WO2010054482A1

WO2010054482A1 - Immunogenic human papillomavirus compositions

Info

Publication number: WO2010054482A1
Application number: PCT/CA2009/001650
Authority: WO
Inventors: Peter Emtage
Original assignee: Nventa Biopharmaceuticals Corporation
Priority date: 2008-11-12
Filing date: 2009-11-12
Publication date: 2010-05-20

Abstract

A fusion protein comprising a heat shock protein, or immunostimulatory portion thereof, and two or more human papillomavirus (HPV) proteins, or immunogenic portions thereof is disclosed.

Description

IMMUNOGENIC HUMAN PAPILLOMAVIRUS COMPOSITIONS FIELD OF INVENTION

[0001] The present invention relates to immunogenic human papillomavirus compositions.

BACKGROUND OF THE INVENTION

[0002] Human papillomavirus (HPV) is a family of viruses that affect all parts of the body - over 100 types of HPV are known. HPV Infection is common in the population, and while the majority of infections may be asymptomatic, several types are associated with benign tumors (e.g., warts) or malignant progression. HPV is one of the most common sexually transmitted infections - with an overall prevalence as high as 44% in some population groups (Dunne et al., 2007. JAMA 297:813-819).

[0003] HPV types associated with genital infections include types 5, 6, 11, 18, 31, 33, 35, 39, 45, 51, 52, 54, 58, 60, 66, 68, 69 and 70, and may also be associated with an increased risk of cancer of the genitourinary tract, or cancers of other tissues (Vandepapeliere 2005. J. Inf Dis.l92:2099-2107; zur Hausen, 2000. J. Natl. Cancer Inst. 92: 690-698; zur Hausen, 2008). The observed pathologies may vary with the virus type - for example, types 16 and 18 are found associated with a majority of cervical carcinomas, while types 6 and 11 are frequently associated with anogenital warts. Papillomaviruses and their related pathologies are reviewed by zur Hausen, 2000 (supra) and references cited therein.

[0004] Vaccines for prevention of HPV infections are known. GARDASIL™ and CERVARIX™ are two commercially available vaccine preparations that comprise HPV structural proteins. While conventional vaccines may be effective in preventing establishment of an HPV infection, they may have little therapeutic effect on an individual who has been previously infected. Further, some HPV infections may involve multiple HPV types, each independently capable of establishing an HPV infection related pathology. A treatment regimen would optimally include medicaments or other therapeutic compositions able to address an infection associated with more than one type of HPV. [0005] PCT Publication WO 98/04706 discloses a fusion protein of HPV proteins L2 and E7.

[0006] PCT Publication WO 01/51081 discloses a method of inducing a CD8+ CTL response by administering to a subject a portion of a heat shock protein comprising an ATP binding domain.

[0007] PCT Publication WO 2007/058235 discloses a fusion protein comprising ubiquitin, a cancer antigen protein or infection antigen protein and the C-terminus of a heat shock protein presented thereon as an antigen.

[0008] PCT Publication WO 2007 038083 discloses a heat shock protein from Mycobacterium leprae and its use to treat atopic conditions, or as a vaccine against M. leprae.

[0009] PCT Publication WO 96/00583 discloses nucleic acid constructs encoding papillomavirus gene products.

[0010] The present invention provides for immunogenic human papillomavirus compositions, methods of making such compositions and uses of such compositions.

SUMMARY OF THE INVENTION [001 1] The present invention relates to immunogenic human papillomavirus compositions

[0012] In accordance with one aspect of the invention, there is provided a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof.

[0013] hi accordance with another aspect of the invention, there is provided a pharmaceutical composition comprising a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof. [0014] In accordance with another aspect of the invention, there is provided a nucleic acid encoding a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof.

[0015] In accordance with another aspect of the invention, there is provided an expression vector comprising a nucleic acid encoding a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof.

[0016] In accordance with another aspect of the invention, there is provided a cell comprising an expression vector comprising a nucleic acid encoding a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof.

[0017] In accordance with another aspect of the invention, there provided a method of making a fusion protein comprising providing a cell comprising an expression vector comprising a nucleic acid encoding a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof; and culturing the cell under conditions that permit expression of the nucleic acid.

[0018] In accordance with another aspect of the invention, there is provided a method of inducing or enhancing an immune response against a human papillomavirus antigen, the method comprising administering to the subject an effective amount of the fusion protein of a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof, or a pharmaceutical composition comprising a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof.

[0019] In accordance with another aspect of the invention, there is provided a method of inducing or enhancing an immune response against a human papillomavirus antigen, the method comprising administering to the subject an effective amount of pharmaceutical composition compπsing a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portion thereof.

[0020] In accordance with another aspect of the invention, there is provided a composition for inducing a cell-mediated cytolytic immune response to a human papillomavirus (HPV) in a mammal, the composition compπsing a fusion protein compπsing a stress protein or immunostimulatory portion thereof, and two or more human papillomavirus proteins, or immunogenic portions thereof

[0021] In accordance with another aspect of the invention, there is provide a fusion protein for inducing a cell-mediated cytolytic immune response to a human papillomavirus (HPV) in a mammal, the fusion protein compπsing two or more HPV polypeptides, or portions thereof, and a stress protein, or immunostimulatory portion thereof.

[0022] In accordance with another aspect of the invention, the two or more HPV polypeptides, or portion thereof, may be El, E2, E3, E4, E5, E6 and E7 or one or more portions thereof

[0023] hi accordance with another aspect of the invention, the stress protein or immunostimulatory portion thereof may be a heat shock protein

[0024] In accordance with another aspect of the invention, the stress protein or immunostimulatory portion thereof may be HspόO, Hsp65, Hsp70, Hsp 100-200, HsplOO, Hsp90, Hsp20-30, hsp65, Hsp 10 and ubiquitin.

[0025] In accordance with another aspect of the invention, the stress protein or immunostimulatory portion thereof may be a mycobacteπal heat shock protein.

[0026] In accordance with another aspect of the invention, the stress protein or immunostimulatory portion thereof may be an M bovis BCG stress protein.

[0027] In accordance with another aspect of the invention, the M bovis BCG stress protein may be an M bovis BCG hsp65 heat shock protein [0028] In accordance with another aspect of the invention, the pharmaceutical composition may further comprise a pharmaceutically acceptable carrier or excipient, or an adjuvant.

[0029] hi accordance with another aspect of the invention, the adjuvant may be a TLR3 agonist, or a TLR9 agonist.

[0030] In accordance with another aspect of the invention, the TLR3 agonist may be double- stranded RNA (dsRNA), Poly I:C, Poly I: C with poly-L-lysine and poly I:C with polyarginine.

[0031] In accordance with another aspect of the invention, the TLR agonist is CpG ODN 2395.

[0032] In accordance with another aspect of the invention, the fusion protein comprises the sequence of SEQ ID NO: 41.

[0033] In accordance with another aspect of the invention, the immunostimulatory portion of a heat shock protein comprises the sequence of SEQ ID NO: 41.

[0034] In accordance with another aspect of the invention, the two or more HPV polypeptides, or immunogenic portions thereof are selected from group comprising of HPV E2, HPV E6 and HPV E7.

[0035] In accordance with another aspect of the invention, the two or more HPV polypeptides, or immunogenic portions thereof are selected from a group comprising SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 32, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 49 and SEQ ID NO: 50.

[0036] In accordance with another aspect of the invention, the cell-mediated cytolytic immune response comprises CD8+ lymphocyte stimulation.

[0037] In accordance with another aspect of the invention, the cell-mediated cytolytic immune response comprises CD4+ lymphocyte stimulation. [0038] In accordance with another aspect of the invention, the fusion protein comprises the sequence of SEQ ID NO: 46.

[0039] hi accordance with another aspect of the invention, the nucleic acid encoding a fusion protein comprising a stress protein, or immunostimulatory portion thereof, and a human papillomavirus protein, or immunogenic portion thereof comprises SEQ ID NO: 45.

[0040] A fusion protein comprising epitopes from two or more proteins fused to a stress protein or portion thereof provides an advantage of stimulating immune cells specific for two or more antigens. For example, a composition comprising a fusion protein according to some aspects of the invention may be used in a polyvalent vaccine, while only requiring production of a single protein molecule. This may allow for prophylactic immunization against two or more strains of the same pathogen, or against two or more pathogens. A similar advantage may be realized when such fusion proteins are used to treat a subject, or prepare a composition to treat a subject, the subject having a disease or condition associated with two or more strains of the same pathogen, or two or more pathogens.

[0041] A fusion protein comprising an immunostimulatory portion of a stress protein fused to epitopes of two or more proteins further provides an advantage of being smaller in size than a fusion protein comprising most or all of a stress protein. An immunostimulatory portion of a stress protein according to some embodiments of the invention maintains the immunostimulatory effects of the full size stress protein, but allows for a smaller fusion protein - the subject is exposed to fewer epitopes, thus reducing the opportunity for undesired or adverse responses.

[0042] This summary of the invention does not necessarily describe all features of the invention. Other aspects, features and advantages of the present invention will become apparent to those of ordinary skill in the art upon review of the following description of specific embodiments of the invention. BRIEF DESCRIPTION OF THE DRAWINGS

[0043] These and other features of the invention will become more apparent from the following description in which reference is made to the appended drawings wherein:

[0044] FIGURE 1 shows the location of HPV6/11 peptides on a plate map for the ELISPOT experiments.

[0045] FIGURE 2 shows the ELISPOT counts for each well of the plate map.

[0046] FIGURE 3 SDS-PAGE results of expression of hsp6/l 1. A) SDS-PAGE of CLD209 shaker-flasks. Lane 1, MW marker; lane 2, UI (Uninduced) supernatant (3h); lane, 3 UI (Uninduced) insoluble (3h); lane 4, UI (Uninduced) supernatant (20H); lane 5, UI (Uninduced) insoluble (2Oh); lane 6, 0.ImM IPTG soluble (3h); lane 7, 0.ImM IPTG insoluble (3h); lane 8, 0.ImM IPTG soluble (2Oh); lane 9, O.lmM IPTG insoluble (2Oh); lane

10, LOmM IPTG soluble (3h); lane 11, LOmM IPTG insoluble (3h); lane 12, LOmM IPTG soluble (20h); lane 13, LOmM IPTG insoluble (2Oh). B) SDS-PAGE of CLD210 shaker- flask. Lane 1, MW marker; lane 2, MW marker; lane 3, UI (Uninduced) supernatant (3h); lane 4, UI (Uninduced) insoluble (3h); lane 5, UI (Uninduced) supernatant (2Oh); lane 6, UI (Uninduced) insoluble (2Oh); lane 7, O.lmM IPTG soluble (3h); lane 8, O.lmM IPTG insoluble (3h); lane 9, O.lmM IPTG soluble (2Oh); lane 10, O.lmM IPTG insoluble (2Oh); lane

11, 1.0 niM IPTG soluble (3h); lane 12, 1.0 mM IPTG insoluble (3h); lane 13, 1.0 mM IPTG soluble (2Oh); lane 14, 1.0 mM IPTG insoluble (2Oh); lane 15, MW marker.

