WO2007041432A2 - Cross-neutralization of hcv with recombinant proteins - Google Patents

Cross-neutralization of hcv with recombinant proteins Download PDF

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Publication number
WO2007041432A2
WO2007041432A2 PCT/US2006/038315 US2006038315W WO2007041432A2 WO 2007041432 A2 WO2007041432 A2 WO 2007041432A2 US 2006038315 W US2006038315 W US 2006038315W WO 2007041432 A2 WO2007041432 A2 WO 2007041432A2
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hcv
composition
polypeptide
envelope polypeptide
polypeptides
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PCT/US2006/038315
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French (fr)
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WO2007041432A3 (en
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Michael Houghton
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Novartis Vaccines And Diagnostics, Inc.
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Publication of WO2007041432A3 publication Critical patent/WO2007041432A3/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • A61K39/29—Hepatitis virus
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/24011—Flaviviridae
    • C12N2770/24211—Hepacivirus, e.g. hepatitis C virus, hepatitis G virus
    • C12N2770/24222—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/24011—Flaviviridae
    • C12N2770/24211—Hepacivirus, e.g. hepatitis C virus, hepatitis G virus
    • C12N2770/24234—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Definitions

  • the present invention pertains generally to immunogenic compositions comprising HCV immunogenic polypeptides that cross-neutralize the infectivity of multiple HCV genotypes.
  • the invention relates to compositions comprising HCV envelope polypeptides that cross-neutralize the infectivity of HCV genotypes selected from HCV-I, HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6.
  • HCV Hepatitis C virus
  • HCV has a 9.5 kb positive-sense, single-stranded RNA genome and is a member of the Flaviridae family of viruses. At least six distinct, but related genotypes of HCV, based on phylogenetic analyses, have been identified (Simmonds et al., J. Gen. Virol (1993) 74:2391-2399).
  • the virus encodes a single polyprotein having about 3000 amino acid residues (Choo et al., Science (1989) 244:359-362: Choo et al., Proc. Natl Acad. ScL USA (1991) 88:2451-2455; Han et al., Proc. Natl Acad. Sci. USA (1991) 88:1711-1715).
  • several proteins are encoded by the HCV genome.
  • the order and nomenclature of the cleavage products of the HCV polyprotein is as follows: NH 2 -C-El-E2- ⁇ 7-NS2-NS3-NS4a-NS4b-NS5a-NS5b- COOH.
  • Another protein (F) has also been identified and results from translational frame-shifting within the C gene. Branch et al., Semin. Liver Dis. (2005) 25: 105-117. Initial cleavage of the polyprotein is catalyzed by host proteases which liberate three structural proteins, the N-terminal nucleocapsid protein (termed “core”) and two envelope glycoproteins, gpEl (also known as E) and gpE2 (also known as E2/NS1), as well as nonstructural (NS) proteins that encode the viral enzymes and other activities.
  • the NS regions are termed NS2, NS3, NS4 and NS5.
  • NS2 is an integral membrane protein with proteolytic activity and, in combination withNS3, cleaves the NS2-NS3 junction.
  • the NS3 protease along with its NS4a cofactor, serves to process the remaining polyprotein.
  • NS3 liberates an NS3 cofactor (NS4a), two proteins (NS4b and NS5a), and an RNA-dependent RNA polymerase (NS5b).
  • NS4a NS3 cofactor
  • NS4b two proteins
  • NS5b RNA-dependent RNA polymerase
  • Completion of polyprotein maturation is initiated by autocatalytic cleavage at the NS3-NS4a junction, catalyzed by the NS3 serine protease.
  • El is detected as a 32-35 kDa glycoprotein species and is converted by endoglycosidase H into an approximately 18 kDa species.
  • E2 glycoprotein displays a complex pattern upon immunoprecipitation consistent with the generation of multiple species (Spaete et al., Virol. (1992) 188:819-830; Selby et al., J. Virol (1996) 70:5177-5182; Grakoui et al., J. Virol (1993) 67:1385-1395; Tomei et al., J. Virol (1993) 67:4017-4026.).
  • HCV envelope glycoproteins El and E2 form a stable complex that is co-immunoprecipitable (Grakoui et al., J. Virol. (1993) 67:1385-1395; Lanford et al., Virology (1993) 197:225-235; Ralston et al., J. Virol (1993) 67:6753-6761).
  • El and E2 are retained within the endoplasmic reticulum of cells and lack complex carbohydrate when expressed stably or in a transient Vaccinia virus system (Spaete et al., Virology (1992) 188:819-830; Ralston et al., J. Virol. (1993) 67:6753-6761). Since the El and E2 proteins are normally membrane-bound in these expression systems, secreted truncated forms have been produced in order to facilitate purification of the proteins. See, e.g., U.S. Patent No. 6,121,020. Additionally, intracellular production of E1E2 in HeIa cells has been described. See, e.g., International Publication No.
  • HCV El and E2 glycoproteins are of considerable interest because they have been shown to be protective against viral challenge in primate studies. (Choo et al, Proc. Natl. Acad. Sci. USA (1994) 91:1294-1298; Houghton, M. and Abrignani, S., Nature (2005) 436:961-966). Meunier et al., Proc. Natl. Acad. Sci.
  • the present invention provides a means for providing broad-based immunity to HCV.
  • the present invention provides compositions and methods for treating and/or preventing HCV infection caused by more than one of HCV genotypes 1, 2, 3, 4, 5 and 6, and preferably all of these HCV genotypes.
  • the invention eliminates the need for multiple vaccinations using immunogens from each of these genotypes.
  • the compositions and methods of the invention include immunogenic HCV envelope polypeptides from one or more HCV genotypes selected from HCV 1, 4, 5 and/or 6, in combination with one or more immunogenic envelope polypeptides selected from HCV 2 and/or 3. The use of such combinations provides an effective approach for treating and/or preventing HCV infection caused by multiple HCV genotypes.
  • the invention is directed to a composition
  • a composition comprising: (a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV- 5 and HCV-6; and (b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
  • HCV hepatitis C virus
  • the composition comprises an HCV envelope polypeptide from HCV-I and an HCV envelope polypeptide from HCV-2. In other embodiments, the composition comprises an HCV envelope polypeptide from HCV-4 and an HCV envelope polypeptide from HCV-2. In additional embodiments, the composition comprises an HCV envelope polypeptide from HCV-5 and an HCV envelope polypeptide from HCV-2. In further embodiments, the composition comprises an HCV envelope polypeptide from HCV-6 and an HCV envelope polypeptide from HCV-2.
  • composition further comprises an HCV envelope polypeptide from HCV-3.
  • the envelope polypeptide of (a) is an El polypeptide, an E2 polypeptide or an HCV E1E2 complex, such as a complex produced by a method comprising expressing a polynucleotide encoding an HCV El/E2/p7 region.
  • the envelope polypeptide of (b) is an El polypeptide, an E2 polypeptide or an HCV E1E2 complex, such as a complex produced by a method comprising expressing a polynucleotide encoding an HCV E l/E2/p7 region.
  • the envelope polypeptide of (a) and (b) is an El polypeptide, an E2 polypeptide or an HCV E1E2 complex, such as a complex produced by a method comprising expressing a polynucleotide encoding an HCV El/E2/p7 region.
  • the composition further comprises an adjuvant and/or another immunostimulatory compound such as an immunostimulatory sequence, or a small molecule immune potentiator.
  • the immunostimulatory sequence can be a CpG sequence.
  • the envelope polypeptide is produced recombinantly in a mammalian host cell.
  • the invention is directed to a method of stimulating an immune response in a vertebrate subject which comprises administering to the subject a therapeutically effective amount of any one of the compositions above.
  • the invention is directed to a method of stimulating an immune response in a vertebrate subject.
  • the method comprises administering to the subject a therapeutically effective amount of
  • HCV hepatitis C virus envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV- 5 and HCV-6; and (b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
  • HCV hepatitis C virus
  • (a) is administered prior to (b). In alternative embodiments, (b) is administered prior to (a). In yet further embodiments, (a) and (b) are administered concurrently. In additional embodiments, (a) and (b) are present in the same composition.
  • the envelope polypeptide is produced recombinantly in a mammalian host cell.
  • the invention is directed to a method of making a composition
  • a composition comprising: combining (a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV-5 and HCV-6; with (b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
  • HCV hepatitis C virus
  • Figure 1 is a diagrammatic representation of the HCV genome, depicting the various regions of the HCV polyprotein.
  • Figures 2A-2C (SEQ ID NOS: 1 and 2) show the nucleotide and corresponding amino acid sequence for the HCV-Ia El/E2/p7 region. The numbers shown in the figure are relative to the full-length HCV-Ia polyprotein. The El, E2 and p7 regions are shown.
  • Figure 3 shows neutralization antibody titers against an HCV type Ia pseudoparticle in sera from patients infected with different strains of HCV.
  • Glutamic acid GIu (E)
  • Glycine GIy (G)
  • Threonine Thr (T) Tryptophan: Trp (W)
  • polypeptide refers to a protein which includes modifications, such as deletions, additions and substitutions (generally conservative in nature), to the native sequence, so long as the protein maintains the desired activity. These modifications may be deliberate, as through site-directed mutagenesis, or may be accidental, such as through mutations of hosts which produce the proteins or errors due to PCR amplification.
  • an "El polypeptide” is meant a molecule derived from an HCV El region.
  • the mature El region of HCV-Ia begins at approximately amino acid 192 of the polyprotein and continues to approximately amino acid 383, numbered relative to the full-length HCV-Ia polyprotein.
  • Amino acids 192-383 of Figures 2A-2C correspond to amino acid positions 20-211 of SEQ ID NO:2.
  • Amino acids at around 173 through approximately 191 (amino acids 1-19 of SEQ ID NO:2) serve as a signal sequence for El.
  • the corresponding region for other HCV genotypes and subtypes are known and readily determined by comparison to the HCV-Ia polyprotein.
  • an "El polypeptide” also encompasses El polypeptides from any of the various HCV genotypes, such as HCV- 1, HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6 and subtypes thereof, such as HCV- Ia, HCV-2a, HCV-3a, HCV-4a, HCV-5a and HCV-6a.
  • an "El polypeptide” is meant either a precursor El protein, including the signal sequence, or a mature El polypeptide which lacks this sequence, or even an El polypeptide with a heterologous signal sequence.
  • the El polypeptide includes a C-terminal membrane anchor sequence which occurs at approximately amino acid positions 360-383, numbered relative to the HCV-Ia polyprotein (see, International Publication No. WO 96/04301, published February 15, 1996).
  • An El polypeptide, as defined herein, may or may not include the C-terminal anchor sequence or portions thereof. Moreover, the El polypeptide may or may not be glycosylated.
  • an "E2 polypeptide” is meant a molecule derived from an HCV E2 region.
  • the mature E2 region of HCV-Ia begins at approximately amino acid 383-385, numbered relative to the full-length HCV-I polyprotein. (See, Figures 1 and 2A-2C. Amino acids 383-385 of Figures 2A-2C correspond to amino acid positions 211-213 of SEQ ID NO:2.) A signal peptide begins at approximately amino acid 364 of the polyprotein. The corresponding region for other HCV genotypes and subtypes are known and readily determined by comparison to the HCV-Ia polyprotein.
  • E2 polypeptide also encompasses E2 polypeptides from any of the various HCV genotypes, such as HCV-I, HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6 and subtypes thereof, such as HCV-Ia, HCV-2a, HCV-3a, HCV-4a, HCV-5a and HCV-6a.
  • an "E2 polypeptide” is meant either a precursor E2 protein, including the signal sequence, or a mature E2 polypeptide which lacks this sequence, or even an E2 polypeptide with a heterologous signal sequence.
  • the E2 polypeptide includes a C-terminal membrane anchor sequence which occurs at approximately amino acid positions 715-730 and may extend as far as approximately amino acid residue 746, numbered relative to the HCV-Ia polyprotein (see, Lin et al., J. Virol. (1994) 68:5063-5073).
  • An E2 polypeptide, as defined herein, may or may not include the C-terminal anchor sequence or portions thereof. Additionally, the E2 polypeptide may or may not be glycosylated.
  • an E2 polypeptide may also include all or a portion of the p7 region which occurs immediately adjacent to the C-terminus of E2. As shown in Figures 1 and 2A-2C, the p7 region of the HCV-Ia polyprotein is found at positions 747-809, numbered relative to the full-length HCV-I polyprotein (amino acid positions 575-637 of SEQ ID NO:2). Additionally, it is known that multiple species of HCV E2 exist (Spaete et al., Virol. (1992) 188:819-830; Selby et al., J. Virol. (1996) 70:5177-5182; Grakoui et al., J. Virol.
  • E2 encompasses any of these species of E2 including, without limitation, species that have deletions of 1-20 or more of the amino acids from the N-terminus of the E2, such as, e.g, deletions of 1, 2, 3, 4, 5....10...15, 16, 17, 18, 19... etc. amino acids.
  • Such E2 species include those beginning at amino acid 387, amino acid 402, amino acid 403, etc.
  • Representative El and E2 regions from HCV-Ia are shown in Figures 2A-2C and SEQ ID NO:2.
  • HCV genotypes 2, 3, 4, 5 and 6, and subtypes thereof are known and discussed more fully below.
  • the El and E2 regions are defined with respect to the amino acid number of the polyprotein encoded by the genome of HCV-Ia, with the initiator methionine being designated position 1. See, e.g., Choo et al., Proc. Natl. Acad. ScL USA (1991) 88:2451-2455.
  • an "El polypeptide” or an “E2 polypeptide” as defined herein is not limited to a polypeptide having the exact sequence depicted in the Figures. Indeed, the HCV genome is in a state of constant flux in vivo and contains several variable domains which exhibit relatively high degrees of variability between isolates. A number of conserved and variable regions are known between these strains and, in general, the amino acid sequences of epitopes derived from these regions will have a high degree of sequence homology, e.g., amino acid sequence homology of more than 30%, preferably more than 40%, more than 60%, and even more than 80-90% homology, when the two sequences are aligned.
