WO2020106983A1 - Methods and compositions for treating cancer - Google Patents
Methods and compositions for treating cancerInfo
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- WO2020106983A1 WO2020106983A1 PCT/US2019/062659 US2019062659W WO2020106983A1 WO 2020106983 A1 WO2020106983 A1 WO 2020106983A1 US 2019062659 W US2019062659 W US 2019062659W WO 2020106983 A1 WO2020106983 A1 WO 2020106983A1
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- 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
- A61K35/741—Probiotics
- A61K35/744—Lactic acid bacteria, e.g. enterococci, pediococci, lactococci, streptococci or leuconostocs
- A61K35/747—Lactobacilli, e.g. L. acidophilus or L. brevis
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- 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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- 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
- A61K35/741—Probiotics
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- 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
- A61K35/741—Probiotics
- A61K35/742—Spore-forming bacteria, e.g. Bacillus coagulans, Bacillus subtilis, clostridium or Lactobacillus sporogenes
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
- A61K39/39533—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals
- A61K39/3955—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals against proteinaceous materials, e.g. enzymes, hormones, lymphokines
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
- C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
Definitions
- This invention relates to the field of molecular biology and medicine.
- anti-CTLA-4 and anti -PD-1 combination therapy provides a superior rate of response than the same agents given as monotherapies, however this is offset by much greater risk of developing severe toxicities.
- the high frequency of developing severe to life threatening toxicity to anti-CTLA-4 and anti -PD-1 combination therapy has become a limiting factor for clinicians to prescribe this form of therapy.
- the disclosure relates to methods of treating cancer and/or reducing toxicity to a therapy in a subject comprising administering to the subject a composition comprising at least one isolated or purified population of bacteria belonging to one or more of the genera or species Flavonifractor, Dielma, Akkermansia, Alistipes, Bacteroides, Butyricimonas, Vampirovibrio, Tyzzerella, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacdlus secaliphdus, Bacteroides finegoldii, Lactobacillus
- the composition comprises at least one isolated or purified population of bacteria belonging to one or more of the genera or species Flavonifractor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Bacteroides stercoris, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum.
- the disclosure relates to methods of treating cancer and/or reducing toxicity of a therapy in a subject comprising administering to the subject a composition comprising fecal matter from a healthy patient, from a patient determined to respond to immune checkpoint blockade mono or combination therapy, or from a patient determined to have a non-toxic response to immune checkpoint blockade mono or combination therapy, wherein the method further comprises treating the subject with a combination of (i) a PD-1, PDL1, or PDL2 inhibitor and (ii) a CTLA-4, B7-1, or B7-2 inhibitor.
- the fecal matter is transplanted into the colon or rectum of the subject.
- the disclosure relates to methods of reducing or preventing adverse events associated with combination checkpoint blockade therapy, comprising the step of administering a composition to the subject a composition comprising at least one isolated or purified population of bacteria belonging to one or more of the genera or species Flavonifractor, Dielma, Akkermansia, Alistipes, Bacteroides, Butyricimonas, Vampirovibrio, Tyzzerella, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides finegoldii, Lactobacillus johnsonii, Parapedobacter composti, and Anaerotignum lactatifermentans or
- the disclosure relates to methods of treating cancer and/or reducing toxicity to a therapy in a subject comprising administering to a subject determined to have a favorable microbial profile in the gut microbiome a combination of (i) a PD-1, PDL1, or PDL2 inhibitor and (ii) a CTLA-4, B7-1, or B7-2 inhibitor.
- the disclosure relates to methods for predicting a response to combination immune checkpoint inhibitor therapy in a subject having cancer, the method comprising: detecting a microbial profile in a sample obtained from the subject; predicting a toxic response to the therapy when bacteria of one or one or more of the genera Bacteroides, Dialister, Coprobacter, Intestinibacter, and Parasutterella is detected in a sample from the subject; or predicting a non-toxic response to the therapy when bacteria of one or more of the genera or species Bacteroides fragilis, Vampirovibrio, Tyzzerella, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans is detected in a sample from the subject.
- the disclosure relates to methods for predicting a response to combination immune checkpoint inhibitor therapy in a subject having cancer, the method comprising: detecting a microbial profile in a sample obtained from the subject; predicting a toxic response to the therapy when a favorable microbial profile is detected in a sample from the subject; or predicting a non-toxic response to the therapy when a non-favorable microbial profile is detected in a sample from the subject.
- a toxic-response comprises one or more irAEs.
- a toxic response comprises grade 3 or higher adverse events.
- a toxic response comprises one or more of interstitial pneumonia, colitis, hypothyroidism, liver dysfunction, skin rash, vitiligo, hypophysitis, type 1 diabetes, renal dysfunction, myasthenia gravis, neuropathy, myositis, and uveitis.
- a toxic response excludes one or more of interstitial pneumonia, colitis, hypothyroidism, liver dysfunction, skin rash, vitiligo, hypophysitis, type 1 diabetes, renal dysfunction, myasthenia gravis, neuropathy, myositis, and uveitis is excluded.
- the irAE comprises one or more of interstitial pneumonia, colitis, hypothyroidism, liver dysfunction, skin rash, vitiligo, hypophysitis, type 1 diabetes, renal dysfunction, myasthenia gravis, neuropathy, myositis, and uveitis.
- one or more of interstitial pneumonia, colitis, hypothyroidism, liver dysfunction, skin rash, vitiligo, hypophysitis, type 1 diabetes, renal dysfunction, myasthenia gravis, neuropathy, myositis, and uveitis is excluded.
- the methods exclude treatment of colitis and/or exclude patients diagnosed with or having colitis.
- a subject is predicted to be a non-responder to CICB when one or more of Robertkochia marina, Adlerrcreutizia equolifaciens, Lawsonia intracellularis, or Lactobacillus satsumensis is detected in a biological sample from the subject.
- the disclosure relates to methods of treating cancer in a subject comprising (1) first administering to the subject a composition comprising an isolated or purified population of bacteria comprising at least one bacterial species belonging to a genus or species selected from the group consisting of Flavonifractor, Dielma, Akkermansia, Alistipes, Bacteroides, Butyricimonas, Vampirovibrio, Tyzzerella, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides fmegoldii, Lactobacillus johnsonii, Parapedobacter composti, and Anaerotignum lactatifermentans ,
- the isolated or purified population of bacteria comprises at least one bacterial species belonging to the genera or species: Flavonifractor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Bacteroides stercoris, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum.
- the disclosure relates to methods for predicting a response to combination immune checkpoint inhibitor therapy in a subject having cancer, the method comprising: detecting a microbial profile in a sample obtained from the subject; predicting an effective response to the therapy when bacteria of one or more of the genera or species Bacteroides stercoris, Butyricimonas, Flavonifractor, Dielma, Alistipes, and Akkermansia muciniphila is detected in a sample from the subject; or predicting a non-effective response to the therapy when bacteria of one or more of the genera or species Lactobacillus, Bacteroides fragilis, and Prevotella is detected in a sample from the subject.
- the disclosure relates to methods for predicting a response to combination immune checkpoint inhibitor therapy in a subject having cancer, the method comprising: detecting a microbial profile in a sample obtained from the subject; predicting an effective response to the therapy when a favorable profile is detected in a sample from the subject; or predicting a non-effective response to the therapy when an unfavorable profile is detected in a sample from the subject.
- the disclosure relates to methods comprising detecting one or more of Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Dialister, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Bacteroides stercoris, Flavonifractor plautii, Butyricimonas faecihominis, Alistipes indistinctus, Dielma fastidiosa, Akkermansia muciniphila, Lactobacillus rogosae, Bacteroides fragilis, Prevotella copri, and Prevotella shahii in a subject.
- the disclosure relates to methods comprising detecting one or more of Bacteroides stercoris, Bacteroides caccae , Bacteroides intestinalis, Dialister, Bacteroides fragilis , Vampirovibrio , Tyzzerella, Flavonifractor plautii, Dielma fastidiosa, Butyricimonas faecihominis, Alistipes, Akkermansia muciniphila , Lactobacillus rogosae, Prevotella copri, Prevotella shahii, Citrobacter, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Hafniaceae, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafnia alvei, Hafnia, Roseb
- the disclosure relates to methods comprising detecting one or more of Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Dialister, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Bacteroides stercoris, Flavonifractor plautii, Dielma fastidiosa, Akkermansia muciniphila, Lactobacillus rogosae, Bacteroides fragilis, Prevotella copri, Prevotella shahii, Firmicutes, Clostridiales, Ruminococcaceae, Alistipes indistinctus, Bacteroides stercorirosoris, Clostridium lactatifermentans orus, Abyssivirga alkaniphila, Acetatifactor muris, Acetivibrio cellulolyticus, Acetivibrio ethanolgignens, Acholeplasma vituli, Achromo
- compositions comprising at least one isolated or purified population of bacteria belonging to one or more of the genera or species Flavonifr actor, Dielma, Akkermansia, Alistipes, Bacteroides, Butyricimonas, Vampirovibrio, Tyzzerella, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides finegoldii, Lactobacillus johnsonii, Parapedobacter composti, and Anaerotignum lactatifermentans.
- the composition comprises at least one isolated or purified population of bacteria belonging to one or more of the genera or species: Flavonifr actor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Bacteroides stercoris, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum.
- compositions comprising at least two isolated or purified population of bacteria belonging to one or more of the genera or species Flavonifr actor, Dielma, Akkermansia, Alistipes, Bacteroides, Butyricimonas, Vampirovibrio, Tyzzerella, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides finegoldii, Lactobacillus johnsonii, Parapedobacter composti, and Anaerotignum lactatifermentans.
- the composition comprises at least two isolated or purified populations of bacteria belonging to one or more of the genera or species: Flavonifr actor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Bacteroides stercoris, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum.
- compositions comprising an isolated or purified population of at least one, at least two, or 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 (or any derivable range therein) of Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides finegoldii, Lactobacillus johnsonii, Parapedobacter composti, Flavonifractor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Anaerotignum lactatifermentans, Bacteroides coprophilus, Bacteroides stercoris, Bacteroides caccae, Bacter
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to one or more of the OF species Flavonifractor, Bacteroides stercoris, Butyricimonas faecihominis, Dielma, Akkermansia, and Alistipes indistinctus .
- the composition excludes Bacteroides stercoris.
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to one or more of the genera Dielma and Akkermansia.
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to one or more of the genera Alistipes, Dielma, and Akkermansia. In some embodiments, the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to the Akkermansia genus. In some embodiments, the composition comprises or further comprises at least one isolated or purified population of Akkermansia muciniphila. In some embodiments, the composition comprises or further comprises a population of bacteria comprising one or more of Akkermansia muciniphila and Dielma fastidiosa but also Alistipes indistinctus.
- the bacteria of the genera Flavonifractor comprises Flavonifractor plautii.
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to one or more of the genera or species Bacteroides fragilis, Vampirovibrio, Tyzzerella, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans.
- the composition comprises or further comprises at least one isolated or purified population of Bacteroides intestinalis.
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to phylum Firmicutes, order Clostridiales, and family Ruminococcaceae .
- the composition comprises or further comprises Flavonifractor plautii and/or Dielma fastidiosa.
- the composition comprises or further comprises Bacteroides stercoris, Butyricimonas faecihominis, Flavonifractor plautii, Dielma fastidiosa, Alistipes indistinctus, and Akkermansia muciniphila [0024]
- the composition comprises less than 1 x 10 5 , 1 x 10 4 , 1 x 10 3 , or l x lO 2 CFU or cells (or any derivable range therein) of bacteria classified as Firmicutes , Clostridiales , and Ruminococcaceae .
- the composition comprises less than l x lO 5 , l x lO 4 , l x lO 3 , or l x lO 2 CFU or cells (or any derivable range therein) of bacteria belonging to the family Ruminococcaceae , Clostridiaceae , Lachnospiraceae , Micrococcaceae , and/or Veilonellaceae .
- the cancer is a skin cancer.
- the cancer is basal-cell skin cancer, squamous-cell skin cancer, melanoma, dermatofibrosarcoma protuberans, Merkel cell carcinoma, Kaposi’s sarcoma, keratoacanthoma, spindle cell tumors, sebaceous carcinomas, microcystic adnexal carcinoma, Paget’s disease of the breast, atypical fibroxanthoma, leiomyosarcoma, or angiosarcoma.
- the cancer is melanoma.
- the melanoma is metastatic melanoma, Lentigo Maligna, Lentigo Maligna Melanoma, Superficial Spreading Melanoma, Nodular Melanoma, Acral Lentiginous Melanoma, Cutaneous Melanoma, or Desmoplastic Melanoma.
- the cancer comprises Cutaneous Melanoma.
- the cancer comprises recurrent cancer. In some embodiments, the cancer comprises recurrent metastatic cancer. In some embodiments, the cancer comprises a recurrence of the cancer in the area of the primary tumor. In some embodiments, the cancer comprises a metastatic cancer. In some embodiments, the cancer comprises a stage III or IV cancer. In some embodiments, the cancer comprises a stage I or II cancer. In some embodiments, the cancer excludes stage I or II cancer.
- the method further comprises administering at least one additional anticancer treatment.
- the at least one additional anticancer treatment is surgical therapy, chemotherapy, radiation therapy, hormonal therapy, immunotherapy, small molecule therapy, receptor kinase inhibitor therapy, anti-angiogenic therapy, cytokine therapy, cryotherapy or a biological therapy.
- the additional anticancer treatment comprises a cancer treatment described herein.
- a PD-1, PDL1, or PDL2 inhibitor, (ii) a CTLA-4, B7-1, or B7-2 inhibitor, and/or at least one additional anticancer treatment is administered intratumorally, intraarterially, intravenously, intravascularly, intrapleurally, intraperitoneally, intratracheally, intrathecally, intramuscularly, endoscopically, intralesionally, percutaneously, subcutaneously, regionally, stereotactically, orally or by direct injection or perfusion.
- the route of administration is a route described herein.
- the method is defined as method of treating a cancer in a subject diagnosed with cancer.
- the method comprises or further comprises reducing or preventing one or more adverse events.
- the method comprises or further comprises reducing or preventing one or more severe adverse events.
- treating cancer comprises reducing or preventing one or more severe adverse events.
- the method is for reducing the toxicity of an immunotherapy, such as combination immune checkpoint blockade therapy.
- reducing toxicity comprises reducing adverse events.
- the adverse event or severe adverse event is further classified as an immune-related adverse event.
- the method comprises preventing or reducing immune-related adverse events.
- the adverse event is classified as a severe adverse event. In some embodiments, grade 3 or higher adverse events are prevented.
- the grade of adverse events is scored by methods known in the art, for example, scoring according to the NCI Common Terminology Criteria for Adverse Events (CTCAE).
- the subject has been determined to have an unfavorable microbial profile in the gut microbiome.
- the unfavorable profile comprises a population of bacteria comprising bacteria belonging to one or one or more of the genera Bacteroides, Dialister, Coprobacter, Intestinibacter, and Parasutterella.
- the unfavorable profile comprises a population of bacteria comprising one or more of Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Parasutterella secunda, and Dialister propionicifaciens.
- the unfavorable profile comprises Erysipelatoclostridium ramosum. In some embodiments, the unfavorable profile comprises a population of bacteria comprising bacteria belonging to one or more of the genera Lactobacillus, Bacteroides, Prevotella, Citrobacter, Clostridium, Hungateiclostridium, Eubacterium, Hafniaceae, Enterobacter, Hafiiia, Roseburia, Weissella, Bacilli, Lactobacillales, and Klebsiella.
- the unfavorable profile comprises a population of bacteria comprising one or more of Lactobacillus rogosae, Bacteroides fragilis, Prevotella copri, and Prevotella shahii.
- the unfavorable profile comprises one or more of Prevotella copri, prevotella shahii, Butyrivibrio, Blautia hydrogenotrophica, Bacteroides fragilis, Butyrivibrio corssotus, Lactobacillales, Lactobacillus, Lactobacillaceae, Lactobacillus rogosae, Clostridium saccharagumia, and Me gasphaera massiliensis.
- the unfavorable profile comprises at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 (or any derivable range thereof) of Citrobacter, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Hafniaceae, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hajhia alvei, Hajhia, Roseburia hominis, Weissella paramesenteroides, Enterobacter, Bacilli, Lactobacillales, Klebsiella aerogenes, Klebsiella, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Intestinibacter, Parasutterella secunda, Dialister propionicifaciens, Prevotella copri, prevotella shahii, But
- the unfavorable profile is further classified as a non-responsive or non-effective profile.
- a non-responsive profile refers to a microbial profile in the subject, particularly in the gut of the subject, that is present in subjects that are non-responsive to combination immune checkpoint blockade therapy.
- the non-responsive profile comprises at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 (or any derivable range thereof) of Citrobacter, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Hafniaceae, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafiiia alvei, Hafiiia, Roseburia hominis, Weissella paramesenteroides, Enterobacter, Lactobacillus rogosae, Bacilli, Lactobacillales, Klebsiella aerogenes, Klebsiella, Prevotella copri, Prevotella shahii, Butyrivibrio, Blautia hydrogenotrophica, Bacteroides fragilis,
- the unfavorable profile comprises one or more of Bacteroides stercoris, Bacteroides caccae, Negativicutes, Bacteroides intestinalis, Clostridium species, Clostridium clostridioforme, and Dialister.
- the unfavorable profile comprises at least, at most, or exactly 1, 2, 3, 4, 5, 6, or 7 (or any derivable range thereof) of Coprobacter, Intestinibacter bartletti, Intestinibacter, Parasutterella secunda, Dialister propionicifaciens, Bacteroides stercoris, Bacteroides caccae, Negativicutes, Bacteroides intestinalis, Clostridium species, Clostridium clostridioforme, and Dialister.
- the unfavorable profile is further classified as a toxicity-associated profile.
- a toxicity-associated profile refers to a microbial profile in the subject, particularly in the gut of the subject, that is present in subjects that experience toxicity in response to combination immune checkpoint blockade therapy.
- the non-responsive profile comprises at least, at most, or exactly 1, 2, 3, 4, 5, 6, or 7 (or any derivable range thereof) of Bacteroides stercoris, Bacteroides caccae, Negativicutes, Bacteroides intestinalis, Clostridium species, Clostridium clostridioforme, and Dialister.
- the bacteria belonging to the Citrobacter, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Hafniaceae, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafiiia alvei, Hafiiia, Roseburia hominis, Weissella paramesenteroides, Enterobacter, Lactobacillus rogosae, Bacilli, Lactobacillales, Klebsiella aerogenes, Klebsiella, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Intestinibacter, Parasutterella secunda, Dialister propionicifaciens, Bacteroides, Dialister, Lactobacillus, and/or Prevotella genera or species were determined to be at least 10% in relative abundance
- the term relative abundance is the percent composition of an organism of a particular kind relative to the total number of organisms in the area, such as the sample from the subject.
- the combined relative abundances of bacteria classified as one or more of Citrobacter, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Hafniaceae, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafiiia alvei, Hafiiia, Roseburia hominis, Weissella paramesenteroides, Enterobacter, Lactobacillus rogosae, Bacilli, Lactobacillales, Klebsiella aerogenes, Klebsiella, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Intestinibacter, Parasutterella secunda, Dialister propionicifaciens, Dialister, Lactobacillus, Bacteroides, and/or Prevotella were determined to be at least 2, 3, 5,
- the relative abundance of bacteria belonging to the Bacteroides genera was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein). In some embodiments, the relative abundance of bacteria belonging to the Dialister genera was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to the Lactobacillus, genera was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein). In some embodiments, the relative abundance of bacteria belonging to the Prevotella genera was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the method further comprises comparing a microbial profile determined in a sample from a patient with a control sample.
- the control may be a microbial profile derived from a sample taken from a patient that is a non-responder, a responder, experienced toxicity, or did not experience toxicity to combination immune checkpoint blockade therapy.
- the subject was or is determined to comprise an unfavorable microbial profile by analyzing the microbiome in a sample from the subject.
- the sample is a fecal sample or buccal sample.
- the analyzing comprises performing 16S ribosomal sequencing and/or metagenomics whole genome sequencing.
