which is also thought to modulate inflammation (see, Example 15).
  • Glycan therapeutics when administered in an effective amount may modulate bacterial species, such as, e.g., Akkermansia that play a role in the reduction of inflammation.
  • Glycan treatment may alter inflammatory pathways in the gastrointestinal tract and decrease inflammation in the gastrointestinal tract, which may prevent the development of cancer.
  • mice normal mice were administered glycans (non-fermentable Acacia fiber, Glu100 or Man52glu29gal19) in their drinking water over a period of 21 days. On days 8-13 all mice were treated with 2.5% Dextran sulfate sodium (DSS) to induce intestinal inflammation. Dextran sulfate sodium is a chemical that drives inflammation in the intestine of animals. On day 21 mice were sacrificed by CO 2 asphyxiation. Two 3-5 mm adjacent sections of flushed colon were placed in 2 separate freezer vials and snap frozen. Messenger RNA was extracted and sequenced on Illumina HiSeq sequencer.
  • DSS Dextran sulfate sodium
  • mice treated with glycans were involved in Notch signaling and Wnt signaling pathways, which control cell proliferation, migration and tissue regeneration. This could be a sign of more active epithelial regeneration induced by functional shifts of the microbiota as a result of the glycan treatment.
  • Bacteria can elicit both pro- and anti-inflammatory responses from host (mammalian) cells, and different bacterial species can elicit different host responses.
  • the immune system and pro-and anti-inflammatory responses are linked to diseases, disorders or pathological conditions realted to, e.g., immune imbalances, nutritional imbalances which can lead to and may be associated with cancers.
  • Preparations of glycans are used to alter the bacterial population to elicit a desired host response.
  • An in vitro co-culture model is used to measure the host responses elicited by bacterial populations grown in the presence of glycans. Glycans that promote bacterial populations that elicit beneficial host responses or minimize detrimental host responses are selected using this assay.
  • Epithelial cell lines or tissues from the intestine are used in a co-culture model (Haller D, Bode C, Hammes W P, Pfeifer A M A, Schiffrin E J, Blum S, 2000.
  • Non-pathogenic bacteria elicit a differential cytokine response by intestinal epithelial cell/leucocyte co-cultures.
  • Gut. 47:79-97 Bacillus subtilis
  • Human enterocyte-like CaCO-2 cells are seeded at a density of 2.5 ⁇ 10 5 cells/ml on 25 mm cell culture inserts (0.4 ⁇ m nucleopore size; Becton Dickinson).
  • the inserts are placed into 6-well tissue culture plates (Nunc) and cultured 18-22 days at 37° C./10% CO 2 in DMEM (glutamine, high glucose; Amimed) supplemented with 20% heat-inactivated fetal calf serum (56° C., 30 minutes; Amimed), 1% MEM non-essential amino acids (Gibco BRL), 10 ⁇ m/ml gentamycin (Gibco BRL), and 0.1% penicillin/streptomycin (10 000 IU/ml/10 000 UG/ml; Gibco BRL).
  • the cell culture medium is changed every second day until the cells are fully differentiated.
  • a 3D reconstructed tissue model produced from normal, human cell-derived small intestine epithelial and endothelial cells and fibrobasts (Epilntestinal model; MatTek Corporation, Ashland, Mass.) is used.
  • Transepithelial electrical resistance (TEER) is determined using a MultiCell-ERS voltmeter/ohmmeter. Tissue culture inserts are washed twice with prewarmed antibiotic-free medium prior to challenge with bacterial cultures. Separately, bacterial cultures are grown in the presence of preparations of glycan.
  • the bacterial suspensions are prepared in antibiotic-free medium and 10 6 -10 8 CFU are added to confluent cell or tissue cultures.
  • the co-cultures are incubated at 37° C. for 4-24 hours.