  • El and E2 polypeptides from any of the various HCV strains and isolates including isolates having any of the 6 genotypes of HCV described in Simmonds et al., J. Gen. Virol. (1993) 74:2391-2399 (e.g., strains 1, 2, 3, 4 etc.), as well as newly identified isolates, and subtypes of these isolates, such as HCVIa, HCVIb etc.
  • El or E2 polypeptide refers to native El or
  • E2 sequences from any of the various HCV genotypes unless specifically identified, as well as analogs, muteins and immunogenic fragments, as defined further below.
  • the complete genotypes of many of these strains are known. See, e.g., U.S. Patent No. 6,150,087 and GenBank Accession Nos. AJ238800 and AJ238799.
  • El polypeptide and E2 polypeptide encompass proteins which include modifications to the native sequence, such as internal deletions, additions and substitutions (generally conservative in nature), such as proteins substantially homologous to the parent sequence. These modifications may be deliberate, as through site-directed mutagenesis, or may be accidental, such as through naturally occurring mutational events.
  • modifications are encompassed in the present invention so long as the modified El and E2 polypeptides function for their intended purpose.
  • the modifications must be such that immunological activity (i.e., the ability to elicit a humoral or cellular immune response to the polypeptide) is not lost.
  • E1E2 complex is meant a protein containing at least one El polypeptide and at least one E2 polypeptide, as described above. Such a complex may also include all or a portion of the p7 region which occurs immediately adjacent to the C-terminus of E2. As shown in Figures 1 and 2A-2C, the p7 region is found at positions 747-809, numbered relative to the full-length HCV-I polyprotein (amino acid positions 575-637 of SEQ ID NO:2). A representative E1E2 complex which includes the p7 protein is termed "ElE2go9" herein. The mode of association of El and E2 in an E1E2 complex is immaterial. The
  • El and E2 polypeptides may be associated through non-covalent interactions such as through electrostatic forces, or by covalent bonds.
  • the E1E2 polypeptides of the present invention may be in the form of a fusion protein which includes an immunogenic El polypeptide and an immunogenic E2 polypeptide, as defined above.
  • the fusion may be expressed from a polynucleotide encoding an E1E2 chimera.
  • E1E2 complexes may form spontaneously simply by mixing El and E2 proteins which have been produced individually. Similarly, when co-expressed and secreted into media, the El and E2 proteins can form a complex spontaneously.
  • E1E2 complexes also called aggregates
  • Such aggregates may include one or more El monomers in association with one or more E2 monomers.
  • the number of El and E2 monomers present need not be equal so long as at least one El monomer and one E2 monomer are present.
  • Detection of the presence of an E1E2 complex is readily determined using standard protein detection techniques such as polyacrylamide gel electrophoresis and immunological techniques such as immunoprecipitation.
  • analogs and mutants refer to biologically active derivatives of the reference molecule, such as E1E2 BO9 , or fragments of such derivatives, that retain desired activity, such as immunoreactivity in assays described herein.
  • analog refers to compounds having a native polypeptide sequence and structure with one or more amino acid additions, substitutions (generally conservative in nature) and/or deletions, relative to the native molecule, so long as the modifications do not destroy immunogenic activity.
  • mutant refers to polypeptides having one or more amino acid-like molecules including but not limited to compounds comprising only amino and/or imino molecules, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), polypeptides with substituted linkages, as well as other modifications known in the art, both naturally occurring and non-naturally occurring (e.g., synthetic), cyclized, branched molecules and the like.
  • the term also includes molecules comprising one or more N-substituted glycine residues (a "peptoid") and other synthetic amino acids or peptides. (See, e.g., U.S. Patent ⁇ os.
  • the analog or mutein has at least the same immunoreactivity as the native molecule.
  • Methods for making polypeptide analogs and muteins are known in the art and are described further below.
  • amino acids are generally divided into four families: (1) acidic ⁇ aspartate and glutamate; (2) basic — lysine, arginine, histidine; (3) non-polar ⁇ alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar — glycine, asparagine, glutamine, cysteine, serine threonine, tyrosine.
  • Phenylalanine, tryptophan, and tyrosine are sometimes classified as aromatic amino acids.
  • an isolated replacement of leucine with isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar conservative replacement of an amino acid with a structurally related amino acid will not have a major effect on the biological activity.
  • the polypeptide of interest such as an E1E2 polypeptide, may include up to about 5-10 conservative or non-conservative amino acid substitutions, or even up to about 15-25 or 50 conservative or non-conservative amino acid substitutions, or any integer between 5-50, so long as the desired function of the molecule remains intact.
  • fragment is intended a polypeptide consisting of only a part of the intact full-length polypeptide sequence and structure.
  • the fragment can include a
  • an "immunogenic fragment" of a particular HCV protein will generally include at least about 5-10 contiguous amino acid residues of the full-length molecule, preferably at least about 15-25 contiguous amino acid residues of the full-length molecule, and most preferably at least about 20-50 or more contiguous amino acid residues of the full-length molecule, that define an epitope, or any integer between 5 amino acids and the full-length sequence, provided that the fragment in question retains the ability to elicit an immunological response as defined herein.
  • known immunogenic fragments of HCV El and E2 see, e.g., Chien et al., International Publication No. WO 93/00365.
  • epitope refers to a sequence of at least about 3 to 5, preferably about 5 to 10 or 15, and not more than about 500 amino acids (or any integer therebetween), which define a sequence that by itself or as part of a larger sequence, elicits an immunological response in the subject to which it is administered. Often, an epitope will bind to an antibody generated in response to such sequence. There is no critical upper limit to the length of the fragment, which may comprise nearly the full-length of the protein sequence, or even a fusion protein comprising two or more epitopes from the HCV polyprotein. An epitope for use in the subject invention is not limited to a polypeptide having the exact sequence of the portion of the parent protein from which it is derived.
  • epitopes encompasses sequences identical to the native sequence, as well as modifications to the native sequence, such as deletions, additions and substitutions (generally conservative in nature).
  • Regions of a given polypeptide that include an epitope can be identified using any number of epitope mapping techniques, well known in the art. See, e.g., Epitope Mapping Protocols in Methods in Molecular Biology, Vol. 66 (Glenn E. Morris, Ed., 1996) Humana Press, Totowa, New Jersey.
  • linear epitopes may be determined by e.g., concurrently synthesizing large numbers of peptides on solid supports, the peptides corresponding to portions of the protein molecule, and reacting the peptides with antibodies while the peptides are still attached to the supports. Such techniques are known in the art and described in, e.g., U.S. Patent No.
  • conformational epitopes are readily identified by determining spatial conformation of amino acids such as by, e.g., x-ray crystallography and 2-dimensional nuclear magnetic resonance. See, e.g., Epitope Mapping Protocols, supra.
  • Antigenic regions of proteins can also be identified using standard antigenicity and hydropathy plots, such as those calculated using, e.g., the Omiga version 1.0 software program available from the Oxford Molecular Group. This computer program employs the Hopp/ Woods method, Hopp et al., Proc. Natl. Acad. Sd USA (1981) 78:3824-3828 for determining antigenicity profiles, and the Kyte-Doolittle technique, Kyte et al., J. MoI.
  • the term “conformational epitope” refers to a portion of a full-length protein, or an analog or mutein thereof, having structural features native to the amino acid sequence encoding the epitope within the full-length natural protein. Native structural features include, but are not limited to, glycosylation and three dimensional structure. The length of the epitope defining sequence can be subject to wide variations as these epitopes are believed to be formed by the three-dimensional shape of the antigen (e.g., folding).
  • amino acids defining the epitope can be relatively few in number, but widely dispersed along the length of the molecule (or even on different molecules in the case of dimers, etc.), being brought into correct epitope conformation via folding.
  • the portions of the antigen between the residues defining the epitope may not be critical to the conformational structure of the epitope. For example, deletion or substitution of these intervening sequences may not affect the conformational epitope provided sequences critical to epitope conformation are maintained (e.g., cysteines involved in disulfide bonding, glycosylation sites, etc.). Conformational epitopes are readily identified using methods discussed above.
  • the presence or absence of a conformational epitope in a given polypeptide can be readily determined through screening the antigen of interest with an antibody (polyclonal serum or monoclonal to the conformational epitope) and comparing its reactivity to that of a denatured version of the antigen which retains only linear epitopes (if any). In such screening using polyclonal antibodies, it may be advantageous to absorb the polyclonal serum first with the denatured antigen and see if it retains antibodies to the antigen of interest. Conformational epitopes derived from the El and E2 regions are described in, e.g., International Publication No. WO 94/01778.
  • an "immunological response" to an HCV antigen or composition is the development in a subject of a humoral and/or a cellular immune response to molecules present in the composition of interest.
  • a “humoral immune response” refers to an immune response mediated by antibody molecules
  • a "cellular immune response” is one mediated by T-lymphocytes and/or other white blood cells.
  • CTLs cytolytic T-cells
  • CTLs have specificity for peptide antigens that are presented in association with proteins encoded by the major histocompatibility complex (MHC) and expressed on the surfaces of cells.
  • helper T-cells help induce and promote the intracellular destruction of intracellular microbes, or the lysis of cells infected with such microbes.
  • Another aspect of cellular immunity involves an antigen-specific response by helper T-cells.
  • Helper T-cells act to help stimulate the function, and focus the activity of, nonspecific effector cells against cells displaying peptide antigens in association with MHC molecules on their surface.
  • a "cellular immune response” also refers to the production of cytokines, chemokines and other such molecules produced by activated T-cells and/or other white blood cells, including those derived from CD4+ and CD8+ T-cells.
  • a composition or vaccine that elicits a cellular immune response may serve to sensitize a vertebrate subject by the presentation of antigen in association with MHC molecules at the cell surface.
  • the cell-mediated immune response is directed at, or near, cells presenting antigen at their surface.
  • antigen-specific T-lymphocytes can be generated to allow for the future protection of an immunized host.
  • the ability of a particular antigen to stimulate a cell-mediated immunological response may be determined by a number of assays, such as by lymphoproliferation (lymphocyte activation) assays, CTL cytotoxic cell assays, or by assaying for T-lymphocytes specific for the antigen in a sensitized subject.
  • assays are well known in the art. See, e.g., Erickson et al., J. Immunol. (1993) 151:4189-4199; Doe et al., Eur. J. Immunol. (1994) 24:2369-
  • an immunological response as used herein may be one which stimulates the production of CTLs, and/or the production or activation of helper T- cells.
  • the antigen of interest may also elicit an antibody-mediated immune response, including, or example, neutralization of binding (NOB) antibodies.
  • NOB neutralization of binding
  • an immunological response may include one or more of the following effects: the production of antibodies by B-cells; and/or the activation of suppressor T-cells and/or ⁇ T-cells directed specifically to an antigen or antigens present in the composition or vaccine of interest.
  • responses may serve to neutralize infectivity, and/or mediate antibody-complement, or antibody dependent cell cytotoxicity (ADCC) to provide protection or alleviation of symptoms to an immunized host.
  • ADCC antibody dependent cell cytotoxicity
  • Such responses can be determined using standard immunoassays and neutralization assays, well known in the art.
  • isolated is meant, when referring to a polypeptide, that the indicated molecule is separate and discrete from the whole organism with which the molecule is found in nature or is present in the substantial absence of other biological macro-molecules of the same type.
  • isolated with respect to a polynucleotide is a nucleic acid molecule devoid, in whole or part, of sequences normally associated with it in nature; or a sequence, as it exists in nature, but having heterologous sequences in association therewith; or a molecule disassociated from the chromosome.
  • equivalent antigenic determinant an antigenic determinant from different sub-species or strains of HCV, such as from strains 1, 2, 3, etc., of HCV which antigenic determinants are not necessarily identical due to sequence variation, but which occur in equivalent positions in the HCV sequence in question.
  • amino acid sequences of equivalent antigenic determinants will have a high degree of sequence homology, e.g., amino acid sequence homology of more than 30%, usually more than 40%, such as more than 60%, and even more than 80-90% homology, when the two sequences are aligned.
  • Homology refers to the percent identity between two polynucleotide or two polypeptide moieties.
  • Two DNA, or two polypeptide sequences are "substantially homologous" to each other when the sequences exhibit at least about 50% , preferably at least about 75%, more preferably at least about 80%-85%, preferably at least about 90%, and most preferably at least about 95%-98% sequence identity over a defined length of the molecules.
  • substantially homologous also refers to sequences showing complete identity to the specified DNA or polypeptide sequence.
  • identity refers to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Percent identity can be determined by a direct comparison of the sequence information between two molecules by aligning the sequences, counting the exact number of matches between the two aligned sequences, dividing by the length of the shorter sequence, and multiplying the result by 100. Readily available computer programs can be used to aid in the analysis, such as ALIGN, Dayhoff, M.O. in Atlas of Protein Sequence and Structure M.O. Dayhoff ed., 5 Suppl.
  • percent identity of a particular nucleotide sequence to a reference sequence can be determined using the homology algorithm of Smith and Waterman with a default scoring table and a gap penalty of six nucleotide positions.
  • Another method of establishing percent identity in the context of the present invention is to use the MPSRCH package of programs copyrighted by the University of Edinburgh, developed by John F. Collins and Shane S. Sturrok, and distributed by IntelliGenetics, Inc. (Mountain View, CA). From this suite of packages the Smith- Waterman algorithm can be employed where default parameters are used for the scoring table (for example, gap open penalty of 12, gap extension penalty of one, and a gap of six).
  • homology can be determined by hybridization of polynucleotides under conditions which form stable duplexes between homologous regions, followed by digestion with single-stranded-specific nuclease(s), and size determination of the digested fragments.
  • DNA sequences that are substantially homologous can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art. See, e.g., Sambrook et al., supra; DNA Cloning, supra; Nucleic Acid Hybridization, supra.
  • Recombinant as used herein to describe a nucleic acid molecule means a polynucleotide of genomic, RNA, DNA, cDNA, viral, semisynthetic, or synthetic origin which, by virtue of its origin or manipulation is not associated with all or a portion of the polynucleotide with which it is associated in nature.
