WO2008097863A2

WO2008097863A2 - Methods for producing yeast-based vaccines

Info

Publication number: WO2008097863A2
Application number: PCT/US2008/052843
Authority: WO
Inventors: Alex Franzusoff; Deborah Quick
Original assignee: Globeimmune, Inc.
Priority date: 2007-02-02
Filing date: 2008-02-01
Publication date: 2008-08-14
Also published as: EP2121013B1; CN104120086A; KR20090116757A; IL237406A0; JP2014223072A; US20100189749A1; US9549970B2; US9066893B2; WO2008097863A3; KR20150006022A; KR101555641B1; IL200176A; DK2121013T3; CA2676783C; CN101687030B; ES2527756T3; SG171577A1; IL200176A0; PL2121013T3; US20130309269A1

Abstract

The invention provides methods for culturing yeast at a neutral pH level. Yeast cultured under neutral pH conditions exhibit desirable characteristics useful for biological purposes, such as the development of vaccines, prophylactics and therapeutics. The invention also provides for compositions and kits comprising yeast grown using the methodologies disclosed herein.

Description

IMPROVED METHODS FOR PRODUCING YEAST-BASED VACCINES

RELATED APPLICATIONS

[0001] This patent application claims the priority of U.S. Serial No. 60/899,281, filed on

February 2, 2008, which is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

[0002] The invention relates to methods of growing yeast cultures at a neutral pH to improve yields and certain characteristics of yeast cultures. The method also relates to compositions produced by these methods.

BACKGROUND OF THE INVENTION

[0003] Vaccines are one of the most cost-effective measures available to the health care industry. There remains, however, an urgent need to develop safe and effective vaccines and adjuvants for a variety of diseases, including those due to infection by pathogenic agents, cancers, genetic defects and other disorders of the immune system. Publications on vaccine, for example, Rabinovich et al., Science 265, 1401-1404 (1994), state that there is still a need for safe and heat- stable vaccines that can be administered orally and that need to be administered only a few times, preferably early in life. Also preferred are combination vaccines that can protect individuals from more than one disease, as well as vaccines that do not require an adjuvant and that can elicit mucosal immunity. To date very few, if any, vaccines meet all of these criteria.

[0004] Subunit vaccines, the development of which was made possible by recombinant

DNA technology, have been disappointing to date as they exhibit only limited immunogenicity. One example is the recent clinical testing of several HIV (human immunodeficiency virus) subunit vaccines which has been stopped due not only to limited efficacy of the vaccines but also because in some cases immunized individuals showed accelerated disease progression when they were subsequently exposed to HIV; see, for example, Cohen, Science 264:1839(1994); and Cohen, Science 264: 660 (1994). One disadvantage of subunit vaccines, as well as of killed virus and recombinant live virus vaccines, is that while they appear to stimulate a strong humoral immune response, they fail to elicit protective cellular immunity. A major conclusion at the 1994 International AIDS Conference was that there remains a need for a cytotoxic T cell- mediated response to prevent, or reduce, HIV infectivity, which to date is lacking in vaccines in the clinic. In addition, HIV vaccines tested to date have failed to elicit immunity at the mucosal surfaces where primary HIV infection occurs.

[0005] Furthermore, the only adjuvants approved for use in the United States are the aluminum salts aluminum hydroxide and aluminum phosphate, neither of which stimulates cell- mediated immunity. In addition, aluminum salt formulations cannot be frozen or lyophilized, and such adjuvants are not effective with all antigens.

[0006] Yeast cells have been used in the production of subunit protein vaccines, including some of those tested in the aforementioned HIV vaccine trials. Yeast has also been fed to animals prior to immunization to try to prime the immune response in a non-specific manner (i.e., to stimulate phagocytosis as well as the production of complement and interferon). The results have been ambiguous, and such protocols have not generated protective cellular immunity; see, for example, Fattal-German et al., Dev. Biol. Stand. 77: 115-120 (1992) and Bizzini et al., FEMS Microbiol. Immunol. 2: 155-167 (1990).

[0007] In addition to vaccines, many gene and drug therapies require efficient and specific delivery vehicles to ensure the greatest possible benefit. Lack of an adequate delivery vehicle is a major roadblock to the application of gene therapy and significantly limits the therapeutic potential of many drugs. For example, recent reports have indicated that adenovirus vectors, which are currently being tested in the clinic for gene therapy applications, are stimulating undesirable immune and inflammatory responses and do not appear to be integrating in a desired manner; see, for example, Engelhardt et al., Human Gene Therapy 5: 1217-1229 (1994) and references cited therein.

[0008] Another major hurdle for yeast vaccine technology is the manufacturing process.

Yeast cells have been cultured in the laboratories for many years and standard culture conditions have been established. See, for example, Methods ofEnzymology, Vol. 194, Guthrie et al., eds., Cold Spring Harbor Laboratory Press (1990). Standard operating protocols generally involve culturing yeast in media that is acidic as measured by pH levels. However, culturing yeast in acidic media may result in the yeast exhibiting different biological properties that are not optimal for using yeast as antigen-bearing vehicles for purposes of immunomodulation or making vaccines. Thus, there is a need for methods for growing yeast such that the yeast exhibit properties that make them better suited for being antigen-bearing vehicles. The invention disclosed herein in based, in part, on the discovery that while yeast can grow in acidic media, the biological properties that the yeast exhibit when grown in acidic media is not as desirable as when yeast are grown in media that is at neutral pH levels.

[0009] The disclosure of all patents, patent applications, and publications cited herein are hereby incorporated by reference in their entirety for all purposes.

BRIEF SUMMARY OF THE INVENTION

[0010] The invention provides a method for growing yeast by culturing the yeast in medium wherein the media is maintained at a pH level of between 5.5 and 8 for at least 50% of time that the yeast are in culture. The invention also provides for a method for growing yeast by culturing the yeast in medium wherein the media is maintained at a pH level of between 5.5 and 8 and wherein the density of the yeast is at least 0.5 yeast units/mL.