  • the supernatant is collected and analyzed for inflammatory and immunomodulatory cytokines including IL-1 ⁇ , IL-1 ⁇ , TNF, IL-8, RANTES, IL-10, TGF- ⁇ , IFN- ⁇ , IL-4, IL-6, IL-12, IL-17, and IL-23.
  • This analysis is performed by enzyme linked immunosorbent assay (ELISA) or other comparable quantification technique (e.g., Luminex Assay; Life Technologies, Carlsbad, Calif.) following standard protocols.
  • gene expression e.g., by microarray
  • transcriptomic e.g., by RNA-Seq
  • This procedure is used to analyze the expression of genes encoding inflammatory cytokines, immunomodulatory cytokines, antimicrobial peptides, and other relevant host responses.
  • Bacteroidete Bacteroides uniformis ATCC 8492 “BUN.80” was tested in 100 mM potassium phosphate buffer (pH 7.2), 15 mM sodium chloride, 8.5 mM ammonium sulfate, 4 mM L-cysteine, 1.9 ⁇ M hematin, 200 ⁇ M L-histidine, 100 ⁇ M magnesium chloride, 1.4 ⁇ M iron sulfate heptahydrate, 50 ⁇ M calcium chloride, 1 ⁇ g/mL vitamin K3 and 5 ng/mL vitamin B12 (Martens E C et al. Cell Host & Microbe 2008; 4, 447-457).
  • the Lachnospiracea Dorea longicatena (DSM 13814) “DLO.76” was tested in 900 mg/L sodium chloride, 26 mg/L calcium chloride dihydrate, 20 mg/L magnesium chloride hexahydrate, 10 mg/L manganese chloride tetrahydrate, 40 mg/L ammonium sulfate, 4 mg/L iron sulfate heptahydrate, 1 mg/L cobalt chloride hexahydrate, 300 mg/L potassium phosphate dibasic, 1.5 g/L sodium phosphate dibasic, 5 g/L sodium bicarbonate, 0.125 mg/L biotin, 1 mg/L pyridoxine, 1 m/L pantothenate, 75 mg/L histidine, 75 mg/L glycine, 75 mg/L tryptophan, 150 mg/L arginine, 150 mg/L methionine, 150 mg/L threonine, 225 mg/L valine, 225 mg/L iso
  • Short chain fatty acid (SCFA) analysis was performed on the filtered culture supernatants using a cold extraction of short chain fatty acids, measured by EI-CGMS without derivatization.
  • FIG. 13 summarizes the results obtained.
  • cultures of Bacteroidete BUN.80 and Lachnospiracea DLO.76 grown with either glycan glu80man20 or FOS produced supernatants with total SCFA concentrations in excess of 5,000 ⁇ M.
  • Acetate was the SCFA produced in the highest concentrations in the assay, and propionate was produced at the second-highest levels. Butyrate, isovalerate, valerate, hexanoate and octanoate were also detected in the assay.
  • the decrease in short chain fatty acids due to glycan treatment may increase the propensity of T cells that differentiate in the gastrointestinal tract to become inflammatory T cells (e.g. Th17) that can traffic to tumor sites and drive inflammatory responses against the tumor.
  • SCFAs constitute an important energy source for colonocytes and also function as signaling molecules, modulating intestinal inflammation, and metabolism. SCFAs, in particular acetate, propionate, and butyrate, favor histone H3K27 acetylation and increased expression of the Treg-specific transcription factor gene, Foxp3, thereby boosting Treg development in the gastrointestinal tract (Furusawa et al., 2013. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells.
  • Tregs are absent in germfree mice that lack both commensal bacteria and their metabolites, such as the short-chain fatty acid (SCFA) butyrate, and are necessary for their development (Arpaia et al., 2013 Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504, 451-455; Atarashi et al., 2011 Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337-341; Furusawa et al., 2013).
  • the modulation of T cell function by the microbiota, through SCFAs, toward tolerance (IL-10 secretion) rather than inflammation (IL-17 secretion) has also been proposed for IL-10/IL-17 double-secreting T cells.
