Classifications

• • 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
  • A61K39/0005—Vertebrate antigens
  • A61K39/0011—Cancer antigens
• • 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
  • A61K39/0005—Vertebrate antigens
  • A61K39/0011—Cancer antigens
  • A61K39/001154—Enzymes
  • A61K39/001162—Kinases, e.g. Raf or Src
• • 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
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
  • A61K2039/52—Bacterial cells; Fungal cells; Protozoal cells
  • A61K2039/522—Bacterial cells; Fungal cells; Protozoal cells avirulent or attenuated
• • 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
  • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
  • A61K2039/52—Bacterial cells; Fungal cells; Protozoal cells
  • A61K2039/523—Bacterial cells; Fungal cells; Protozoal cells expressing foreign proteins
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K2300/00—Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
  • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

• the present invention in some embodiments thereof, relates to bacterial vaccines which may be manipulated to comprise disease-associated antigens.
• bacteria may trigger a vast immune response against itself and consequently against the delivered neoantigen.
• bacterial vectors that deliver antigenic messages are also able to deliver a strong danger signal mediated by their pathogen-associated molecular patterns (PAMPs), such as lipopolysaccharides, lipoproteins, flagellin and CpG.
• PAMPs pathogen-associated molecular patterns
• PAMPs derived from different classes of pathogens bind to diverse families of pathogen recognition receptors (PRRs) that include Toll-like receptors (TLRs), C-type lectin-like receptors (CLRs), retinoic acid- induciblegene(RIG)-like receptors (RLRs) and nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs).
• PRRs pathogen recognition receptors
• TLRs Toll-like receptors
• CLRs C-type lectin-like receptors
• RLRs retinoic acid- induciblegene(RIG)-like receptors
• NOD nucleotide-binding oligomerization domain
• NLRs nucleotide-binding oligomerization domain
• a vaccine comprising tumor-homing bacteria which are genetically modified to express at least one cancer-associated antigen and a pharmaceutically acceptable carrier.
• a method of treating cancer of a subject in need thereof comprising administering to the subject a therapeutically effective amount of the vaccine of any one of claims 1-14, thereby treating the cancer.
• a first vaccine comprising a first bacteria which is genetically modified to express at least one cancer-associated antigen; and subsequently;
• a second vaccine comprising a second bacteria which is genetically modified to express at least one cancer-associated antigen, thereby treating the cancer.
• a method of preventing cancer of a subject in need thereof comprising administering to the subject a prophylatically effective amount of the vaccine described herein, thereby preventing the cancer.
• the bacteria is a gram positive bacteria.
• the bacteria is a gram negative bacteria.
• the bacteria is aerobic.
• the bacteria is anaerobic.
• the bacteria are live bacteria.
• the bacteria are attenuated bacteria.
• the bacteria is of a species or genus set forth in any of Tables 1-3.
• the genome of the bacteria comprises a 16S rRNA sequence as set forth in any one of SEQ ID NOs: 24-310.
• the cancer-associated antigen is a neoantigen.
• the bacteria are genetically modified to express a therapeutic protein.
• the therapeutic protein is a cytokine.
• the vaccine is devoid of an aluminium salt.
• the carrier is devoid of adjuvant.
• the first bacteria are viable bacteria and the second bacteria are non-viable bacteria.
• the first bacteria comprises a first strain of bacteria that is genetically modified to express a cancer-associated antigen and the second bacteria comprises a second strain of bacteria that is non-identical to the first strain of bacteria, the second bacteria being genetically modified to express the cancer-associated antigen.
• the cancer is selected from the group consisting of breast, melanoma, colorectal cancer, lung cancer, gastric cancer, pancreatic cancer, ovarian cancer, bone cancer and brain cancer.
• the brain cancer comprises glioblastoma.
• the at least one cancer-associated antigen of the first vaccine is identical to the at least one cancer-associated antigen of the second vaccine.
• the at least one cancer-associated antigen of the first vaccine is non-identical to the at least one cancer-associated antigen of the second vaccine.
• the cancer is selected from the group consisting of breast, melanoma, colorectal cancer, gastric cancer, lung cancer, pancreatic cancer, ovarian cancer, bone cancer and brain cancer.
• the brain cancer comprises glioblastoma.
• all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains.
• methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control.
• the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.
• FIGs. 1A-B Long-term efficacy of vaccination by OVA expressing bacteria in B 16-OVA tumor model.
• A Experiment time line.
• B Tumor growth curves from start of treatment.
• FIGs. 2A-G Short-term efficacy and immunogenicity of vaccination by OVA expressing bacteria in B16-OVA tumor model.
• A Experiment time line.
• C Tumor volume percentage at day 16 relative to day 0. P-values were obtained by two sided Mann-Whitney test. Below are the percentage values of fully cured mice per cohort.
• D Mice from the cohort treated with Anti -PD 1 or Anti -PD 1 together with PACMAN-OVA. While the tumor of the mouse treated with PACMAN-OVA gradually disappears, the tumor of the mouse treated with anti -PD 1 only continued to grow exponentially.
• E CFU count of tumor and liver extracts.
• mice Following 16 days from vaccination, bacteria from tumors and livers were seeded on LB plates with resistance to AMP. Per mouse, CFU count and tumor volumes are given. Of note, 4 out of 5 mice of the PACMAN-OVA cohort exhibited complete clearance of bacteria. Bacteria were present in the mouse with the biggest tumor, suggesting that the tumor tissue enables bacteria proliferation.
• Sera of mice cohorts were subjected to IFNg ELISA. The PACMAN-OVA cohort exhibited the highest IFNg serum level indicating high systemic immune activation. Green dot refers to mouse 836 in F. Mouse 836 was the only case where bacteria were present in the liver, probably resulting in the highest serum level of IFNg.
• FIGs. 3A-D Alternate administration of different bacterial vaccines may overcome acquired immunity.
• A Experiment time table.
• B Tumor growth curves.
• D Weight change (percentage of initial weight) during the first 40 days of treatment.
• FIGs. 4A-B Immune memory of vaccination by OVA expressing bacteria in B16-OVA tumor model.
• A Experiment time table.
• B Tumor growth curves.
• FIGs. 5A-C Long-term efficacy of vaccination by Adpgk expressing bacteria in MC38 CRC tumor model.
• A Experiment time line.
• B Tumor growth curves from treatment start. As shown, tumor growth was significantly inhibited in the PACMAN-Adpgk cohort relative to the other mice cohorts. Following two cycles of immunization, one mouse in the PACMAN-Adpgk cohort was fully cured.
• mice vaccinated with PACMAN-Adpgk were re-challenged with 10 5 MC38 cells and tumor growth was compared to naive mice injected with the same amount of cells. While naive mice exhibited exponentially growing tumors shortly after injection, re-challenged mouse which was vaccinated with PACKMAN-Adpgk remained tumor free, indicating the establishment of long term immune memory against MC38 cells.
• FIG. 6 is a graph illustrating tumor homing of attenuated (STM3120) Salmonella bacteria.
• FIG. 7 is a graph illustrating toxicity of i.v. administration of attenuated (STM3120) vs parental (14028) Salmonella.
• FIGs. 8A-B are graphs illustrating splenocytes immune profiling following vaccination by OVA expressing bacteria in B16-OVA tumor model.
• Figure 8A Quantification of IFNg positive CD8 T-cells by FACS.
• Figure 8B Quantification of T cells killing capacity.
• FIGs. 9A-C illustrate long-term efficacy of vaccination by Adpgk expressing P. Aeruginosa in MC38 tumor model.
