immunotherapeutic compositions of brachyury yeast, and their uses

专利摘要:
IMMUNOTHERAPEUTIC COMPOSITIONS OF BRACHYURY YEAST. The invention describes yeast-based immunotherapeutic compositions comprising Brachyury antigens, and methods for preventing and / or treating cancers characterized by the expression or overexpression of Brachyury.
公开号:BR112013023456B1
申请号:R112013023456-3
申请日:2012-03-19
公开日:2020-11-17
发明作者:Claudia Palena；Zhimin Guo；David Apelian；Jeffrey Schlom
申请人:Globeimmune, Inc.；The United States Of America, As Represented By The Secretary, Department Of Health And Human Services；
IPC主号:

专利说明:

CROSS REFERENCE WITH RELATED REQUESTS
[0001] This claim claims priority benefit under 35 USC § 119 (e) at US Provisional Request. No. 61 / 453,656, filed March 17, 2011. Full description of US Interim Order. No. 61 / 453,656, filed on March 17, 2011 is incorporated as a reference in this report. GOVERNMENT RIGHTS
[0002] This invention was created in the performance of a Cooperative Research and Development Agreement with the National Institute of Health (National Institutes of Health), an Agency of the Department of Health and Human Services. The United States Government has certain rights in this invention. DECLARATION WITH REGARD TO JOINT RESEARCH AGREEMENT
[0003] This invention was made by, or on behalf of, parties to a Cooperative Research and Development Agreement, executed on May 8, 2008. The parties to the Cooperative Research and Development Agreement are: Globelmmune, Inc. and the Department of Health and Human Services, as represented by the National Cancer Institute, an Institute, Centers or Division of the National Institute of Health. REFERENCE TO A SEQUENCE LISTING
[0004] This order contains a Sequence listing submitted electronically as a text file via EFS-Web. The text file, called "3923-34-PCT ST25", has a size in bytes of 76 KB, and was registered on March 13, 2012. The information contained in the text file is incorporated as a reference in this report in its entirety. compliance with 37 CFR § 1.52 (e) (5). FIELD OF THE INVENTION
[0005] The present invention generally relates to yeast-based immunotherapeutic compositions and methods for the prevention and / or treatment of cancers characterized by the expression or overexpression of Brachyury. BACKGROUND OF THE INVENTION
[0006] Brachyury, also known as "T", is a mesodermal transcription factor and a member of the T-box gene complex. The gene encoding Brachyury (termed as the T gene or Brachyury gene in humans) was initially identified in 1927 by Nadine DobrovolskaTa-ZavadskaTa through a mutation in mice that affected the length of the tail and sacral vertebrae in heterozygous animals. The Brachyury gene was cloned in mice in 1990 by Hermann et al. (Herrmann et al., 1990, Nature343: 617-622) and in humans in 1996 by Edwards et al. (Edwards et al., 1996, Genome Res.6: 226-223), who also described the deduced amino acid sequence for human Brachyury.
[0007] As a member of the T-box family of transcription factors, Brachyury contains the motif (motif) of the highly conserved DNA binding domain, called the "T-box" or T-domain, which binds to a sequence palindromic consensus. Brachyury, like other T-box proteins, has been shown to play a role in early development, and is vital for the formation and differentiation of posterior mesoderm and axial development in vertebrates (see, for example, Wilkinson et al., 1990, Nature343 (6259): 657-659); Beddington et al., 1992, Development (Suppl.yAδJ-lβS; Schulte-Merker et al., 1994, Development 120: 1009-1015; Kispert and Herrmann, 1994, Dev. Biol. 161: 179-193; Showell et al., 2004 , Dev. Dyn. 229: 201-218). More recently, Palena et al. have shown that Brachyury is expressed in a variety of human tumor tissues and cancer cell lines and have demonstrated that Brachyury peptides can be used to generate Brachyury-specific T cell lines in normal donors and cancer patients (Palena et al., 2007 , Clin Res. 13 (8): 2471-2478). Studies by Fernando and others have shown that Brachyury promotes the epithelial-mesenchymal transition (EMT) in human tumor cells, which confers a mesenchymal phenotype in tumor cells, as well as migratory and invasive capacities, while attenuating the progression of the tumor cell cycle ( Fernando et al., 2010, J. Clin. Invest.120 (2): 533-544). Consequently, Brachyury is involved in the metastatic progression of cancer.
[0008] Cancer is a leading cause of death in the world, and the development of effective cancer therapies remains one of the most active areas of clinical research and development. Although a variety of innovative approaches to treat and prevent cancers are proposed, many cancers continue to have a high mortality rate and can be difficult to treat or relatively insensitive to conventional therapies. Cancers associated with Brachyury expression can be found in a variety of tissues, including breast, small intestine, stomach, kidney, bladder, uterus, ovary, testicles, lungs, colon and prostate, and includes metastatic and end-stage cancers. In addition, Brachyury is expressed in tumors of B cell origin, such as chronic lymphocytic leukemia (CLL), B cell viruses transformed by Epstein-Barr virus, Burkitt's and Hodgkin's lymphomas. Therefore, Brachyury appears to play a role in a large number of human cancers. Although Brachyury, it has been proposed to be a target for cancer immunotherapy (see, for example, Palena and others, supra, Fernando and others, supra, and WO 2008/106551), since this is a relatively new cancer target, there is a need in the state of the art for new immunotherapeutic products that effectively treat and / or prevent cancers associated with Brachyury expression or overexpression. SUMMARY OF THE INVENTION
[0009] One embodiment of the invention relates to a method of reducing, stopping, reversing, delaying or preventing the metastatic progression of cancer in an individual who has cancer. The method includes the stage of administering, to an individual who has a type of cancer that is suffering from metastatic progression, is at risk of suffering metastatic progression, or is predicted to start suffering metastatic progression, an immunotherapeutic composition that comprises: (a) a yeast vehicle; and (b) a cancer antigen comprising at least one Brachyury antigen. Another embodiment of the invention relates to the use of an immunotherapeutic composition comprising a yeast vehicle and a cancer antigen comprising at least one Brachyury antigen, to reduce, arrest, reverse or prevent metastatic progression of cancer in an individual who has cancer.
[00010] In one aspect, of these modalities of the invention, Brachyury is not detected in the individual's cancer, the moment the composition is first administered. In one aspect, Brachyury expression is detected in the individual's cancer the moment the composition is first administered. The individual may have stage I cancer, stage II cancer, stage III cancer, or stage IV cancer.
[00011] Another embodiment of the invention relates to a method of preventing or delaying the onset of a cancer expressing Brachyury. The method includes the step of administering an immunotherapeutic composition to an individual comprising: (a) a yeast vehicle; and (b) a cancer antigen comprising at least one Brachyury antigen. Another embodiment of the invention relates to the use of an immunotherapeutic composition comprising a yeast vehicle and a cancer antigen comprising at least one Brachyury antigen to prevent or delay the onset of a cancer expressing Brachyury.
[00012] In one aspect of these modalities, cancer is not detected in the individual. In one aspect, the individual is at high risk of developing cancer (for example, via a genetic predisposition). In one aspect, the individual has a precancerous lesion.
[00013] In one aspect of these modalities, the individual has cancer, but cancer cells expressing Brachyury have not been detected in the cancer. In one respect, cancer is not yet metastatic. In one aspect, cancer has a high risk of metastasis. In one aspect, the individual has stage I cancer. In one aspect, the individual has stage II cancer.
[00014] Another embodiment of the invention relates to a method of reducing or preventing resistance to chemotherapy or resistance to tumor cell radiation in a cancer patient. The method includes the steps of administration to an individual who has cancer and is receiving chemotherapy and / or radiation therapy from an immunotherapeutic composition that comprises: (a) a yeast vehicle; and (b) a cancer antigen comprising at least one Brachyury antigen. Another embodiment of the invention relates to the use of an immunotherapeutic composition comprising a yeast vehicle and a cancer antigen comprising at least one Brachyury antigen to reduce or prevent resistance to chemotherapy or resistance to radiation from tumor cells in a cancer patient . In one aspect of this embodiment of the invention, Brachyury is not detected in the individual's cancer the moment the composition is first administered. In one aspect, Brachyury expression is detected in the individual's cancer, the moment the composition is first administered.
[00015] Yet another embodiment of the invention relates to a method for treating cancer. The method includes the steps of: (a) administering to an individual who has cancer in which Brachyury expression is not detected, a first immunotherapeutic composition that comprises a yeast vehicle and a first cancer antigen that does not comprise a Brachyury antigen, (b) administering to the subject, prior to, simultaneously with, sequentially with, or subsequent to, administration of the first immunotherapeutic composition, a second immunotherapeutic composition comprising a yeast vehicle and a second cancer antigen comprising a Brachyury antigen. In one aspect, the method additionally comprises, in step (a), administering one or more additional immunotherapeutic compositions, wherein each or more of the additional immunotherapeutic compositions comprises an additional cancer antigen. In one aspect, from each modality above, the cancer antigen is selected from: Ras mutant, carcinoembryonic antigen (CEA), MUC-1, EGFR, BCR-Ab1, MART-1, MAGE-1, MAGE-3, GAGE, GP-100, MUC-2, PSMA, tyrosinase, TRP-1 (gp75), NY-ESO-1, TRP-2, TAG72, KSA, CA-125, PSA, HER-2 / neu / c-erb / B2 , hTERT, p73, B-RAF, coli adenomatous polyposis (APC), Myc, von Hippel-Lindau protein (VHL), Rb-1, Rb-2, androgen receptor (RA), Smad4, MDR1, Flt-3, BRCA-1, BRCA-2, pax3-fkhr, ews-fli-1, HERV-H, HERV-K, TWIST, Mesothelin and NGEP. In one aspect, the cancer antigen is selected from the group consisting of: Ras mutant, carcinoembryonic antigen (CEA) and MUC-1. Another embodiment of the invention relates to the use of a combination of immunotherapeutic compositions to treat cancer, immunotherapeutic compositions comprising: (a) a first immunotherapeutic composition comprising a yeast vehicle and a first cancer antigen that does not comprise a Brachyury antigen; and (b) a second immunotherapeutic composition comprising a yeast vehicle and a second cancer antigen comprising a Brachyury antigen.
[00016] Yet another embodiment of the invention relates to a method for treating cancer. The method includes the steps of: (a) administering to an individual who has cancer a first immunotherapeutic composition comprising a yeast vehicle and a mutant Ras antigen; (b) administering to the individual from (a) a second immunotherapeutic composition comprising a yeast vehicle and an antigen selected from the group consisting of carcinoembryonic antigen (CEA) and mucin-1 (MUC-1); and (c) administering to the individual of (a) and (b) a third immunotherapeutic composition comprising a yeast vehicle and a Brachyury antigen. In one aspect, the administration steps in (a), (b) and (c) are concurrent. Another embodiment of the invention relates to the use of a combination of immunotherapeutic compositions to treat cancer, the immunotherapeutic compositions comprising: (a) a first immunotherapeutic composition comprising a yeast vehicle and a mutant Ras antigen; (b) a second immunotherapeutic composition comprising a yeast vehicle and an antigen selected from the group consisting of carcinoembryonic antigen (CEA) and mucin-1 (MUC-1); and (c) a third immunotherapeutic composition comprising a yeast vehicle and a Brachyury antigen.
[00017] In any of the modalities or aspects of the invention described above or anywhere else in this report, where the individual has cancer or a precancerous lesion, in one aspect of the invention, the individual is being treated or has been treated with another cancer therapy. For example, such therapy may include, but is not limited to, chemotherapy, cancer-targeted therapy, radiation therapy, adoptive T cell transfer, and / or administration of one or more additional immunotherapeutic compositions. In one aspect, an additional immunotherapeutic composition comprises a yeast vehicle and a second cancer antigen that does not include Brachyury antigen. The second cancer antigen may include, but is not limited to, mutant Ras, carcinoembryonic antigen (CEA), MUC-1, EGFR, BCR-Ab1, MART-1, MAGE-1, MAGE-3, GAGE, GP-100 , MUC-2, PSMA, tyrosinase, TRP-1 (gp75), NY-ESO-1, TRP-2, TAG72, KSA, CA-125, PSA, HER-2 / neu / c-erb / B2, hTERT, p73, B-RAF, coli adenomatous polyposis (APC), Myc, von Hippel-Lindau protein (VHL), Rb-1, Rb-2, androgen receptor (RA), Smad4, MDR1, Flt-3, BRCA-1 , BRCA-2, pax3-fkhr, ews-fli-1, HERV-H, HERV-K, TWIST, Mesothelin and NGEP. In one aspect, the second cancer antigen is selected from: Ras mutant, carcinoembryonic antigen (CEA), and MUC-1.
[00018] In one aspect of any of the modalities or aspects of the invention described above, or anywhere else in this report, the method or use reduces tumor burden on the individual, increases survival of the individual, and / or inhibits tumor growth in the individual.
[00019] In one aspect of any of the modalities or aspects of the invention described above or elsewhere in this report, the method additionally comprises surgical resection of a tumor from the individual.
[00020] In one aspect of any of the modalities or aspects of the invention described above or elsewhere in this report, the cancer is of epithelial cell origin. In one aspect, cancer can include, but is not limited to, breast cancer, small intestine cancer, stomach cancer, pancreatic cancer, kidney cancer, bladder cancer, uterine cancer, ovarian cancer, testicular cancer, cancer of lung, colon cancer, prostate cancer, chronic lymphocytic leukemia (LLC), B cells transformed by Epstein-Barr virus, Burkitt lymphoma, Hodgkine lymphoma, metastatic cancers of these.
[00021] In one aspect of any of the embodiments or aspects of the invention described above, the Brachyury antigen is full-length human Brachyury. In one respect, the Brachyury antigen is not a full-length Brachyury. In one aspect, the Brachyury antigen has an amino acid sequence represented by SEQ ID NO: 6, SEQ ID NO: 18, SEQ ID NO: 2, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 6, SEQ ID NO: 18, or SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises at least position 1 or 2 between position 255 and the C terminus of SEQ ID NO: 6, SEQ ID NO: 18, or SEQ ID NO: 2. In one aspect, Brachyury antigen comprises at least position 1 or 2 between position 430 and end C of SEQ ID NO: 6, SEQ ID NO: 18 , or SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises positions 246 to 254 of SEQ ID NO: 6, SEQ ID NO: 18, or SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises SEQ ID NO: 6; positions 2-435 of SEQ ID NO: 6, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 6. In one aspect, the Brachyury antigen comprises SEQ ID NO: 18; positions 2-435 of SEQ ID NO: 18, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 18. In one aspect, Brachyury antigen comprises SEQ ID NO: 2, positions 2-435, of SEQ ID NO: 2, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises SEQ ID NO: 6, positions 2-435, of SEQ ID NO : 6, or an amino acid sequence that is at least 99% identical to SEQ ID NO: 6. In one aspect, Brachyury antigen comprises SEQ ID NO: 18, positions 2-435 of SEQ ID NO: 18, or an amino acid sequence that is at least 99% identical to SEQ ID NO: 18. In one aspect, the Brachyury antigen comprises SEQ ID NO: 2; positions 2-435 of SEQ ID NO: 2, or an amino acid sequence that is at least 99% identical to SEQ ID NO: 2. In one aspect, the cancer antigen is at least 25 amino acids in length. In one aspect, the Brachyury antigen is at least 25 amino acids in length. In one respect, the Brachyury antigen is greater than 30 amino acids in length. In one aspect, the cancer antigen comprises two or more immunogenic Brachyury domains.
[00022] In one aspect of any of the modalities or aspects of the invention described above or elsewhere in this report, the cancer antigen is a fusion protein. In one aspect, the fusion protein has an amino acid sequence represented by SEQ ID NO: 8, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 8. In one aspect, the fusion protein has a amino acid sequence represented by SEQ ID NO: 20, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 20.
[00023] Another embodiment of the invention relates to a Brachyury yeast immunotherapeutic composition, wherein the immunotherapeutic composition comprises: (a) a yeast vehicle; and (b) an antigen expressed by the yeast vehicle and comprising at least one Brachyury antigen, wherein the Brachyury antigen comprises more than 30 amino acids from an amino acid sequence represented by SEQ ID NO: 6, SEQ ID NO: 18 or SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises an amino acid sequence that is at least 95% identical to SEQ ID NO: 6, SEQ ID NO: 18 or SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises of at least position 1 or 2 between position 255 and end C of SEQ ID NO: 6, SEQ ID NO: 18 or SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises of, at least, position 1 or 2 between position 430 and the end C of SEQ ID NO: 6, SEQ ID NO: 18 or SEQ ID NO: 2. In one aspect, Brachyury antigen comprises positions 246 to 254 of SEQ ID NO : 6, SEQ ID NO: 18 or SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises SEQ ID NO: 6; positions 2-435 of SEQ ID NO: 6, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 6. In one aspect, the Brachyury antigen comprises SEQ ID NO: 18; positions 2-435 of SEQ ID NO: 18, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 18. In one aspect, the Brachyury antigen comprises SEQ ID NO: 2; positions 2-435 of SEQ ID NO: 2, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 2. In one aspect, the Brachyury antigen comprises SEQ ID NO: 6; positions 2-435 of SEQ ID NO: 6, or an amino acid sequence that is at least 99% identical to SEQ ID NO: 6. In one aspect, the Brachyury antigen comprises SEQ ID NO: 18; positions 2-435 of SEQ ID NO: 18, or an amino acid sequence that is at least 99% identical to SEQ ID NO: 18. In one aspect, the Brachyury antigen comprises SEQ ID NO: 2; positions 2-435 of SEQ ID NO: 2, or an amino acid sequence that is at least 99% identical to SEQ ID NO: 2. In one aspect, the cancer antigen is a fusion protein. In one aspect, the fusion protein has an amino acid sequence that is SEQ ID NO: 8, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 8. In one aspect, the fusion protein has a amino acid sequence of SEQ ID NO: 20, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 20. In one aspect, the yeast vehicle is a total yeast. In one aspect, the total yeast is inactivated by heat.
[00024] Yet another embodiment of the invention relates to a Brachyury yeast immunotherapeutic composition comprising: (a) a total inactivated yeast; and (b) a Brachyury fusion protein comprising the amino acid sequence of positions 2-435 of SEQ ID NO: 6. The expression of the Brachyury fusion protein is under the control of the CUP1 promoter, the Brachyury fusion protein is expressed by yeast , and the composition induces a Brachyury-specific T cell response. In one aspect, the fusion protein comprises the amino acid sequence of SEQ ID NO: 8.
[00025] Yet another embodiment of the invention relates to a Brachyury yeast immunotherapeutic composition comprising: (a) a total, inactivated yeast; and (b) a Brachyury fusion protein comprising the amino acid sequence of positions 2-435 of SEQ ID NO: 18. The expression of the Brachyury fusion protein is under the control of the CPU1 promoter, the Brachyury fusion protein is expressed by yeast , and the composition induces a Brachyury-specific T cell response. In one aspect, the fusion protein comprises the amino acid sequence of SEQ ID NO: 20.
[00026] In one aspect of any of the modalities or aspects of the invention described above or elsewhere in this report, the yeast vehicle is a total yeast. In one aspect, the total yeast is killed. In one aspect, the total yeast is inactivated by heat. In one respect, yeast expresses the antigen. In one aspect, yeast is from a genus selected from the group consisting of: Saccharomyces, Candida, Cryptococcus, Hansenula, Kluyveromyces, Pichia, Rhodotorula, Schizosaccharomyces and Yarrowia. In one respect, the yeast is from Saccharomyces. In one aspect, the yeast is from Saccharomyces cerevisiae.
[00027] In one aspect of any of the embodiments of the invention described above or elsewhere in this report, the composition is formulated in a pharmaceutically acceptable excipient suitable for administration to an individual.
[00028] Yet another embodiment of the invention relates to the use of any of the Brachyury yeast immunotherapeutic compositions described in this report to treat a disease. In one aspect, the disease is cancer. In one aspect, the disease is associated with an infectious agent. In one aspect, the disease is associated with a virus or viral infection. Such a virus may include, but is not limited to, Epstein-Barr Virus (EBV).
[00029] Another embodiment of the invention relates to a method for treating or preventing a disease or condition associated with Epstein-Barr Virus (EBV) infection. The method includes the step of administering to any individual any of the Brachyury yeast immunotherapeutic compositions described in this report.
[00030] Yet another embodiment of the invention relates to a method for producing a Brachyury yeast immunotherapeutic composition. The method includes the steps of: (a) cultivating yeast that has been transformed with a recombinant nucleic acid molecule that encodes a Brachyury antigen under the control of a CUP1 promoter in a suitable medium in the absence of CuSCXi until the yeast reaches its growth stage medium; (b) induce expression of Brachyury antigen in yeast by adding CuSθ4 to the medium; (c) cultivate the yeast after step (b) for up to 6 to 8 hours; and (d) harvesting the yeast. In one aspect, the yeast in step (a) is grown at a cell density of between 1.0 and 2.0 Y. U. per milliliter of total culture volume. In one aspect, the yeast in step (a) is grown at a cell density of between 1.0 and 1.5 Y. U. per milliliter of total culture volume. In one aspect, yeast is grown in steps (a) - (c) in a medium where the pH is maintained at pH 5.5 or higher. In one aspect, the method additionally includes a yeast heat inactivation step after step (d). For example, in one aspect, the yeast is heat inactivated at approximately 56 ° C for about 1 hour. In a further aspect of this embodiment, the yeast can be formulated for injection with a pharmaceutically acceptable excipient. In one respect, the yeast is from Saccharomyces. In one aspect, the yeast is from Saccharomyces cerevisiae. BRIEF DESCRIPTION OF THE FIGURES
[00031] Fig. 1A is a scanned image of a Western blot showing anti-Brachyury detection of Brachyury expression in a Brachyury yeast immunotherapeutic composition, with both U2 and UL2 media.
[00032] Fig. 1B is a scanned image of a Western blot showing anti-His detection of Brachyury expression in a Brachyury yeast immunotherapeutic composition, with both U2 and UL2 media.
[00033] Fig. 2 is a scanned image of a Western blot showing Brachyury expression in a Brachyury yeast immunotherapeutic composition, in which cell density under antigen induction and harvest time after antigen induction were variable.
[00034] Figures 3A-3C are graphs showing that peripheral blood mononuclear cells (PBMCs) from two out of three healthy donors, pulsed with Brachyury yeast for two cycles of stimulation, followed by pulsation with Brachyury's CTL peptide, were able to generate CD8 + CTLs that can kill SW480 carcinoma cells (HLA-A2 positive / high Brachyury), with minimal lysis of MCF7 carcinoma (HLA-A2 positive / low Brachyury) -, (Fig. 3A, donor 07706; Fig. 3B, donor 17663; Fig. 3C, donor 26532).
[00035] Fig. 4A is a graph showing healthy donor-specific Brachyury T cells PBMCs stimulated with a Brachyury yeast immunotherapeutic composition specifically lysis of tumor cells that show MHC carcinoma cells (SW480, HLA-A2 positive / high Brachyury) versus appropriate H226 (HLA-A2 negative / high Brachyury).
[00036] Fig. 4B is a graph showing the expression of Brachyury mRNA in relation to that of a control gene (GAPDH) in tumor cells SW480 and H226 used in the experiment shown in Fig. 4A.
[00037] Fig. 5 is a graph showing proliferation of CD4 + T cells isolated from the spleen of mice that were vaccinated with Brachyury yeast (GI-6301, circles) or control yeast (yeast control, triangles) in response to indicated doses of purified Brachyury protein or control β-gal protein.
[00038] Fig. 6 is a graph showing that administration of a Brachyury yeast immunotherapeutic composition (GI-6301, circles) of the invention shows a trend towards reducing tumors expressing Brachyury in mice compared to mice receiving yeast alone (no antigen) of Brachyury).
[00039] Figures 7A and 7B are flow cytometry analyzes showing that the Brachyury-specific T cell line, T-2-BR-A, binds to a Brachyury-specific HLA-A2 tetramer (Fig. 7B) and not to a control tetramer (Fig. 7A).
[00040] Fig. 8 is a flow cytometry analysis showing the expression of perforin in the Brachyury-specific T cell line, T-2-BR-A, after stimulation with autologous B cells pulsed by Brachyury agonist peptide. DETAILED DESCRIPTION OF THE INVENTION
[00041] This invention generally relates to yeast-based immunotherapeutic compositions and methods for the prevention and / or treatment of cancers that express or overexpress Brachyury. The invention includes the use of a yeast-based immunotherapeutic composition (also referred to as yeast-based immunotherapy), which comprises a yeast vehicle and Brachyury antigens or immunogenic domains thereof (also referred to in this report as "Brachyury yeast immunotherapy" ^ 'or "Brachyury yeast immunotherapeutic compositions”). The inventors describe in this report, the construction and production of new Brachyury yeast immunotherapeutic products, and demonstrated that Brachyury yeast immunotherapy expands Brachyury-specific T cells, including CD8 'CTLs, from normal individuals and from cancer patients. In addition, mice immunized with Brachyury yeast immunotherapeutic compositions generated Brachyury-specific T cell responses in vivo, and tumor growth expressing Brachyury was inhibited in these mice. Taken together, the data presented in this report show that Brachyury yeast immunotherapy is useful for eliciting Brachyury-specific cellular immune responses (CD4 + and CD8 +) and for the prevention and treatment of tumors expressing Brachyury, offering new therapy for the prevention and / or treatment of metastatic cancers and associated conditions.
[00042] Brachyury yeast immunotherapeutic compositions useful in the present invention are uniquely adapted for cancers expressing Brachyury effectively targeted for several reasons. First Brachyury is involved in EMT processes, and therefore, without being bound by theory, the inventors believe that Brachyury plays a role in late stage tumors and metastatic processes. Consequently, in one aspect of the invention, Brachyury yeast immunotherapy is effective in targeting tumor cells, before or in the moment, during which time they begin to acquire motility and invade other tissues, thereby preventing, inhibiting, stopping, reversing or delaying the onset of metastatic cancer and / or the progression of cancer, and especially, metastatic cancer. There is a great need for effective therapies for late-stage cancers, especially metastatic cancers, which may have few treatment options since conventional cancer therapy was insufficient. Brachyury yeast presents a new approach for the treatment of such cancers, or to delay, inhibit, reverse, or prevent them altogether. In addition, Brachyury yeast immunotherapy can be used to prevent or delay metastatic cancer or cancer progression in individuals who have early stage cancer. Therapy is useful, in one modality, in cancers that have a high rate of metastatic progression, and may be useful in stopping cancer progression. In addition, Brachyury yeast immunotherapy is useful in individuals who have a pre-cancerous (pre-malignant) lesion or tumor, in individuals who are at a high risk of developing cancer, particularly one who has a high rate of metastases, and also in normal individuals, as a prophylactic agent for cancer prevention, which can be used in conjunction with other prophylactic immunotherapies for cancer, as described in this report.
[00043] Brachyury yeast immunotherapy also provides a benefit to individuals who are undergoing other cancer therapy, including chemotherapy and radiation therapy. More particularly, metastatic cancers are known in some cases to be more resistant to chemotherapy and / or radiation therapy than primary cancers. Therefore, the Brachyury yeast immunotherapy compositions of the invention, can be used to inhibit or reduce, or eliminate resistance to chemotherapy or resistance to radiation that can occur in metastatic cancers by inhibiting Brachyury expression in cancer (and thus , inhibiting antiproliferative influences), and the compositions of the invention may enhance the performance of chemotherapy or radiation therapy in an individual.
[00044] Brachyury yeast immunotherapy can also be used to treat conditions or diseases associated with Brachyury expression that may be non-oncological in nature, or that may precede malignant transformation. For example, Brachyury can be induced in cells that are infected with an infectious agent, for example, a virus, such as Epstein-Barr Virus (EBV). Consequently, Brachyury yeast immunotherapy can be used to treat or prevent any disease or condition associated with Brachyury expression, including, but not limited to, infectious diseases, such as viral infection, including, but not limited to, conditions associated with Epstein-Barr virus (for example, mononucleosis).
[00045] Brachyury yeast immunotherapy is also readily adaptable for the use of additional tumor antigens within the same yeast composition, or for use in combination with other yeast-based immunotherapeutics that target other tumor antigens (sequentially or concurrently) or other immunotherapeutics and cancer treatments / therapies. Consequently, Brachyury yeast immunotherapy can be adapted to the type of cancer; the stage of cancer, the degree of cancer, the antigens expressed by the tumor, and the general medical condition of the individual (that is, the therapy is easily personalized), and for the individual who already has cancer, its use can be modified when the cancer evolves in an individual in order to provide maximum effectiveness under a variety of tumor stages. Brachyury yeast immunotherapy offers the opportunity to design individualized, sophisticated and effective approaches to prophylactic and / or therapeutic treatment based on a wide range of cancers.
[00046] Brachyury yeast compositions described in this report induce innate immune responses, as well as adaptive immune responses against the target antigen (Brachyury), including CD4-dependent T cell, TH 17 and TH1 responses and CD8 + T cell responses antigens, which include cytotoxic T lymphocyte responses (CTL), all without the use of exogenous adjuvants, cytokines, or other immunostimulatory molecules, many of which have toxic tissues. In addition, Brachyury yeast immunotherapeutic compositions inhibit regulatory numbers of T cells (Treg) and / or functionality, thereby intensifying effector T cell responses that could normally be suppressed by the presence of the tumor, for example. In addition, when compared to immunotherapeutic compositions that immunize by generating antibody responses, broad-based and potent antigen-specific cellular immune responses induced by Brachyury yeast immunotherapy are believed to be particularly effective in targeting cells tumoral. In fact, numerous studies have shown that immunotherapeutic approaches are enhanced when tumor cells are targeted via CD8 + CTLs, which recognize tumor peptides in the context of MHC Class I molecules.
[00047] Brachyury yeast immunotherapy is highly competent in activating cells presenting antigen, and has a unique ability to cross-prime to the immune response, generating CD8 + CTL responses that are typically effective against tumors, even if they may otherwise be one. suppressive environment. Since this type of immunotherapy uses the cell's natural ability to present antigen that displays relevant immunogens, it is not necessary to know the exact identity of CTL epitopes or Brachyury MHC Class II epitopes to produce an effective immunotherapeutic in accordance with the present invention. . In fact, CD4 + and CD8 + T cell epitopes can be targeted in a single Brachyury yeast immunotherapeutic composition, and thus the Brachyury yeast immunotherapeutics of the invention are not limited to the use of short peptides and, in fact, the use of longer polypeptides , and fusion proteins in these compositions becomes effective. Consequently, using Brachyury yeast immunotherapy, the use of complex algorithms and formulas to identify putative T cell epitopes is eliminated.
[00048] Furthermore, since Brachyury is not expressed by more normal (non-tumor) tissues, and is typically overexpressed in tumor cells, any "off-target" effects related to normal tissues are not of concern. As mentioned above, Brachyury's yeast can be effectively used in an immunization protocol (prophylactic or therapeutic) without the use of exogenous adjuvants, immunostimulatory agents or molecules, co-stimulatory molecules, or cytokines, although such agents can be included, if desired. In addition, Brachyury yeast immunotherapy can be administered repeatedly without losing effectiveness, as it can be problematic with other types of immunotherapy. Compositions of the Invention
[00049] One embodiment of the present invention relates to a yeast-based immunotherapeutic composition that can be used to prevent and / or treat cancers characterized by Brachyury expression or overexpression (including, cancers that may not contain cells expressing detectable Brachyury initially , but which may or will contain cells expressing Brachyury in later stages of cancer development). The composition is a Brachyury yeast immunotherapeutic composition comprising: (a) a yeast vehicle; and (b) a cancer antigen comprising one or more Brachyury antigens and / or immunogenic domain (s) thereof. The Brachyury antigen or its immunogenic domain is more typically expressed as a recombinant protein by the yeast vehicle (for example, by an intact yeast or yeast spheroplasty, which can be optional and further processed into a yeast cytoplasm, yeast spectrum or yeast membrane extract or fraction thereof), although it is an embodiment of the invention that one or more Brachyury antigens are loaded into a yeast vehicle, or otherwise complexed with, bound to, mixed with, or administered with a vehicle yeast as described in this report to form a composition of the present invention.
[00050] A "Brachyury yeast immunotherapeutic composition" is a specific type of "yeast-based immunotherapeutic composition" that contains at least one Brachyury antigen or its immunogenic domain. The term "yeast-based immunotherapeutic composition" may be used interchangeably with "yeast-based immunotherapy product", "yeast-based immunotherapy composition", "yeast-based composition", "yeast-based immunotherapy", "yeast-based vaccine", or derivatives of those expressions. An "immunotherapeutic composition" is a composition that induces an immune response sufficient to obtain at least one therapeutic benefit in an individual. As used in this report, yeast-based immunotherapeutic composition refers to a composition that includes a yeast carrier component and that induces an immune response sufficient to obtain at least one therapeutic benefit in an individual. More particularly, a yeast-based immunotherapeutic composition is a composition that includes a yeast carrier component and typically an antigen component, and can elicit or induce an immune response, such as a cellular immune response, including, without limitation, a cellular response. T cell-mediated cellular immune response. In one aspect, a yeast-based immunotherapeutic composition useful in the invention is capable of inducing a CD8 + and / or CD4 + T cell-mediated immune response and, in one aspect, a T cell-mediated immune response. CD8 + and CD4 +, particularly, against a target antigen (for example, a cancer antigen). A CD4 + immune response can include TH1 immune responses, TH2 immune responses, TH 17 immune responses, or any combination of the above. Yeast-based immunotherapeutics are particularly capable of generating TH1 and TH 17 responses. A CD8 + immune response can include a T lymphocyte cytotoxic response (CTL), and yeast-based immunotherapeutics are capable of generating such responses. In one aspect, a yeast-based immunotherapeutic composition modulates the number and / or functionality of regulatory T cells (Tregs) in an individual. Yeast-based immunotherapy can also be modified to promote one type of response over another, for example, by adding cytokines, antibodies, and / or modulating the yeast production process. Optionally, a yeast-based immunotherapeutic composition is capable of inducing a humoral immune response.
[00051] Brachyury yeast immunotherapeutic compositions of the invention may be "prophylactic" or "therapeutic". When provided prophylactically, the compositions of the present invention are provided with anticipation of the development of, or the detection of the development of, a cancer that expresses Brachyury, with the aim of preventing, inhibiting or delaying the development of tumors expressing Brachyury, and / or preventing , inhibit or delay tumor migration and / or tumor invasion from other tissues (metastases); and / or generally prevent or inhibit cancer progression in an individual. As discussed in this report, Brachyury is expressed in a number of cancers, including advanced stage cancers, and has been shown to be involved in the EMT process, which is a process associated with invasiveness and tumor migration, such as metastatic cancer. Therefore, prophylactic compositions can be administered to individuals who appear to be cancer-free (healthy, or normal individuals), to individuals with pre-cancerous lesions (pre-malignant lesions) and also to individuals who have cancer, but where Brachyury has not yet been detected (that is, before the expression of Brachyury by tumor cells in cancer). Individuals who are at high risk of developing cancer, particularly cancer with which Brachyury expression and / or metastases are typically associated, may be treated prophylactically with a composition of the invention. When provided therapeutically, the immunotherapy compositions are provided to an individual with a cancer expressing Brachyury, for the purpose of improving the cancer, such as reducing the tumor burden on the individual; inhibiting tumor growth in the individual; increasing the individual's survival; preventing, inhibiting, reversing, or delaying the development of tumor migration and / or invasion of the tumor from other tissues (metastatic cancer) and / or preventing, inhibiting, reversing or delaying the progression of cancer in the individual. In one aspect, Brachyury yeast immunotherapy is used therapeutically to inhibit, reduce or eliminate resistance to chemotherapy or resistance to radiation that can occur in metastatic cancer by inhibiting Brachyury expression in cancer, and compositions of the invention can improve performance of chemotherapy or radiation therapy in an individual.
[00052] Typically, a yeast Brachyury immunotherapy composition includes a yeast vehicle and at least one cancer antigen comprising a Brachyury antigen or immunogenic domain thereof, in which the cancer antigen is expressed, linked with, loaded onto, or mixed with the yeast vehicle. In some embodiments, the cancer antigen, Brachyury antigen, or its immunogenic domain, is provided as a fusion protein. Several Brachyury proteins and fusion proteins suitable for use in the compositions and methods of the invention are described below. In some modalities, the cancer antigen and the Brachyury antigen are the same elements. In some embodiments, the cancer antigen includes other antigens, including other cancer antigens, in addition to the Brachyury antigen. In one aspect of the invention, a fusion protein useful as a cancer antigen may include two or more antigens, for example, a Brachyury antigen and another cancer antigen that is not a Brachyury antigen, or two different Brachyury antigens. In one aspect, the fusion protein may include two or more immunogenic domains of one or more antigens, such as, two or more immunogenic domains of a Brachyury antigen, or two or more epitopes of one or more antigens, such as, two or more epitopes of a Brachyury antigen.
[00053] According to the present invention, a yeast vehicle used in a Brachyury yeast immunotherapy composition is any yeast cell (for example, a total or intact cell) or a derivative thereof (see below) that can be used together with one or more antigens, domains thereof, or epitopes thereof, in a composition of the invention (for example, a therapeutic or prophylactic composition). The yeast vehicle can therefore include, but is not limited to, an intact (total) live yeast microorganism (i.e., a yeast cell with all its components, including a cell wall), a yeast microorganism destroyed (killed) or inactivated intact yeast microorganism, or intact yeast derivatives, including: a yeast spheroplast (ie, a yeast cell devoid of a cell wall), a yeast cytoplasm (ie, a yeast cell devoid of a cell wall and nucleus), a yeast spectrum (that is, a yeast cell devoid of a cell wall, nucleus and cytoplasm), a subcellular yeast membrane extract or fraction thereof (also referred to as a yeast membrane particle and, previously, as a subcellular yeast particle), any other yeast particle, or a yeast cell wall preparation.
[00054] Yeast spheroplasts are typically produced by enzymatic digestion of the yeast cell wall. Such a method is described, for example, in Franzusoff et al., 1991, Meth. Enzymol. 194, 662-674, incorporated in this report as a reference in its entirety.
[00055] Yeast cytoplasts are typically produced by enucleation of yeast cells. Such a method is described, for example, in Coon, 1978, Natl. Cancer Inst. Monogr. 48, 45-55 incorporated in this report as a reference in its entirety.
[00056] Yeast spectra are typically produced by resealing a permeabilized or lysed cell and may, but not necessarily, contain at least some of the cell's organelles. Such a method is described, for example, in Franzusoff et al., 1983, J. Biol. Chem. 258, 3608-3614, and Bussey et al., 1979, Biochim. Biophvs. Acta553, 185-196, each of which is incorporated in this report as a reference in its entirety.
[00057] A yeast membrane particle (subcellular yeast membrane extract or fraction thereof) refers to a yeast membrane that lacks a natural nucleus or cytoplasm. The particle can be of any size, including sizes ranging from the size of a natural yeast membrane to microparticles produced by ultrasound or by other membrane disruption methods known to those skilled in the art, followed by resealing. A method for producing subcellular yeast membrane extracts is described, for example, in Franzusoff et al., 1991, Meth. Enzymol. 194, 662- 674. A method may also use particular fractions of the yeast membrane that contain portions of the yeast membrane and, when the antigen, or other proteins were expressed recombinantly by the yeast prior to the preparation of the yeast membrane particles, the antigen or other proteins of interest. Antigens, or other proteins of interest, can be carried into the membrane, on any surface of the membrane, or combinations thereof (that is, the protein can be both inside and outside the membrane and / or spanning the membrane of the particle of yeast membrane). In one embodiment, a yeast membrane particle is a recombinant yeast membrane particle that can be an intact, broken yeast membrane; or broken and resealed that includes at least one desired antigen or other protein of interest, on the surface of the membrane or, at least, partially embedded within the membrane.
[00058] An example of a yeast cell wall preparation is an isolated yeast cell wall preparation that carries an antigen on its surface, or at least partially embedded within the cell wall, such that the cell wall preparation of yeast, when administered to an animal, stimulates a desired immune response against a target disease.
[00059] Any yeast strain can be used to produce a yeast vehicle of the present invention. Yeast are single-celled microorganisms that belong to one of three classes: Ascomycetes, Basidiomycetese Fungi Imperfect. One consideration for selecting a type of yeast for use as an immune modulator is the pathogenicity of yeast. In one embodiment, yeast is a non-pathogenic strain, such as Saccharomyces cerevisiae. The selection of a non-pathogenic yeast strain minimizes any adverse effects to the individual, to whom the yeast vehicle is administered. However, pathogenic yeast may be used if the pathogenicity of the yeast can be negated by any means known to the person skilled in the art (for example, mutant strains). According to one aspect of the present invention, non-pathogenic yeast strains are used.
[00060] Genera of yeast strains that can be used in the invention include, but are not limited to, Saccharomyces, Candida (which may be pathogenic), Cryptococcus, Hansenula, Kluyveromyces, Pichia, Rhodotorula, Schizosaccharomyces and Yarrowia. In one aspect, yeast genera are selected from Saccharomyces, Candida, Hansenula, Pichia or Schizosaccharomyces, and in one aspect, Saccharomyces is used. Species of yeast strains which can be used in the invention include, but are not limited to, Saccharomyces cerevisiae, Saccharomyces carlsbergensis, Candida albicans, Candida kefyr, Candida tropicalis, Cryptococcus laurentii, Cryptococcus neoformans, Hansenula anomala, Hansenula polymor Kluyveromyces lactis, Kluyveromyces marxianus var. lactis, Pichia pastoris, Rhodotorula rubra, Schizosaccharomyces pombe and Yarrowia lipolytica.It should be considered that several of these species include a variety of subspecies, types, subtypes, etc., which are intended to be included in the above mentioned species. In one aspect, yeast species used in the invention include S. cerevisiae, C. albicans, H. polymorpha, P. pastoris and S. pombe. S. cerevisiae is useful as it is relatively easy to manipulate and to be "generally recognized as safe" "Generally Recognized As Safe" or ("GRAS") for use as food additives (GRAS, FDA proposed Rule 62FR18938, April 17, 1997). One embodiment of the present invention is a yeast strain that is capable of replicating plasmids up to a particularly high copy number, such as a strain of S. cerevisiae cif. The S. cerevisiae strain is that strain that is capable of supporting expression vectors that allow one or more target antigens and / or antigen fusion protein (s), and / or other proteins that must be expressed at high levels. Another strain of yeast that is useful in the invention is Saccharomyces cerevisiae W303a. In addition, any mutant yeast strains can be used in the present invention, including those that exhibit reduced post-translational modifications of expressed target antigens or other proteins, such as mutations in enzymes that extend to N-linked glycosylation.
[00061] The Brachyury yeast immunotherapy composition of the invention includes at least one cancer antigen comprising a Brachyury antigen. According to the present invention, the general use in this report of the term "antigen" refers to: any portion of a protein (for example, peptide, partial protein, full-length protein), in which the protein occurs naturally or derived synthetically or designed, for a cellular composition (total cell, cell lysate or ruptured cells), for an organism (total organism, lysate or ruptured cells); or a carbohydrate, or another molecule, or a portion of it. An antigen can induce an antigen-specific immune response (for example, a humoral response and / or a cell-mediated immune response) against the same or similar antigens that are found by an element of the immune system (for example, T cells, antibodies ).
[00062] An antigen can be as small as a single epitope, a single immunogenic domain or larger, and can include multiple epitopes or immunogenic domains. As such, the size of an antigen can be as small as about 8-11 amino acids (ie, a peptide) and as large as: a full-length protein, a multimer, a fusion protein, a chimeric protein, a total cell, an entire microorganism, or any portion thereof (for example, protein fragments (polypeptides), whole cell lysates or extracts of microorganisms). Antigens useful in the Brachyury yeast immunotherapeutic of the present invention are peptides, polypeptides, full-length proteins, multimers, fusion proteins and chimeric proteins. In addition, antigens can include carbohydrates, which can be loaded into a yeast vehicle or a composition of the invention. It will be considered that in some embodiments (for example, when the antigen is expressed by the yeast vehicle from a recombinant nucleic acid molecule), the antigen is a protein, fusion protein, chimeric protein, or fragment thereof, rather than an entire cell or microorganism. For expression in yeast, an antigen is of a minimum size capable of being expressed recombinantly in yeast, if the antigen is the entire protein that must be expressed by yeast, and is typically at least or greater than 25 amino acids in length, or at least, or greater than 26, at least or greater than 27, at least or greater than 28, at least or greater than 29, at least or greater than 30, at least or greater than 31, at least or greater than 32 , at least or greater than 33, at least or greater than 34, at least or greater than 35, at least or greater than 36, at least or greater than 37, at least or greater than 38, at least or greater than 38, at least or greater than 39, at least or greater than 40, at least or greater than 41, at least or greater than 42, at least or greater than 43, at least or greater than 44, at least or greater than 45, at least less than or greater than 46, at least or greater than 47, at least or greater than 48, at least or greater than 49, or at least or greater than 50 am inoacids in length, or at least or greater than 25-50 amino acids in length, or at least or greater than 30-50 amino acids in length, or at least or greater than 35-50 amino acids in length, or at least or greater than 40-50 amino acids in length, or at least or greater than 45-50 amino acids in length, although smaller proteins can be expressed, and considerably larger proteins (for example, hundreds of amino acids in length, or even a few thousand long amino acids) can be expressed. In one aspect, a full-length protein or protein that is devoid of between 1 and 20 amino acids of the N-terminus and / or the C-terminus can be expressed. Fusion proteins and chimeric proteins are also antigens that can be expressed in the invention. A "target antigen" is an antigen that is specifically targeted by an immunotherapeutic composition of the invention (i.e., an antigen against which the elicitation of an immune response is desired). A "cancer antigen" is an antigen that comprises at least one antigen that is associated with cancer; such as an antigen expressed by a tumor cell, such that targeting the antigen also directs cancer. A cancer antigen can include one or more antigens from one or more proteins, including one or more tumor-associated proteins. A "Brachyury antigen" is an antigen derived, designed or produced, from a Brachyury protein.
[00063] When referring to the stimulation of an immune response, the term "immunogen" is a subset of the term "antigen", and therefore, in some examples, may be used interchangeably with the term "antigen". An immunogen, as used in this report, describes an antigen that induces a humoral and / or cell-mediated (i.e., immunogenic) immune response, such that administration of the immunogen to an individual increases an antigen-specific immune response against the same or similar antigens that are found by the individual's immune system. In one embodiment, the immunogen induces a cell-mediated immune response, including, a CD4 + T cell response (eg, TH1, TH2 and / or TH17) and / or a CD8 + T cell response (eg, a CTL).
[00064] An "immunogenic domain" of a given antigen can be any portion, fragment or epitope of an antigen (for example, a peptide fragment or subunit, or an antibody epitope or other conformational epitope) that contains at least one epitope that can act as an immunogen when administered to an animal. Therefore, an immunogenic domain is larger than a single amino acid and is at least large enough to contain at least one epitope that can act as an immunogen. For example, a single protein can contain several different immunogenic domains. Immunogenic domains do not need to be linear sequences within a protein, as in the case of a humoral immune response, where conformational domains are considered.
[00065] An epitope is defined in this report as a single immunogenic site within a given antigen that is sufficient to induce an immune response, when provided to the immune system, in the context of appropriate costimulatory signals and / or activated cells of the immune system. In other words, an epitope is the part of an antigen that is recognized by components of the immune system, and can also be referred to as an antigenic determinant. Those skilled in the art will recognize that T cell epitopes differ in the size and composition of B cell epitopes or antibodies, and that the epitopes presented via the MHC Class I pathway differ in the size and structural attributes of epitopes presented through of the Class II MHC pathway. For example, T cell epitopes displayed by MHC Class I molecules are typically between 8 and 11 amino acids in length, since the epitopes displayed by MHC Class II molecules are less restricted in length and can be up to 25 amino acids or more. In addition, T cell epitopes have predicted structural characteristics depending on the specific MHC molecules linked by the epitope. Epitopes can be linear sequence epitopes or conformational epitopes (conserved binding regions). Most antibodies recognize conformational epitopes.
[00066] Brachyury (which may also be referred to as "T") is a highly conserved protein among multiple different species of animals and is a transcription factor that contains a "T-box" or "T domain", a motif (motif) DNA binding domain shared between several different proteins, collectively called the T-box family of proteins. Human Brachyury was first cloned in 1996 (Edwards et al; supra). A nucleotide sequence encoding human Brachyury is represented here by SEQ ID NO: 1, which is an mRNA sequence that was obtained from GENBANK® Accession No. NM_003181 (Gl: 19743811). SEQ ID NO: 1 encodes a 435 amino acid human Brachyury protein, the amino acid sequence of which is represented here, as SEQ ID NO: 2 (also found in GENBANK® Accession No. NP_003172; Gl: 4507339).
[00067] Another human Brachyury protein described in this report is a variant of the human Brachyury protein represented by SEQ ID NO: 2, and has the amino acid sequence of SEQ ID NO: 6. SEQ ID NO: 6, also a protein of 435 amino acids, is encoded by a nucleotide sequence represented here, by SEQ ID NO: 5. SEQ ID NO: 6 is approximately 99% identical to SEQ ID NO: 2 over the total length of the protein. SEQ ID NO: 6 differs from SEQ ID NO: 2 at position 177 (Asp vs. Gly, respectively), position 368 (Thr vs. Ser, respectively) and position 409 (Asn vs. Asp, respectively).
[00068] Another human Brachyury protein described in this report is an agonist of the human Brachyury protein represented by SEQ ID NO: 2 or SEQ ID NO: 6. As commonly used in this report, an "agonist" is any compound or agent, including , without limitation, small molecules, proteins, peptides, antibodies, nucleic acid binding agents, etc., which binds to a receptor or ligand and produces or causes a response, which may include agents that mimic or enhance the action of a naturally occurring substance, which binds to the receptor or ligand. When used in the context of a Brachyury antigen of the invention, an "agonist" antigen or protein refers to an antigen or protein that comprises at least one epitope of T cell agonist, which can also be referred to as a "mimotope" . A mimotope peptide is a peptide that mimics the structure of a wild type epitope and, like an agonist, the mimotope mimics or enhances the action (biological function) of the natural epitope. For example, the amino acid sequence of SEQ ID NO: 12 (WLLPGTSTL) is a T cell epitope of a wild-type Brachyury protein. The amino acid sequence of SEQ ID NO: 13 (WLLPGTSTV) is a mimotope or agonist of the T cell epitope of SEQ ID NO: 12.