  • T cells can switch from a tolerance to inflammatory phenotype and vice versa based on the presence or absence of SCFAs (Ruff and Kriegel, 2015, Autoimmune host-microbiota interaction at barrier sites and beyond. Trends Mol. Med. 21, 233-244), and the decrease of SCFAs driven by glycans likely leads to an increase in inflammatory T cells.
  • Th17 cells primed in the intestine could traffic to peripheral sites, undergo functional plasticity, and mediate inflammation: A number of mouse models of chronic inflammation residing in distant, non-mucosal tissues, where an impact of the gut microbiota was demonstrated, outlined the pro-inflammatory role of intestinal Th17 cells (Lee et al., 2011, Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc. Natl. Acad. Sci. USA 108 (Suppl 1), 4615-4622; Wu et al., 2010, Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells.
  • Untargeted metabolomics was performed on 30-50 mg of cecal contents from mice fed either a High Fat diet (Research Diets D12492), Normal Mouse chow (Research Diets D12450), or High Fat diet+glycan using Metabolon's LC-MS based DiscoveryHD4 platform. A total of 538 metabolites were identified and 149 were differentially abundant in High Fat vs. Normal Chow, 26 with treatment with glu100 0.3%, and 36 with treatment with man52glu29gal19 1% (Tables 18 and 19). Treatment with glycans significantly shifted the composition of the mouse cecal metabolome (P ⁇ 0.01, adonis, FIG. 15 ).
  • glycan treatment modulates the total metabolite output of the GI tract microbiota in the animal including SCFAs (see Example 16) and bile acids (see Example 18).
  • SCFAs see Example 16
  • bile acids see Example 18.
  • Metabolic changes and potential links to the immune system and inflammatory responses are thought to play a role in diseases, disorders or pathological conditions realted to, e.g., immune imbalances, nutritional imbalances and cancers.
  • DOC deoxycholic acid
  • LCA Lithocholic acid
  • DOC can be considered as a microbial co-carcinogen that not only contributes to colon carcinogenesis, but that also participates to the development of liver cancer, presumably by inducing the senescence-associated secretory phenotype of hepatic stellate cells, thereby stimulating pro-inflammatory and tumor-promoting reactions in a mouse model of obesity-associated hepatocellular carcinoma (Yoshimoto et al., 2013, Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature 499, 97-101).
  • DOC may well cooperate with other bacterial products, including LPS, in promoting hepatocellular carcinoma (Dapito et al., 2012, Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. Cancer Cell 21, 504-516). Numerous other studies have shown that DOC induces apoptosis in colon cells in short-term cultures.
  • Bile acid analysis was performed on 30-50 mg of cecal contents from mice fed either a High Fat diet (Research Diets D12492), Normal Mouse chow (Research Diets D12450), or High Fat diet+glycan using Biocrates LC-MS based Bile Acid Kit. Glycan treatment significantly altered the bile acid composition of the mouse cecum ( FIG. 16 , Table 20), while total bile acid pool size did not change.
  • Bile acid species that are significantly different with glycan treatment (P ⁇ 0.05, Wilcoxon Rank Sum with FDR correction for multiple hypotheses) Bile Acid Type Glycodeoxycholic acid Secondary Glycolithocholic acid Secondary Alpha-Muricholic acid Primary Beta-Muricholic acid Primary Taurocholic acid Primary Taurochenodeoxycholic acid Primary
  • glycan treatment resulted in a reduction of (A) DCA (deoxycholic acid) and (B) LCA (lithocholic acid) compared to high fat control.
  • DCA deoxycholic acid
  • LCA lithocholic acid
  • Glycan treatment may modulate the bile acids present in the gastrointestinal tract of subjects consuming a high fat diet to prevent cancer development.