• Figure 9A Experiment timetable.
• Figure 9B Tumor growth curves. Mice treated with PACMAN- ADPGK i.v, exhibited a considerable delayed tumor growth. Per treatment, indicated number of fully cured mice.
• Figure 9C Average tumor growth curves of the mice cohorts in Fig 9B. Whiskers indicate standard error.
• FIGs. 10A-B illustrates long-term efficacy of vaccination by Adpgk expressing Bacillus Subtilis spores in MC38 tumor model.
• Figure 10A Experimental timetable.
• Figure 10B Tumor growth curves. Mice treated with PACMAN-ADPGK spores p.o or i.v, exhibited a considerable delayed tumor growth. Per treatment, indicated number of fully cured mice.
• FIGs. 11A-B illustrates long-term efficacy of vaccination by Adpgk expressing attenuated Salmonella (STM3120) in MC38 tumor model.
• Figure 11 A Experiment timetable.
• Figure 11B Tumor growth curves. Mice treated with PACMAN-ADPGK exhibited a considerable delayed tumor growth. Per treatment, indicated number of fully cured mice.
• the present invention in some embodiments thereof, relates to bacterial vaccines which may be manipulated to contain disease-associated antigens on their outer surface.
• the bacteria is genetically modified to express (and even secrete) the disease antigen.
• the bacteria may be used to deliver plasmid cDNA which encode the disease antigen to the immune system.
• the present inventors have now conceived of a novel vaccine which includes tumor-homing bacteria.
• the bacteria are genetically modified to express disease associated antigens. These vaccines are referred to herein as Personalized Anti-Cancer Microbiome-Assisted VaccinatioN (PACMAN).
• PACMAN Personalized Anti-Cancer Microbiome-Assisted VaccinatioN
• the present inventors show that it is possible to genetically modify bacteria to express tumor antigens.
• the genetically modified bacteria serve two purposes 1) as a targeting vehicle - homing to the tumor site and 2) as an adjuvant, stimulating the immune system.
• the Inventors demonstrated the ability to produce effective vaccines using a number of different bacteria including Salmonella Typhimurium ( Figures 1A-B, 2A-G, 3A-D, 4A-B, 5A-C), P. aeruginosa ( Figures 9A-B) and B. Subtilis ( Figures 10A-C).
• Salmonella Typhimurium Figures 1A-B, 2A-G, 3A-D, 4A-B, 5A-C
• P. aeruginosa Figures 9A-B
• B. Subtilis Figures 10A-C
• the bacteria were genetically modified to express various tumor specific antigens including OVA ( Figures 1 A-B, 2A-G, 3A-D, 4A-B) and ADPGK ( Figures 5A-C, 9A-B, 10A-C and 11 A-B).
• a vaccine comprising tumor-homing bacteria which are genetically modified to express at least one cancer-associated antigen and a pharmaceutically acceptable carrier.
• the term “vaccine” refers to a pharmaceutical preparation (pharmaceutical composition) that upon administration induces an immune response, in particular a cellular immune response, which recognizes and attacks a cancer cell.
• the vaccine results in the formation of long-term immune memory towards the targeted antigen.
• the vaccine of the present invention preferably also includes a pharmaceutically acceptable carrier (e.g. a liquid composition which carries the bacteria).
• the carrier is one which retains the viability of the bacteria.
• the isolated bacteria of this aspect of the present invention may be gram positive or gram negative bacteria or may be a combination of both.
• the bacteria may be aerobic or anaerobic bacteria.
• the bacteria are capable of homing to a tumor site.
• the bacteria which are capable of homing to a tumor are present in a tumor microbiome of the subject.
• tumor microbiome refers to the totality of microbes (bacteria, fungae, protists), their genetic elements (genomes) in a defined environment, e.g. within the tumor of a host.
• the microbiome refers only to the totality of bacteria in a defined environment, e.g. within the tumor of a host.
• the tumor may be a primary tumor or a secondary tumor (i.e. metastasized tumor).
• Examples of bacteria known to be present in a breast tumor microbiome are set forth in Table 1, herein below. Such bacteria may be particular relevant for use in vaccines for treating breast cancer.
• the sequence provided refers to the 16S rRNA sequence for each bacteria.
• Table 2 includes bacterial taxa that may be particular relevant for use in a vaccine for treating breast, lung or ovarian cancers. Bacteria are sorted according to their p-values (lowest to highest) for enrichment per tumor type. Table 2
• Table 3 summarizes the different bacterial species that are prevalent in specific tumor types.
• the bacteria is Salmonella Typhimurium - e.g. the Salmonella Typhimurium attenuated strain VNP20009, Salmonella Typhimurium 14028 strain STM3120, Salmonella Typhimurium 14028 strain STM1414, Pseudomonas aeruginosa (strain CHA-OST) and/or Bacillus Subtillis (strain PY79).
• Salmonella Typhimurium e.g. the Salmonella Typhimurium attenuated strain VNP20009, Salmonella Typhimurium 14028 strain STM3120, Salmonella Typhimurium 14028 strain STM1414, Pseudomonas aeruginosa (strain CHA-OST) and/or Bacillus Subtillis (strain PY79).
• isolated or “enriched” encompasses bacteria 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 microbes 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. In some embodiments, isolated microbes 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 microbe 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 microbe or a microbial population may be considered purified if it is isolated at, or after production, such as from a material or environment containing the microbe or microbial population, and a purified microbe or microbial 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 microbes or microbial population 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 microbial types present in the composition can be independently purified from one or more other microbes produced and/or present in the material or environment containing the microbial type.
• Microbial compositions and the microbial components thereof are generally purified from residual habitat products.
• At least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% of the bacteria in the vaccine are of a genus, species or strain listed in Tables 1-3.
• the genome of the bacteria comprises a 16S rRNA sequence at least 90 %, 91 %, 92 %, 93 %, 94 %, 95 %, 96 %, 97 %, 98 % 99 %, 99.1 %, 99.2 %, 99.3 %, 99.4 %, 99.5 %, 99.6 %, 99.7 %, 99.8 %, 99.9 %, 99.95 % identical to any one of the sequences as set forth in SEQ ID NO: 24-310.
• percent homology As used herein, “percent homology”, “percent identity”, “sequence identity” or “identity” or grammatical equivalents as used herein in the context of two nucleic acid or polypeptide sequences includes reference to the residues in the two sequences which are the same when aligned. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g . charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution.
• Sequences which differ by such conservative substitutions are considered to have "sequence similarity" or "similarity". Means for making this adjustment are well-known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g ., according to the algorithm of Henikoff S and Henikoff JG. [Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 1992, 89(22): 10915- 9] ⁇
• Percent identity can be determined using any homology comparison software, including for example, the BlastN software of the National Center of Biotechnology Information (NCBI) such as by using default parameters.
• Other exemplary sequence alignment programs that may be used to determine % homology or identity between two sequences include, but are not limited to, the FASTA package (including rigorous (S SEARCH, LALIGN, GGSEARCH and GL SEARCH) and heuristic (FASTA, FASTX/Y, TFASTX/Y and FASTS/M/F) algorithms, the EMBOSS package (Needle, stretcher, water and matcher), the BLAST programs (including, but not limited to BLASTN, BLASTX, TBLASTX, BLASTP, TBLASTN), megablast and BLAT.
• the sequence alignment program is BLASTN.
• 95% homology refers to 95% sequence identity determined by BLASTN, by combining all non-overlapping alignment segments (BLAST HSPs), summing their numbers of identical matches and dividing this sum with the length of the shorter sequence.
