# Patent

## Title
Method for the oral/mucosal vaccination by means of recombinant yeasts

## Abstract

Recombinant yeast cells are produced which are used for vaccination, among other uses for the oral vaccination by feeding.

## Background
BACKGROUND OF THE INVENTION
Controlling infectious diseases is still one of the greatest challenges in both human and veterinary medicine. The situation is particularly complex in the case of viral infections, which, in contrast to bacterial infections, generally cannot be treated with broad-spectrum active substances and are the cause of major economic damages. Developing novel, effective vaccination strategies against viral illnesses is therefore extremely important.
“Attenuated” viruses, i.e. viruses modified by mutagenesis that have significantly reduced or no virulence (“live vaccines”) or inactivated viruses (“dead vaccines”) are traditionally used for prophylactic and also for therapeutic vaccination against viral diseases. Recently so-called “subunit vaccines” or “subunit marker vaccines” have become more established, wherein defined genetically produced “major antigens” of the pathogen are used for vaccination. The term “marker vaccine” implies that vaccinated individuals may be clearly differentiated from naturally infected individuals using subsequent diagnostic analysis. Major antigens are for instance proteins of the virus shell or virus capsid that may induce a humoral and/or cellular immune response in the host in the absence of a complete virus particle, and as a result of this viral infection may be preventively or therapeutically defended or combated. A “subunit vaccination” requires that major antigens are characterized. Production (expression) and immunogenic formulation of such proteins (“antigen formulation”) become key for the vaccination process, especially since virus shell proteins are generally not water-soluble and may only rarely be produced recombinantly in bacterial expression systems. Methods for obtaining “subunit” vaccines in a purified form and for assuring their storability are correspondingly complex.
SUMMARY OF THE INVENTION
Yeasts for expression systems for recombinant proteins combine the economic advantages of bacterial systems with the organizational form typical of higher cells. They are compartmented by intracellular membrane systems, which fundamentally distinguishes them from bacterial host systems and enables the expression of membrane-anchored viral shell proteins or even entire virus capsids. In addition, the beta-glucanes, glucose polymers from which the yeast cell wall is constructed, have an immune-stimulating effect that has been known for some time. It was therefore the object to develop a method in which complete yeasts may be employed for vaccination. The object was attained in that by means of genetic methods genes for immunogenic determinants are planted into the genome of non-pathogenic yeasts and expressed and these recombinant yeast cells are employed directly for vaccination, inter alia for oral vaccination by feeding.
Kluyveromyces lactis 
Kluyveromyces lactis belongs to the so-called food grade yeasts with GRAS status (generally regarded as safe). Like baker's yeast, which has been tested and proven as a food additive over centuries, the K. lactis yeast, which is frequently used in dairy products, is also considered safe in the food industry.
Oral/Mucosal Vaccination
The following options are available for administering vaccines/antigens: subcutaneous, intramuscular, parenteral or mucosal/oral options. While in the first three cases cited the antigens travel directly into the blood or lymphatic system, with mucosal/oral application the exposition of the antigen occurs via mucosa of the bronchial or gastrointestinal tract. The term mucosal/oral thus includes both nasal/bronchial administration and oral administration of antigens. Both bronchial and intestinal mucosa are permanently exposed to pathogens and represent per se a significant barrier to absorption of infectious agents. In the human body, the immune system associated with mucosal surfaces, especially that of the mucosal intestinal epithelium, includes e.g. approx. 90% of all immunocompetent cells. The antigen is absorbed and presented by the dendritic cells and M cells of the “Peyer's patches” (known collectively as MALT, mucosa-associated lymphoid tissue) in the intestinal mucosa, in the so-called inductive sites, but also by enterocytes and intestinal epithelium cells according to recent findings. The situation with the nasal/bronchial mucosa (BALT, bronchial associated lymphoid tissue) is analogous. After the immune response subsides, specific memory immune cells that as a rule provide long-lasting protection against the original antigen/pathogen occur in the entire organism, but also in the so-called effector sites of the mucosa.
Advantages of Oral/Mucosal Vaccination Methods.
Compared to parenteral immunization, oral/mucosal immunization requires the use of significantly higher quantities of antigens. In contrast to parenteral immunization, however, with oral/mucosal vaccination it is possible to induce a local immune response at the effector sites of the mucosa in addition to the systemic immune response. Especially with pathogens (such as e.g. bovine viral diarrhea virus, BVDV, and classical swine fever virus, CSFV; also see below), which also are transmitted via mucosa, a mucosal/oral vaccination has the potential to produce active and long-lasting immunity. Additional major advantages of oral vaccination are good acceptance and economy. In the most favorable case the vaccines may be produced at low cost and may be uncomplicated to administer with food. Moreover, vaccines of the invention having long storability outside a cold train can be produced according to the invention.
Mucosal/oral administration of yeast strains that express virus antigens is therefore not only safe but might also have additional health-promoting and adjuvant effects.
Again, the object was to develop an expression system based on Kluyveromyces lactis, which system permits the deliberate integration of foreign genes in the yeast genome and thus permits corresponding antigen formulations. An additional object was to employ a recombinant K. lactis strain that expresses a specific virus antigen for a vaccination, inter alia for a mucosal/oral vaccination.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic illustration relating to exemplary embodiment 1; and
FIG. 2 is a schematic illustration relating to exemplary embodiment 2.