  • the decrease in inflammation resulting from alterations of bile acids may systemically decrease inflammatory cell numbers across the body and thereby may influence diseases that are related to aberrant immune inflammatory activation, e.g., auto-immune diseases and other diseases related to immune imbalances and nutritional imbalances.
  • mice 75 male Sprague-Dawley rats (Charles River Laboratories) were randomized into five groups of fifteen animals each, and each animal was individually housed. The rats were allowed to acclimate for four days following arrival, and starting on Day ⁇ 7, animals in four glycan-treated groups began treatment with novel glycan compositions (glu100, glu50/gal50, glu33/gal33/fuc33, or man100) at 2.5% wt/wt ad libitum in drinking water; treatment with glycans continued through Day 9. During this same period, animals in the control group received plain water.
  • novel glycan compositions glu100, glu50/gal50, glu33/gal33/fuc33, or man100
  • Treatment with 5-FU elicits a number of off-target toxicities, including neutropenia and leukopenia.
  • treatment of rats with glu/gal/fuc increased the white blood cell count compared to 5-FU treatment alone.
  • white blood cells leukocytes, neutrophils, macrophages, or monocytes
  • SCFAs short chain fatty acids
  • SCFAs Bacterially-derived SCFAs have demonstrated both pro- and anti-inflammatory actions, depending upon the cell type affected; SCFAs may inhibit leukocyte function and migration, but may also increase accumulation of neutrophils (Vinolo et al., Regulation of inflammation by short chain fatty acids, Nutrients. 2011 October; 3(10)). While further analysis is required to determine the subpopulation(s) of white blood cells affected by glu/gal/fuc, the increase in WBCs seen with glu/gal/fuc may confer an increased ability to react to bacterial infiltration across the gut membrane and thus ameliorate some of the toxic effects of 5-FU treatment.
  • glu/gal/fuc or similar glycans may decrease the presentation or severity of side effects and possibly prevent the need to decrease 5-FU dose or frequency.
  • drug toxicities are also related to or associated with immune imbalances and nutritional imbalances apart from cancer.
  • mice normal mice are dosed with glycan or control for several days and then administered a dose of morphine sufficient to produce decreased gastrointestinal (GI) transit and colonic propulsion (Coates et al. 2006 Neurogastroenterol Motil 18:464-471).
  • GI gastrointestinal
  • morphine and related opiate drugs are known to cause constipation. They act on neurons in the myenteric plexus as mu-opioid receptor agonists, leading to decreased GI motility and propulsion.
  • opioids are the most efficacious analgesics in this setting. Dose limitation of opioids in cancer patients due to side-effects may result in a lack of adequate pain management.
  • Chemotherapeutic agents themselves can cause constipation.
  • Vinca alkaloids, platinum agents, thalidomide and hormonal agents result in a high incidence of constipation (Gibson, Rachel J., and Dorothy M K Keefe. “Cancer chemotherapy-induced diarrhoea and constipation: mechanisms of damage and prevention strategies.” Supportive Care in Cancer 14.9 (2006): 890-900).
  • mice Male ICR; CD-1, 6-7 weeks old, 25-30 grams; Charles River Laboratories, Wilmington, Mass. were individually housed.
  • mice were treated with either commercially-available fiber polydextrose (PDX; “Litesse”, Dupont Danisco, Surrey, United Kingdom) or xylo-oligosaccharide (XOS; “Llife-Oligo XOS”, Bio Nutrition, Inc., Island Park, N.Y.) or novel glycan compositions (xyl100, ara100, glu100); all administered at 1% ad libitum in drinking water for 11 days.
  • a control group received plain drinking water.
  • all mice were administered morphine at a dose of 3 mg/kg subcutaneously to reduce colonic propulsion.
  • One control group of mice were treated with naloxone, a mu-receptor inverse agonist 30 minutes prior to morphine administration.