• the sequence alignment program is a basic local alignment program, e.g., BLAST. In some embodiments, the sequence alignment program is a pairwise global alignment program. In some embodiments, the pairwise global alignment program is used for protein-protein alignments. In some embodiments, the pairwise global alignment program is Needle. In some embodiments, the sequence alignment program is a multiple alignment program. In some embodiments, the multiple alignment program is MAFFT. In some embodiments, the sequence alignment program is a whole genome alignment program. In some embodiments, the whole genome alignment is performed using BLASTN. In some embodiments, BLASTN is utilized without any changes to the default parameters.
• the identity is a global identity, i.e., an identity over the entire nucleic acid sequences of the invention and not over portions thereof.
• determining a presence of one or more bacteria or components or products thereof comprises determining a level or set of levels of one or more DNA sequences.
• one or more DNA sequences comprises any DNA sequence that can be used to differentiate between different bacterial types.
• one or more DNA sequences comprises 16S rRNA gene sequences.
• one or more DNA sequences comprises 18S rRNA gene sequences. In some embodiments, 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, 100, 1,000, 5,000 or more sequences are amplified.
• a microbiota sample e.g. tumor sample
• DNA is isolated from a tumor microbiota sample and isolated DNA is assayed for a level or set of levels of one or more DNA sequences.
• Methods of isolating microbial DNA are well known in the art. Examples include but are not limited to phenol-chloroform extraction and a wide variety of commercially available kits, including QIAamp DNA Stool Mini Kit (Qiagen, Valencia, Calif.).
• a presence, a level or set of levels of one or more DNA sequences is determined by amplifying DNA sequences using PCR (e.g., standard PCR, semi-quantitative, or quantitative PCR). In some embodiments, a level or set of levels of one or more DNA sequences is determined by amplifying DNA sequences using quantitative PCR.
• PCR e.g., standard PCR, semi-quantitative, or quantitative PCR.
• a level or set of levels of one or more DNA sequences is determined by amplifying DNA sequences using quantitative PCR.
• DNA sequences are amplified using primers specific for one or more sequence that differentiate(s) individual microbial types from other, different microbial types.
• 16S rRNA gene sequences or fragments thereof are amplified using primers specific for 16S rRNA gene sequences.
• 18S DNA sequences are amplified using primers specific for 18S DNA sequences.
• a presence, a level or set of levels of one or more 16S rRNA gene sequences is determined using phylochip technology.
• Use of phylochips is well known in the art and is described in Hazen et al. ("Deep-sea oil plume enriches indigenous oil-degrading bacteria.” Science, 330, 204-208, 2010), the entirety of which is incorporated by reference. Briefly, 16S rRNA genes sequences are amplified and labeled from DNA extracted from a microbiota sample. Amplified DNA is then hybridized to an array containing probes for microbial 16S rRNA genes.
• Level of binding to each probe is then quantified providing a sample level of microbial type corresponding to 16S rRNA gene sequence probed.
• phylochip analysis is performed by a commercial vendor. Examples include but are not limited to Second Genome Inc. (San Francisco, Calif.).
• determining a presence, a level or set of levels of one or more types of microbes or components or products thereof comprises determining a presence, a level or set of levels of one or more microbial RNA molecules (e.g., transcripts).
• Methods of quantifying levels of RNA transcripts are well known in the art and include but are not limited to northern analysis, semi-quantitative reverse transcriptase PCR, quantitative reverse transcriptase PCR, and microarray analysis.
• determining a presence, a level or set of levels of one or more types of microbes or components or products thereof comprises determining a presence, a level or set of levels of one or more microbial polypeptides.
• Methods of quantifying polypeptide levels are well known in the art and include but are not limited to Western analysis and mass spectrometry. These and all other basic polypeptide detection procedures are described in Ausebel et al.
• determining a presence, a level or set of levels of one or more types of microbes or components or products thereof comprises determining a presence, a level or set of levels of one or more microbial metabolites.
• levels of metabolites are determined by mass spectrometry.
• levels of metabolites are determined by nuclear magnetic resonance spectroscopy.
• levels of metabolites are determined by enzyme-linked immunosorbent assay (ELISA).
• ELISA enzyme-linked immunosorbent assay
• levels of metabolites are determined by colorimetry.
• levels of metabolites are determined by spectrophotometry.
• the vaccine comprises at least lxlO 3 colony forming units (CFUs), lxlO 4 colony forming units (CFUs), lxlO 5 colony forming units (CFUs), lxlO 6 colony forming units (CFUs), lxlO 7 colony forming units (CFUs), lxlO 8 colony forming units (CFUs), 1x109 colony forming units (CFUs), lxlO 10 colony forming units (CFUs) of bacteria of a family/genus/species/strain listed in Tables 1-3.
• Methods for producing bacteria may include three main processing steps. The steps are: organism banking, organism production, and preservation.
• the strains included in the bacteria may be (1) isolated directly from a specimen or taken from a banked stock, (2) optionally cultured on a nutrient agar or broth that supports growth to generate viable biomass, and (3) the biomass optionally preserved in multiple aliquots in long-term storage.
• the agar or broth may contain nutrients that provide essential elements and specific factors that enable growth.
• An example would be a medium composed of 20 g/L glucose, 10 g/L yeast extract, 10 g/L soy peptone, 2 g/L citric acid, 1.5 g/L sodium phosphate monobasic, 100 mg/L ferric ammonium citrate, 80 mg/L magnesium sulfate, 10 mg/L hemin chloride, 2 mg/L calcium chloride, 1 mg/L menadione.
• Another examples would be a medium composed of 10 g/L beef extract, 10 g/L peptone, 5 g/L sodium chloride, 5 g/L dextrose, 3 g/L yeast extract, 3 g/L sodium acetate, 1 g/L soluble starch, and 0.5 g/L L-cysteine HC1, at pH 6.8.
• a variety of microbiological media and variations are well known in the art (e.g., R. M. Atlas, Handbook of Microbiological Media (2010) CRC Press). Culture media can be added to the culture at the start, may be added during the culture, or may be intermittently/continuously flowed through the culture.
• the strains in the vaccine may be cultivated alone, as a subset of the microbial composition, or as an entire collection comprising the microbial composition.
• a first strain may be cultivated together with a second strain in a mixed continuous culture, at a dilution rate lower than the maximum growth rate of either cell to prevent the culture from washing out of the cultivation.
• the inoculated culture is incubated under favorable conditions for a time sufficient to build biomass.
• microbial compositions for human use this is often at 37 °C temperature, pH, and other parameter with values similar to the normal human niche.
• the environment may be actively controlled, passively controlled (e.g., via buffers), or allowed to drift.
• an anoxic/reducing environment may be employed. This can be accomplished by addition of reducing agents such as cysteine to the broth, and/or stripping it of oxygen.
• a culture of a bacterial composition may be grown at 37 °C, pH 7, in the medium above, pre-reduced with 1 g/L cysteine-HCl.
• the organisms may be placed into a chemical milieu that protects from freezing (adding ' cryoprotectants ' ), drying ( ' lyoprotectants ' ), and/or osmotic shock ( ' osmoprotectants ' ), dispensing into multiple (optionally identical) containers to create a uniform bank, and then treating the culture for preservation.
• Containers are generally impermeable and have closures that assure isolation from the environment.
• Cryopreservation treatment is accomplished by freezing a liquid at ultra-low temperatures (e.g., at or below -80 °C).