[00069] A human Brachyury agonist antigen is represented here by SEQ ID NO: 18. SEQ ID NO: 18 is a 435 amino acid protein that is encoded by a nucleotide sequence represented in this report by SEQ ID NO: 17. SEQ ID NO: 18 is identical to SEQ ID NO: 6, except for a replacement of a leucine at position 254 relative to SEQ ID NO: 6, with a valine at SEQ ID NO: 18. This substitution creates a T cell agonist epitope in SEQ ID NO: 18 in positions 246 to 254 which, without being bound in theory, are believed to induce enhanced T cell responses against Brachyury, when compared to the wild type epitope (positions 246 to 254 of SEQ ID NO: 6 ).
[00070] Positions 41 to 223 of any of SEQ ID NO: 2, SEQ ID NO: 6 or SEQ ID NO: 18 represent the human Brachyury T-Box DNA binding domain, and the T-box domain in others Brachyury sequences, including Brachyury sequences from other species, can be readily identified by comparison with those sequences. As used in this report, reference to a T-box domain of any Brachyury protein described in this report, or known in the art and used in the invention may include an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39 or 40 consecutive amino acids of the Brachyury sequence at the N-terminus and / or the C-terminus of the defined T-box domain (for example, on each side of positions 41 -223 of SEQ ID NOs: 2, 6 or 18). Human Brachyury, including the two human Brachyury proteins described in this report, also contain several epitopes of CD4 + and CD8 + T cells. Such epitopes are described, for example, in WO 2008/106551, and include an epitope from CTL CD8 +, WLLPGTSTL (also referred to in this report as Tp2, SEQ ID NO: 12), in positions 246 to 254 of SEQ ID NO: 2 or SEQ ID NO: 6. As discussed above, SEQ ID NO: 18 comprises an agonist epitope of SEQ ID NO: 12, represented in this report by SEQ ID NO: 13.
[00071] Human Brachyury has very high homology with Brachyury from other animal species and, therefore, the one skilled in the art is able to use Brachyury sequences from other organisms in the preparation of an immunotherapeutic composition of Brachyury yeast from invention, particularly, where these sequences are identical, substantially homologous, and induce an effective immune response against the target antigen (eg, native Brachyury expressed by a tumor cell). For example, murine Brachyury, which was first cloned by Hermann et al., In 1990 (Herman et al., Supra), is approximately 85% identical to human Brachyury at the nucleotide level, and approximately 91% identical at the amino acid level. With respect to Brachyury from other animals, at the amino acid level, human Brachyury is 99.5% identical to Brachyuryde Pan troglodytes, 90.1% identical to Brachyury from Canis lupus familiaris, 88.5% identical to Brachyuryde Bos Taurus, 92, 2% identical to Brachyury from Rattus norvegicus, and 80.9% identical to Brachyury from Gallus gallus. Among amino acids 1-223 of Brachyury, which contains the T-box domain, mouse and human Brachyury differ in only two amino acids (at positions 26 and 96). A nucleotide sequence encoding murine Brachyury is represented in this report by SEQ ID NO: 3, which is an mRNA sequence that was obtained from GENBANK ® Accession No. NM_009309 (Gl: 118130357). SEQ ID NO: 3 encodes a 436 amino acid murine Brachyury protein, the amino acid sequence which is represented here as SEQ ID NO: 4. Positions 41 to 223 of SEQ ID NO: 4; represents the murine Brachyury T-box DNA binding domain.
[00072] In one embodiment of the invention, a Brachyury antigen comprises or consists of the amino acid sequence represented by SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 18, or at least one immunogenic domain. In one embodiment, a Brachyury antigen comprises or consists of two, three, four, five, or more immunogenic Brachyury domains. In one embodiment of the invention, a Brachyury antigen comprises or consists of the amino acid sequence represented by positions 1 or 2 of amino acids by means of one of the last 25 amino acids at the C-terminus of SEQ ID NO: 2, SEQ ID NO: 4, ID SEQ NO: 6 or SEQ ID NO: 18 (that is, by means of any of positions 441 to 435 of SEQ ID NO: 2 or SEQ ID NO: 6 or SEQ ID NO: 18, or by means of one of the positions 442 to 436 of SEQ ID NO: 4). Another Brachyury antigen useful in the invention also includes at least 1-223 positions of Brachyury amino acids (for example, positions 1-223 of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 or SEQ ID NO: 18) or Brachyury positions 41-223 (for example, positions 41-223 of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 or SEQ ID NO: 18). Another Brachyury antigen useful in the invention includes at least amino acid positions 1 to 85, between position 255 and the C-terminus of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 or SEQ ID NO: 18. Another Brachyury antigen useful in the invention includes at least amino acid positions 1 to 85, between position 430 and end C of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 or ID SEQ NO: 18. Another Brachyury antigen useful in the invention includes at least amino acid positions 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 between position 255 and the C terminus of ID SEQ NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 or SEQ ID NO: 18.
[00073] In accordance with any embodiment of the present invention, reference to a "full length" protein (or a full length functional domain or full length immune domain) includes the full length amino acid sequence of the protein or functional domain or immunological domain, as described in this report, or as otherwise known, or described in a publicly available sequence. A protein or domain that is "close to full length", which is also a type of homologue of a protein, differs from a protein or domain to full length, by adding or deleting, or omitting 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids, starting from the N and / or C terminus of such full-length protein or full-length domain. By way of example, several of the fusion proteins described herein comprise a "close-total-length" Brachyury antigen, since the antigen omits methionine at position 1, and replaces a terminating N peptide. General reference to a protein or a domain, or antigen, can include both full-length and close-length proteins, as well as other homologues thereof.
[00074] In one aspect of any modalities reported for a Brachyury antigen, a cancer antigen or a Brachyury antigen is of a minimum size sufficient to allow the antigen to be expressed by yeast. For expression in yeast, a protein is typically at least approximately 25 amino acids in length, although smaller proteins can be expressed, and considerably larger proteins can be expressed by yeast. For example, a Brachyury antigen useful in the invention is a fragment of a Brachyury protein that can be expressed recombinantly by yeast and that contains at least one immunogenic Brachyury domain, which can include at least one immunogenic domain of any one of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 or SEQ ID NO: 18. In one aspect, such an antigen is at least 25 amino acids in length, and contains at least one Brachyury immunogenic domain. In one aspect, such an antigen is greater than 30 amino acids in length, and contains at least one Brachyury immunogenic domain. In one aspect, such an antigen is at least 25-50 amino acids in length, and contains at least one Brachyury immunogenic domain. In one aspect, such an antigen is at least 30-50 amino acids in length, and contains at least one Brachyury immunogenic domain. In one aspect, such an antigen is at least 35-50 amino acids in length, and contains at least one Brachyury immunogenic domain. In one aspect, such an antigen is at least 40-50 amino acids in length, and contains at least one Brachyury immunogenic domain. In one aspect, such an antigen is at least 45-50 amino acids in length, and contains at least one Brachyury immunogenic domain. In one embodiment, the Brachyury antigen useful in the present invention is at least 25 amino acids in length, or at least: 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90 , 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215 , 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 305, 310, 315, 320, 325, 330, 335, 340 , 345, 350, 355, 360, 365, 370, 375, 380, 385, 390, 395, 400, 405, 410, 415, 420, 425 or 430 amino acids in length, which can include any fragment of at least any one of these lengths of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 or SEQ ID NO: 18.
[00075] In one aspect, a Brachyury antigen comprises one or more epitopes from CTL, which may include; two or more copies of any one, two, three or more of the CTL epitopes described in this report. In one aspect, the Brachyury antigen comprises one or more epitopes of CD4 + T cells. In one aspect, the T cell, the Brachyury antigen comprises one or more epitopes of CTL and one or more epitopes of CD4 + T cells. In one aspect, the T cell epitope is an agonist epitope.
[00076] In one aspect, a Brachyury antigen comprises an amino acid sequence of WLLPGTSTL (SEQ ID NO: 12, also represented by positions 245 to 254 of SEQ ID NO: 2 or SEQ ID NO: 6). In one aspect, the Brachyury antigen comprises an amino acid sequence of WLLPGTSTV (SEQ ID NO: 13, also represented by positions 245 to 254 of SEQ ID NO: 18). In one aspect, the amino acid at position 4 of each SEQ ID NO: 12 or SEQ ID NO: 13 (a proline or P in these sequences) is replaced with a serine (S), a threonine (T), an isoleucine (I ), or a valine (V).
[00077] In one aspect, the Brachyury antigen comprises an amino acid sequence of SQYPSLWSV (SEQ ID NO: 14). In one aspect, the amino acid at position 2 of SEQ ID NO: 14 (a glutamine or Q in that sequence) is replaced with a leucine (L). In one aspect, the amino acid at position 4 of SEQ ID NO: 14 (a proline or P in that sequence) is replaced with a serine (S), threonine (T), leucine (L), or valine (V). In one aspect, the amino acid at position 7 of SEQ ID NO: 14 (a tryptophan or W in that sequence) is replaced with a valine (V), leucine (L), isoleucine (I), serine (S), or threonine ( T). In one aspect, the amino acid at position 9 of SEQ ID NO: 14 (a valine or V in that sequence) is replaced with a leucine (L). An antigen comprising a sequence having any combination of one or more of these substitutions in SEQ ID NO: 14 is considered by the invention.
[00078] In one aspect, the Brachyury antigen comprises an amino acid sequence of RLIASWTPV (SEQ ID NO: 15). In one aspect, the amino acid at position 1 of SEQ ID NO: 15 (an arginine or R in that sequence) is replaced with a tyrosine (Y) or a tryptophan (W). In one aspect, the amino acid at position 6 of SEQ ID NO: 15 (a tryptophan or W in that sequence) is replaced with a valine (V), a lysine (L), an isoleucine (I), a serine (S) or a threonine (T). An antigen comprising a sequence that exhibits any combination of one or both of these substitutions in SEQ ID NO: 15 is considered by the invention.
[00079] In one aspect, the Brachyury antigen comprises an amino acid sequence of AMYSFLLDFV (SEQ ID NO: 16). In one aspect, the amino acid at position 2 of SEQ ID NO: 16 (a methionine or M in that sequence) is replaced with a leucine (L).
[00080] In one embodiment of the invention, a Brachyury antigen comprises, consists essentially of, or consists of a fusion protein that has the amino acid sequence of SEQ ID NO: 8. The fusion protein of SEQ ID NO: 8 is a single polypeptide with the following sequence elements fused in structure from N terminus to C terminus: (1) an N terminating peptide confers resistance to proteasome degradation and stabilizes expression in yeast (positions 1-6 of SEQ ID NO: 8 ); (2) a human Brachyury antigen consisting of positions 2-435 of SEQ ID NO: 6 (positions 7-440 of SEQ ID NO: 8); and (3) a hexa-histidine tail (positions 441-446 of SEQ ID NO: 8). The amino acid sequence of SEQ ID NO: 8 is encoded by the polynucleotide sequence of SEQ ID NO: 7.
[00081] In another embodiment of the invention, a Brachyury antigen comprises, consists essentially of, or consists of a fusion protein that has the amino acid sequence of SEQ ID NO: 10. The fusion protein of SEQ ID NO: 10 is a single polypeptide with the following sequence elements fused in structure from N terminus to C terminus: (1) an N termination peptide confers resistance to proteasome degradation and stabilizes expression in yeast (positions 1-6 of SEQ ID NO: 10 ); (2) a murine Brachyury antigen consisting of positions 2-436 of SEQ ID NO: 4 (positions 7-441 of SEQ ID NO: 10); and (3) a hexa-histidine tail (positions 442-447 of SEQ ID NO: 10). The amino acid sequence of SEQ ID NO: 10 is encoded by the polynucleotide sequence of SEQ ID NO: 9.
[00082] In another embodiment of the invention, a Brachyury antigen comprises, consists essentially of, or consists of a fusion protein having the amino acid sequence of SEQ ID NO: 20. The fusion protein of SEQ ID NO: 20 is a single polypeptide with the following sequence elements fused in structure from N to C terminus: (1) an N-terminated peptide confers resistance to proteasome degradation and stabilizes expression in yeast (positions 1-6 of SEQ ID NO: 20); the peptide sequence also represented in this report by SEQ ID NO: 11); (2) 2-435 amino acids of SEQ ID NO: 18 (positions 7-440 of SEQ ID NO: 20), SEQ ID NO: 18 representing a full-length human Brachyury agonist protein; and (3) a hexa-histidine tail (positions 441-446 of SEQ ID NO: 20). The agonist epitope (SEQ ID NO: 13) is located at positions 251 to 259 of SEQ ID NO: 20 (positions 246 to 254 of SEQ ID NO: 18). The amino acid sequence of SEQ ID NO: 20 is encoded by the polynucleotide sequence of SEQ ID NO: 19.
[00083] A Brachyury antigen useful in the present invention also includes proteins that have an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93% , 94%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequence of any of the Brachyury proteins or antigens described in this report, on the total length of the protein, or with respect to a fragment or defined domain (for example, an immune domain or functional domain (domain with at least one biological activity)) that forms part of the protein. For example, a domain of the Brachyury protein described in this report includes the T-box domain. An immune domain has been described in detail above.
[00084] In some aspects of the invention, amino acid insertions, deletions, and / or substitutions can be made by one, two, three, four, five, six, seven, eight, nine, ten or more amino acids of a Brachyury protein wild-type or reference, provided that the resulting Brachyury protein, when used as an antigen in a Brachyury yeast immunotherapeutic composition of the invention, induces an immune response against a native Brachyury protein such as the wild-type or reference Brachyury protein, which may include a marked immune response, a decreased immune response, or a substantially similar immune response. For example, the invention includes the use of Brachyury agonist antigens, which can include one or more T cell epitopes that have been mutated to increase the T cell response against the Brachyury agonist, such as, improving the avit or affinity of the epitope to an MHC molecule or to the T cell receptor that recognizes the epitope in the context of MHC presentation. Brachyury agonists can therefore improve the potency or efficiency of a T cell response against native Brachyury expressed by a tumor cell. The Brachyury antigen having the amino acid sequence of SEQ ID NO: 18 is a non-limiting example of a Brachyury agonist (or a Brachyury antigen comprising an agonist epitope).
[00085] In addition, N-termination expression sequences and C-termination tails, such as those described above, with respect to the fusion proteins of SEQ ID NO: 8, SEQ ID NO: 10, or SEQ ID NO: 20 are optional, but can be selected from several different sequences described elsewhere in this report to improve or assist with expression, stability, and / or allow protein identification and / or purification. Also, many different promoters suitable for use in yeast are known in the art. In addition, short intervening ligand sequences (for example, 1, 2, 3, 4, 5 or amino acid peptides) can be inserted between portions of a fusion protein that comprises a Brachyury antigen for a variety of reasons, including, the introduction of restriction enzyme sites to facilitate cloning, such as cleavage sites for phagosomal host proteases, to accelerate protein or antigen processing, and for future manipulation of constructs.
[00086] Optionally, proteins, including fusion proteins, which are used as a component of the Brachyury yeast immunotherapeutic composition of the invention are produced using antigen constructs which are particularly useful for enhancing or stabilizing the expression of heterologous antigens in yeast. In one embodiment, the desired antigenic proteins or peptides are fused at their amino terminus to: (a) a specific synthetic peptide that stabilizes the expression of the fusion protein in the yeast vehicle or prevents post-translational modification of the expressed fusion protein (such peptides are described in detail, for example, in United States Patent Publication No. 2004-0156858 A1, published on August 12, 2004, incorporated herein by reference in their entirety), (b) at least a portion of an endogenous yeast protein, including, but not limited to, a leading yeast factor-alpha sequence, in which each of the fusion partners provides better protein expression stability in yeast and / or prevents a post-translational modification of yeast proteins by yeast cells (such proteins are also described in detail, for example, United States Patent Publication No. 2004-0156858 A1, supra) and / or (c) at least a portion of a yeast protein that leads to the fusion protein being expressed on the surface of the yeast (for example, an Aga protein, described in more detail in this report). In addition, the present invention optionally includes the use of peptides that are fused to the C-terminus of the construct encoding the antigen, particularly for use in protein selection and identification. Such peptides include, but are not limited to, any synthetic or natural peptide, such as a peptide tag (e.g., 6X His or hexapeptide) or any other short epitope tag. The peptides attached to the C-terminus of an antigen according to the invention can be used with or without the addition of the N-terminated peptides discussed above, and vice versa.
[00087] In one embodiment, a synthetic peptide useful in a fusion protein must be expressed in a yeast that is linked to the N-terminus of the antigen, the peptide consisting of at least two amino acid positions that are heterologous to the antigen, where the peptide stabilizes the expression of the fusion protein in the yeast vehicle or prevents post-translational modification of the expressed fusion protein. The synthetic peptide and N-terminus of the antigen together form a fusion protein that has the following requirements: (1) the amino acid residue at position one, of the fusion protein is methionine (ie, the first amino acid in the synthetic peptide is a methionine); (2) the amino acid residue at position two of the fusion protein is not a glycine or a proline (that is, the second amino acid in the synthetic peptide is not a glycine or a proline); (3) none of the amino acid positions at positions 2-6 of the fusion protein is a methionine (ie, the amino acids at positions 2-6, if part of the synthetic peptide or protein, if the synthetic peptide is less than 6 amino acids, does not include methionine); and (4) none of the amino acids at positions 2-6 of the fusion protein is a lysine, or an arginine (that is, the amino acids at positions 2-6, if part of the synthetic peptide or protein, whether the synthetic peptide is less than 5 amino acids, does not include lysine or arginine). The synthetic peptide can be as small as two amino acids, but in one aspect, it is 2-6 amino acids (including 3, 4, 5 amino acids), and can be greater than 6 amino acids, in whole numbers, up to about 200 amino acids, 300 amino acids, 400 amino acids, 500 amino acids, or more.
[00088] In one embodiment, a fusion protein comprises an amino acid sequence of M-X2-X3-X4-X5-X6, where M is methionine; where X2 is any amino acid, except glycine, proline, lysine or arginine; where X3 is any amino acid, except methionine, lysine or arginine; where X4 is any amino acid, except methionine, lysine or arginine; where X5 is any amino acid, except methionine, lysine or arginine; and where X6 is any amino acid, except methionine, lysine or arginine. In one embodiment, residue X6 is proline. An exemplary synthetic sequence that enhances the expression stability of an antigen in a yeast cell and / or prevents post-translational modification of the protein in yeast includes the sequence M-A-D-E-A-P (represented in this report by SEQ ID NO: 11). In addition to the enhanced stability of the expression product, this fusion partner does not appear to have a negative impact on the immune response against the immunization antigen in the construct. In addition, synthetic fusion peptides can be designed to provide an epitope that can be recognized by a selection agent, such as an antibody.
[00089] In one aspect of the invention, the yeast vehicle is manipulated in such a way that the antigen is expressed or provided by transferring or translocating a protein product expressed, partially or totally, onto the surface of the yeast vehicle ( extracellular expression). One method for carrying out this aspect of the invention is to use a spacer arm for positioning one or more proteins on the surface of the yeast vehicle. For example, a spacer arm can be used to create a fusion protein of the antigen (s) or other protein of interest with a protein that targets the antigen (s) or other protein of interest to the yeast cell wall. For example, one such protein that can be used to target other proteins is a yeast protein (for example, cell wall protein 2 (cwp2), protein Aga2, Pir4 or Flo1) that allows the antigen (s) ( s) or another protein is directed to the yeast cell wall, such that the antigen, or another protein is located on the surface of the yeast. Proteins other than yeast proteins can be used for the spacer arm, however, for any spacer arm protein, it is more desirable to present the immunogenic response directed against the target antigen, rather than the spacer arm protein. As such, if other proteins are used for the spacer arm, then the spacer arm protein that is used should not generate a large immune response to the spacer arm protein itself, such that the immune response to the antigen (s) (s) target is overloaded. One skilled in the art should aim at a small immune response to the spacer arm protein, in relation to the immune response to the target antigen (s). Spacer arms can be constructed to have cleavage sites (for example, protease cleavage sites) that allow the antigen to be readily removed, or processed outside the yeast, if desired. Any known method of determining the magnitude of immune responses can be used (for example, antibody production, lytic assays, etc.), and are readily known to the person skilled in the art.
[00090] Another method for positioning the target antigen (s), or other proteins to be exposed on the surface of the yeast is the use of signal sequences, such as glycosylphosphatidyl inositol (GPI) to anchor the target to the wall yeast cell. Alternatively, positioning can be performed by adding signal sequences that target the antigen (s) or other proteins of interest in the secretory pathway through translocation to the endoplasmic reticulum (ER), in such a way that the antigen binds if a protein that is bound to the cell wall (for example, cwp).
[00091] In one aspect, the spacer arm protein is a yeast protein. The yeast protein can consist of between approximately two and approximately 800 amino acids of a yeast protein. In one embodiment, the yeast protein is approximately 10 to 700 amino acids. In another embodiment, the yeast protein is approximately 40 to 600 amino acids. Other embodiments of the invention include yeast protein being at least 250 amino acids, at least 300 amino acids, at least 350 amino acids, at least 400 amino acids, at least 450 amino acids, at least 500 amino acids, at least 550 amino acids, at least 600 amino acids , or at least 650 amino acids. In one embodiment, the yeast protein is at least 450 amino acids in length. Another consideration for optimizing the surface expression of the antigen, if this is desired, is whether the combination of the antigen and the spacer arm should be expressed as a monomer or as a dimer or as a trimer, or even more units linked together. This use of monomers, dimers, trimers, etc .; allows appropriate spacing or unfolding of the antigen in such a way that some, if not all, of the antigen is displayed on the surface of the yeast vehicle in a way that makes it more immunogenic.
[00092] Use of yeast proteins can stabilize the expression of fusion proteins in the yeast vehicle, prevent post-translational modification of the expressed fusion protein, and / or direct the fusion protein to a particular compartment in the yeast (for example, to be expressed on the surface of the yeast cell). For transfer to the yeast secretory pathway, exemplary yeast proteins to use include, but are not limited to: Aga (including, but not limited to, Agal and / or Aga2); SUC2 (yeast invertase); leading alpha signal factor sequence; CPY; Cwp2p for its location and retention in the cell wall, BUD genes for yeast cell bud localization during the initial phase of daughter cell formation; Flolp; Pir2p and Pir4p.
[00093] Other sequences can be used to target, retain and / or stabilize the protein to other parts of the yeast vehicle, for example, in the cytosol or mitochondria or endoplasmic reticulum, or in the nucleus. Examples of suitable yeast protein that can be used for any of the above embodiments include, but are not limited to, TK, AF SEC7; phosphoenolpyruvate carboxykinase PCK1, phosphoglycerokinase PGK and gene products triose phosphate isomerase (TPI) for its repressible expression in glucose and cytosolic location; heat shock proteins, SSA1 SSA3, SSA4, SSC1, whose expression is induced and whose proteins are more thermostable after exposure of cells to a heat treatment, the mitochondrial protein CYC1 of import into mitochondria; ACT 1.
[00094] Methods of producing yeast vehicles and expression, combining and / or associating yeast vehicles with antigens and / or other proteins and / or agents of interest for producing yeast-based immunotherapy compositions are considered by the invention.
[00095] In accordance with the present invention, the term "yeast carrier antigen complex" or "yeast antigen complex" is used generically to describe any combination of an antigen, and can be used interchangeably with "immunotherapy composition to yeast base "when such a composition is used to induce an immune response, as described above. Such an association includes expression of the antigen by yeast (a recombinant yeast), introduction of an antigen into a yeast, physical attachment of the antigen to the yeast, and mixing the yeast and antigen together, such as in a buffer or other solution, or formulation. These types of complexes are described in detail below.
[00096] In one embodiment, the yeast cell used to prepare the yeast vehicle is transfected with a heterologous nucleic acid molecule that encodes a protein (for example, the antigen) such that the protein is expressed by the yeast cell. Such yeast is also referred to in this report as a recombinant yeast or a recombinant yeast vehicle. The yeast cell can then be formulated with a pharmaceutically acceptable excipient and administered directly to a patient, stored for later administration, or loaded into a dendritic cell as an intact cell. The yeast cell can also be killed, or can be derived such as by forming yeast spheroplasts, cytoplasts, spectra or subcellular particles, any of which can be followed by storing, administering or loading the derivative into the dendritic cell. Yeast spheroplasts can also be directly transfected with a recombinant nucleic acid molecule (for example, the spheroplast is produced from a total yeast and then transfected) in order to produce a recombinant spheroplast that expresses the antigen. Yeast cells or yeast spheroplasts that recombinantly express the antigen (s) can be used to produce a yeast vehicle that comprises a yeast cytoplasm, a yeast spectrum, or a yeast membrane particle or yeast cell wall particle, or fraction thereof.
[00097] In general, the yeast and antigen (s) vehicle and / or other agents can be associated by any technique described in this report. In one aspect, the yeast vehicle was loaded intracellularly with the antigen (s) and / or agent (s). In another aspect, the antigen (s) and / or agent (s) was (were) covalently or non-covalently linked to the yeast vehicle. In yet another aspect, the yeast vehicle and the antigen (s) and / or agent (s) were mixed together. In another aspect, and in one embodiment, the antigen (s) and / or agent (s) are expressed recombinantly by the yeast vehicle or by the yeast cell or yeast spheroplast from which the yeast vehicle was derived.
[00098] A number of antigens and / or other proteins to be produced by a yeast vehicle of the present invention is any number of antigens and / or other proteins that can reasonably be produced by a yeast vehicle, and typically, varies by at least one to at least about 6 or more, including from approximately 2 to approximately 6 antigens and or other proteins.
[00099] Expression of an antigen or other protein in a yeast vehicle of the present invention is carried out using techniques known to those skilled in the art. Briefly, a nucleic acid molecule that encodes at least one desired antigen or other protein is inserted into an expression vector, such that the nucleic acid molecule is operably linked to a transcription control sequence in order to be able to effecting either constitutive or regulated expression of the nucleic acid molecule when transformed into a host yeast cell. The nucleic acid molecules that encode one or more antigens and / or other proteins can be in one or more expression vectors operably linked to one or more expression control sequences. Particularly important expression control sequences are those that control initiation of transcription, such as upstream promoter and activation sequences. Any suitable yeast promoter can be used in the present invention and a variety of such promoters are known to those skilled in the art. Promoters for expression in Saccharomyces cerevisiae include, but are not limited to, promoters of genes encoding the following yeast proteins: alcohol dehydrogenase I (ADH1) or II (ADH2), CUP1, phosphoglycerate kinase (PGK), phosphate isomerase triose (TPI), translational elongation factor EF-1 alpha (TEF2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH; also referred to as TDH3, for triose phosphate dehydrogenase), galactokinase (GAL1), galactose-1-uridyl transferase ( GAL7), UDP-galactose epimerase (GAL10), cytochrome d (CYC1), Sec7 protein (SEC7) and acid phosphatase (PHO5), including hybrid promoters, such as ADH2 / GAPDH and CYC1 / GAL10 promoters, and including the promoter ADH2 / GAPDH, which is induced when glucose concentrations in the cell are low (for example, about 0.1 to about 0.2 percent), as well as the CUP1 promoter and the TEF2 promoter. Likewise, several upstream activation sequences (UASs), also referred to as enhancers, are known. Upstream activation sequences for expression in Saccharomyces cerevisiae include, but are not limited to, UASs of genes encoding the following proteins: PCK1, TPI, TDH3, CYC1, ADH1, ADH2, SUC2, GAL1, GAL7 and GAL10, as well as other UASs activated by the GAL4 gene product, with ADH2 UAS being used in one respect. Since ADH2 UAS is activated by the product of the ADR1 gene, it may be preferable to overexpress the ADR1 gene when a heterologous gene is operationally linked with ADH2 UAS. Transcription termination sequences for expression in Saccharomyces cerevisiae include a-factor, GAPDH and CYC1 genes termination sequences.
[000100] Transcriptional control sequences expressing genes in methyltrophic yeast include the transcriptional control regions of the regions encoding alcohol oxidase and dehydrogenase format.
[000101] Transfection of a nucleic acid molecule into a yeast cell, according to the present invention, can be carried out by any method by which a nucleic acid molecule can be introduced into the cell and includes, but is not limited to , diffusion, active transport, ultrasound baths, electroporation, microinjection, lipofection, adsorption, and protoplast fusion. The transfected nucleic acid molecules can be integrated into a yeast chromosome or maintained in extrachromosomal vectors using techniques known to those skilled in the art. Examples of yeast vehicles that carry such nucleic acid molecules are described in detail in this report. As discussed above, yeast cytoplasm particles, yeast spectra and yeast membrane or cell wall preparations can also be produced recombinantly by transfecting intact yeast microorganisms or yeast spheroplasts with nucleic acid molecules desired, producing the antigen therein, and then, additionally, manipulating microorganisms or spheroplasts using techniques known to those skilled in the art to produce cytoplasmic extract, spectrum, or subcellular yeast membrane, or fractions thereof containing antigens or other proteins desired.
[000102] Effective conditions for the production of recombinant yeast vehicles and expression of antigen and / or other protein by the yeast vehicle include an effective medium, in which a yeast strain can be grown. An effective medium is typically an aqueous medium comprising assimilable sources of carbohydrates, nitrogen and phosphate, as well as salts, minerals, metals and other appropriate nutrients, such as vitamins and growth factors. The medium can comprise complex nutrients or it can be a defined minimum medium. The yeast strains of the present invention can be grown in a variety of containers, including, but not limited to, bioreactors, Erlenmeyer flasks, test tubes, microtiter plates, and Petri dishes. The culture is carried out under a temperature, pH and oxygen content suitable for the yeast strain. Such culture conditions are well within the skill of the person skilled in the art (see, for example, Guthrie et al. (Eds.), 1991, Methods in Enzymology, vol. 194, Academic Press, San Diego). a protocol, liquid cultures containing a suitable medium, can be inoculated using cultures obtained from starter plates and / or starter cultures from Brachyury yeast immunotherapy compositions, and are grown for about 20 hours at 30 ° C, with agitation at 250 rpm. The primary cultures can then be expanded into larger cultures as desired. Protein expression from vectors into which yeast has been transformed (for example, Brachyury expression) can be constitutive if the promoter used is a constitutive promoter, or it can be induced by adding the appropriate induction conditions for the promoter, if the promoter used is an inducible promoter (eg copper sulphate, in the case of the CUP1 promoter). In the case of an inducible promoter, induction of protein expression can be initiated after the culture has grown to an appropriate cell density, which can be about 0.2 Y.U./ml, or greater densities.
[000103] A non-limiting example of a medium suitable for culturing a Brachyury yeast immunotherapy composition of the invention is U2 medium. U2 medium comprises the following components: 20 g / L glucose, 6.7 g / L yeast nitrogen base, containing ammonium sulfate, and 0.04 mg / mL each of histidine, leucine, tryptophan, and adenine. Another non-limiting example of a medium suitable for culturing the Brachyury yeast immunotherapy composition of the invention is UL2 medium. UL2 medium comprises the following components: 20 g / L of glucose, 6.7 g / L of yeast nitrogen base, containing ammonium sulfate, and 0.04 mg / mL of each of histidine, tryptophan and adenine.
[000104] In an embodiment of the invention, when an inducible promoter is used (for example, the CUP1 promoter) to express a Brachyury protein in a yeast vehicle, according to the invention, induction of protein expression is initiated in a superior cell density when compared to the cell density that would be suitable for most proteins expressed by yeast using such a promoter. More specifically, the present inventors have found that optimal expression of Brachyury antigen driven by the CUP1 promoter occurs when the yeast that expresses Brachyury antigen is allowed to grow to a cell density of at least between 0.5 YU / ml and approximately 2 , 0 YU / ml and in one aspect, between 0.5 YU / ml and about 1.5 YU / ml, and in one aspect, at least between 1.0 YU / ml and about 2.0 YU / ml, and in another aspect, at least about 1.0 YU / ml, before inducing the expression of Brachyury antigen in yeast. The present inventors found that, after inducing Brachyury expression, yeast would only double from about 1X to 1.5X. Furthermore, after inducing Brachyury expression, the inventors found that yeast growth to more cell densities elevated than about 2.0 YU / ml, or for more than about 6-8 hours, results in decreased crop viability, without substantially improving yeast antigen accumulation. Therefore, in one embodiment of the invention, a yeast-Brachyury immunotherapy composition showing antigen expression, under the control of an inducible promoter, such as the CUP1 promoter, is cultivated to the middle stage before induction of antigen expression. In one aspect, the cells are grown to between about 1 and 2 Y.U./ml before induction of antigen expression. In one aspect, antigen expression is induced (for example, by the addition of copper sulfate), and continues for up to 6; 6.5; 7; 7.5 or 8 hours. In one aspect, induction occurs at a temperature of about 30 ° C and a stirring rate of 250 rpm.
[000105] In some embodiments of the invention, yeast is grown under conditions of neutral pH. As used in this report, the general use of the term "neutral pH" refers to a pH range between, approximately pH 5.5 and approximately pH 8, and in one aspect, between approximately pH 6 and approximately pH 8. That The person skilled in the art will appreciate that minor fluctuations (for example, tenths or hundredths) may occur when measuring with a pH meter. As such, the use of a neutral pH to grow yeast cells means that the yeast cells are grown at neutral pH for most of the time that they are in culture. In one embodiment, yeast is grown in a medium maintained at a pH level of at least 5.5 (that is, the pH of the culture medium is not allowed to drop below pH 5.5). In another aspect, yeast is grown at a pH level maintained at about 6; 6.5; 7; 7.5 or 8. The use of a neutral pH in yeast culture promotes several biological effects, which are desirable characteristics for the use of yeast, as vehicles for immunomodulation. For example, yeast culture at neutral pH allows for good yeast growth without negative effect on cell generation time (for example, reducing duplication time). Yeast can continue to grow at high densities, without losing its flexibility of the cell wall. The use of a neutral pH allows the production of yeast with flexible cell walls and / or yeast, which are more sensitive to cell wall digesting enzymes (eg, glucanase) at all harvest densities. This characteristic is desirable, because yeast with flexible cell walls can induce different or improved immune responses, when compared with yeast grown under more acidic conditions, for example, by promoting the secretion of cytokines by cells that present antigen that phagocytosed the yeast. (for example, TH1 type cytokines, including, but not limited to, IFN-y, interleukin-12 (IL-12) and IL-2, as well as pro-inflammatory cytokines, such as IL-6). In addition, greater accessibility to antigens located on the cell wall is provided by such culture methods. In another aspect, the use of neutral pH for some antigens allows the release of the disulfide-bound antigen through treatment with dithiothreitol (DTT), which is not possible when such a yeast expressing antigen is grown in lower pH media (for example , pH 5).
[000106] In one embodiment, control of the amount of yeast glycosylation is used to control the expression of antigens by the yeast, particularly on the surface. The amount of yeast glycosylation can affect the immunogenicity and antigenicity of the antigen, particularly that expressed on the surface, since portions of sugar tend to be bulky. As such, the existence of portions of sugar on the yeast surface and its impact on the three-dimensional space around the target antigen (s) must be considered in the modulation of the yeast, according to the invention. Either method can be used to reduce the amount of yeast glycosylation (or increase it, if desired). For example, a mutant strain of yeast that has been selected for low glycosylation (for example, mnn1, ochlh and mnn9 mutants) can be used, or can be eliminated by mutating the glycosylation acceptor sequences in the target antigen. Alternatively, yeast with abbreviated glycosylation patterns can be used, for example, Pichia. Yeast can also be treated using methods that reduce or alter glycosylation.
[000107] In one embodiment of the present invention, as an alternative for expressing recombinantly an antigen or other protein in the yeast vehicle, a yeast vehicle is loaded intracellularly with the protein or peptide, or with carbohydrates or other molecules that work as an antigen and / or are useful as immunomodulating agents or biological response modifiers according to the invention. Subsequently, the yeast vehicle, which now contains the antigen and / or other intracellular proteins, can be administered to an individual or loaded onto a carrier, such as a dendritic cell. Peptides and proteins can be inserted directly into the yeast vehicles of the present invention using techniques known to those skilled in the art, such as, by diffusion, active transport, liposome fusion, electroporation, phagocytosis, freeze-thaw cycles and ultrasound baths. Yeast vehicles that can be directly loaded with peptides, proteins, carbohydrates, or other molecules include intact yeasts, as well as spheroplasts, cytoplasts or spectra, which can be loaded with antigens and other agents after production. Alternatively, the intact yeast can be loaded with the antigen and / or the agent and then spheroplasts, spectra, cytoplasts, or subcellular particles can be prepared from these. Any number of antigens and / or other agents can be loaded into a yeast vehicle in this modality, from at least 1, 2, 3, 4, or any whole number up to hundreds or thousands of antigens and / or other agents, as it would be provided by loading a microorganism or portions of it, for example.
[000108] In another embodiment of the present invention, an antigen and / or another agent is physically bound to the yeast vehicle. Physical attachment of the antigen and / or other agent to the yeast vehicle can be accomplished by any suitable method in the prior art, including, covalent and non-covalent association methods, which include, but are not limited to, chemical cross-linking of the antigen, and / or another agent to the outer surface of the yeast vehicle, or biologically binding the antigen and / or another agent to the outer surface of the yeast vehicle, such as, using an antibody or other binding partner. Chemical cross-linking can be achieved, for example, by methods including glutaraldehyde binding, photo-affinity labeling, treatment with carbodiimides, treatment with disulfide-bonding chemicals, and treatment with other standard cross-linking chemicals in the prior art. Alternatively, a chemical can be contacted with the yeast vehicle that alters the yeast membrane lipid bilayer load, or the composition of the cell wall, so that the outer surface of the yeast is more likely to fuse or bond. antigen and / or other agent that has specific charge characteristics. Targeting agents, such as antibodies, binding peptides, soluble receptors, and other ligands, can also be incorporated into an antigen such as a fusion protein or otherwise associated with an antigen for binding the antigen to the yeast vehicle.
[000109] When the antigen or other protein is expressed on, or physically attached to, the yeast surface, spacer arms can, in one aspect, be carefully selected to optimize expression of antigen or other proteins or content on the surface. The size of the spacer arm (s) can affect the amount of antigen or other protein that is exposed to binding on the surface of the yeast. Thus, depending on which antigen (s) or other protein (s) are used, the one skilled in the art will select a spacer arm that performs the proper spacing for the antigen or other protein on the surface of the yeast. In one embodiment, the spacer arm is a yeast protein of at least 450 amino acids. Spacer arms are discussed in detail above.
[000110] In yet another embodiment, the yeast vehicle and the antigen or other protein are associated with each other, by a more passive, non-specific or non-covalent binding mechanism, such as by gently mixing the yeast vehicle and the antigen, or other proteins together in a buffer or other suitable formulation (eg, mixture).
[000111] In one embodiment, intact yeast (with or without expression of heterologous antigens or other proteins) can be milled or processed to produce yeast cell wall preparations, yeast membrane particles or yeast fragments (ie, not intact) and yeast fragments may, in some embodiments, be provided with, or administered with, other compositions that include antigens (for example, DNA vaccines, protein subunit vaccines, dead or inactivated pathogens, viral vector vaccines) to increase immune responses. For example, enzymatic treatment, chemical treatment or physical strength (for example, mechanical breakdown or ultrasound) can be used to break the yeast into parts that are used as an adjuvant.
[000112] In one embodiment of the invention, yeast vehicles useful in the invention include yeast vehicles that are killed or inactivated. Yeast death or inactivation can be accomplished by any of a variety of suitable methods known in the art. For example, heat inactivation of yeast is a standard form of yeast inactivation, and one skilled in the art can monitor structural changes to the target antigen, if desired, using standard methods known in the art. Alternatively, other methods of inactivating yeast can be used, such as chemical, electrical, radioactive or UV methods. See, for example, the methodology described in standard yeast culture textbooks, such as Methods of Enzymology, vol. 194, Cold Spring Harbor Publishing (1990). Any of the inactivation strategies used must assume the secondary, tertiary or quaternary structure of the target antigen for consideration and preserve that structure when optimizing its immunogenicity.
[000113] Yeast vehicles can be formulated in immunotherapy compositions based on yeast or products of the present invention using various techniques known to those skilled in the art. For example, yeast vehicles can be dried by lyophilization. Formulations comprising yeast vehicles can also be prepared by packaging the yeast in a cake or a tablet, just as it is done for the yeast used in cooking or brewing operations. In addition, yeast vehicles can be mixed with a pharmaceutically acceptable excipient, such as an isotonic buffer that is tolerated by a host or host cell. Examples of such excipients include water, saline, Ringer's solution, dextrose solution, Hank's solution, and other physiologically balanced aqueous saline solutions. Non-aqueous vehicles, such as fixed oils, sesame oil, ethyl oleate, or triglycerides can also be used. Other useful formulations include suspensions containing viscosity-increasing agents, such as sodium carboxymethyl cellulose, sorbitol, glycerol, or dextran. Excipients can also contain minor amounts of additives, such as substances that increase isotonicity and chemical stability. Examples of buffers include phosphate buffer, bicarbonate buffer and Tris buffer, while examples of preservatives include thimerosal, m-cresol or o-cresol, formalin and benzyl alcohol. Standard formulations can be either liquid or solid injectables that can be taken in an appropriate liquid such as a suspension or solution for injection. Thus, in a non-liquid formulation, the excipient may comprise, for example, dextrose, human serum albumin, and / or preservatives to which sterile water or saline can be added prior to administration.
[000114] In one embodiment of the present invention, a composition can include additional agents, which can also be referred to as biological response modifying compounds, or the ability to produce such agents / modifiers. For example, a yeast vehicle can be transfected with or loaded with at least one antigen and at least one biological response modifying agent / compound, or a composition of the invention can be administered together with at least one biological response modifying agent / agent. Biological response modifiers include adjuvants and other compounds that can modulate immune responses, which can be referred to as immunomodulatory compounds, as well as compounds that modify the biological activity of another compound or agent, such as a yeast-based immunotherapeutic, such activity biological activity and is not limited to the effects of the immune system. Certain immunomodulatory compounds can stimulate a protective immune response, whereas others can suppress a harmful immune response, and whether an immunomodulator is useful in combination with yeast-based immunotherapeutic data may depend, at least in part, on the condition or condition of the disease that should be treated or prevented, and / or the individual that should be treated. Certain biological response modifiers preferentially improve a cell-mediated immune response, while others preferentially improve a humoral immune response (that is, it can stimulate an immune response in which there is an increase in the level of mediated cells compared to immunity. humoral, or vice versa.). Certain biological response modifiers have one or more properties in common with the biological properties of yeast-based immunotherapeutics or enhance or complement the biological properties of yeast-based immunotherapeutics. There are several techniques known to those skilled in the art to measure stimulation or suppression of immune responses, as well as to differentiate cell-mediated immune responses from humoral immune responses, and to differentiate one type of cell-mediated response from others ( for example, a TH 17 response versus a TH1 response).
[000115] Biological response agents / modifiers useful in the invention may include, but are not limited to, cytokines, chemokines, hormones, lipid derivatives, peptides, proteins, polysaccharides, small molecule drugs, antibodies and antigen binding fragments thereof (including, but not limited to, anti-cytokine antibodies, anti-cytokine receptor antibodies, anti-chemokine antibodies), vitamins, polynucleotides, nucleic acid binding moieties, aptamers, and growth modulators. Some suitable agents include, but are not limited to, IL-1 or IL-1 or IL-1R agonists, anti-IL-1 or other IL-1 antagonists; IL-6 or agonists of IL-6 or IL-6R, anti-IL-6 or other antagonists of IL-6, IL-12 or agonists of IL-12 or IL-12R, anti-IL-12 or others IL-12 antagonists; IL-17 or IL-17 or IL-17R agonists, anti-IL-17 or other IL-17 antagonists; IL-21 or IL-21 or IL-21R agonists, anti-IL-21 or other IL-21 antagonists; IL-22 or agonists of IL-22 or IL-22R, anti-IL-22 or other antagonists of IL-22, IL-23, or agonists of IL-23 or IL-23R, anti-IL-23 or other IL-23 antagonists; IL-25 or IL-25 or IL-25R agonists, anti-IL-25 or other IL-25 antagonists; IL-27, or IL-27 or IL-27R agonists, anti-IL-27 or other IL-27 antagonists; type I interferon (including, IFN-a) or type I interferon agonists or antagonists or a receptor therefor; type II interferon (including, IFN-y) or type II interferon agonists or antagonists or a receptor therefor; anti-CD40, CD40L, protein lymphocyte activation gene 3 (LAG3) and / or IMP321 (T cell immunostimulatory factor derived from the soluble form of LAG3), anti-CTLA-4 antibody (for example, to release anergic T cells ); T cell co-stimulators (for example, anti-CD137, anti-CD28, anti-CD40); alentuzumab (for example, CamPath®), denileucine diphthitox (for example, ONTAK®), anti-CD4, anti-CD25; anti-PD-1, anti-PD-L1, anti-PD-L2; agents that block FOXP3 (for example, to revoke CD4 + / CD25 + regulatory T cell activity / kill); ligand Flt3, imiquimod (Aldara ™), granulocyte-macrophage colony stimulating factor (GM-CSF); granulocyte colony stimulating factor (G-CSF); sargramostima (Leukine®); hormones, including, without limitation, prolactin and growth hormone; receptor agonists such as Toll (TLR), including, but not limited to, TLR-2 agonists, TLR-4 agonists, TLR-7 agonists, and TLR-9 agonists; TLR antagonists, including, but not limited to, TLR-2 antagonists, TLR-4 antagonists, TLR-7 antagonists and TLR-9 antagonists; anti-inflammatory and immunomodulatory agents, including, but not limited to, COX-2 inhibitors (eg, Celecoxib, NSAIDs), glucocorticoids, statins, and thalidomide and their analogues, including, IMiD ™ s (which are structural and functional properties of thalidomide (eg REVLIMID® (lenalidomide), ACTIMID® (pomalidomide)); pro-inflammatory agents, such as fungal or bacterial components, or any pro-inflammatory cytokine or chemokine; immunotherapeutic vaccines, including, but not limited to, limit to, virus-based vaccines, bacterial-based vaccines, or antibody-based vaccines; and any other immunomodulatory, immunopotentiating, and anti-inflammatory agents, pro-inflammatory agents, and any agents that modulate the number of, modulate the state of activation and / or modulating the survival of cells presenting antigen or of TH 17, TH1, and / or Treg cells. Any combination of such agents is considered by the invention, and any of such comb agents Inhaled with, or administered in a protocol with (for example, simultaneously, sequentially, or in other formats with) a yeast-based immunotherapeutic is a composition covered by the invention. Such agents are well known in the art. These agents can be used alone or in combination with other agents described in this report.
[000116] Agents can include agonists and antagonists of a given protein or peptide or domain thereof. As used in this report, an "agonist" is any compound or agent, including, but not limited to, small molecules, proteins, peptides, antibodies, nucleic acid binding agents, etc., that bind to a receptor or ligand and produces or elicits a response, which may include agents that mimic or enhance the action of a naturally occurring substance that binds to the receptor or ligand. An "antagonist" is any compound or agent, including, without limitation, small molecules, proteins, peptides, antibodies, nucleic acid binding agents, etc., that blocks or inhibits, or reduces the action of an agonist.
[000117] Compositions of the invention may additionally include or may be administered with (simultaneous, sequentially, or intermittently with) any other agents or compositions, or protocols that are useful for the prevention or treatment of cancer or any compounds that treat or alleviate any symptoms cancer, and particularly, cancers associated with Brachyury expression or overexpression. In addition, the compositions of the invention can be used in conjunction with other immunotherapeutic compositions, including prophylactic and / or therapeutic immunotherapy. In fact, the compositions of the invention can be used to inhibit or reduce resistance to chemotherapy or resistance to radiation, which can occur in metastatic cancer by inhibiting Brachyury expression in cancer (and thereby inhibiting anti-proliferative influences ) or the compositions of the invention can increase the performance of chemotherapy or radiation therapy in an individual. Additional agents, compositions or protocols (for example, therapeutic protocols) that are useful for the treatment of cancer include, but are not limited to, chemotherapy, surgical resection of a tumor, radiation therapy, allogeneic or autologous stem cell transplantation , and / or targeted cancer therapies (for example, small molecule drugs, biological products, or monoclonal antibody therapies that specifically target molecules involved in tumor growth and progression, including, but not limited to, estrogen receptor modulators (SERMs), aromatase inhibitors, tyrosine kinase inhibitors, serine / threonine kinase inhibitors, histone deacetylase inhibitors (HDAC), retinoid receptor activators, apoptosis stimulators, angiogenesis inhibitors, poly (ADP-ribose inhibitors) ) polymerase (PARP) or immunostimulators). Any of these additional therapeutic agents and / or therapeutic protocols can be administered before, simultaneously with, alternating with, or after the immunotherapy compositions of the invention, or at different time points. For example, when administered to an individual in conjunction with chemotherapy or cancer-targeted therapy, it may be desirable to administer the Brachyury yeast immunotherapy compositions during the "vacation" between doses of chemotherapy or cancer-directed therapy in order to maximize effectiveness immunotherapy compositions. Surgical resection of a tumor can often precede the administration of a Brachyury yeast immunotherapy composition, but additional or primary surgery may occur during or after the administration of a Brachyury yeast immunotherapy composition.