- the subject has previously been treated for the cancer.
- the subject has been determined to be a non-responder to the previous treatment.
- the patient has been determined to have a toxic response to the previous treatment.
- the previous treatment comprises immune checkpoint blockade monotherapy or immune checkpoint blockade combination therapy.
- the previous treatment comprises immune checkpoint blockade monotherapy comprising only one of a PD-1, PDL1, PDL2, CTLA-4, B7-1, or B7-2 inhibitor.
- the combination immune checkpoint blockade therapy comprises a combination of (i) a PD-1, PDL1, or PDL2 inhibitor and (ii) a CTLA-4, B7-1, or B7-2 inhibitor.
- (i) is a PD-1 antibody and/inhibitor (ii) is a CTLA-4 inhibitor.
- (i) is an anti -PD-1 monoclonal antibody and/or (ii) is an anti-CTLA-4 monoclonal antibody.
- (i) comprises nivolumab, pembrolizumab, or pidilizumab.
- (ii) comprises ipilimumab or tremelimumab.
- the subject has not been previously treated with immune checkpoint blockade monotherapy or combination immune checkpoint blockade therapy.
- the subject is treated with the isolated population of bacteria prior to or concurrent with the treatment in (i) and (ii). In some embodiments, the subject is treated with the isolated population of bacteria after the treatment in (i) and (ii). In some embodiments, the treatment with the microbial composition occurs at least or at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, or 24 hours or 1 2, 3, 4, 5, or 6 days or 1, 2, 3, 4, 5, or 6 weeks (or any derivable range therein) before or after treatment with the inhibitors of (i) and (ii). ).
- the treatment with the microbial composition occurs within at least or at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, or 24 hours or 1 2, 3, 4, 5, or 6 days or 1, 2, 3, 4, 5, or 6 weeks (or any derivable range therein) of treatment with the inhibitors of (i) and (ii).
- the purified population of bacteria comprises bacteria from at least two genera or species, and wherein the ratio of the two bacteria is 1 : 1.
- the purified population of bacteria comprises bacteria from at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 16, 20, 30, 40, or 50 (or any derivable range therein) different families, genera, or species of bacteria.
- the ratio of one family, genera, or species of bacteria to another family, genera, or species of bacteria present in the composition is at least, at most, or exactly 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 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, 1:95, 1:100, 1:150, 1:200, 1:250, 1:300, 1:350, 1:400, 1:450, 1:500, 1:600, 1:700, 1:800, 1:900, 1:1000, 1:1500, 1:2000, 1:2500, 1:3000, 1:3500, 1:4000, 1:4500, 1:5000, 1:1550, 1:6000, 1:6500, 1:7000, 1:7500, 1:8000, 1:8500, 1:9000, 1:9500,
- the compositions provide for an alpha diversity of at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20.
- Methods of calculating alpha diversity are known in the art. For example, taxonomic alpha-diversity of samples can be estimated using the Inverse Simpson Index, which is described in Example 1.
- the compositions are administered in an effective amount.
- the effective amount comprises an amount that provides for an an alpha diversity of at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 (or any derivable range therein) in the subject.
- the bacteria belonging to the genera or species Flavonifractor, Dielma, Akkermansia, Alistipes, Bacteroides, Butyricimonas, Vampirovibrio, Tyzzerella, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacdlus secaliphdus, Bacteroides finegoldii, Lactobacillus johnsonii, Parapedobacter composti, and Anaerotignum lactatifermentans are administered in an amount of at least, at most, or exactly lxlO 3 , UIO 4 , UIO 5 , UIO 6 , UIO 7 , UIO 8 , I c IO 9
- the bacteria belonging to the genera or species Flavonifractor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Bacteroides stercoris, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum are administered in an amount of at least, at most, or exactly 1 c 10 3 , lxlO 4 , lxlO 5 , lxlO 6 , lxlO 7 , lxlO 8 , lxlO 9 , lxlO 10 , lxlO 11 , lxlO 12 , lxlO 13 , lxlO 14 , lxlO 15 , or lxlO 16 cells or CFU (or any derivable range therein).
- the total amount of bacteria administered is at least, at most, or exactly U10 3 , lxlO 4 , I c IO 5 , I c IO 6 , I c IO 7 , I c IO 8 , I c IO 9 , I c IO 10 , I c IO 11 , I c IO 12 , lxlO 13 , 1 x 10 14 , 1 x 10 15 , or lxlO 16 cells or CFU (or any derivable range therein).
- a particular amount of bacteria such as a particular species of bacteria may be at least, at most, or exactly in an amount of at least, at most, or exactly lxlO 3 , lxlO 4 , lxlO 5 , lxlO 6 , lxlO 7 , lxlO 8 , lxlO 9 , lxlO 10 , lxlO 11 , lxlO 12 , lxlO 13 , lxlO 14 , lxlO 15 , or lxlO 16 cells or CFU (or any derivable range therein).
- the composition may contain at least, at most, or exactly at least, at most, or exactly UIO 3 , UIO 4 , UIO 5 , UIO 6 , UIO 7 , UIO 8 , UIO 9 , UIO 10 , lxlO 11 , lxlO 12 , lxlO 13 , lxlO 14 , UIO 15 , or UIO 16 cells or CFU (or any derivable range therein) from a phylum, family, genera or species of bacteria described herein.
- the composition may contain less than at least, at most, or exactly 1 c 10 6 , 1 c 10 5 , 1 c 10 4 , 1 c 10 3 , or 1 x 10 2 cells or CFU (or any derivable range therein) from a phylum, family, genus or species of bacteria described herein.
- the method further comprises administration of an antibiotic.
- the antibiotic may be a broad-spectrum antibiotic.
- a mixture of at least 1, 2, 3, 4, or 5 antibiotics is administered.
- the antibiotics comprises ampicillin, streptomycin, and colistin, and combinations thereof.
- the antibiotic is administered prior to the composition comprising at least one isolated or purified population of bacteria.
- the antibiotic is administered concurrent with the composition comprising at least one isolated or purified population of bacteria.
- the antibiotic is administered at least or at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, or 24 hours or 12, 3, 4, 5, or 6 days or 1, 2, 3, 4, 5, or 6 weeks (or any derivable range therein) before or after the microbial composition.
- the favorable profile comprises a population of bacteria comprising bacteria belonging to one or more of the genera Bacteroides, Vampirovibrio, and Tyzzerella.
- the favourable profile comprises a population of bacteria comprising one or more of Bacteroides fragilis, Vampirovibrio, Tyzzerella, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans.
- the favorable profile comprises a relative abundance of less than 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1% of bacteria from one or more of the phylum Firmicutes, order Clostridiales, and family Ruminococcaceae.
- the favorable profile comprises a population of bacteria comprising one or more of Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Akkermansia muciniphila, Bacteroides stercoris, Dielma fastidiosa, Firmicutes, Clostridiales, Ruminococcaceae, Flavonifractor plautii, Alistipes indistinctus, Akkermansia muciniphila, Bacteroides stercorirosoris, Clostridium lactatifermentans
- the favorable profile comprises a population of bacteria excluding one or more of Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatif ermentans, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Akkermansia muciniphila, Bacteroides stercoris, Dielma fastidiosa, Firmicutes, Clostridiales, Ruminococcaceae, Flavonifr actor plautii, Alistipes indistinctus, Akkermansia muciniphila, Bacteroides stercorirosoris, Clostridium
- the favorable profile comprises a population of bacteria comprising 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, 75, 80, 85, 90, 95, or 100 of (or any derivable range therein) Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Akkermansia muciniphila, Bacteroides stercoris, Dielma fastidiosa, Firmi cutes, Clostridiales, Rum
- the favorable profile comprises a population of bacteria comprising one or more of Parabacteroides distasonis, Fournier ella, Fournier ella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Akkermansia muciniphila, Bacteroides stercoris, Dielma fastidiosa, Firmicutes, Clostridiales, Ruminococcaceae, Flavonifractor plautii, Alistipes indistinctus, Akkermansia muciniphila, Bacteroides stercorirosoris, Clostri
- the favorable profile is further classified as a non-toxicity- associated profile.
- a non-toxic-associated profile refers to a microbial profile in the subject, particularly in the gut of the subject, that is present in subjects that do not experience toxicity, experience a low level of toxicity, or experience less than grade 3 immune related adverse in response to combination immune checkpoint blockade therapy.
- the favorable profile comprises a population of bacteria comprising bacteria belonging to one or more of the genera Dorea, Caloramator, Muricomes, Geosporobacter, Geosporobacter, Anaerotignum, Bacteroides, Butyricimonas, Flavonifractor, Dielma, Alistipes, and Akkermansia.
- the favorable profile comprises a population of bacteria comprising one or more of Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans, Bacteroides stercoris, Butyricimonas faecihominis, Flavonifractor plautii, Dielma fastidiosa, Alistipes indistinctus, and Akkermansia muciniphila.
- the favorable profile is further defined as an effective profile.
- an effective profile refers to a microbial profile in the subject, particularly in the gut of the subject, that is present in subjects that respond to combination immune checkpoint blockade therapy.
- an effective response comprises an increase in CD8+ cells in tumor samples or infiltrates.
- an effective response comprises an increase in the number and/or density of T cells or in the entropy of tumor T cell infiltrates.
- the entropy can be determined by methods known in the art and described herein. For example, Shannon entropy and Renyi entropy can been used to compare the TCR diversities between different people or between different T-cell phenotypes.
- the relative abundances of Alistipes, Bacteroides, Butyricimonas, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides fmegoldii, Lactobacillus johnsonii, ParapedobAnaerotignum lactatifermentans, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Flavonifractor, Dielma or Akkermansia combined were determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Bacteroides fragilis was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein). In some embodiments, the relative abundance of bacteria belonging to Vampirovibrio was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Tyzzerella was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein). In some embodiments, the relative abundance of bacteria belonging to Flavonifractor was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Dielma was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein). In some embodiments, the relative abundance of bacteria belonging to Akkermansia was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- a toxic response is predicted when one or more of Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Parasutterella secunda, and Dialister propionicifaciens is detected in a sample from the subject.
- a toxic response is predicted when one or more of Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Parasutterella secunda, and Dialister propionicifaciens is determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein) in relative abundance.
- the bacteria belonging to Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Parasutterella secunda, and Dialister propionicifaciens were determined to be present at a relative abundance of at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundances of Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Parasutterella secunda, and Dialister propionicifaciens combined were determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Bacteroides stercoris was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Bacteroides caccae was determined to be at least
- the relative abundance of bacteria belonging to Bacteroides intestinalis was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Dialister was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- a non-toxic response is predicted when one or more of Bacteroides fragilis, Vampirovibrio, Tyzzerella, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans is detected.
- a non-toxic response is predicted when one or more of Bacteroides fragilis, Vampirovibrio, Tyzzerella, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans is determined to be at least 2,
- the bacteria belonging to Bacteroides fragilis, Vampirovibrio, Tyzzerella, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans were determined to be present at a relative abundance of at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundances of Bacteroides fragilis, Vampirovibrio, Tyzzerella, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans combined were determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Bacteroides fragilis was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein). In some embodiments, the relative abundance of bacteria belonging to Vampirovibrio was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Tyzzerella was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- an effective response is predicted when one or more of Parabacteroides distasonis, Fournierella, Fournier ella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Bacteroides stercoris, Flavonifractor plautii, Dielma fastidiosa and Akkermansia muciniphila is detected in a sample from the subject.
- an effective response is predicted when one or more of Parabacteroides, Fournierella, Eisenbergiella, Tissierellales, Hungateiclostridium, Bacteroides, Butyricimonas, Flavonifractor, Dielma, Alistipes, and Akkermansia is detected in a sample from the subject.
- an effective response is predicted when one or more of Bacteroides stercoris, Butyricimonas faecihominis, Flavonifractor plautii, Dielma fastidiosa, Alistipes indistinctus, and Akkermansia muciniphila is detected in a sample from the subject.
- an effective response is predicted when one or more of Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Bacteroides stercoris, Butyricimonas faecihominis, Flavonifractor plautii, Dielma fastidiosa, Alistipes indistinctus, and Akkermansia muciniphila is determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein) in relative abundance.
- Hungateiclostridium thermocellum Bacteroides stercoris, Butyricimonas faecihominis, Flavonifractor plautii, Dielma fastidiosa, Alistipes indistinctus, and Akkermansia muciniphila were determined to be present at a relative abundance of at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- Hungateiclostridium thermocellum Bacteroides stercoris, Butyricimonas faecihominis, Flavonifractor plautii, Dielma fastidiosa, Alistipes indistinctus, and Akkermansia muciniphila combined were determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Bacteroides stercoris was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Flavonifractor plautii was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Dielma fastidiosa was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Akkermansia muciniphila was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Butyricimonas faecihominis was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Alistipes indistinctus was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- a non-effective response is predicted when one or more of Lactobacillus rogosae, Bacteroides fragilis, Prevotella copri, Prevotella shahii, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafnia alvei, Roseburia hominis, Weissella paramesenteroides, and Klebsiella aerogenes is detected.
- a non-effective response is predicted when one or more of Lactobacillus rogosae, Bacteroides fragilis, Prevotella copri, Prevotella shahii, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafnia alvei, Roseburia hominis, Weissella paramesenteroides, and Klebsiella aerogenes is determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein) in relative abundance.
- the relative abundances of Lactobacillus rogosae, Bacteroides fragilis, Prevotella copri, Prevotella shahii, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafnia alvei, Roseburia hominis, Weissella paramesenteroides, and Klebsiella aerogenes combined were determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Lactobacillus rogosae was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein). In some embodiments, the relative abundance of bacteria belonging to Bacteroides fragilis was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- the relative abundance of bacteria belonging to Prevotella copri was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein). In some embodiments, the relative abundance of bacteria belonging to Prevotella shahii was determined to be at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90% (or any derivable range therein).
- a favorable profile, non-toxicity-associated profile, and/or effective profile excludes bacteria from one or more of the families Ruminococcaceae, Clostridiaceae, Lachnospiraceae, Micrococcaceae, and/or Veilonellaceae or includes a relative abundance of less than 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1% (or any derivable range therein) of bacteria from one or more of the families Ruminococcaceae, Clostridiaceae, Lachnospiraceae, Micrococcaceae, and/or Veilonellaceae.
- a favorable profile, non-toxicity-associated profile, and/or effective profile excludes bacteria from one or more of the following or comprises a relative abundance of less than 30%, 25%, 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% (or any derivable range therein) of bacteria from one or more of the following: Bacteroides stercoris, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans, Bacteroides coagulans, Clostridium aldenense , Clostridium aldrichii , Clostri
- Desulfuricans Desulfovibrio idahonensis, Desulfovibrio litoralis, Desulfovibrio piger, Desulfovibrio simplex, Desulfovibrio zosterae, Desulfuromonas acetoxidans, Dethiobacter alkaliphilus AHT 1, Dethiosulfatibacter aminovorans, Dialister invisus, Dialister propionicifaciens, Dielma fastidiosa, Dietzia alimentaria 72, Dorea longicatena, Dysgonomonas gadei ATCC BAA-286, Dysgonomonas mossii, Eggerthella lenta, Eikenella corrodens, Eisenbergiella tayi, Emergencia timonensis, Enorma massiliensis phi, Enterococcus faecalis, Enterorhabdus muris, Ethanoligenens harbinense YUAN
- a non-favorable profile, toxicity-associated profile, and/or non-effective profile excludes one or more of Citrobacter, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Hafniaceae, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafhia alvei, Hafnia, Roseburia hominis, Weissella paramesenteroides, Enterobacter, Lactobacillus rogosae, Bacilli, Lactobacillales, Klebsiella aerogenes, Klebsiella, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Intestinibacter, Parasutterella secunda, Dialister propionicifaciens, Anaerotruncus colihominis, Kle
- CAG:255 Lachnospiraceae, Streptococcus pasteurianus, Lactococcus lactis, Clostridiales, Streptococcus mutans, Ruminococcaceae bacterium D16, Firmicutes bacterium CAG:102, Oscillibacter, Clostridium clostridioforme, Bacteroides massiliensis, Clostridium scindens, Parabacteroides merdae, Eubacterium sp.
- CAG:161 Ruminococcus gnavus, Clostridium clostridioforme , or includes a relative abundance of less than 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1% (or any derivable range therein) of bacteria from one or more of Citrobacter, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Hafniaceae, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafnia alvei, Hafnia, Roseburia hominis, Weissella paramesenteroides, Enterobacter, Lactobacillus rogosae, Bacilli, Lactobacillales, Klebsiella aerogenes, Klebsiella, Bacteroides intestinalis, Coprobacter, Intestinibacter bartletti, Intestini
- CAG 255, Lachnospiraceae, Streptococcus pasteurianus, Lactococcus lactis, Clostridiales, Streptococcus mutans, Ruminococcaceae bacterium D16, Firmicutes bacterium C AG: 102, Oscillibacter, Clostridium clostridioforme, Bacteroides massiliensis, Clostridium scindens, Parabacteroides merdae, Eubacterium sp. C AG: 161, Ruminococcus gnavus, and Clostridium clostridioforme .
- the microbial compositions of the disclosure exclude bacteria from one or more of the families Ruminococcaceae , Clostridiaceae , Lachnospiraceae , Micrococcaceae , and/or Veilonellaceae or includes less than lxlO 6 , lxlO 5 , lxlO 4 , lxlO 3 , or lxlO 2 cells or CFU (or any derivable range therein) of bacteria from one or more of the families Ruminococcaceae, Clostridiaceae, Lachnospiraceae, Micrococcaceae, and/or Veilonellaceae.
- the microbial compositions of the disclosure exclude bacteria from one or more of the following or comprises less than l x lO 6 , l x lO 5 , l x lO 4 , 1 x 10 3 , or 1 x 10 2 cells or CFU (or any derivable range therein) of bacteria from one or more of the following: Bacteroides coagulans, Clostridium aldenense , Clostridium aldrichii , Clostridium alkalicellulosi , Clostridium amygdalinum , Clostridium asparagiforme, Clostridium cellulosi , Clostridium citroniae , Clostridium clariflavum DSM 19732, Clostridium clostridioforme, Clostridium colinum, Clostridium fimetarium, Clostridium hiranonis, Clostridium hungatei, Clostridium hylemona
- Desulfuricans Desulfovibrio idahonensis, Desulfovibrio litoralis, Desulfovibrio piger, Desulfovibrio simplex, Desulfovibrio zosterae, Desulfuromonas acetoxidans, Dethiobacter alkaliphilus AHT 1, Dethiosulfatibacter aminovorans, Dialister invisus, Dialister propionicifaciens, Dielma fastidiosa, Dietzia alimentaria 72, Dorea longicatena, Dysgonomonas gadei ATCC BAA-286, Dysgonomonas mossii, Eggerthella lenta, Eikenella corrodens, Eisenbergiella tayi, Emergencia timonensis, Enorma massiliensis phi, Enterococcus faecalis, Enterorhabdus muris, Ethanoligenens harbinense YUAN
- the method further comprises treating the subject predicted to have a non-toxic or effective response with combination immune checkpoint blockade therapy. In some embodiments, the method further comprises treating the subject predicted to have a toxic and/or non-effective response with a composition of the disclosure. In some embodiments, the method further comprises treating the subject with a combination of (i) a PD-1, PDL1, or PDL2 inhibitor and (ii) a CTLA-4, B7-1, or B 7-2 inhibitor.
- a toxic, non-toxic, effective, or non-effective response is predicted when one or more bacteria of a phylum, order, family, genera or species described herein is determined to be at least 2%, 3%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or 90% (or any derivable range therein) in relative abundance.
- a combination of bacteria is determined to have a total relative abundance of at least 2%, 3%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or 90% (or any derivable range therein).
- the compositions of the disclosure may exclude one or more bacteria genera or species described herein or may include less than I c IO 6 , I c IO 5 , I c IO 4 , l x lO 3 , or l x lO 2 cells or CFU (or any derivable range therein) of one or more of the bacteria described herein.
- the favorable or unfavorable profiles described herein may exclude one or more bacteria described herein or may comprise a relative abundance of less than 30%, 25%, 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% (or any derivable range therein) of one or more of the bacteria described herein.