• Dried preservation removes water from the culture by evaporation (in the case of spray drying or ' cool drying' ) or by sublimation (e.g., for freeze drying, spray freeze drying). Removal of water improves long-term microbial composition storage stability at temperatures elevated above cryogenic. If the microbial composition comprises, for example, spore forming species and results in the production of spores, the final composition may be purified by additional means such as density gradient centrifugation preserved using the techniques described above. Microbial composition banking may be done by culturing and preserving the strains individually, or by mixing the strains together to create a combined bank.
• a microbial composition culture may be harvested by centrifugation to pellet the cells from the culture medium, the supernatant decanted and replaced with fresh culture broth containing 15 % glycerol. The culture can then be aliquoted into 1 mL cryotubes, sealed, and placed at -80 °C for long-term viability retention. This procedure achieves acceptable viability upon recovery from frozen storage.
• Microbial production may be conducted using similar culture steps to banking, including medium composition and culture conditions. It may be conducted at larger scales of operation, especially for clinical development or commercial production. At larger scales, there may be several subcultivations of the microbial composition prior to the final cultivation.
• the culture is harvested to enable further formulation into a dosage form for administration. This can involve concentration, removal of undesirable medium components, and/or introduction into a chemical milieu that preserves the microbial composition and renders it acceptable for administration via the chosen route.
• the powder may be blended to an appropriate potency, and mixed with other cultures and/or a filler such as microcrystalline cellulose for consistency and ease of handling, and the bacterial composition formulated as provided herein.
• vaccines i.e. bacterial compositions
• the bacteria are combined with additional active and/or inactive materials in order to produce a final product, which may be in single dosage unit or in a multi-dose format.
• the bacteria present in the vaccine may be viable (e.g. capable of propagating when cultured in the appropriate medium, or inside the body, following administration).
• the bacteria present in the vaccine are non-viable.
• the bacteria are attenuated such that they are not capable of causing disease.
• the bacteria of the vaccine disclosed herein express at least one cancer associated antigen.
• Cancer-associated antigens are typically short peptides corresponding to one or more antigenic determinants of a protein.
• the cancer-associated antigen typically binds to a class I or II MHC receptor thus forming a ternary complex that can be recognized by a T-cell bearing a matching T-cell receptor binding to the MHC/peptide complex with appropriate affinity.
• Peptides binding to MHC class I molecules are typically about 8-14 amino acids in length.
• T-cell epitopes that bind to MHC class II molecules are typically about 12-30 amino acids in length.
• the same peptide and corresponding T cell epitope may share a common core segment, but differ in the overall length due to flanking sequences of differing lengths upstream of the amino-terminus of the core sequence and downstream of its carboxy terminus, respectively.
• a T-cell epitope may be classified as an antigen if it elicits an immune response.
• the antigens for cancers can be antigens from testicular cancer, ovarian cancer, brain cancer such as glioblastoma, pancreatic cancer, melanoma, lung cancer, prostate cancer, hepatic cancer, breast cancer, rectal cancer, colon cancer, esophageal cancer, gastric cancer, renal cancer, sarcoma, neuroblastoma, Hodgkins and non-Hodgkins lymphoma and leukemia.
• the cancer-associated antigen is a cancer testis antigen (e.g. a member of the melanoma antigen protein (MAGE) family, Squamous Cell Carcinoma- 1 (NY-ESO-1), BAGE (B melanoma antigen), LAGE-1 antigen, Brother of the Regulator of Imprinted Sites (BORIS) and members of the GAGE family).
• MAGE melanoma antigen protein
• NY-ESO-1 Squamous Cell Carcinoma- 1
• BAGE B melanoma antigen
• LAGE-1 antigen e.g. a member of the melanoma antigen protein (MAGE) family, Squamous Cell Carcinoma- 1 (NY-ESO-1), BAGE (B melanoma antigen), LAGE-1 antigen, Brother of the Regulator of Imprinted Sites (BORIS) and members of the GAGE family).
• BORIS Regulator of Imprinted Sites
• the cancer-associated antigen is derived from MART- 1 /Mel an- A protein e g. (MARTI MHC class I peptides (Melan-A:26-35(L27), ELAGIGILTV; SEQ ID NO: 1) and MHC class II peptides (Melan-A:51-73(RR-23) RNGYRALMDKSLHVGTQCALTRR; SEQ ID NO: 2).
• the cancer-associated antigen is derived from glycoprotein 70, glycoprotein 100 (gpl00:25-33 (MHC class I (EGSRNQDWL - SEQ ID NO: 7)) or gpl00:44-59 MHC class II (WNRQLYPEWTEAQRLD - SEQ ID NO: 8) peptides).
• the cancer-associated antigen is derived from tyrosinase, tyrosinase-related protein 1 (TRPl), tyrosinase-related protein 2 (TRP-2) or TRP-2/INT2 (TRP- 2/intron2).
• the cancer-associated antigen comprises MUT30 (mutation in Kinesin family member 18B, Kifl8b - P SKP SF QEF VDWENV SPELNSTDQPFL - SEQ ID NO: 9) or MUT44 (cleavage and polyadenylation specific factor 3-like, Cpsf31 - EFKHIK AFDRTF ANNPGPM VVF ATPGM - SEQ ID NO: 10).
• the cancer-associated antigen is derived from stimulator of prostatic adenocarcinoma-specific T cells- SPAS-1.
• the cancer-associated antigen is derived from human telomerase reverse transcriptase (hTERT) or hTRT (human telomerase reverse transcriptase).
• the cancer-associated antigen is derived from ovalbumin (OVA) for example OVA 25 7-264 MHCI H-2Kb (SIINFEKL - SEQ ID NO: 11) and OVA323-339 MHCII I-A(d) (I S Q A VH A AH AEINE AGR SEQ ID NO: 12), a RAS mutation, mutant oncogenic forms of p53 (TP53) (p53mut (peptide antigen of mouse mutated P53 RI72H sequence VVRHCPHHER - SEQ ID NO: 4 (human mutated p53 Ri75H sequence EVVRHCPHHE - SEQ ID NO: 5)), or from BRAF-V600E peptide (GDFGLATEKSRWSGS - SEQ ID NO: 13).
• OVA ovalbumin
• TP53 mutant oncogenic forms of p53
• p53mut peptide antigen of mouse mutated P53 RI72H sequence VVRHCPHHER - SEQ ID NO: 4
• the cancer-associated antigen is a breast cancer associated disease antigen including but not limited to a-Lactalbumin (a-Lac), Her2/neu, BRCA-2 or BRCA- 1 (RNF53), KNG1K438-R457 (kininogen-1 peptide) and C3fS1304-R1320 (peptides that distinguish BRCA1 mutated from other BC and non-cancer mutated BRCA1).
• a-Lac a-Lactalbumin
• Her2/neu Her2/neu
• BRCA-2 or BRCA- 1 RRF53
• KNG1K438-R457 kininogen-1 peptide
• C3fS1304-R1320 peptides that distinguish BRCA1 mutated from other BC and non-cancer mutated BRCA1.
• the cacer-associated antigen is a colorectal cancer associated disease antigen including but not limited to MUC1, KRAS, CEA (CAP-1-6-D [Asp6]; YLSGADLNL - SEQ ID NO: 14) and Adpgk R30 4 M MC38 (MHCI-Adpgk: ASMTNMELM SEQ ID NO: 15; MHCII-Adpgk: GIP VHLEL ASMTNMELMS SIVHQQ VFPT SEQ ID NO: 16).
• the cancer-associated antigen is a pancreatic cancer associated disease antigen including but not limited to CEA, CA 19-9, MUC1, KRAS, p53mut (peptide antigen of mouse mutated P53 RI72H sequence VVRHCPHHER - SEQ ID NO: 4 (human mutated p53 Ri75H sequence EVVRHCPHHE - SEQ ID NO: 5)) and MUC4 or MUC13, MUC3A or CEACAM5, KRAS peptides (e g.