  • Naloxone is known to counteract the action of morphine at the mu-receptor. Colonic propulsion was assessed as follows: thirty minutes post morphine dosing, a 3 mm glass bead was inserted at a depth of 2 cm into the distal colon through each mouse's anus. Mice were observed for 30 minutes for expulsion of the bead, and the time in seconds to expulsion was noted. A cutoff of 30 minutes was used as a maximum time.
  • naloxone, XOS and PDX had significant effects on the time to bead expulsion, with overall latency decreased ( FIG. 19 ).
  • Xyl100-treated animals had an overall average decrease in expulsion time, but this did not reach significance.
  • Naloxone, XOS and xyl100-treated groups fell into two groups, those mice that responded and ones that responded significantly less to the treatments. This effect was seen less in the PDX-treated animals. Seventy-five percent of mice in the vehicle-treated group reached the maximal cutoff time.
  • Ara100 and glu100 had a non-statistically significant effect on bead expulsion.
  • a second analysis was performed using a reduction in expulsion of >25% of maximum expulsion time as a cutoff to define a “responder” (1350 seconds)).
  • naloxone had 6/8 mice respond to treatment, PDX, 7 had responders, XOS had 5 responders, and xyl100 and ara100 had 4 responders each, and glu100 and vehicle had 1 responder.
  • a third analysis was performed to determine the average time to bead expulsion in the responder versus non-responder animals in each treatment group ( FIGS. 20 a and 20 b ).
  • a cutoff time for bead expulsion was set at 1800 seconds.
  • naloxone had the expected effect of reversing the effects of morphine, as it is a direct inverse agonist, competing with morphine for mu-receptor occupancy and blocking its known effects on gastrointestinal motility.
  • XOS and PDX have been shown to have efficacy in clinical constipation settings (Shimada et al, 2015 J.
  • mice To study efficacy of the therapeutic glycans described herein in the treatment of cancer, an animal model of melanoma was chosen. In this model, mice usually develop tumors within 7-21 days and a treatment effect can be observed by measuring the kinetics of tumor growth. For example, a treatment effect can be in the form of delaying tumor growth.
  • Melanoma is a cancer of the skin, but is mostly observed in skin exposed to sunlight. Melanoma is most commonly diagnosed in non-Hispanic whites; 1 per 100,000 in African Americans, 4 per 100,000 in Hispanics, and 25 per 100,000 in non-Hispanic whites. The number of deaths in 2015 was 2.7 per 100,000 men and women per year. The rates of melanoma have been rising for at least 30 years. The estimated 5-year survival rate for patients whose melanoma is detected early is about 98 percent in the U.S. The survival rate falls to 63 percent when the disease reaches the lymph nodes, and 17 percent when the disease metastasizes to distant organs.
  • New checkpoint inhibitor therapies have improved the outlook for patients with metastatic melanoma.
  • Anti-PD-1 therapies e.g. nivolumab and pembrolizumab
  • nivolumab FDA label and pembrolizumab FDA label
  • Combination studies of anti-PD-1 therapy with anti-CTLA4 therapy have shown 60% overall response rate (compared to 11% with anti-CTLA4 therapy alone) and a median progression-free survival of 8.9 months (nivolumab FDA label).
  • Some commensal bacterial species may be implicated in regulating gut immunity and responses to immunotherapies in physically distant tumors (V effetzou M et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 2015 Nov. 27; 350:1079).
  • Sivan et al. showed decreased tumor growth kinetics of B16 melanoma cells in mice by combining bifidobacteria species with anti-PD-L1 therapy (Sivan A et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 2015 Nov. 27; 350:1084).
  • Therapeutic glycans capable of modulating the microbiota may be useful in cancer therapy, in some cases by promoting anti-tumor immunity, in some cases by increased melanoma-specific effector T-cell responses.
  • Therapeutic glycans combined with existing immunotherapies may produce an additive or synergistic effect.