[0011] In other aspect, the invention provides for growing yeast by culturing the yeast in medium with a pH level of at least 5.5. The invention also provides a method for growing yeast by culturing the yeast in medium wherein the media is maintained at a pH level of between 5.5 and 8. In an aspect of the invention, the yeast is Saccharomyces cerevisiae. In aspects of the invention the medium is buffered with succinate or succinic acid or the medium may additionally contain soytone. In other aspects of the invention, the yeast elicits an immune response. In other aspects of the invention, the yeast expresses an antigen, in some cases the antigen is a heterologous antigen. In some cases, the heterologous antigen is expressed on the surface of the yeast.

[0012] The invention provides for a composition comprising yeast cultured by any the methods and related aspects above.

[0013] The invention provides for a method for producing antigen-expressing yeast by culturing yeast containing an expression system for expressing the antigen in a medium wherein the pH of the media is at least 5.5. The invention also provides for a method for producing antigen-expressing yeast by culturing yeast containing an expression system for expressing the antigen wherein the media is maintained at a pH level of between 5.5 and 8. In one aspect, the yeast is Saccharomyces cerevisiae. In other aspects, the medium is buffered with succinate or succinic acid or the medium may additionally contain soytone. In other aspects of the invention, the yeast elicits an immune response. In other aspects of the invention, the yeast expresses an antigen, in some cases the antigen is a heterologous antigen. In some cases, the heterologous antigen is expressed on the surface of the yeast. In some aspects, the heterologous antigen is more readily accessible for interaction with other cells or agents than when the yeast is grown at a pH of less than 5.5.

[0014] The invention also provides for a composition comprising yeast cultured by the method disclosed above.

[0015] The invention also provides for a method of inducing a ThI -type response in an individual by administering to the individual a composition comprising antigen-expressing yeast wherein the yeast has been cultured in a medium with a pH level of at least 5.5.

[0016] The invention also provides for a method of inducing a ThI -type response in an individual by administering to the individual a composition comprising antigen-expressing yeast wherein the yeast has been cultured in media wherein the media is maintained at a pH level of between 5.5 and 8. In one aspect, the composition comprises dendritic cells loaded with yeast which have been cultured, maintained or harvested at a neutral pH. In another aspect, the yeast is Saccharomyces cerevisiae. In other aspects, the medium is buffered with succinate or succinic acid or the medium may additionally contain soytone. In other aspects of the invention, the yeast elicits an immune response. In other aspects of the invention, the yeast expresses an antigen, in some cases the antigen is a heterologous antigen. In some cases, the heterologous antigen is expressed on the surface of the yeast. In one aspect, the Thl-type response is interferon-gamma production. In another aspect, the Thl-type response is IL-12 production.

[0017] The invention also provides for a kit for culturing yeast comprising media wherein the pH of the media is at least 5.5 and instructions for the use of the media to culture yeast. The invention also provides for a kit for culturing yeast comprising media wherein the pH of the media is maintained at a pH level of between 5.5 and 8 and instructions for the use of the media to culture yeast. In other aspects, the medium is buffered with succinate or succinic acid or the medium may additionally contain soytone. In one aspect, the kit additionally includes yeast. In some cases, the yeast is frozen or lyophilized. In some cases, the yeast has been cultured in a media of at least pH 5.5 or has been cultured in a media wherein the pH of the media is maintained at a pH level of between 5.5 and 8. In other cases, the yeast is capable of replication.

BRIEF DESCRIPTION OF THE DRAWINGS

[0018] Figure 1 depicts the effects of media pH levels on cell growth and also on the pH levels of the culture.

[0019] Figure 2 depicts the effect of media pH levels on cell wall thickness.

[0020] Figure 3 depicts the results from testing different buffers at a pH of about 6.5.

The effects on the growth of 75-15 cells and the culture pH are shown.

[0021] Figure 4 depicts the effect of various buffering agents on the cell wall thickness, as measured by lysis by glucanase. The culture media was buffered using either succinate or citrate to buffer the culture media to a pH level of about 6.5.

[0022] Figure 5 depicts the results of a media formulation study wherein various additives were tested for its effect on growth and pH levels.

[0023] Figure 6 depicts the results for yeast cell viability as part of a media formulation study. The surface expression of HA on yeast cell surface was measured using flow cytometry.

[0024] Figure 7 depicts the results of a media formulation study on cell growth and pH profiles in which various additives were tested.

[0025] Figure 8 depicts the results from an immunoblot assay of releasable hemagglutinin (HA) from intact yeast showing the difference in HA accessibility when yeast are grown at neutral versus when yeast are grown at lower pH conditions. The immunoblot is a western blot of DTT elutate from YEX and GI- 8103.

[0026] Figure 9 depicts the effect of culturing yeast cells at neutral and low pH levels on the secretion of cytokines by dendritic cells that have been loaded with yeast cells. DETAILED DESCRIPTION OF THE INVENTION

[0027] The invention disclosed herein is based on the discovery that growing yeast at a neutral pH, at least pH 5.5, or between pH 5.5 and 8, or between pH 6 and 8, results in yeast with more desirable biological characteristics. Some of these desirable characteristics, which are detailed infra, include but are not limited to, ability to grow well at increased cell density, keeping yeast cell wall pliable and sensitive to digestion with cell wall digesting enzymes, and display of antigens in a manner that makes them more accessible to other cells and/or agents.