  • the term "recombinant” as used with respect to a protein or polypeptide means a polypeptide produced by expression of a recombinant polynucleotide.
  • the gene of interest is cloned and then expressed in transformed organisms, as described further below. The host organism expresses the foreign gene to produce the protein under expression conditions.
  • an effective amount or “pharmaceutically effective amount” of an immunogenic composition refers to a nontoxic but sufficient amount of the composition to provide the desired response, such as an immunological response, and optionally, a corresponding therapeutic effect.
  • the exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the condition being treated, and the particular macromolecule of interest, mode of administration, and the like. An appropriate "effective" amount in any individual case may be determined by one of ordinary skill in the art using routine experimentation.
  • vertebrate subject any member of the subphylum chordata, including, without limitation, humans and other primates, including non-human primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs; birds, including domestic, wild and game birds such as chickens, turkeys and other gallinaceous birds, ducks, geese, and the like.
  • the term does not denote a particular age. Thus, both adult and newborn individuals are intended to be covered.
  • treatment refers to either (1) the prevention of infection or reinfection (prophylaxis), or (2) the reduction or elimination of symptoms of the disease of interest (therapy).
  • HCV envelope polypeptides from HCV genotypes capable of cross-neutralizing multiple HCV genotypes.
  • HCV-Ia neutralizing antibodies produced by infection with HCV-Ia are capable of cross-neutralizing HCV genotypes 4a, 5a and 6a.
  • the use of envelope polypeptides from one or more of HCV genotypes 1, 4, 5 and 6, when combined with the use of envelope polypeptides from HCV-2 and/or 3, may provide broad-based protection and/or treatment against multiple HCV genotypes.
  • subjects can be administered envelope polypeptides from all of these genotypes, or envelope polypeptides from some of the genotypes, such as from two, three, four, five or all six of these genotypes, so long as neutralizing antibodies are produced that are directed against more than one of the six genotypes.
  • the HCV envelope polypeptides can be administered together, in the same composition, or can be administered in separate compositions. If delivered in separate compositions, administration can be, but need not be, concurrent.
  • an HCV envelope polypeptide from an HCV genotype selected from one or more of HCV-I, HCV-4, HCV-5 and HCV-6 can be delivered prior to, subsequent to, or concurrent with an HCV envelope polypeptide from an HCV genotype selected from HCV-2 and/or HCV-3.
  • Subjects can subsequently be boosted with either protein or DNA compositions that deliver HCV envelope polypeptides, such as HCV E1E2 protein complexes.
  • HCV envelope polypeptides such as HCV E1E2 protein complexes.
  • the molecules used for boosting can be either the same as initially administered, or can be different HCV envelope polypeptides, as described further below, so long as an immune response is generated.
  • the compositions above can be used alone, or in combination with other compositions, such as compositions comprising other HCV proteins, compositions comprising DNA encoding other HCV proteins, as well as compositions comprising ancillary substances. If used in combination with other compositions, such compositions can be administered prior to, concurrent with, or subsequent to the HCV envelope compositions.
  • HCV polypeptides and compositions for use in the subject methods are provided below.
  • compositions of the invention include HCV envelope polypeptides from more than one HCV genotype.
  • HCV-Ia amino acid positions discussed below are generally with reference to HCV-Ia.
  • the corresponding region for other HCV genotypes and subtypes are known and readily determined by comparison to the HCV-Ia polyprotein.
  • polypeptides and polynucleotides from any of the various HCV genotypes such as HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6 and subtypes thereof, including but not limited to HCV-2a, HCV-3a, HCV-4a, HCV-5a and HCV-6a, are also intended.
  • the complete sequences for several HCV-I isolates are reported.
  • HCV-3 isolates are also reported. See, e.g., NCBI accession nos. AF046866, D17763, D28917, D49374, D63821, X76918.
  • the complete sequences for HCV-4 isolates are also known. See, e.g., NCBI accession no. Yl 1604.
  • the complete sequences for several HCV-5 isolates are known. See, e.g., NCBI accession nos. AF064490 and Y13184.
  • the complete sequences for several HCV-6 isolates are also known. See, e.g., NCBI accession nos. AY859526, AY878650, D63822, D84262, D84263, D84264, D84265, Y12083.
  • HCV Jl.1 is described in Kubo et al. (1989) Japan. Nucl. Acids Res. 17:10367-10372; Takeuchi et al.(1990) Gene 91:287-291; Takeuchi et al. (1990) J. Gen. Virol. 71:3027-3033; and Takeuchi et al. (1990) Nucl. Acids Res.18:4626.
  • the complete coding sequences of two independent isolates, HCV-J and BK are described by Kato et al., (1990) Proc. Natl. Acad. ScL USA 87:9524-9528 and Takamizawa et al., (1991) J. Virol.
  • HCV-I isolates are described by Choo et al. (1990) Brit. Med. Bull. 46:423-441; Choo et al. (1991) Proc. Natl. Acad. Sci. USA 88:2451-2455 and Han et al. (1991) Proc. Natl. Acad. Sci. USA 88:1711-1715.
  • HCV isolates HC-Jl and HC-J4 are described in Okamoto et al. (1991) Japan J. Exp. Med. 60: 167-177.
  • HCV isolates HCT 18, HCT 23, Th, HCT 27, ECl and EClO are described in Weiner et al. (1991) Virol. 180:842-848.
  • HCV isolates Pt-I, HCV-Kl and HCV-K2 are described in Enomoto et al. (1990) Biochem. Biophys. Res. Commun. 170:1021-1025.
  • HCV isolates A, C, D & E are described in Tsukiyama-Kohara et al. (1991) Virus Genes 5:243-254.
  • the HCV El polypeptide is a glycoprotein and extends from approximately amino acid 192 to amino acid 383, numbered relative to the polyprotein of HCV-Ia. See, Choo et al., Proc. Natl. Acad. Sci. USA (1991) 88:2451-2455. Amino acids at around 173 through approximately 191 represent a signal sequence for El.
  • the HCV E2 polypeptide is also a glycoprotein and extends from approximately amino acid 383 or 384 to amino acid 746. A signal peptide for E2 begins at approximately amino acid 364 of the polyprotein.
  • full-length El or “not truncated” El refers to polypeptides that include, at least, amino acids 192-383 of an HCV polyprotein (numbered relative to HCV-Ia).
  • full-length or “not truncated” as used herein refers to polypeptides that include, at least, amino acids 383 or 384 to amino acid 746 of an HCV polyprotein (numbered relative to HCV-Ia).
  • E2 polypeptides for use with the present invention may include additional amino acids from the p7 region, such as amino acids 747-809, numbered relative to HCV-Ia.
  • an E2 polypeptide for use herein may comprise at least amino acids 405-661, e.g., 400, 401, 402...
  • preferable El polypeptides for use herein can comprise amino acids 192-326, 192-330, 192-333, 192-360, 192-363, 192-383, or 192 to any C-terminus between 326-383, of an HCV polyprotein.
  • El and E2 polypeptides for use in the subject compositions and methods also include immunogenic fragments of El and E2 which comprise epitopes.
  • fragments of El polypeptides can comprise from about 5 to nearly the full-length of the molecule, such as 6, 10, 25, 50, 75, 100, 125, 150, 175, 185 or more amino acids of an El polypeptide, or any integer between the stated numbers.
  • fragments of E2 polypeptides can comprise 6, 10, 25, 50, 75, 100, 150, 200, 250, 300, or 350 amino acids of an E2 polypeptide, or any integer between the stated numbers.
  • the El and E2 polypeptides may be from the same or different HCV strains.
  • epitopes derived from, e.g., the hypervariable region of E2, such as a region spanning amino acids 384-410 or 390-410, can be included in the E2 polypeptide.
  • a particularly effective E2 epitope to incorporate into the E2 sequence is one which includes a consensus sequence derived from this region, such as the consensus sequence
  • Gly-Ser-Ala-Ala-Arg-Thr-Thr-Ser-Gly-Phe-Val-Ser-Leu-Phe-Ala-Pro-Gly-Ala-Lys- Gln-Asn (SEQ ID NO:3), which represents a consensus sequence for amino acids 390-410 of the HCV type 1 genome. Additional epitopes of El and E2 are known and described in, e.g., Chien et al., International Publication No. WO 93/00365.
  • the El and E2 polypeptides may lack all or a portion of the membrane spanning domain.
  • the membrane anchor sequence functions to associate the polypeptide to the endoplasmic reticulum.
  • polypeptides are capable of secretion into growth medium in which an organism expressing the protein is cultured.
  • polypeptides may also be recovered intracellularly. Secretion into growth medium is readily determined using a number of detection techniques, including, e.g., polyacrylamide gel electrophoresis and the like, and immunological techniques such as immunoprecipitation assays as described in, e.g., International Publication No. WO 96/04301, published February 15, 1996.
  • polypeptides terminating with about amino acid position 370 and higher will be retained by the ER and hence not secreted into growth media.
  • polypeptides terminating with about amino acid position 731 and higher will be retained by the ER and not secreted.
  • these amino acid positions are not absolute and may vary to some degree.
  • the present invention contemplates the use of El and E2 polypeptides which retain the transmembrane binding domain, as well as polypeptides which lack all or a portion of the transmembrane binding domain, including El polypeptides terminating at about amino acids 369 and lower, and E2 polypeptides, terminating at about amino acids 730 and lower, are intended to be captured by the present invention.
  • the C-terminal truncation can extend beyond the transmembrane spanning domain towards the N-terminus.
  • El truncations occurring at positions lower than, e.g., 360 and E2 truncations occurring at positions lower than, e.g., 715 are also encompassed by the present invention.
  • truncated El and E2 polypeptides remain functional for their intended purpose.
  • particularly preferred truncated El constructs are those that do not extend beyond about amino acid 300. Most preferred are those terminating at position 360.
  • Preferred truncated E2 constructs are those with C-terminal truncations that do not extend beyond about amino acid position 715.
  • Particularly preferred E2 truncations are those molecules truncated after any of amino acids 715-730, such as 725. If truncated molecules are used, it is preferable to use El and E2 molecules that are both truncated.
  • compositions and methods of the invention are complexes of El and E2 polypeptides as described above.
  • the El and E2 polypeptides in such complexes can be associated either through non-covalent or covalent interactions.
  • Such complexes may also include all or a portion of the p7 region which occurs immediately adjacent to the C-terminus of E2.
  • Representative HCV E1E2 complexes are described in PCT Publication No. WO 03/002065, incorporated herein by reference in its entirety.
  • the El and E2 polypeptides and complexes thereof may also be present as asialoglycoproteins. Such asialoglycoproteins are produced by methods known in the art, such as by using cells in which terminal glycosylation is blocked.
  • the E1E2 complexes may comprise a heterogeneous mixture of molecules, due to clipping and proteolytic cleavage, as described above.
  • a composition including E1E2 complexes may include multiple species of E1E2, such as E1E2 terminating at amino acid 746 (EIE2746), E1E2 terminating at amino acid 809 (ElE2gQ9), or any of the other various El and E2 molecules described above, such as E2 molecules with N-terminal truncations of from 1-20 amino acids, such as E2 species beginning at amino acid 387, amino acid 402, amino acid 403, etc.
  • EIE2746 EIE2746
  • ElE2gQ9 E1E2 terminating at amino acid 809
  • E2gQ9 E1E2 terminating at amino acid 809
  • E2gQ9 E1E2 terminating at amino acid 809
  • E2gQ9 E1E2 terminating at amino acid 809
  • E2gQ9 E1E2 terminating at amino acid
  • E1E2 polypeptides may be associated through non-covalent interactions such as through electrostatic forces, or by covalent bonds.
  • E1E2 complexes form spontaneously by mixing El and E2 proteins which have been produced individually.
  • the El and E2 proteins can form a complex spontaneously.
  • E1E2 complexes also called aggregates
  • the number of El and E2 monomers present need not be equal so long as at least one El monomer and one E2 monomer are present.
  • E1E2 complexes are readily produced recombinantly. If E1E2 complexes are desired, they can be produced either as fusion proteins or by e.g., cotransfecting host cells with constructs encoding for the El and E2 polypeptides of interest. Cotransfection can be accomplished either in trans or cis, i.e., by using separate vectors or by using a single vector which bears both of the El and E2 genes. If done using a single vector, both genes can be driven by a single set of control elements or, alternatively, the genes can be present on the vector in individual expression cassettes, driven by individual control elements. Following expression, the El or E2 proteins will spontaneously associate.
  • the complexes can be formed by mixing the individual proteins together which have been produced separately, either in purified or semi-purified form, or even by mixing culture media in which host cells expressing the proteins, have been cultured, if the proteins are secreted.
  • the E1E2 complexes of may be expressed as a fusion protein wherein the desired portion of El is fused to the desired portion of E2.
  • Polynucleotides encoding HCV El and E2 polypeptides, to be used for expressing El and E2 polypeptides for use either alone or in complexes can be made using standard techniques of molecular biology.
  • polynucleotide sequences coding for the above-described molecules can be obtained using recombinant methods, such as by screening cDNA and genomic libraries from cells expressing the gene, or by deriving the gene from a vector known to include the same.
  • the desired gene can be isolated directly from viral nucleic acid molecules, using techniques described in the art, such as in Houghton et al., U.S. Patent No. 5,350,671.
  • the gene of interest can also be produced synthetically, rather than cloned.
  • the molecules can be designed with appropriate codons for the particular sequence.
  • the complete sequence is then assembled from overlapping oligonucleotides prepared by standard methods and assembled into a complete coding sequence. See, e.g., Edge (1981) Nature 292:756; Nambair et al. (1984) Science 223:1299; and Jay et al. (1984) J. Biol. Chem. 259:6311.
  • nucleotide sequences can be obtained from vectors harboring the desired sequences or synthesized completely or in part using various oligonucleotide synthesis techniques known in the art, such as site-directed mutagenesis and polymerase chain reaction (PCR) techniques where appropriate. See, e.g., Sambrook, supra.