[000118] The invention also includes a kit comprising any of the compositions described in this report, or any of the individual components of the compositions described in this report. Kits may include additional reagents and written instructions or directions for using any of the compositions of the invention to prevent or treat cancer associated with Brachyury expression or overexpression. Methods for Administration or Use of Compositions of the Invention
[000119] Brachyury yeast immunotherapeutic compositions of the invention are designed for use to prevent or treat cancers that are associated with, or characterized by, expression or overexpression of Brachyury, including, preventing the onset of such types of cancer, halting the progression of such cancers or eliminating such types of cancers. More particularly, Brachyury yeast immunotherapeutic compositions can be used to prevent, inhibit or delay the development of tumors expressing Brachyury, and / or to prevent, inhibit or delay tumor migration and / or tumor invasion from other tissues (metastases) and / or to generally prevent or inhibit the progression of cancer in an individual. Immunotherapeutic compositions of Brachyury yeast can also be used to improve at least one symptom of cancer, such as by reducing the individual's tumor burden; prevent, inhibit tumor growth in the individual; increase the individual's survival; prevent, inhibit, reverse or delay the development of tumor migration and / or tumor invasion from other tissues (metastatic cancer) and / or prevent, inhibit, reverse or delay the progression of cancer in the individual. Brachyury yeast immunotherapy can also be used therapeutically to inhibit, reduce or eliminate resistance to chemotherapy or resistance to radiation, which can occur in metastatic cancer by inhibiting Brachyury expression in cancer, and the compositions of the invention can increase the performance of chemotherapy or radiation therapy in an individual.
[000120] Cancers that are relevant to the compositions and methods of the invention are any cancer that expresses, or can express, Brachyury, or cancers in the vicinity of cancers that express or can express Brachyury, and include, but are not limited to, cancer of the breast, small intestine, stomach, kidney, bladder, uterus, ovary, testicles, lung, colon, pancreas, or prostate, and include metastatic and end-stage cancers. In addition, Brachyury is expressed in tumors of B cell origin, such as chronic lymphocytic leukemia (CLL), B cells transformed by Epstein-Barr virus, Burkitt's and Hodgkin's lymphomas, as well as their metastatic cancers.
[000121] One embodiment of the invention relates to a method of inhibiting tumor migration and / or reducing, stopping (stopping), reversing or preventing metastatic progression of cancer in an individual who has cancer, or to reverse the development of events metastatic in cancer. As discussed above, Brachyury promotes epithelial-mesenchymal transition (EMT) in human tumor cells, which confers a mesenchymal phenotype on tumor cells, as well as migratory and invasive capabilities, while attenuating the progression of the tumor cell cycle. Therefore, Brachyury's involvement in metastatic processes makes him an ideal target for the prevention or inhibition of metastatic processes, including, stopping cancer at a pre-metastatic stage. Use of a Brachyury yeast immunotherapeutic composition of the invention may be effective in preventing or treating metastatic cancer, including, arresting cancer progression, in the face of cancer escape (or attempted escape) from traditional therapy, such as chemotherapy and radiation . The method includes the steps of administering to an individual who has cancer, a Brachyury yeast immunotherapeutic composition of the invention as described in this report, including, but not limited to: (a) a yeast vehicle; and (b) a cancer antigen comprising at least one Brachyury antigen.
[000122] In one aspect, Brachyury is not detected in the individual's cancer when the composition is first administered. In general, when Brachyury is not detected in the individual's cancer, the individual may have a premature stage cancer, in which Brachyury expression has not yet been manifested (for example, stage I or stage II), or in which Brachyury expression does not it is still detectable in any event (ie, Brachyury may or may not be expressed at a reduced level, or in a small number of tumor cells, but it is not yet easily detectable using standard detection methods). In that aspect of the invention, the development of tumor cells that express Brachyury is prevented, delayed or inhibited by using the yeast immunotherapeutic composition Brachyury. As a result, tumor migration and / or other metastatic processes that lead to metastatic progression of the tumor, are prevented, delayed or inhibited and / or general arrest of tumor progression occurs in the individual.
[000123] In another aspect, Brachyury expression is or can be detected in the individual's cancer, at the moment when the composition is first administered. The individual may have stage I, stage II, stage III, or stage IV cancer in this aspect of the invention. In this respect, the use of the yeast immunotherapeutic composition Brachyury reduces, eliminates or decreases, or stops the growth of tumors that express Brachyury, which may result in the reduction of tumor burden in the individual, inhibition of tumor growth expressing Brachyury and / or an increase in the individual's survival. The individual may experience arrest, reduction or reversal in metastatic processes, improved patient survival and health, and, in addition, allowing other therapeutic protocols for the treatment of cancer.
[000124] In fact, metastatic cancer can be associated with resistance, or greater resistance, to cancer therapies, such as chemotherapy, radiation or cancer-targeted therapy, whereby cancer "escapes" from therapy or is simply less impacted by therapy and advances. Consequently there is a need to reduce or eliminate resistance to such therapies to improve or increase the effectiveness of the therapy and to improve the patient's health and survival. Thus, an embodiment of the invention relates to a method for reducing or preventing resistance to chemotherapy, resistance to cancer-directed therapy, or resistance to radiation in a cancer patient. The method comprises administration to an individual who has cancer and is receiving chemotherapy and / or radiation therapy for cancer, an immunotherapeutic composition of Brachyury yeast as described in this report, which may include a composition comprising: (a) a yeast; and (b) a cancer antigen comprising at least one Brachyury antigen. This method of the invention can also be used to treat resistance associated with other therapeutic cancer treatments, including, but not limited to, cancer-targeted therapy.
[000125] In one aspect of this modality, Brachyury is not detected in the individual's cancer, at the moment when the composition is first administered. In this regard, administration of an immunotherapeutic composition of yeast Brachyury prevents or inhibits the onset of resistance to chemotherapy or radiation therapy, inhibiting the development of tumor cells expressing Brachyury in cancer. In another aspect, Brachyury expression is detected in the individual's cancer, at the moment when the composition is first administered. In this regard, the individual may or may not already be experiencing resistance to chemotherapy or radiation. In each case, administration of the Brachyury yeast immunotherapeutic composition of the invention prevents or inhibits chemotherapy resistance or radiation resistance therapy, or increases the ability of chemotherapy or radiation therapy to treat the individual by reducing or eliminating tumor cells. expressing Brachyury in the patient.
[000126] Another embodiment of the invention relates to a method for treating cancer, and particularly, a cancer expressing Brachyury. The method includes administering to an individual who has Brachyury-expressing cancer a Brachyury yeast immunotherapeutic composition described in this report, which may include a composition comprising: (a) a yeast vehicle; and (b) a cancer antigen comprising at least one Brachyury antigen. In one aspect, the method reduces tumor burden on the patient. In one aspect, the method increases the patient's survival. In one aspect, the method inhibits tumor growth in the individual. In one aspect, the method prevents, stops or reverses the metastatic progression of the tumor.
[000127] Since Brachyury's expression is believed to be more prevalent as an advance or progression of cancer in higher stages (for example, from stage I, stage II, stage III, stage IV, depending on the particular cancer) and it is associated with metastatic processes, it is a modality of the invention, to provide a method of preventing or delaying the onset of a cancer expressing Brachyury, or to stop the cancer in a pre-metastatic or pre-malignant stage. Such a method includes administration to an individual in whom cancer cells expressing Brachyury are not detected, of a Brachyury yeast immunotherapeutic composition described in this report, which may include a composition comprising: (a) a yeast vehicle; and (b) a cancer antigen comprising at least one Brachyury antigen. In one aspect of this modality, cancer is known to express or is believed to be susceptible to expressing Brachyury at some stage of cancer in at least a subset of individuals with cancer. In an aspect of this modality, the individual already has a cancer, but Brachyury is not detected in the cancer, at the moment, when the composition is first, administered, which means that the individual can present an earlier stage of cancer in which the Brachyury expression has not yet been manifested, or where Brachyury expression is not yet detectable in any event (ie, Brachyury may or may not be expressed at a low level, or in a small number of tumor cells, but it is not still easily detectable using standard detection methods). In some cases, the type of cancer may be known to have a high rate of metastatic progression. In this regard, administration of the Brachyury yeast immunotherapeutic composition prevents, delays or inhibits the development of tumor cells expressing Brachyury in the patient's cancer, and therefore prevents, detains, delays or inhibits metastatic processes that accompany Brachyury expression. In another aspect, the individual does not have cancer when the composition is administered. Such an individual may be "predisposed" or prone to developing cancer, perhaps due to family history or a genetic marker, or because the individual has shown signs of precancerous cells or lesions, or has precancerous cells or lesions (precancerous). malignant).
[000128] In one aspect, the individual is additionally treated with at least one other therapeutic compound or therapeutic protocol useful for the treatment of cancer. Such therapeutic agents and protocols are discussed in detail elsewhere in this report. For example, in any of the modalities with respect to the methods of the invention described in this report, in one aspect, when the individual has cancer (regardless of the status of Brachyury expression detectable in tumor cells), the individual being treated or has been treated with another cancer therapy. Such therapy may include any of the therapeutic protocols, or the use of any therapeutic compound or agent previously described herein, including, but not limited to, chemotherapy, radiation therapy, cancer-directed therapy, surgical resection of a tumor, transfer of stem cells, cytokine therapy, transfer of adoptive T cells, and / or administration of a second immunotherapeutic composition. In the case of administration of a second immunotherapeutic composition, such compositions may include, but are not limited to, additional yeast-based immunotherapy, recombinant virus-based immunotherapy (viral vectors), cytokine therapy, immunostimulatory therapy (including, chemotherapy with immunostimulating properties), DNA vaccines, and other immunotherapy compositions.
[000129] In one aspect, the second immunotherapeutic composition includes a second cancer antigen that does not include Brachyury antigen. For example, a second immunotherapeutic composition useful in combination with a yeast Brachyury immunotherapeutic composition is a yeast immunotherapeutic composition comprising another cancer antigen. Such cancer antigens may include, but are not limited to, carcinoembryonic antigen (CEA), Ras mutated point oncoprotein, MUC-1, EGFR, BCR-Ab1, MART-1, MAGE-1, MAGE-3, GAGE, GP-100, MUC-2, normal and mutated p53 oncoproteins, PSMA, tyrosinase, TRP-1 (gp75), NY-ESO-1, TRP-2, TAG72, KSA, CA-125, PSA, HER-2 / neu / c-erb / B2, hTERT, p73, B-RAF, adenomatous polyposis coli (APC), Myo, von Hippel-Lindau protein (VHL), Rb-1, Rb-2, androgen receptor (RA) , Smad4, MDR1, Flt-3, BRCA-1, BRCA-2, pax3-fkhr, ews-fli-1, HERV-H, HERV-K, TWIST, Mesothelin, NGEP, modifications of such antigens, junction variants such antigens, and epitope agonists of such antigens, as well as combinations of such antigens, and / or immunogenic domains thereof, modifications thereof, variants thereof, and / or epitope agonists thereof.
[000130] As used in this report, to "treat" a cancer, or any permutation of it (for example, "cancer treaty", etc.) generally refers to the administration of a composition of the invention, once the cancer has occurred (for example, once the cancer was diagnosed or detected in an individual), with at least one therapeutic purpose of the treatment (when compared in the absence of that treatment), including: reduction in tumor burden, inhibition of tumor growth, increase in individual survival, delaying, inhibiting, stopping or preventing the onset or development of metastatic cancer (such as, delaying, inhibiting, stopping or preventing the onset of tumor migration and / or tumor invasion of tissues outside of primary cancer and / or other processes associated with metastatic cancer progression), slowing or arresting cancer progression, improving immune responses against the tumor, improving long-term memory immune responses o against tumor antigens, and / or improving the individual's overall health. To "prevent" or "protect" from a cancer, or any permutation of it (for example, "cancer prevention", etc.), generally refers to administering a composition of the invention before a cancer has occurred , or before, a specific stage of cancer or tumor antigen expression in a cancer has occurred (for example, before Brachyury expression is detected in cancer), with at least one treatment goal (when compared to absence of such treatment), including: preventing or delaying the onset or development of a cancer, or, if the cancer occurs after treatment, at least reducing the severity of the cancer (for example, reducing the level of tumor growth, halting progression cancer, improving the immune response against cancer, inhibiting metastatic processes) or improving outcomes in the individual (for example, improving survival).
[000131] The present invention includes the transfer (administration, immunization) of a Brachyury yeast immunotherapeutic composition of the invention to a subject or individual. The administration process can be carried out ex vivo or in vivo, but it is typically carried out in vivo. Administration, ex vivore refers to the part of carrying out the regulatory step outside the patient, such as administering a composition of the present invention to a population of cells (dendritic cells) removed from a patient under conditions, such as a yeast vehicle, antigen (s) and any other agents or compositions are loaded into the cell, and returning the cells to the patient. The therapeutic composition of the present invention can be returned to a patient, or administered to a patient, by any suitable mode of administration.
[000132] Administration of a composition can be systemic, mucous and / or proximal to the location of the target site (for example, close to a tumor site). Adequate routes of administration will be evident to those skilled in the art, depending on the type of cancer that must be prevented or treated and / or the target cell or tissue population. Various acceptable methods of administration include, but are not limited to, intravenous administration, intraperitoneal administration, intramuscular administration, intranodal administration, intracoronary administration, intraarterial administration (for example, in a carotid artery), subcutaneous administration, transdermal administration, administration intratracheal, intra-articular administration, intraventricular administration, inhalation (for example, aerosol), intracranial intracranial, intraocular, aural, intranasal, oral, pulmonary administration, impregnation of a catheter and direct injection into tissue. In one aspect, routes of administration include: intravenous, intraperitoneal, subcutaneous, intradermal, intranodal, intramuscular, transdermal, inhalation, intranasal, oral, intraocular, intra-articular, intracranial, intraspinal. Parenteral transfer can include routes: intradermal, intramuscular, intraperitoneal, intrapleural, intrapulmonary, intravenous, subcutaneous, atrial catheter and venal catheter. Ear transfer can include ear drops, intranasal transfer can include nasal drops or intranasal injection, and intraocular transfer can include eye drops. Aerosol transfer (inhalation) can also be performed using standard methods in the prior art (see, for example, Stribling et al .; Proc. Natl. Acad. Sci. USA 189: 11277-11281, 1992). In one aspect, a Brachyury yeast immunotherapeutic composition of the invention is administered subcutaneously. In one aspect, the Brachyury yeast immunotherapeutic composition is administered directly to a tumor medium.
[000133] In general, a single adequate dose of a Brachyury yeast immunotherapeutic composition is a dose that is capable of effectively providing a yeast vehicle and Brachyury antigen for a given cell type, tissue, or region of the patient's body in an amount effective to induce a tumor-specific immune response against one or more Brachyury antigens or epitopes, when administered one or more times over an appropriate period of time. For example, in one embodiment, a single dose of a Brachyury yeast of the present invention is approximately 1 x 10 5 to approximately 5 x 10 7 yeast cell equivalents per kilogram of body weight of the organism that is to be administered the composition. In one aspect, a single dose of a yeast vehicle of the present invention is approximately 0.1 Yeast Unit (Y.U., which is 1 x 106 yeast cells or yeast cell equivalents), at about 100 Y.U. (1 x 109 cells) per dose (ie, per organism), including any interim dose, in increments of 0.1 x 106 cells (ie, 1.1 x 106, 1.2 x 106, 1.3 x 106 ...). In one embodiment, a suitable dose includes doses between 1 Y.U. and 40 Y.U. and in one respect, between 10 Y.U. and 40 Y.U. In one embodiment, doses are administered at different sites in the individual, but over the same dosage period. For example, a dose of 40 Y.U. may be administered by injection of 10 Y.U. to four different sites in the individual over a dosing period. The invention includes administration of a quantity of the yeast immunotherapy composition Brachyury (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16 , 17, 18, 19, 20 YU or more) at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more different sites in an individual to form a single dose. One Yeast Unit (Y.U.) is 1 x 107 yeast cells or yeast cell equivalents.
[000134] "Boosters" or "boosters" of a therapeutic composition are administered, for example, when the immune response against the antigen has decreased or as needed, provide an immune response or induce a memory response against a specific antigen or antigens. Boosters can be administered about 1, 2, 3, 4, 5, 6, 7 or 8 weeks apart, or monthly, bimonthly, quarterly, annually, and / or in some or several annual increments after the original administration , depending on the state of the individual being treated and the purpose of therapy at the time of administration (eg prophylactic, active treatment, maintenance). In one embodiment, an administration program is one in which doses of Brachyury yeast immunotherapeutic composition are administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more times over a period of weeks, months, or even years. In one embodiment, doses are administered weekly or fortnightly, for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more doses, followed by fortnightly or monthly doses, as needed to achieve preventive treatment. or desired therapy for cancer. Additional boosters can then be given at similar or longer intervals (months or years) as maintenance or remission therapy, if desired.
[000135] In one aspect of the invention, one or more additional therapeutic agents or therapeutic protocols are administered or performed, sequentially and / or simultaneously with the administration of the Brachyury yeast immunotherapy composition (e.g., surgical resection of the tumor, administration of chemotherapy , administration of radiation therapy, administration of another immunotherapy composition or protocol, cytokine therapy, transfer of adoptive T cells, or stem cell transplantation). For example, one or more therapies can be administered or performed before the first dose of Brachyury yeast immunotherapy composition or after the first dose is administered. In one embodiment, one or more therapies can be administered or performed in an alternating manner, with the dosage of the Brachyury yeast immunotherapy composition, as in a protocol in which the Brachyury yeast composition is administered at prescribed intervals, between one or more consecutive doses of chemotherapy or other therapy. In one embodiment, the Brachyury yeast immunotherapy composition is administered in one or more doses, over a period of time before initiating additional therapies. In other words, the Brachyury yeast immunotherapeutic composition is administered as a monotherapy for a period of time and then additional therapy is added (for example, chemotherapy), either simultaneously, with new doses of Brachyury yeast immunotherapy, or in an alternating form with Brachyury yeast immunotherapy. Alternatively, or in addition, another therapy can be administered for a period of time before starting administration of the yeast immunotherapy composition Brachyury, and the concepts can be combined (for example, surgical resection of a tumor, followed by monotherapy with immunotherapy of Brachyury yeast for several weeks, followed by alternating doses of chemotherapy and Brachyury yeast immunotherapy, for weeks or months, optionally, followed by monotherapy using Brachyury yeast immunotherapy or other therapy, or by a new protocol combination therapy provided, sequentially, simultaneously, or alternatively). Various protocols for the treatment of cancer using Brachyury yeast immunotherapy are considered by the invention, and these examples should be considered as non-limiting examples of several possible protocols.
[000136] In one aspect of the invention, additional antigens other than Brachyury are also targeted using yeast-based immunotherapy, in addition to Brachyury targeting. Such additional target antigens can be included within the same yeast vehicle as Brachyury antigens, or additional yeast-based immunotherapy compositions targeting different antigens can be produced and then combined as desired, depending on the individual to be treated , the antigens expressed by the type of cancer or the specific tumor of the individual, and / or depending on the stage of cancer in the individual, or the stage of treatment of the individual. For examples, a combination of antigens can be selected that covers: (1) antigens involved in seminal events in cancer development, such as Ras mutant, antigens involved in, or associated with deregulation of cellular processes, such as CEA, and (3 ) Brachyury, who is involved in metastatic processes. For example, in, or more other yeast-based immunotherapy compositions, they may express one or more antigens, including, but not limited to, carcinoembryonic antigen (CEA), Ras mutant oncoprotein, MUC-1, EGFR, BCR -Ab1, MART-1, MAGE-1, MAGE-3, GAGE, GP-100, MUC-2, normal and sharp mutant p53 oncoproteins, PSMA, tyrosinase, TRP-1 (gp75), NY-ESO-1, TRP-2, TAG72, KSA, CA-125, PSA, HER-2 / neu / c-erb / B2, hTERT, p73, B-RAF, coli adenomatous polyposis (APC), Myc, von Hippel-Lindau protein (VHL ), Rb-1, Rb-2, androgen receptor (RA), Smad4, MDR1, Flt-3, BRCA-1, BRCA-2, pax3-fkhr, ews-fli-1, HERV-H, HERV-K , TWIST, Mesothelin, NGEP, modifications of such antigens, junction variants of such antigens, and agonists of the epitope of such antigens, as well as combinations of such antigens, and / or their immunogenic domains, modifications thereof, variants thereof, and / or epitope agonists of these. One, two, three or more of these yeast-based immunotherapy compositions can be administered to an individual before, simultaneously, or alternating with, and / or after administration of a Brachyury yeast immunotherapy composition, in order to optimize antigen targeting in the individual's tumor. As above, additional therapies can also be used in such protocols (for example, surgical tumor resection, chemotherapy, cancer-targeted therapy, radiation therapy, etc.).
[000137] In an embodiment of the invention, a method for treating cancer is provided. The method includes the steps of: (a) administering to an individual who has cancer in which Brachyury expression was not detected, a first immunotherapeutic composition comprising a yeast vehicle and a first cancer antigen that does not comprise a Brachyury antigen, and (b) administering to the individual, prior to, simultaneously with, or subsequent to, administration of the first immunotherapeutic composition, a second immunotherapeutic composition comprising a yeast vehicle and a second cancer antigen comprising a Brachyury antigen. In additional embodiments, the method may include administering one or more additional immunotherapeutic compositions, wherein each of the one or more additional immunotherapeutic compositions comprises an additional cancer antigen. The additional antigen can be any of those known in the art or described in this report, including, but not limited to, mutant Ras, carcinoembryonic antigen (CEA) and MUC-1.
[000138] In another embodiment of the invention, a method for treating cancer includes the following steps: (a) administering to an individual who has cancer, a first immunotherapeutic composition comprising a yeast vehicle and a mutant Ras antigen; (b) administering to the individual from (a) a second immunotherapeutic composition comprising a yeast vehicle and an antigen selected from the group consisting of carcinoembryonic antigen (CEA) and mucin-1 (MUC-1); and (c) administering to the individual of (a) and (b) a third immunotherapeutic composition comprising a yeast vehicle and a Brachyury antigen. One or more of the administration steps in (a), (b) and (c) can be performed simultaneously, or sequentially. The steps can be repeated as needed to treat an individual's specific cancer, and the cancer antigens can be modified before or during treatment to specifically address the individual's specific cancer.
[000139] In the method of the present invention, therapeutic compositions and compositions can be administered to animals, including any vertebrate, and particularly, to any member of the vertebrate class, Mammalia, including, without limitation, primates, rodents, cattle and domestic animals. Cattle include mammals to be consumed or that produce useful products (for example, sheep for wool production). Mammals to treat or protect using the invention include humans, non-human primates, dogs, cats, mice, rats, goats, sheep, cattle, horses and pigs.
[000140] An "individual" is a vertebrate, just like a mammal, including, without limitation, a human being. Mammals include, but are not limited to, farm animals, sport animals, pets, primates, mice and rats. The term "individual" can be used interchangeably with the term "animal", "subject" or "patient". General Techniques Useful in the Invention
[000141] The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology (including, recombinant techniques), microbiology, cell biology, biochemistry, nucleic acid chemistry, and immunology, which are well known those skilled in the art. Such techniques are fully explained in the literature, such as, Methods of Enzymology, (Methods of Enzymology), vol. 194, Guthrie et al., Eds., Cold Spring Harbor Laboratory Press (1990); Biology and activities of yeasts, (Biology and yeast activities), Skinner, et al., Eds., Academic Press (1980); Methods in yeast genetics: a laboratory course manual, (Rose yeast genetics methods: a laboratory course manual), Rose et al., Cold Spring Harbor Laboratory Press (1990); The Yeast Saccharomyces: Cell Cycle and Cell Biology, (The Yeast Saccharomyces'.Cell Cycle and Cell Biology, Pringle et al., Eds., Cold Spring Harbor Laboratory Press (1997); The Yeast Saccharomyces: Gene Expression, (The Saccharomyces Yeast ' Gene Expression, Jones et al., Cold Spring Harbor Laboratory Press (1993); The Yeast Saccaromyces: Genome Dynamics, Protein Synthesis and Energetics, (Genome Dynamics, Protein and Energy Synthesis), Broach and others, Eds., Cold Spring Harbor Laboratory Press (1992); Molecular Cloning: A Laboratory Manual, second edition (Sambrook et al., 1989) and Molecular Cloning: A Laboratory Manual, third edition ( Sambrook and Russel, 2001), (together referred to in this report as "Sambrook"); Current Protocols in Molecular Biology, (Current Protocols in Molecular Biology) (FM Ausubel et al., Eds., 1987, including supplements up to 2001); PCR: The Polymerase Chain Re action, (RCP: Polymerase Chain Reaction), (Mullis et al., Eds., 1994); Harlow and Lane (1988), Antibodies, A Laboratory Manual, (Antibodies, A Laboratory Manual), Cold Spring Harbor Publications, New York; Harlow and Lane (1999) Using Antibodies: A Laboratory Manual, (Cold Antibodies: A Laboratory Manual), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (hereinafter referred to as "Harlow and Lane"), Beaucage and others, Eds., Current Protocols in Nucleic Acid Chemistry, (Current Protocols in Nucleic Acid Chemistry), John Wiley & Sons, Inc. New York, 2000); Casarett and Doull’s Toxicology The Basic Science of Poisons, (Toxicology, The Basic Science of Poison), C. Klaassen, Ed., 6a. edition (2001), and Vaccines, (Vaccines), S. Plotkin, W. Orenstein and P. Offit, eds., fifth edition (2008). General Settings
[000142] A "TARMOGEN®" (Globelmmune, Inc., Louisville, Colorado) generally refers to a yeast vehicle that expresses one or more heterologous antigens extracellularly (on its surface), intracellularly (internally or cytosolically) or both , extracellular and intracellular. TARMOGENs® have generally been described (see, for example, United States Patent No. 5,830,463). Certain yeast-based immunotherapy compositions, and methods of producing and generally using it, are also described in detail, for example, United States Patent No. 5,830,463, United States Patent No. 7,083,787, United States Patent No. 7,736,642, Stubbs et al., Nat. Med. Chem. 7: 625-629 (2001), Lu et al., Cancer Research 64: 5084-5088 (2004), and Bernstein et al., Vaccine, January 24, 2008; 26 (4): 509-21, each of which is incorporated as a reference in this report in its entirety.
[000143] As used in this report, the term "analog" refers to a chemical compound that is structurally similar to another compound, but differs slightly in composition (as in the replacement of an atom by an atom of a different element or in the presence of a particular functional group, or the replacement of a functional group with another functional group). Thus, an analog is a compound that is similar or comparable in function and appearance, but has a different structure or origin with respect to the reference compound.
[000144] The terms, "substituted", "substituted derivative" and "derivative", when used to describe a compound, mean that at least one hydrogen bonded to the unsubstituted compound is replaced with a different atom or a chemical moiety.
[000145] Although a derivative has a physical structure similar to that of the original compound, the derivative may have different chemical and / or biological properties than the original compound. Such properties may include, but are not limited to, increased or reduced activity of the original compound, new activity, compared to the original compound, increased or reduced bioavailability, increased or reduced efficacy, increased or reduced stability in vitroe / or in vivo, and / or increased or reduced absorption properties.
[000146] In general, the term "biologically active" indicates that a compound (including, a protein or peptide) exhibits at least one detectable activity that has an effect on the metabolic, physiological, chemical, or other processes of a cell, a tissue, or an organism, when measured or observed in vivo (ie, in a natural physiological environment) or in vitro (ie, under laboratory conditions).
[000147] According to the present invention, the term "modular" can be used interchangeably with "regular" and generally refers to over-regulation or deregulation of a specific activity. As used herein, the term "super-regular" can be used in general to describe any of: elicitation, initiation, increase, elevation, reinforcement, improvement, intensification, amplification, promotion or supply, in relation to a particular activity. Similarly, the term "unregulated" can be used generally to describe any of: decrease, decrease, inhibition, improvement, decrease, reduction, block, or impediment, in relation to a particular activity.
[000148] In one embodiment of the present invention, any of the amino acid sequences described in this report can be produced with at least one, and up to approximately 20, additional heterologous amino acids that flank each of the C and / or N termini of the sequence specified amino acid. The resulting protein or polypeptide can be referred to as "consisting essentially of" the specified amino acid sequence. According to the present invention, heterologous amino acids are sequences of amino acids that are not found naturally (i.e., not found in nature, in vivo), that flank the specified amino acid sequence, or that are not related to the function of the sequence specified amino acid sequence, or that would not be encoded by the nucleotides that flank the naturally occurring nucleic acid sequence encoding the specified amino acid sequence when it occurs in the gene, if such nucleotides in the naturally occurring sequence have been translated using standard codon to the organism, from which the specified amino acid sequence is derived. Similarly, the term "consisting essentially of", when used with reference to a nucleic acid sequence in this report, refers to a nucleic acid sequence that encodes a specified amino acid sequence that can be flanked by at least one, or even as many as approximately 60; additional heterologous nucleotides at each of the 5 'and / or 3' ends of the nucleic acid sequence encoding the specified amino acid sequence. Heterologous nucleotides are not naturally found (that is, not found in nature, in vivo) that flank the nucleic acid sequence that encodes the specified amino acid sequence when it occurs in the natural gene or, it does not encode a protein that confers any additional function to the protein or changes the function of the protein that has the specified amino acid sequence.
[000149] According to the present invention, the term "selectively binds" refers to the ability of an antibody, antigen-binding fragment or binding partner of the present invention to bind preferentially to specific proteins. More specifically, the term "selectively binds" refers to the specific binding of one protein to another (for example, an antibody, fragment thereof, or antigen binding partner), where the level of binding, as measured by any standard assay (for example, an immunoassay), it is statistically and significantly larger than the base control for the assay. For example, when performing an immunoassay, controls typically include a reaction well / tube that contains isolated antigen binding antibody or fragment (ie, in the absence of antigen), where an amount of reactivity (for example, non-binding) well) by the antibody or antigen-binding fragment thereof in the absence of the antigen, is considered to be the basis. Binding can be measured using a variety of standard methods in the art, including enzyme immunoassays (eg, ELISA, immunoblot assays, etc.).
[000150] General reference to a protein or polypeptide used in the present invention includes proteins of full length, proteins of near full length (defined above), or any fragment; domain (structural, functional or immunogenic), conformational epitope, or a homolog or variant of a specific protein. A fusion protein can also be generally referred to as a protein or polypeptide. An isolated protein according to the present invention is a protein (including, a polypeptide or peptide) that has been removed from its natural environment (that is, that has been subjected to human manipulation), and may include purified proteins, partially purified proteins , proteins produced recombinantly, and proteins produced synthetically, for example. As such, "isolated" does not reflect the extent to which the protein has been purified. Preferably, an isolated protein of the present invention is produced recombinantly. According to the present invention, the terms "modification" and "mutation" can be used interchangeably, in particular, with respect to modifications / mutations with the amino acid sequence of proteins or portions thereof (or nucleic acid sequences) described in this report .
[000151] As used in this report, the term "homologous" or "variant" is used to refer to a protein or peptide that differs from a reference protein or peptide (that is, the "prototype" or "wild type" protein ) for minor modifications with the reference protein or peptide, but which maintains the basic and side-chain protein structure as it occurs naturally. Such changes include, but are not limited to: changes in one or a few amino acid side chains, changes in one or a few amino acids, including deletions (for example, a truncated version of the protein or peptide), insertions and / or substitutions; changes in the stereochemistry of one or a few atoms; and / or minor derivatizations, including, but not limited to: methylation, glycosylation, phosphorylation, acetylation, myristylation, prenylation, palmitation, amidation and / or addition of glycosylphosphatidyl inositol. A homolog or variant may have increased, decreased, or substantially similar properties, compared to the reference protein or peptide. A homolog or variant can include a protein agonist or a protein antagonist. Homologues or variants can be produced using techniques known in the art for protein production, including, but not limited to, direct modifications to the isolated reference protein, direct protein synthesis; or modifications to the nucleic acid sequence encoding the protein using, for example, classical or recombinant DNA techniques to effect random or targeted mutagenesis, resulting in the encoding of a protein variant. In addition, there may be naturally occurring variants of a reference protein (for example, isoforms, allelic variants, or other natural variants that can occur from individual to individual) and can be isolated, produced and / or used in the invention.
[000152] A homologue or variant of a specified protein may comprise, essentially consist of, or consist of, an amino acid sequence that is at least about 45%, or at least about 50%, or at least about 55 %, or at least about 60%, or at least about 65%, or at least about 70%, or at least about 75%, or at least about 80%, or at least about 85%, or at least about 86% identical, or at least about 87% identical, or at least about 88% identical, or at least about 89% identical, or at least about 90%, or at least about 91 % identical, or at least about 92% identical, or at least about 93% identical, or at least about 94% identical, or at least about 95% identical, or at least about 96% identical, or at least at least about 97% identical, or at least about 98% identical, or at least about 99% identical (or any percentage of identity between 45% and 99%, in increment the totals of an integer), with the amino acid sequence of the reference protein (for example, an amino acid sequence specified here, or the amino acid sequence of a specified protein). In one embodiment, the homologous or variant comprises, consists essentially of, or consists of, a sequence of amino acids that is less than 100% identical, less than about 99% identical, less than about 98% identical, unless of about 97% identical, less than about 96% identical, less than about 95% identical, and so on, in 1% increments, unless about 70% identical to the amino acid sequence of reference protein.
[000153] As used in this report, unless otherwise specified, reference to a percentage (%) of identity refers to a homology assessment that is performed using: (1) a basic homology survey, Basic Local Alignment Search Tool (BLAST) using blastp for amino acid searches and blastn for nucleic acid searches with standard (default) parameters, where the query string is filtered for low complexity regions by default (as described in Altschul, SF, Madden, TL, Schããffer, AA, Zhang, J., Zhang, Z., Miller, W. & Lipman, DJ (1997); "gapped BLAST and PSI-BLAST: a new generation of protein database research programs "Nucleic Acids Res. 25: 3389-3402, hereby incorporated by reference in their entirety), (2) a two-sequence BLAST alignment (for example, using the parameters described below) , (3) and / or PSI-BLAST with the standard parameters (position- Specific Iterated BLAST. It is noted that, due to some differences in the standard parameters between basic BLAST and BLAST for two sequences, two specific sequences can be recognized as presenting significant homology using the BLAST program, since a research carried out in Basic BLAST using one of the strings as the query string may not identify the second string in the top combination. In addition, PSI-BLAST provides an automated, easy-to-use version of a search "profile", which is a sensitive way to search for sequence counterparts. The first program performs a search of the gapped BLAST database. The PSI-BLAST program uses information from any significant alignments returned for the construction of a position-specific scoring matrix, which replaces the query string for the next round of database research. Therefore, it must be understood that the percentage of identity can be determined using any of these programs.
[000154] Two specific sequences can be aligned to each other using BLAST as described in Tatusova and Madden, (1999), "Blast 2 sequences - a new tool for comparing protein and nucleotide sequences", FEMS Microbiol. Lett. 174: 247-250, hereby incorporated by reference in its entirety. Such alignment of the sequence is performed in blastp or blastn using the BLAST 2.0 algorithm to perform a BLAST gapped search (BLAST 2.0) between the two sequences that allow the introduction of gaps (deletions and insertions) in the resulting alignment. For the sake of clarity, here, a BLAST alignment sequence for two sequences is done using the standard parameters as follows.
[000155] For blastn, using matrix BLOSUM62 0:
[000156] Reward for correspondence = 1
[000157] Penalty for incompatibility = -2
[000158] Open gap (5) and extension gap (2) penalties
[000159] Gap xdropoff (50) wait (10) express size (11) filter (in)
[000160] For blastp, using matrix BLOSUM62 0:
[000161] Open gap (11) and extension gap (1) penalties
[000162] x_dropoff gap (50) wait (10) express size (3) filter (in).
[000163] An isolated nucleic acid molecule is a nucleic acid molecule that has been removed from its natural environment (ie, that has been subjected to human manipulation), its natural environment, being the genome or chromosome in which the nucleic acid molecule is found in nature. As such, "isolated" does not necessarily reflect the extent to which the nucleic acid molecule has been purified, but it does indicate that the molecule does not include an entire genome or an entire chromosome or a segment of the genome that contains more than one gene, where the nucleic acid molecule that is found in nature. An isolated nucleic acid molecule can include a complete gene. An isolated nucleic acid molecule that includes a gene that is not a fragment of a chromosome that includes such a gene, but instead includes the coding region and regulatory regions associated with the gene, but additional genes that are not naturally found in the same chromosome. An isolated nucleic acid molecule can also include portions of a gene. An isolated nucleic acid molecule may also include a specified nucleic acid sequence, flanked by (i.e., at the 5 'and / or 3' end of the sequence) additional nucleic acids that do not normally flank the specified nucleic acid sequence in nature (that is, heterologous sequences). Isolated nucleic acid molecule can include DNA, RNA (for example, mRNA), or derivatives of DNA or RNA (for example, cDNA). Although the term "nucleic acid molecule" refers primarily to the physical nucleic acid molecule and the term "nucleic acid sequence" refers primarily to the nucleotide sequence in the nucleic acid molecule, the two expressions can be used interchangeably , in particular, with respect to a nucleic acid molecule, or a nucleic acid sequence, being able to encode a protein or a domain of a protein.
[000164] A recombinant nucleic acid molecule is a molecule that can include at least one of any nucleic acid sequence encoding one or more proteins described herein operably linked to at least one of any transcription control sequence capable of regulating effectively expressing the nucleic acid molecule in the cell to be transfected. Although the term "nucleic acid molecule" mainly refers to the physical nucleic acid molecule and the term "nucleic acid sequence" mainly refers to the nucleotide sequence in the nucleic acid molecule, both expressions can be used alternately, in particular, with respect to a nucleic acid molecule, or a nucleic acid sequence, being able to encode a protein. In addition, the term "recombinant molecule" refers primarily to a nucleic acid molecule operably linked to a transcription control sequence, but can be used interchangeably with the term "nucleic acid molecule", which is administered to a animal.
[000165] A recombinant nucleic acid molecule includes a recombinant vector, which is any nucleic acid sequence, typically a heterologous sequence that is operably linked to the isolated nucleic acid molecule that encodes a fusion protein of the present invention, which is capable of allowing recombinant production of the fusion protein, and which is capable of transferring the nucleic acid molecule to a host cell according to the present invention. Such a vector can contain nucleic acid sequences that are not naturally found adjacent to isolated nucleic acid molecules that must be inserted into the vector. The vector can be RNA or DNA, either prokaryotic or eukaryotic, and preferably, in the present invention, it is a plasmid useful for yeast transfection. Recombinant vectors can be used in the cloning, sequencing, and / or otherwise manipulation of nucleic acid molecules, and can be used in the transfer of such molecules (for example, as in a DNA composition or a viral vector-based composition ). Recombinant vectors are preferably used in the expression of nucleic acid molecules, and can also be referred to as expression vectors. Preferred recombinant vectors are capable of being expressed in a transfected host cell, such as a yeast.
[000166] In a recombinant molecule of the present invention, nucleic acid molecules are operably linked to expression vectors that contain regulatory sequences, such as transcription control sequences, translation control sequences, origins of replication and other regulatory sequences that are compatible with the host cell and which control the expression of nucleic acid molecules of the present invention. In particular, the recombinant molecules of the present invention include nucleic acid molecules that are operably linked to one or more expression control sequences. The term "operably linked" refers to the binding of a nucleic acid molecule to an expression control sequence such that the molecule is expressed when transfected (i.e., transformed, translated or transfected) into a host cell.
[000167] In accordance with the present invention, the term "transfection" is used to refer to any method by which an exogenous nucleic acid molecule (i.e., a recombinant nucleic acid molecule) can be inserted into a cell . The term "transformation" can be used interchangeably with the term "transfection", when that term is used to refer to the introduction of nucleic acid molecules into microbial cells, such as algae, bacteria and yeast. In microbial systems, the term "transformation" is used to describe an inherited change due to the acquisition of exogenous nucleic acids by the microorganism and is essentially synonymous with the term "transfection". Therefore, transfection techniques include, but are not limited to, transformation, chemical treatment of cells, bombardment of particles, electroporation, microinjection, lipofection, adsorption, infection and fusion of protoplasts.
[000168] The following experimental results are provided for purposes of illustration, and are not intended to limit the scope of the invention. EXAMPLES Example 1
[000169] The following example describes the production of an immunotherapeutic composition of yeast Brachyury.
[000170] In this experiment, yeast (Saccharomyces cerevisiae) was manipulated to express human Brachyury under the control of the copper-inducible promoter, CUP1, or the constitutive promoter, TEF2, producing yeast Brachyury immunotherapy compositions. In each case, a fusion protein comprising a Brachyury antigen was produced as a single polypeptide with the following sequence elements fused to the structure from N terminus to C terminus, represented by SEQ ID NO: 8 (1) a peptide terminating N to confer resistance to proteasome degradation and stabilize expression (positions 1 to 6 of SEQ ID NO: 8, the peptide sequence also represented here by SEQ ID NO: 11); (2) amino acids 2- 435 of SEQ ID NO: 6, SEQ ID NO: 6, which represents a near-length Brachyuryhuman protein (positions 7-440 of SEQ ID NO: 8); and (3) a hexa-histidine tail (positions 441-446 of SEQ ID NO: 8). The amino acid sequences used in this fusion protein can be modified by using additional or alternating amino acids that flank each end of the Brachyury antigen, if desired, and the shorter portions of the Brachyury antigen can also be used. A nucleic acid sequence encoding the SEQ ID NO: 8 fusion protein (codon optimized for yeast expression) is represented here by SEQ ID NO: 7.
[000171] Briefly, DNA encoding a full-length human Brachyury protein from a plasmid pCRI -Brachyury provided by the National Cancer Institute (Dr. Jeffrey Schlom) was amplified using CPR, and then inserted into cloning sites EcoRI and Spel behind the CUP1 promoter (vector pGI-100) or the TEF2 promoter (vectors plu011 or pGI-172), in 2 pm yeast expression vectors. The nucleotide sequences encoding the N-terminating stabilizing peptide, MADEAP (SEQ ID NO: 11) and a C-terminating hexahistidine peptide were also added to the plasmid vector to encode the complete fusion protein, represented by ID SEQ NO: 8. The resulting plasmids were transformed into DH5a for plasmid storage, and Saccharomyces cerevisiae W303a for the production of the immunotherapeutic compositions of yeast Brachyury.
[000172] Transformation into Saccharomyces cerevisiae was performed by transfection of lithium acetate / polyethylene glycol, and primary transfectants were selected in minimal solid plates devoid of uracil (UDM; uridine abandonment medium). Colonies were selected by growth in U2 (uridine abandonment medium) or UL2 (uridine and leucine abandonment medium) medium at 30 ° C.
[000173] The yeast Brachyury immunotherapy composition comprising a polynucleotide encoding the human Brachyury fusion protein represented by SEQ ID NO: 8, under the control of the CUP1 promoter is also referred to here as GI-6301. The Brachyury yeast immunotherapy composition comprising a polynucleotide encoding the human Brachyury fusion protein represented by SEQ ID NO: 8, under the control of the TEF2 promoter (in vector plu011) is also referred to here as GI-6302. The Brachyury yeast immunotherapy composition comprising a polynucleotide encoding the human Brachyury fusion protein represented by SEQ ID NO: 8, under the control of the TEF2 promoter (in vector pGI-172) is also referred to here as GI-6303.
[000174] Liquid cultures lacking uridine (U2) or missing uridine and leucine (UL2) were inoculated using the plates and starter cultures described above, and were grown for 20 hours at 30 ° C, 250 rpm. PH buffering media containing 4.2 g / L of Bis-Tris (BT-U2; BT-UL2) were also inoculated to evaluate yeast-Brachyury immunotherapeutic products produced under neutral pH production conditions (data not shown). Primary cultures were used to inoculate final cultures of the same formulation. U2 liquid media recipe: • 15 g / L glucose • 6.7 g / L ammonium sulphate containing yeast nitrogen base • 0.04 g / L each of histidine, tryptophan, adenine and 0.06 g / L of leucine. UL2 liquid media recipe: • 15 g / L glucose • 6.7 g / L ammonium sulfate containing yeast nitrogen base • 0.04 g / L each of histidine, tryptophan, and adenine.
[000175] In initial experiments comparing immunotherapeutic compositions of Brachyury yeast under the control of different promoters, CUP1-directed (inducible expression) expression of evedura-Brachyury was initiated by the addition of 0.5 mM copper sulfate, after eveduva culture -Brachyury reached a density of approximately 0.2 YU / ml, and was continued until the culture reached a density of 0.5-1.5 YU ( evedura-Brachyury doubled only approximately 1-1.5, after the addition of copper sulfate, but a large amount of Brachyury protein was produced by the cells). TEF2-directed expression of eveduva-Brachyury is constitutive, and the growth of these cells was continued until the cultures reached a density of, between 1.1 to 4.0 Y.U./ml. The cells of each culture were then harvested, washed and killed by heat at 56 ° C for 1 hour in PBS. The live cells from each culture were also processed for comparison.
[000176] After death by heat from the cultures, the cells were washed three times in PBS. Total protein expression was measured by a TCA precipitation / nitrocellulose binding and Western blot assay using an anti-his labeling monoclonal antibody and an anti-Brachyury antibody (Abeam, Cambridge, MA). The protein content was quantified using semiquantitative digital imaging methods.
[000177] The results of the initial expression experiments (data not shown) demonstrated that each of the Brachyury yeast immunotherapy compositions of the invention expressed to the Brachyury fusion protein, that is, using the CUP1 promoter or the TEF2 promoter, and expression was detected using means (U2 and UL2). In addition, antigen expression was detected in both heat-dead and live yeast cells (data not shown). Brachyury expression was significantly higher in the Brachyury yeast immunotherapeutic composition comprising the CUP1 promoter (GI-6301), and so that composition was selected for further studies, including, expression optimization and for in vivo experiments in vivo (see, Examples below ).
[000178] Fig. 1A shows Brachyury expression in GI-6301 using both U2 and UL2 media using anti-Brachyury antibody for detection. Control yeast that expresses a non-Brachyury antigen does not stain with the antibody. Fig. 1B shows Brachyury expression in the same GI-6301 preparations, using anti-His antibodies to identify the hexa-histidine tag on the Brachyury fusion protein. Control yeast that expresses a non-Brachyury antigen, but showing a hexahystidine tail is also shown. These results showed good expression of Brachyury using each medium, although expression in UL2 media was significantly higher. Example 2
[000179] The following example describes the identification of conditions for antigen expression and production of the yeast immunotherapeutic composition Brachyury, GI-6301.
[000180] To determine the optimal density for copper induction of GI-6301 antigen expression, GI-6301 starter and intermediate cultures were prepared using the standard growth conditions in UL2 media described in Example 1 above. Culture aliquots were then diluted to 0.5 YU / ml, 1.0 YU / ml and 1.5 YU / ml and incubated at 30 ° C for 1 hour. 0.5 mM CuSO4 was added to the cultures to induce Brachyury expression, and the culture was continued. The cells were collected and counted at 6 hours and 14 hours to measure cell density. 20 YU of yeast killed by the heat of each condition was lysed, total protein was measured, and Western blots were generated using anti-His antibodies.