General Techniques

[0028] 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 to those skilled in the art. Such techniques are explained fully in the literature, such as, Methods ofEnzymology, Vol. 194, Guthrie et al., eds., Cold Spring Harbor Laboratory Press (1990); Biology and activities of yeasts, Skinner, et al., eds., Academic Press (1980); Methods in yeast genetics : a laboratory course manual, Rose et al., Cold Spring Harbor Laboratory Press (1990); The Yeast Saccharomyces: Cell Cycle and Cell Biology, Pringle et al., eds., Cold Spring Harbor Laboratory Press (1997); The Yeast Saccharomyces: Gene Expression, Jones et al., eds., Cold Spring Harbor Laboratory Press (1993); The Yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics, Broach et al., 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 Russell, 2001), (jointly referred to herein as "Sambrook"); Current Protocols in Molecular Biology (F.M. Ausubel et al., eds., 1987, including supplements through 2001); PCR: The Polymerase Chain Reaction, (Mullis et al., eds., 1994); Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York; Harlow and Lane (1999) Using Antibodies: A Laboratory Manual Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (jointly referred to herein as "Harlow and Lane"), Beaucage et al. eds., Current Protocols in Nucleic Acid Chemistry John Wiley & Sons, Inc., New York, 2000) and Vaccines, S. Plotkin and W. Orenstein, eds., 3^rd edition (1999). Definitions

[0029] As used herein, the general use of the term "neutral pH" refers to a pH level of at least 5.5. The neutral pH range can be between about pH 5.5 and about pH 8, preferably between about pH 6 and about 8. One of skill the art will appreciate that minor fluctuations (e.g., tenths or hundredths) can occur when measuring with a pH meter and, as such, should take this into account when determining the pH level at any given time.

[0030] As used herein, the general use of the term "antigen" refers any molecule that can be recognized by the adaptive immune system. In one aspect, an antigen is a molecule that binds specifically to an antibody. The molecule can be any portion of a protein (peptide, partial protein, full-length protein) wherein the protein is naturally occurring or synthetically derived, or part of a cellular composition (whole cell, cell lysate or disrupted cells), part of an organism (whole organism, lysate or disrupted cells) or a carbohydrate or a portion thereof. The antigen can elicit an antigen-specific humoral immune response by itself or with the use of another compound such as an adjuvant (like crushed yeast cells). In another aspect, an antigen is recognized by T lymphocytes (or T cells) in the context of major histocompatibility complexes (MHCs). In another aspect, the antigen can act as a toleragen, against the same or similar antigens that are encountered within the cells and tissues of the animal to which the antigen is administered.

[0031] In one aspect of the present invention, when referring to the stimulation of an immune response, the "antigen" can be an "immunogen." Immunogens are molecules which can elicit an adaptive immune response, e.g., induction of antibody production. The immunogen can in some cases generate memory cells that will produce antibodies which recognize the antigen upon future exposure to the antigen. As is well-known to all persons of skill in this field, immunogens can also be recognized by T lymphocytes, although the form of the immunogen recognized by T lymphocytes will be different from the form of the immunogen that the antibody recognizes. Methods of Culturing Yeast

[0032] The invention provides for methods for culturing yeast that produces desirable characteristics, such as high expression of a desired antigen, cell wall pliability, and display of antigen.

[0033] These methods are broadly applicable to all yeast. Yeast are unicellular microorganisms that belong to one of three classes: Ascomycetes, Basidiomycetes and Fungi Imperfecti. While pathogenic yeast strains, or nonpathogenic mutants thereof can be used in accordance with the present invention, in one aspect, nonpathogenic yeast strains are used. Examples of nonpathogenic yeast strains include Saccharomyces, Candida, Cryptococcus, Hansenula, Kluyveromyces, Pichia, Rhodotorula, Schizosaccharomyces and Yarrowia. In one aspect, Saccharomyces, Candida, Hansenula, Pichia and Schizosaccharomyces are used. In yet other aspects, Saccharomyces cerevisiae, Saccharomyces carlsbergensis, Candida albicans, Candida kefyr, Candida tropicalis, Cryptococcus laurentii, Cryptococcus neoformans, Hansenula anomala, Hansenula polymorpha, Kluyveromyces fragilis, Kluyveromyces lactis, Kluyveromyces marxianus var. lactis, Pichia pastoris, Rhodotorula rubra, Schizosaccharomyces pombe, and Yarrowia lipolytica are used. It is understood the invention is not limited to the species list above and that one of skill in the art can apply the teachings here in any type of yeast. In another aspect, Saccharomyces cerevisiae (S. cerevisiae) is used to practice the methods of the invention. S. cerevisiae is preferred due to it ease for molecular manipulation and being "Generally Recognized As Safe" or "GRAS" for use as food additives (GRAS, FDA proposed Rule 62FR18938, Apr. 17, 1997).

[0034] The pH level is important in the culturing of yeast. One of skill in the art will appreciate that the culturing process includes not only the start of the yeast culture but the maintenance of the culture as well. The yeast culture may be started at any pH level, however, since the media of a yeast culture tends to become more acidic (i.e., lowering the pH) over time, care must be taken to monitor the pH level during the culturing process.

[0035] In some aspects of the invention, the yeast is grown in a media at a pH level of at least 5.5. In other aspects, the yeast is grown at a pH level of about 5.5. In other aspects, the yeast is grown at a pH level of between 5.5 and 8. In some cases, the yeast culture is maintained at a pH level of between 5.5 and 8. In other aspects, the yeast is grown at a pH level of between 6 and 8. In some cases, the yeast culture is maintained at a pH level of between 6 and 8. In other aspects, the yeast is grown and/or maintained at a pH level of between 6.1 and 8.1. In other aspects, the yeast is grown and/or maintained at a pH level of between 6.2 and 8.2. In other aspects, the yeast is grown and/or maintained at a pH level of between 6.3 and 8.3. In other aspects, the yeast is grown and/or maintained at a pH level of between 6.4 and 8.4. In other aspects, the yeast is grown and/or maintained at a pH level of between 5.5 and 8.5. In other aspects, the yeast is grown and/or maintained at a pH level of between 6.5 and 8.5. In other aspects, the yeast is grown at a pH level of about 5.6, 5.7, 5.8 or 5.9. In another aspect, the yeast is grown at a pH level of about 6. In another aspect, the yeast is grown at a pH level of about 6.5. In other aspects, the yeast is grown at a pH level of about 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9 or 7.0. In other aspects, the yeast is grown at a pH level of about 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. In other aspects, the yeast is grown at a level of above 8.