- each of the populations of bacteria is present in the composition at a concentration of at least l x lO 3 CFU.
- the composition is a live bacterial product or a live biotherapeutic product.
- the bacteria are lyophilized, freeze dried, or frozen.
- the composition is formulated for oral delivery.
- the composition formulated for oral delivery is a tablet or capsule.
- the tablet or capsule comprises an acid-resistant enteric coating.
- the composition is formulated for administration rectally, via colonoscopy, sigmoidoscopy by nasogastric tube, or enema.
- the composition is capable of being re-formulated for final delivery as comprising a liquid, a suspension, a gel, a geltab, a semisolid, a tablet, a sachet, a lozenge, a capsule, or as an enteral formulation.
- the composition is formulated for multiple administrations.
- the composition further comprises a pharmaceutically acceptable excipient.
- any limitation discussed with respect to one embodiment of the invention may apply to any other embodiment of the invention.
- any composition of the invention may be used in any method of the invention, and any method of the invention may be used to produce or to utilize any composition of the invention.
- Aspects of an embodiment set forth in the Examples are also embodiments that may be implemented in the context of embodiments discussed elsewhere in a different Example or elsewhere in the application, such as in the Summary of Invention, Detailed Description of the Embodiments, Claims, and description of Figure Legends.
- FIG. 2A-G Molecular and immune predictors of response.
- NSV Non- synonymous variant
- C Significantly copy number variant (CNV)-affected genes.
- (D) CNV landscape assessed by whole-exome sequencing (n 26 tumors), showing CNV losses and gains affecting selected genes recurrently mutated in melanoma, IFN-signaling genes and antigen processing/presentation genes.
- FIG. 3A-F Circulating T cell repertoire composition and phenotype predict toxicity.
- D Percentage of CD27+ cells within CD4+ T effectors (Teff) and (E) of CD28+ cells within CD8+ Teff in pre-treatment peripheral blood samples (Mann-Whitney tests as shown; receipt of prior immunotherapy indicated by color).
- FIG. 4A-F Gut microbiome profiles are associated with response and toxicity to CICB.
- LDA linear discriminant analysis.
- (F) Heatmap of correlation (Spearman’s rho) between key toxicity-associated or non-toxicity-associated bacterial taxa and circulating immune subsets quantitated by multiparameter flow cytometry of baseline blood samples (n 9).
- Teff T effector cells
- TCM T central memory
- TEM T effector memory
- Treg regulatory T cell.
- FIG. 5A-E Microbiome shifts with CICB are associated with tumor size.
- A MCA205 sarcoma (left panels) or RET melanoma (right panels) tumor size after 4 injections of indicated antibody (x-axis).
- mice were treated with 6 or 5 injections of anti-PD-1 and anti-CTLA-4 respectively, or the relevant isotype control.
- Beta-diversity of fecal microbiota according to time (orange: before treatment initiation, blue: 48h after 2 injections, red: 48h after 5 injections) in MCA205 (left panel) and RET (right panel).
- C Beta-diversity coloured according to tumor size in MCA205 (left panel) and RET (right panel), intensity of purple indicates increasing tumor size.
- ANOSIM defines the separation of the groups; the p value defines the significance of such separation after 999 permutations of the samples.
- FIG. D Venn diagram showing the overlay of bacterial species prior to treatment initiation, shared or not shared between tumor models, corresponding to responders to CICB (left panel). Flavonifractor plautii preferentially found in R mice (right panel) which is shared with melanoma patients ( Figure 4D-E).
- E Time course of relative abundances in mice of taxa detected prior to therapy that were found to be differentially-abundant between R (in blue) and NR (in red) in both patients and murine tumor types, contrasting species-level variations in abundance over time.
- FIG. 6A-I Microbiota-dependent ileitis and colitis in tumor- bearing mice.
- A-B Representative micrographs of ilei from MCA205-bearing mice treated with isotype control, CICB or CICB+ATB followed by recolonization with Erysipelatoclostridium ramosum or Bacteroides intestinalis (scale bar: 50 pm).
- Detailed scoring of H&E-stained ileum of MCA205 tumor bearing mice treated with isotype control or CICB, or antibiotics alone or followed by monocolonisation with Bacteroides intestinalis (BI), Dielma fastidiosa (DF), or E. ramosum (ER), n 9-22/group.
- Beta diversity (Bray-Curtis dissimilarity) of the fecal microbiota assessed in 16S rDNA sequencing of gene amplicons colored according to score of colonic inflammatory infiltrates in RET tumor bearing mice, intensity of purple indicating increasing inflammatory infiltrate score (left panel).
- Relative abundance of Bacteroides intestinalis and Vampirovibrio chlorellavorus which are shared between mice and patients (right panel) contrasting abundance by response (NR, red; R blue) and hosts exhibiting colon toxicity from those who did not (high inflammatory score, green; low inflammatory score, yellow).
- FIG. 7A-B relating to FIG. 1 and Table 3 : Patient treatment outcomes.
- B Swimmer plot indicating per-patient best overall response (color shading), duration of best overall response (length of shaded portion of bar), and duration of overall follow-up (shaded+unshaded portion of bar), measured from the day of first dose of combined immune checkpoint blockade therapy.
- FIG. 8A-E relating to FIG. 2: Molecular markers of combined immune checkpoint blockade.
- D Barplot of number of genes affected by copy number losses by chromosome demonstrating dominant burden within chromosomes 5, 10 and 15.
- E genome-wide SGOL scores show enrichment of CNVs affecting chromosome 10
- FIG. 9A-E relating to FIG. 2 and FIG. 3 : Immune markers of CICB response and toxicity.
- FIG. 10A-E relating to FIG. 4: Fecal microbiome characterestics associated with CICB response and toxicity.
- B-C Volcano plots of pairwise comparisons of OTUs (all taxonomic levels) by dichotomized response categories (B) or development of high-grade toxicity (C).
- FIG. 11A-D relating to FIG. 5. Kinetics of therapy -induced shifts in intestinal bacteria composition and correlations with tumor sizes.
- A, C LEfSe plot of discriminating species 48 hours after 2 (A) or 5 (C) mAb injections (orange: isotype control antibody, purple: anti-PD-1 antibody, green: CICB).
- Linear discriminant analysis (LDA) was coupled with effect size measurements to represent species differentially present among each treatment group.
- FIG. 12A Microbiota-dependent inflammatory cytokine patterns of ilei and colons in tumor- bearing mice.
- FIG. 13A-F Gut microbiome influences responses to anti -PD 1 therapy in late-stage melanoma patients through beneficial changes in the anti-tumor immune infiltrate
- C) Spearman correlation matrix between pro-R gut bacteria and immune infiltrate within the tumor (n 15) as quantified by immunohistochemistry.
- D Experimental design of studies in germ-free mice.
- FIG. 15A-D Molecular and immune predictors of response
- CNV Copy number loss burden
- binarized best overall response p ⁇ 0.05, Mann-Whitney test.
- 16A-C Characterization of the gut microbiome by 16S rRNA sequencing.
- A) Stacked bar plot depicting microbial composition of each analyzed fecal sample from the cutaneous and unknown primary cohort at the order level (n 40).
- FIG. 19A-B Association between circulating immune populations and most differentially enriched bacterial taxa by phenotype.
- TEff T effector cells
- TCM T central memory
- TEM T effector memory
- Treg regulatory T cell.
- FIG. 20A-C Gut microbial associations with CICB response.
- PLS-DA Partial Least Squares Discriminant Analysis
- LV latent variable.
- VIP Variable importance score barplot highlighting bacterial species present at TO significantly enriched (*p ⁇ 0.05, **/; ⁇ 0 01 , ***/; ⁇ 0.001 ) in the group defined by the bar color compared to the group defined by the border color, indicating mice that were eventually tumor-free versus tumor-bearing following CICB treatment (RET and MCA205 models).
- the bar color depicts the cohort with the highest mean relative abundance for a defined species, whilst the border color indicates the cohort with the lowest mean relative abundance.
- An absent border indicates mean relative abundance of zero in the compared cohort(s).
- C Pearson correlation of the relative abundance of Parabacteroides distasonis (at TO, T2, and T5) in CICB treated mice with tumor size at T5.
- TEff T effector cells
- TCM T central memory
- TEM T effector memory
- Treg regulatory T cell.
- FIG. 22A-G Gut microbiome profiles are associated with response and toxicity to CICB.
- B Heat map of log2-fold change of pro-inflammatory immune gene expression (CICB-treated vs isotype) in ilea and colons of MCA205 and RET tumor-bearing mice ⁇ antibiotics (left panel).
- C Relative ileal Illb expression in tumor-bearing mice treated with isotype/CICB ⁇ antibiotics. Mann-Whitney test.
- n 10-22 mice/group.
- mice were classified according to low (score 0 or 1) vs high toxicity (score 2, 3 or 4), Chi-square test. Ileal Illb expression analyzed using Mann-Whitney test.
- G Ileal toxicity scores following CICB (or isotype) treatment comparing mice colonized with B.intestinalis-high versus -low donor FMT. *p ⁇ 0.05, **p ⁇ 0.01 , ***p ⁇ 0.001
- FIG. 24A-D Immune markers of CICB response and toxicity.
- A,B and CD8+ Teff (C,D) from a separate CICB-treated cohort, in pre-treatment peripheral blood samples (p values from Mann-Whitney tests as shown).
- FIG. 25 Prior immunotherapy and toxicity-associated T cell phenotype.
- Stacked bar plot (above) and contingency table (below) depicting the relationship between exposure to prior immunotherapy and risk of developing >Gr3 irAE following combination anti-CTLA-4 and anti -PD- 1 blockade in patients with cutaneous or unknown primary melanomas (p 0.028, Fisher’s exact test).
- FIG. 27A-D Microbiome and response in murine models.
- B Microbial alpha diversity (upper panel) and Partial Least Square Discriminant Analysis (PLS-DA) of fecal microbial beta diversity (lower panel) in fecal samples taken before treatment initiation (TO, orange), 48 hours after 2 injections (T2, blue) and 48 hours after 5 injections (T5, red) of CICB or isotype control in MCA205 (left panel) and RET (right panel) tumor-bearing mice assessed by sequencing of 16S rRNA gene amplicons using the Shannon index.
- Mann-Whitney U test *p ⁇ 0.05, **/K0.01.
- ANOSIM and PERMANOVA define the separation of the groups; p values define the significance of group separation after 999 permutations of the samples.
- FIG. 28A-H Representative micrographs of ilea from MCA205 and RET- bearing mice treated with isotype or CICB (scale bar: 50 pm, magnification: 100X) (left panel).
- C Heatmap of correlation (Pearson’s rho) between colonic infiltrate score and relative abundance of taxa at TO, T2 and T5 for RET in combined discovery and validation cohort data. Red represents a positive correlation, whilst blue represents a negative correlation with colonic infiltrate score.
- Beta diversity ordination (Bray-Curtis dissimilarity) of the fecal microbiota assessed by sequencing of 16S rRNA gene amplicons colored according to score of colonic inflammatory infiltrate in RET tumor-bearing mice, intensity of purple indicates increasing inflammatory infiltrate score in the discovery (left panel) and validation (right panel) cohort.
- Bacterial relative abundances and colonic inflammatory infiltrate were both normalized and standardized before correlation analysis. Pearson correlation and associated p-values comparing each principal component with inflammatory infiltrate are indicated.
- CICB immune checkpoint blockade
- CICB cytotoxic T lymphocyte antigen-4
- PD-1 programmed death receptor-1
- the term“antibody” refers to an immunoglobulin, derivatives thereof which maintain specific binding ability, and proteins having a binding domain which is homologous or largely homologous to an immunoglobulin binding domain. These proteins may be derived from natural sources, or partly or wholly synthetically produced.
- An antibody may be monoclonal or polyclonal.
- the antibody may be a member of any immunoglobulin class, including any of the human classes: IgG, IgM, IgA, IgD, and IgE.
- Antibodies used with the methods and compositions described herein are generally derivatives of the IgG class.
- the term antibody also refers to antigen-binding antibody fragments.
- antibody fragments include, but are not limited to, Fab, Fab', F(ab')2, scFv, Fv, dsFv diabody, and Fd fragments.
- Antibody fragments may be produced by any means.
- the antibody fragment may be enzymatically or chemically produced by fragmentation of an intact antibody, it may be recombinantly produced from a gene encoding the partial antibody sequence, or it may be wholly or partially synthetically produced.
- the antibody fragment may optionally be a single chain antibody fragment. Alternatively, the fragment may comprise multiple chains which are linked together, for instance, by disulfide linkages.
- the fragment may also optionally be a multimolecular complex.
- a functional antibody fragment retains the ability to bind its cognate antigen at comparable affinity to the full antibody.
- the term“monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, e.g., the individual antibodies comprising the population are identical except for possible mutations, e.g., naturally occurring mutations, that may be present in minor amounts.
- the modifier“monoclonal” indicates the character of the antibody as not being a mixture of antibodies with different epitope specificities.
- such a monoclonal antibody typically includes an antibody comprising a polypeptide sequence that binds a target, wherein the target-binding polypeptide sequence was obtained by a process that includes the selection of a single target binding polypeptide sequence from a plurality of polypeptide sequences.
- the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of hybridoma clones, phage clones, or recombinant DNA clones.
- a selected target binding sequence can be further altered, for example, to improve affinity for the target, to humanize the target binding sequence, to improve its production in cell culture, to reduce its immunogenicity in vivo, to create a multispecific antibody, etc., and that an antibody comprising the altered target binding sequence is also a monoclonal antibody of this disclosure.
- each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen.
- monoclonal antibody preparations are advantageous in that they are typically uncontaminated by other immunoglobulins.
- composition refers to molecular entities and compositions that do not produce an adverse, allergic, or other untoward reaction when administered to an animal, such as a human, as appropriate.
- preparation of a pharmaceutical composition comprising an antibody or additional active ingredient will be known to those of skill in the art in light of the present disclosure.
- animal e.g., human
- preparations should meet sterility, pyrogenicity, general safety, and purity standards as required by FDA Office of Biological Standards.
- “pharmaceutically acceptable carrier” includes any and all aqueous solvents (e.g., water, alcoholic/aqueous solutions, saline solutions, parenteral vehicles, such as sodium chloride, and Ringer's dextrose), non-aqueous solvents (e.g., propylene glycol, polyethylene glycol, vegetable oil, and injectable organic esters, such as ethyloleate), dispersion media, coatings, surfactants, antioxidants, preservatives (e.g., antibacterial or antifungal agents, anti-oxidants, chelating agents, and inert gases), isotonic agents, absorption delaying agents, salts, drugs, drug stabilizers, gels, binders, excipients, disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, fluid and nutrient replenishers, such like materials and combinations thereof, as would be known to one of ordinary skill in the art.
- aqueous solvents e.g., water
- unit dose refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the therapeutic composition calculated to produce the desired responses discussed herein in association with its administration, i.e., the appropriate route and treatment regimen.
- the quantity to be administered depends on the effect desired.
- the actual dosage amount of a composition of the present embodiments administered to a patient or subject can be determined by physical and physiological factors, such as body weight, the age, health, and sex of the subject, the type of disease being treated, the extent of disease penetration, previous or concurrent therapeutic interventions, idiopathy of the patient, the route of administration, and the potency, stability, and toxicity of the particular therapeutic substance.
- a dose may also comprise from about 1 pg/kg/body weight to about 1000 mg/kg/body weight (this such range includes intervening doses) or more per administration, and any particular dose derivable therein.
- a range derivable from the numbers listed herein a range of about 5 pg/kg/body weight to about 100 mg/kg/body weight, about 5 pg/kg/body weight to about 500 mg/kg/body weight, etc., can be administered.
- the practitioner responsible for administration will, in any event, determine the concentration of active ingredient(s) in a composition and appropriate dose(s) for the individual subject.
- A“population” of bacteria may refer to a composition of bacteria comprising a single species, or a mixture of different species?
- immune checkpoint refers to various stimulatory, co-stimulatory and inhibitory signals that regulate the breadth and magnitude of the immune response that are essential for the maintenance of immune homeostasis and host survival.
- Known immune checkpoint proteins comprise CTLA-4, PD-1 and its ligands PD-L1 and PD-L2 and in addition LAG-3, BTLA, B7H3, B7H4, TIM3, KIR.
- LAG3, BTLA, B7H3, B7H4, TIM3, and KIR are recognized in the art to constitute immune checkpoint pathways similar to the CTLA-4 and PD-1 dependent pathways (see e.g. Pardoll, 2012, Nature Rev Cancer 12:252-264; Mellman et ah, 2011, Nature 480:480- 489).
- inhibitor refers to a molecule that may be organic or inorganic, a protein, polypeptide, antibody, small molecule, carbohydrate, or nucleic acid that blocks or decreases one or more functions of the protein.
- the inhibitor may be a direct inhibitor that acts by directly interacting with the protein or an indirect inhibitor that may not interact directly with the protein but still inhibits one or more functions of the protein.
- an“immune checkpoint inhibitor” refers to any compound inhibiting the function of an immune checkpoint protein. Inhibition includes reduction of function and full blockade.
- the immune checkpoint protein is a human immune checkpoint protein.
- the immune checkpoint protein inhibitor in particular is an inhibitor of a human immune checkpoint protein.
- Subject and“patient” refer to either a human or non-human, such as primates, mammals, and vertebrates. In particular embodiments, the subject is a human.
- the terms “treat,” “treatment,” “treating,” “ameliorating”, or “amelioration” when used in reference to a disease, disorder or medical condition refer to therapeutic treatments for a condition, wherein the object is to reverse, alleviate, ameliorate, inhibit, slow down or stop the progression or severity of a symptom or condition.
- the term “treating” includes reducing or alleviating at least one adverse effect or symptom of a condition.
- Treatment is generally“effective” if one or more symptoms or clinical markers are reduced. Alternatively, treatment is“effective” if the progression of a condition is reduced or halted.
- treatment includes not just the improvement of symptoms or markers, but also a cessation or at least slowing of progress or worsening of symptoms that would be expected in the absence of treatment.
- Beneficial or desired clinical results include, but are not limited to, alleviation of one or more symptom(s), diminishment of extent of the deficit, stabilized (i.e., not worsening) state of a tumor or malignancy, delay or slowing of tumor growth and/or metastasis, and an increased lifespan as compared to that expected in the absence of treatment.
- the “gut microbiota” or “gut microbiome” designates the population of microorganisms (and their genomes) living in the intestine of a subject.
- alpha diversity is a measure of intra-sample diversity and refers to the distribution and assembly patterns of all microbiota within samples and is calculated as a scalar value for each sample.
- Beta diversity is a term for inter-sample diversity, and involves the comparison of samples to each which provides a measure of the distance or dissimilarity between each sample pair.
- relative amount which can also be designated as the “relative abundance” is defined as the number of bacteria of a particular taxonomic level (from phylum to species) as a percentage of the total number of bacteria of that level in a biological sample. This relative abundance can be assessed, for example, by measuring the percentage of 16S rRNA gene sequences present in the sample which are assigned to these bacteria. It can be measured by any appropriate technique known by the skilled artisan, such as 454 pyrosequencing of the specific bacterial 16S rRNA gene markers or quantitative PCR of a specific gene.
- a“good responder to a treatment” also called a“responder” or “responsive” patient or in other words a patient who“benefits from” this treatment, refers to a patient who is affected with a cancer and who shows or will show a clinically significant relief in the cancer after receiving this treatment.
- a“bad responder” or“non-responder” is one who does not or will not show a clinically significant relief in the cancer after receiving this treatment.
- the decreased response to treatment may be assessed according to the standards recognized in the art, such as immune- related response criteria (irRC), WHO or RECIST criteria.
- a responsive patient may be one identified as having a complete response (CR), which is disappearance of all target lesions or a partial response (PR), which is at least a 30% decrease in the sum of the longest diameter (LD) target lesions (taking as reference the baseline sum LD), and a non-responsive patient may be identified as having stable disease (SD), which corresponds to neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for progressive disease (PD) (taking as reference the smallest LD sum since the treatment started) or progressive disease (PD), which is at least a 20% increase in the sum of the LD of target lesions (taking as reference the smallest sum LD recorded since the treatment started or the appearance of one or more new lesions).