  • PCR polymerase chain reaction
  • one method of obtaining nucleotide sequences encoding the desired sequences is by annealing complementary sets of overlapping synthetic oligonucleotides produced in a conventional, automated polynucleotide synthesizer, followed by ligation with an appropriate DNA ligase and amplification of the ligated nucleotide sequence via PCR. See, e.g., Jayaraman et al.
  • Proc. Natl. Acad. ScL USA 86"-10029-100383 can be used to provide molecules having altered or enhanced antigen-binding capabilities and immunogenicity.
  • coding sequences Once coding sequences have been prepared or isolated, such sequences can be cloned into any suitable vector or replicon.
  • suitable vectors include, but are not limited to, plasmids, phages, transposons, cosmids, chromosomes or viruses which are capable of replication when associated with the proper control elements.
  • the coding sequence is then placed under the control of suitable control elements, depending on the system to be used for expression.
  • the coding sequence can be placed under the control of a promoter, ribosome binding site (for bacterial expression) and, optionally, an operator, so that the DNA sequence of interest is transcribed into RNA by a suitable transformant.
  • the coding sequence may or may not contain a signal peptide or leader sequence which can later be removed by the host in post-translational processing. See, e.g., U.S. Patent Nos. 4,431,739; 4,425,437; 4,338,397.
  • regulatory sequences which allow for regulation of the expression of the sequences relative to the growth of the host cell.
  • Regulatory sequences are known to those of skill in the art, and examples include those which cause the expression of a gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound.
  • Other types of regulatory elements may also be present in the vector.
  • enhancer elements may be used herein to increase expression levels of the constructs. Examples include the SV40 early gene enhancer (Dijkema et al. (1985) EMBOJ. 4:761), the enhancer/promoter derived from the long terminal repeat (LTR) of the Rous Sarcoma Virus (Gorman et al.
  • the expression cassette may further include an origin of replication for autonomous replication in a suitable host cell, one or more selectable markers, one or more restriction sites, a potential for high copy number and a strong promoter.
  • An expression vector is constructed so that the particular coding sequence is located in the vector with the appropriate regulatory sequences, the positioning and orientation of the coding sequence with respect to the control sequences being such that the coding sequence is transcribed under the "control" of the control sequences (i.e., RNA polymerase which binds to the DNA molecule at the control sequences transcribes the coding sequence).
  • Modification of the sequences encoding the molecule of interest may be desirable to achieve this end. For example, in some cases it may be necessary to modify the sequence so that it can be attached to the control sequences in the appropriate orientation; i.e., to maintain the reading frame.
  • the control sequences and other regulatory sequences may be ligated to the coding sequence prior to insertion into a vector.
  • the coding sequence can be cloned directly into an expression vector which already contains the control sequences and an appropriate restriction site.
  • Mutants or analogs of HCV polypeptides for use in the subject compositions may be prepared by the deletion of a portion of the sequence encoding the polypeptide of interest, by insertion of a sequence, and/or by substitution of one or more nucleotides within the sequence.
  • Techniques for modifying nucleotide sequences, such as site-directed mutagenesis, and the like, are well known to those skilled in the art. See, e.g., Sambrook et al., supra; Kunkel, T.A. (1985) Proc. Natl. Acad. Sci. USA (1985) 82:448; Geisselsoder et al. (1987) BioTechniques 5:786; Zoller and Smith (1983) Methods Enzymol. 100:468; Dalbie-McFarland et al. (1982) Proc. Natl. Acad Sci USA 79:6409.
  • the molecules can be expressed in a wide variety of systems, including insect, mammalian, bacterial, viral and yeast expression systems, all well known in the art.
  • insect cell expression systems such as baculovirus systems
  • baculovirus systems are known to those of skill in the art and described in, e.g., Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987).
  • Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego CA ("MaxBac" kit).
  • bacterial and mammalian cell expression systems are well known in the art and described in, e.g., Sambrook et al., supra.
  • Yeast expression systems are also known in the art and described in, e.g., Yeast Genetic Engineering (Barr et al., eds., 1989) Butterworths, London.
  • a number of appropriate host cells for use with the above systems are also known.
  • mammalian cell lines are known in the art and include immortalized cell lines available from the American Type Culture Collection (ATCC), such as, but not limited to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human embryonic kidney cells, human hepatocellular carcinoma cells (e.g., Hep G2), Madin-Darby bovine kidney (“MDBK”) cells, as well as others.
  • ATCC American Type Culture Collection
  • bacterial hosts such as E. coli, Bacillus subtilis, and Streptococcus spp., will find use with the present expression constructs.
  • Yeast hosts useful in the present invention include inter alia, Saccharomyces cerevisiae, Candida albicans, Candida maltosa, Hansenula polymorpha, Kluyveromyces fragilis, Kl ⁇ yveromyces lactis, Pichia guillerimondii,
  • Pichia pastoris Schizosaccharomyces pombe and Yarrowia lipolytica.
  • Insect cells for use with baculovirus expression vectors include, inter alia, Aedes aegypti, Autographa californica, Bombyx mori, Drosophila melanogaster, Spodoptera frugiperda, and T ⁇ choplusia ni.
  • Nucleic acid molecules comprising nucleotide sequences of interest can be stably integrated into a host cell genome or maintained on a stable episomal element in a suitable host cell using various gene delivery techniques well known in the art. See, e.g., U.S. Patent No. 5,399,346.
  • the molecules are produced by growing host cells transformed by an expression vector described above under conditions whereby the protein is expressed.
  • the expressed protein is then isolated from the host cells and purified. If the expression system secretes the protein into growth media, the product can be purified directly from the media. If it is not secreted, it can be isolated from cell lysates.
  • the selection of the appropriate growth conditions and recovery methods are within the skill of the art.
  • compositions comprising HCV immunogens or DNA encoding such immunogens.
  • Such compositions can be delivered prior to, subsequent to, or concurrent with the above envelope compositions, as well as prior to, subsequent to, or concurrent with compositions for boosting the immune response, if used.
  • the genome of the hepatitis C virus typically contains a single open reading frame of approximately 9,600 nucleotides, which is transcribed into a polyprotein.
  • the full-length sequence of the polyprotein is disclosed in European Publication No. 388,232 and U.S. Patent No. 6,150,087, incorporated herein by reference in their entireties.
  • An HCV polyprotein upon cleavage, produces at least ten distinct products, in the order of NH 2 _Core-El-E2-p7-NS2-NS3-NS4a-NS4b-NS5a-NS5b-COOH.
  • the core polypeptide occurs at positions 1-191, numbered relative to HCV-Ia (see, Choo et al.
  • HCV-I Human immunodeficiency virus
  • This polypeptide is further processed to produce an HCV polypeptide with approximately amino acids 1-173.
  • the envelope polypeptides, El and E2 occur at about positions 192-383 and 384-746, respectively.
  • the P7 domain is found at about positions 747-809.
  • NS2 is an integral membrane protein with proteolytic activity and is found at about positions 810-1026 of the polyprotein.
  • NS2 either alone or in combination with NS3 (found at about positions 1027- 1657), cleaves the NS2-NS3 sissle bond which in turn generates the NS3 N-terminus and releases a large polyprotein that includes both serine protease and RNA helicase activities.
  • the NS3 protease found at about positions 1027-1207, serves to process the remaining polyprotein.
  • the helicase activity is found at about positions 1193-1657. Completion of polyprotein maturation is initiated by autocatalytic cleavage at the NS3-NS4a junction, catalyzed by the NS3 serine protease.
  • NS3-mediated cleavages of the HCV polyprotein appear to involve recognition of polyprotein cleavage junctions by an NS3 molecule of another polypeptide.
  • NS3 liberates anNS3 cofactor (NS4a, found about positions 1658-1711), two proteins (NS4b found at about positions 1712-1972, and NS5a found at about positions 1973-2420), and an RNA-dependent RNA polymerase (NS5b found at about positions 2421-3011).
  • HCV polypeptides derived from the Core region such as polypeptides derived from the region found between amino acids 1-191; amino acids 10-53; amino acids 10-45; amino acids 67-88; amino acids 86-100; 81-130; amino acids 121-135; amino acids 120-130; amino acids 121-170; and any of the Core epitopes identified in, e.g., Houghton et al., U.S. Patent No. 5,350,671; Chien et al. Proc. Natl. Acad. ScL USA (1992) 89:10011-10015; Chien et al. J.
  • polypeptides derived from the nonstructural regions of the virus will also find use herein.
  • the NS3/4a region of the HCV polyprotein has been described and the amino acid sequence and overall structure of the protein are disclosed in Yao et al. Structure (November 1999) 7:1353-1363. See, also, Dasmahapatra et al., U.S. Patent No. 5,843,752, incorporated herein by reference in its entirety. As explained above, either the native sequence or immunogenic analogs can be used in the subject formulations. Dasmahapatra et al., U.S. Patent No. 5,843,752 and Zhang et al., U.S. Patent No. 5,990,276, both describe analogs of NS3/4a and methods of making the same.
  • polypeptides for use in the subject compositions and methods may be derived from the NS3 region of the HCV polyprotein.
  • a number of such polypeptides are known, including, but not limited to polypeptides derived from the c33c and clOO regions, as well as fusion proteins comprising an NS3 epitope, such as c25.
  • These and other NS3 polypeptides are useful in the present compositions and are known in the art and described in, e.g., Houghton et al, U.S. Patent No. 5,350,671; Chien et al. Proc. Natl. Acad. ScL USA (1992) 89:10011-10015; Chien et al. J. Gastroent.
  • MEFAs multiple epitope fusion antigens
  • Such MEFAs include multiple epitopes derived from two or more of the various viral regions. The epitopes are preferably from more than one HCV strain, thus providing the added ability to protect against multiple strains of HCV in a single vaccine.
  • HCV polypeptides and polynucleotides for use with the present invention are not limited to those derived from the HCV-Ia sequence and any strain or isolate of HCV can serve as the basis for providing antigenic sequences for use with the invention.
  • the corresponding regions in another HCV isolate can be readily determined by aligning sequences from the two isolates in a manner that brings the sequences into maximum alignment.
  • HCV J 1.1 is described in Kubo et al. (1989) Japan. Nucl. Acids Res. 17:10367-10372; Takeuchi et al.(1990) Gene 91:287-291; Takeuchi et al. (1990) J. Gen. Virol. 71:3027-3033; and Takeuchi et al. (1990) Nucl. Acids Res.18:4626.
  • HCV-J and BK The complete coding sequences of two independent isolates, HCV-J and BK, are described by Kato et al., (1990) Proc. Natl. Acad. ScL USA 87:9524-9528 and Takamizawa et al., (1991) J. Virol. 65:1105-1113, respectively.
  • HCV-I isolates are described by Choo et al. (1990) Brit. Med. Bull. 46:423-441; Choo et al. (1991) Proc. Natl. Acad. Sci. USA 88:2451-2455 and Han et al. (1991) Proc. Natl. Acad. Sci. USA 88:1711-1715.
  • HCV isolates HC-Jl and HC-J4 are described in Okamoto et al. (1991) Japan J. Exp. Med. 60:167-177.
  • HCV isolates HCT 18, HCT 23, Th, HCT 27, ECl and EClO are described in Weiner et al. (1991) Virol. 180:842-848.
  • HCV isolates Pt-I, HCV-Kl and HCV-K2 are described in Enomoto et al. (1990) Biochem. Biophys. Res. Commun. 170:1021-1025.
  • HCV isolates A, C, D & E are described in Tsukiyama-Kohara et al. (1991) Virus Genes 5:243-254.
  • HCV E1E2 polynucleotides and polypeptides for use in the compositions and methods of the invention can be obtained from any of the above cited strains of HCV or from newly discovered isolates isolated from tissues or fluids of infected patients
  • compositions A. Compositions
  • the envelope polypeptides or other immunogens may be provided in immunogenic compositions, in e.g., prophylactic (i.e., to prevent infection) or therapeutic (to treat HCV following infection) vaccine compositions.
  • the compositions can comprise mixtures of more than one envelope polypeptide, at least one of the polypeptides derived from any one of HCV genotypes 1, 4, 5 and/or 6, and at least one of the polypeptides derived from HCV genotype 2 and/or 3.
  • HCV envelope polypeptides from all of these genotypes can be present, if desired.
  • the compositions will include at least an envelope polypeptide from HCV genotype 1, 4, 5 or 6, such as from HCV-Ia, 4a, 5a or 6a, and at least an envelope polypeptide from HCV genotype 2 or 3, preferably both of 2 and 3 such as HCV-2a and 3a.
  • two or more compositions can be provided, one including at least one envelope polypeptides derived from HCV genotypes 1, 4, 5 and/or 6, such as from HCV-Ia, 4a, 5a and/or 6a, and another composition including at least one envelope polypeptide derived from HCV genotype 2 and/or 3, such as HCV-2a and/or 3 a.
  • separate compositions, each with an HCV envelope polypeptide from each of these six genotypes can be provided, if desired.
  • compositions will generally include one or more "pharmaceutically acceptable excipients or vehicles" such as water, saline, glycerol, ethanol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.
  • pharmaceutically acceptable excipients or vehicles such as water, saline, glycerol, ethanol, etc.
  • auxiliary substances such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.
  • a carrier is optionally present which is a molecule that does not itself induce the production of antibodies harmful to the individual receiving the composition.
  • Suitable carriers are typically large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycollic acids, polymeric amino acids, amino acid copolymers, lipid aggregates (such as oil droplets or liposomes), and inactive virus particles.
  • Such carriers are well known to those of ordinary skill in the art.
  • the HCV polypeptide may be conjugated to a bacterial toxoid, such as toxoid from diphtheria, tetanus, cholera, etc.
  • compositions of the invention can also be used in compositions of the invention, for example, mineral salts such as hydrochlorides, hydrobromides, phosphates, or sulfates, as well as salts of organic acids such as acetates, proprionates, malonates, or benzoates.
  • mineral salts such as hydrochlorides, hydrobromides, phosphates, or sulfates
  • organic acids such as acetates, proprionates, malonates, or benzoates.