[0036] In one aspect, yeast is cultured such that the pH level of the medium does not drop below pH 5.5. In some cases, the drop below pH 5.5 is not more than 5 minutes. In other cases, the drop below pH 5.5 is not more than 10 minutes, preferably 20, 30, 40, 50 or 60 minutes. In other cases, the drop below pH 5.5 is not more than 1 hour. In another aspect, yeast is cultured such that the pH level of the medium does not drop below 5.0. In some cases, the drop below pH 5.0 is not more than 5 minutes. In other cases, the drop below pH 5.0 is not more than 10 minutes, preferably 20, 30, 40, 50 or 60 minutes. In other cases, the drop below pH 5.0 is not more than 1 hour. As such, the longer time the yeast are grown in a medium that is at least pH 5.5 or above, the better the results will be in terms of obtaining yeast with desirable characteristics described infra.

[0037] In one aspect, the use of neutral pH methods to grow yeast cells means that the yeast cells are grown in neutral pH for at least 50% of the time that the yeast are in culture. It is more preferable that the yeast are grown at neutral pH for at least 60% of the time they are in culture, more preferably at least 70% of the time they are in culture, more preferably at least 80% of the time they are in culture, and most preferably at least 90% of the time they are in culture .

[0038] In another aspect, growing yeast at neutral pH includes culturing yeast cells for at least five minutes at neutral pH, preferably at least 15 minutes at neutral pH, more preferably at least one hour at neutral pH, more preferably at least two hours, even more preferably, at least three hours or longer.

[0039] As noted earlier, as yeast grow and replicate, the cell densities become greater and the acidity level in the culture media rises. As such, it is recommended that as the yeast are cultured at a pH level of at least 5.5 and/or maintained at at least pH 5.5 as the yeast density increases. In one aspect, the yeast are grown and/or maintained between a pH of 5.5 and 8 as the yeast density is 0.5 yeast units (YU)/ml or above. In other aspects, the yeast are grown and/or maintained between a pH of 5.5 and 8 when the yeast density is at least 0.6 YU/ml or above, preferably 0.7 YU/ml or above, 0.8 YU/ml or above, 0.9 YU/ml or above, or 1 YU/ml or above. In another aspect, the yeast are grown and/or maintained between a pH of 6 and 8 as the yeast density is 0.5 YU/ml or above. In other aspects, the yeast are grown and/or maintained between a pH of 6 and 8 when the yeast density is at least 0.6 YU/ml or above, preferably 0.7 YU/ml or above, 0.8 YU/ml or above, 0.9 YU/ml or above, or 1 YU/ml or above.

[0040] In some aspects, it is preferable at the time of harvest that the yeast culture is at a neutral pH level. In some cases, the yeast culture, at the time of harvest, will be at a pH level of between 6 and 8. In other cases, the yeast culture, at the time of harvest, will be at a pH level of between 5.5 and 8.

[0041] The culture media can be brought to a pH level of at least 5.5 by any means. In one aspect, succinic acid (and any related forms, e.g., the anion succinate) is used for buffering the culture media. As further detailed in the Examples, the use of succinate to buffer the culture media to at least pH 5.5 allows for yeast to have a doubling time of about two to two and a half hours. Succinate is available from commercially available sources (e.g., Sigma Chemicals). In other aspects, citrate may be used to bring the media to a pH of at least 5.5. One of skill in the art will be able to readily determine other buffering agents which may be used to bring the media to a pH of at least 5.5 while keeping the yeast viable. The concept of buffering agents to keep a solution at a steady pH level is well-known in the art and as such, will not be discussed in detail herein. If yeast grown according to the invention are being used for pharmaceutical formulations (e.g., vaccines), it is recommended that GMP grade material be used.

[0042] In addition, other supplements may be added to the culture media to improve the media. Other supplements which are particularly helpful to add to the culture media include soytone. Soytone is readily available from commercial sources (e.g., BD Difco). As shown in the Examples and figures, the addition of soytone to the culture media supports higher density for growth at neutral pH. Furthermore, the addition of soytone supports expression of an antigen of interest, hemagglutinin (HA) of the influenza virus.

[0043] Other additives may be added to the yeast culture for other purposes, such as inducing expression of heterologous genes. In some aspects, copper is used to induce the expression of hemagglutinin expression. However, the use of copper is not ideal at neutral pH thus, for control of inducible genes to be expressed in yeast grown at neutral pH; an additive other than copper would be recommended.

Effects of Neutral pH on Yeast Culture

[0044] The use of a neutral pH in culturing yeast promotes several biological effects that are desirable characteristics for using the yeast as vehicles for immunomodulation and/or eliciting immune responses. In one aspect, culturing the yeast in neutral pH allows for good growth of the yeast without any negative effect on the doubling time (e.g., slowing down the doubling time). The yeast can continue to grow to high densities without losing their cell wall pliability.

[0045] In another aspect, the use of a neutral pH, such as a pH of at least 5.5 or between pH 5.5 and 8, allows for the production of yeast with pliable cell walls and/or yeast that have a sensitivity to cell wall digesting enzymes (e.g., glucanase) at all harvest densities. As such, the invention provides for methods and compositions of yeast with cell wall pliability as measured by traditional assays (e.g., sensitivity to glucanase). Prior experiments had established that yeast lost its sensitivity to digestion with cell wall digesting enzymes at harvest densities of about 0.5 YU (yeast units)/ml. As such, one advantage is that comparisons done with yeast cultured in standard growth media at 0.5 YU/ml can be used for comparison with neutral pH growth at any density. This trait is desirable because yeast with flexible cell walls can exhibit unique immune responses, such as promoting the secretion of cytokines (e.g., INF-gamma) in the cells hosting the yeast. Another reason why one of skill in the art would use the neutral pH methodology is that it allows for greater accessibility to the antigens located in the cell wall. This is useful for greater immunogenicity and also for antibody detection of expressed protein, measured by standard techniques such as flow cytometry. [0046] Yet another desirable characteristic that is observed in yeast cultured at neutral pH is the expression of antigens in a way that is beneficial for purposes of immunomodulation. In one aspect, the yeast are used as vehicles for antigen expression (see, for example, U.S. Patent Nos., 5,830,463 and 7,083,787). The antigen may be an antigen native to yeast or alternatively, a heterologous antigen that is expressed by the yeast. In some aspects, the use of yeast for expression of antigens is helpful for development of vaccines, prophylactics, and therapeutics to combat various diseases and ailments (e.g., infectious diseases or cancer). Using neutral pH methodology, one of skill in the art can produce antigen-bearing yeast wherein the antigen is more accessible to other cells (e.g., for immune co- stimulatory functions or immune regulation) or to other agents (e.g., antibodies for detection). In addition, the use of neutral pH for some antigens, such as the influenza HA antigen, allows for release of the di-sulfide bonded HA by treatment with dithiothreitol (DTT) that is not possible when the HA-expressing yeast is cultured in media where the pH drops below pH 5. In some cases, this occurs when the pH drops below pH 5 for any length of time. In other cases, this occurs when the pH drops below pH 5 for one or a few minutes or one or more hours.