DETAILED DESCRIPTION OF THE INVENTION
In accordance with the invention, a K. lactis strain, preferably VAK367-D4 and variants of this strain, was generated using genetic methods and permits the deliberate integration of foreign genes on the LAC4 locus of the yeast genome without it being necessary to introduce additional DNA sequences (selection marker or the like). The recombinant yeast strains are stable without selection pressure and may be cultivated under fermentation conditions to create high densities. Foreign gene expression may be induced by metered lactose or galactose or, after turning off the KIGAL80 regulator gene, may be constitutively activated. Foreign gene expression may be quantified indirectly using expression of an endogenous reporter gene.
A series of recombinant variants building on the K. lactis VAK367-D4 strain was generated. In general these variants express inducibly significant quantities of a protein, or domains of this protein, or domains of this protein fused with heterogenous protein domains. The related heterogenous protein domains act to deliberately stimulate the immune response (adjuvant purposes) and to deliberately compartmentalize the expressed foreign protein in the yeast cell. In addition to adjuvant effects, compartmentalization of the expressed foreign protein is important for optimizing expression and for formulating the expression product. One of these recombinant K. lactis strains was successfully employed for mucosal/oral vaccination (see exemplary embodiments).
Exemplary Embodiments
1. Production of the K. lactis VAK367-D4 Strain (Met′ ura3 lac4::ScURA3).
The initial VAK367 strain for heterologous expression of foreign proteins has the following properties: It permits cultivation to produce high cell density without intracellular proteins being detectably released. This strain is distinguished from many closely related K. lactis strains in this regard. The VAK367 strain was derived from two rounds of mutagenesis of the CBS 2359 strain (Central bureau voor Schimmelcultures, Fungal Biodiversity Centre) and is auxotrophic for the amino acid methionine and the nucleobase uracil. Using genetic methods, the VAK367-D4 strain was derived from the VAK367 strain (deposited with the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) in Braunschweig) in that the sequence of +358 to +1181 of the LAC4 gene was replaced with the ScURA3 gene using the plasmid pD4-2. The VAK367-D4 strain now permits the integration of foreign genes at the LAC4 locus without additional markers in that lactose growth is selected. When using a suitable integration vector such as e.g. Klp3 (see below) by homologous recombination, the disruption cassette is replaced such that an intact LAC4 gene is reconstituted and the ScURA3 marker is lost. (FIG. 1)
2. Production of an Integration Vector that Permits the Inducible Expression of Foreign genes.
Vector: Klp3
The Klp3 vector is an E. coli vector based on YRp7 that cannot replicate autonomically in yeasts because the ARS1 sequence was deleted. Klp3 includes K. lactis sequences that make it possible to integrate at the LAC4 locus using homologous recombination (upstream region of LAC4 and 5′ end of the LAC4 reading frame). A DNA segment that includes the TEF1 terminator and the KIGAL80 promotor was inserted between the LAC4 promotor and the transcription start. Thus the LAC4 reading frame is under control of the KIGAL80 promotor that is co-regulated via the KIGal4 transcription factor with the LAC4 promotor (Zenke et al. 1993, Molecular and Cellular Biology, 13:7566-7576). This design makes it possible to track induction of foreign gene expression by measuring the LAC4-coded β-galactosidase. Klp3 permits the integration of the foreign gene between LAC4 promotor and TEF1 terminator via the unical Sall interface. For integrating the expression cassette, Klp3 is digested with Hpal or EcoRl and transformed into K. lactis VAK367-D4. In doing so the expression cassette is separated form the E. coli vector portion so that the resulting strains do not contain any bacterial sequences.
Plasmid Klp3-E2-1 (9437 bp) (FIG. 2)
The gene segment of the BVDV virus that codes for the viral structure protein E2 was inserted into the Sal interface between LAC4 promotor and TEF1 terminator as Sall-Xhol fragment. The KIGAL80 promotor is downstream and was fused to the 5′ end of the LAC4 ORF.
The plasmid was cut with HPal and the larger Hpal fragment was integrated with the E2-ORF chromosomally using homologous recombination. The lac4::URA3 gene locus was replaced and the intact LAC4 gene was reconstituted. Growth on lactose medium was used for selection. The loss of the URA3 gene was confirmed by the uracil auxotrophy. The sequence for the corresponding gene locus was confirmed using DNA sequencing. (Sequence log 1)
3. Formulation of the E2 Major Antigens of BVDV and CSFV.
A major antigen is characterized by BVDV (bovine viral diarrhea virus), the pathogen of bovine viral diarrhea and mucosal disease (BVD/MD), and also by CSFV (classical swine fever virus), the pathogen of classical swine fever (CSF). This is the “envelope” (virus-shell integrated) protein E2. Even in the absence of a virus particle, E2 induces a massive humoral immune response, i.e. the formation of effectively virus-neutralizing antibodies. Genetically formulating E2 made it possible to further strengthen the immunogenic potential of the protein and also to produce a cellular immune response. The specific and exclusive immune response to individual protein domains of E2, some of which were genetically formulated, made it possible to discriminate between vaccinated animals and animals infected with the field virus, e.g. by means of the ELISA method.
4. Design of a K. lactis Strain that Expresses the BVDV E2 Protein VAK367-E2-1, a K. lactis strain, was produced by means of the inventive technology. In this strain, a segment of the BVDV genome (CP7 strain) was integrated into the yeast genome. The corresponding BVDV gene segment included the area that included protein for the E2 and parts of the adjacent E1 and p7-coding regions of the BVDV genome. The E1 and p7 regions include the signal sequences needed for correctly processing the E2 protein (sequence log 2). Correct processing (maturation) of the BVDV E2 protein occurs via signalases.
Expression of E2 in cells of the VAK367-E2-1 K. lactis strain may be established by means of a specifically developed immunofluorescence detection method. An ELISA method specially developed for detecting the BVDV E2 permits detection and quantification of the heterologously expressed antigen. It was possible to use the analog ELISA method for precisely quantifying the antibody titer of immunized animals. Virus neutralization methods and methods for characterizing antibodies and T cells were employed as routine methods.
A novel qRT-PCR method makes it possible to detect and quantify BVDV RNA genomes from serum and cell culture supernatants.
5. Demonstrating the Effectiveness of K. lactis Strain VAK367-E2-1 in Mucosal/Oral Immunization Studies
Study 1
In animal testing an emulsion of naive K. lactis was applied to a significant number of mice under standard conditions. Various immunization schemes were used.
The main criteria were different quantities of supplied yeasts (3—max. 8% portion of daily food intake) and different “booster intervals.”
Results:
(i) General tolerance for K. lactis was demonstrated: oral administration of the yeast emulsions did not cause any visible changes in the findings for the animals.
(ii) Administration of K. lactis led to a clearly detectable humoral immune response to certain yeast proteins. Using the western blot method it was possible to establish a significant and specific antibody response to yeast proteins in the animals that had been fed with K. lactis compared to control animals. Yeast proteins thus have an immunogenic effect per se. In addition to the proof of principle that an immune response may be produced with the oral application of K. lactis, it was indicated that the oral administration of yeasts in combination with a recombinant antigen may attain an additional adjuvant effect.