  • Cancer models, such as the animal melanoma model are informative with respect to efficacy of agents for the treatment of immune imbalances and/or nutritional imbalances.
  • B16.F10.SIY cells were cultured at subconfluence in Dulbecco's Modified Eagle's Medium with (DMEM) supplemented with 10% fetal bovine serum (FBS) and standard Pen/Step supplement (Life Technologies). Cell expression of GFP-SIY fusion was ascertained via flow cytometry and cells were only injected if >90% of cells were positive for SIY peptide expression. Cells were trypsinized and counted, and cell viability determined via trypan blue exclusion assay prior to injection.
  • DMEM Dulbecco's Modified Eagle's Medium with
  • FBS fetal bovine serum
  • Pen/Step supplement Life Technologies
  • mice Six to eight week old female C57BL/6 mice were acquired from Taconic, housed under SPF conditions, and fed a chow of Harlan Teklan 2018 ad libitum. At the beginning of the study, a total of 1 ⁇ 10 ⁇ 6 cells of the syngeneic melanoma cell line B16.F10.SIY were injected subcutaneously into each of the mice. Tumor size was measured twice per week by multiplying length times the square of the width times 0.5.
  • Bifidobacterium mixture e.g. B. bifidum, B. longum, B. lactis , and B.
  • anti-PD-L1 was included as a control group, as anti-PD-L1 has been previously shown to delay tumor growth kinetics in this mouse model of melanoma (Sivan A et al.).
  • FIG. 21 shows tumor growth curves for Group 1 mice that received vehicle treatment (gray long-dashed line) and Group 2 mice that received Man100 in the drinking water at 1% from 5 days prior to tumor inoculation through the duration of the study (black solid line).
  • the tumor growth curves were suppressed in mice that received man100 in the drinking water (Group 2) compared to the vehicle control (Group 1).
  • mice receiving anti-PD-L1 (Group 3) showed superior tumor growth suppression (gray shortest-dashed line), and addition of the bifidobacteria mix (Group 4, gray medium-dashed line) did not show significant tumor growth changes compared to Group 1.
  • FIG. 22 shows the spider plots of the individual tumor growth curves for Group 1 (vehicle control, thin gray dotted lines), Group 2 (Man100, thick black solid lines), and Group 3 ( ) anti-PD-L1, thick gray solid lines).
  • Group 1 vehicle control, thin gray dotted lines
  • Group 2 Man100, thick black solid lines
  • Group 3 anti-PD-L1, thick gray solid lines
  • Example 22 Glycan Treatment in Patients with Melanoma
  • TIL tumor-infiltrating lymphocytes
  • Fecal samples are expected to reveal that treatment with glycan increases the absolute and relative proportion of Bifidobacterium species in the feces.
  • Tumor biopsies are expected to reveal that treatment with glycan increases the proportion of TIL from baseline, and the magnitude of increase is larger than the placebo group.
  • the glycan-treated patients are expected to experience less tumor growth over the period of treatment than the placebo controls.
  • TIL tumor-infiltrating lymphocytes
  • Fecal samples are expected to reveal that treatment with glycan increases the absolute and relative proportion of Bifidobacterium species in the feces.
  • Tumor biopsies are expected to reveal that treatment with glycan increases the proportion of TIL from baseline, and the magnitude of increase is larger than the placebo group.
  • TIL tumor-infiltrating lymphocytes
  • Fecal samples are expected to reveal that treatment with glycan increases the absolute and relative proportion of Bifidobacterium species in the feces.
  • Tumor biopsies are expected to reveal that treatment with glycan increases the proportion of TIL from baseline, and the magnitude of increase is larger than the placebo group.
  • the glycan-treated patients experience less tumor growth over the period of treatment than the placebo controls.
  • Example 24 Properties of the Glycan Therapeutic in the Treatment, Co-Treatment and Prevention of Different Oncological Processes/Diseases
  • a repression of the expression of oncogenes jun myc and fos may be detected with respect to the control group.