[0047] Another desirable characteristic that yeast cultured following the neutral pH methodologies exhibit is the secretion of Thl-type cytokines from cells that have been exposed to the yeast. Examples of Thl-type cytokines include, but are not limited to, interferon-gamma, IL- 12, and IL-2. As further detailed in the Examples, dendritic cells that were loaded with yeast that had been grown following neutral pH protocols exhibit increased levels of interferon- gamma secretion and expression as compared to yeast grown at low (acidic) pH media. There was no reduction in the levels of IL- 12 secretion when using the neutral pH culturing methods. As such, one of skill in the art can use the neutral pH methodologies disclosed herein for immunomodulation purposes, e.g., inducing a Thl-type response in an individual that is afflicted with a disease or disorder that would benefit from an enhanced Thl-type response.

Compositions of Yeast Grown Using Neutral pH Methodology

[0048] The invention also contemplates compositions comprising yeast which are grown using the neutral pH methodologies disclosed herein. In one aspect, the composition comprises yeast that express native antigens, either on its surface or internally or both. This composition can be useful for various purposes, such as administration as an adjuvant. In another aspect, the composition comprises yeast that express heterologous antigens, either on its surface or internally or both. This composition can be useful for various purposes, such as immunomodulation in an individual in need thereof and the development of vaccines.

[0049] These compositions can also include pharmaceutically acceptable excipients and/or carriers. Pharmaceutically acceptable carriers may include sterile aqueous or nonaqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, antioxidants, chelating agents, and inert gases and the like. The formulation of compositions comprising yeast grown under neutral pH conditions with a pharmaceutically acceptable excipient is generally routine for one of skill in the art.

Kits of the Invention

[0050] The invention contemplates kits comprising media components for culturing yeast under neutral pH conditions. In one aspect, the kit includes media components containing succinate or succinic acid which can be used to bring the media to a pH of at least 5.5 and a set of instructions for its use. In another aspect, the kit further includes soytone as an additional component. In another aspect, the kit further includes yeast cells. The yeast cells can be frozen for starting a culture using the protocols disclosed herein. In another aspect, the yeast cells can have already been cultured by the methods disclosed herein prior to being frozen for packaging as part of the kit. In another aspect, the yeast cells can be lyophilized and optionally be included in the kit. In another aspect, the kit comprises yeast prepared according to the methods disclosed herein that is capable of replication.

[0051] The following examples are provided to illustrate certain aspects of the invention.

They are not intended to limit the invention in any manner. EXAMPLES

Example 1 Yeast Media Formulations

[0052] Various types of media can be used to culture yeast and be adjusted such that the pH level is neutral. Several examples of media which can be used are given below, however, it is to be understood that the invention is not limited to the use of these media components or media protocols.

[0053] One standard media recipe is ULDM media which is as follows:

[0055] Another standard media recipe is UL3 media which is as follows:

[0056] Another standard media recipe is UL4 media which is as follows:

[0057] Another standard media recipe is UDM media which is as follows:

[0058] Another standard media recipe is U2 media which is as follows:

[0059] Another standard media recipe is U3 media which is as follows:

[0060] Another standard media recipe is U4 media which is as follows:

[0061] Standard media formulations may be supplemented with additional amino acids.

The following protocols are exemplary media formulations.

[0062] The ULDMaa media formulation is as follows:

[0064] The UL3aa media formulation is as follows:

[0065] The UDMaa media formulation is as follows:

[0067] The U3aa media formulation is as follows:

[0068] In another aspect, succinate-containing buffered media is used. Examples of succinate-containing yeast media are below. The UDMS media formulation, adjusted to pH 6.9 is as follows:

[0069] The U2S media formulation, adjusted to pH 6.9 is as follows:

[0070] The U3S media formulation, adjusted to pH 6.9 is as follows:

Example 2 Effect of media pH on cell growth and culture pH

[0072] The effect of media pH on cell growth and culture pH were tested, as shown in

Figure 1. Cells were grown in U2 media supplemented with Bis-Tris buffer, pH 7.2 or phosphate buffer, pH 7.2. Control cultures were gown in U2 media without buffer added to the media. For conditions marked as control (same as media pH 5.5) or media pH 7.2, the growth media for these controls was either adjusted to pH 5.5 or pH 7.2 with base (NaOH) prior to inoculating with the yeast. The cultures were incubated at 3O⁰C and monitored for cell count and culture pH for up to 16 hours. The results indicate that buffers at varying pH levels affected growth rates of the yeast. As shown in Figure 1, the doubling times ranged from 2.8 to 4.5 hours. The pH in unbuffered pH 7 media was -5.5 at 2.0 YU/mL, which indicates the need for some form of buffering agent to keep the pH at a neutral level.

Example 3 Effect of media pH on Cell Wall Thickness

[0073] The effect of media pH was tested to determine if it had any effect on cell wall thickness. Growth media and conditions were the same as in Example 1. Cultures were harvested at densities ranging from 0.5 to 2.0 YU/mL. In the legend for Figure 2, the density when the cultures were harvested is listed as the number following the dash mark, e.g. control- 0.6 means cells grown in unbuffered media at pH 5.5, then harvested when cells reached 0.6 YU/mL density. The conditions for flasks 1-3 (e.g. 1-0.5, 2-2.0 or 3-1.0) are listed below the figure and the cell density at harvest is marked in the legend. The lysis assay protocol used was as follows: (1) re-suspend IOYU of washed cells in ImL of Tris-BME; (2) pull a "Time 0" sample and measure the OD at 600nm; (3) add 20 U of glucanase; (4) rotate at 3O⁰C; (5) every 10 minutes, take a sample and measure the OD.