[0047] FIGURE 4 shows a flow chart of the steps for production and purification of Hsp6/11.

[0048] FIGURE 5 shows SDS-PAGE results of cells and cell fractions during homogenization. Lane 1, MW marker; lane 2, resuspended cells; lane 3, first homogenization pass; lane 4, second homogenization pass; lane 5 supernattant of homogenate; lane 6, solubilized inclusion body preparation; lane 7, supernatant of solubilized inclusion body preparation; lane 8, pellet of solubilized inclusion body preparation. [0049] FIGURE 6 shows a full-scale chromatogram of the IMAC metal affinity chromatography.

[0050] FIGURE 7 shows SDS-PAGE results of selected elution fractions from IMAC affinity chromatography. Gel A- Lane 1, MW marker; lane 2, column load; lane 3, flow through; lane 4, high salt wash; lane 5, low salt wash; lanes 6-14, fractions 2-7. Gel B - lane 1 MW marker; lanes 2-14, fractions 8-20. Gel C - lane 1 MW marker; lane 2, MW marker; lanes 3-14, fractions 21-32. Gel D - lane 1 MW marker; lanes 2-13, fractions 33-44.

[0051] FIGURE 8 shows a full chromatogram of IEX chromatography of fractions 1-11 and 14-30 of the MAC chromatography step.

[0052] FIGURE 9 shows SDS-PAGE results of elution fractions from IEX chromatography. Gel A - Lane 1, MW marker; lane 2, column load; lane 3, flow through; lanes 4-15, fractions 1-12. Gel B - Lane 1, MW marker; lanes 2-12, fractions 13-23. Gel C - lane 1 MW marker; lanes 2-14, fractions 24-36.

[0053] FIGURE 10 shows SDS-PAGE results of elution fractions from the second IEX chromatography. Gel A - lane 1, MW marker; lanes 2-13, fractions A-L; lanes 14-15, fractions 37-38. Gel B - Lane 1, MW marker; lanes 2-12, fractions 39-49.

[0054] FIGURE 11 shows SDS PAGE analysis of the final samples. Lane 1, MW marker; lane 2, IMAC before concentration; lane 3, IMAC after 10 fold concentration; lane 4, IMAC permeate; lane 5, Q1Q2 fractions before concentration; lane 6, Q1Q2 fractions after 10x concentration; lane 7, Q1Q2 fractions permeate; lane 8, Q2FT fractions before concentration; Iane9, Q2FT fractions after 10x concentration; lane 10, Q2 fraction permeate.

[0055] FIGURE 12 shows the sequence of SEQ ID NO: 45.

DETAILED DESCRIPTION

[0056] In the description that follows, a number of terms are used extensively, the following definitions are provided to facilitate understanding of various aspects of the invention. Use of examples in the specification, including examples of terms, is for illustrative purposes only and is not intended to limit the scope and meaning of the embodiments of the invention herein.

[0057] Use of the term 'a' or 'an' includes both singular and plural references.

[0058] The present invention provides a fusion protein comprising a heat shock protein protein, or immunostimulatory portion thereof, and one or more Human Papillomavirus (HPV) proteins, or immunogenic portions thereof.

[0059] The present invention further provides for a composition comprising a fusion protein and an adjuvant, the fusion protein comprising a heat shock protein, or immunostimulatory portion thereof, and one or more HPV proteins, or immunogenic portions thereof.

[0060] The double-stranded, circular DNA genome of HPV encodes both structural and regulatory gene products. The genome sequences of many types of HPV are fully sequenced and cloned, and the sequence information deposited in sequence databases (e.g., GenBank). Vectors comprising complete or partial HPV genome sequences may be obtained from the American Type Culture Collection (ATCC).

[0061] Of the open reading frames of the HPV genome, Ll and L2 encode capsid proteins; and El, E2 , E4, E5, E6 and E7 encode proteins with roles in regulation and expression of the viral proteins and interact with the host genes and proteins. El, E2 and E4 have roles in viral DNA replication , while E6 and E7 are oncogenic and, when expressed, may be capable of transforming cells in vitro.

[0062] Multiple HPV types are known, and may cause or be associated with various pathologies. For example HPV types 5, 6, 7, 11, 16, 18, 31, 32, 33, 35, 39, 45, 51, 52, 54, 58, 60, 66, 68, 69 and 70 may cause, or be associated with diseases or disorders including anogenital warts, plantars warts, cervical cancer, cervical dysplasia, vulvar cancer, vulvar intraepithelial neoplasia, penile intraepithelia neoplasia, cervical intraepithelial neoplasia, anal cancer, anal dysplasia, some head-and-neck cancers and recurrent respiratory papillomatosis. HPV types 5, 8, 9, 12, 14, 15, 17, 19, 25, 36, 38, 47, 50 may cause, or be associated with epidermodysplasia verruciformis. HPV types 1, 2, 3, 4, 7 and 10 may cause, or be associated with, common warts, plantars warts or flat warts.

[0063] An HPV protein, or immunogenic portion thereof, according to some embodiments of the invention may include any polypeptide encoded by one or more HPV types. As non- limiting examples, the HPV protein, or immunogenic portion thereof, may be selected from the group comprising E2, E6 and E7 from HPV types 6 and 11. The full length polypeptide may be used, or a fragment or portion thereof, providing the fragment or portion thereof is immunogenic.

[0064] A "full-length" protein, fusion protein or polypeptide, etc. includes a polypeptide comprising all, or most of the amino acid complement of a particular protein or polypeptide. For example, a few amino acids from the C and/or N terminus may be absent relative to the protein or polypeptide, but identifying domains, functional sequence, amino acids present in an active site or binding site of the immunogen, and sufficient amino acid sequence to specifically identify the protein are present in the "full-length" protein or polypeptide.

Alternately, a "full-length" protein, fusion protein or polypeptide, etc. includes a polypeptide comprising one or more than one additional amino acids added to the C and/or N terminus, relative to the protein or polypeptide. A full-length protein may be fused to other amino acids, proteins or peptides of interest. For example, a cysteine amino acid may be added to facilitate a disulfide bridge, or to allow for fusion, coupling or other linkages to another peptide or a surface. As another example, a "His-tag" sequence (4-10 histidine residues) or a FLAG sequence may be added to the C or N terminus of the fusion protein to facilitate isolation of the protein or polypeptide. As another example, a cleavage sequence may be included to separate domains of a fusion protein, or to allow for post-isolation removal of the His-tag.

[0065] A fragment or portion of a protein, fusion protein or polypeptide includes a peptide or polypeptide comprising a subset of the amino acid complement of a particular protein or polypeptide. The fragment may, for example, comprise an immunogenic region, a stress- response-inducing region, or a region comprising a functional domain of the protein or polypeptide. The fragment may also comprise a region or domain common to proteins of the same general family, or the fragment may include sufficient amino acid sequence to specifically identify the full-length protein from which it is derived.

[0066] A protein or polypeptide, or fragment or portion of a protein or polypeptide may range in size from as small as 4-6 amino acids to the "full-length" of the protein or polypeptide. The protein or polypeptide may be described with reference to a database accession number (e.g., a Genbank accession number, or to a SEQ ID NO. or combination thereof. For example, a fragment or portion may be from about 1% to about 10%, from about 10% to about 20%, from about 20% to about 30%, from about 30% to about 40% , from about 40% to about 50%, from about 50% to about 60%, from about 60% to about 70%, from about 70% to about 80%, from about 80% to about 90% or from about 90% to about 100% of the full-length protein or polypeptide. Alternately, a fragment or portion may be from about 4 to about 10 amino acids, or any amount therebetween, from 10 to about 50 amino acids, or any amount therebetween, from about 50 to about 100 amino acids or any amount therebetween, from about 100 to about 150 amino acids, or any amount therebetween, from about 150 to about 250 amino acids or any amount therebetween, from about 250 to about 500 amino acids or any amount therebetween. Alternately, a fragment or portion maybe 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, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more amino acids long.

[0067] A protein or polypeptide, or fragment or portion of a protein or polypeptide is specifically identified when its sequence may be differentiated from others found in the same phylogenetic Species, Genus, Family or Order. Such differentiation may be identified by comparison of sequences. Comparisons of a sequence or sequences may be done using a BLAST algorithm (Altschul et al. 1009. J. MoI Biol 215:403-410). A BLAST search allows for comparision of a query sequence with a specific sequence or group of sequences, or with a larger library or database (e.g., GenBank or GenPept) of sequences, and identify not only sequences that exhibit 100% identity, but also those with lesser degrees of identity. [0068] Sequence identity or sequence similarity may be determined using a nucleotide sequence comparison program, such as that provided within DNASIS (for example, using, but not limited to, the following parameters: GAP penalty 5, #of top diagonals 5, fixed GAP penalty 10, k-tuple 2, floating gap 10, and window size 5). However, other methods of alignment of sequences for comparison are well-known in the art for example the algorithms of Smith & Waterman (1981, Adv. Appl. Math. 2:482), Needleman & Wunsch (J. MoI. Biol. 48:443, 1970), Pearson & Lipman (1988, Proc. Nat'l. Acad. Sci. USA 85:2444), and by computerized implementations of these algorithms (e.g., GAP, BESTFIT, FASTA, and BLAST), or by manual alignment and visual inspection.

[0069] In some embodiments of the invention the immunogenic fragment or portion of the E2 HPV protein comprises SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40 SEQ ID NO: 49, or SEQ ID NO: 50, or a portion or fragment thereof; for example, SEQ ID NO: 32, SEQ ID NO: 49, SEQ ID NO: 50, or a portion thereof (Examples 5-7). In some embodiments the immunogenic fragment of the E2 HPV polypeptide may comprise some or all of amino acids 181-200, or some or all of amino acids 311-350.