[000181] As shown in Table 1, yeast only doubled in approximately 1 hour after copper induction (other experiments showed up to 1.5X duplication), and cell density and viability (not shown) decreased after 6 hours of copper induction. Fig. 2 shows that all three induction densities resulted in significant Brachyury expression, with a trend towards greater Brachyury expression at the highest induction densities. However, additional experiments using induction starting densities of 2.1 YU / ml and 2.8 YU / ml and 375 pM CuSO4 showed that protein expression began to decrease as the density of cultures at the beginning of induction of copper increased, and did not improve significantly after approximately 6-8 hours (data not shown).
[000182] Then, the effect of the amount of CuSO4 on Brachyury expression was investigated. GI-6301 was grown from starter and intermediate cultures in UL2 media, as described in Example 1. Aliquots of the culture were then diluted to 1.0 Y.U./ml and incubated at 30 ° C for 1 hour. CuSO4 was added to each culture at a concentration of 375 pM, or 500 pM, and induction of protein expression was allowed to proceed at various time points (2 hours, 4 hours, 6 hours, 8 hours, 24 hours), in which At this point the cells were harvested, killed by heat, and processed for protein expression evaluation using anti-His Western Blots as described above. Although both concentrations of CuSO4 resulted in good Brachyury expression, expression of the protein using 375 pM appeared to be slightly better, particularly at later time points (data not shown).
[000183] Consequently, for CUP1-directed Brachyury yeast (inducible expression), the inventors found that induction of expression of antigens in yeast middle phase growth was optimal for antigen production. For the production of the yeast-Brachyury immunotherapeutic composition (GI-6301) used in the following Examples, cells were grown in UL2 media as described in Example 1 for between 1 and 2 YU / ml, and were then induced by the addition of 0.375 -0.5 mM copper sulfate for up to 6-8 hours at 30 ° C, 250 rpm. The cells were harvested, washed and killed by heat at 56 ° C for 1 hour in PBS. Example 3
[000184] The following example describes the construction and production of an additional Brachyury yeast immunotherapeutic composition, wherein the Brachyury antigen contains an agonist T cell epitope.
[000185] In this experiment, yeast (Saccharomyces cerevisiae) was engineered to express a human Brachyury antigen which is a close-length Brachyury protein comprising the T cell epitope WLLPGTSTV (SEQ ID NO: 13), which is an epitope agonist. The native Brachyury T cell epitope, present in SEQ ID NO: 6 or 8, for example, is WLLPGTSTL (SEQ ID NO: 12). The human Brachyury agonist antigen was expressed under the control of the copper-inducible promoter, CUP1, producing a yeast-Brachyury immunotherapy composition. More particularly, a fusion protein comprising a Brachyury agonist antigen (i.e., a Brachyury agonist antigen Brachyury protein containing at least one agonist epitope), was produced as a single polypeptide with the following sequence elements fused to the structure from termination N to termination C, represented by SEQ ID NO: 20 (1), a terminating peptide N to confer resistance to proteosomal degradation and to stabilize expression (positions 1 to 6 of SEQ ID NO: 20, the peptide sequence also represented here by SEQ ID NO: 11), (2) amino acids 2-435 of SEQ ID NO: 18 (represented by positions 7-440 of SEQ ID NO: 20; SEQ ID NO: 18 represents a full-length human Brachyury agonist protein that has a single amino acid substitution at position 254 when compared to protein d the wild type Brachyury), and (3) a hexa-histidine tag (positions 441-446 of SEQ ID NO: 20). The agonist epitope (SEQ ID NO: 13) is located at positions 251 to 259 of SEQ ID NO: 20 (positions 246 to 254 of SEQ ID NO: 18). The amino acid sequences used in this fusion protein can be modified by using additional or alternative amino acids that flank each end of the Brachyury antigen, if desired, and the shorter portions of the Brachyury antigen can also be used. A nucleic acid sequence encoding the SEQ ID NO: 20 fusion protein (codon optimized for yeast expression) is represented herein by SEQ ID NO: 19.
[000186] Briefly, the DNA encoding the human full-length Brachyury protein, as described in Example 1 (i.e., full-length Brachyury minus the N-terminating methionine), modified by site-directed mutagenesis to introduce a substitution of valine by leucine at position 254 relative to the full-length Brachyury protein, was amplified using PCR, and then inserted into the EcoRI and Spel cloning sites behind the CUP1 promoter (vector pGI-100) in expression vectors 2 pM yeast. The nucleotide sequences encoding the N-terminating stabilization peptide, MADEAP (SEQ ID NO: 11) and a C-terminating hexa-histidine peptide were also added to the plasmid vector to encode the complete fusion protein, represented by ID SEQ NO: 20. The resulting plasmids were transformed into DH5a for plasmid storage, and Saccharomyces cerevisiae W303a for production of the yeast immunotherapeutic composition Brachyury.
[000187] Transformation into Saccharomyces cerevisiae was performed by means of transfection of lithium acetate / polyethylene glycol, and primary transfectants were selected in minimal solid plates lacking uracil (UDM; uridine abandonment medium). Colonies were selected by growing on UL2 medium (uridine and leucine abandonment medium) at 30 ° C.
[000188] The Brachyury yeast immunotherapy composition comprising a polynucleotide encoding the human Brachyury agonist fusion protein represented by SEQ ID NO: 20 under the control of the CUP1 promoter is also referred to in this report as Gl-6305.
[000189] GI-6305 cells were cultured in UL2 media as described in Example 1 for between 1 and 2 YU / ml, and were then induced by the addition of 0.375-0.5 mM copper sulfate for up to 6- 8 hours at 30 ° C, 250 rpm, using the conditions developed by the inventors for GI-6301, as described in Example 2. The cells were harvested, washed and killed by heat, at 56 ° C for 1 hour in PBS.
[000190] After death by heat from the cultures, the cells were washed three times in PBS. Total protein expression was measured by means of a TCA precipitation / nitrocellulose binding assay and by Western blot using an anti-his brand monoclonal antibody and an anti-Brachyury antibody (Abeam, Cambridge, MA). The protein content was quantified using semiquantitative digital imaging methods.
[000191] Fig. 1C shows the robust expression of Brachyury agonist antigen in GI-6305 using anti-His to identify the hexa-histidine tag on the Brachyury fusion protein. The approximate antigen content for growth of GI-6305 in UL2 medium in this experiment was> 22615 ng / Y.U. Example 4
[000192] The following example demonstrates the expansion of Brachyury-specific T cells using a Brachyury yeast immunotherapeutic composition of the invention.
[000193] To determine whether T cells from normal donors were able to generate T cells, which are specific for Brachyury antigen, dendritic cells (DCs) were prepared from peripheral blood mononuclear cells (PBMCs) from two normal donors . Briefly, isolated PBMCs were grown for 5 days in the presence of GM-CSF and IL-4, and were subsequently incubated in a control yeast (also denoted "YVEC", which is a yeast from Saccharomyces cerevisiae, which is transformed ∞m an empty vector, or a vector that does not have an antigen-altering insert) or Brachyury's yeast (G1-6301, described in Examples 1 and 2 above), in a yeast ratio: DCs = 1: 1. After 48 hours of cultura-culture, DCs were used in APCs for stimulation of autologous T cells. Each stimulation cycle, called ∞mo IVS (in vitro stimulation), was cultured for 3 days in the absence of IL-2, followed by an additional 4 days in the presence of recombinant IL-2 (20 U / ml). At the end of IVS 2, T cells were labeled ∞ with a control tetramer or a specific tetramer of the Brachyury Tp2 peptide (WLLPGTSTL, positions 246 to 254 of SEQ ID NO: 2 or SEQ ID NO: 6). Table 2 shows the percentage of CD8 + T cells stained positively with each tetramer.