  • Especially useful protein substrates are serum albumins, keyhole limpet hemocyanin, immunoglobulin molecules, thyroglobulin, ovalbumin, tetanus toxoid, and other proteins well known to those of skill in the art.
  • compositions of the invention can also contain liquids or excipients, such as water, saline, glycerol, dextrose, ethanol, or the like, singly or in combination, as well as substances such as wetting agents, emulsifying agents, or pH buffering agents.
  • the proteins or polynucleotides of the invention can also be adsorbed to, entrapped within or otherwise associated with liposomes and particulate carriers such as PLG. Liposomes and other particulate carriers are described above.
  • co-stimulatory molecules which improve immunogen presentation to lymphocytes, such as B7-1 or B7-2, or cytokines, lymphokines, and chemokines, including but not limited to cytokines such as IL-2, modified IL-2 (cysl25 to serl25), GM-CSF, IL-12, ⁇ - interferon, IP-IO, MlPl ⁇ , FLP-3, ribavirin and RANTES, may be included in the composition.
  • adjuvants can also be included in a composition.
  • Adjuvants which can be used include, but are not limited to: (1) aluminum salts (alum), such as aluminum hydroxide, aluminum phosphate, aluminum sulfate, etc; (2) oil-in-water emulsion formulations (with or without other specific immunostimulating agents such as muramyl peptides (see below) or bacterial cell wall components), such as for example (a) MF59 (PCT Publ. No.
  • aluminum salts alum
  • oil-in-water emulsion formulations with or without other specific immunostimulating agents such as muramyl peptides (see below) or bacterial cell wall components
  • a) MF59 PCT Publ. No.
  • WO 90/14837 containing 5% Squalene, 0.5% TWEEN 80, and 0.5% SPAN 85 (optionally containing various amounts of MTP-PE ), formulated into submicron particles using a microfluidizer such as Model HOY microfluidizer (Microfluidics, Newton, MA), (b) SAF, containing 10% Squalane, 0.4% TWEEN 80, 5% pluronic-blocked polymer L 121, and thr-MDP (see below) either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion, and (c) RibiTM adjuvant system (RAS), (Ribi Immunochem, Hamilton, MT) containing 2% Squalene, 0.2% TWEEN 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton
  • MPL monophosphorylipid A
  • CWS preferably MPL + CWS (DetoxTM);
  • saponin adjuvants such as QS21 or StimulonTM (Cambridge Bioscience, Worcester, MA) may be used or particles generated therefrom such as ISCOMs (immunostimulating complexes), which ISCOMs may be devoid of additional detergent (see, e.g., International Publication No. WO 00/07621);
  • CFA Complete Freunds Adjuvant
  • IFA Incomplete Freunds Adjuvant
  • cytokines such as interleukins, such as IL-I, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 etc. (see, e.g., International Publication No.
  • interferons such as gamma interferon, macrophage colony stimulating factor (M-CSF), tumor necrosis factor (TNF), etc.
  • M-CSF macrophage colony stimulating factor
  • TNF tumor necrosis factor
  • a bacterial ADP-ribosylating toxin such as a cholera toxin (CT), a pertussis toxin (PT), or an E.
  • coli heat-labile toxin particularly LT-K63 (where lysine is substituted for the wild-type amino acid at position 63)
  • LT-R72 where arginine is substituted for the wild-type amino acid at position 72
  • CT-S 109 where serine is substituted for the wild-type amino acid at position 109
  • PT-K9/G129 where lysine is substituted for the wild-type amino acid at position 9 and glycine substituted at position 129)
  • W093/13202 and W092/19265 monophosporyl lipid A (MPL) or 3-O-deacylated MPL (3dMPL) (see, e.g., GB 2220221; EPA 0689454), optionally in the substantial absence of alum (see, e.g., International Publication No. WO 00/56358); (8) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulations (see, e.g., EPA 0835318; EPA 0735898; EPA 0761231); (9) a polyoxyethylene ether or a polyoxyethylene ester (see, e.g., International Publication No.
  • WO 99/52549 (10) an immunostimulatory oligonucleotide such as a CpG oligonucleotide, or a saponin and an immunostimulatory oligonucleotide, such as a CpG oligonucleotide (see, e.g., International Publication No. WO 00/62800); (11) an immunostimulant and a particle of a metal salt (see, e.g., International Publication No. WO 00/23105); (12) a saponin and an oil-in-water emulsion (see, e.g., International Publication No.
  • WO 99/11241 (13) a saponin (e.g., QS21) + 3dMPL + IL-12 (optionally + a sterol) (see, e.g., International Publication No. WO 98/57659); (14) the MPL derivative RC529; and (15) other substances that act as immunostimulating agents to enhance the effectiveness of the composition.
  • Alum and MF59 are preferred.
  • muramyl peptides include, but are not limited to,
  • HCV polypeptides can be adsorbed to, or entrapped within, an
  • ISCOM Classic ISCOMs are formed by combination of cholesterol, saponin, phospholipid, and immunogens. Generally, immunogens (usually with a hydrophobic region) are solubilized in detergent and added to the reaction mixture, whereby ISCOMs are formed with the immunogen incorporated therein. ISCOM matrix compositions are formed identically, but without viral proteins. Proteins with high positive charge may be electrostatically bound in the ISCOM particles, rather than through hydrophobic forces.
  • ISCOMs for use with the present invention are produced using standard techniques, well known in the art, and are described in e.g., U.S. Patent Nos. 4,981,684, 5,178,860, 5,679,354 and 6,027,732; European Publ. Nos. EPA 109,942; 180,564 and 231,039; Coulter et al. (1998) Vaccine 16:1243.
  • the term "ISCOM" refers to immunogenic complexes formed between glycosides, such as triterpenoid saponins (particularly Quil A), and antigens which contain a hydrophobic region. See, e.g., European Publ. Nos. EPA 109,942 and 180,564.
  • the HCV polypeptides (usually with a hydrophobic region) are solubilized in detergent and added to the reaction mixture, whereby ISCOMs are formed with the polypeptides incorporated therein.
  • the HCV polypeptide ISCOMs are readily made with HCV polypeptides which show amphipathic properties.
  • proteins and peptides which lack the desirable hydrophobic properties may be incorporated into the immunogenic complexes after coupling with peptides having hydrophobic amino acids, fatty acid radicals, alkyl radicals and the like.
  • the presence of antigen is not necessary in order to form the basic ISCOM structure (referred to as a matrix or ISCOMATRIX), which may be formed from a sterol, such as cholesterol, a phospholipid, such as phosphatidylethanolamine, and a glycoside, such as Quil A.
  • a matrix or ISCOMATRIX which may be formed from a sterol, such as cholesterol, a phospholipid, such as phosphatidylethanolamine, and a glycoside, such as Quil A.
  • the HCV polypeptide of interest rather than being incorporated into the matrix, is present on the outside of the matrix, for example adsorbed to the matrix via electrostatic interactions.
  • HCV polypeptides with high positive charge may be electrostatically bound to the ISCOM particles, rather than through hydrophobic forces.
  • the ISCOM matrix may be prepared, for example, by mixing together solubilized sterol, glycoside and (optionally) phospholipid. If phospholipids are not used, two dimensional structures are formed. See, e.g., European Publ. No. EPA 231 ,039.
  • the term "ISCOM matrix" is used to refer to both the 3-dimensional and 2- dimensional structures.
  • the glycosides to be used are generally glycosides which display amphipathic properties and comprise hydrophobic and hydrophilic regions in the molecule.
  • saponins are used, such as the saponin extract from Quillaja saponaria Molina and Quil A. Other preferred saponins are aescine from Aesculus hippocastanum (Part et al.
  • glycosides are used in at least a critical micelle-forming concentration. In the case of Quil A, this concentration is about 0.03% by weight.
  • the sterols used to produce ISCOMs may be known sterols of animal or vegetable origin, such as cholesterol, lanosterol, lumisterol, stigmasterol and sitosterol. Suitable phospholipids include phosphatidylcholine and phosphatidylethanolamine.
  • the molar ratio of glycoside (especially when it is Quil A) to sterol (especially when it is cholesterol) to phospholipid is 1:1:0-1, + 20% (preferably not more than +10%) for each figure. This is equivalent to a weight ratio of about 5:1 for the Quil Axholesterol.
  • a solubilizing agent may also be present and may be, for example a detergent, urea or guanidine.
  • a non-ionic, ionic or zwitter-ionic detergent or a cholic acid based detergent such as sodium desoxycholate, cholate and CTAB
  • detergents include, but are not limited to, octylglucoside, nonyl N-methyl glucamide or decanoyl N-methyl glucamide, alkylphenyl polyoxyethylene ethers such as a polyethylene glycol p-isooctyl-phenylether having 9 to 10 oxyethylene groups (commercialized under the trade name TRITON X- 100RTM) 5 acylpolyoxy ethylene esters such as acylpolyoxyethylene sorbitane esters (commercialized under the trade name TWEEN 2 ⁇ TM , TWEEN 80TM and the like).
  • the solubilizing agent is generally removed for formation of the ISCOMs, such as by ultrafiltration, dialysis, ultracentrifugation or chromatography, however, in certain methods, this step is unnecessary. (See, e.g., U.S. Patent No. 4,981,684).
  • the ratio of glycoside, such as QuilA, to HCV fusion by weight is in the range of 5:1 to 0.5:1.
  • the ratio by weight is approximately 3:1 to 1:1, and more preferably the ratio is 2:1.
  • the ISCOMs may be formulated into compositions and administered to animals, as described herein. If desired, the solutions of the immunogenic complexes obtained may be lyophilized and then reconstituted before use.
  • HCV envelope polypeptides including E1E2 complexes
  • compositions that include a submicron oil-in-water emulsion such as MF59 and/or oligonucleotides containing immunostimulatory nucleic acid sequences (ISS), such as CpY, CpR and unmethylated CpG motifs (a cytosine followed by guanosine and linked by a phosphate bond).
  • ISS immunostimulatory nucleic acid sequences
  • CpY, CpR and unmethylated CpG motifs a cytosine followed by guanosine and linked by a phosphate bond
  • compositions including the HCV envelope polypeptides or polynucleotides described above can be used in combination with other HCV immunogenic proteins, and/or compositions comprising the same.
  • the HCV envelope proteins can be used in combination with any of the various HCV immunogenic proteins derived from one or more of the regions of the HCV polyprotein described in Table 1.
  • the additional HCV immunogenic proteins can be provided in compositions with excipients, adjuvants, immunstimulatory molecules and the like, as described above.
  • the compositions of the present invention may be administered in conjunction with a number of immunoregulatory agents and will usually include an adjuvant.
  • agents and adjuvants for use with the compositions include, but are not limited to, any of those substances described above, as well as one or more of the following set forth below.
  • Mineral containing compositions suitable for use as adjuvants in the invention include mineral salts, such as aluminum salts and calcium salts.
  • the invention includes mineral salts such as hydroxides (e.g. oxyhydroxides), phosphates (e.g. hydroxyphosphates, orthophosphates), sulfates, etc. (e.g. see chapters 8 & 9 of Vaccine Design (1995) eds. Powell & Newman. ISBN: 030644867X. Plenum), or mixtures of different mineral compounds (e.g. a mixture of a phosphate and a hydroxide adjuvant, optionally with an excess of the phosphate), with the compounds taking any suitable form (e.g. gel, crystalline, amorphous, etc.), and with adsorption to the salt(s) being preferred.
  • the mineral containing compositions may also be formulated as a particle of metal salt (PCT Publication No. WO00/23105).
  • Aluminum salts may be included in compositions of the invention such that the dose OfAl 3+ is between 0.2 and 1.0 mg per dose.
  • the aluminum- based adjuvant for use in the present compositions is alum' (aluminum potassium sulfate (AlK(SCU) 2 )), or an alum derivative, such as that formed in situ by mixing an antigen in phosphate buffer with alum, followed by titration and precipitation with a base such as ammonium hydroxide or sodium hydroxide.
  • Aluminum-based adjuvant for use in vaccine formulations of the present invention is aluminum hydroxide adjuvant (A1(OH)3) or crystalline aluminum oxyhydroxide (AlOOH), which is an excellent adsorbant, having a surface area of approximately 500m 2 /g.
  • AlPO 4 aluminum phosphate adjuvant
  • Al hydroxyphosphate aluminum hydroxyphosphate, which contains phosphate groups in place of some or all of the hydroxyl groups of aluminum hydroxide adjuvant is provided.
  • Preferred aluminum phosphate adjuvants provided herein are amorphous and soluble in acidic, basic and neutral media.
  • the adjuvant for use with the present compositions comprises both aluminum phosphate and aluminum hydroxide.
  • the adjuvant has a greater amount of aluminum phosphate than aluminum hydroxide, such as a ratio of 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1 or greater than 9:1, by weight aluminum phosphate to aluminum hydroxide.
  • aluminum salts may be present at 0.4 to 1.0 mg per vaccine dose, or 0.4 to 0.8 mg per vaccine dose, or 0.5 to 0.7 mg per vaccine dose, or about 0.6 mg per vaccine dose.
  • the preferred aluminum-based adjuvant(s), or ratio of multiple aluminum-based adjuvants, such as aluminum phosphate to aluminum hydroxide is selected by optimization of electrostatic attraction between molecules such that the antigen carries an opposite charge as the adjuvant at the desired pH.
  • adsorbs lysozyme but not albumin at pH 7.4.
  • albumin be the target
  • aluminum hydroxide adjuvant would be selected (iep 11.4).
  • pretreatment of aluminum hydroxide with phosphate lowers its isoelectric point, making it a preferred adjuvant for more basic antigens.
  • Oil emulsion compositions suitable for use as adjuvants in the compositions include squalene-water emulsions. Particularly preferred adjuvants are submicron oil- in-water emulsions. Preferred submicron oil-in-water emulsions for use herein are squalene/water emulsions optionally containing varying amounts of MTP-PE, such as a submicron oil-in-water emulsion containing 4-5% w/v squalene, 0.25-1.0% w/v Tween 80TM (polyoxyelthylenesorbitan monooleate), and/or 0.25-1.0% Span 85TM (sorbitan trioleate), and, optionally, N-acetylmuramyl-L-alanyl-D-isogluatminyl-L- alanine-2-(l'-2'-dipalmitoyl-5 «-glycero-3-huydroxyphosphophoryloxy)-
  • MF59 contains 4-5% w/v Squalene (e.g.