[0070] In some embodiments of the invention, the immunogenic fragment or portion of the E6 HPV protein comprises SEQ ID NO: 1 , SEQ ID NO:2, SEQ ID NO: 3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 or SEQ ID NO: 14, or a portion or fragment thereof; or SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 13 or SEQ ID NO: 14, or a portion thereof (Examples 5-7). In some embodiments, the immunogenic fragment of the E6 HPV polypeptide may comprise some or all of amino acids 1-150 of SEQ ID NO: 42. [0071] In some embodiments of the invention, the immunogenic fragment or portion of the E7 HPV protein sequence comprises SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, or SEQ ID NO: 22, or a portion or fragment thereof; or SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 or SEQ ID NO: 18, or a portion thereof (Examples 5-7). In some embodiments, the immunogenic fragment of the E7 HPV polypeptide may comprise some or all of amino acids 1-80 of SEQ ID NO: 43.

[0072] In some embodiments of the invention, the E2 HPV protein comprises SEQ ID NO: 44; the E6 HPV protein comprises SEQ ID NO: 42; and the E7 HPV protein comprises SEQ ID NO: 43, and the E2, E6 and E7 proteins are fused to a heat shock protein, or immunostimulatory portion thereof.

[0073] hi some embodiments of the invention, the HPV proteins or portions thereof are fused in any of several sequential orders (from N-terminal to C-terminal), for example E6-E7-E2, E6-E2-E7, E7-E2-E6, E7-E6-E2, E2-E6-E7 or E2-E7-E6. The fusion of HPV proteins or portions thereof may be subsequently fused N-terminally or C-terminally to a heat shock protein, or immunostimulatory portion thereof. In some embodiments of the invention, the heat shock protein or immunostimulatory portion thereof and the HPV proteins or portions thereof are fused in the sequential order (from N-terminal to C-terminal) Hsp-E6-E7-E2.

[0074] Numbering of amino acids in any given sequence are relative to the particular sequence, however one of skill can readily determine the 'equivalency' of a particular amino acid in a sequence based on structure and/or sequence. For example, if 6 N terminal amino acids were removed when constructing a clone for crystallography, this would change the specific numerical identity of the amino acid (e.g., relative to the full length of the protein), but would not alter the relative position of the amino acid in the structure.

[0075] Comparisons of a sequence or sequences may be done using a BLAST algorithm

(Altschul et al., 1990. J. MoI Biol 215:403-410). A BLAST search allows for comparison of a query sequence with a specific sequence or group of sequences, or with a larger library or database (e.g., GenBank or GenPept) of sequences, and identify not only sequences that exhibit 100% identity, but also those with lesser degrees of identity. Nucleic acid or amino acid sequences may be compared using a BLAST algorithm. Furthermore the identity between two or more sequences may be determined by aligning the sequences together and determining the % identity between the sequences. Alignment may be carried out using the BLAST Algorithm (for example as available through GenBank; URL: ncbi.nlm.nih.gov/cgi- bin/BLAST/ using default parameters: Program: blastn; Database: nr; Expect 10; filter: default; Alignment: pairwise; Query genetic Codes: Standard(l)), or BLAST2 through EMBL URL: embl-heidelberg.de/Services/ index.html using default parameters: Matrix BLOSUM62; Filter: default, echofilter: on, Expect: 10, cutoff: default; Strand: both; Descriptions: 50, Alignments: 50; or FASTA, using default parameters), or by manually comparing the sequences and calculating the % identity.

[0076] Heat shock proteins, or fragments or portions thereof, are immunostimulatory proteins found in many species, and are evolutionarily conserved and present in both prokaryotic and eukaryotic cells. Heat shock proteins, alternately referred to as stress proteins, are generally produced by the cell in response to a stress. Heat shock proteins are encoded by heat shock genes. Heat shock genes (alternately referred to as stress genes) are those whose expression is upregulated when the cell or organism is exposed to a stress, for example temperature changes, hypoxia, nutrient depravation, heavy metal exposure, inhibition of energy metabolism such as electron transport, or the like. Heat shock proteins known in the art and which may be used in some embodiments of the present invention include but are not limited to HspόO, Hsp65, Hsp70, Hsp 100-200, HsplOO, Hsp90, Hsp20-30, hsp65, HsplO and ubiquitin (reviewed in US Patent 523833; Parsell DA & Lindquist S, 1993 Ann. Rev. Genet. 27:437-496; Moseley P 2000. Immunopharmacology 48:299-302). Expression of heat shock proteins by an infecting pathogen may have a role in modulation of the general inflammatory response in an infected host. Some individuals, including healthy individuals with no history of mycobacterial infection or autoimmune disease also carry T cells that recognize both bacterial and human HspόO epitopes; a considerable fraction of T cells in healthy individuals that are characterized by expression of the gamma-delta T cell receptor recognize both self and foreign stress proteins (O'Brien, R. et al.. Cell 57: 664-674 (1989); O' Brien et al 2001. Proc. Natl Acad. Sci 92:4348^352). Full-length hsp60 has also been demonstrated to activate T-cells (Osterloh et al 2004. J. Biol Chem. 279:47906-4791. An immunostimulatory fragment or portion of a heat shock protein is one that facilitates an immune response to an antigen. The fragment or derivative, for example, may induce an immune response that would not otherwise occur or may enhance an immune response that would be expected to occur.

[0077] Examples of fragments or portions that may be used include, but are not limited to fragments comprising amino acids 1-190 of M. tuberculosis Hsp65 (SEQ ID NO: 41), amino acids 161-370 of mycobacterial Hsp70 (particularly M. tuberculosis Hsp70) (Huang et al., J. Exp. Med. 17:403-408; 2000); amino acids 280-385 of murine Hsc70 (Udono et al., Intl.

Immunology 3: 1233-1242, 2001); amino acids 359-610 of M. Tuberculosis Hsp70 (Wand et al., Immunity 15: 971-983, 2001); amino acids 1 to 200 of mycobacterial Hsp65 (Chu et al., US 6495347).

[0078] Heat shock proteins, or immunostimulatory fragments or portions thereof, may be obtained from bacteria, such as E. coli, enterobacteria, or mycobacteria, for example M. tuberculosis, M. bovis, M. leprae or the like. Other sources of heat shock proteins include, but are not limited to mammals, humans, birds, rats, mice, fruit flies, Xenopus, amphibians, reptiles or the like, hi some embodiments of the invention, the heat shock protein is a mycobacterial hsp65, for example M. bovis BCG Hsp65. An immunostimulatory portion of hsp65 includes a portion that is capable of stimulating an immune response. SEQ ID NO: 41 is an example of an immunostimulatory portion of M. bovis BCG Hsp65, comprising amino acids 1-190.

[0079] Heat shock proteins and HPV polypeptides may be produced or obtained using known techniques. Nucleic acids encoding the heat shock protein and HPV polypeptides may be obtained from a biological repository; alternately, such nucleic acids may be obtained using conventional molecular cloning techniques. Such nucleic acids may also be synthesized chemically, using conventional techniques. Once the nucleic acid is obtained, it may be manipulated to add or remove sequences (e.g., affinity tags for aiding purification, restriction endonuclease sites to facilitate cloning, etc), alter amino acid expression (e.g., codon optimization) to suit a preferred expression system or expression vector, or the like. Many prokaryotic and eukaryotic expression vectors are known, for example the pET vector and system (Invitrogen), pAVEway™ vectors (Avecia Biologies Limited), retroviral expression vectors, baculovirus expression vectors, yeast expression vectors and the like. Other examples of expression systems are described in, for example, PCT Publication No. WO 99/05297, PCT Publication No. WO 2007/088371, PCT Publication No. WO 2005/071089. Choice of vector may depend on the intended use of the expressed protein; for example, some expression systems provide post-translational modifications that may or may not be suitable; some expressed polypeptides may be toxic to particular expression system hosts, some expression systems may preferably form inclusion bodies comprising the expressed polypeptide, others may exhibit reduced expression levels that do not induce formation of inclusion bodies. The expressed polypeptide may be isolated by conventional methods. For example, cells may be lysed and inclusion bodies collected by centrifugation, followed by solubilization. If the expressed polypeptide is secreted into the culture media, the culture media may be collected by centrifugation or filtration. Alternately, whole cell lysate may be centrifuged to remove insoluble matter. The resulting solution comprising the polypeptide (solubilized inclusion bodies, cell lysate or culture medium for example) may be subjected to antibody-based purification methods (e.g., antibody labeled beads), or chromatographic separation methods (ion exchange chromatography, metal ion affinity chromatography, immunoaffinity chromatography or the like). Such methods and techniques are known in the art. See, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, 3d Ed.. Cold Spring Harbor Laboratory Press (2001); Deutscher. M., Guide to Protein Purification Methods in Enzymology, vol. 182. Academic Press, Inc.. San Diego, CA (1990).

[0080] A fusion protein is a chimeric polypeptide comprising amino acid sequences of two or more polypeptides. The two or more polypeptides may have complementary functions, one of the polypeptides may provide a supplementary functional property, or one of the polypeptides may have a function unrelated to the others in the fusion protein. One or more polypeptides comprising organelle targeting or retention sequences may be fused with a desired polypeptide to target the desired polypeptide to a specific cellular organelle, or retain the desired polypeptide within the cell. One or more polypeptides comprising a carrier sequence that aids in expression, purification and/or detection of the fusion polypeptide may be fused with a desired polypeptide (e.g., FLAG (Sigma), a 6x HIS tag, GST fusions and the like). An immunostimulatory polypeptide may be fused with one or more immunogenic polypeptides. Nucleic acids encoding the two or more polypeptides may be joined and cloned in a suitable vector so that a single polypeptide is expressed, hi some embodiments of the invention, a heat shock protein, or immunostimulatory portion thereof, is fused with one or more than one HPV polypeptides, or portions thereof. Examples of a heat shock protein or immunostimulatory portions thereof include Hsp60, Hsp65, Hsp70, Hsp 100-200, HsplOO, Hsp90, Hsp20-30, hsp65, Hsp 10 and ubiquitin from eukaryotic or prokaryotic cells, hi some examples, the heat shock protein is from M. tuberculosis, M. bovis or M. leprae. In some examples, the immunostimulatory portion may comprise amino acids 1-190 of M. tuberculosis Hsp65 (SEQ ID NO: 41), amino acids 161-370 of mycobacterial Hsp70 (particularly M. tuberculosis Hsp70) (Huang et al., J. Exp. Med. 17:403-408; 2000); amino acids 280-385 of murine Hsc70 (Udono et al., Intl. Immunology 3: 1233-1242, 2001); amino acids 359-610 of M. Tuberculosis Hsp70 (Wand et al., Immunity 15: 971-983, 2001); amino acids 1 to 200 of mycobacterial Hsp65 (Chu et al., US 6495347).