- CR complete response
- PR partial response
- SD stable disease
- PD progressive disease
- PD progressive disease
- isolated encompasses a bacterium or other entity or substance that has been (1) separated from at least some of the components with which it was associated when initially produced (whether in nature or in an experimental setting), and/or (2) produced, prepared, purified, and/or manufactured by the hand of man.
- Isolated bacteria may be separated from at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or more of the other components with which they were initially associated.
- isolated bacteria are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure.
- a substance is“pure” if it is substantially free of other components.
- the terms“purify,”“purifying” and“purified” refer to a bacterium or other material that has been separated from at least some of the components with which it was associated either when initially produced or generated (e.g., whether in nature or in an experimental setting), or during any time after its initial production.
- a bacterium or a bacterial population may be considered purified if it is isolated at or after production, such as from a material or environment containing the bacterium or bacterial population, and a purified bacterium or bacterial population may contain other materials up to about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or above about 90% and still be considered“isolated.”
- purified bacteria and bacterial populations are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure.
- the one or more bacterial types present in the composition can be independently purified from one or more other bacteria produced and/or present in the material or environment containing the bacterial type.
- Bacterial compositions and the bacterial components thereof are generally purified from residual habitat products.
- the term“determined to have” refers to a patient population that has been tested and reported as having a certain outcome, such as microbiome status.
- “lower,”“reduced,”“reduction,”“decrease,” or“inhibit” are all used herein generally to mean a decrease by a statistically significant amount.
- “lower,”’’reduced,”“reduction,“decrease,” or“inhibit” means a decrease by at least 10% as compared to a reference level, for example a decrease by at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% decrease (i.e. absent level as compared to a reference sample), or any decrease between 10- 100% as compared to a reference level.
- the terms“increased,”’’increase,”“enhance,” or“activate” are all used herein to generally mean an increase by a statically significant amount; for the avoidance of any doubt, the terms“increased,”“increase,”“enhance,” or“activate” means an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10- fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level.
- the term“comprising,” which is synonymous with“including,”“containing,” or “characterized by,” is inclusive or open-ended and does not exclude additional, unrecited elements or method steps.
- the term“consisting essentially of’ includes the active ingredients recited, excludes any other active ingredients, but does not exclude any pharmaceutical excipients or other components that are not therapeutically active.
- references to“the method” includes one or more methods, and/or steps of the type described herein and/or which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.
- essentially free in terms of a specified component, is used herein to mean that none of the specified component has been purposefully formulated into a composition and/or is present only as a contaminant or in trace amounts. The total amount of the specified component resulting from any unintended contamination of a composition is therefore well below 0.01%. Most preferred is a composition in which no amount of the specified component can be detected with standard analytical methods.
- the terms“or” and“and/or” are utilized to describe multiple components in combination or exclusive of one another.
- “x, y, and/or z” can refer to“x” alone,“y” alone,“z” alone,“x, y, and z,”“(x and y) or z,”“x or (y and z),” or“x or y or z.” It is specifically contemplated that x, y, or z may be specifically excluded from an embodiment.
- the phrase“effective amount” or“therapeutically effective amount” or“sufficient amount” means a dosage of a drug or agent sufficient to produce a desired result.
- the desired result can be a decrease in tumor size, a decrease in the rate of growth of cancer cells, a decrease in metastasis, increase in CD8+ T lymphocytes in the tumor or tumor immune infiltrate, an increase in CD45+, CD3+/CD20+/CD56+, CD68+ and/or HLA-DR+ cells in the tumor, an increase in CD3, CD8, PD1, FoxP3, Granzyme B and/or PD-L1 expression in a tumor immune infiltrate, a decrease in RORyT expression in a tumor immune infiltrate, an increase of effector CD4+, CD8+ T, monocytes and/or myeloid dendritic cell in the systemic circulation or the peripheral blood, a decrease of B cells, regulatory T cells and/or myeloid derived suppressor cells in the systemic circulation or the peripheral blood of the subject or
- Embodiments relate to a combination treatment comprising a) a CTLA-4, B7-1, and/or B7-2 inhibitor and b) a PD-1, PDL1, and/or PDL2 inhibitor.
- the treatment is with a combination of an inhibitor that blocks the interaction between CTLA-4 and B7-1 or B7-2 and an inhibitor that blocks the interaction of PD-1 and PDL1 or PDL2.
- the immune checkpoint inhibitor is a small molecule inhibitor. In some embodiments of any one of the methods, compositions or kits provided, the immune checkpoint inhibitor is a polypeptide that inhibits an immune checkpoint pathway. In some embodiments of any one of the methods, compositions or kits provided, the inhibitor is a fusion protein. In some embodiments of any one of the methods, compositions or kits provided, the immune checkpoint inhibitor is an antibody. In some embodiments of any one of the methods, compositions or kits provided, the antibody is a monoclonal antibody.
- PD-1 can act in the tumor microenvironment where T cells encounter an infection or tumor. Activated T cells upregulate PD-1 and continue to express it in the peripheral tissues. Cytokines such as IFN-gamma induce the expression of PDL1 on epithelial cells and tumor cells. The main role of PD-1 is to limit the activity of effector T cells in the periphery and prevent excessive damage to the tissues during an immune response. Inhibitors of the disclosure may block one or more functions of PD-1 and/or PDL1 activity.
- Alternative names for“PD-1” include CD279 and SLEB2.
- Alternative names for “PDL1” include B7-H1, B7-4, CD274, and B7-H.
- Alternative names for“PDL2” include B7- DC, Btdc, and CD273.
- PD-1, PDL1, and PDL2 are human PD-1, PDL1 and PDL2.
- the PD-1 inhibitor is a molecule that inhibits the binding of PD-1 to its ligand binding partners.
- the PD-1 ligand binding partners are PDL1 and/or PDL2.
- a PDL1 inhibitor is a molecule that inhibits the binding of PDL1 to its binding partners.
- PDL1 binding partners are PD-1 and/or B7-1.
- the PDL2 inhibitor is a molecule that inhibits the binding of PDL2 to its binding partners.
- a PDL2 binding partner is PD-1.
- the inhibitor may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
- Exemplary antibodies are described in U.S. Patent Nos. 8,735,553, 8,354,509, and 8,008,449, all incorporated herein by reference.
- Other PD-1 inhibitors for use in the methods and compositions provided herein are known in the art such as described in U.S. Patent Application Nos. US2014/0294898, US2014/022021, and US2011/0008369, all incorporated herein by reference.
- the PD-1 inhibitor is an anti-PD-1 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody).
- the anti-PD- 1 antibody is selected from the group consisting of nivolumab, pembrolizumab, and pidilizumab.
- the PD-1 inhibitor is an immunoadhesin (e.g, an immunoadhesin comprising an extracellular or PD-1 binding portion of PDL1 or PDL2 fused to a constant region (e.g, an Fc region of an immunoglobulin sequence).
- the PDL1 inhibitor comprises AMP- 224.
- Nivolumab also known as MDX-1106-04, MDX- 1106, ONO-4538, BMS-936558, and OPDIVO ® , is an anti-PD-1 antibody described in W02006/121168.
- Pembrolizumab also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA ® , and SCH-900475, is an anti-PD-1 antibody described in W02009/114335.
- Pidilizumab also known as CT-011, hBAT, or hBAT-1, is an anti-PD-1 antibody described in W02009/101611.
- AMP-224 also known as B7-DCIg, is a PDL2-Fc fusion soluble receptor described in W02010/027827 and WO2011/066342.
- Additional PD-1 inhibitors include MEDI0680, also known as AMP-514, and REGN2810.
- the immune checkpoint inhibitor is a PDL1 inhibitor such as Durvalumab, also known as MEDI4736, atezolizumab, also known as MPDL3280A, avelumab, also known as MSB00010118C, MDX-1105, BMS-936559, or combinations thereof.
- the immune checkpoint inhibitor is a PDL2 inhibitor such as rHIgM12B7.
- the antibody described herein (such as an anti-PD-1 antibody, an anti-PDLl antibody, or an anti-PDL2 antibody) further comprises a human or murine constant region.
- the human constant region is selected from the group consisting of IgGl, IgG2, IgG2, IgG3, and IgG4.
- the human constant region is IgGl.
- the murine constant region is selected from the group consisting of IgGl, IgG2A, IgG2B, and IgG3.
- the antibody has reduced or minimal effector function.
- the minimal effector function results from production in prokaryotic cells.
- the minimal effector function results from an“effector-less Fc mutation” or aglycosylation.
- the inhibitor comprises the heavy and light chain CDRs or VRs of nivolumab, pembrolizumab, or pidilizumab. Accordingly, in one embodiment, the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of nivolumab, pembrolizumab, or pidilizumab, and the CDR1, CDR2 and CDR3 domains of the VL region of nivolumab, pembrolizumab, or pidilizumab.
- the antibody competes for binding with and/or binds to the same epitope on PD-1, PDL1, or PDL2 as the above- mentioned antibodies.
- the antibody has at least about 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range therein) variable region amino acid sequence identity with the above-mentioned antibodies.
- an antibody used herein can be aglycosylated.
- Glycosylation of antibodies is typically either N-linked or O-linked.
- N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue.
- the tripeptide sequences asparagine- X-serine and asparagine-X-threonine, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain.
- X is any amino acid except proline
- O-linked glycosylation refers to the attachment of one of the sugars N-acetylgalactosamine, galactose, or xylose to a hydroxy amino acid, most commonly serine or threonine, although 5-hydroxyproline or 5-hydroxylysine may also be used.
- Removal of glycosylation sites from an antibody is conveniently accomplished by altering the amino acid sequence such that one of the above-described tripeptide sequences (for N-linked glycosylation sites) is removed. The alteration may be made by substitution of an asparagine, serine or threonine residue within the glycosylation site another amino acid residue (e.g ., glycine, alanine or a conservative substitution).
- the antibody or antigen binding fragment thereof may be made using methods known in the art, for example, by a process comprising culturing a host cell containing nucleic acid encoding any of the previously described anti-PDLl, anti-PD-1, or anti-PDL2 antibodies or antigen-binding fragment in a form suitable for expression, under conditions suitable to produce such antibody or fragment, and recovering the antibody or fragment.
- CTLA-4 cytotoxic T-lymphocyte-associated protein 4
- CD152 cytotoxic T-lymphocyte-associated protein 4
- the complete cDNA sequence of human CTLA-4 has the Genbank accession number LI 5006.
- CTLA-4 is found on the surface of T cells and acts as an“off’ switch when bound to B7-1 (CD80) or B7-2 (CD86) on the surface of antigen-presenting cells.
- CTLA4 is a member of the immunoglobulin superfamily that is expressed on the surface of Helper T cells and transmits an inhibitory signal to T cells.
- CTLA4 is similar to the T-cell co-stimulatory protein, CD28, and both molecules bind to B7-1 and B7-2 on antigen-presenting cells.
- CTLA-4 transmits an inhibitory signal to T cells, whereas CD28 transmits a co-stimulatory signal.
- Intracellular CTLA-4 is also found in regulatory T cells and may be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules.
- Inhibitors of the disclosure may block one or more functions of CTLA-4, B7-1, and/or B7-2 activity. In some embodiments, the inhibitor blocks the CTLA-4 and B7-1 interaction. In some embodiments, the inhibitor blocks the CTLA-4 and B7-2 interaction.
- the immune checkpoint inhibitor is an anti-CTLA-4 antibody (e.g ., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
- an anti-CTLA-4 antibody e.g ., a human antibody, a humanized antibody, or a chimeric antibody
- an antigen binding fragment thereof e.g a human antibody, a humanized antibody, or a chimeric antibody
- an immunoadhesin e.g., a human antibody, a humanized antibody, or a chimeric antibody
- an antigen binding fragment thereof e.g., an immunoadhesin, a fusion protein, or oligopeptide.
- Anti-human-CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art.
- art recognized anti-CTLA-4 antibodies can be used.
- the anti- CTLA-4 antibodies disclosed in: US 8, 119,129, WO 01/14424, WO 98/42752; WO 00/37504 (CP675,206, also known as tremelimumab; formerly ticilimumab), U.S. Patent No. 6,207,156; Hurwitz et al ., 1998; can be used in the methods disclosed herein.
- the teachings of each of the aforementioned publications are hereby incorporated by reference.
- Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used.
- a humanized CTLA-4 antibody is described in International Patent Application No. W02001/014424, W02000/037504, and U.S. Patent No. 8,017,114; all incorporated herein by reference.
- a further anti-CTLA-4 antibody useful as a checkpoint inhibitor in the methods and compositions of the disclosure is ipilimumab (also known as 10D1, MDX- 010, MDX- 101, and Yervoy®) or antigen binding fragments and variants thereof (see, e.g. , WOO 1/14424).
- the inhibitor comprises the heavy and light chain CDRs or VRs of tremelimumab or ipilimumab. Accordingly, in one embodiment, the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of tremelimumab or ipilimumab, and the CDR1, CDR2 and CDR3 domains of the VL region of tremelimumab or ipilimumab.
- the antibody competes for binding with and/or binds to the same epitope on PD-1, B7-1, or B7-2 as the above- mentioned antibodies. In another embodiment, the antibody has at least about 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range therein) variable region amino acid sequence identity with the above-mentioned antibodies.
- CTLA-4 Other molecules for modulating CTLA-4 include soluble CTLA-4 ligands and receptors such as described in U.S. Patent Nos. US5844905, US5885796 and International Patent Application Nos. WO1995001994 and WO1998042752; all incorporated herein by reference, and immunoadhesins such as described in U.S. Patent No. US8329867, incorporated herein by reference.
- the disclosure relates to methods comprising detecting one or more of Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Dialister, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Flavonifractor plautii, Dielma fastidiosa, Butyricimonas faecihominis, Alistipes, Akkermansia muciniphila, Lactobacillus rogosae, Prevotella copri, Prevotella shahii, Citrobacter, Clostridium hylemonae, Hungateiclostridium aldrichii, Citrobacter rodentium, Eubacterium sulci, Hafniaceae, Citrobacter freundii, Eubacterium halii, Enterobacter cloacae, Hafinia alvei, Hafnia, Roseburia hominis,
- the disclosure relates to methods comprising detecting one or more of Bacteroides stercoris, Bacteroides caccae, Bacteroides intestinalis, Dialister, Bacteroides fragilis, Vampirovibrio, Tyzzerella, Bacteroides stercoris, Flavonifractor plautii, Dielma fastidiosa, Akkermansia muciniphila, Lactobacillus rogosae, Bacteroides fragilis, Prevotella copri, Prevotella shahii, Firmicutes, Clostridiales, Ruminococcaceae, Alistipes indistinctus, Bacteroides stercorirosoris, Clostridium lactatifermentans orus, Abyssivirga alkaniphila, Acetatifactor muris, Acetivibrio cellulolyticus, Acetivibrio ethanolgignens, Acholeplasma vituli, Achromo
- compositions comprising at least one isolated or purified population of bacteria belonging to one or more of the genera or species Flavonifr actor, Dielma, Akkermansia, Alistipes, Bacteroides, Butyricimonas, Vampirovibrio, Tyzzerella, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides finegoldii, Lactobacillus johnsonii, Parapedobacter composti, and Anaerotignum lactatifermentans.
- the composition comprises at least one isolated or purified population of bacteria belonging to one or more of the genera or species: Flavonifr actor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Bacteroides stercoris, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum.
- compositions comprising at least two isolated or purified population of bacteria belonging to one or more of the genera or species Flavonifr actor, Dielma, Akkermansia, Alistipes, Bacteroides, Butyricimonas, Vampirovibrio, Tyzzerella, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides finegoldii, Lactobacillus johnsonii, Parapedobacter composti, and Anaerotignum lactatifermentans.
- the composition comprises at least two isolated or purified populations of bacteria belonging to one or more of the genera or species: Flavonifr actor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Bacteroides stercoris, Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Bacteroides coprophilus, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum.
- compositions comprising an isolated or purified population of at least one, at least two, or 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 (or any derivable range therein) of Parabacteroides distasonis, Fournierella, Fournierella massiliensis, Eisenbergiella tayi, Tissierellales, Hungateiclostridium thermocellum, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Geosporobacter, Prevotella paludivivens, Lactobacillus secaliphilus, Bacteroides finegoldii, Lactobacillus johnsonii, Parapedobacter composti, Flavonifractor, Bacteroides, Butyricimonas, Dielma, Akkermansia, Alistipes, Anaerotignum lactatifermentans, Bacteroides coprophilus, Bacteroides stercoris, Bacteroides caccae, Bacter
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to one or more of the OF species Flavonifractor, Bacteroides stercoris, Butyricimonas faecihominis, Dielma, Akkermansia, and Alistipes indistinctus .
- the composition excludes Bacteroides stercoris.
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to one or more of the genera Dielma and Akkermansia.
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to one or more of the genera Alistipes, Dielma, and Akkermansia. In some embodiments, the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to the Akkermansia genus. In some embodiments, the composition comprises or further comprises at least one isolated or purified population of Akkermansia muciniphila. In some embodiments, the composition comprises or further comprises a population of bacteria comprising one or more of Akkermansia muciniphila and Dielma fastidiosa but also Alistipes indistinctus.
- the bacteria of the genera Flavonifractor comprises Flavonifractor plautii.
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to one or more of the genera or species Bacteroides fragilis, Vampirovibrio, Tyzzerella, Dorea formicigenerans, Caloramator coolhaasi, Muricomes, Muricomes intestini, Geosporobacter, Geosporobacter subterraneus, Anaerotignum lactatifermentans.
- the composition comprises or further comprises at least one isolated or purified population of Bacteroides intestinalis.
- the composition comprises or further comprises at least one isolated or purified population of bacteria belonging to phylum Firmicutes, order Clostridiales, and family Ruminococcaceae .
- the composition comprises or further comprises Flavonifractor plautii and/or Dielma fastidiosa.
- the composition comprises or further comprises Bacteroides stercoris, Butyricimonas faecihominis, Flavonifractor plautii, Dielma fastidiosa, Alistipes indistinctus, and Akkermansia muciniphila [0141]
- the composition comprises less than 1 x 10 5 , 1 x 10 4 , 1 x 10 3 , or l x lO 2 CFU or cells (or any derivable range therein) of bacteria classified as Firmicutes , Clostridiales , and Ruminococcaceae .
- the composition comprises less than l x lO 5 , l x lO 4 , l x lO 3 , or l x lO 2 CFU or cells (or any derivable range therein) of bacteria belonging to the family Ruminococcaceae , Clostridiaceae , Lachnospiraceae , Micrococcaceae , and/or Veilonellaceae .
- Ruminococcaceae Clostridiaceae
- Lachnospiraceae Lachnospiraceae
- Micrococcaceae and/or Veilonellaceae .
- the present disclosure also provides a pharmaceutical composition comprising one or more microbial populations as described above and at, for example, in the summary of the invention.
- the bacterial species therefore are present in the dose form as live bacteria, whether in dried, lyophilized, or sporulated form. This may be preferably adapted for suitable administration; for example, in tablet or powder form, potentially with an enteric coating, for oral treatment.
- the composition is formulated for oral administration.
- Oral administration may be achieved using a chewable formulation, a dissolving formulation, an encapsulated/coated formulation, a multi-layered lozenge (to separate active ingredients and/or active ingredients and excipients), a slow release/timed release formulation, or other suitable formulations known to persons skilled in the art.
- the word“tablet” is used herein, the formulation may take a variety of physical forms that may commonly be referred to by other terms, such as lozenge, pill, capsule, or the like.
- compositions of the present disclosure are preferably formulated for oral administration
- other routes of administration can be employed, however, including, but not limited to, subcutaneous, intramuscular, intradermal, transdermal, intraocular, intraperitoneal, mucosal, vaginal, rectal, and intravenous.
- the desired dose of the composition of the present disclosure may be presented in multiple (e.g ., two, three, four, five, six, or more) sub-doses administered at appropriate intervals throughout the day.