  • MTP-PE may be present in an amount of about 0-500 ⁇ g/dose, more preferably 0-250 ⁇ g/dose and most preferably, 0-100 ⁇ g/dose.
  • MF59-0 refers to the above submicron oil-in-water emulsion lacking MTP-PE, while the term MF59-MTP denotes a formulation that contains MTP-PE.
  • MF59-100 contains 100 ⁇ g MTP-PE per dose, and so on.
  • MF69 another submicron oil-in-water emulsion for use herein, contains 4.3% w/v squalene, 0.25% w/v Tween 80TM, and 0.75% w/v Span 85TM and optionally MTP-PE.
  • MF75 also known as SAF, containing 10% squalene, 0.4% Tween 80TM, 5% pluronic- blocked polymer L121, and thr-MDP, also microfluidized into a submicron emulsion.
  • MF75-MTP denotes an MF75 formulation that includes MTP, such as from 100-400 ⁇ g MTP-PE per dose.
  • Submicron oil-in-water emulsions methods of making the same and immunostimulating agents, such as muramyl peptides, for use in the compositions, are described in detail in International Publication No. WO90/14837 and US Patent Nos. 6,299,884 and 6,451,325.
  • Complete Freund's adjuvant (CFA) and incomplete Freund's adjuvant (IFA) may also be used as adjuvants in the subject compositions.
  • Saponin formulations may also be used as adjuvants in the compositions.
  • Saponins are a heterologous group of sterol glycosides and triterpenoid glycosides that are found in the bark, leaves, stems, roots and even flowers of a wide range of plant species. Saponins isolated from the bark of the Quillaia saponaria Molina tree have been widely studied as adjuvants. Saponins can also be commercially obtained from Smilax ornata (sarsaprilla), Gypsophilla paniculata (brides veil), and Saponaria offidanalis (soap root).
  • Saponin adjuvant formulations include purified formulations, such as QS21, as well as lipid formulations, such as ISCOMs.
  • the saponin is QS21.
  • a method of production of QS21 is disclosed in US
  • Saponin formulations may also comprise a sterol, such as cholesterol (see, PCT Publication No. WO96/33739).
  • ISCOMs Immunostimulating Complexes
  • phospholipid such as phosphatidylethanolamine or phosphatidylcholine.
  • the ISCOM includes one or more of Quil A, QHA and QHC.
  • ISCOMs are further described in EP0109942,
  • the ISCOMS may be devoid of (an) additional detergent(s). See WO00/07621.
  • VLPs Virosomes and Virus Like Particles
  • Virosomes and Virus Like Particles can also be used as adjuvants with the present compositions.
  • These structures generally contain one or more proteins from a virus optionally combined or formulated with a phospholipid. They are generally non-pathogenic, non-replicating and generally do not contain any of the native viral genome. The viral proteins may be recombinantly produced or isolated from whole viruses.
  • viral proteins suitable for use in virosomes or VLPs include proteins derived from influenza virus (such as HA or NA), Hepatitis B virus (such as core or capsid proteins), Hepatitis E virus, measles virus, Sindbis virus, Rotavirus, Foot-and-Mouth Disease virus, Retrovirus, Norwalk virus, human Papilloma virus, HIV, RNA-phages, Q ⁇ -phage (such as coat proteins), GA-phage, fr- phage, AP205 phage, and Ty (such as retrotransposon Ty protein pi).
  • influenza virus such as HA or NA
  • Hepatitis B virus such as core or capsid proteins
  • Hepatitis E virus measles virus
  • Sindbis virus Rotavirus
  • Foot-and-Mouth Disease virus Retrovirus
  • Norwalk virus Norwalk virus
  • human Papilloma virus HIV
  • RNA-phages Q ⁇ -phage (such as coat proteins)
  • GA-phage such as fr- phag
  • VLPs are discussed further in WO03/024480, WO03/024481, and Niikura et al., "Chimeric Recombinant Hepatitis E Virus-Like Particles as an Oral Vaccine Vehicle Presenting Foreign Epitopes", Virology (2002) 293:273-280; Lenz et al., “Papillomarivurs-Like Particles Induce Acute Activation of Dendritic Cells", Journal of Immunology (2001) 5246-5355; Pinto, et al., “Cellular Immune Responses to Human Papillomavirus (HPV)-16 Ll Healthy Volunteers Immunized with Recombinant HPV-16 Ll Virus- Like Particles", Journal of Infectious Diseases (2003) 188:327-338; and Gerber et al., "Human Papillomavrisu Virus-Like Particles Are Efficient Oral Immunogens when Coadministered with Es
  • Virosomes are discussed further in, for example, Gluck et al., "New Technology Platforms in the Development of Vaccines for the Future", Vaccine (2002) 20:B10 -B16.
  • Immunopotentiating reconstituted influenza virosomes are used as the subunit antigen delivery system in the intranasal trivalent INFLEXALTM product (Mischler & Metcalfe (2002) Vaccine 20 Suppl 5:B17-23) and the INFLUVAC PLUSTM product.
  • Adjuvants suitable for use in the present compositions include bacterial or microbial derivatives such as: (1) Non-toxic derivatives of enterobacterial lipopolysaccharide (LPS)
  • Such derivatives include Monophosphoryl lipid A (MPL) and 3-O-deacylated MPL (3dMPL).
  • 3dMPL is a mixture of 3 De-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains.
  • a preferred "small particle" form of 3 De-O-acylated monophosphoryl lipid A is disclosed in EP 0 689454. Such "small particles" of 3dMPL are small enough to be sterile filtered through a 0.22 micron membrane (see EP 0 689 454).
  • Other non-toxic LPS derivatives include monophosphoryl lipid A mimics, such as aminoalkyl glucosaminide phosphate derivatives e.g. RC-529. See Johnson et al. (1999) BioorgMed Chem Lett 9:2273-2278.
  • Lipid A derivatives include derivatives of lipid A from Escherichia coli such as OM-174.
  • OM-174 is described for example in Meraldi et al., "OM-174, a New Adjuvant with a Potential for Human Use, Induces a Protective Response with Administered with the Synthetic C-Terminal Fragment 242-310 from the circumsporozoite protein of Plasmodium berghei", Vaccine (2003) 21:2485-2491; and Pajak, et al., "The Adjuvant OM-174 induces both the migration and maturation of murine dendritic cells in vivo", Vaccine (2003) 21:836-842.
  • Immunostimulatory oligonucleotides are described for example in Meraldi et al., "OM-174, a New Adjuvant with a Potential for Human Use, Induces a Protective Response with Administered with the Synthetic C-Terminal Fragment 242-310 from
  • Immunostimulatory oligonucleotides suitable for use as adjuvants include nucleotide sequences containing a CpG motif (a sequence containing an unmethylated cytosine followed by guanosine and linked by a phosphate bond). Bacterial double stranded RNA or oligonucleotides containing palindromic or poly(dG) sequences have also been shown to be immunostimulatory.
  • the CpG' s can include nucleotide modifications/analogs such as phosphorothioate modifications and can be double-stranded or single-stranded.
  • the guanosine may be replaced with an analog such as 2'-deoxy-7- deazaguanosine.
  • Kandimalla, et al. "Divergent synthetic nucleotide motif recognition pattern: design and development of potent immunomodulatory oligodeoxyribonucleotide agents with distinct cytokine induction profiles", Nucleic Acids Research (2003) 3_1(9): 2393-2400; WO02/26757 and WO99/62923 for examples of possible analog substitutions.
  • the adjuvant effect of CpG oligonucleotides is further discussed in Krieg, "CpG motifs: the active ingredient in bacterial extracts?”, Nature Medicine (2003) 9(7): 831-835; McCluskie, et al.,
  • mice with hepatitis B surface antigen and CpG DNA FEMS Immunology and Medical Microbiology (2002) 32:179-185; WO98/40100; US Patent No. 6,207,646; US Patent No. 6,239,116 and US Patent No. 6,429,199.
  • the CpG sequence may be directed to TLR9, such as the motif GTCGTT or
  • the CpG sequence may be specific for inducing a ThI immune response, such as a CpG-A ODN, or it may be more specific for inducing a B cell response, such a CpG-B ODN.
  • CpG-A and CpG-B ODNs are discussed in Blackwell, et al., "CpG-A-Induced Monocyte IFN-gamma-Inducible Protein- 10 Production is Regulated by Plasmacytoid Dendritic Cell Derived IFN- alpha", J. Immunol. (2003) 170(8):4061-4068; Krieg, “From A to Z on CpG”, TRENDS in Immunology (2002) 23(2): 64-65 and WO01/95935.
  • the CpG is a CpG-A ODN.
  • the CpG oligonucleotide is constructed so that the 5' end is accessible for receptor recognition.
  • two CpG oligonucleotide sequences may be attached at their 3' ends to form "immunomers".
  • Kandimalla "Secondary structures in CpG oligonucleotides affect immunostimulatory activity" BBRC (2003) 306:948-953; Kandimalla, et al., "Toll- like receptor 9: modulation of recognition and cytokine induction by novel synthetic GpG DNAs", Biochemical Society Transactions (2003) 3J,(part 3):664-658; Bhagat et al., "CpG penta- and hexadeoxyribonucleotides as potent immunomodulatory agents” BBRC (2003) 300:853-861 and WO03/035836.
  • ADP-ribosylating toxins and detoxified derivatives thereof Bacterial ADP-ribosylating toxins and detoxified derivatives thereof may be used as adjuvants in the compositions.
  • the protein is derived from E. coli (i.e., E. coli heat labile enterotoxin "LT), cholera ("CT"), or pertussis ("PT").
  • E. coli heat labile enterotoxin
  • CT cholera
  • PT pertussis
  • the use of detoxified ADP-ribosylating toxins as mucosal adjuvants is described in WO95/17211 and as parenteral adjuvants in WO98/42375.
  • the adjuvant is a detoxified LT mutant such as LT-K63, LT-R72, and LTR192G.
  • LT-K63 LT-K63
  • LT-R72 LT-R72
  • LTR192G LTR192G
  • Numerical reference for amino acid substitutions is preferably based on the alignments of the A and B subunits of ADP-ribosylating toxins set forth in Domenighini et al., MoI. Microbiol (1995) JJ5(6):1165-1167.
  • Bioadhesives and mucoadhesives may also be used as adjuvants in the subject compositions.
  • Suitable bioadhesives include esterified hyaluronic acid microspheres (Singh et al. (2001) J. Cont. ReIe. 70:267-276) or mucoadhesives such as cross-linked derivatives of polyacrylic acid, polyvinyl alcohol, polyvinyl pyrollidone, polysaccharides and carboxymethylcellulose. Chitosan and derivatives thereof may also be used as adjuvants in the compositions. See, e.g., WO99/27960.
  • Microparticles may also be used as adjuvants in the compositions.
  • Microparticles i.e. a particle of ⁇ 100 nm to ⁇ 150 ⁇ m in diameter, more preferably ⁇ 200 nm to ⁇ 30 ⁇ m in diameter, and most preferably ⁇ 500 nm to ⁇ 10 ⁇ m in diameter
  • materials that are biodegradable and non-toxic e.g. a poly( ⁇ -hydroxy acid), a polyhydroxybutyric acid, a polyorthoester, a polyanhydride, a polycaprolactone, etc.
  • a negatively-charged surface e.g. with SDS
  • a positively-charged surface e.g. with a cationic detergent, such as CTAB
  • liposome formulations suitable for use as adjuvants are described in US Patent No. 6,090,406, US Patent No. 5,916,588, and EP 0 626 169.
  • Adjuvants suitable for use in the compositions include polyoxyethylene ethers and polyoxyethylene esters. See, e.g., WO99/52549. Such formulations further include polyoxyethylene sorbitan ester surfactants in combination with an octoxynol (WO01/21207) as well as polyoxyethylene alkyl ethers or ester surfactants in combination with at least one additional non-ionic surfactant such as an octoxynol (WO01/21152).
  • Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether (laureth 9), polyoxyethylene-9-steoryl ether, polyoxytheylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35- lauryl ether, and polyoxyethylene-23-lauryl ether.
  • PCPP J. Polvphosphazene
  • PCPP formulations are described, for example, in Andrianov et al., "Preparation of hydrogel microspheres by coacervation of aqueous polyphophazene solutions", Biomaterials (1998) 19(1-3): 109-115 and Payne et al., “Protein Release from Polyphosphazene Matrices", Adv. Drug. Delivery Review (1998) 31(3): 185- 196.
  • Muramyl peptides examples include N-acetyl- muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-1-alanyl-d- isoglutamine (nor-MDP), and N ⁇ acetylmuramyl-l-alanyl-d-isoglutaminyl-l-alanine-2- ( 1 '-2'-dipalmitoyl-sn-glycero-3 -hydroxyphosphoryloxy)-ethylamine MTP-PE) .
  • thr-MDP N-acetyl- muramyl-L-threonyl-D-isoglutamine
  • nor-MDP N-acetyl-normuramyl-1-alanyl-d- isoglutamine
  • imidazoquinoline compounds suitable for use as adjuvants in the compositions include Imiquimod and its analogues, described further in Stanley, “Imiquimod and the imidazoquinolines: mechanism of action and therapeutic potential” Clin Exp Dermatol (2002) 27(7):571-577; Jones, “Resiquimod 3M", Curr Opin Investig Drugs (2003) 4(2):214-218; Wu et al. (2004) Antiviral Res. 64(2):79- 83; Vasilakos et al. (2000) Cell Immunol.
  • Preferred SMIPs include:
  • thiosemicarbazone compounds as well as methods of formulating, manufacturing, and screening for compounds all suitable for use as adjuvants in the compositions include those described in WO04/60308.
  • the thiosemicarbazones are particularly effective in the stimulation of human peripheral blood mononuclear cells for the production of cytokines, such as TNF- ⁇ .