[0081] The one or more HPV polypeptides, or portions thereof, fused to a heat shock protein may include, but is not limited to, Ll , L2, El , E2, E4, E5, E6 or E7; for example, E2, E6 or E7. As a further example, the immunogenic fragment or portion of the E2 HPV protein comprises SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40 SEQ ID NO: 49, or SEQ ID NO: 50, or a portion or fragment thereof; for example, SEQ ID NO: 32, SEQ ID NO: 49, SEQ ID NO: 50, or a portion thereof (Examples 5-7). As a further example, the immunogenic fragment of the E2 HPV polypeptide may comprise some or all of amino acids 181-200, or some or all of amino acids 311-350. [0082] As a farther example, the immunogenic fragment or portion of the E6 HPV protein comprises SEQ ID NO: 1, SEQ ID NO.2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 or SEQ ID NO: 14, or a portion or fragment thereof; or SEQ ID NO: 1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 13 or SEQ ID NO: 14, or a portion thereof (Examples 5-7). As a further example, the immunogenic fragment of the E6 HPV polypeptide may comprise some or all of amino acids 1-150 of SEQ ID NO: 42.

[0083] As a further example, the immunogenic fragment or portion of the E7 HPV protein sequence comprises SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, or SEQ ID NO: 22, or a portion or fragment thereof; or SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 or SEQ ID NO: 18, or a portion thereof (Examples 5-7). As a further example, the immunogenic fragment of the E7 HPV polypeptide may comprise some or all of amino acids 1-80 of SEQ ID NO: 43.

[0084] As a further example, the E2 HPV protein comprises SEQ ID NO: 44; the E6 HPV protein comprises SEQ ID NO: 42; and the E7 HPV protein comprises SEQ ED NO: 43, and the E2, E6 and E7 proteins are fused to a heat shock protein, or immunostimulatory portion thereof.

[0085] The one or more HPV proteins or portions thereof may be fused in any of several sequential orders (from N-terminal to C-terminal), for example E6-E7-E2, E6-E2-E7, E7-E2- E6, E7-E6-E2, E2-E6-E7 or E2-E7-E6. The fusion of HPV proteins or portions thereof may be subsequently fused N-terminally or C-terminally to a heat shock protein, or immunostimulatory portion thereof. In some embodiments of the invention, the heat shock protein or immunostimulatory portion thereof and the HPV proteins or portions thereof are fused in the sequential order (from N-terminal to C-terminal) Hsp-E6-E7-E2. [0086] An example of a fusion protein is Hsp6/11. Hsp6/11 comprises an immunostimulatory fragment of a heat shock protein (M bovis BCG hsp65) fused in frame, without intervening stop codons, with polypeptides encoding HPV type 6 E6 protein, HPV type 6 E7 protein and HPV type 11 E2 protein, or portions thereof. The Hsp6/11 fusion protein comprises SEQ ID NO: 46; a nucleic acid encoding Hsp6/11 comprises SEQ ID NO: 45.

[0087] Therefore, the present invention provides for a fusion protein comprising a heat shock protein or immunostimulatory portion thereof, and one or more Human Papillomavirus (HPV) proteins, or immunogenic portions thereof.

[0088] Therefore, the present invention further provides for a method of making a fusion protein, comprising providing a cell comprising an expression vector, the expression vector comprising a nucleic acid encoding a fusion protein comprising heat shock protein, or immunostimulatory portion thereof, and one or more Human Papillomavirus (HPV) proteins, or immunogenic portions thereof, and culturing the cell under conditions that permit expression of the nucleic acid.

[0089] An adjuvant is an immunostimulatory agent that has no antigen- or immunogen- specific effect by itself, but stimulates the immune system to increase the response to a specific immunogen, or group of immunogens. The ability of an immunogen to induce a response of the innate or adaptive immune system is referred to as the "biological activity" of the immunogen. An adjuvant may mediate, augment or stimulate the biological activity of an immunogen. In some examples, the immunogen may have very little or negligible biological activity in the absence of an adjuvant.

[0090] hi other examples, an adjuvant or adjuvant composition may have an immunogenic effect that is independent of a specific antigen. For example, adjuvant compositions may induce maturation of some immune cells, or may induce clonal expansion of some immune cells, or may induce cytokine production in some immune cells. Examples of immune cells include peripheral blood mononuclear cells (PBMC), granulocytes (CD 15+), monocytes, (CD 14+), T-lymphocytes (CD3+), T helper cells ( CD4+), cytotoxic T cells (CD8+), B lymphocytes (CD 19+, CD20+), dendritic cells and natural killer cells (CD 16+, CD56+).

[0091] Examples of adjuvants include, but are not limited to, poly IC/polyarginine (described in U.S. Patent Application 61/085,673), carboxymethylcellulose, poly-L-lysine, aluminium hydroxide, alum, aluminum trihydrate or other aluminium salts, virosomes, nucleic acids comprising CpG motifs, nucleic acids comprising both CpG motifs and locked nucleic acids (see, for example PCT Publication WO 2008/106803), squalene, oils, saponins, virus-like particles, monophosphoryl-lipidA/trehalose dicorynomycolate, toll-like receptor agonists or copolymers such as polyoxypropylene and polyoxyethylene.

[0092] hi some embodiments of the invention, the adjuvant composition may be a selective agonist for TLR9 or TLR3. Examples of such adjuvants include, but are not limited to, CpG- containing oligonucleotides, for example, CpG ODN 2395 from InvivoGen (a TLR9 agonist), A TLR3 agonist for example double-stranded RNA(dsRNA) or Poly I:C, Poly I:C with poly- L-lysine (po IyICLC) or poly I: C with polyarginine (described in U.S. Patent Application 61/085,673), mono-phosphoryl-lipid A (MPL; a TLR4 agonist) or MPL- trehalose 6,6'- dimycolate (MPL-TDM), and anti-CD-40.

[0093] Therefore, the invention provides for a composition comprising a fusion protein and an adjuvant, the fusion protein comprising a heat shock protein, or immunostimulatory portion thereof, and one or more Human Papillomavirus proteins, or immunogenic portions thereof.

[0094] Fusion proteins according to some embodiments of the invention may be used to prepare a pharmaceutical composition for administration to a subject. When such a pharmaceutical composition is administered to a subject in a suitable dosage regimen, the subject receives a therapeutically effective amount of the fusion protein.

[0095] Thee terms "subject" and "patient" may be used interchangeably. A "subject" refers to an animal, or a mammal, including, but not limited to, a mouse, rat, dog, cat, pig, or primate, including but not limited to a monkey, chimpanzee or human. The subject may be immunologically naive with respect to a particular immunogen or group of immunogens, or the subject may have been previously exposed to a particular immunogen or group of immunogens, for example by immunization or previous or existing infection.

[0096] Pharmaceutical compositions according to various embodiments of the invention may be formulated with any of a variety of pharmaceutically acceptable excipients or carriers, frequently in an aqueous vehicle such as Water for Injection, Ringer's lactate, isotonic saline or the like. Pharmaceutically acceptable excipients may include, for example, salts, buffers, antioxidants, complexing agents, tonicity agents, cryoprotectants, lyoprotectants, suspending agents, emulsifying agents, antimicrobial agents, preservatives, chelating agents, binding agents, surfactants, wetting agents, anti-adherents agents, disentegrants, coatings, glidants, deflocculating agents, anti-nucleating agents, surfactants, stabilizing agents, non-aqueous vehicles such as fixed oils, or polymers for sustained or controlled release. See, for example, Berge et al. (1977. J. Pharm Sci. 66:1-19), or Remington - The Science and Practice of Pharmacy, 21^st edition. Gennaro et al editors. Lippincott Williams & Wilkins Philadelphia (both of which are herein incorporated by reference).

[0097] The amount of a pharmaceutical composition administered, where it is administered, the method of administration, the nature of the subject (e.g., age, gender, health status) and the timeframe over which it is administered may all contribute to the observed effect. As an example, a composition may be administered systemically e.g., intravenous administration and have a toxic or undesirable effect, while the same composition administered subcutaneously may not yield the same undesirable effect. In some embodiments, localized stimulation of immune cells in the lymph nodes close to the site of subcutaneous injection may be advantageous, while a systemic immune stimulation may not.

[0098] Quantities and/or concentrations may be calculated on a mass/mass basis (e.g., micrograms or milligrams of fusion protein per kilogram of subject), or maybe calculated on a mass/volume basis (e.g., concentration, micrograms or milligrams of fusion protein per milliliter). Using a mass/volume unit, a fusion protein may be present at an amount from about 0.1 ug/ml to about 20 mg/ml, or any amount therebetween, for example 0.1, 0.5, 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160 180, 200, 250, 500, 750, 1000, 1500, 2000, 5000, 10000, 20000 ug/ml, or any amount therebetween; or from about 1 ug/ml to about 2000 ug/ml, or any amount therebetween, for example 1.0, 2.0, 5.0, 10.0, 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 50.0 60.0, 70.0, 80.0, 90.0, 1OQ 120, 140, 160 180, 200, 250, 500, 750, 1000, 1500, 2000, ug/ml or any amount therebetween; or from about lOug/ml to about 1000ug/ml or any amount therebetween, for example 10.0, 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 50.0 60.0, 70.0, 80.0, 90.0, 1OQ 120, 140, 160 180, 200, 250, 500, 750, 1000 ug/ml, or any amount therebetween; or from about 30ug/ml to about lOOOug/ml or any amount therebetween, for example 30.0, 35.0, 40.0, 50.0 60.0, 70.0, 80.0, 90.0, 1OQ 120, 140, 160 180, 200, 250, 500, 750, 1000 ug/ml.

[0099] An "effective amount" of a fusion protein as used herein refers to the amount of fusion protein required to achieve a therapeutic effect in the subject to whom it is administered. A therapeutic effect may include one or more than one of prevention of infection with a bacterial or viral pathogen, amelioration of infection caused by or associated with a bacterial or viral pathogen, reduction in size or elimination of one or more warts, growths, lesions or tumors caused by or associated with a bacterial or viral pathogen.