[000194] In a second experiment, dendritic cells (DCs) were prepared from PBMCs from nine normal donors, using a 5-day culture in the presence of GM-CSF and IL-4, subsequently incubated with Brachyury yeast (G1 -6301), in a yeast ratio: DCs = 1: 1, as described above. After 48 hours in co-culture, DCs were used as APCs for stimulation of autologous T cells. Each IVS cycle was performed as described above. At the end of IVS 2, T cells were labeled with a control tetramer or a specific tetramer of the Brachyury Tp2 peptide. Table 3 shows the percentage of CD8 + T cells stained positively with each tetramer.

[000195] The results in Tables 2 and 3 show that stimulation of normal donor T cells with a Brachyury yeast immunotherapeutic of the invention increases the percentage of tetramer-positive CD8 + T cells in a majority of normal donors, compared to controls, indicating that Normal human T cells have the ability to recognize Brachyury as an immunogen. Example 5
[000196] The following example demonstrates the ability of a Brachyury yeast immunotherapeutic composition to generate Brachyury-specific CTLs from normal donor PBMCs that lyse targets expressing Brachyury
[000197] In this experiment, Brachyury-specific T cells from three of the normal donors in Table 2 above were expanded in vitro, using DCs incubated with Brachyury yeast (GI-6301) for 2 cycles of IVS (as described in Example 4). A third IVS was performed with mature DCs, in the presence of CD40L and pulsed with Brachyury-specific Tp2 peptide (WLLPGTSTL, positions 246 to 254 of SEQ ID NO: 2 or SEQ ID NO: 6). On day 5, CD8 + T cells were isolated and used in a cytotoxic T lymphocyte (CTL) assay overnight against SW480 (HLA-A2 + / high Brachyury) and MCF7 (H J -A2 + iBrachyury low) cell targets tumor, at the indicated effector target ratios (AE) (see, Figure 3.). Table 4 shows the percentage of CD8 + T cells that have been positively stained with a control tetramer versus a Brachyury-specific Tp2 tetramer.