Study 2

In other animal studies that used a significant number of mice, oral vaccinations were administered with an optimized immunization scheme (see Study 1) and with recombinant K. lactis of the VAK367-E2-1 strain.
Results:
(i) Using the special ELISA method it was possible to detect the formation of anti-BVDV E2 antibodies in the mice vaccinated with K. lactis strain VAK367-E2-1 compared to control mice (immunized with naïve K. lactis).
(ii) In a neutralization test with BVDV on bovine culture cells it was possible to detect a neutralizing effect of anti-sera from mice that had been immunized with K. lactis of the VAK367-E2-1 strain, again in comparison to the sera from control mice.
(iii) The immune response could be increased by using adjuvants such as CpG-ODN and QuilA.
(iv) It was possible to attain effective protection using mucosal/oral immunization with the recombinant K. lactis VAK367-E2-1 strain. This could be demonstrated in challenge experiments with recombinant vaccine viruses that express the BVDV E2 protein.
The results of the study prove that in accordance with the invention foreign genes without additional selection markers may be deliberately integrated into them by means of producing a K. lactis strain and variants of this strain. The resulting recombinant descendants of the K. lactis strains in question may be used for expression purposes for the subsequent biochemical representation of a heterologous protein. The cells of the corresponding recombinant K. lactis strains may be employed directly for mucosal/oral or parenteral immunization.