[00100] The effective amount may be calculated on a mass/mass basis (e.g., micrograms or milligrams per kilogram of subject), or may be calculated on a mass/volume basis (e.g., concentration, micrograms or milligrams per milliliter). Using a mass/volume unit, an immunogen may be present at an amount from about 0.1 ug/ml to about 20 mg/ml, or any amount therebetween, for example 0.1, 0.5, 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160 180, 200, 250, 500, 750, 1000, 1500, 2000, 5000, 10000, 20000 ug/ml, or any amount therebetween; or from about 1 ug/ml to about 2000 ug/ml, or any amount therebetween, for example 1.0, 2.0, 5.0, 10.0, 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 50.0 60.0, 70.0, 80.0, 90.0, 100, 120, 140, 160 180, 200, 250, 500, 750, 1000, 1500, 2000, ug/ml or any amount therebetween; or from about 10ug/ml to about 1000ug/ml or any amount therebetween, for example 10.0, 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 50.0 60.0, 70.0, 80.0, 90.0, 100, 120, 140, 160 180, 200, 250, 500, 750, 1000 ug/ml, or any amount therebetween; or from about 30ug/ml to about 1000ug/ml or any amount therebetween, for example 30.0, 35.0, 40.0,

50.0 60.0, 70.0, 80.0, 90.0, 1OQ 120, 140, 160 180, 200, 250, 500, 750, 1000 ug/ml. [00101] One of skill in the art will be readily able to interconvert such mass/mass or mass/volume units as necessary, given the mass of the subject, the concentration of the fusion protein, individual components of the pharmaceutical composition, or combinations thereof, or volume of the pharmaceutical composition, individual components of the pharmaceutical composition or combinations thereof, into a format suitable for the desired application.

[00102] Pharmaceutical compositions of the present invention may be administered by any suitable method, for example orally, intradermally, intranasally, intramuscularly, intraperitoneally, intravenously, or subcutaneously. The suitability of any particular method may depend upon the concentration and nature of the fusion protein and other components of the pharmaceutical composition, including but not limited to adjuvants, excipients and carriers.

[00103] Therefore, the present invention provides for a pharmaceutical composition comprising a fusion protein comprising heat shock protein protein, or immunostimulatory portion thereof, and one or more Human Papillomavirus (HPV) proteins, or immunogenic portions thereof, and a pharmaceutically acceptable carrier or excipient.

[00104] Therefore, the present invention further provides for a composition comprising

Hsp6/11, and methods of using such a composition. The composition may further comprise an adjuvant, such as a TLR agonist, and optionally other pharmaceutically acceptable ingredients.

[00105] Fusion proteins of the present invention may comprise one or more immunogens from bacterial or fungal pathogens, or viral pathogens. Other examples of immunogens include, but are not limited to a protein, a peptide, a fusion protein, a fusion peptide, a recombinant protein or recombinant peptide or an amino acid sequence comprising an antigen from bacterial, fungal or viral pathogens, or one or more than one fragment or portion thereof. Examples of bacterial, fungal or viral pathogens other than HPV include, but are not limited to, causative agents of the following diseases or disorders: papilloma, genital warts, influenza, hepatitis A, hepatitis B, hepatitis C, hepatitis D, hepatitis E, hepatitis G, Cytomegalovirus, Epstein,Barr virus, AIDS, AIDS Related Complex , Chickenpox (Varicella), tooth decay (e.g., Streptococcus mutans), Common cold , Cytomegalovirus Infection , Colorado tick fever, Dengue fever , Ebola haemorrhagic fever, Hand, foot and mouth disease, Hepatitis , Herpes simplex , Herpes zoster , human papillomavirus (HPV) , Influenza (Flu), Lassa fever , Measles , Marburg haemorrhagic fever , Infectious mononucleosis , Mumps , Poliomyelitis , Progressive multifocal leukencephalopathy , Rabies, Rubella , SARS, Smallpox (Variola) , Viral encephalitis , Viral gastroenteritis (e.g., Norwalk virus, Rotavirus and the like), Viral meningitis, fifth disease, Viral pneumonia , West Nile disease , Yellow fever, Anthrax , Bacterial Meningitis , Botulism , Brucellosis, Campylobacteriosis, Cat Scratch Disease, Cholera, Diphtheria, Epidemic Typhus, Gonorrhea, Impetigo, Legionellosis, Leprosy (Hansen's Disease), Leptospirosis, Listeriosis, Lyme Disease, Melioidosis, MRSA infection, Nocardiosis, Pertussis (Whooping Cough), Plague, bacterial pneumonia, fungal pneumonia, Pneumococcal pneumonia, Psittacosis, Q fever, Roseola, Rocky Mountain Spotted Fever (RMSF), Salmonellosis, Scarlet Fever, Shigellosis, Syphilis, Tetanus, Trachoma, Tuberculosis, Tularemia, Typhoid Fever, Typhus, urinary tract infections, aspergillosis, basidiobolomycosis, candidiasis, cryptococcosis, coccidioidomycosis, dermatophytosis, ringworm, histoplasmosis, fungemia, paracoccidioidomycosis, Pneumocystis pneumonia, and the like. Recombinant immunogens may be expressed using a recombinant expression system, for example bacterial, yeast, baculoviral, mammalian cell or plant expression system.

[00106] In some embodiments of the invention, an immunogen may be a tumor antigen, a tumor-derived antigen, or an antigen found in association with a cancer. The cancer may be associated with, or caused by a papillomavirus, for example a human papillomavirus.

[00107] In some embodiments of the invention, the immunogen may be a fusion polypeptide comprising polypeptide sequences from two or more viral pathogens, or two or more proteins from a single viral pathogen, or fragments or portions thereof.

[00108] The biological activity of fusion proteins, or compositions comprising fusion proteins, may be measured by any of several assays known in the art. Alternately, the immunostimulatory effect of an adjuvant in combination with an fusion protein according to some embodiments of the invention may also be assessed in a similar assay. Some aspects of biological activity may be indicative of induction of a cell-mediated cytolytic immune response, and thus indicate the suitability of the fusion protein or composition comprising the fusion protein as an inducer of a cell mediated cytolytic immune response.

[00109] For example, induction of antigen-specific CD8-positive T lymphocytes may be quantified through use of an ELISPOT assay (Asai et al 2000 Clin. Diag. Lab Immunol 7: 145-154). Other versions of an ELISPOT assay may be used for other cytokines, see, for example, Kalyzhny et al 2005. Methods MoI Biol 302:15-31; Ott, et al. J. Immunol. Methods. 2004 Feb 15; 285(2):223-35; Forsthuber, et al. Science, 271: 1728-1730. Other T-cell assays that may be useful for monitoring a response to an immunogen include intracellular cytokine flow cytometry, proliferation assays, antibody microarrays, and the like. See, for example Nagorsen et al 2004. Expert Opin Biol Ther 4: 1677-84, or Handbook of Experimental Immunology, VoIs. 1-IV, D. M. Weir and C. C. Blackwell, eds., 1986, Blackwell Scientific Publications. Interferon-α (alpha), β (beta) and γ (gamma) may be quantified, for example, with an Interferon ELISA kit (Kim et al 2004. Nature Biotechnology 22:321-325), or an ELISpot kit (R&D Systems Catalogue # EL485) Multiplexed assays, for example, bead-based systems (Luminex, Panomics and the like) allow for simultaneous quantification of a plurality of cytokines, and are available from various suppliers (e.g., R&D Systems, Millipore and the like). Examples of cytokines include IL- lα, IL-I β, IL-2, 11-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL- 10, IL- 12 (p70), IL-13, IL-15, IL-17, IL-18, IFNα (alpha), IFNβ (beta), IFNγ (gamma), GM- CSF, TNFα (alpha), G-CSF, MIP- lα (alpha) , MIP- Iβ (beta), MCP-I, EOTAXIN, RANTES, FGF-basic, VEGF and the like. For clarity, the term 'cytokine' includes alternative nomenclatures such as lymphokines, interleukins, or chemokines. Antigen-specific antibodies may be detected and/or quantified using any of several assays known in the art. Examples include ELISA, western blot, flow-cytometry or bead-based methods such as RapidQuant™ (Guava Technologies) or the like. Antibodies may be of several isotypes such as IgA, IgM, IgG, IgD and IgE, with particular isotypes being predominant in certain tissues, in response to type of pathogens (bacterial, viral, parasite or protozoan) and/or at certain stages in the immune response.

[00110] Biological activity, including cytokine production, may be assessed with regards to the subject as a whole (e.g., via a serum, blood or other fluid or tissue sample), or with regards to cells, or a particular cell type. The cells may be, for example, peripheral blood mononuclear cells (PBMCs) or particular immune cells, such as CD8+ cells or CD4+ cells.

[0011 1] Therefore, the invention provides for a composition for inducing a cell- mediated cytolytic immune response to a human papillomavirus in a mammal, the composition comprising a fusion protein comprising heat shock protein protein, or immunostimulatory portion thereof, and one or more Human Papillomavirus (HPV) proteins, or immunogenic portions thereof.

[00112] Immunostimulatory agents are compounds or compositions that initiate an immune response, or provide a catalytic effect in initiating an immune response. The immune response may be solely an innate (or non-adaptive) immune response, such as inducing the production and secretion of cytokines (for example interferons, interleukins, colony stimulating factors and the like) which in turn incite phagocytic cells to migrate and ingest foreign immunogens nonspecifϊcally and present the immunogens for recognition by the adaptive immune system. Alternatively, the immune response may be an adaptive immune response, in response to the presence of particular immunogens (such as those presented by an phagocytic cell, also referred to as an antigen-presenting cell).

[00113] An "immune response" generally refers to a response of the adaptive immune system. The adaptive immune system generally comprises a humoral response, and a cell- mediated response. The humoral response is the aspect of immunity that is mediated by secreted antibodies, produced in the cells of the B lymphocyte lineage (B cell). Secreted antibodies bind to antigens on the surfaces of invading microbes (such as viruses or bacteria), which flags them for destruction. Humoral immunity is used generally to refer to antibody production and the processes that accompany it, as well as the effector functions of antibodies, including Th2 cell activation and cytokine production, memory cell generation, opsonin promotion of phagocytosis, pathogen elimination and the like. The terms "modulate" or "modulation" or the like refer to an increase or decrease in a particular response or parameter, as determined by any of several assays generally known or used, some of which are exemplified herein.

[00114] A cell-mediated response is an immune response that does not involve antibodies but rather involves the activation of macrophages, natural killer cells (NK), antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen. Cell-mediated immunity is used generally to refer to some Th cell activation, Tc cell activation and T-cell mediated responses. Cell mediated immunity is of particular importance in responding to viral infections.

[00115] For example, the induction of antigen specific CD8 positive T lymphocytes may be measured using an ELISPOT assay; stimulation of CD4 positive T-lymphocytes may be measured using a proliferation assay. Specific antibody titres may be quantified using an ELISA assay; isotypes of antigen-specific or cross reactive antibodies may also be measured using anti-isotype antibodies (e.g., anti - IgG, IgA, IgE or IgM). Methods and techniques for performing such assays are well-known in the art.