[000198] Figures 3A (donor 07706), 3B (donor 17663) and 3C (donor 26532) show that PBMCs from two of the three normal donors were able to generate CD8 + CTLs that could kill targets expressing Brachyury. Taken together, these data demonstrate that Brachyury yeast immunotherapeutic compositions can generate Brachyury-specific CTLs that are capable of killing a tumor cell that expresses Brachyury.
[000199] In order to show that Brachyury yeast immunotherapy can induce Brachyury-specific CTLs in the absence of pulsation with a specific peptide (ie, by generating CTLs against potentially several different CTL epitopes), additional experiments were performed using cells Normal donor T expanded in vitrout using only the Brachyury yeast immunotherapeutic composition, GI-6301 (i.e., no peptide pulse). Briefly, PBMC-specific Brachyury T cells from normal donors (donor 19063) were expanded in vitrusing using DCs incubated with GI-6301 for 2 cycles of IVS (as described in Example 4). On day 5, CD8 + T cells were isolated and used in an overnight CTL assay against tumor cells SW480 (HLA-A2 positive / high Brachyury) and H226 (HLA-A2 negative / high Brachyury), in a ratio of 15: 1 target effector (EA). Fig. 4A shows the percentage of specific lysis of tumor cells SW480 and H226. Fig. 4B shows the expression of Brachyury mRNA in relation to that of GAPDH in tumor cells SW480 and H226 by RT-RCP in real time. These experiments further demonstrate that the evedura-Brachyury immunotherapeutic composition can generate Brachyury-specific CTLs that are capable of killing a tumor cell that expresses Brachyury. Example 6
[000200] The following example demonstrates that a Brachyury yeast composition of the invention can expand Brachyury-specific T cells from cancer patients.
[000201] In this experiment, DCs were prepared from the PBMCs of two patients with breast cancer, post-vaccination with viral veto vaccines comprising CEA and MUC-1 antigens. DCs were prepared in a 5-day culture in the presence of GM-CSF and IL-4, as described in Example 4, followed by incubation in the presence of Brachyury yeast (GI-6301), in a yeast ratio: DCs = 1 :1. After 48 hours of co-culture, DCs were used as APCs for stimulation of autologous T cells. Each IVS cycle consisted of three days, in the absence of IL-2, followed by an additional four days in the presence of 20 U / ml of recombinant IL-2. Shown in Table 5 is the percentage of CD8 + T cells (IVS1) that have been positively stained with a control tetramer or a specific tetramer of the Brachyury Tp2 peptide.