• KRAS-G12R, KRAS-G13D p5-21 sequence KL V V V GAGGV GK S ALTI (SEQ ID NO: 17), p5-21 G12D sequence KLVVVGADGVGKSALTI (SEQ ID NO: 18), pi 7-31 sequence SALTIQLIQNHFVDE (SEQ ID NO: 19), p78-92 sequence FLCVFAINNTKSFED (SEQ ID NO: 20), pl56-170 sequence FYTLVREIRKHKEKM (SEQ ID NO: 21), NRAS (e g. NRAS-Q61R), PI3K (e g.
• PIK3CA- H1047R C-Kit-D816V
• the cancer-associated antigen is a lung cancer associated disease antigen including but not limited to Sperm Protein 17 (SP17), A-kinase anchor protein 4 (AKAP4) and Pituitary Tumor Transforming Gene 1 (PTTG1), Aurora kinase A, HER2/neu, and p53mut.
• SP17 Sperm Protein 17
• AKAP4 A-kinase anchor protein 4
• PTTG1 Pituitary Tumor Transforming Gene 1
• Aurora kinase A HER2/neu
• p53mut a lung cancer associated disease antigen including but not limited to Sperm Protein 17 (SP17), A-kinase anchor protein 4 (AKAP4) and Pituitary Tumor Transforming Gene 1 (PTTG1), Aurora kinase A, HER2/neu, and p53mut.
• the cancer-associated antigen is a prostate cancer associated disease antigen such as prostate cancer antigen (PCA), prostate-specific antigen (PSA) or prostate-specific membrane antigen (PSMA).
• PCA prostate cancer antigen
• PSA prostate-specific antigen
• PSMA prostate-specific membrane antigen
• the cancer-associated antigen is a brain cancer, specifically glioblastoma cancer associated disease antigen such as GL261 neoantigen (mlmp3 D81N AALLNKLYA - SEQ ID NO: 6).
• the cancer-associated antigen is a neoantigen.
• neoantigen is an epitope that has at least one alteration that makes it distinct from the corresponding wild-type, parental antigen, e.g., via mutation in a tumor cell or post-translational modification specific to a tumor cell.
• a neoantigen can include a polypeptide sequence or a nucleotide sequence.
• a mutation can include a frameshift or nonframeshift indel, missense or nonsense substitution, splice site alteration, genomic rearrangement or gene fusion, or any genomic or expression alteration giving rise to a neoORF.
• a mutation can also include a splice variant.
• Post-translational modifications specific to a tumor cell can include aberrant phosphorylation.
• Post-translational modifications specific to a tumor cell can also include a proteasome-generated spliced antigen.
• APC antigen is QATEAERSF (SEQ ID NO: 3).
• BRCA mutated epitopes are YIHTHTFYV (SEQ ID NO: 22) and SQIWNLNPV (SEQ ID NO: 23) HLA-A*02:01 restricted neoepitopes.
• a universal HLA-DR-binding T helper synthetic epitope (AKFVAAWTLKAAA, SEQ ID NO: 311) is the pan DR-biding epitope (PADRE), which is a 13 amino acid peptide that activates CD4+ T cells.
• PADRE pan DR-biding epitope
• Another contemplated cancer-associated neoantigen is the GL261 neoantigen (mlmp3 D81N, sequence AALLNKLYA - SEQ ID NO: 6).
• the bacteria described herein are genetically modified to express the cancer associated antigen, intracellularly and/or on the bacterial surface (i.e., genetic surface display). In another embodiment, the bacteria are genetically modified to secrete the cancer associated antigen.
• the bacteria comprises a nucleic acid encoding the cancer-associated antigen operably linked to transcriptional regulatory elements, such as a bacterial promotor.
• the transcriptional regulatory element can further comprise a secretion signal.
• the cancer-associated antigen is constitutively expressed by the bacteria.
• the cancer-associated antigen is inducibly expressed by the bacteria (e.g., it is expressed upon exposure to a sugar or an environmental stimulus like low pH or an anaerobic environment).
• the bacteria comprises a plurality of nucleic acid sequences that encode for multiple different cancer-associated antigens that can be expressed by the same bacterial cell.
• the bacteria displays a recombinantly produced cancer-associated antigen on its surface using a bacterial surface display system.
• bacterial surface display systems include outer membrane protein systems (e.g., LamB, FhuA, Ompl, OmpA, OmpC, OmpT, eCPX derived from OmpX, OprF, and PgsA), surface appendage systems (e.g., F pillin, FimH, FimA, FliC, and FliD), lipoprotein systems (e.g., INP, Lpp-OmpA, PAL, Tat- dependent, and TraT), and virulence factor-based systems (e.g., AIDA-1, EaeA, EstA, EspP, MSP1 a, and invasin).
• Exemplary surface display systems are described, for example, in van Bloois, E., et al., Trends in Biotechnology, 2011, 29:79-86, which is hereby incorporated by reference.
• bacterial promoters include but are not limited to STM1787 promoter, pepT promoter, pflE promoter, ansB promoter, vhb promoter, FF+20* promoter or p(luxl) promoter.
• the genetically modified bacteria described herein comprise a cancer therapeutic (e.g., the cancer therapeutic is loaded into the bacteria prior to administration to a subject, or is genetically modified to express the cancer therapeutic).
• the cancer therapeutic is loaded into the bacteria by growing the bacteria in a medium that contains a high concentration (e.g., at least 1 mM) of the cancer therapeutic, which leads to either uptake of the cancer therapeutic during cell growth or binding of the cancer therapeutic to the outside of the bacteria.
• the cancer therapeutic can be taken up passively (e.g. by diffusion and/or partitioning into the lipophilic cell membrane) or actively through membrane channels or transporters.
• drug loading is improved by adding additional substances to the growth medium that either increase uptake of the molecule of interest (e.g., Pluronic F-127) or prevent extrusion of the molecules after uptake by the bacterium (e.g., efflux pump inhibitors like Verapamil, Reserpine, Carsonic acid, or Piperine).
• the bacteria is loaded with the cancer therapeutic by mixing the bacteria with the cancer therapeutic and then subjecting the mixture to electroporation, for example, as described in Sustarsic M., et al., Cell Biol., 2014, 142(1): 113-24, which is hereby incorporated by reference.
• the cells can also be treated with an efflux pump inhibitor (see above) after the electroporation to prevent extrusion of the loaded molecules.
• the bacteria is genetically modified to express the cancer therapeutic.
• the bacteria of the vaccine comprise an inhibitory antibody or small molecule directed against the immune checkpoint protein - e.g. anti-CTLA4, anti-CD40, anti- 4 IBB, anti-OX40, anti -PD 1 and anti-PDLl.
• an inhibitory antibody or small molecule directed against the immune checkpoint protein e.g. anti-CTLA4, anti-CD40, anti- 4 IBB, anti-OX40, anti -PD 1 and anti-PDLl.
• the bacteria of the vaccine may comprise therapeutic agents attached to the outside of the bacteria using an attachment method such as CLICK chemistry.
• an attachment method such as CLICK chemistry.
• therapeutic agents include immune modulatory proteins, such as a cytokine.