[00116] Cytokine presence or levels may also be quantified. For example a T-helper cell response (Thl/Th2) will be characterized by the measurement of IFN-γ and IL-4 secreting cells using by ELISA (e.g., BD Biosciences OptEIA kits). Peripheral blood mononuclear cells (PBMC) or splenocytes obtained from a subject may be cultured, and the supernatant analyzed. T lymphocytes may also be quantified by fluorescence-activated cell sorting (FACS), using marker specific fluorescent labels and methods as are known in the art.

[001 17] A microneutralization assay may also be conducted to characterize an immune response in a subject, see for example the methods of Rowe et al., 1973. Virus neutralization titers may be obtained several ways, including: 1) enumeration of lysis plaques (plaque assay) following crystal violet fixation/coloration of cells; 2) microscopic observation of cell lysis in culture; 3) ELISA and spectrophotometric detection of a specific virus protein or proteins (correlate with virus infection of host cells), for example, Ll, L2, El, E2, D4, E5, E6 and/or E7 HPV proteins.

[00118] A murine tumor cell line TC-I expressing HPV E7, may be used as a model of

HPV-associated carcinoma. Tumor regression in response to administration of one or more fusion proteins according to the present invention may be determined using an assay comprising a TC-I cell line stably transfected with HPVE6, HPVE7, HPV E6 and E7, HPV E2 and E6, HPV E2 and E7, or HPV E2, E6 and E7. The transfected TC-I cells maybe implanted in C57BL/6 mice, and followed by injection of one or more than one fusion proteins or controls 7 days later. Tumor development (growth, regression or maintenance) is monitored. Examples of similar experiments are described by Chu N. R., et. al. (Chu N. R. et al., 2000, CHn Exp Immunol 121 (2):216-225).

[00119] In some embodiments of the invention, an immunogenic fragment or portion of the E2 HPV protein may induces CD8 positive T lymphocytes; examples of such fragments or portions include SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40 SEQ ID NO: 49, or SEQ ID NO: 50, or a portion or fragment thereof; or SEQ ID NO: 32, or a portion or fragment thereof; or some or all of amino acids 181-200 of SEQ ID NO: 44, or a portion or fragment thereof.

[00120] In some embodiments of the invention, the fusion protein comprising an immunogenic fragment or portion of the E6 HPV protein may induces CD8 positive T lymphocytes; examples of such fragments or portions include SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 or SEQ ID NO: 14, or a portion or fragment thereof; or SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO: 10 or SEQ ID NO: 14, or a portion or fragment thereof; or some or all of amino acids 1-150 of SEQ ID NO: 42, or a portion or fragment thereof.

[00121 ] hi some embodiments of the invention, the fusion protein comprising an immunogenic fragment or portion of the E7 HPV protein may induces CD8 positive T lymphocytes; examples of such fragments or portions include SEQ ID NO: 15, SEQ ID

NO:16, SEQ ID NO:17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, or SEQ ID NO: 22, or a portion or fragment thereof; or SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 or SEQ ID NO: 18, or a portion or fragment thereof. In some embodiments, the immunogenic fragment of the E7 HPV polypeptide may comprise some or all of amino acids 1-80 of SEQ ID NO: 43, or a portion or fragment thereof.

[00122] hi some embodiments of the invention, the fusion protein comprising an immunogenic fragment or portion of the E2 HPV protein may induce CD4 positive T lymphocytes; examples of such fragments or portions include SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40 SEQ ID NO: 49, or SEQ ID NO: 50, or a portion or fragment thereof; or SEQ ID NO: 32, SEQ ID NO: 49, SEQ ID NO: 50, or a portion or fragment thereof, hi some embodiments the immunogenic fragment of the E2 HPV polypeptide may comprise some or all of amino acids 181 -200, or some or all of amino acids 31 1 -350 of SEQ ID NO: 44, or a portion or fragment thereof.

[00123] hi some embodiments of the invention, the fusion protein comprising an immunogenic fragment or portion of the E6 HPV protein may induce CD4 positive T lymphocytes; examples of such fragments or portions include SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 or SEQ ID NO: 14, or a portion or fragment thereof; or SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 12, SEQ ID NO: 13 or SEQ ID NO: 14, or a portion thereof, hi some embodiments, the immunogenic fragment of the E6 HPV polypeptide may comprise some or all of amino acids 1-150 of SEQ ID NO: 42, or a portion or fragment thereof.

[00124] Therefore, the invention provides for a fusion protein comprising a heat shock protein or immunostimulatory portion thereof, and one or more HPV proteins or immunogenic portion thereof, wherein the one or more immunogenic portions induce a CD4 positive lymphocyte response, or a CD8 positive lymphocyte response, or a CD4 positive lymphocyte response and a CD8 positive lymphocyte response.

[00125] Table 1 : Summary table of sequences and SEQ ID NOs.

[00126] ANALYTICAL METHODS

[00127] Wet and dry cell weight, and optical density were determined using standard methods.

[00128] Quantitation using SDS-PAGE. Samples of well-mixed fresh culture were centrifuged to obtain cell pellets which were processed immediately or stored frozen pending analysis. Samples and standards were mixed with NuPAGE LDS Sample Buffer (Invitrogen LC2676) and NuPAGE Reducing Agent (Invitrogen NP004) (65 uL sample, 25 uL of sample buffer, and 10 uL of reducing agent). The samples were boiled for 10 minutes and centrifuged in a microfuge for 3 minutes before applying to the gel. NuPAGE Bis-Tris 4-12 % Gels (Invitrogen NP0322) were used, with MES Running buffer (Invitrogen NP002). Gels were run using the NuPAGE Gel programme and stained using Coomassie G-250 (Invitrogen SimplyBlue Safestain). Gels were scanned by densitometry.

[00129] Microbiological purity.

[00130] Samples of fresh culture were analysed by microscopic examination of stained slides and visual inspection of colonial morphology on agar plates.

[00131] Example 1: Construction of Hsp6/ll Expression vector

[00132] The coding sequence for Hsp6/11 (SEQ ID NO: 45) was codon optimized and synthesized with flanking Nde I and Xho I sites by DNA2.0.

[00133] The plasmids were digested with Nde I (New England Biolabs, Catalogue

ROl 1 IS) and Xho I (New England Biolabs, Catalogue RO 1463). The pAVEway™ vectors (Avecia Biologies Limited, described in PCT Application No. PCT/GB2007/000351) were digested with the same enzymes. The three reaction mixes were run on 1% Low Melting Point (LMP) agarose (Sigma Catalogue A9414) gel for 40 minutes at 100 V. After electrophoresis the relevant bands were cut from the gel with a scalpel and recovered from the gel fragments using a Qiaexll gel extraction kit (Qiagen, Catalogue 20021, Lot 12190118). The fragment was ligated to pAVEway™ using the NEB (New England Biolabs) Quick Ligation™ kit (Catalogue #M2200S) and transformed into XL-I Blue MR (Stratagene, Catalogue 200229), plated onto Luria Agar (+tet,) and grown at 37°C overnight. Single colonies were picked into 5mL Luria broth (+tet,) and grown overnight prior to plasmid miniprep (Qiaprep minispin kit Qiagen, Catalogue 27106, lot 12106620). Plasmid DNA was digested with Nde I and Xho I to screen for presence of the insert. One clone from each ligation was transformed by electroporation into host strain BL21. [00134] The Hsp6/11 expressed polypeptide (802 amino acids; SEQ K) NO: 45) had a calculated molecular weight of 89402.65 Da; an Average Residue Weight of 11 1.475 Da; an Isoelectric Point of 6.4703; an A_28O Molar Extinction Coefficient of 98430; and an A₂₈₀ Extinction Coefficient at 1 mg/ml = 1.10. Details of the strains are provided in Table 2.

[00135] Table 2: Recombinant Strains, hosts and plasmids

[00136] A 250ml baffled flask containing 50ml LB with Tet antibiotic (10 ug/ml final concentration) was inoculated with a single colony from the transformed plates from 3.3. The flasks were incubated at 37oC, 200 rpm overnight for approx 16 hrs. The following morning ODs were taken (OD600) and the flasks harvested. Each flask was aliquoted into two 50ml centrifuge tubes and spun down at 4000 rpm for 15mins at 4⁰C. Pellets were resuspended in 1/4 of the original volume (12.5ml) of fresh culture medium without antibiotic and pooled into a sterile 250ml flask containing magnetic stirrer. An equal volume of Glycerol (12.5ml) was added to the flask and mixed gently. 1.0ml aliquots dispensed into 25 Cryovials and the vials frozen at -70⁰C.

Example 2: Growth of recombinant strains

[00137] Cells were grown at 37⁰C overnight with agitation (200 rpm) in LB+ 10 ug/ml tetracycline. 50 ul of overnight culture was transferred to 50 ml of LB+ 10 ug/ml tetracycline, and grown to mid log phase. IPTG was added to a final concentration of ImM to the culture to induce expression from the Hsp6/11 vector. Samples were taken at 0-4 and 20 hours post- induction for analysis of biomass and protein expression (Table 3). [00138] Table 3: Data from CLD209 and CLD210 strains in shake flask culture.

[00139] In the shake flask experiment the 3h and 20h samples were analysed by SDS-

PAGE. The samples were prepared with Bugbuster™ protein extraction solution from Novagen follow the manufacture recommendation. This determines whether the HSP6/11 is in the soluble or insoluble fraction. The HSP6/11 protein has a MW of -90KDa. In Figure 3a the CLD209 strain shows a low level protein band in the insoluble fraction (Lane 7, 9) around 90 KDa region. The protein accumulation correlated with the grow curve, whilst the higher amount of IPTG concentration has negative effect. A similar analysis was performed for the CLD210 strain (Figure 3b). The CLD210 strain was selected for further fermentation and purification studies.

Example 3: Expression and Purification of Hsp6/ll

[00140] Fermentation of HSP6/11 for large scale purification.

[00141] Inocula for fermenters were grown in shake flasks containing an LB type liquid medium supplemented with glucose and tetracycline. The cultures were incubated overnight at 37⁰C with agitation then transferred to a 15 L fermentor containing a glycerol-salts growth medium supplemented with yeast extract and tetracycline. The cultures were grown with agitation at 37°C and pH 7.0, maintained by automatic titration with ammonium hydroxide and/or ortho-phosphoric acid. Gas flow rate was maintained at 1 wm. The DO was maintained at or above 30% of saturation by adjusting agitator speed and/or oxygen content of the inlet gas stream. At the end of batch growth a glycerol/magnesium sulphate feed solution was introduced. Induction of the target protein was achieved by adding IPTG to a final concentration of 0.5 mM when the OD₆₀₀ had reached 50 Au. After a further 12 h the culture was harvested and centrifuged to recover the cell paste.