[000202] The results in Table 5 demonstrate that stimulation of T cells from breast cancer donors with a Brachyury yeast immunotherapeutic of the invention increases the percentage of tetramer-positive CD8 + T cells in most donors, when compared with controls, indicating that T cells from donors with existing cancer have the ability to recognize Brachyury as an immunogen. Example 7
[000203] The following example demonstrates the generation of Brachyury-specific CD4 + T cell responses in vivo using Brachyury yeast immunotherapy.
[000204] In this experiment, C57BL / 6 mice were vaccinated weekly for a total of 4 times with 4 Y.U. yBrachyury yeast (GI-6301), administered at four separate injection sites in 1 Y.U. by location). Two weeks after the final boost, the mice were sacrificed and the CD4 + T cells were purified and tested for proliferation in the presence of various concentrations of purified Brachyury protein (obtained from insect cells). As a control, β-Gal was used at 40 pg / ml.
[000205] Results showing the proliferation of CD4 + T cells isolated from the spleens of animals vaccinated with the control yeast (YVEC, see Example 4) and hBrachyury yeast (GI-6301), are shown in Fig. 5. Fig 5 shows that immunization with Brachyury evedura (GI-6301) generates Brachyury-specific CD4 + T cells. Example 8
[000206] The following example demonstrates that immunization with Brachyury yeast immunotherapeutic composition reduces tumors expressing Brachyury in vivo.
[000207] In this experiment, C57BL / 6 mice received 1 x 106 MC38-phBrachyury cells (tumor cells MC38 expressing a recombinant human Brachyury) via the tail vein (day 0). Four days after tumor implantation, the animals started receiving weekly vaccines with yeast control (YVEC, see Example 4) versus hBrachyury yeast (GI-6301), administered at a dose of 1 YU per site in four different locations (4 Total YU per dose). On day 40 post-tumor implantation, the animals were sacrificed and the number of pulmonary tumor nodules was assessed. The results of two combined experiments are shown in Fig. 6. Table 6 shows the number of average lung tumors (± SEM) and the number (and percentage) of animals with> 5 pulmonary nodules.