- the disclosed composition may be prepared as a capsule.
- the capsule i.e the carrier
- the capsule may be a hollow, generally cylindrical capsule formed from various substances, such as gelatin, cellulose, carbohydrate or the like.
- the disclosed composition may be prepared as a suppository.
- the suppository may include but is not limited to the bacteria and one or more carriers, such as polyethylene glycol, acacia, acetylated monoglycerides, camauba wax, cellulose acetate phthalate, com starch, dibutyl phthalate, docusate sodium, gelatin, glycerin, iron oxides, kaolin, lactose, magnesium stearate, methyl paraben, pharmaceutical glaze, povidone, propyl paraben, sodium benzoate, sorbitan monooleate, sucrose talc, titanium dioxide, white wax and coloring agents.
- carriers such as polyethylene glycol, acacia, acetylated monoglycerides, camauba wax, cellulose acetate phthalate, com starch, dibutyl phthalate, docusate sodium, gelatin, glycerin, iron oxides, kaolin, lactose, magnesium
- the disclosed microbial modulator composition may be prepared as a tablet.
- the tablet may include the bacteria and one or more tableting agents (i.e., carriers), such as dibasic calcium phosphate, stearic acid, croscarmellose, silica, cellulose and cellulose coating.
- tableting agents i.e., carriers
- the tablets may be formed using a direct compression process, though those skilled in the art will appreciate that various techniques may be used to form the tablets.
- the disclosed microbial modulator composition may be formed as food or drink or, alternatively, as an additive to food or drink, wherein an appropriate quantity of bacteria is added to the food or drink to render the food or drink the carrier.
- the microbial modulator compositions of the present disclosure may further comprise one or more prebiotics known in the art, such as lactitol, inulin, or a combination thereof.
- the microbial modulator composition may further comprise a food or a nutritional supplement effective to stimulate the growth of bacteria of the order Clostri diales present in the gastrointestinal tract of the subject.
- the nutritional supplement is produced by a bacterium associated with a healthy human gut microbiome.
- the current methods and compositions of the disclosure may include one or more additional therapies known in the art and/or described herein.
- the additional therapy comprises an additional cancer treatment. Examples of such treatments are described herein.
- the additional therapy comprises a further cancer immunotherapy.
- Cancer immunotherapy (sometimes called immuno-oncology, abbreviated IO) is the use of the immune system to treat cancer.
- Immunotherapies can be categorized as active, passive or hybrid (active and passive). These approaches exploit the fact that cancer cells often have molecules on their surface that can be detected by the immune system, known as tumor-associated antigens (TAAs); they are often proteins or other macromolecules (e.g. carbohydrates).
- TAAs tumor-associated antigens
- Passive immunotherapies enhance existing anti-tumor responses and include the use of monoclonal antibodies, lymphocytes and cytokines. Immunotherapies are known in the art, and some are described below. 1. Inhibition of co-stimulatory molecules
- the immunotherapy comprises an inhibitor of a co stimulatory molecule.
- the inhibitor comprises an inhibitor of B7-1 (CD80), B7-2 (CD86), CD28, ICOS, 0X40 (TNFRSF4), 4-1BB (CD137; TNFRSF9), CD40L (CD40LG), GITR (TNFRSF18), and combinations thereof.
- Inhibitors include inhibitory antibodies, polypeptides, compounds, and nucleic acids.
- Dendritic cell therapy provokes anti-tumor responses by causing dendritic cells to present tumor antigens to lymphocytes, which activates them, priming them to kill other cells that present the antigen.
- Dendritic cells are antigen presenting cells (APCs) in the mammalian immune system. In cancer treatment they aid cancer antigen targeting.
- APCs antigen presenting cells
- One example of cellular cancer therapy based on dendritic cells is sipuleucel-T, marketed as Provenge(R).
- One method of inducing dendritic cells to present tumor antigens is by vaccination with autologous tumor lysates or short peptides (small parts of protein that correspond to the protein antigens on cancer cells). These peptides are often given in combination with adjuvants (highly immunogenic substances) to increase the immune and anti-tumor responses.
- adjuvants include proteins or other chemicals that attract and/or activate dendritic cells, such as granulocyte macrophage colony-stimulating factor (GM-CSF).
- Dendritic cells can also be activated in vivo by making tumor cells express GM- CSF. This can be achieved by either genetically engineering tumor cells to produce GM-CSF or by infecting tumor cells with an oncolytic virus that expresses GM-CSF.
- Another strategy is to remove dendritic cells from the blood of a patient and activate them outside the body.
- the dendritic cells are activated in the presence of tumor antigens, which may be a single tumor-specific peptide/protein or a tumor cell lysate (a solution of lysed tumor cells). These cells (with optional adjuvants) are infused and provoke an immune response.
- Dendritic cell therapies include the use of antibodies that bind to receptors on the surface of dendritic cells. Antigens can be added to the antibody and can induce the dendritic cells to mature and provide immunity to the tumor. Dendritic cell receptors such as TLR3, TLR7, TLR8 or CD40 have been used as antibody targets. 3. CAR-T cell therapy
- Chimeric antigen receptors are engineered receptors that combine a new, non-MHC restricted specificity with an immune cell to target cancer cells. Typically, these receptors graft the specificity of a monoclonal antibody onto a T cell. The receptors are called chimeric because they are fused of parts from different sources.
- CAR-T cell therapy refers to a treatment that uses such transformed cells for therapeutic purposes, such as cancer, for example.
- CAR-T cell design involves recombinant receptors that combine antigen-binding and T-cell activating functions.
- the general premise of CAR-T cells is to artificially generate T-cells targeted to markers found on cancer cells.
- scientists can remove T-cells from a person, genetically alter them, and put them back into the patient for them to attack the cancer cells.
- CAR-T cells create a link between an extracellular ligand recognition domain to an intracellular signaling molecule which in turn activates T cells.
- the extracellular ligand recognition domain is usually a single-chain variable fragment (scFv) derived from an antibody.
- scFv single-chain variable fragment
- Exemplary CAR-T therapies include Tisagenlecleucel (Kymriah(R)) and Axicabtagene ciloleucel (Yescarta(R)).
- the CAR-T therapy targets CD 19.
- Cytokines are proteins produced by many types of cells present within a tumor. They can modulate immune responses. The tumor often employs them to allow it to grow and reduce the immune response. These immune-modulating effects allow them to be used as drugs to provoke an immune response. Two commonly used cytokines are interferons and interleukins.
- Interferons are produced by cells of the immune system. They are usually involved in anti-viral response, but also have impact on cancer. They are classified in three groups: type I (IFNa and PTNGb), type II (IFNy) and type III (IFNI).
- Interleukins have an array of immune system effects.
- IL-2 is an exemplary interleukin cytokine therapy. 5.
- Adoptive T-cell therapy is an exemplary interleukin cytokine therapy.
- T cells are found in blood and tissue and usually activate when they find foreign pathogens. Specifically, they activate when the T cell receptor (TCR) encounter cells that display parts of foreign proteins on their surface antigens. These can be either infected cells, or antigen presenting cells (APCs). They are found in normal tissue and in tumor tissue, where they are known as tumor infiltrating lymphocytes (TILs). They are activated by the presence of APCs such as dendritic cells that present tumor antigens. Although these cells can attack the tumor, the environment within the tumor is highly immunosuppressive, preventing immune-mediated tumor death.
- TCR T cell receptor
- APCs antigen presenting cells
- TILs tumor infiltrating lymphocytes
- T-cells specific to a tumor antigen can be removed from a tumor sample (TILs) or filtered from blood. Subsequent activation and culturing is performed ex vivo, with the resulting preparation of activated T cells reinfused. Activation can take place by exposing the T cells to tumor antigens.
- TILs tumor sample
- Activation can take place by exposing the T cells to tumor antigens.
- the additional therapy comprises an oncolytic virus.
- An oncolytic virus is a virus that preferentially infects and kills cancer cells. As the infected cancer cells are destroyed by oncolysis, they release new infectious virus particles or virions to help destroy the remaining tumor. Oncolytic viruses are thought not only to cause direct destruction of the tumor cells, but also to stimulate host anti-tumor immune responses for long-term immunotherapy
- the additional therapy comprises polysaccharides.
- Certain compounds found in mushrooms primarily polysaccharides, can up-regulate the immune system and may have anti-cancer properties.
- beta-glucans such as lentinan have been shown in laboratory studies to stimulate macrophage, NK cells, T cells and immune system cytokines and have been investigated in clinical trials as immunologic adjuvants.
- the additional therapy comprises neoantigen administration.
- Many tumors express mutations. These mutations potentially create new targetable antigens (neoantigens) for use in T cell immunotherapy.
- the presence of CD8+ T cells in cancer lesions, as identified using RNA sequencing data, is higher in tumors with a high mutational burden.
- the level of transcripts associated with cytolytic activity of natural killer cells and T cells positively correlates with mutational load in many human tumors.
- the additional therapy comprises a chemotherapy.
- chemotherapeutic agents include (a) Alkylating Agents, such as nitrogen mustards (e.g., mechlorethamine, cylophosphamide, ifosfamide, melphalan, chlorambucil), ethylenimines and methylmelamines (e.g., hexamethylmelamine, thiotepa), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomustine, chlorozoticin, streptozocin) and triazines (e.g., dacarbazine), (b) Antimetabolites, such as folic acid analogs (e.g., methotrexate), pyrimidine analogs (e.g., 5-fluorouracil, floxuridine, cytarabine, azauridine) and purine analogs
- nitrogen mustards e.g.
- Cisplatin has been widely used to treat cancers such as, for example, metastatic testicular or ovarian carcinoma, advanced bladder cancer, head or neck cancer, cervical cancer, lung cancer or other tumors. Cisplatin is not absorbed orally and must therefore be delivered via other routes such as, for example, intravenous, subcutaneous, intratumoral or intraperitoneal injection. Cisplatin can be used alone or in combination with other agents, with efficacious doses used in clinical applications including about 15 mg/m 2 to about 20 mg/m 2 for 5 days every three weeks for a total of three courses being contemplated in certain embodiments.
- the amount of cisplatin delivered to the cell and/or subject in conjunction with the construct comprising an Egr-1 promoter operably linked to a polynucleotide encoding the therapeutic polypeptide is less than the amount that would be delivered when using cisplatin alone.
- Other suitable chemotherapeutic agents include antimicrotubule agents, e.g., Paclitaxel (“Taxol”) and doxorubicin hydrochloride (“doxorubicin”).
- Doxorubicin is absorbed poorly and is preferably administered intravenously.
- appropriate intravenous doses for an adult include about 60 mg/m 2 to about 75 mg/m 2 at about 21-day intervals or about 25 mg/m 2 to about 30 mg/m 2 on each of 2 or 3 successive days repeated at about 3 week to about 4 week intervals or about 20 mg/m 2 once a week.
- the lowest dose should be used in elderly patients, when there is prior bone- marrow depression caused by prior chemotherapy or neoplastic marrow invasion, or when the drug is combined with other myelopoietic suppressant drugs.
- Nitrogen mustards are another suitable chemotherapeutic agent useful in the methods of the disclosure.
- a nitrogen mustard may include, but is not limited to, mechlorethamine (HN2), cyclophosphamide and/or ifosfamide, melphalan (L-sarcolysin), and chlorambucil.
- Cyclophosphamide (CYTOXAN®) is available from Mead Johnson and NEOSTAR® is available from Adria), is another suitable chemotherapeutic agent.
- Suitable oral doses for adults include, for example, about 1 mg/kg/day to about 5 mg/kg/day
- intravenous doses include, for example, initially about 40 mg/kg to about 50 mg/kg in divided doses over a period of about 2 days to about 5 days or about 10 mg/kg to about 15 mg/kg about every 7 days to about 10 days or about 3 mg/kg to about 5 mg/kg twice a week or about 1.5 mg/kg/day to about 3 mg/kg/day.
- the intravenous route is preferred.
- the drug also sometimes is administered intramuscularly, by infiltration or into body cavities.
- Additional suitable chemotherapeutic agents include pyrimidine analogs, such as cytarabine (cytosine arabinoside), 5-fluorouracil (fluorouracil; 5-FU) and floxuridine (fluorode-oxyuridine; FudR).
- 5-FU may be administered to a subject in a dosage of anywhere between about 7.5 to about 1000 mg/m2. Further, 5-FU dosing schedules may be for a variety of time periods, for example up to six weeks, or as determined by one of ordinary skill in the art to which this disclosure pertains.
- Gemcitabine diphosphate (GEMZAR®, Eli Lilly & Co.,“gemcitabine”), another suitable chemotherapeutic agent, is recommended for treatment of advanced and metastatic pancreatic cancer, and will therefore be useful in the present disclosure for these cancers as well.
- the amount of the chemotherapeutic agent delivered to the patient may be variable.
- the chemotherapeutic agent may be administered in an amount effective to cause arrest or regression of the cancer in a host, when the chemotherapy is administered with the construct.
- the chemotherapeutic agent may be administered in an amount that is anywhere between 2 Z to 10,000 z fold less than the chemotherapeutic effective dose of the chemotherapeutic agent.
- chemotherapeutics of the disclosure can be tested in vivo for the desired therapeutic activity in combination with the construct, as well as for determination of effective dosages.
- suitable animal model systems prior to testing in humans, including, but not limited to, rats, mice, chicken, cows, monkeys, rabbits, etc.
- In vitro testing may also be used to determine suitable combinations and dosages, as described in the examples.
- the additional therapy or prior therapy comprises radiation, such as ionizing radiation.
- ionizing radiation means radiation comprising particles or photons that have sufficient energy or can produce sufficient energy via nuclear interactions to produce ionization (gain or loss of electrons).
- An exemplary and preferred ionizing radiation is an x-radiation. Means for delivering x-radiation to a target tissue or cell are well known in the art.
- the amount of ionizing radiation is greater than 20 Grays (Gy) and is administered in one dose. In some embodiments, the amount of ionizing radiation is 18 Gy and is administered in three doses. In some embodiments, the amount of ionizing radiation is at least, at most, or exactly 2, 4, 6, 8, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 40 Gy (or any derivable range therein).
- the ionizing radiation is administered in at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 does (or any derivable range therein).
- the does may be about 1, 4, 8, 12, or 24 hours or 1, 2, 3, 4, 5, 6, 7, or 8 days or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, or 16 weeks apart, or any derivable range therein.
- the amount of IR may be presented as a total dose of IR, which is then administered in fractionated doses.
- the total dose is 50 Gy administered in 10 fractionated doses of 5 Gy each.
- the total dose is 50-90 Gy, administered in 20-60 fractionated doses of 2-3 Gy each.
- the total dose of IR is at least, at most, or about 20, 21, 22, 23, 24, 25, 26, 27,
- the total dose is administered in fractionated doses of at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 20, 25, 30, 35, 40, 45, or 50 Gy (or any derivable range therein. In some embodiments, at least, at most, or exactly 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
- fractionated doses are administered (or any derivable range therein).
- at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 (or any derivable range therein) fractionated doses are administered per day.
- at least, at most, or exactly 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, or 30 (or any derivable range therein) fractionated doses are administered per week.
- Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed and may be used in conjunction with other therapies, such as the treatment of the present embodiments, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy, and/or alternative therapies.
- Tumor resection refers to physical removal of at least part of a tumor.
- treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically-controlled surgery (Mohs’ surgery).
- a cavity may be formed in the body.
- Treatment may be accomplished by perfusion, direct injection, or local application of the area with an additional anti-cancer therapy. Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. These treatments may be of varying dosages as well.
- agents may be used in combination with certain aspects of the present embodiments to improve the therapeutic efficacy of treatment.
- additional agents include agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adhesion, agents that increase the sensitivity of the hyperproliferative cells to apoptotic inducers, or other biological agents. Increases in intercellular signaling by elevating the number of GAP junctions would increase the anti-hyperproliferative effects on the neighboring hyperproliferative cell population.
- cytostatic or differentiation agents can be used in combination with certain aspects of the present embodiments to improve the anti-hyperproliferative efficacy of the treatments.
- Inhibitors of cell adhesion are contemplated to improve the efficacy of the present embodiments.
- Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin. It is further contemplated that other agents that increase the sensitivity of a hyperproliferative cell to apoptosis, such as the antibody c225, could be used in combination with certain aspects of the present embodiments to improve the treatment efficacy.
- the therapy provided herein comprises administration of a combination of immune checkpoint inhibitors and a microbial modulator.
- the therapy may be administered in any suitable manner known in the art.
- an immune checkpoint inhibitor e.g PD-1 inhibitor and/or CTLA-4 inhibitor
- the microbial modulator may be administered sequentially (at different times) or concurrently (at the same time).
- the immune checkpoint inhibitors are in a separate composition as the microbial modulator.
- the immune checkpoint inhibitor is in the same composition as the microbial modulator.
- Embodiments of the disclosure relate to compositions and methods comprising one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor in combination with one or more of a PD- 1, PDL1, and/or PDL2 inhibitor.
- the immune checkpoint inhibitors may be administered in one composition or in more than one composition such as 2 compositions, 3 compositions, or 4 compositions.
- Various combinations of the inhibitors may be employed, for example, a CTLA-4, B7-1, or B7-2 inhibitor is“A” and a PD-1, PDL1, or PDL2 inhibitor is“B”:
- the method comprises administration of one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor at the same time as one or more of a PD-1, PDL1, and/or PDL2 inhibitor.
- one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor is administered prior to one or more of a PD-1, PDL1, and/or PDL2 inhibitor.
- one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor is administered at least, at most, or exactly 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) prior to one or more of a PD-1, PDL1, and/or PDL2 inhibitor.
- one or more of a PD-1, PDL1, and/or PDL2 inhibitor is administered prior to one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor.
- one or more of a PD-1, PDL1, and/or PDL2 inhibitor is administered at least, at most, or exactly 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) prior to one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor.
- one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor is administered within 1, 2, 3, 4, 5, 6, 7, days or 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, or 20 weeks (or any derivable range therein) of administration of one or more of a PD-1, PDL1, and/or PDL2 inhibitor.
- the microbial modulator composition is administered prior to the immune checkpoint inhibitors. In some embodiments, the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) prior to the immune checkpoint inhibitors. In some embodiments, at least 1, 2, 3, 4, 5, 6, or 7 doses (or any derivable range therein) of the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) prior to the immune checkpoint inhibitors.
- the microbial modulator composition is administered after the immune checkpoint inhibitors. In some embodiments, the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) after the immune checkpoint inhibitors or after at least one of the immune checkpoint inhibitors or after at least 2 of the immune checkpoint inhibitors.
- At least 1, 2, 3, 4, 5, 6, or 7 doses (or any derivable range therein) of the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) afterthe immune checkpoint inhibitors or after at least one of the immune checkpoint inhibitors or after at least 2 of the immune checkpoint inhibitors.
- the combination therapy of the disclosure also includes a microbial modulator composition.
- the microbial modulator composition is administered prior to one or more of a PD-1, PDL1, and/or PDL2 inhibitor.
- the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) prior to one or more of a PD-1, PDL1, and/or PDL2 inhibitor.
- 1, 2, 3, 4, 5, 6, or 7 doses (or any derivable range therein) of the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) prior to one or more of a PD-1, PDL1, and/or PDL2 inhibitor.
- the microbial modulator composition is administered after one or more of a PD-1, PDL1, and/or PDL2 inhibitor.
- the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) after one or more of a PD-1, PDL1, and/or PDL2 inhibitor or after at least one of, or at least two of a PD-1, PDL1, or PDL2.
- at least 1, 2, 3, 4, 5, 6, or 7 doses (or any derivable range therein) of the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or
- the combination therapy of the disclosure also includes a microbial modulator composition.
- the microbial modulator composition is administered prior to one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor.
- the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) prior to one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor.
- At least 1, 2, 3, 4, 5, 6, or 7 doses (or any derivable range therein) of the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) prior to one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor.
- the microbial modulator composition is administered after one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor.
- the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) after one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor or after at least one of, or at least two of a CTLA-4, B7-1, or B7-2 inhibitor.