[00142] Homogenisation, IB isolation and IB solubilisation

[00143] The cell pellet was resuspended in 5L chilled Buffer B. Using an Ultraturrax mixer the cells were suspended and loaded into the homogenizer (Niro Soavi Panda). The pressure was 950-1050 bar under 2 passes. The IB was isolated by centrifugation, using the same conditions as the cell harvesting. The IB was solubilised overnight at room temperature in Buffer B solution at gentle agitation using a magnetic stirrer. The SDS gel data in Figure 5 shows no HSP6/11 product in the supernatant of the homogenate, with all HSP6/11 in the inclusion body. After solubilisation a centrifuge was used to clarify the IB (15000 x g 20 minutes). No product was seen in the pellet fraction in lane 8. The pellet was large gel type material. The solubilised IB was filtered by Sartorius sartopure 3 um filter. A lO L fermentor yielded -300 g of wet IB.

[00144] IMAC Chromatography

[00145] For metal affinity chromatography GE IMAC FF resin was packed into a

BPGIOO column (GE LifeSciences) to 1 L bed volume. The resin was charged with 100 mM NiSO₄.

[00146] The chromatography method: 5 CV water wash, 3 CV equilibration Buffer B20, 4.5 CV Load (B20), 2CV post load wash high salt Buffer B20, 2CV post load wash low salt C20, 5CV Elution 0-2CV linear gradient C20-C300, 5CV water wash, 50 ml fractions were collected. [00147] A full scale chromatogram is shown in Figure 6. The fractions were collected manually and analyzed by SDS-PAGE. The results are shown in Figure 7 A-D.

[00148] For further IEX purification, fractions 1-11 and 14-30 were pooled; fractions

12 and 13 exhibited aberrant impurities and were omitted.

[00149] Q-Sepharose purification

[00150] An XK26 column was packed with GE Q-Sepharose FF at bed volume of 100 ml. The method for chromatography: -2 CV high salt wash buffer B, -5 CV low salt wash and equilibrate Buffer C20. -15 CV load, -3 CV post load wash Buffer C, -12 CV elution lOCV gradient 0-100% Buffer C - Buffer B, -15 ml fractions collected. Figure 8 shows a representative chromatograph of the elution profile of the Q-sepharose column.

[00151 ] A large amount of material flowed through the resin. In the post load wash the pH dropped due to incorrect pH setting of Buffer C, therefore the bound material started to elute from the column. The program was stopped, and the buffer changed to the correct pH and the chromatography continued. In the salt gradient one peak eluted. All these fractions were analyzed by SDS-PAGE. The results are shown in Figure 9. In gel A in lane 3 a large amount of material did not bind to the column. In that gel lane 9 and 10 are the peak area of the pH drop elution. There is a 25KDa protein band which co-eluted with HSP6/11. Gel B represent the very sharp second peak area with more pure HSP6/11 product. In gel C we can see the fractions around the peak which eluted by salt gradient. Because a large amount of protein did not bind to the Q Sepharose, we repeated the run and loaded the flow through again to the same column.

[00152] Second Q-Sepharose purification

[00153] The flow through fraction from the first Q sepharose purification was re-loaded onto the Q-sepharose column, and the separation repeated. Peak fractions were analyzed by SDS-PAGE (Figure 10). The majority of the Hsp6/11 product is found in fractions 40-41 (-30 ml volume). [00154] In summary, the target concentration was less than 1-2 mg/ml Hsp6/11. IMAC fractions 12 and 13 were pooled (-100 ml volume); concentration of this sample was ~0.9 mg/ml. First and second Q sepharose elution fractions were -60 ml; with a concentration was -0.3-0.4 mg/ml. The second Q sepharose purification flow through was -1.5 L; with a concentration of -0.2 mg/ml. (Table 4).

[00155] Table 4: Concentration and volume of the final samples.

A280 Extinction Coefficient 1 mg/ml = 1.10

[00156] All pooled fractions were diluted 2x with 5OmM Tris pH 7.5 and concentrated to approximately 1/10 of the original volume. The IMAC and Q sepharose elution fractions were concentrated by Millipore Amicon Ultra 1 K concentrator; the Q sepharose flow through was concentrated by Millipore TFF system, using Pellicon XL filter with 5K cut off range.

[00157] After concentration the samples were analyzed by SDS-PAGE and A280 measurement. The SDS-PAGE data is shown in Figure 11, and the A280 data in Table 5. No material was found in the permeate following concentration.

[00158] Table 5: Summary of product concentration

[00159] Protein Identification IMAC Fraction 12 from the large scale purification demonstrated two major bands of -90 kDa and -25 kDa. These bands were N-terminally sequenced and fingerprinted by LC/MS/MS.

[00160] The -25 kDa band yielded an N terminal sequence of MKVAKDLWS (SEQ

ID NO: 47). This is indicative of a host strain protein, FKBP-type peptidyl -prolyl cis-trans isomerase.

[00161 ] The -90 kDa band yielded an N terminal sequence of AKTIA YDEEA (SEQ

ID NO: 48), corresponding to residues 2-1 1 of the sequence of the Hsp6/1 1 polypeptide (SEQ ID NO: 46) encoded by SEQ ID NO: 45. This sequence information, in combination with the observed and predicted MW of the Hsp6/11 protein identified this band as the Hsp6/11 protein.

[00162] Further LC/MS/MS fingerprints confirm the results of N-terminal sequencing, as several peptides were identified in this band corresponding to as human papillomavirus protein and heatshock protein from the 90 KDa band.

[00163] LC/MS/MS fingerprinting of the 25 kDa band confirmed the N-terminal sequencing results.

[00164] Endotoxin level determination

[00165] The three concentrated samples in Table 5 were assessed for endotoxin content, and found to comprise > 2500 EU/ml. Following filtration with Pall Mustang E endotoxin removal membrane, the endotoxin content was assessed, but this had little effect on the observed concentration. Buffer control yielded -0.25 EU/ml, suggesting that the HSP6/11 protein or one of the contaminant proteins copurifying with the Hsp6/1 1 is associated with endotoxin activity.

[00166] Another possibility that the HSP6/11 causes a false positive result. Without wishing to be bound by theory, this may be the more likely explanation, as the purification method employed to obtain the Hsp6/11 expressed protein (IMAC and 2x Q-sepharose IEX ) is expected to remove endotoxins and provide a low level of endotoxin in the final sample, even without use of an endotoxin removal membrane.

[00167] Each of the three fractions yielded Hsp6/ 11 at -70 % purity.

[00168] Therefore, the novel protein (Hsp6/11) was successfully cloned and expressed, and may be purified from inclusion bodies. A 1OL fermentation platform provided a final overall yield of- 4g/L.

Example 4: Preparation of mice splenocytes and Flt3L-mobilized DCs

[00169] Hsp6/11 is a fusion protein (SEQ ID NO: 46) comprising SEQ ID NOs: (41, 42, 43 and 44). A TLR3 agonist (PolyIC/R) and TLR9 agonist (CpG/ODN2395; (InvivoGen Cat # tlrl-odnc) were used in the immunization protocols

[00170] To determine if co-immunization of Hsp6/11 with PolyIC/R and CPG will augment the ability of a heat shock protein, or a portion of a heat shock protein to induce T- cell response, female C57BL/6 mice (7 to 8 weeks old) were immunized subcutaneously on the scruff at the back of the neck with the following combinations (total volume of 200 ul per mouse):

1. CpG ODN 2395 (InvivoGen Cat # tlrl-odnc) (100μg/100μl) + Hsp6/1 1

(lOOμg/lOOμl).

2. PolyIC/R (100 μg/lOOμl) + Hsp6/1 1 (lOOμg/lOOμl). [00171] Immunized mice were sacrificed and spleens were removed 7 and 14 days after immunization. Spleens were placed in 15 ml RPMI 1640 with 10% FBS, kept on ice until ready to prepare single cell suspension.

[00172] Table 6: Culture media for splenocytes

[00173] Single cell suspension of spleen was obtained by pushing the spleen with the plunger of a 5 ml syringe through a 100 μm nylon mesh (Falcon Cat # 2360) into 10 ml of splenocytes media (Table 6) contained in a petri dish. Cell suspensions were rinsed through the mesh a couple of times and placed into a 50-ml centrifuge tube. The screen was rinsed again with 20 ml of media, and cells were pooled into the centrifuge tube for a total volume of 30 ml cell suspension.

[00174] Cells were centrifuged at 1200 rpm for 5 minutes. Supernatant were aspirated off and then cells were resuspended in 30 ml of media as a second wash. Cells were centrifuged again at 1200 rpm for 5 minutes. The second wash was aspirated off.

[00175] Before counting the total number of lymphocytes in spleen cells suspension,

RBC depletion was accomplished by resuspending pellet of spleen cells in lysing buffer (Gibco cat # 1821) using 5 ml per spleen. Cells were incubated with lysing buffer for 5 minutes at RT with occasional shaking. Media was added to fill the tube to 50 ml then cells were spun down in a low-speed centrifuge at 1200 rpm for 10 minutes. The supernatant were discarded. This washing was performed twice. After washing, the cells were resuspended in 1 ml of splenocytes media and live cells were counted by trypan blue exclusion method. Cell requirement were calculated using cell density of 2.5x10⁵ splenocytes per well.

[00176] An appropriate number of vials of Flt3L-mobilized dendritic cells was removed from liquid nitrogen. One complete 96-well plate requires approximately Ix 10⁷ Flt3L-mobilized DCs or IxIO⁵ cells per well. Cells were thawed in a 37⁰C water bath until ice crystals are no longer visible. The outside of the vial was wiped with 70% isopropyl alcohol or ethanol and then aseptically transferred into a 50 ml centrifuge tube. While gently agitating the cell suspension, 9 ml of cold RPMI culture medium was added per vial then the cells were pelleted at 1000 rpm for 10 minutes in room temperature. Supernatant were aspirated off and the cells were dislodged by flicking the tube with fingers, and then resuspended in 4 ml of cold RPMI culture media per vial thawed. Cell count was determined using trypan blue exclusion procedure. For each 96-well plate, prepare IxIO⁷ Flt3L-moblized DCs plus 2.5xlO⁷ splenocytes in 10 ml of cold RMI media.

[00177] Culture media were added at 100 μl per well to all the wells on the plate.

Peptides (stock concentration of 10mg/ml) were further diluted by adding 1 ul of each peptide per well, done in duplicate; amino acid sequences of the peptides are provided in Table 1. Location of Hsp6/11 peptides was shown on the plate map (Figure 1). Cells were then added at 100 ul giving a total volume of 200μl per well. Plates were incubated overnight in a humidified 37⁰C CO₂ incubator.