[000208] The results in Fig. 6 and Table 6 demonstrate that administration of a Brachyury yeast immunotherapeutic composition of the invention is capable of reducing tumors expressing Brachyury in mice, when compared to mice that received yeast alone (no Brachyury antigen). Example 9
[000209] The following example demonstrates the generation of Brachyury-specific CD4 + T cell responses in vitroutizing Brachyury yeast immunotherapy on human peripheral blood mononuclear cells (PBMCs) obtained from healthy donors.
[000210] In the following experiments, a full-length human Brachyury protein was expressed in insect cells via baculovirus expression and subsequently purified.
[000211] Dendritic cells (DCs) were prepared from PBMCs from healthy donors by 5-day culture with GM-CSF and IL-4 and subsequently treated in vitro with yeast control (YVEC, see Example 4), or Brachyury yeast (GI-6301, see examples 1 and 2) (yeast ratio: DCs = 1: 1). After 48 hours, DCs were harvested, irradiated (30 Gy) and used for stimulation of autologous PBMCs, in a DC: PBMC ratio = 1:10. On day 3, IL-2 (10 U / ml) was added to the cultures. On day 7, stimulated T cells were harvested and subsequently tested for IFN-y production in response to irradiated, autologous PBMCs (ratio T cells: PBMC = 1: 3), alone or in the presence of 10 pg / ml of purified protein Brachyury or human serum albumin protein control. After 96 hours of stimulation, supernatants were collected and assessed for IFN-γ levels by ELISA assay. A total of 9 healthy donors were evaluated, with 3/9 donors demonstrating Brachyury-specific CD4 + T cell responses after in vitro stimulation with DCs treated with Brachyury yeast. The results for 3 positive cases are shown in Table 7 (values indicate IFN-y levels in response to Brachyury protein, after subtracting baseline levels induced by stimulation with human serum albumin control protein; in relation to 3 donors, two cycles stimulation tests were performed before assessing response to Brachyury protein).

[000212] Six additional healthy donors were evaluated for CD4 + T cell responses to Brachyury protein, after in vitro stimulation with DCs treated with eveduva-Brachyury (GI-6301) by staining intracellular IFN-y cytokines in CD4 + cells . Dendritic cells were prepared from PBMCs from healthy donors, by culturing 5 days with GMCSF and IL-4 and subsequently treated in vitro with yeast control (YVEC) or Brachyury yeast (GI-6301) (yeast ratio: DCs = 1: 1). After 48 hours, DCs were harvested, irradiated (30 Gy) and used for stimulation of autologous PBMCs, in a DC: PBMCs ratio = 1:10. On day 3, IL-2 (10 U / ml) was added to the cultures. On day 7, stimulated T cells were harvested and subsequently tested for IFN-y production in response to autologous PBMCs (T cell ratio: PBMCs = 1: 3), alone or in the presence of 10 pg / ml of purified Brachyury protein or control of human serum albumin protein. After 2 hours of stimulation, BD GOLGISTOP ™ protein transport inhibitor (BD Biosciences) was added to the cultures. After 4 hours of stimulation, cells were harvested, permeabilized, and stained for CD4 + and IFN-y using anti-CD4 PerCP-Cy5.5 and anti-IFN-y FITC antibodies (BD Biosciences). A total of 6 healthy donors were evaluated, with 2/6 donors demonstrating Brachyury-specific CD4 + T cell responses after in vitro stimulation with DCs treated with Brachyury yeast. The results for positive cases are shown in Table 8 (values indicate the percentage of T cells that were simultaneously positive for CD4 and intracellular IFN-y in response to control of human serum albumin (HSA) or human Brachyury protein, after subtracting the levels induced by stimulation with isolated PBMCs).
Example 10
[000213] The following example demonstrates that a Brachyury yeast immunotherapy composition expressing a Brachyury agonist antigen generates Brachyury-specific T cells from a patient with prostate cancer.
[000214] To generate a Brachyury-specific T cell line, immature autologous dendritic cells (DCs) were exposed to the Brachyury yeast immunotherapy composition known in GI-6305 (see, Example 3) in a DC ratio: GI- 6305 = 1: 1 for 48 hours, and subsequently used as antigen presenting cells (APCs) to stimulate non-adherent autologous cells in a 10: 1 effector-to-APC ratio. Cultures were incubated for 3 days at 37 ° C, in a humidified atmosphere containing 5% CO2, and subsequently supplemented with recombinant human IL-2 at a concentration of 20 U / ml for an additional 7 days. The culture on day 10, consisting of an in vitro stimulation cycle (IVS). T cells were again stimulated with autologous DCs exposed to GI-6305, as described above, on day 11, to begin the next IVS cycle. Autologous DCs exposed to GI-6305 were used as APCs for three cycles of IVS. After the third IVS, irradiated autologous EBV-transformed B cells (23,000 rads.), Pulsed with a Brachyury agonist peptide, WLLPGTSTV (SEQ ID NO: 13), were used as APCs. A Brachyury-specific T cell line, denoted, T-2-BR-A, was established. This T cell line was used in the immunoassays described below.
[000215] Table 9 demonstrates that Brachyury-specific T cells (T-2-BR-A) release significant levels of IFN-y after stimulation with allogeneic DCs treated with GI-6305, whereas in yeast control (YVEC, see Example 4), did not stimulate the release of IFN-y by T-2-BR-A cells. Results are expressed in pg / ml / 105 T cells. Briefly, HLA-A2 positive allogeneic DCs from a normal donor were treated with GI-6305 for 48 hours in various yeast to DC ratios (shown in Table 9), and , then used to stimulate specific T cells of the Brachyury agonist epitope (T-2-BR-A). In this experiment, the DC to T cell ratio was 1:10.

[000216] Table 10 demonstrates that Brachyury-specific T cells established using GI-6305-treated DCs can effectively lysis MDA-MB-231 breast cancer cells that are HLA-A2 positive / Brachyury positive, but do not lysis of ASPC-1 pancreatic cancer cells that are HLA-A2 negative / Brachyury positive. Briefly, the Brachyury-specific T-cell line T-2-BR-A was used in IVS-6 in a cytotoxic T lymphocyte assay at night against tumor cell targets MDA-MB-231 (HLA-A27Brac / 7yurj ^) and ASPC-1 (HLA-A2 / Brachyury ''), in the indicated effective ratios (EA) (see Table 10). The results are expressed as the percentage of specific lysis.

[000217] In another experiment, the ability of the T-2-BR-A cell line to bind to Brachyury-specific HLA-A2 tetramers was evaluated. Briefly, T-2-BR-A cells (used in IVS-4) were stained with a control tetramer or a tetramer specific for the Brachyury agonist peptide. Figures 7A and 7B show that 10.8% of CD8 + T cells in the T-2-BR-A cell line generated with DCs treated with GI-6305 specifically bind to a Brachyury HLA-A2 tetramer (Fig. 7B) and not to a control tetramer (Fig. 7A).
[000218] Perforin expression from the T cell lineage, T-2-BR-A was analyzed by flow cytometry (perforin is a mediator of the cytolytic activity of cytotoxic T lymphocytes (CTLs)). Briefly, T cells were tested on day 5 after restimulation with EBV-transformed autologous B cells pulsed with Brachyury agonist peptide. Fig. 8 shows the expression of perforin in the T-2-BR-A cell line, after stimulation with autologous B cells pulsed with Brachyury agonist peptide, further demonstrating the cytotoxic capacity of this Brachyury-specific T cell line, which was generated using DCs treated with GI-6305. Example 11
[000219] The following example describes a phase 1 clinical trial in individuals with Brachyury-positive cancer.
[000220] A phase 1 open-label, sequential dose escalation clinical trial was initiated using the Brachyury yeast immunotherapy composition known as GI-6301, described in Examples 1, 2 and 4-9. Under this clinical trial protocol, 9-18 cancer patients (3-6 patients per dose group) are administered the Brachyury yeast immunotherapeutic composition known as GI-6301 in a dose group escalation protocol. sequentially using 4 YU dose ranges (1 Y.U. x 4 sites, meaning that 1 Y.U. of Gl-6301 is administered at 4 different sites in the patient's area at each visit), 16 Y.U. (4 Y.U x 4 sites) and 40 Y.U. (10 Y.U. x 4 sites), administered subcutaneously. GI-6301 is administered at 2-week intervals for a total of seven visits (~ 3 months), and thereafter, monthly, for ∞following, until patients meet out-of-study criteria. A group of expansion patients (n = 10), at maximum tolerated dose (DMT) or the best observed dose are selected for further study. The results are safety monitoring and tolerability - as a primary end point, and in the expansion group, if a significant change in T cell precursors is detectable when measured by an increase in Brachyury-specific T cells in the ELISpot assay and proliferation in response to Brachyury protein (for example, Brachyury-specific CD8 + or CD4 + T cells or emerging or expansive in treatment). As secondary end points, clinical benefit such as progression-free survival, radiographic clinical response, reduction in serum markers and / or reduction in circulating tumor cells is measured, as well as general immune activation parameters, including, frequency of subsets of immune cells in peripheral blood (CD8 + memory / effector T cells, CD4 + memory / effector cells, Tregs, NK cells, dendritic cells-DCs), and changes in s0ri∞s levels of cytokines ( for example, IFN-y, IL-10, IL-12, IL-2, ILA TGF-β, etc.).
[000221] GI-6301 is expected to be safe and well tolerated, without significant toxicities. In addition, GI-6301 is expected to produce Brachyury-specific T-cell responses emerging from treatment or an improvement in pre-existing Brachyury-specific baseline T-cell responses, at least some, or a majority of patients. Some patients are also expected to have stabilized disease.
[000222] In an additional study or an expansion of that study, the Brachyury yeast immunotherapeutic composition known as GI-6305 (see Example 3) is administered to an additional group of patients, using the maximum tolerated dose or the best observed dose determined above , and the same primary and secondary end points are measured. GI-6305, is also expected to be safe and well tolerated, without significant toxicities, as well as to produce Brachyury-specific T cell responses emerging from treatment or an improvement in pre-existing Brachyury-specific baseline T-cell responses , at least some, or a majority of patients. Some patients are also expected to have stabilized disease. Example 12
[000223] The following example describes a phase 2 clinical trial using Brachyury yeast immunotherapeutic compositions.
[000224] A phase 2 randomized clinical trial in patients with breast cancer is performed using a Brachyury yeast immunotherapeutic composition, as described in Example 1 and 2 (eg GI-6301) or, in Example 3 (GI- 6305). At least 100 or more individuals with stage I, II or III positive Brachyury breast cancer are enrolled. Inclusion criteria for individuals may include individuals with grade 1, 2 or 3 cancers. Criteria, including individuals may also include individuals with "triple negative" breast cancer (cancers that are negative for each of estrogen receptors (ER), progesterone receptor (RP) and HER2). Criteria for inclusion of individuals may also include patients with lymph node negative cancer.
[000225] The trial is run as a multicentre, double-blind, or open, placebo-controlled trial. All patients receive standard patient care therapy from the treatment arm receiving multiple injections in series of Brachyury yeast immunotherapeutic composition during treatment. The primary end point is recurrence-free survival or total survival. Additional end points may include antigen-specific T cell responses (eg, emerging or expansive Brachyury-specific CD8 + T cells in treatment), maintenance of lymph node negativity, progression to metastasis, and Brachyury expression in tumor cells.
[000226] The immunotherapeutic composition of yeast Brachyury is expected to be safe and well tolerated, without significant toxicities. In addition, the Brachyury yeast immunotherapeutic composition is expected to produce Brachyury-specific T cell responses emerging from treatment and / or an improvement in pre-existing Brachyury-specific baseline T cell responses in at least some or majority of patients. Some or a majority of patients are also expected to have stabilized disease, maintain lymph node negativity, and / or prevent, reduce or halt metastatic progression.
[000227] Although various modalities of the present invention are described in detail, it is evident that modifications and adaptations of these modalities will occur to those skilled in the art. It should be expressly understood, however, that such modifications and adaptations are within the scope of the present invention, as presented in the following exemplary claims.

权利要求:
Claims (15)
[0001]
1. Use of an immunotherapeutic composition comprising: (a) an entire inactivated yeast; and (b) a Brachyury fusion protein, characterized by the fact that it is in the preparation of a drug to reduce, stop, reverse, delay or prevent the metastatic progression of cancer in an individual who has cancer, in which the fusion protein de Brachyury has an amino acid sequence represented by SEQ ID NO: 6, positions 2-435 of SEQ ID NO: 6, SEQ ID NO: 18 or positions 2-435 of SEQ ID NO: 18.
[0002]
2. Use according to claim 1, characterized by the fact that Brachyury expression is not detected in the individual's cancer at the time the composition is first administered.
[0003]
3. Use according to claim 1, characterized by the fact that Brachyury expression is detected in the individual's cancer at the time the composition is first administered.
[0004]
4. Use according to any one of claims 1 to 3, characterized by the fact that the cancer is selected from the group consisting of: breast cancer, small intestine cancer, stomach cancer, pancreatic cancer, kidney cancer, bladder cancer, uterine cancer, ovarian cancer, testicular cancer, lung cancer, colon cancer, prostate cancer, chronic lymphocytic leukemia (CLL), B cells transformed by the Epstein-Barr virus, Burkitt's lymphoma, Hodgkine's lymphoma metastatic of these.
[0005]
Use according to claim 1, characterized in that the additional immunotherapeutic compositions comprise a yeast vehicle and a second cancer antigen that does not include Brachyury antigen.
[0006]
6. Use according to claim 5, characterized by the fact that the second cancer antigen is selected from the group consisting of: Ras mutant, carcinoembryonic antigen (CEA), MUC-1, EGFR, BCR-Ab1, MART- 1, MAGE-1, MAGE-3, GAGE, GP-100, MUC-2, PSMA, tyrosinase, TRP-1 (gp75), NY-ESO-1, TRP-2, TAG72, KSA, CA-125, PSA , HER-2 / neu / c-erb / B2, hTERT, p73, B-RAF, adenomatous polyposis coli (APC), Myc, von Hippel-Lindau protein (VHL), Rb-1, Rb-2, androgen receptor (RA), Smad4, MDR1, Flt-3, BRCA-1, BRCA-2, pax3-fkhr, ews-fli-1, HERV-H, HERV-K, TWIST, Mesothelin and NGEP.
[0007]
Use according to any one of claims 1 to 6, characterized by the fact that the Brachyury fusion protein has an amino acid sequence represented by SEQ ID NO: 18 or SEQ ID NO: 6.
[0008]
Use according to any one of claims 1 to 7, characterized in that the fusion protein has an amino acid sequence represented by SEQ ID NO: 8 or SEQ ID NO: 20.
[0009]
Use according to claim 8, characterized by the fact that the expression of the fusion protein is under the control of the CUP1 promoter.
[0010]
Use according to any one of claims 1 to 9, characterized in that the Brachyury fusion protein is expressed by a yeast.
[0011]
Use according to any one of claims 1 to 10, characterized in that the composition is formulated in a pharmaceutically acceptable excipient suitable for administration to an individual.
[0012]
12. Brachyury yeast immunotherapeutic composition, characterized by the fact that it comprises: (a) an entire inactivated yeast; (b) an antigen expressed by the yeast vehicle and comprising at least one Brachyury antigen, wherein the Brachyury antigen comprises an amino acid sequence represented by SEQ ID NO: 18, positions 2-435 of SEQ ID NO: 18, SEQ ID NO: 6 or positions 2-435 of SEQ ID NO: 6, and (c) a pharmaceutically acceptable excipient suitable for administration to a human.
[0013]
13. Brachyury yeast immunotherapeutic composition according to claim 12, characterized by the fact that it is for use in the treatment of a disease.
[0014]
14. Use according to claim 1, characterized by the fact that the individual has stage I cancer, stage II cancer, stage III cancer or stage IV cancer.
[0015]
Use according to any one of claims 1 to 11, characterized by the fact that the yeast is Saccharomyces cerevisiae.

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同族专利:

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公开号 | 公开日

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RU2690180C2|2019-05-31|

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RU2017116350A|2018-10-17|

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PT2685995T|2017-08-09|

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SG193396A1|2013-10-30|

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JP2014509595A|2014-04-21|

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CN103648513A|2014-03-19|

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CN103648513B|2018-10-12|

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KR20140038387A|2014-03-28|

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US20190374624A1|2019-12-12|

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JP2017061570A|2017-03-30|

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RU2619850C2|2017-05-18|

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JP2019199484A|2019-11-21|

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RU2017116350A3|2018-10-17|

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AU2017200715B2|2018-05-31|

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US10363294B2|2019-07-30|

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EP2685995A1|2014-01-22|

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US20160106824A1|2016-04-21|

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MX2013010475A|2014-05-28|

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PL2685995T3|2017-10-31|

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AU2017200715A1|2017-02-23|

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CA2835475A1|2012-09-20|

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DK2685995T3|2017-08-21|

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IL228421A|2019-02-28|

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US20140004135A1|2014-01-02|

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HK1245649A1|2018-08-31|

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MX350661B|2017-09-13|

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US20210106666A1|2021-04-15|

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ES2627979T3|2017-08-01|

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IL228421D0|2013-12-31|

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US20170246276A1|2017-08-31|

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KR102046449B1|2019-11-19|

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EP2685995A4|2014-12-24|

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JP6309607B2|2018-04-11|

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US9198941B2|2015-12-01|

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EP2685995B1|2017-05-03|

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WO2012125998A1|2012-09-20|

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NZ616696A|2015-09-25|

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JP6580733B2|2019-09-25|

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EP3238731B1|2021-02-17|

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JP2018090634A|2018-06-14|

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EP3238731A1|2017-11-01|

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RU2013146324A|2015-04-27|

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AU2012228937B2|2016-11-03|

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HUE033491T2|2017-12-28|

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CA2835475C|2020-06-30|

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JP6068368B2|2017-01-25|

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BR112013023456A2|2016-12-06|

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AU2018202972B2|2019-08-29|

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AU2012228937A1|2013-10-31|

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SG10201601913RA|2016-05-30|

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AU2018202972A1|2018-05-17|

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US9623097B2|2017-04-18|

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法律状态:
2017-10-24| B07D| Technical examination (opinion) related to article 229 of industrial property law [chapter 7.4 patent gazette]|

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2018-04-03| B06F| Objections, documents and/or translations needed after an examination request according [chapter 6.6 patent gazette]|

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2019-04-24| B07E| Notice of approval relating to section 229 industrial property law [chapter 7.5 patent gazette]|Free format text: NOTIFICACAO DE ANUENCIA RELACIONADA COM O ART 229 DA LPI |

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2019-08-20| B06U| Preliminary requirement: requests with searches performed by other patent offices: procedure suspended [chapter 6.21 patent gazette]|

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2020-03-10| B07A| Application suspended after technical examination (opinion) [chapter 7.1 patent gazette]|

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2020-08-04| B09A| Decision: intention to grant [chapter 9.1 patent gazette]|

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2020-11-17| B16A| Patent or certificate of addition of invention granted [chapter 16.1 patent gazette]|Free format text: PRAZO DE VALIDADE: 20 (VINTE) ANOS CONTADOS A PARTIR DE 19/03/2012, OBSERVADAS AS CONDICOES LEGAIS. |

优先权:

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申请号 | 申请日 | 专利标题

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US201161453656P| true| 2011-03-17|2011-03-17|

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US61/453,656|2011-03-17|

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PCT/US2012/029636|WO2012125998A1|2011-03-17|2012-03-19|Yeast-brachyury immunotherapeutic compositions|

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