- At least 1, 2, 3, 4, 5, 6, or 7 doses (or any derivable range therein) of the microbial modulator composition is administered at least, at most, or exactly 1, 2, 3, 5, 6, 12, 24 hours or 2, 3, 4, 6, 8, 10, days or 2, 3, 4, 5, 6, 7, or 8 weeks (or any derivable range therein) after one or more of a CTLA-4, B7-1, and/or B7-2 inhibitor or after at least one of, or at least two of a CTLA-4, B7-
- the microbial modulator composition is formulated for oral administration.
- the skilled artisan knows a variety of formulas which can encompass living or killed microorganisms and which can present as food supplements (e.g ., pills, tablets and the like) or as functional food such as drinks or fermented yogurts.
- the immune checkpoint inhibitors and microbial modulator may be administered by the same route of administration or by different routes of administration.
- the immune checkpoint inhibitor is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally.
- the microbial modulator is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally.
- the immune checkpoint inhibitors are administered intravenously and the microbial modulator is administered orally.
- An effective amount of the immune checkpoint inhibitor and the microbial modulator may be administered for prevention or treatment of disease.
- the appropriate dosage of immune checkpoint inhibitor and/or the microbial modulator may be determined based on the type of disease to be treated, severity and course of the disease, the clinical condition of the individual, the individual's clinical history and response to the treatment, and the discretion of the attending physician.
- I I, 12, 13, 14, or 15 isolated or purified populations of bacteria of the microbial modulator compositions of the embodiments that is administered to a human will be at least about 1 c 10 3 colony forming units (CFU) of bacteria or at least about lxlO 4 lxlO 5 , lxlO 6 , lxlO 7 , lxlO 8 , lxlO 9 , lxlO 10 , lxlO 11 , lxlO 12 , lxlO 13 , lxlO 14 , lxlO 15 CFU (or any derivable range therein).
- CFU colony forming units
- a single dose will contain an amount of bacteria (such as a specific bacteria or species, genus, or family described herein) of at least, at most, or exactly 1 10 4 , lxlO 5 , lxlO 6 , lxlO 7 , lxlO 8 , U10 9 , UIO 10 , lxlO 11 , U10 12 , U10 13 , U10 14 , U10 15 or greater than lxlO 15 CFU (or any derivable range therein) of a specified bacteria.
- bacteria such as a specific bacteria or species, genus, or family described herein
- a single dose will contain at least, at most, or exactly UIO 4 , UIO 5 , UIO 6 , lxlO 7 , lxlO 8 , lxlO 9 , lxlO 10 , lxlO 11 , U10 12 , U10 13 , U10 14 , U10 15 or greater than U10 15 CFU (or any derivable range therein) of total bacteria.
- the bacteria are provided in spore form or as sporulated bacteria.
- the concentration of spores of each isolated or purified population of bacteria is at least, at most, or exactly 1 c 10 4 , 1 c 10 5 , 1 c 10 6 , 1 c 10 7 , 1 c 10 8 , lxlO 9 , lxlO 10 , lxlO 11 , lxlO 12 , lxlO 13 , lxlO 14 , lxlO 15 or greater than lxlO 15 (or any derivable range therein) viable bacterial spores per gram of composition or per administered dose.
- the composition comprises or the method comprises administration of at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 40, or 50 (or any derivable range therein) of different bacterial species, different bacterial genus, or different bacterial family.
- the therapeutically effective or sufficient amount of each of the at least one isolated or purified population of bacteria or each of the at least two, 3, 4, 5, 6, 7, 8, 9, 1011, 12, 13, 14, or 15 isolated or purified populations of bacteria of the microbial modulator compositions of the embodiments that is administered to a human will be at least about lxlO 3 cells of bacteria or at least about lxlO 4 , 1 c 10 5 , lxlO 6 , lxlO 7 , lxlO 8 , lxlO 9 , lxlO 10 , lxlO 11 , lxlO 12 , lxlO 13 , lxlO 14 , lxlO 15 cells (or any derivable range therein).
- a single dose will contain an amount of bacteria (such as a specific bacteria or species, genus, or family described herein) of at least, at most, or exactly 1 c 10 4 , 1 c 10 5 , 1 c 10 6 , lxlO 7 , lxlO 8 , lxlO 9 , lxlO 10 , lxlO 11 , lxlO 12 , lxlO 13 , lxlO 14 , lxlO 15 or greater than lxlO 15 cells (or any derivable range therein) of a specified bacteria.
- bacteria such as a specific bacteria or species, genus, or family described herein
- a single dose will contain at least, at most, or exactly 1 c 10 4 , 1 c 10 5 , 1 c 10 6 , 1 c 10 7 , 1 c 10 8 , 1 c 10 9 , 1 c 10 10 , lxlO 11 , lxlO 12 , lxlO 13 , lxlO 14 , lxlO 15 or greater than lxlO 15 cells (or any derivable range therein) of total bacteria.
- the bacteria are provided in spore form or as sporulated bacteria.
- the concentration of spores of each isolated or purified population of bacteria is at least, at most, or exactly lxlO 4 , lxlO 5 , lxlO 6 , lxlO 7 , lxlO 8 , lxlO 9 , lxlO 10 , lxlO 11 , lxlO 12 , lxlO 13 , 1 c 10 14 , 1 10 15 or greater than l x lO 15 (or any derivable range therein) viable bacterial spores per gram of composition or per administered dose.
- the composition comprises or the method comprises administration of at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 40, or 50 (or any derivable range therein) of different bacterial species, different bacterial genus, or different bacterial family.
- Intratumoral injection, or injection into the tumor vasculature is specifically contemplated for discrete, solid, accessible tumors.
- Local, regional or systemic administration also may be appropriate.
- the volume to be administered will be about 4- 10 ml (in particular 10 ml), while for tumors of ⁇ 4 cm, a volume of about 1-3 ml will be used (in particular 3 ml).
- Multiple injections delivered as single dose comprise about 0.1 to about 0.5 ml volumes.
- adenoviral particles may advantageously be contacted by administering multiple injections to the tumor.
- Treatment regimens may vary as well, and often depend on tumor type, tumor location, disease progression, and health and age of the patient. Obviously, certain types of tumors will require more aggressive treatment, while at the same time, certain patients cannot tolerate more taxing protocols. The clinician will be best suited to make such decisions based on the known efficacy and toxicity (if any) of the therapeutic formulations.
- the tumor being treated may not, at least initially, be resectable.
- Treatments with therapeutic viral constructs may increase the resectability of the tumor due to shrinkage at the margins or by elimination of certain particularly invasive portions. Following treatments, resection may be possible. Additional treatments subsequent to resection will serve to eliminate microscopic residual disease at the tumor site.
- the treatments may include various“unit doses.”
- Unit dose is defined as containing a predetermined-quantity of the therapeutic composition.
- the quantity to be administered, and the particular route and formulation, is within the skill of determination of those in the clinical arts.
- a unit dose need not be administered as a single injection but may comprise continuous infusion over a set period of time.
- a unit dose comprises a single administrable dose.
- the quantity to be administered depends on the treatment effect desired.
- An effective dose is understood to refer to an amount necessary to achieve a particular effect. In the practice in certain embodiments, it is contemplated that doses in the range from 10 mg/kg to 200 mg/kg can affect the protective capability of these agents.
- doses include doses of about 0.1, 0.5, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, and 200, 300, 400, 500, 1000 pg/kg, mg/kg, pg/day, or mg/day or any range derivable therein.
- doses can be administered at multiple times during a day, and/or on multiple days, weeks, or months.
- the therapeutically effective or sufficient amount of the immune checkpoint inhibitor, such as an antibody and/or microbial modulator, that is administered to a human will be in the range of about 0.01 to about 50 mg/kg of patient body weight whether by one or more administrations.
- the inhibitor used is about 0.01 to about 45 mg/kg, about 0.01 to about 40 mg/kg, about 0.01 to about 35 mg/kg, about 0.01 to about 30 mg/kg, about 0.01 to about 25 mg/kg, about 0.01 to about 20 mg/kg, about 0.01 to about 15 mg/kg, about 0.01 to about 10 mg/kg, about 0.01 to about 5 mg/kg, or about 0.01 to about 1 mg/kg administered daily, for example.
- the inhibitor is administered at 15 mg/kg.
- an inhibitor described herein is administered to a subject at a dose of about 100 mg, about 200 mg, about 300 mg, about 400 mg, about 500 mg, about 600 mg, about 700 mg, about 800 mg, about 900 mg, about 1000 mg, about 1100 mg, about 1200 mg, about 1300 mg or about 1400 mg on day 1 of 21-day cycles.
- the dose may be administered as a single dose or as multiple doses ( e.g ., 2 or 3 doses), such as infusions. The progress of this therapy is easily monitored by conventional techniques.
- the effective dose of the pharmaceutical composition is one which can provide a blood level of about 1 mM to 150 mM.
- the effective dose provides a blood level of about 4 mM to 100 mM ; or about 1 mM to 100 mM; or about 1 mM to 50 mM; or about 1 mM to 40 mM; or about 1 mM to 30 mM; or about 1 mM to 20 mM; or about 1 mM to 10 mM; or about 10 mM to 150 mM; or about 10 mM to 100 mM; or about 10 mM to 50 mM; or about 25 mM to 150 mM; or about 25 mM to 100 mM; or about 25 mM to 50 mM; or about 50 mM to 150 mM; or about 50 mM to 100 mM (or any range derivable therein).
- the dose can provide the following blood level of the agent that results from a therapeutic agent being administered to a subject: about, at least about, or at most 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,
- the therapeutic agent that is administered to a subject is metabolized in the body to a metabolized therapeutic agent, in which case the blood levels may refer to the amount of that agent.
- the blood levels discussed herein may refer to the unmetabolized therapeutic agent.
- Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment (alleviation of symptoms versus cure) and the potency, stability and toxicity of the particular therapeutic substance or other therapies a subject may be undergoing.
- dosage units of pg/kg or mg/kg of body weight can be converted and expressed in comparable concentration units of pg/ml or mM (blood levels), such as 4 mM to 100 mM. It is also understood that uptake is species and organ/tissue dependent. The applicable conversion factors and physiological assumptions to be made concerning uptake and concentration measurement are well-known and would permit those of skill in the art to convert one concentration measurement to another and make reasonable comparisons and conclusions regarding the doses, efficacies and results described herein.
- kits for treating or delaying progression of cancer in an individual comprising administering to the individual an effective of microbial modifier compositions to a subject who has been or is currently being administered immune checkpoint therapy. Also provided herein are methods of selecting subjects who will respond favorably to immune checkpoint therapy by assessing the microbial profile of the subject and administering immune checkpoint inhibitor to a subject identified to have a favorable microbial profile.
- the treatment results in a sustained response in the individual after cessation of the treatment.
- the methods described herein may find use in treating conditions where enhanced immunogenicity is desired such as increasing tumor immunogenicity for the treatment of cancer.
- methods of enhancing immune function such as in an individual having cancer comprising administering to the individual an effective amount of an immune checkpoint inhibitor (e.g PD-1 inhibitor and/or CTLA-4 inhibitor) and a microbial modulator.
- the individual is a human.
- the individual has cancer that is resistant (has been demonstrated to be resistant) to one or more anti-cancer therapies.
- resistance to anti-cancer therapy includes recurrence of cancer or refractory cancer.
- Recurrence may refer to the reappearance of cancer, in the original site or a new site, after treatment.
- resistance to anti-cancer therapy includes progression of the cancer during treatment with the anti-cancer therapy.
- the cancer is at early stage or at late stage.
- the cancer has low levels of T cell infiltration. In some embodiments, the cancer has no detectable T cell infiltrate. In some embodiments, the cancer is a non-immunogenic cancer (e.g ., non-immunogenic colorectal cancer and/or ovarian cancer).
- the combination treatment may increase T cell (e.g., CD4 + T cell, CD8 + T cell, memory T cell) priming, activation, proliferation, and/or infiltration relative to prior to the administration of the combination.
- the cancer may be a solid tumor, metastatic cancer, or non-metastatic cancer.
- the cancer may originate in the bladder, blood, bone, bone marrow, brain, breast, urinary, cervix, esophagus, duodenum, small intestine, large intestine, colon, rectum, anus, gum, head, kidney, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, testis, tongue, or uterus.
- the cancer may specifically be of the following histological type, though it is not limited to these: neoplasm, malignant; carcinoma; undifferentiated, bladder, blood, bone, brain, breast, urinary, esophageal, thymomas, duodenum, colon, rectal, anal, gum, head, kidney, soft tissue, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, testicular, tongue, uterine, thymic, cutaneous squamous-cell, noncolorectal gastrointestinal, colorectal, melanoma, Merkel-cell, renal-cell, cervical, hepatocellular, urothelial, non-small cell lung, head and neck, endometrial, esophagogastric, small-cell lung mesothelioma, ovarian, esophagogastric, glioblastoma, adrencorical, uveal, pancreatic, germ
- the cancer comprises cutaneous squamous-cell carcinoma, non-colorectal and colorectal gastrointestinal cancer, Merkel-cell carcinoma, anal cancer, cervical cancer, hepatocellular cancer, urothelial cancer, melanoma, lung cancer, non-small cell lung cancer, small cell lung cancer, head and neck cancer, kidney cancer, bladder cancer, Hodgkin's lymphoma, pancreatic cancer, or skin cancer.
- the cancer comprises lung cancer, pancreatic cancer, metastatic melanoma, kidney cancer, bladder cancer, head and neck cancer, or Hodgkin’s lymphoma.
- Methods may involve the determination, administration, or selection of an appropriate cancer“management regimen” and predicting the outcome of the same.
- the phrase“management regimen” refers to a management plan that specifies the type of examination, screening, diagnosis, surveillance, care, and treatment (such as dosage, schedule and/or duration of a treatment) provided to a subject in need thereof (e.g., a subject diagnosed with cancer).
- treatment means any treatment of a disease in a mammal, including: (i) preventing the disease, that is, causing the clinical symptoms of the disease not to develop by administration of a protective composition prior to the induction of the disease; (ii) suppressing the disease, that is, causing the clinical symptoms of the disease not to develop by administration of a protective composition after the inductive event but prior to the clinical appearance or reappearance of the disease; (iii) inhibiting the disease, that is, arresting the development of clinical symptoms by administration of a protective composition after their initial appearance; and/or (iv) relieving the disease, that is, causing the regression of clinical symptoms by administration of a protective composition after their initial appearance.
- the treatment may exclude prevention of the disease.
- further cancer or metastasis examination or screening or further diagnosis such as contrast enhanced computed tomography (CT), positron emission tomography-CT (PET-CT), and magnetic resonance imaging (MRI) may be performed for the detection of cancer or cancer metastasis in patients determined to have a certain gut microbiome composition.
- CT contrast enhanced computed tomography
- PET-CT positron emission tomography-CT
- MRI magnetic resonance imaging
- the methods relate to obtaining a microbiome profile.
- obtaining a microbiome profile comprises the steps of or the ordered steps of: i) obtaining a sample obtained from a subject ( e.g a human subject), ii) isolating one or more bacterial species from the sample, iii) isolating one or more nucleic acids from at least one bacterial species, iv) sequencing the isolated nucleic acids, and v) comparing the sequenced nucleic acids to a reference nucleic acid sequence.
- any genotyping assay can be used. For example, this can be done by sequencing the 16S or the 23 S ribosomal subunit or by metagenomics shotgun sequencing associated with metatranscriptomics.
- Methods for determining microbiome composition may include one or more microbiology methods such as sequencing, next generation sequencing, wester blotting, comparative genomic hybridization, PCR, ELISA, etc.
- kits for performing the methods of the disclosure can be prepared from readily available materials and reagents.
- such kits can comprise any one or more of the following materials: enzymes, reaction tubes, buffers, detergent, primers, probes, antibodies.
- these kits allow a practitioner to obtain samples of neoplastic cells in blood, tears, semen, saliva, urine, tissue, serum, stool, sputum, cerebrospinal fluid and supernatant from cell lysate.
- these kits include the needed apparatus for performing RNA extraction, RT-PCR, and gel electrophoresis. Instructions for performing the assays can also be included in the kits.
- kits may comprise a plurality of agents for assessing or identifying microorganisms, wherein the kit is housed in a container.
- the kits may further comprise instructions for using the kit for assessing sequences, means for converting and/or analyzing sequence data to generate prognosis.
- the agents in the kit for measuring biomarker expression may comprise a plurality of PCR probes and/or primers for qRT-PCR and/or a plurality of antibody or fragments thereof for assessing expression of the biomarkers.
- the agents in the kit for measuring biomarker expression may comprise an array of polynucleotides complementary to the mRNAs of the biomarkers of the invention. Possible means for converting the expression data into expression values and for analyzing the expression values to generate scores that predict survival or prognosis may be also included.
- Kits may comprise a container with a label.
- Suitable containers include, for example, bottles, vials, and test tubes.
- the containers may be formed from a variety of materials such as glass or plastic.
- the container may hold a composition which includes a probe that is useful for prognostic or non-prognostic applications, such as described above.
- the label on the container may indicate that the composition is used for a specific prognostic or non-prognostic application, and may also indicate directions for either in vivo or in vitro use, such as those described above.
- the kit may comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.
- kits comprising the therapeutic compositions of the disclosure.
- the kits may be useful in the treatment methods of the disclosure and comprise instructions for use.
- Example 1 Molecular, immune and microbial factors in response & toxicity to combined CTLA-4 and PD-1 blockade
- the inventors sought to identify potential tumor-derived and systemic molecular, immune and gut microbial biomarkers of both response and immune-related toxicity in melanoma patients receiving CICB.
- One fifth (n l l, 20.8%) of patients had received some form of prior immunotherapy; ipilimumab or anti -PD- 1 not as combined therapy, anti-PD-Ll agent, cytokine agent alone or as part of a biochemotherapy regimen with adjuvant or palliative intent (Table 2) ⁇
- the median number of doses of combination ipilimumab + anti -PD- 1 agent was 3 (range 1-4) (Table 3), with a median number of anti -PD- 1 agent monotherapy doses after initial combination dosing of 1 (range 0-44).
- the overall response rate was 77.4% (41/53 patients) and after a median follow-up time of 15.6 months, progression had occurred in 21 patients (median PFS not reached overall, median time-to-progression 3.0 months in progressors; Figure 1).
- Severe irAEs are particularly common in patients receiving CICB, and occurrence of grade 3 or higher irAEs often leads to discontinuation of therapy despite clinical response. Precise immune mechanisms of irAEs from CICB and reliable predictive biomarkers are lacking (Carlino and Long, 2016).
- the inventors studied the association between systemic immune parameters and toxicity, hypothesizing that the systemic circulation represented the most readily accessible compartment from which to sample potentially auto-reactive immune cells and thus identify immune signatures of a patient's susceptibility to irAEs with CICB.
- the inventors performed comprehensive immune profiling of peripheral blood leukocytes using multiparameter flow cytometry, and evaluated the circulating T cell repertoire with TCR sequencing.
- fecal microbial composition was quite varied, with Bacteroidales and Clostridiales being the most abundant in all fecal samples (FIG. 4A).
- compositional differences between R and NR to CICB using linear discriminant analysis of effect size (LEfSe) (Segata et ak, 2011), and pairwise comparison of relative taxonomic abundances.
- LfSe linear discriminant analysis of effect size
- FIG. 10D The inventors then performed similar analyses between circulating immune populations and bacterial taxa associated with development of, or freedom from, high-grade irAE. Consistently positive correlations were observed between the abundance of several toxicity-associated Bacteroides taxa and PD-1+ T cell populations, consistent with the potential (re)activation of diverse immune specificities upon CICB initiation leading to toxicity (FIG. 4F).
- NR mice non-responder mice, defined as mice whose tumors enlarged over two consecutive measurements (5/6 anti-PD-1 -treated and 2/10 CICB-treated were NR; FIG. 5A, right panel).
- the inventors next compared bacteria present in the pre-treatment gut microbiota of mice that subsequently responded to CICB in either of the two tumor models (MCA205 and RET), finding 169 taxa present in both models, including Alistipes indistinctus and Akkermansia muciniphila. Furthermore, Flavonifractor plautii was also enriched in human patients responding to CICB (FIG. 4D, FIG. 5D, Table 4). To identify further commonalities in bacteria across patient samples and murine tumor models, the inventors compared response- associated taxa identified by LEfSe in patients with those identified as differentially enriched between R and NR mice to CICB using LEfSe in both murine tumor models.