[00178] HPV6 and 11 peptide pools

[00179] The E2, E6 and E7 proteins of HPV6 are 86% identical with HPVl 1 compared to 56% with HPV 16. The HPV6 E6 (SEQ ID NO: 42) and E7 (SEQ ID NO: 43) amino acid sequence were the basis for the synthesis of 20mer peptides overlapping by 10 amino acids (Synthetic Biomolecules, San Diego, CA). The 20mer peptides (non-overlapping) for E2 were synthesized (Synthetic Biomolecules, San Diego, CA) based on the E2 protein sequence ofHPV6 (SEQ ID NO: 44).

[00180] Individual peptides were solubilized in dimethyl sulphoxide (DMSO) or dimethylformamide (DMF) to provide 10 mg/ml stock solutions and were frozen in small aliquots then stored at -8O⁰C freezer for storage.

[00181 ] A set of HP V6 E2 ( 18 peptides), HP V6 E6 ( 14 peptides) and HPV6 E7 peptides were indicated by the first and last amino acids in the protein of E2, E6 or E7, i.e. first residues E2i_-2o, E6i_₂₀, E7j_-2o and last residues E2341.360, E613M50 and E7si-9₈, respectively (SEQ ID NO: 1-40, Table 1). These peptides were used for the screening of CD4⁺ and CD8⁺ T-cell responses by determining the amount of IFN-gamma secreted by the cells.

[00182] Example 5: Identification of T-cell type producing IFN-gamma using

ELISA assay

[00183] IFN-gamma producing HPV-specific T cells were quantified using ELISA assay (Peprotech Cat # 900-K98).

[00184] Capture antibody ( 100 μg of antigen-affinity purified rabbit anti-mIFN-gamma) were reconstituted in 1 ml sterile water for a concentration of 100ug/ml. It was then diluted with PBS to a working concentration of 1 μg/ml. Maxisorp ELISA plates were coated with 100 ul of the diluted capture antibody. The plates were sealed and incubated at room temperature for at least 2 hours or at 4⁰C overnight. The liquid were then removed from the wells and the plates were washed 4 times using 300 ul of wash buffer (0.05% Tween-20 in PBS) per well. After each wash, the plates were blotted on absorbent paper to remove residual buffer. About 300 ul of block buffer (1% BSA in PBS) were added to each well. Plates were sealed and incubated for at least 1 hour at room temperature or at 4⁰C overnight. After the blocking time was achieved, the plates were washed with wash buffer for four (4) times. [00185] Supernatants from each well were harvested and 100 μl added in triplicate to the pre-coated ELISA plates. The plates were sealed and incubated at room temperature for 1 to 2 hours. The liquid were then aspirated off and plates were washed with wash buffer for four (4) times.

[00186] Detection antibody (biotinylated antigen-affinity purified rabbit anti-mlFN- gamma) was reconstituted in 0.25 ml sterile water for a concentration of 100ug/ml. It was then diluted in diluent (0.05% Tween-20, 0.1% BSA in PBS) to a concentration of 0.25 μg/ml, and 100 ul were added per well. Plates were sealed and incubated at room temperature for 1 to 2 hours. The liquid were then aspirated off and plates were washed with wash buffer for four (4) times.

[00187] Avidin-HRP conjugate were diluted to 1 :2000 by adding 5.5 μl into 1 1 ml of diluent buffer and 100 μl were added per well. Plates were sealed and incubated at room temperature for 20 to 30 minutes. The liquid were then aspirated off and plates were washed with wash buffer for four (4) times.

[00188] ABTS liquid substrate (2,2'-Azino-Bis(3-ethylbenzthiazoline-6-sulfonic acid) was then added at 100 μl per well. Plates were incubated at room temperature for color development for about 5 to 10 minutes. Stop solution (1% SDS) were then added at 100 μl per well. Plates were read using an ELISA plate reader at 450 nm.

[00189] ELISA results indicated that peptides E6 1 -20, E6 11 -30, E6 21 -40, E6 31 -50, E641-60, E6 51-70, E6 61-80, E6 71-90, E6 81-100, E6 91-110, E6 111-130, E6 121-140, E6 131-150, E7 1-20, E7 11-30, E7 21-40, E7 31-50, E2 181-200, E2 311-330 and E2 331-350 stimulated secretion of IFN-gamma from isolated splenocytes. ELISA results were confirmed with ELISPOT.

[00190] Example 6: ELISPOT Assay of IFN-gamma Release

[00191] The mouse IFN-gamma ELISPOT assay (R&D Systems Cat # EL485) is designed for the detection of IFN-gamma secreting cells at the individual single cell level and can be used to quantitate the frequency of mouse IFN-gamma secreting cells. It employs the quantitative sandwich enzyme-linked immunosorbent assay (ELISA) technique.

[00192] A monoclonal antibody specific for mouse IFN-gamma had been pre-coated onto a PVDF (polyvinylidene diflouride)-backed microplate. Culture media were added at 100 μl per well to all the wells on the plate. One microlitre of E6, E7 or E2 peptides (stock concentration of 10mg/ml) were added to the wells (in duplicate) according to the plate map (Figure 1). A single cell suspension of mice splenocytes and CDl Ic⁺ cells were subsequently loaded into the microplate at cell density per well of 1 x 10⁵ and 2.5xlO⁵ cells, respectively. The microplate was placed into a humidified 37⁰C CO₂ incubator overnight. After washing, a biotinylated polyclonal antibody specific for mouse IFN-gamma was added to the wells. Following a wash to remove any unbound biotinylated antibody, alkaline-phosphatase conjugated streptavidin was added. Unbound enzyme was subsequently removed by washing and a substrate solution (BCIP/NBT) was added. A blue-black colored precipitate formed at the sites of the cytokine localization and appeared as spots, with each individual spot representing an individual IFN-gamma secreting cell. The spots were counted with an automated ELISPOT reader system using a stereomicroscope. Number of spots per well is shown on the ELISA plate map (Figure 2).

[00193] The E6 peptides comprising some or all of amino acids 1-110 and 131 - 150 demonstrated a significant number of spots, relative to controls.

[00194] The E6 131-150 peptide comprises an epitope that stimulates IFN-gamma secretion in the mouse splenocytes. As the E6 121-140 peptide does not result in similar stimulation, it may be deduced that one or more stimulatory epitopes comprise at least some or all of amino acids 141-150. Alternately, one or more stimulatory epitopes may comprise a larger fragment or portion of the E6 polypeptide.

[00195] The E7 peptides comprising amino acids 1-50 demonstrated a significant number of spots, relative to controls. [00196] The E2 peptides comprising amino acids 181 -200 demonstrated a significant number of spots, relative to controls.

[00197] Example 7: ELISPOT assay of CD4+ and CD8+ lymphocytes

[00198] Splenocytes isolated from immunized or control mice as described were obtained. CD4 positive and CD8 positive lymphocytes were separated out and assayed for IFN-gamma secretion by ELISPOT as described.

[00199] Peptides that specifically stimulated CD8 positive lymphocytes to secrete IFN- gamma included E6 1-20, E6 21-40, E6 31-50, E6 41-60, E6 61-80, E6 71-90 and E6 91-110.

[00200] Peptides that specifically stimulated CD4 positive lymphocytes to secrete IFN- gamma included E6 51-70, E6 61-80, E6 11 1-130, E6 121-140, E6 131-150 E2 181-200, E2 311-330 and E2 331-350.

[00201 ] All citations are herein incorporated by reference.

[00202] One or more currently preferred embodiments have been described by way of example. It will be apparent to persons skilled in the art that a number of variations and modifications can be made without departing from the scope of the invention as defined in the claims.

Claims

WHAT IS CLAIMED IS:

I . A fiision protein comprising a heat shock protein, or immunostimulatory portion thereof, and two or more human papillomavirus (HPV) polypeptides, or immunogenic portions thereof.

2. The fusion protein of claim 1 wherein the heat shock protein or immunostimulatory portion thereof, comprises SEQ ID NO: 41.

3. A fusion protein comprising the sequence of SEQ ID NO: 46.

4. A composition comprising the fusion protein of claim 1.

5. A nucleic acid encoding the fusion protein of claim 3.

6. An expression vector comprising the nucleic acid of claim 4.

7. A cell comprising the expression vector of claim 6.

8. A method of making a fusion protein, the method comprising:

a. providing the cell of claim 7 and

b. culturing the cell under conditions that permit expression of the nucleic acid.

9. The composition of claim 4 further comprising an adjuvant.

10. The composition of claim 9 wherein the adjuvant is a TLR3 agonist or a TLR9 agonist.

I I . A composition for inducing a cell-mediated cytolytic immune response to a human papillomavirus (HPV) in a mammal, the composition comprising two or more HPV polypeptides, or portions thereof, and a heat shock protein, or immunostimulatory portion thereof.

12. A fusion protein for inducing a cell-mediated cytolytic immune response to a human papillomavirus (HPV) in a mammal, the fusion protein comprising two or more HPV polypeptides, or one or more portions thereof, and a heat protein, or immunostimulatory portion thereof.

13. The fusion protein of claim 1, wherein the two or more HPV polypeptides, or immunogenic portions thereof are selected from the group consisting of HPV E2, HPV E6 and HPV E7.

14. The fusion protein of claim 13, wherein the two or more HPV polypeptides, or immunogenic portions thereof are selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18,

SEQ ID NO: 32, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 49 and SEQ ID NO: 50.

15. The composition of claim 1 1, wherein the cell-mediated cytolytic immune response comprises CD8+ lymphocyte stimulation.

16. The composition of claim 1 1, wherein the cell-mediated cytolytic immune response comprises CD4+ lymphocyte stimulation.

17. The composition of claim 1 1, wherein the two or more HPV polypeptides, or immunogenic portions thereof are selected from the group consisting of HPV E2, HPV E6 and HPV E7.

18. The composition of claim 17, wherein the two or more HPV polypeptides, or immunogenic portions thereof are selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 32, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 49 and SEQ ID NO: 50.

19. The fusion protein of claim 12, wherein the cell-mediated cytolytic immune response comprises CD8+ lymphocyte stimulation.

20. The fusion protein of claim 12, wherein the cell-mediated cytolytic immune response comprises CD4+ lymphocyte stimulation.

21. The fusion protein of claim 12, wherein the two or more HPV polypeptides, or immunogenic portions thereof are selected from the group consisting of HPV E2, HPV E6 and HPV E7.

22. The fusion protein of claim 21, wherein the two or more HPV polypeptides, or immunogenic portions thereof are selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7,

SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 32, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 49 and SEQ ID NO: 50.