  • cytokines such as TNF- ⁇ .
  • tryptanthrin compounds as well as methods of formulating, manufacturing, and screening for compounds all suitable for use as adjuvants in the compositions include those described in WO04/64759.
  • the tryptanthrin compounds are particularly effective in the stimulation of human peripheral blood mononuclear cells for the production of cytokines, such as TNF- ⁇ .
  • nucleoside analogs examples include: (a) Isatorabine (ANA-245; 7- thia-8-oxoguanosine):
  • Rl and R2 are each independently H, halo, -NRaRb, -OH, C 1 -6 alkoxy, substituted C 1-6 alkoxy, heterocyclyl, substituted heterocyclyl, C6-10 aryl, substituted C6-10 aryl, C 1-6 alkyl, or substituted C 1-6 alkyl;
  • R3 is absent, H, C 1-6 alkyl, substituted C 1-6 alkyl, C6-10 aryl, substituted C6-
  • R4 and R5 are each independently H, halo, heterocyclyl, substituted heterocyclyl, C(O)-Rd, C 1-6 alkyl, substituted C 1-6 alkyl, or bound together to form a 5 membered ring as in R4-5:
  • the binding being achieved at the bonds indicated by a - ⁇ > ⁇ - Xl and X2 are each independently N, C, O, or S;
  • R8 is H, halo, -OH, Cl-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, -OH, -NRaRb, -(CH2)n- O-Rc, -0-(C 1 -6 alkyl), -S(O)pRe, or -C(O)-Rd;
  • R9 is H, Cl-6 alkyl, substituted Cl-6 alkyl, heterocyclyl, substituted heterocyclyl or R9a, wherein R9a is:
  • RlO and RIl are each independently H, halo, Cl-6 alkoxy, substituted Cl-6 alkoxy, -
  • Human immunomodulators suitable for use as adjuvants in the compositions include cytokines, such as interleukins (e.g. IL-I, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (e.g. interferon- ⁇ ), macrophage colony stimulating factor, and tumor necrosis factor.
  • cytokines such as interleukins (e.g. IL-I, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (e.g. interferon- ⁇ ), macrophage colony stimulating factor, and tumor necrosis factor.
  • the compositions may also comprise combinations of aspects of one or more of the adjuvants identified above.
  • the following adjuvant compositions may be used in the invention:
  • combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulsions See European patent applications 0835318, 0735898 and 0761231); (6) SAF, containing 10% Squalane, 0.4% Tween 80, 5% pluronic-block polymer L121, and thr-MDP, either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion.
  • RibiTM adjuvant system (RAS), (Ribi Immunochem) containing 2% Squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphory lipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL + CWS (DetoxTM); and
  • one or more mineral salts such as an aluminum salt
  • a non-toxic derivative of LPS such as 3dPML
  • one or more mineral salts such as an aluminum salt
  • an immunostimulatory oligonucleotide such as a nucleotide sequence including a CpG motif
  • Aluminum salts and MF59 are preferred adjuvants for use with injectable vaccines.
  • Bacterial toxins and bioadhesives are preferred adjuvants for use with mucosally-delivered vaccines, such as nasal vaccines.
  • mucosally-delivered vaccines such as nasal vaccines.
  • compositions described above are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared.
  • the compositions are conventionally administered parenterally, e.g., by injection, either subcutaneously or intramuscularly. Additional formulations suitable for other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications.
  • Dosage treatment may be a single dose schedule or a multiple dose schedule.
  • the effective amount is sufficient to bring about treatment or prevention of disease symptoms.
  • the exact amount necessary will vary depending on the subject being treated; the age and general condition of the individual to be treated; the capacity of the individual's immune system to synthesize antibodies; the degree of protection desired; the severity of the condition being treated; the particular macromolecule selected and its mode of administration, among other factors.
  • An appropriate effective amount can be readily determined by one of skill in the art.
  • a "therapeutically effective amount” will fall in a relatively broad range that can be determined through routine trials using in vitro and in vivo models known in the art.
  • the composition is preferably injected intramuscularly to a large mammal, such as a primate, for example, a baboon, chimpanzee, or human.
  • the amount of polypeptide administered will generally be about 0.1 ⁇ g to about 5.0 mg per dose, or any amount between the stated ranges, such as .5 ⁇ g to about 10 mg, 1 ⁇ g to about 2 mg, 2.5 ⁇ g to about 250 ⁇ g, 4 ⁇ g to about 200 ⁇ g, such as 4, 5, 6, 7, 8, 9, 10...20...30...40...50...60...70...80...90...100, etc., ⁇ g per dose.
  • the compositions can be administered either to a mammal that is not infected with an HCV or can be administered to an HCV-infected mammal.
  • HCV polypeptides can elicit a cellular immune response, and/or an anti-El, anti-E2 and/or anti-El E2 antibody titer in the mammal that lasts for at least 1 week, 2 weeks, 1 month, 2 months, 3 months, 4 months, 6 months, 1 year, or longer.
  • the HCV envelope polypeptides can also be administered to provide a memory response. If such a response is achieved, antibody titers may decline over time, however exposure to the HCV virus or immunogen results in the rapid induction of antibodies, e.g., within only a few days.
  • antibody titers can be maintained in a mammal by providing one or more booster injections of the polypeptides at 2 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 1 year, or more after the primary injection.
  • an antibody titer of at least 10, 100, 150, 175, 200, 300, 400, 500, 750, 1,000, 1,500, 2,000, 3,000, 5,000, 10,000, 20,000, 30,000, 40,000, 50,000 (geometric mean titer), or higher, is elicited, or any number between the stated titer, as determined using a standard immunoassay, such as the immunoassay described in, e.g., Chien et al., Lancet (1993) 342:933; and Chien et al., Proc. Natl. Acad. ScL USA (1992) 89:10011.
  • neutralization assays can be performed using techniques well known in the art. For example sera can be isolated from an immunized subject and analyzed using an HCV pseudotyped retroviral particle (HCVpp) assay, as described in e.g., Meunier et al., Proc. Natl. Acad. ScL USA (2005) 102:4560-4565; Bartosch et al., J. Exp. Med. (2003) 197:633-642.
  • HCVpp HCV pseudotyped retroviral particle
  • compositions of the invention can be given in a single dose schedule, or preferably in a multiple dose schedule in which a primary course of vaccination includes 1-10 separate doses, followed by other doses given at subsequent time intervals required to maintain and/or reinforce an immune response, for example, at 1-4 months for a second dose, and if needed, a subsequent dose or doses after several months.

Abstract

Immunogenic compositions comprising HCV immunogenic polypeptides that cross-neutralize multiple HCV genotypes, as well as methods of using the immunogenic polypeptides are described. In particular, the invention relates to compositions comprising HCV envelope polypeptides that cross-neutralize at least two HCV genotypes selected from HCV-1, HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6. Preferably, the HCV envelope polypeptides cross-neutralize all six of these HCV genotypes.

Description

CROSS-NEUTRALIZATION OF HCV WITH RECOMBINANT PROTEINS
CROSS-REFERENCE TO RELATED APPLICATION
This application claims the benefit under 35 U.S.C. §119(e)(l) of U.S. Provisional Application 60/722,635, filed September 30, 2006, which application is incorporated herein by reference in its entirety.
TECHNICAL FIELD
The present invention pertains generally to immunogenic compositions comprising HCV immunogenic polypeptides that cross-neutralize the infectivity of multiple HCV genotypes. In particular, the invention relates to compositions comprising HCV envelope polypeptides that cross-neutralize the infectivity of HCV genotypes selected from HCV-I, HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6.
BACKGROUND Hepatitis C virus (HCV) was identified over a decade ago and is now known to be the leading cause of non-A and non-B viral hepatitis (Choo et al., Science (1989) 244:359-362; Armstrong et al., Hepatology (2000) 3k777). HCV infects approximately 3% of the world population, an estimated 200 million people (Cohen, J., Science (1999) 285:26). About 30,000 newly acquired HCV infections occur in the United States annually. Additionally, there is a large incidence of HCV infection in developing countries. Although the immune response is capable of clearing HCV infection, the majority of infections become chronic. Most acute infections remain asymptomatic and liver disease usually occurs only after years of chronic infection. The viral genomic sequence of HCV is known, as are methods for obtaining the sequence. See, e.g., International Publication Nos. WO 89/04669; WO 90/11089; and WO 90/14436. HCV has a 9.5 kb positive-sense, single-stranded RNA genome and is a member of the Flaviridae family of viruses. At least six distinct, but related genotypes of HCV, based on phylogenetic analyses, have been identified (Simmonds et al., J. Gen. Virol (1993) 74:2391-2399). The virus encodes a single polyprotein having about 3000 amino acid residues (Choo et al., Science (1989) 244:359-362: Choo et al., Proc. Natl Acad. ScL USA (1991) 88:2451-2455; Han et al., Proc. Natl Acad. Sci. USA (1991) 88:1711-1715). In particular, as shown in Figure 1, several proteins are encoded by the HCV genome. The order and nomenclature of the cleavage products of the HCV polyprotein is as follows: NH2-C-El-E2-ρ7-NS2-NS3-NS4a-NS4b-NS5a-NS5b- COOH. Another protein (F) has also been identified and results from translational frame-shifting within the C gene. Branch et al., Semin. Liver Dis. (2005) 25: 105-117. Initial cleavage of the polyprotein is catalyzed by host proteases which liberate three structural proteins, the N-terminal nucleocapsid protein (termed "core") and two envelope glycoproteins, gpEl (also known as E) and gpE2 (also known as E2/NS1), as well as nonstructural (NS) proteins that encode the viral enzymes and other activities. The NS regions are termed NS2, NS3, NS4 and NS5. NS2 is an integral membrane protein with proteolytic activity and, in combination withNS3, cleaves the NS2-NS3 junction. The NS3 protease, along with its NS4a cofactor, serves to process the remaining polyprotein. In these reactions, NS3 liberates an NS3 cofactor (NS4a), two proteins (NS4b and NS5a), and an RNA-dependent RNA polymerase (NS5b). Completion of polyprotein maturation is initiated by autocatalytic cleavage at the NS3-NS4a junction, catalyzed by the NS3 serine protease.
El is detected as a 32-35 kDa glycoprotein species and is converted by endoglycosidase H into an approximately 18 kDa species. By contrast, E2 glycoprotein displays a complex pattern upon immunoprecipitation consistent with the generation of multiple species (Spaete et al., Virol. (1992) 188:819-830; Selby et al., J. Virol (1996) 70:5177-5182; Grakoui et al., J. Virol (1993) 67:1385-1395; Tomei et al., J. Virol (1993) 67:4017-4026.). The HCV envelope glycoproteins El and E2 form a stable complex that is co-immunoprecipitable (Grakoui et al., J. Virol. (1993) 67:1385-1395; Lanford et al., Virology (1993) 197:225-235; Ralston et al., J. Virol (1993) 67:6753-6761).
Full-length El and E2 are retained within the endoplasmic reticulum of cells and lack complex carbohydrate when expressed stably or in a transient Vaccinia virus system (Spaete et al., Virology (1992) 188:819-830; Ralston et al., J. Virol. (1993) 67:6753-6761). Since the El and E2 proteins are normally membrane-bound in these expression systems, secreted truncated forms have been produced in order to facilitate purification of the proteins. See, e.g., U.S. Patent No. 6,121,020. Additionally, intracellular production of E1E2 in HeIa cells has been described. See, e.g., International Publication No. WO 98/50556. The HCV El and E2 glycoproteins are of considerable interest because they have been shown to be protective against viral challenge in primate studies. (Choo et al, Proc. Natl. Acad. Sci. USA (1994) 91:1294-1298; Houghton, M. and Abrignani, S., Nature (2005) 436:961-966). Meunier et al., Proc. Natl. Acad. Sci. USA (2005) 102:4560-4565 used retroviral pseudoparticles displaying intact El and E2 glycoproteins and found that viral-neutralizing antibodies raised during HCV-I infections are also able to neutralize HCV genotypes 4, 5 and 6, but have only limited neutralization against HCV genotypes 2 and 3.
Currently, the only available therapies for HCV are IFN-α and ribavirin. Unfortunately, these agents are effective in less than half the patients treated (Poynard et al., Lancet (1998) 352:1426; McHutchison et al., Engl. J. Med. (1998) 339:1485V Therefore, there is an urgent need for the development of efficacious vaccines to prevent HCV infection, as well as for immunotherapies to be used as an alternative, or in conjunction with existing therapies.
SUMMARY OF THE INVENTION
The present invention provides a means for providing broad-based immunity to HCV. In particular, the present invention provides compositions and methods for treating and/or preventing HCV infection caused by more than one of HCV genotypes 1, 2, 3, 4, 5 and 6, and preferably all of these HCV genotypes. Thus, the invention eliminates the need for multiple vaccinations using immunogens from each of these genotypes. In particular, the compositions and methods of the invention include immunogenic HCV envelope polypeptides from one or more HCV genotypes selected from HCV 1, 4, 5 and/or 6, in combination with one or more immunogenic envelope polypeptides selected from HCV 2 and/or 3. The use of such combinations provides an effective approach for treating and/or preventing HCV infection caused by multiple HCV genotypes.
Accordingly, in one embodiment, the invention is directed to a composition comprising: (a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV- 5 and HCV-6; and (b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
In certain embodiments, the composition comprises an HCV envelope polypeptide from HCV-I and an HCV envelope polypeptide from HCV-2. In other embodiments, the composition comprises an HCV envelope polypeptide from HCV-4 and an HCV envelope polypeptide from HCV-2. In additional embodiments, the composition comprises an HCV envelope polypeptide from HCV-5 and an HCV envelope polypeptide from HCV-2. In further embodiments, the composition comprises an HCV envelope polypeptide from HCV-6 and an HCV envelope polypeptide from HCV-2.
In additional embodiments of any of the above compositions, the composition further comprises an HCV envelope polypeptide from HCV-3.