- the inventors sought to enrich the taxonomic discovery with additional biological information by focusing on human response-associated taxa which became or remained differentially enriched in either mouse model during the course of CICB, and which were correlated (or anti-correlated) with tumor size (FIG. 11A-D).
- the inventors examined two timepoints in an attempt to determine if treatment and tumor size were associated with the gut microbiota, and if the gut microbiota remained stable after commencing therapy.
- Flavonifractor F. plautii in MCA205
- Dielma D.
- the inventors analyzed potential correlations between the gut microbiota and toxicity in mouse models, focusing on gut toxicity (colonic and ileal).
- murine models poorly reproduce overt colonic irAE (e.g. : weight loss, mucosal bleeding, altered stool volume and consistency)
- the inventors first scored histologic abnormalities of the gut epithelium and lamina basement (irregularities or destruction or length reduction of villi and crypts, presence of inflammatory infiltrates) after administration of CICB alone or co administered with broad-spectrum antibiotics (ATB), with or without monocolonization by specific commensal bacteria informed by the parallel analyses in humans.
- ATB broad-spectrum antibiotics
- FIG. 6C ramosum , but not B. intestinalis or I fastidiosa
- FIG. 6D Consistent with a specific role for IL-Ib in the genesis of ileal inflammation in response to CICB, IL-1R1 blockade concomitant with CICB alleviated ileal toxicity (FIG. 6D).
- muciniphila which has been previously identified as a species associated with anti -PD- 1 response (Routy et al., 2018), or fecal material from a RCC patient who responded to therapy and did not experience grade 3-4 irAE, as monitored by immunohistochemistry and fecal levels of the antimicrobial peptide lipocalin-2 (FIG. 6H-I).
- Metagenomic analysis of responding RCC patient feces indicated the presence of A. indistinctus which was also present in the fecal microbiota of responding melanoma patients (FIG. 4D) and responding mice (FIG. 5E) but absent in the non-responding RCC patient feces.
- the gut microbiota may also represent a critical - and modifiable - influence on the likelihood of developing checkpoint immunotherapy-related autoimmune toxicities.
- the inventors identified several taxa as strongly associated either with the development of, or freedom from high-grade immune-related toxicities. Importantly, most response-associated bacterial taxa were not highly associated with toxicity, except for B. stercoris, and apparent species-level variation in the correlation to toxicity-associated systemic lymphocyte sub populations. This data suggests that potentially distinct immunomodulatory microbial mechanisms underlying associations with irAE extend to very low (species) levels of taxonomy such that even closely-related taxa can have conflicting associations with irAE.
- CICB was more toxic at the ileal than the colonic level, with a clear causative role of distinct ecosystems. Indeed, therapy with broad spectrum antibiotics or fecal microbial transplantation could ameliorate the ileitis or colitis score. Some bacterial species appeared more toxic than others (such as E. ramosum). CICB-induced ileitis might be ascribed to the capacity of toxicity- associated commensals to induce mucosal IL-Ib, as IL-1R1 blockade mitigated the CICB- induced ileitis. It was also found commonalities across mammals with respect to the commensals associated with gut toxicity. B.
- intestmalis featured among the commensals associated with grade 3-4 toxicity in the present cohort of metastatic melanoma patinets treated with CICB as well as in (C)ICB-treated RET/MCA205 tumor bearing mice.
- CICB combination immune checkpoint blockade
- mice experiments were approved by the local institutional board and performed in accordance with government and institutional guidelines and regulations.
- Female C57B1/6 and BALB/c were purchased from Harlan (France) and Janvier (France), respectively. Mice were used between 8 and 16 weeks of age. All mice experiments were performed at Gustave Roussy Cancer Campus and mice were housed in specific pathogen-free conditions or maintained in isolators.
- MCA205 and RET melanoma (a transgene-enforced expression of the Ret protooncogene under the control of the metallothionein-1 promoter driving spontaneous melanomagenesis, kindly provided by Professor Viktor Umansky) (syngeneic from C57BL/6J mice) and luciferase-transfected renal cancer (RENCA) cell lines (syngeneic for BALB/c mice, kindly provided by Transgene, Illkirch, France) were cultured at 37°C under 5% CO2 in RPMI- 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin/streptomycin, 2 mM L-glutamine and 1% of sodium pyruvate and non-essential amino acids (all from Gibco-Invitrogen), referred herein as complete RPMI medium.
- FBS heat-inactivated fetal bovine serum
- penicillin/streptomycin 2 m
- RENCA was maintained in complete RPMI supplemented with 0.7mg/ml geneticin (Invitrogen, LifeTechnologies). Cell lines were regularly tested for mycoplasma contamination and cells were not used for more than 10 passages. D. METHOD DETAILS
- Clinical response annotation was performed independently by at least two clinical investigators per patient (MCA, PAP, HT). Treatment responses were defined using the best overall response (BOR) according to RECIST 1.1 criteria (Eisenhauer et al., 2009) comparing tumor burden on restaging imaging performed at standard disease re assessment time points studies with baseline (pre-treatment) studies. Longitudinal restaging scans were evaluated throughout the period of treatment until the initiation of a subsequent line of therapy or last known follow-up date. Imaging modality was matched whenever possible, favoring contrast-enhanced CT of the chest, abdomen and pelvis, contrast-enhanced MRI or CT brain, and imaging of the neck or extremities as indicated by known sites of disease.
- R refers to patients that were classified as“responders” (R) if they achieved objective complete response (CR; 100% reduction in tumor burden) or partial response (PR; >30% reduction in tumor burden) attributable to CICB. Patients were classified as non-responders if they achieved a BOR of progressive disease (PD; >20% increase in disease burden) or stable disease (SD; not meeting criteria for CR/PR/PD). Mice were defined as responders (R) if their tumors either regressed or were stable during treatment, or as non-responders (NR) when tumors increased in size over two consecutive measurements.
- CR objective complete response
- PR partial response
- SD stable disease
- Biospecimen collections Available tumor and peripheral blood samples were identified by querying institutional research biospecimen holdings and, when necessary, archival pathology holdings from diagnostic specimens. Tumor biopsies were obtained as punch, core needle, or excisional biopsies and preserved as snap-frozen (for RNA/DNA extraction) or formalin-fixed paraffin-embedded (FFPE; for immunohistochemistry or DNA extraction) specimens. Peripheral blood samples underwent density-gradient centrifugation to isolate peripheral blood mononuclear cells (PBMC) prior to cryopreservation until required for germline DNA extraction or flow cytometry.
- PBMC peripheral blood mononuclear cells
- Biospecimens were retrieved, collected and analyzed under UT MD Anderson Cancer Center Institutional Review Board-approved protocols in accordance with the Declaration of Helsinki. Fecal samples were obtained on an outpatient basis using the OMNIgene-GUT Kit (DNA Genotek Inc, Ottawa, Canada) according to the manufacturer’s recommendations after detailed explanation and instruction by treating clinicians. Stabilized fecal samples were returned in person or by mail within 30 days of collection.
- Target enrichment was performed using the Agilent SureSelectXT Target Enrichment (#5190-8646) protocol as per the manufacturer’s instructions, using 650- 750 ng of prepared libraries. Enriched libraries were normalized to equal concentrations using an Eppendorf Mastercycler EP Gradient instrument, pooled to equimolar amounts on the Agilent Bravo B platform and quantified using the KAPA LibraryQuantification Kit (#KK4824). Pooled libraries were adjusted to 2 nM, denatured with 0.2 MNaOH, diluted using Illumina hybridization buffer, and underwent cluster amplification using HiSeq v3 cluster chemistry and the Illumina Multiplexing Sequencing Primer Kit as per manufacturer’s instructions.
- Additional post-calling filters were then applied, including: (a) total read count in tumor sample > 30, (b) total read count in matched normal sample > 10, (c) VAF (Variant Allele Frequency) in tumor sample > 0.05, (d) VAF in matched normal sample ⁇ 0.01, and (e) SNVs reported in dbSNP129 and 1000 Genomes Project were removed.
- Copy number alteration analysis Copy number alteration analysis was performed as previously described (Roh et al., 2017). Essentially, Sequenza (v2.1.2) algorithm was applied to the aligned BAM data to obtain the log2 copy number ratio (tumor/normal) for each tumor sample. Using R package“CNTools” (vl .24.0), copy number gain (log2 copy ratios > log2l .5) and loss (log2 copy ratios ⁇ -log2l .5) at the gene level were identified. The burden of copy number gain or loss was defined as the total number of genes with copy number gain or loss per sample.
- R package“cghMCR” (vl .26.0) was applied to the calculated log2 copy ratios (tumor/normal) to identify genomic regions of recurrent CNAs (minimum common regions, MCRs).
- MCRs minimum common regions
- Fisher’s exact test was performed at each gene location, and statistical significance was defined by FDR adjusted p ⁇ 0.05. Genes with CNA in less than 3 samples were excluded.
- Neoantigen prediction Non-synonymous exonic mutations (NSEM) from WES were reviewed and all possible 8- to 12-mer peptides encompassing NSEM were used for neoantigen prediction and compared with wild type peptides. ELLA of each case was predicted using PHLAT (Bai et ah, 2014). Binding affinity was evaluated, taking into account patient HLA, by the NetMHCpan (v2.8) algorithm (Hoof et ah, 2009). Candidate peptides with a predicted IC50 ⁇ 500 nM were considered HLA-binding.
- PBMCs Peripheral blood mononuclear cells obtained from the study patients were analyzed by members of the MD Anderson Immunotherapy Platform. Pre treatment and post-treatment blood samples were drawn for immunophenotypic analysis of PBMCs. PBMC samples were available from 20 patients, including 10 patients with >Grade 3 irAE, and 10 patients with ⁇ Grade 3 irAE.
- Multiparametric flow cytometry analysis of PBMCs was performed using fluorescently conjugated monoclonal antibodies across several panels: CD4 AF532 (SK3, eBioscience), CD3 PerCP-Cy5.5 (UCHT1, Biolegend) CD8 AF700 (RPA- T8, BD Biosciences), CD127 BV711 (HIL-7R-M21, BD Biosciences), ICOS PE-Cy7 (ISA-3, eBioscience), PD-1 BV650 (EH12.1 BD Biosciences) and FOXP3 PE-e610 (PCH101; eBioscience); CD3 PE-CF594, CD4 Pe-Cy5.5, CD8 AF532, CD45RA BV650 (HI100, Biolegend), CCR7 BV785 (G043H7, Biolegend) CD27 PeCy5 (0323, eBioscience), CD28 APC-e780 (CD28.2 eBioscience), PD-1 BV650 (EH12.1 BD Biosciences),
- Live/Dead fixable yellow stain was obtained from Thermo Fisher Scientific. Samples were run using an LSR Fortessa (BD Biosciences) and analyzed using the FlowJo software program. After appropriate forward/side scatter and live single cell gating, the inventors determined the frequency of total CD3+ T cells, CD8+ T cells (CD3+CD8+) and CD4+ T cells (CD3+CD4+). Among the CD4, CD4+ effector T cells (CD4+FOXP3-) and CD4+ regulatory T cells (CD4+FOXP3+CD127-/low). PD-1 and ICOS expression were evaluated on these populations.
- CD45RA and CCR7 expression on CD4 and CD8 T cells was used to define naive, T central memory (TCM), T effector memory (TEM) and effector T (Teff) sub-populations.
- TCM T central memory
- TEM T effector memory
- Teff effector T sub-populations.
- PD-1, CD28, CD27, EOMES and TBET expression was evaluated in each of these compartments.
- the selected antibody panel included programmed death-ligand 1 (PD-L1) clone E1L3N (1 : 100, Cell Signaling Technology), PD-1 clone EPR4877 (1 :250, Epitomics), CD3 polyclonal (1 : 100, DAKO), CD4 clone 4B12 (1 :80, Leica Biosystems), CD8 clone C8/144B (1 :25, Thermo Scientific), FOXP3 clone 206D (1 :50, BioLegend) and Granzyme B clone 11F1 (ready to use, Leica Microsystems).
- PD-L1 programmed death-ligand 1
- IHC staining of a limited antibody panel was performed using a Leica Bond Max automated Stainer (Leica Biosystems, Buffalo Grove, IL). The IHC reaction was preformed using Leica Bond Polymer Refine detection kit (Leica Biosystems) and diaminobenzidine (DAB) was used as chromogen. Counterstaining was with hematoxylin. All IHC slides were scanned using an Aperio AT Turbo (Leica Biosystems) prior to all downstream IHC analyses. Using the Aperio Image Toolbox analysis software (Leica Biosystems), average values for each marker from five randomly-selected 1mm 2 areas within the tumor region were selected for digital analysis as previously described (Chen et ah, 2016). PD-L1 expression was evaluated by H-score, which evaluates the percentage of positive cells (0 to 100) and the intensity of staining (0 to 3+), with a total score ranging from 0 to 300. The remaining markers were scored as density of cells.
- TCR Sequencing DNA was extracted from available FFPE tumor tissues (19R, 6NR) and PBMC (15 patients with >Grade 3 irAE, and 12 patients with ⁇ Grade 3 irAE) using the QIAamp DNA FFPE Tissue Kit (Qiagen).
- Next generation TCR sequencing of CDR3 variable regions was performed using the ImmunoSeq hsTCRB kit (Adaptive Biotechnologies) followed by sequencing on a MiSeq 150x (Illumina) and analysis using the ImmunoSeqTM Analyzer software v3.0 (Adaptive Biotechnologies), considering only samples for which a minimum of 1000 unique templates were detected.
- Clonality is an index inversely correlated with TCR diversity and was measured as 1 -(entropy )/log2(# of productive unique sequences).
- Preferential clonal expansion was defined as the number of T cell clones significantly expanded in post-treatment compared to pre-treatment blood samples. 4.
- mice were treated with an antibiotic solution (ATB) containing ampicillin (1 mg/ml), streptomycin (5 mg/ml), and colistin (1 mg/ml) (Sigma- Aldrich), with or without the addition of vancomycin (0.25 mg/ml) via the drinking water. Solutions and bottles were replaced 3 times and once weekly, respectively. Antibiotic activity was confirmed by cultivating fecal pellets resuspended in BHI+15% glycerol at 0.1 g/ml on COS (Columbia Agar with 5% Sheep Blood) plates for 48 h at 37°C in aerobic and anaerobic conditions. The duration of ATB treatments was slightly different based on the experimental settings. In brief, mice were treated for 2 weeks prior to tumor implantation and continuously throughout the experiment in MCA205 and RET experiments, whilst in experiments where RENCA was used, ATB treatment was administered for 3 days prior to fecal microbiota transfer.
- ATB antibiotic solution
- mice were subcutaneously (s.c.) injected with 0.8 x 10 6 MCA205 or 0.5 x 10 6 RET cells. Treatment commenced when tumors reached 20 to 30 mm 2 .
- Mice were injected intraperitoneally (i.p) with anti-PD-1 mAh (250 pg/mouse; clone RMP1-14) and/or anti-CTLA-4 mAh (100 pg/mouse, clone 9D9), with or without anti- IL1R (anakinra, 500 pg/mouse) or respective isotype controls as indicated in figures. All mAbs for in vivo use were obtained from BioXcell (West Riverside, NH, USA), using the recommended isotype control mAbs except anakinra (Swedish Orphan Biovitrum, Sweden).
- FMT fecal microbiota transfer
- Treatment began 5 days after tumor inoculation. Mice were treated with anti-PD-1 mAh and anti CTLA-4 with or without oral gavage of fecal samples from responding patients or of Akkermansia muciniphila. Tumor growth was monitored once weekly on an IVIS Imaging System 50 Series (Analytic Jenap).
- Oral gavages of 10 8 or 10 9 CFU in 100 pL were administered 24 hours prior to antibody treatment and with each antibody treatment. Bacteria were verified using a Matrix- Assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) mass spectrometer (Microflex LT analyser, Bruker Daltonics, Germany).
- MALDI-TOF Matrix- Assisted Laser Desorption/Ionization Time of Flight
- Gut tissue was preserved in either formalin fixed paraffin embedded (FFPE) or optimum cutting temperature compound (OCT).
- FFPE formalin fixed paraffin embedded
- OCT optimum cutting temperature compound
- Tissues were then either paraffin-embedded with a Tissue-Tek® VIP® 6 Vacuum Infiltration Processor (Sakura) or rehydrated in 15% sucrose for lh followed by 30% sucrose overnight, OCT embedded (Sakura) and snap frozen. Longitudinal sections were counterstained with hematoxylin, eosin & safran stain (H&E).
- Colon Inflammatory infiltrate, defined as either physiological (0), low (1), moderate (2) and high (3) levels were scored.
- OTUs Operational Taxonomic Units
- Microbiota and OTU-level analyses Measurements of a diversity (within sample diversity) such as observed otus and Shannon index, were calculated at OTU level using the SciKit-learn package v.0.4.1. Exploratory analysis of b-diversity (between sample diversity) was calculated using the Bray-Curtis measure of dissimilarity calculated with Mothur and represented in Principal Coordinate Analyses (PCoA), while for Hierarchical Clustering Analysis (HCA)‘Bray-Curtis’ metrics and‘complete linkage’ method were implemented using custom scripts (Python v.2.7.11).
- PCoA Principal Coordinate Analyses
- Taxonomic alpha- diversity of patient samples was estimated using the Inverse Simpson Index calculated as
- D l/ (pi is the proportion of the total species S that is comprised by the species i) (Morgan and Huttenhower, 2012), and additional diversity metrics as indicated in figures.
- ANalysis Of SIMilarity (ANOSIM, which represents the difference of datasets’ centroids) or, when indicated, Pearson correlation coefficient, were computed with Python 2.7.11.
- Permutation testing was performed by randomly permuting sample labels for a total of 1000 iterations. In murine studies, statistical analyses gathering more than two groups were performed using ANOVA followed with pairwise comparisons with Bonferroni adjustments. Otherwise, for two groups, statistical analyses were performed using the unpaired t-test. Outliers within a given distribution were tested using Grubbs’ test (found online at graphpad.com/quickcalcs/Grubbsl .cfm) with a threshold at p ⁇ 0.05. All tumor growth curves were analyzed using software developed in Professor Guido Kroemer’s laboratory and information about statistical analyses can be found at this following link: found online at kroemerlab.shinyapps.io/TumGrowth/.
- Prior immunotherapies IL-2, IFN, anti-CTLA-4, anti-PD-1 (pembrolizumab, nivolumab).
- Gr3+ irAE grade 3 or higher immune-related adverse event.
- Pre/Post/Early time point of specimen sampling relative to CICB initiation.
- BOR best overall response by RECIST vl. l.
- Lactobacillus faecis Lactobacillus faecis
- Example 2 Therapeutic efficacy and tolerability of combined immune checkpoint blockade in metastatic melanoma is influenced by the gut microbiome
- the gut microbiome is increasingly being recognized as a strong modulator of anti- PD1 based cancer immunotherapy.
- Compelling evidence demonstrates differential bacterial enrichment and diversity in responders (R) versus non-responders (NR), mediated by profound influences on systemic and anti-tumor immune infiltrates.
- R responders
- NR non-responders
- CICB combined immune checkpoint blockade
- FIGS. 13-19 demonstrate that, while there were no major differences in gut diversity by response or toxicity, notable differences existed in terms of taxonomic enrichment, specifically Bacteroides stercoris in R and Lactobacillus rogosae in NR (also associated with PFS); and Bacteroides intestinalis in patients with Grade 3 (or higher irAE), and Anaerotignum lactatifermentans in patients with less than Grade 3 irAE.
- Example 3 Peripheral immune repertoire and gut microbiome signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade
- CICB immune checkpoint blockade
- irAE immune-related adverse events
- the inventors profiled the blood, tumor and gut microbiome of 77 advanced melanoma patients treated with CICB, with a high rate of any >Grade 3 irAEs (49%).