  • the jun and fos products are transcription factors that dimerize to form the transcription complex called AP-1 (Activating Protein-1).
  • AP-1 is a transcription factor that regulates expression of genes induced by growth factors and tumor promoters. Overexpression of oncogenes Jun and/or fos is associated with several cancers such as breast, ovarian, colon, osteosarcoma, cervical, lung and bladder cancer. Therefore, AP-1 is used as a target for chemotherapeutic treatment of cancer.
  • Myc oncogene product is a protein that regulates the expression of the transcription factor E2F and phosphatase responsible for activation of Cdc cyclins, which are involved in cell cycle regulation.
  • the myc oncogene is overexpressed in many human cancers, including pancreatic, cervical, breast and colon cancer.
  • Myc oncogene product is also used as target for cancer treatment.
  • a study in humans showed that in the intestinal mucosa there is a repression in the expression of oncogenes jun, fos and myc after infusion of the membrane with a strain of Lactobacillus .
  • Adamts1 a disintegrin-like and metalloproteinase (reprolysin type) with thrombospondin type 1 motif
  • Adamts1 gene product is a protein that has a metalloproteinase domain and disintegrin domain. This protein is involved in inflammatory processes and the development of cancer cachexia as tested in animal models of colon cancer. It has been demonstrated overexpression of Adamts1 gene in breast cancer with high metastatic activity. It has been speculated that overexpression of this gene might promote tumor growth by recruiting fibroblasts.
  • ATF3 activating transcription factor 3
  • ATF3 gene product is a transcription factor expressed in conditions of stress and DNA damage in various tissues. In many breast tumors has been reported overexpression of ATF3. This protein is used as a marker of prostate cancer since its involvement has been shown in developing this type of cancer and is therefore a potential therapeutic target.
  • Ddit4 gene DNA-damage-inducible transcript 4
  • Ddit4 gene product is a protein called RTP801 or REDD1, which inhibits the pathway mTOR/S6K1, involved in cell proliferation. Inhibitors of this route are being evaluated as cancer therapy.
  • RTP801 or REDD1 which inhibits the pathway mTOR/S6K1, involved in cell proliferation. Inhibitors of this route are being evaluated as cancer therapy.
  • mice has been described that the gene Ddti4 deficiency promotes tumor growth, while in humans has been described repression of the gene in various cancers.
  • a repression on the expression of Egr1 gene (early growth response 1) may be detected with respect to the control group.
  • the Egr1 gene product is a transcription factor involved in various cellular processes and its involvement has been demonstrated in cell growth and survival of prostate cancer. In animal models of prostate cancer has shown that lack of Egr1 gene retards tumor growth.
  • Sox9 gene produces a protein that acts as a transcription factor with DNA-binding domain type HMG (High Mobility Group). It has been shown an implication of Sox9 gene product in the proliferation of pancreatic cancer and overexpression of the same in different cell lines of colon cancer.
  • IL1a interleukin 1 alpha gene
  • the IL1a gene is overexpressed in various cancers, including lung cancer, colon and melanoma.
  • colon cancer IL1a stimulates the cell migration and angiogenesis and its expression is induced by prostaglandin E2.
  • Protaglandin E2 In a study in humans showed that in the intestinal mucosa occurs a repression in the IL1a gene expression after the infusion of the membrane with a strain of Lactobacillus .
  • an activation of the expression of Gadd45b gene growth arrest and DNA-damage-inducible 45 beta
  • Gadd45q gene growth arrest and DNA-damage-inducible 45 gamma
  • Gadd45g and Gadd45b genes are proteins related with cell cycle control. In mice models of melanoma have been shown that a lack of function of Gadd45b produces higher tumor growth. The product of this gene is required for activation of p38 kinase. The p38 protein is involved in tumor suppression. The expression of Gadd45g and Gadd45b genes is repressed in various cancers.

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