[0074] As can be observed in Figure 2, the control culture (media pH~5.5) shows less efficient lysis as cell density increases. Flask 2 shows the effect of media at pH 7.2 with no buffer. Flask 2 shows the effect of media at pH 7.2 with Bis-Tris buffer. Flask 3 shows the effect of media at pH 7.2 with phosphate buffer.

[0075] Thus, the results indicate that growing yeast buffered at about pH 5.5 or higher keeps the cell wall pliable and sensitive to digestion with cell wall digesting enzymes (e.g., making spheroplasts with lyticase/glucanase) at all harvest densities. In contrast, with the standard process commonly used in many yeast laboratories, the sensitivity was lost at harvest densities >0.5 YU/mL. For ease of comparison, 0.5 YU/mL with standard growth media is often used for comparison with neutral pH growth at any density.

Example 4 Construction of 75-15 cells

[0076] A fusion protein denoted TK75-15 was engineered to express influenza HA protein on the cell wall using the Aga2 sequence, driven by the TEF2 promoter. In this construct, the protein was constructed with the HA sequence C-terminal to the Aga2 sequence. This protein, when expressed in cells that also express Agalp (in this case, driven by the CUPl promoter), localizes to the outer cell wall of the yeast cell, as well as to the cytosol. The fusion protein comprising the influenza HA antigen is a single polypeptide with the following sequence elements fused in frame from N- to C-terminus (the amino acid sequence of the fusion protein being represented herein by SEQ ID NO:1): 1) the full length S. cerevisiae Aga2 protein sequence (positions 1 to 87 of SEQ ID NO:1), including its natural 18 amino acid ER-targeting signal sequence (positions 1 to 18 of SEQ ID NO:1; 2) a spacer to separate the Aga2 from the HA body (positions 88 and 89); 3) influenza HA protein lacking its signal sequence (positions 90 to 600 of SEQ ID NO:1), and lacking 36 C-terminal residues of HA, thus eliminating its C- terminal membrane anchor and cytoplasmic tail; 4) a triglycine spacer to separate the body of HA protein from the histidine tag (positions 601-603 of SEQ ID NO:1); and 5) a C-terminal hexahistidine tag (positions 604-609 of SEQ ID NO:1). A nucleic acid sequence encoding the fusion protein of SEQ ID NO:1 is represented herein by SEQ ID NO:2. This fusion protein and the Tarmogen expressing it can be called 75-15.

[0077] The protein sequence used is as follows (SEQ ID NO: 1):

MQLLRCFSIFSVIASVLAQELTTICEQIPSPTLESTPYSLSTTTILANGK SO AMQGVFEYYKSVTFVSNCGSHPSTTSKGSPINTQYVFTSDTICIGYHANN IOO STDTVDTVLEKNVTVTHS VNLLEDSHNGKLCRLKGIAPLQLGKCNIAGWL 150 LGNPECDPLLPVRSWSYIVETPNSENGICYPGDFID YEELREQLSSVSSF 200 ERFEIFPKESSWPNHNTNGVTAACSHEGKSSFYRNLLWLTEKEGSYPKLK 250 NSYVNKKGKEVLVLWGIHHPSNSKEQQNLYQNENAYVSVVTSNYNRRFTP SOO EIAERPKVRDQAGRMNYYWTLLKPGDTIIFEANGNLIAPMYAFALSRGFG SSO SGIITSNASMHECNTKCQTPLGAINSSLPYQNIHPVTIGERPKYVRSAKL 400 RMVTGLRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYA 450 ADQKSTQNAINGITNKVNTVIEKMNIQFTAVGKEFNKLEKRMENLNKKVD SOO DGFLDIWTYNAELLVLLENERTLDFHDSNMKNLYEKVKSQLKNNAKEIGN SSO GCFEFYHKCDNECMESVRNGTYD YPKYSEESKLNREKVDGVKLESMGIYQ 600 GGGHHHHHH*

[0078] The corresponding nucleic acid sequence is as follows (SEQ ID NO:2):