- Immune and genomic biomarkers of response to CICB were similar to those identified for anti-CTLA-4 and anti-PD-1 monotherapy. Toxicity from CICB was associated with a more diverse T cell repertoire and a less antigen-experienced phenotype.
- the inventors interrogated the phenotype of PBL in patients with grade 3 or above irAEs via multi-parameter flow cytometry at baseline and on-treatment.
- TCR sequencing data suggest that a more diverse T cell repertoire harboring greater numbers of potentially auto-reactive clones may contribute to irAEs following CICB.
- the inventors first queried associations of gut microbiota with response through studies of compositional differences between R and NR using LEfSE (FIG. 17A) and pairwise comparisons (FIG. 18A).
- LEfSE Lith Generation Partnership Project
- T2 and T5 was negatively correlated with tumor size at T5 (FIG. 20C) and was significantly over-represented at TO and T2 in mice receiving CICB that were eventually tumor-free (FIG. 27D). Additional taxa associated with response in each tumor model were noted (Extended Data Tables 4-5). Together, these data identify a dynamic interplay between CICB and gut commensal microbiota, with commonalities in enriched taxa between the two murine tumor models and human patients, such as P. distasonis , which was positively associated with beneficial tumor responses.
- the inventors After assessing the potential impact of gut microbiota on response, the inventors next interrogated associations between the gut microbiota and toxicity to therapy in the patient cohort and in the murine models.
- taxa associated with freedom from >Grade 3 irAEs such as Dorea formicigenerans, Muricomes intestini and Anaerotignum lactatifermentans were inversely correlated with the abundance of previously implicated CD4+ and CD8+ T cells expressing CD27 and CD28, suggestive of a potential route for immunomodulation linking these taxa to the observed clinical outcome.
- the inventors did not detect any association between microbial alpha diversity and >Grade 3 irAEs (FIG. 16C).
- the inventors first assessed for toxicity after administration of CICB with or without co-administration of broad-spectrum antibiotics (ATB).
- treatment with CICB was associated with subclinical ileal toxicity that was highly mitigated by sterilization of the intestines with ATB (FIG. 22A).
- this ileitis was accompanied by a prompt and selective upregulation of transcription of the pro-inflammatory cytokine Illb but not nf or 7/d, and only in the presence of intact gut microflora (FIG. 22B-C).
- the inventors next interrogated human tissues of patients who developed colitis and observed a significant increase in IL1B expression in colitis samples versus healthy colon controls (data not shown).
- FIG. 22E rendered the ileum sensitive to CICB-induced damage
- FIG. 22F rendered the ileum sensitive to CICB-induced damage
- Clinical response annotation was performed independently by at least two clinical investigators per patient (MCA, PAP, HT). Treatment responses were defined using the best overall response (BOR) according to RECIST 1.1 criteria (Eisenhauer, 2009 #29) comparing tumor burden on restaging imaging performed at standard disease re assessment time points studies with baseline (pre-treatment) studies. Longitudinal restaging scans were evaluated throughout the period of treatment until the initiation of a subsequent line of therapy or last known follow-up date. Imaging modality was matched whenever possible, favoring contrast-enhanced CT of the chest, abdomen and pelvis, contrast-enhanced MRI or CT brain, and imaging of the neck or extremities as indicated by known sites of disease.
- Immune-related adverse events was scored according to the NCI Common Terminology Criteria for Adverse Events (CTCAE) 4.0 criteria and immune-relatedness to CICB therapy (“possible”,“probable”,“definite” association) assigned by consensus opinion of at least two independent clinical investigators (MCA, HT, WSC).
- CICB therapy (“possible”,“probable”,“definite” association) assigned by consensus opinion of at least two independent clinical investigators (MCA, HT, WSC).
- Binary toxicity classification was based on whether patients experienced any grade 3 or higher irAE versus less than grade 3 irAE (Extended Data Table 2).
- Biospecimen collections Available pre- and on-treatment tumor and peripheral blood samples were identified by querying institutional research biospecimen holdings and, when necessary, archival pathology holdings from diagnostic specimens. Tumor biopsies were obtained as punch, core needle, or excisional biopsies and preserved as snap-frozen (for RNA/DNA extraction) or formalin-fixed paraffin-embedded (FFPE; for immunohistochemistry or DNA extraction) specimens. Peripheral blood samples underwent density-gradient centrifugation to isolate peripheral blood mononuclear cells (PBMC) prior to cryopreservation until required for germline DNA extraction or flow cytometry.
- PBMC peripheral blood mononuclear cells
- Biospecimens were retrieved, collected and analyzed under UT MD Anderson Cancer Center Institutional Review Board-approved protocols in accordance with the Declaration of Helsinki. Fecal samples were obtained on an outpatient basis using the OMNIgene-GUT Kit (DNA Genotek Inc, Ottawa, Canada) according to the manufacturer’s recommendations after detailed explanation and instruction by treating clinicians. Stabilized fecal samples were returned in person or by mail within 30 days of collection. Patient-level sample utilization is as shown in Extended Data Table 3.
- Target enrichment was performed using the Agilent SureSelectXT Target Enrichment (#5190-8646) protocol as per the manufacturer’s instructions, using 650- 750 ng of prepared libraries. Enriched libraries were normalized to equal concentrations using an Eppendorf Mastercycler EP Gradient instrument, pooled to equimolar amounts on the Agilent Bravo B platform and quantified using the KAPA LibraryQuantification Kit (#KK4824). Pooled libraries were adjusted to 2 nM, denatured with 0.2 MNaOH, diluted using Illumina hybridization buffer, and underwent cluster amplification using HiSeq v3 cluster chemistry and the Illumina Multiplexing Sequencing Primer Kit as per manufacturer’s instructions.
- Additional post-calling filters were then applied, including: (a) total read count in tumor sample > 30, (b) total read count in matched normal sample > 10, (c) VAF (Variant Allele Frequency) in tumor sample > 0.05, (d) VAF in matched normal sample ⁇ 0.01, and (e) SNVs reported in dbSNP129 and 1000 Genomes Project were removed.
- Copy number alteration analysis Copy number alteration analysis was performed as previously described (Roh, 2017 #22). Essentially, Sequenza (v2.1.2) algorithm was applied to the aligned BAM data to obtain the log2 copy number ratio (tumor/normal) for each tumor sample. Using R package“CNTools” (vl .24.0), copy number gain (log2 copy ratios > log21.5) and loss (log2 copy ratios ⁇ -log21.5) at the gene level were identified. The burden of copy number gain or loss was defined as the total number of genes with copy number gain or loss per sample.
- R package“cghMCR” (vl .26.0) was applied to the calculated log2 copy ratios (tumor/normal) to identify genomic regions of recurrent CNAs (minimum common regions, MCRs).
- MCRs minimum common regions
- Fisher’s exact test was performed at each gene location, and statistical significance was defined by FDR adjusted p ⁇ 0.05. Genes with CNA in less than 3 samples were excluded.
- Neoantigen prediction Non-synonymous exonic mutations (NSEM) from WES were reviewed and all possible 8- to 12-mer peptides encompassing NSEM were used for neoantigen prediction and compared with wild type peptides.
- HLA of each case was predicted using PHLAT (Bai, 2014 #38). Binding affinity was evaluated, taking into account patient HLA, by the NetMHCpan (v2.8) algorithm (Nielsen, 2007 #15; Hoof, 2009 #33).
- Candidate peptides with a predicted IC50 ⁇ 500 nM were considered HLA-binding.
- PBMCs Peripheral blood mononuclear cells obtained from the study patients were analyzed by members of the MD Anderson Immunotherapy Platform. Pre treatment and post-treatment blood samples were drawn for immunophenotypic analysis of PBMCs. PBMC samples were available from 20 patients, including 10 patients with >Grade 3 irAE, and 10 patients with ⁇ Grade 3 irAE.
- Multiparametric flow cytometry analysis of PBMCs was performed using fluorescently conjugated monoclonal antibodies across several panels: CD4 AF532 (SK3, eBioscience), CD3 PerCP-Cy5.5 (UCHT1, Biolegend) CD8 AF700 (RPA- T8, BD Biosciences), CD127 BV711 (HIL-7R-M21, BD Biosciences), ICOS PE-Cy7 (ISA-3, eBioscience), PD-1 BV650 (EH12.1 BD Biosciences) and FOXP3 PE-e610 (PCH101; eBioscience); CD3 PE-CF594, CD4 Pe-Cy5.5, CD8 AF532, CD45RA BV650 (HI100, Biolegend), CCR7 BV785 (G043H7, Biolegend) CD27 PeCy5 (0323, eBioscience), CD28 APC-e780 (CD28.2 eBioscience), PD-1 BV650 (EH12.1 BD Biosciences),
- Live/Dead fixable yellow stain was obtained from Thermo Fisher Scientific. Samples were run using an LSR Fortessa (BD Biosciences) and analyzed using the FlowJo software program. After appropriate forward/side scatter and live single cell gating, the inventors determined the frequency of total CD3+ T cells, CD8+ T cells (CD3+CD8+) and CD4+ T cells (CD3+CD4+). Among the CD4, CD4+ effector T cells (CD4+FOXP3-) and CD4+ regulatory T cells (CD4+FOXP3+CD127-/low). PD-1 and ICOS expression were evaluated on these populations.
- CD45RA and CCR7 expression on CD4 and CD8 T cells was used to define naive, T central memory (TCM), T effector memory (TEM) and effector T (Teff) sub-populations.
- TCM T central memory
- TEM T effector memory
- Teff effector T sub-populations.
- PD-1, CD28, CD27, EOMES and TBET expression was evaluated in each of these compartments.
- the selected antibody panel included programmed death-ligand 1 (PD-L1) clone E1L3N (1 : 100, Cell Signaling Technology), PD-1 clone EPR4877 (1 :250, Epitomics), CD3 polyclonal (1 : 100, DAKO), CD4 clone 4B12 (1 :80, Leica Biosystems), CD8 clone C8/144B (1 :25, Thermo Scientific), FOXP3 clone 206D (1 :50, BioLegend) and Granzyme B clone 11F1 (ready to use, Leica Microsystems).
- PD-L1 programmed death-ligand 1
- IHC staining of a limited antibody panel was performed using a Leica Bond Max automated Stainer (Leica Biosystems, Buffalo Grove, IL).
- the IHC reaction was performed using Leica Bond Polymer Refine detection kit (Leica Biosystems) and diaminobenzidine (DAB) was used as chromogen. Counterstaining was with hematoxylin.
- All IHC slides were scanned using an Aperio AT Turbo (Leica Biosystems) prior to all downstream IHC analyses.
- Aperio Image Toolbox analysis software Leica Biosystems
- average values for each marker from five randomly-selected lmm2 areas within the tumor region were selected for digital analysis as previously described (Chen, 2016 #27).
- PD-L1 expression was evaluated by H-score, which evaluates the percentage of positive cells (0 to 100) and the intensity of staining (0 to 3+), with a total score ranging from 0 to 300. The remaining markers were scored as density of cells.
- TCR Sequencing DNA was extracted from available FFPE tumor tissues (19R, 6NR) and PBMC (15 patients with >Grade 3 irAE, and 12 patients with ⁇ Grade 3 irAE) using the QIAamp DNA FFPE Tissue Kit (Qiagen).
- Next generation TCR sequencing of CDR3 variable regions was performed using the ImmunoSeq hsTCRB kit (Adaptive Biotechnologies) followed by sequencing on a MiSeq 150x (Illumina) and analysis using the ImmunoSeqTM Analyzer software v3.0 (Adaptive Biotechnologies), considering only samples for which a minimum of 1000 unique templates were detected.
- Clonality is an index inversely correlated with TCR diversity and was measured as 1 -(entropy )/log2(# of productive unique sequences).
- Preferential clonal expansion was defined as the number of T cell clones significantly expanded in post-treatment compared to pre-treatment blood samples.
- mice were treated with an antibiotic solution (ATB) containing ampicillin (1 mg/ml), streptomycin (5 mg/ml), and colistin (1 mg/ml) (Sigma- Aldrich), with or without the addition of vancomycin (0.25 mg/ml) via the drinking water. Solutions and bottles were replaced 3 times and once weekly, respectively. Antibiotic activity was confirmed by cultivating fecal pellets resuspended in BHI+15% glycerol at 0.1 g/ml on COS (Columbia Agar with 5% Sheep Blood) plates for 48 h at 37°C in aerobic and anaerobic conditions. The duration of ATB treatments was slightly different based on the experimental settings. In brief, mice were treated for 2 weeks prior to tumor implantation and continuously throughout the experiment in MCA205 and RET experiments, whilst in experiments where RENCA was used, ATB treatment was administered for 3 days prior to fecal microbiota transfer.
- ATB antibiotic solution
- mice were subcutaneously (s.c.) injected with 0.8x 10 6 MCA205 or 0.5x 10 6 RET cells. Treatment commenced when tumors reached 20 to 30 mm2. Mice were injected intraperitoneally (i.p) every three days with anti-PD-1 mAb (250 pg/mouse; clone RMP1-14, 6 injections in MCA205, 5 injections in RET) and/or anti- CTLA-4 mAb (100 pg/mouse, clone 9D9, 5 injections in both MCA205 and RET) with or without anti-IL-lR (anakinra, 500 pg/mouse, injected i.p.
- FMT fecal microbiota transfer
- Treatment began 5 days after tumor inoculation. Mice were treated with CICB with or without oral gavage of fecal samples from responding patients who did not experience toxicity. Tumor growth was monitored once weekly on an IVIS Imaging System 50 Series (Analytic Jenap).
- Bacteroides intestinalis CSURP836 (provided by Institut hospitalo-universitaire Mediterranee Infection, Marseille, France; isolated from a human sample), B. intestinalis from everlmmune (isolated from stools of a lung cancer patient prior to immunotherapy) and B. intestinalis (isolated from a mouse sample) were cultured on COS plates in anaerobic conditions using anaerobic generators (Biomerieux) at 37°C for 24 - 72 hours. Suspensions of 109 CFU/mL were obtained using a spectrophotometer (Eppendorf) at an optical density of 1 measured at 600 nm.
- Eppendorf spectrophotometer
- Oral gavages of 109 CFU in 100 pL were administered 24 hours prior to antibody treatment and with each antibody treatment. Bacteria were verified using a Matrix- Assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) mass spectrometer (Microflex LT analyser, Bruker Daltonics, Germany). [0306] Cytokine quantification. Stool samples were collected and stored at -80°C until further processing. Samples were thawed and re-suspended (at 100 mg/mL) in PBS containing 0.1% Tween 20.
- MALDI-TOF Matrix- Assisted Laser Desorption/Ionization Time of Flight
- Lipocalin-2 levels were measured using the mouse Lipocalin-2/NGAL DuoSet ELISA kit (R&D Systems, Minneapolis, MN) following the manufacturer’s instructions.
- Gene expression was analyzed by real-time quantitative PCR (RT-qPCR) using the TaqMan method with TaqMan® Gene Expression Assays and Taqman Universal Master Mix II (Invitrogen) according to the manufacturer’s instructions on the 7500 Fast Real Time PCR system (Applied Biosystems).
- bacterial genomic DNA extracted using the MO BIO PowerSoil DNA Isolation Kit underwent PCR amplification of the 16S rRNA gene V4 region and was sequenced using the MiSeq platform (Illumina, Inc, San Diego, CA). Quality filtered sequences with >97% identity were clustered into bins known as Operational Taxonomic Units (OTUs) by open-reference OTU picking and classified at species level by reference to the NCBI 16S ribosomal RNA sequence database (release date February 1 1, 2017; ncbi-blast+ package 2.5.0). Phylogenetic information was obtained by mapping the representative OTU sequences against the NCBI taxonomy database (release date February 16, 2017) using BLAST.
- OTUs Operational Taxonomic Units
- Mouse fecal DNA extraction and microbiota characterization Preparation and sequencing of mouse fecal samples was performed at IHU Mediterranee Infection, Marseille, France. Briefly, DNA was extracted using two protocols. The first protocol consisted of physical and chemical lysis, using glass powder and proteinase K respectively, then processing using the Macherey-Nagel DNA Tissue extraction kit (Duren, Germany) (Dridi, 2009 #64). The second protocol was identical to the first protocol, with the addition of glycoprotein lysis and de-glycosylation steps (Angelakis, 2016 #65). The resulting DNA was sequenced, targeting the V3-V4 regions of the 16S rRNA gene as previously described (Million, 2016 #63).
- Raw FASTQ files were analyzed with Mothur pipeline v.1.39.5 for quality check and filtering (sequencing errors, chimerae) on a Workstation DELL T7910 (Round Rock, Texas, United States).
- Raw reads (15512959 in total, on average 125104 per sample) were filtered (6342281 in total, on average 51147 per sample) and clustered into Operational Taxonomic
- OTUs OTU Units
- RET and MCA samples 427 bacterial species were identified using a prevalence threshold of >20%. Sample coverage was computed with Mothur and resulted to be on average higher than 99% for all samples, thus meaning a suitable normalization procedure for subsequent analyses.
- Bioinformatic and statistical analyses on recognized OTUs were performed with Python v.2.7.11.
- Genomic DNA was extracted from fecal samples using the QIAamp DNA Stool Mini Kit (Qiagen) following the manufacturer’s instructions.
- Targeted qPCR systems were applied using either TaqMan technology (for systems targeting All Bacteria domain) or SYBR Green for different Bacteroides species. The following primers and probes were used:
- PLS-DA Partial Least Square Discriminant Analysis
- VIP Variable Importance Plot
- bar thickness reports the fold ratio (FR) value of the mean relative abundances for each species among the two cohorts whilst not applicable (N/A) refers to comparisons with a group with zero relative abundance. An absent border indicates mean relative abundance of zero in the compared cohort(s).
- Permutation testing was performed by randomly permuting sample labels for a total of 1000 iterations. In murine studies, statistical analyses gathering more than two groups were performed using ANOVA followed with pairwise comparisons with Bonferroni adjustments. Otherwise, for two groups, statistical analyses were performed using the unpaired t-test. Outliers within a given distribution were tested using Grubbs’ test (found online at graphpad.com/quickcalcs/Grubbsl .cfm) with a threshold at p ⁇ 0.05. All tumor growth curves were analyzed using software developed in Professor Guido Kroemer’s laboratory and information about statistical analyses can be found at this following link online (https): kroemerlab.shinyapps.io/TumGrowth/ (Enot, 2018 #66).
- Percentages are expressed relative to the number of patients within each indicated group. Ties in medians are indicated by non-integer values.
- Gut microbiome modulates response to anti -PD- 1 immunotherapy in melanoma patients. Science 359, 97-103.
- NetMHCpan a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence.
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US11376285B2 (en) | 2020-05-19 | 2022-07-05 | Microbiotica Limited | Bacterial biomarker |
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Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2018115519A1 (en) * | 2016-12-22 | 2018-06-28 | Institut Gustave Roussy | Microbiota composition, as a marker of responsiveness to anti-pd1/pd-l1/pd-l2 antibodies and use of microbial modulators for improving the efficacy of an anti-pd1/pd-l1/pd-l2 ab-based treatment |
US20180303934A1 (en) * | 2016-06-05 | 2018-10-25 | Snipr Technologies Limited | Selectively altering microbiota for immune modulation |
Family Cites Families (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20190282632A1 (en) * | 2014-10-23 | 2019-09-19 | Institut Gustave Roussy | Methods and products for modulating microbiota composition for improving the efficacy of a cancer treatment with an immune checkpoint blocker |
AU2017335732A1 (en) * | 2016-09-27 | 2019-04-04 | Board Of Regents, The University Of Texas System | Methods for enhancing immune checkpoint blockade therapy by modulating the microbiome |
-
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Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20180303934A1 (en) * | 2016-06-05 | 2018-10-25 | Snipr Technologies Limited | Selectively altering microbiota for immune modulation |
WO2018115519A1 (en) * | 2016-12-22 | 2018-06-28 | Institut Gustave Roussy | Microbiota composition, as a marker of responsiveness to anti-pd1/pd-l1/pd-l2 antibodies and use of microbial modulators for improving the efficacy of an anti-pd1/pd-l1/pd-l2 ab-based treatment |
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