• immune modulating proteins include, but are not limited to, B lymphocyte chemoattractant ("BLC”), C— C motif chemokine 11 (“Eotaxin-1”), Eosinophil chemotactic protein 2 (“Eotaxin-2”), Granulocyte colony-stimulating factor (“G-CSF”), Granulocyte macrophage colony-stimulating factor (“GM-CSF”), 1-309, Intercellular Adhesion Molecule 1 ("ICAM-1”), Interferon gamma ("IFN-gamma”), Interlukin-1 alpha (“IL-1 alpha”), Interlukin-1 beta (“IL-1 beta”), Interleukin 1 receptor antagonist (“IL-lra”), Interleukin-2 (“IL-2”), Interleukin-4 (“IL-4"), Interleukin-5 (“IL-5"), Interleukin-6 (“IL-6”), Interleukin-6 soluble receptor (“IL-6 sR”), Interleukin-7 (“IL-7”), Interleukin-8 (“IL-8”), B
• the immune modulatory protein can be made recombinantly using methods known to one skilled in the art.
• the immune modulatory protein can be presented on the surface of a bacterium using bacterial surface display, where the bacterium expresses a genetically engineered protein-protein fusion of e.g., a membrane protein and the immune modulatory protein.
• the bacteria of the vaccine of the present invention may serve as an adjuvant, thereby rendering the use of additional adjuvant not relevant.
• the vaccine is devoid of adjuvant (other than the bacteria itself).
• the vaccine comprises an adjuvant additional to the bacteria.
• Adjuvants are substance that can be added to an immunogen or to a vaccine formulation to enhance the immune-stimulating properties of the immunogenic moiety.
• adjuvants or agents that may add to the effectiveness of proteinaceous immunogens include aluminum hydroxide, aluminum phosphate, aluminum potassium sulfate (alum), beryllium sulfate, silica, kaolin, carbon, water-in-oil emulsions, and oil-in-water emulsions.
• a particular type of adjuvant is muramyl dipeptide (MDP) and various MDP derivatives and formulations, e.g., N-acetyl-D- glucosaminyl-(.beta.l-4)-N-acetylmuramyl-L-alanyl-D-isoglutami- ne (GMDP) (Hornung, R L et al. Ther Immunol 1995 2:7-14) or ISAF-1 (5% squalene, 2.5% pluronic L121, 0.2% Tween 80 in phosphate-buffered solution with 0.4 mg of threonyl-muramyl dipeptide; see Kwak, L W et al. (1992) N. Engl.
• MDP muramyl dipeptide
• GMDP N-acetyl-D- glucosaminyl-(.beta.l-4)-N-acetylmuramyl-L-alanyl-D
• a number of adjuvants are available commercially from various sources, for example, Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.) or Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.), Amphigen (oil-in-water), Alhydrogel (aluminum hydroxide), or a mixture of Amphigen and Alhydrogel.
• Merck Adjuvant 65 Merck and Company, Inc., Rahway, N.J.
• Freund's Incomplete Adjuvant and Complete Adjuvant Difco Laboratories, Detroit, Mich.
• Amphigen oval-in-water
• Alhydrogel aluminum hydroxide
• Aluminum is approved for human use.
• the vaccines described herein may be used to treat and/or prevent cancer.
• the term “treating” includes abrogating, substantially inhibiting, slowing or reversing the progression of a condition, substantially ameliorating clinical or aesthetical symptoms of a condition.
• the term preventing refers to substantially preventing the appearance of clinical or aesthetical symptoms of a condition.
• Particular subjects which are treated are mammalian subjects - e.g. humans.
• the subject has been diagnosed as having cancer.
• carcinomas which are cancers of the epithelial tissue (e.g., skin, squamous cells); sarcomas which are cancers of the connective tissue (e.g., bone, cartilage, fat, muscle, blood vessels, etc.); leukemias which are cancers of blood forming tissue (e.g., bone marrow tissue); lymphomas and myelomas which are cancers of immune cells; and central nervous system cancers which include cancers from brain and spinal tissue.
• carcinomas which are cancers of the epithelial tissue (e.g., skin, squamous cells)
• sarcomas which are cancers of the connective tissue (e.g., bone, cartilage, fat, muscle, blood vessels, etc.)
• leukemias which are cancers of blood forming tissue (e.g., bone marrow tissue)
• lymphomas and myelomas which are cancers of immune cells
• central nervous system cancers which include cancers from brain and spinal tissue.
• cancer refers to all types of cancer or neoplasm or malignant tumors including leukemias, carcinomas and sarcomas, whether new or recurring.
• cancers that may be treated using the bacteria described herein include, but are not limited to adrenocortical carcinoma, hereditary; bladder cancer; breast cancer; breast cancer, ductal; breast cancer, invasive intraductal; breast cancer, sporadic; breast cancer, susceptibility to; breast cancer, type 4; breast cancer, type 4; breast cancer- 1; breast cancer-3; breast-ovarian cancer; triple negative breast cancer, Burkitt’s lymphoma; cervical carcinoma; colorectal adenoma; colorectal cancer; colorectal cancer, hereditary nonpolyposis, type 1; colorectal cancer, hereditary nonpolyposis, type 2; colorectal cancer, hereditary nonpolyposis, type 3; colorectal cancer, hereditary nonpolyposis, type 6; colorectal cancer, hereditary nonpolyposis, type 7; dermatofibrosarcoma protuberans; endometrial carcinoma; esophageal cancer; gastric cancer
• the cancer is melanoma.
• Malignant melanomas are clinically recognized based on the ABCD(E) system, where A stands for asymmetry, B for border irregularity, C for color variation, D for diameter >5 mm, and E for evolving. Further, an excision biopsy can be performed in order to corroborate a diagnosis using microscopic evaluation. Infiltrative malignant melanoma is traditionally divided into four principal histopathological subgroups: superficial spreading melanoma (SSM), nodular malignant melanoma (NMM), lentigo maligna melanoma (LMM), and acral lentiginous melanoma (ALM). Other rare types also exists, such as desmoplastic malignant melanoma.
• SSM superficial spreading melanoma
• NMM nodular malignant melanoma
• LMM lentigo maligna melanoma
• ALM acral lentiginous melanoma
• Other rare types also exists, such as desmoplastic mal
• RGP radial growth phase
• VGP vertical growth phase
• the melanoma is resistant to treatment with inhibitors of BRAF and/or MEK.
• the tumor may be a primary tumor or a secondary tumor (i.e. metastasized tumor).
• compositions may be administered using any route such as for example oral administration, rectal administration, topical administration, inhalation (nasal) or injection.
• Administration by injection includes intravenous (IV), intramuscular (IM), intratumoral (IT), subtumoral (ST), peritumoral (PT), and subcutaneous (SC) administration.
• compositions described herein can be administered in any form by any effective route, including but not limited to intratumoral, oral, parenteral, enteral, intravenous, intraperitoneal, topical, transdermal (e.g., using any standard patch), intradermal, ophthalmic, (intra)nasally, local, non oral, such as aerosol, inhalation, subcutaneous, intramuscular, buccal, sublingual, (trans)rectal, vaginal, intra-arterial, and intrathecal, transmucosal (e.g., sublingual, lingual, (trans)buccal, (trans)urethral, vaginal (e.g., trans- and perivaginally), intravesical, intrapulmonary, intraduodenal, intragastrical, and intrabronchial.
• transdermal e.g., using any standard patch
• intradermal e.g., using any standard patch
• intradermal e.g., using any standard patch
• intradermal e.g.
• compositions described herein are administered orally, rectally, intratumorally, topically, intravesically, by injection into or adjacent to a draining lymph node, intravenously, by inhalation or aerosol, or subcutaneously.