1 ATGCAGTTAC TTCGCTGTTT TTCAATATTT TCTGTTATTG CTTCAGTTTT 51 AGCACAGGAA CTGACAACTA TATGCGAGCA AATCCCCTCA CCAACTTTAG 101 AATCGACGCC GTACTCTTTG TCAACGACTA CTATTTTGGC CAACGGGAAG 151 GCAATGCAAG GAGTTTTTGA ATATTACAAA TCAGTAACGT TTGTCAGTAA 201 TTGCGGTTCT CACCCCTCAA CAACTAGCAA AGGCAGCCCC ATAAACACAC 251 AGTATGTTTT TACTAGTGAC ACAATATGTA TAGGCTACCA TGCGAACAAT 301 TCAACCGACA CTGTTGACAC AGTACTCGAG AAGAATGTGA CAGTGACACA 351 CTCTGTTAAC CTGCTCGAAG ACAGCCACAA CGGAAAACTA TGTAGATTAA 401 AAGGAATAGC CCCACTACAA TTGGGGAAAT GTAACATCGC CGGATGGCTC 451 TTGGGGAATC CAGAATGCGA CCCACTGCTT CCAGTGAGAT CATGGTCCTA 501 CATTGTAGAA ACACCAAACT CTGAGAATGG AATATGTTAT CCAGGAGATT 551 TCATCGACTA TGAGGAGCTG AGGGAGCAAT TGAGCTCAGT GTCATCATTC 601 GAAAGATTCG AAATATTTCC CAAAGAAAGC TCATGGCCCA ACCACAACAC 651 AAACGGAGTA ACGGCAGCAT GCTCCCATGA GGGGAAAAGC AGTTTTTACA 701 GAAATTTGCT ATGGCTGACG GAGAAGGAGG GCTCATACCC AAAGCTGAAA 751 AATTCTTATG TGAACAAAAA AGGGAAAGAA GTCCTTGTAC TGTGGGGTAT 801 TCATCACCCG TCTAACAGTA AGGAACAACA GAATCTCTAT CAGAATGAAA 851 ATGCTTATGT CTCTGTAGTG ACTTCAAATT ATAACAGGAG ATTTACCCCG 901 GAAATAGCAG AAAGACCCAA AGTAAGAGAT CAAGCTGGGA GGATGAACTA 951 TTACTGGACC TTGCTAAAAC CCGGAGACAC AATAATATTT GAGGCAAATG 1001 GAAATCTAAT AGCACCAATG TATGCTTTCG CACTGAGTAG AGGCTTTGGG 1051 TCCGGCATCA TCACCTCAAA CGCATCAATG CATGAGTGTA ACACGAAGTG 1101 TCAAACACCC CTGGGAGCTA TAAACAGCAG TCTCCCTTAC CAGAATATAC 1151 ACCCAGTCAC AATAGGAGAG CGCCCAAAAT ACGTCAGGAG TGCCAAATTG 1201 AGGATGGTTA CAGGACTAAG GAACATTCCG TCCATTCAAT CCAGAGGTCT 1251 ATTTGGAGCC ATTGCCGGTT TTATTGAAGG GGGATGGACT GGAATGATAG 1301 ATGGATGGTA TGGTTATCAT CATCAGAATG AACAGGGATC AGGCTATGCA 1351 GCGGATCAAA AAAGCACACA AAATGCCATT AACGGGATTA CAAACAAGGT 1401 GAACACTGTT ATCGAGAAAA TGAACATTCA ATTCACAGCT GTGGGTAAAG 1451 AATTCAACAA ATTAGAAAAA AGGATGGAAA ATTTAAATAA AAAAGTTGAT 1501 GATGGATTTC TGGACATTTG GACATATAAT GCAGAATTGT TAGTTCTACT 1551 GGAAAATGAA AGGACTCTGG ACTTCCATGA CTCAAATATG AAGAATCTGT 1601 ATGAGAAAGT AAAAAGCCAA TTAAAGAATA ATGCCAAAGA AATCGGAAAT 1651 GGATGTTTTG AGTTCTACCA CAAGTGTGAC AATGAATGCA TGGAAAGTGT 1701 AAGAAATGGG ACTTATGATT ATCCCAAATA TTCAGAAGAG TCAAAGTTGA 1751 ACAGGGAAAA GGTAGATGGA GTGAAATTGG AATCAATGGG GATCTATCAG 1801 GGTGGCGGGC ATCACCATCA CCATCACTAG TGA

Example 5 The effect of different buffers (pH 6.5 media) on 75-15 cell growth and culture pH

[0079] Different buffering agents were tested on 75-15 cells to determine its effect on cell growth and also the effect on the culture pH. These buffers are shown in Figure 3 and included succinate, citrate, and carbonate. None of the buffers caused precipitate to form. All of the buffers used dissolved well in standard growth media. The pH of all test cultures was adjusted to pH 6.5 prior to inoculation with yeast. Cultures were then grown in shake flasks at 3O⁰C for up to 15 hours. There was minimal to no growth seen when the cells were grown in carbonate buffer. As can be seen in Figure 3, the use of different buffering agents affected growth rates. The growth was faster in neutral pH (at least pH 5.5). In particular, the media with succinate buffer performed the best in terms of doubling time (~2.5hr doubling time). In contrast, if the yeast cells were grown in pH less than 5.5 (more acidic conditions), then the doubling time was slower at -3.5 hr. Citrate had similar doubling time (-3.5 hrs). Citrate at 0.05M had a greater buffering capacity than succinate at 0.02M. In these experiments, all the cultures received 0.35mM copper for induction of expression.

Example 6 Effect of various buffering agents on cell lysis

[0080] Figure 4 shows the results from experiments conducted with different buffering agents such as succinate and citrate. Cultures were grown as described in Example 1. The ability of the yeast to be lysed by glucanase was measured using the lysis assay protocol above. The yeast in the control culture (media pH~5.2) showed less efficient lysis by glucanase as the cell density increased (cell densities indicated by the number after the dash, as described above for Figure 2). However, for both succinate and citrate buffered media, the cell density at time of harvest did not have any effect on the ability of the yeast to be lysed by cell wall digestive enzymes in the lysis assay described above. The yeast in the succinate and citrate buffered media remained susceptible to lysis at increasing cell densities (e.g., 0.5 YU/ml, 0.9 YU/ml and 2.1 or 2.2 YU/ml).

Example 7 Media Formulation Study

[0081] The contribution of other agents added to the yeast culture media was tested and the results are shown in Figure 5. U2 or U4 refers to the basic media composition. Since protein expression is under control of the copper-inducible CUPl promoter, 0.35 mM copper is added to the media for yeast cells to be induced to express HA protein. Soytone (Soy in Figure 5), is a commercially available complex mixture of nutrients derived by peptic digestion of soybeans. The addition of soytone gave fastest growth and highest yield (30YU/mL). The use of 0.08M succinic acid showed better buffering capacity. Cells were grown at 3O⁰C for the times indicated on the x-axis.

[0082] Figure 6 shows the results for media formulation study that used Guava

Technologies for determination of cell viability. Yeast strain 75-15 in which express copper- inducible Aga2-HA were grown at 3O⁰C in shake flasks. When copper is added to the culture, the Aga2-HA protein is expressed and will show up on the cell surface, which represents the number of yeast cells that show HA on the surface (% positive signal). Cell viability can also be determined using other methods (e.g., hemacytometer or Trypan blue). The highest signal was observed with U2, even at a cell density of 8YU/mL, which is past the cell density at which cells tend to slow down in its growth rate. The cultures using soytone showed clear effect of cell density, with high densities showing a decline in protein. The use of U4 gave low signal overall. These results also demonstrate the accessibility of detection because of the effects pH has on the cell wall and the ability of HA-specific antibodies to detect the surface expressed protein.