## Claims

1. A method of vaccination, comprising oral/mucosal administration of a vaccine comprising a recombinant yeast, wherein
said recombinant yeast comprises a genomically integrated expression cassette comprising lactose inducible LAC4 promoter from Kluyveromyces lactis, a foreign gene or a part of a foreign gene expressing an immunogenic protein, a transcription terminator and GAL80 promoter from K. lactis (KIGAL80-P) which drives transcription of a LAC4 coding sequence,
wherein the foreign gene or the part of the foreign gene is flanked by the lactose inducible LAC4 promoter and the transcription terminator, which transcription terminator is followed downstream by the KIGAL80-P.

2. The method in accordance with claim 1, wherein the recombinant yeast is Kluyveromyces lactis.

3. The method in accordance with claim 1, in which said recombinant yeast is employed as an expression system.

4. The method in accordance with claim 3, wherein the recombinant yeast allows lactose-inducible expression of the foreign gene or said part of a foreign gene.

5. The method in accordance with claim 1, wherein said recombinant yeast is characterized by absence of any foreign selection markers apart from the foreign gene or said part of a foreign gene.

6. The method in accordance with claim 1, further comprising quantification of the expression of the foreign gene or said part of a foreign gene by expression of an endogenous reporter gene that is a co-regulated Kluyveromyces lactis-intrinsic beta-galactosidase gene (LAC4).

7. The method in accordance with claim 1, wherein the foreign gene or said part of a foreign gene expresses a structure protein from the bovine viral diarrhea virus (BVDV).

8. The method in accordance with claim 1, wherein the vaccine has long storability outside of a cold environment.

9. The method in accordance with claim 1, wherein the recombinant yeast of the vaccine comprises complete yeast cells which provide a specific immunization against the expressed foreign protein or expressed foreign protein part.

10. A method of vaccination comprising inhaled, bronchial, oral or nasal administration of a vaccine, comprising a recombinant yeast comprising complete yeast cells which provide a specific immunization against expressed foreign protein, wherein
the recombinant yeast comprises a genomically integrated expression cassette comprising the lactose inducible LAC4 promoter from Kluyveromyces lactis, a foreign gene or a part of a foreign gene expressing an immunogenic protein, a transcription terminator and GAL80 promoter from K. lactis (KIGAL80-P) which drives transcription of a LAC4 coding sequence,
wherein the foreign gene or the part of the foreign gene is flanked by the lactose inducible LAC4 promoter and the transcription terminator, which transcription terminator is followed downstream by the KIGAL80-P.

11. The method in accordance with claim 1 or 10, further comprising subsequently detecting neutralizing antibodies in sera from individuals who were immunized by said vaccine.

12. The method in accordance with claim 1 or 10, further comprising subsequently detecting neutralizing antibodies against a BVDV E2 protein in sera from individuals who were immunized by said vaccine.

13. The method in accordance with claim 1 or 10, further comprising detecting immunization using a challenge with antigen in individuals who were immunized by said vaccine.

14. The method in accordance with claim 13, wherein the antigen is a viral antigen.

15. The method in accordance with claim 14, wherein the viral antigen is BVDV E2.

16. A method of vaccination comprising oral/mucosal administration of a vaccine comprising a recombinant yeast derived from the strain Kluyveromyces lactis VAK367-D4 by homologous recombination resulting in replacement of the genomic lac4::URA3 locus with an expression cassette comprising
a foreign gene or a part of a foreign gene expressing an immunogenic protein, lactose inducible LAC4 promoter from said strain, a transcription terminator, and GAL80 promoter from K. lactis (KIGAL80-P) which drives transcription of a LAC4 coding sequence, wherein the foreign gene or the part of the foreign gene is flanked by the lactose inducible LAC4 promoter and the transcription terminator, which transcription terminator is followed downstream by the KIGAL80-P.

17. The method of vaccination of claim 1, wherein the vaccine comprises a recombinant yeast of the strain Kluyveromyces lactis in which a foreign gene segment of Bovine Viral Diarrhea Virus coding for viral structure protein E2 is inserted into a gene of the strain, whereby, upon oral or mucosal administration of the vaccine to an animal, an immune response to Bovine Viral Diarrhea Virus is induced in the animal.

18. The method in accordance with claim 1, wherein the foreign gene or part of a foreign gene is deliberately integrated into the yeast genome without introduction of an additional marker.

19. The method of claim 1, 10, 16, or 18, wherein said recombinant yeast is characterized by high genetic stability of the expression cassette even during growth of said recombinant yeast under non-selective conditions due to absence of any extended DNA-sequence repeats in the expression cassette.

20. The recombinant yeast as recited in claim 1.

21. The vaccine as recited in claim 1.