• a first vaccine comprising a first bacteria which is genetically modified to express at least one cancer-associated antigen; and subsequently;
• a second vaccine comprising a second bacteria which is genetically modified to express at least one cancer-associated antigen, thereby treating the cancer.
• the present invention contemplates at least 2 different vaccination cycles for the treatment of cancer, wherein at least one of the vaccination cycles includes one strain of genetically modified bacteria and at least another of the vaccination cycles includes a second (non-identical) genetically modified strain of bacteria.
• the two strains of bacteria may be genetically modified to express the same cancer associated antigens or different cancer associated antigens.
• the present inventors contemplate at least one of the vaccination cycles includes viable bacteria (e,g, the first vaccination) and at least another of the vaccination cycles (e.g. a subsequent vaccination) includes attenuated (or dead) bacteria.
• the vaccine of the present invention may be administered with additional anti-cancer agents.
• the additional anti-cancer agent is an inhibitory antibody or small molecule directed against the immune checkpoint protein - e g. anti-CTLA4, anti-CD40, anti- 4 IBB, anti-OX40, anti -PD 1 and anti-PDLl.
• contemplated anti-cancer agents which may be administered to the subject in combination with the bacteria described herein include, but are not limited to Acivicin; Aclarubicin; Acodazole Hydrochloride; Acronine; Adriamycin; Adozelesin; Aldesleukin; Altretamine; Ambomycin; Ametantrone Acetate; Aminoglutethimide; Amsacrine; Anastrozole; Anthramycin; Asparaginase; Asperlin; Azacitidine; Azetepa; Azotomycin; Batimastat; Benzodepa; Bicalutamide; Bisantrene Hydrochloride; Bisnafide Dimesylate; Bizelesin; Bleomycin Sulfate; Brequinar Sodium; Bropirimine; Busulfan; Cactinomycin; Calusterone; Caracemide; Carbetimer; Carboplatin; Carmustine; Carubicin Hydrochloride; Carzelesin; Cede
• Vincristine Sulfate Vindesine; Vindesine Sulfate; Vinepidine Sulfate; Vinglycinate Sulfate; Vinleursine Sulfate; Vinorelbine Tartrate; Vinrosidine Sulfate; Vinzolidine Sulfate; Vorozole; Zeniplatin; Zinostatin; Zorubicin Hydrochloride.
• Additional antineoplastic agents include those disclosed in Chapter 52, Antineoplastic Agents (Paul Calabresi and Bruce A. Chabner), and the introduction thereto, 1202-1263, of Goodman and Gilman's "The Pharmacological Basis of
• compositions, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.
• a compound or “at least one compound” may include a plurality of compounds, including mixtures thereof.
• range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
• a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range.
• the phrases “ranging/ranges between” a first indicate number and a second indicate number and “ranging/ranges from” a first indicate number “to” a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.
• method refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.
• Ssph2 promoter and secretion signal (aa: 1-200), or the pagC promoter and Ssphl secretion signal (aa: 1-208) were amplified from the Salmonella Typhimurium attenuated strain VNP20009.
• Ssph2 and pagC-Ssphl were inserted into pQE60 by NEBbuilder cloning kit (cat. E5520S).
• Proteins of interest were fused with either Ssphl or Ssph2.
• proteins of interest were fused with the N-terminal 54 amino acids of ExoS in plasmid pEAI3-S54 (a courtesy of Bertrand Toussaint, PMID: 17010670).
• CotC amplified from Bacillus Subtilis 168
• 6His tag element was inserted to allow detection of the protein product.
• the C-terminal of Ovalbumin (aa 252-386) was amplified from pcDNA-OVA (Addgene 64599).
• the amplified oligo contains the sequence which corresponds to SIINFEKL (SEQ ID NO: 11), the epitope of Ovalbumin.
• Adpgk (aa 289-421) was amplified from cDNA of MC38 cells.
• the amplified oligo contains a sequence which corresponds to a validated neoantigen of MC38, based on Yadav et al. (PMID: 25428506).
• Both neoantigens were inserted to the backbone plasmids by NEBuilder cloning kit.
• the attenuated Salmonella Typhimurium strains VNP20009 also named YS1646, ATCC, cat. 202165) and STM3210 were transformed with the relevant plasmids by electroporation. Briefly, bacteria were cultured to OD of 0.6-0.8, washed 3 times with Hepes ImM and suspended in 10% glycerol in DDW. Suspension was electroporated with 0.2 cm, cuivette (BioRad, EC2) and moved to 1 ml cold SOC. Following 1 hour incubation in 37 °C, bacteria were seeded on LB agar plate containing ampicilin. Selected colonies were verified by Sanger sequencing and Western blot using anti-6His tag (Cell Signalling, 2365S).
• the attenuated pseudomonas aeruginosa was transformed as described by Diver et al. PMID: 2126169.
• the Bacillus Subtilis strain PY79 was transformed following incubation in minimal medium and 0.01M MGSO4 in DDW (MC: 80 mM K2HPO4, 30 mM KH2PO4, 2% Glucose, 30 mM Trisodium citrate, 22 pg/ml Ferric ammonium citrate, 0.1% Casein Hydrolysate (CAA), 0.2 % potassium glutamate) for 3 hours to induce competent bacteria.
• MC 80 mM K2HPO4, 30 mM KH2PO4, 2% Glucose, 30 mM Trisodium citrate, 22 pg/ml Ferric ammonium citrate, 0.1% Casein Hydrolysate (CAA), 0.2 % potassium glutamate
• Plasmid pDG364 which contains an antigen fused to CotC protein was cut with Xba and incubated with competent bacteria for 3 hours. Upon integration into the amylase gene, colonies were selected by resistance to chloramphenicol 5pg/ml
• Exponentially growing culture (OD 0.6-0.8), was washed twice in cold PBS. Bacteria pellet was suspended in 25 % glycerol in PBS. A sample from the bacterial stock was serially diluted and seeded on LB agar plate, while the rest of the pool was aliquoted and stored in - 80 °C. To verify viability of bacteria, a frozen aliquot was defrosted and seeded on LB agar plate. Recovery rate following freezing was quantified by calculating the ratio of frozen/fresh CFU count. Calculation of bacteria dosage in mice experiment was based on the CFU count of the frozen culture.
• Freshly resected spleens were mashed on a 70 micron strainer into cold PBS.
• the splenocytes were incubated with ACK lysis buffer (Quality Biological, cat. 118- 156-101), then washed thoroughly in PBS and suspended in FACS labeling buffer.
• 100 m ⁇ of splenocytes were incubated for 1 hour at 4 °C with a mixture containing Fc blocker (BD, cat. 553142, 1 : 100), SIINFEKL (SEQ ID NO: 11) Tetramer (NIH Tetramer Core Facility, 1:500), anti- CD4 (BioLegend, cat.
• Splenocytes were produced as described above. Next, splenocytes were incubated with OVA peptide (final cone. 2.5 pg/ml) for 2 hours at 37 °C. Next, Brafeldin A (BD, 51-2301kz) was added to the cells and incubated for additional 4 hours at 4 °C. FACS staining for CD3, CD8 and INFg were preformed the next day as described above.
• OVA peptide final cone. 2.5 pg/ml
• Brafeldin A BD, 51-2301kz
• MC38 or B16-OVA cells were seeded on 48 well plate.
• Cells were stained with CFSE (5uM) for 20 min at 37 °C, then quenched with culture medium (RPMI with 10% FCS) for 10 min at 37 °C and washed twice with culture medium.
• spleens were resected as described above and cells were counted. Next, 10 5 splenocytes were co-cultured with the tumor cells and incubated for 72 hours at 37 °C.