[0083] Additional experiments were conducted using different concentration of soytone.

Figure 7 illustrates the results. No different in growth or pH was observed between 0.5 g/1 and 1 g/1 soytone. Faster growth was observed in U4-YNB media than in U2 media. Example 8 Difference in HA accessibility when yeast are grown at neutral pH conditions

[0084] The accessibility of particular antigens to interactions from other agents, such as an antibody for detection, was assessed using varying pH levels of the media. Figure 8 shows an immunoblot assay of releasable influenza hemagglutin (HA) from intact yeast when the yeast cells were grown at pH less than 5 and also when yeast were grown at a pH of more than 6. Yeast grown at neutral pH makes the surface displayed HA much more accessible to antibody detection, as determined flow cytometry staining, both in number of cells that express HA and the amount of HA per cell. In addition, the yeast grown at neutral pH were easier to manipulate for the release of the disulfide-bonded HA by treatment with dithiothreitol (disulfide reducing agent).

Example 9 The effect of neutral pH on cytokine production

[0085] The effect of culturing yeast at neutral pH on cytokine production was examined by using dendritic cells (DC) loaded with YVEC yeast (not expressing a heterologous antigen) grown in media where the pH was or was not maintained above pH 5.5. Mouse bone marrow- derived dendritic cells were loaded with 10 yeast per DC by incubating together in RPMI media for 48 hr at 37⁰C. Supernatants were then analyzed for secreted cytokines. Figure 9 shows the results of these experiments. The lower panel show that there is a marked increase of IFN- gamma secretion from dendritic cells loaded with the yeast are grown at a neutral pH (i.e., at least 5.5 or higher) that is absent when the yeast are grown in media where the pH was allowed to drop lower than 5.5.

Claims

CLAIMS What is claimed is:

1. A method for growing yeast comprising culturing the yeast in medium wherein the media is maintained at a pH level of between 5.5 and 8 for at least 50% of time that the yeast are in culture.

2. A method for growing yeast comprising culturing the yeast in medium wherein the media is maintained at a pH level of between 5.5 and 8 and wherein the density of the yeast is at least 0.5 yeast units/mL.

3. A method for growing yeast by culturing the yeast in medium with a pH level of at least 5.5 for at least 50% of time that the yeast are in culture.

4. The method of claim 3 wherein the media is maintained at a pH level of between 5.5 and 8.

5. The method of claim 3 wherein the yeast is Saccharomyces cerevisiae.

6. The method of claim 3 wherein the medium is buffered with succinate or succinic acid.

7. The method of claim 6 wherein the medium additionally contains soytone.

8. The method of claim 3 wherein the yeast elicits an immune response when administered to an individual.

9. The method of claim 8 wherein the yeast expresses a heterologous antigen.

10. The method of claim 9 wherein the heterologous antigen is expressed on the surface of the yeast.

11. A composition comprising yeast cultured by any one the methods of claim 1, 2, or 3.

12. A method for producing antigen-expressing yeast by culturing yeast containing an expression system for expressing the antigen in a medium wherein the pH of the media is at least 5.5.

13. A method for producing antigen-expressing yeast by culturing yeast containing an expression system for expressing the antigen wherein the media is maintained at a pH level of between 5.5 and 8.

14. The method of claim 12 or 13 wherein the yeast is Saccharomyces cerevisiae.

15. The method of claim 14 wherein the medium is buffered with succinate or succinic acid.

16. The method of claim 15 wherein the medium additionally contains soytone.

17. The method of claim 12 or 13 wherein the yeast elicits an immune response when administered to an individual.

18. The method of claim 17 wherein the yeast expresses a heterologous antigen.

19. The method of claim 18 wherein the heterologous antigen is expressed on the surface of the yeast.

20. The method of claim 18 wherein the heterologous antigen is more readily accessible for interaction with other cells or agents than when the yeast is grown at a pH of less than

5.5.

21. A composition comprising yeast cultured by any one of the methods recited in claims 12 or 13.

22. A method of inducing a Thl-type response in an individual by administering to the individual a composition comprising antigen-expressing yeast wherein the yeast has been cultured in a medium with a pH level of at least 5.5.

23. A method of inducing a Thl-type response in an individual by administering to the individual a composition comprising antigen-expressing yeast wherein the yeast has been cultured in media wherein the media is maintained at a pH level of between 5.5 and 8.

24. The method of claim 23 wherein the composition comprises dendritic cells loaded with yeast which has been cultured, maintained or harvested at a neutral pH.

25. The method of claim 23 wherein the yeast is Saccharomyces cerevisiae.

26. The method of claim 23 wherein the medium is buffered with succinate or succinic acid.

27. The method of claim 26 wherein the medium additionally contains soytone.

28. The method of claim 23 wherein the yeast elicits an immune response when administered to an individual.

29. The method of claim 28 wherein the yeast expresses a heterologous antigen.

30. The method of claim 29 wherein the heterologous antigen is expressed on the surface of the yeast.

31. The method of claim 23 wherein the Thl-type response is interferon-gamma production.

32. The method of claim 23 wherein the Thl-type response is IL-12 production.

33. A kit for culturing yeast comprising media wherein the pH of the media is at least 5.5 and instructions for the use of the media to culture yeast.

34. A kit for culturing yeast comprising media wherein the pH of the media is maintained at a pH level of between 5.5 and 8 and instructions for the use of the media to culture yeast.

35. The kit of claim 34 wherein the medium is buffered with succinate or succinic acid.

36. The kit of claim 34 wherein the medium additionally contains soytone.

37. The kit of claim 34 wherein the kit additionally includes yeast.

38. The kit of claim 37 wherein the yeast is frozen or lyophilized.

39. The kit of claim 37 wherein the yeast has been cultured in a media of at least pH 5.5 or has been cultured in a media wherein the pH of the media is maintained at a pH level of between 5.5 and 8.

40. The kit of claim 37 wherein the yeast is capable of replication.