• mice were bled into Eppendorf tube containing 20 m ⁇ Heparin (lOmg/ml). Following centrifugation for 10 mins, 10,000g, sera were transferred to new tubes for long term storage at -20 °C.
• ELISA was performed according to manufacturer instructions (R&D, cat. DY485) using sera diluted 1:4.
• bacteria expressing the Ovalbumin known neoantigen SIINFEKL (SEQ ID NO: 11) were administered to mice bearing the B 16 melanoma tumors which express the Ovalbumin protein (B 16-OVA).
• B 16-OVA Ovalbumin protein
• the OVA neoantigen SIINFEKL (SEQ ID NO: 11) was fused to Ssph2 secretion signal of Salmonella Typhimurium. The resulted oligomer was transformed into the attenuated Salmonella Typhimurium strain VNP20009 (VNP-OVA).
• mice C57BL/6 mice were injected with 10 6 B16 OVA expressing cells in the right flank.
• mice were shuffled into the following treatment cohorts: No treatment control, mice receiving the checkpoint inhibitor, anti -PD 1 (75 pg per mouse, i.p, once a week), and mice receiving anti -PD 1 together with PACMAN-OVA (10 6 CFU, tail vein).
• the experiment time line is shown in Figure 1A.
• Tumor growth curves from treatment start are shown in Figure IB. Tumor growth was completely stopped for 20 days in the PACMAN-OVA cohort versus the exponential growth observed in the other mice cohorts. Following two cycles of immunization, all mice in the VNP-OVA cohort survived significantly longer than the mice in the other cohorts.
• splenocytes were profiled from mice bearing the B 16-OVA tumor following the administration of the PACMAN vaccine.
• the PACMAN-OVA contained the OVA neoantigen SIINFEKL (SEQ ID NO: 11) fused to Ssph2 secretion signal of Salmonella Typhimurium in the attenuated strain STM3210.
• OVA neoantigen was replaced by the MC38 neoantigen, Adpgk (PACMAN-Adpgk), which is not present in B 16-OVA cells.
• mice C57BL/6 mice were injected with 10 6 B16 OVA expressing cells in the right flank.
• mice were shuffled into the following treatment cohorts: No treatment control, mice receiving the checkpoint inhibitor, anti-PDl (75 pg per mouse, i.p, once a week), mice receiving anti-PDl together with PACMAN-OVA (10 6 CFU, tail vein) and mice receiving anti-PDl with PACMAN-Adpgk (10 6 CFU, tail vein).
• PACMAN-OVA 10 6 CFU, tail vein
• mice receiving anti-PDl with PACMAN-Adpgk 10 6 CFU, tail vein.
• mice bearing B 16-Ova tumor were vaccinated consecutively with two attenuated bacteria expressing the OVA neoantigen.
• the first bacteria is the Salmonella attenuated strain STM3210 expressing Ova neoantigen fused to either SshpH2 secretion signal under its endogenous promoter or to Ssphl secretion signal under pagC promoter which is induced upon phagocytosis by macrophages (STM-OVA).
• the second bacteria is the pseudomonas aeruginosa attenuated strain, CHA-OST, expressing Ova neoantigen fused to the secretion signal of ExoS, a toxin of the type-three secretion sysem (TTSS).
• ExoS promoter is activated by the TTSS regulator ExsA, following induction by IPTG (CHA-OST-OVA).
• mice C57BL/6 mice were injected with 10 6 B16 OVA expressing cells in the right flank.
• mice were shuffled into the following treatment cohorts: No treatment control, mice receiving the checkpoint inhibitor, anti-PDl (75 pg per mouse, i.p, once a week), mice receiving anti-PDl together with STM-SspH2-OVA and mice receiving anti- PDl together with STM-pagC-SspHl-OVA.
• the vaccinated mice were treated with 3 doses of STM-OVA (10 6 CFU, tail vein), followed by anti-PDl (75 pg per mouse, i.p, once a week).
• mice were treated with 2 doses of CHA-OST-OVA (10 7 CFU, tail vein, following 3 hours incubation with IPTG 0.5 mM).
• CHA-OST-OVA 10 7 CFU, tail vein, following 3 hours incubation with IPTG 0.5 mM.
• FIG 3B tumor growth was significantly delayed in the mice which were vaccinated with STM-OVA compared to non-vaccinated mice. The majority of tumors in the vaccinated mice regained growth 20-30 days post vaccination, suggesting that the additional injections of the same bacteria did not contribute enough to anti -tumor immunity..
• Strikingly, vaccinating the mice with CHA-OST- OVA slowed down tumor growth and in some cases even caused exponential decay.
• weight decrease is observed following each bacteria administration, however, weight loss is less pronounced after additional vaccination with the same bacteria, further supporting the hypothesis that the mice develop immunity towards the bacteria resulting in fast clearance and thus less effect on body weight.
• mice vaccinated with PACMAN-OVA To test the immune memory of mice vaccinated with PACMAN-OVA, fully cured mice from the experiment described in Figure 3 A were re-challenged with 10 6 B 16-Ova cells and tumor growth was compared to naive mice injected with the same amount of cells. As illustrated in Figure 4B, while naive mice exhibited exponentially growing tumors shortly after injection, re challenged mice remained tumor free, indicating the establishment of long term immune memory against B 16-Ova cells.
• the effect of bacteria expressing the Adpgk neoantigen of MC38 model was tested on mice bearing the MC38 CRC tumors.
• the Adpgk neoantigen was fused to Ssphl secretion signal of Salmonella Typhimurium under pagC promoter which is induced upon phagocytosis by macrophages.
• the oligomer was transformed into the attenuated Salmonella Typhimurium strain VNP20009 (PACMAN- Adpgk). C57BL/6 mice were injected with 10 5 MC38 cells in the right flank.
• mice When tumors reached a volume of -100 mm 3 , mice were shuffled into the following treatment cohorts: mice receiving the checkpoint inhibitor, anti -PD 1 (75 pg per mouse, i.p, once a week), mice receiving anti -PD 1 together with VNP20009 and mice receiving anti -PD 1 together with PACMAN-Adpgk (10 6 CFU, tail vein).
• mice vaccinated with PACMAN-Adpgk were re-challenged with 10 5 MC38 cells and tumor growth was compared to naive mice injected with the same amount of cells. While naive mice exhibited exponentially growing tumors shortly after injection, re-challenged mouse which was vaccinated with PACKMAN-Adpgk remained tumor free, indicating the establishment of long term immune memory against MC38 cells.
• the fully cured mouse following vaccination only with the VNP20009 exhibited tumor growth following re-challenge indicating that the immune memory was a consequence of Adpgk presentation by the bacteria (Figure 5C).
• Figure 8A illustrates the increase in IFNg positive CD8 T-cells following vaccination with the appropriate neoantigen.
• MC38 or B 16-OVA tumor cells were pre-incubated with CFSE (green) to distinguish them from immune cells.
• Harvested splenocytes were co-cultured with tumor cells.
• dead tumor cells CFSE positive
• Significant B 16-OVA specific killing was observed in splenocytes originating from mice vaccinated with STM3120 expressing the OVA neoantigen (Two-tail t-test, Pval ⁇ 0.001).
• Figure 9A is a graphic representation of the treatment protocol. As illustrated in Figure 9B, only mice which where injected with the PACMAN- ADPGK vaccine showed a full cure. Of note, the cured mouse was re-challenged with MC38 cells, however no tumor growth was observed.
• FIG. 10A is a graphic representation of the treatment protocol.
• mice which where injected with the PACMAN-ADPGK vaccine showed a full cure.

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