In yet further embodiments of any of the above compositions, the envelope polypeptide of (a) is an El polypeptide, an E2 polypeptide or an HCV E1E2 complex, such as a complex produced by a method comprising expressing a polynucleotide encoding an HCV El/E2/p7 region.
In certain embodiments of any of the above compositions, the envelope polypeptide of (b) is an El polypeptide, an E2 polypeptide or an HCV E1E2 complex, such as a complex produced by a method comprising expressing a polynucleotide encoding an HCV E l/E2/p7 region.
In additional embodiments of any of the above compositions, the envelope polypeptide of (a) and (b) is an El polypeptide, an E2 polypeptide or an HCV E1E2 complex, such as a complex produced by a method comprising expressing a polynucleotide encoding an HCV El/E2/p7 region. In yet additional embodiments of any of the above compositions, the composition further comprises an adjuvant and/or another immunostimulatory compound such as an immunostimulatory sequence, or a small molecule immune potentiator. In one embodiment, the immunostimulatory sequence can be a CpG sequence. In further embodiments of any of the above compositions, the envelope polypeptide is produced recombinantly in a mammalian host cell. In another embodiment, the invention is directed to a method of stimulating an immune response in a vertebrate subject which comprises administering to the subject a therapeutically effective amount of any one of the compositions above.
In additional embodiments, the invention is directed to a method of stimulating an immune response in a vertebrate subject. The method comprises administering to the subject a therapeutically effective amount of
(a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV- 5 and HCV-6; and (b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
In certain embodiments of the above method, (a) is administered prior to (b). In alternative embodiments, (b) is administered prior to (a). In yet further embodiments, (a) and (b) are administered concurrently. In additional embodiments, (a) and (b) are present in the same composition.
In further embodiments of any of the above methods, the envelope polypeptide is produced recombinantly in a mammalian host cell.
In further embodiments, the invention is directed to a method of making a composition comprising: combining (a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV-5 and HCV-6; with (b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
These and other embodiments of the subject invention will readily occur to those of skill in the art in view of the disclosure herein.
BRIEF DESCRIPTION OF THE FIGURES
Figure 1 is a diagrammatic representation of the HCV genome, depicting the various regions of the HCV polyprotein. Figures 2A-2C (SEQ ID NOS: 1 and 2) show the nucleotide and corresponding amino acid sequence for the HCV-Ia El/E2/p7 region. The numbers shown in the figure are relative to the full-length HCV-Ia polyprotein. The El, E2 and p7 regions are shown. Figure 3 shows neutralization antibody titers against an HCV type Ia pseudoparticle in sera from patients infected with different strains of HCV.
DETAILED DESCRIPTION OF THE INVENTION The practice of the present invention will employ, unless otherwise indicated, conventional methods of chemistry, biochemistry, recombinant DNA techniques and immunology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Fundamental Virology, 2nd Edition, vol. I & II (B.N. Fields and D.M. Knipe, eds.); Handbook of Experimental Immunology, VoIs. I-IV (D.M. Weir and CC. Blackwell eds., Blackwell Scientific Publications); T.E. Creighton, Proteins: Structures and Molecular Properties (W .H. Freeman and Company, 1993); A.L. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.). All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety.
The following amino acid abbreviations are used throughout the text:
Alanine: Ala (A) Arginine: Arg (R)
Asparagine: Asn (N) Aspartic acid: Asp (D)
Cysteine: Cys (C) Glutamine: GIn (Q)
Glutamic acid: GIu (E) Glycine: GIy (G)
Histidine: His (H) Isoleucine: He (I)
Leucine: Leu (L) Lysine: Lys (K)
Methionine: Met (M) Phenylalanine: Phe (F)
Proline: Pro (P) Serine: Ser (S)
Threonine: Thr (T) Tryptophan: Trp (W)
Tyrosine: Tyr (Y) Valine: VaI (V)
1. DEFINITIONS
In describing the present invention, the following terms will be employed, and are intended to be defined as indicated below. It must be noted that, as used in this specification and the appended claims, the singular forms "a", "an" and "the" include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to "an E1E2 complex" includes a mixture of two or more such complexes, and the like. The terms "polypeptide" and "protein" refer to a polymer of amino acid residues and are not limited to a minimum length of the product. Thus, peptides, oligopeptides, dimers, multimers, and the like, are included within the definition. Both full-length proteins and fragments thereof are encompassed by the definition. The terms also include postexpression modifications of the polypeptide, for example, glycosylation, acetylation, phosphorylation and the like. Furthermore, for purposes of the present invention, a "polypeptide" refers to a protein which includes modifications, such as deletions, additions and substitutions (generally conservative in nature), to the native sequence, so long as the protein maintains the desired activity. These modifications may be deliberate, as through site-directed mutagenesis, or may be accidental, such as through mutations of hosts which produce the proteins or errors due to PCR amplification.
By an "El polypeptide" is meant a molecule derived from an HCV El region. The mature El region of HCV-Ia begins at approximately amino acid 192 of the polyprotein and continues to approximately amino acid 383, numbered relative to the full-length HCV-Ia polyprotein. (See, Figures 1 and 2A-2C. Amino acids 192-383 of Figures 2A-2C correspond to amino acid positions 20-211 of SEQ ID NO:2.) Amino acids at around 173 through approximately 191 (amino acids 1-19 of SEQ ID NO:2) serve as a signal sequence for El. The corresponding region for other HCV genotypes and subtypes are known and readily determined by comparison to the HCV-Ia polyprotein. For ease of discussion then, numbering herein is with reference to the HCV-Ia genome, but it is to be understood that an "El polypeptide" also encompasses El polypeptides from any of the various HCV genotypes, such as HCV- 1, HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6 and subtypes thereof, such as HCV- Ia, HCV-2a, HCV-3a, HCV-4a, HCV-5a and HCV-6a. Thus, by an "El polypeptide" is meant either a precursor El protein, including the signal sequence, or a mature El polypeptide which lacks this sequence, or even an El polypeptide with a heterologous signal sequence. The El polypeptide includes a C-terminal membrane anchor sequence which occurs at approximately amino acid positions 360-383, numbered relative to the HCV-Ia polyprotein (see, International Publication No. WO 96/04301, published February 15, 1996). An El polypeptide, as defined herein, may or may not include the C-terminal anchor sequence or portions thereof. Moreover, the El polypeptide may or may not be glycosylated. By an "E2 polypeptide" is meant a molecule derived from an HCV E2 region.
The mature E2 region of HCV-Ia begins at approximately amino acid 383-385, numbered relative to the full-length HCV-I polyprotein. (See, Figures 1 and 2A-2C. Amino acids 383-385 of Figures 2A-2C correspond to amino acid positions 211-213 of SEQ ID NO:2.) A signal peptide begins at approximately amino acid 364 of the polyprotein. The corresponding region for other HCV genotypes and subtypes are known and readily determined by comparison to the HCV-Ia polyprotein. For ease of discussion then, numbering herein is with reference to the HCV-Ia genome, but it is to be understood that an "E2 polypeptide" also encompasses E2 polypeptides from any of the various HCV genotypes, such as HCV-I, HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6 and subtypes thereof, such as HCV-Ia, HCV-2a, HCV-3a, HCV-4a, HCV-5a and HCV-6a.
Thus, by an "E2 polypeptide" is meant either a precursor E2 protein, including the signal sequence, or a mature E2 polypeptide which lacks this sequence, or even an E2 polypeptide with a heterologous signal sequence. The E2 polypeptide includes a C-terminal membrane anchor sequence which occurs at approximately amino acid positions 715-730 and may extend as far as approximately amino acid residue 746, numbered relative to the HCV-Ia polyprotein (see, Lin et al., J. Virol. (1994) 68:5063-5073). An E2 polypeptide, as defined herein, may or may not include the C-terminal anchor sequence or portions thereof. Additionally, the E2 polypeptide may or may not be glycosylated. Moreover, an E2 polypeptide may also include all or a portion of the p7 region which occurs immediately adjacent to the C-terminus of E2. As shown in Figures 1 and 2A-2C, the p7 region of the HCV-Ia polyprotein is found at positions 747-809, numbered relative to the full-length HCV-I polyprotein (amino acid positions 575-637 of SEQ ID NO:2). Additionally, it is known that multiple species of HCV E2 exist (Spaete et al., Virol. (1992) 188:819-830; Selby et al., J. Virol. (1996) 70:5177-5182; Grakoui et al., J. Virol. (1993) 67:1385-1395; Tomei et al., J. Virol. (1993) 67:4017-4026). Accordingly, for purposes of the present invention, the term "E2" encompasses any of these species of E2 including, without limitation, species that have deletions of 1-20 or more of the amino acids from the N-terminus of the E2, such as, e.g, deletions of 1, 2, 3, 4, 5....10...15, 16, 17, 18, 19... etc. amino acids. Such E2 species include those beginning at amino acid 387, amino acid 402, amino acid 403, etc. Representative El and E2 regions from HCV-Ia are shown in Figures 2A-2C and SEQ ID NO:2. The corresponding regions for HCV genotypes 2, 3, 4, 5 and 6, and subtypes thereof are known and discussed more fully below. As explained above, for ease of discussion, the El and E2 regions are defined with respect to the amino acid number of the polyprotein encoded by the genome of HCV-Ia, with the initiator methionine being designated position 1. See, e.g., Choo et al., Proc. Natl. Acad. ScL USA (1991) 88:2451-2455.
Furthermore, an "El polypeptide" or an "E2 polypeptide" as defined herein is not limited to a polypeptide having the exact sequence depicted in the Figures. Indeed, the HCV genome is in a state of constant flux in vivo and contains several variable domains which exhibit relatively high degrees of variability between isolates. A number of conserved and variable regions are known between these strains and, in general, the amino acid sequences of epitopes derived from these regions will have a high degree of sequence homology, e.g., amino acid sequence homology of more than 30%, preferably more than 40%, more than 60%, and even more than 80-90% homology, when the two sequences are aligned. It is readily apparent that the terms encompass El and E2 polypeptides from any of the various HCV strains and isolates including isolates having any of the 6 genotypes of HCV described in Simmonds et al., J. Gen. Virol. (1993) 74:2391-2399 (e.g., strains 1, 2, 3, 4 etc.), as well as newly identified isolates, and subtypes of these isolates, such as HCVIa, HCVIb etc. Thus, for example, the term "El" or "E2" polypeptide refers to native El or
E2 sequences from any of the various HCV genotypes, unless specifically identified, as well as analogs, muteins and immunogenic fragments, as defined further below. The complete genotypes of many of these strains are known. See, e.g., U.S. Patent No. 6,150,087 and GenBank Accession Nos. AJ238800 and AJ238799. Additionally, the terms "El polypeptide" and "E2 polypeptide" encompass proteins which include modifications to the native sequence, such as internal deletions, additions and substitutions (generally conservative in nature), such as proteins substantially homologous to the parent sequence. These modifications may be deliberate, as through site-directed mutagenesis, or may be accidental, such as through naturally occurring mutational events. AU of these modifications are encompassed in the present invention so long as the modified El and E2 polypeptides function for their intended purpose. Thus, for example, if the El and/or E2 polypeptides are to be used in vaccine compositions, the modifications must be such that immunological activity (i.e., the ability to elicit a humoral or cellular immune response to the polypeptide) is not lost.
By "E1E2" complex is meant a protein containing at least one El polypeptide and at least one E2 polypeptide, as described above. Such a complex may also include all or a portion of the p7 region which occurs immediately adjacent to the C-terminus of E2. As shown in Figures 1 and 2A-2C, the p7 region is found at positions 747-809, numbered relative to the full-length HCV-I polyprotein (amino acid positions 575-637 of SEQ ID NO:2). A representative E1E2 complex which includes the p7 protein is termed "ElE2go9" herein. The mode of association of El and E2 in an E1E2 complex is immaterial. The
El and E2 polypeptides may be associated through non-covalent interactions such as through electrostatic forces, or by covalent bonds. For example, the E1E2 polypeptides of the present invention may be in the form of a fusion protein which includes an immunogenic El polypeptide and an immunogenic E2 polypeptide, as defined above. The fusion may be expressed from a polynucleotide encoding an E1E2 chimera. Alternatively, E1E2 complexes may form spontaneously simply by mixing El and E2 proteins which have been produced individually. Similarly, when co-expressed and secreted into media, the El and E2 proteins can form a complex spontaneously. Thus, the term encompasses E1E2 complexes (also called aggregates) that spontaneously form upon purification of El and/or E2. Such aggregates may include one or more El monomers in association with one or more E2 monomers. The number of El and E2 monomers present need not be equal so long as at least one El monomer and one E2 monomer are present. Detection of the presence of an E1E2 complex is readily determined using standard protein detection techniques such as polyacrylamide gel electrophoresis and immunological techniques such as immunoprecipitation.
The terms "analog" and "mutein" refer to biologically active derivatives of the reference molecule, such as E1E2BO9, or fragments of such derivatives, that retain desired activity, such as immunoreactivity in assays described herein. In general, the term "analog" refers to compounds having a native polypeptide sequence and structure with one or more amino acid additions, substitutions (generally conservative in nature) and/or deletions, relative to the native molecule, so long as the modifications do not destroy immunogenic activity. The term "mutein" refers to polypeptides having one or more amino acid-like molecules including but not limited to compounds comprising only amino and/or imino molecules, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), polypeptides with substituted linkages, as well as other modifications known in the art, both naturally occurring and non-naturally occurring (e.g., synthetic), cyclized, branched molecules and the like. The term also includes molecules comprising one or more N-substituted glycine residues (a "peptoid") and other synthetic amino acids or peptides. (See, e.g., U.S. Patent Νos. 5,831,005; 5,877,278; and 5,977,301; Nguyen et al., Chem Biol. (2000) 7:463-473; and Simon et al., Proc. Natl. Acad. ScL USA (1992) 89:9367-9371 for descriptions of peptoids). Preferably, the analog or mutein has at least the same immunoreactivity as the native molecule. Methods for making polypeptide analogs and muteins are known in the art and are described further below.
Particularly preferred analogs include substitutions that are conservative in nature, i.e., those substitutions that take place within a family of amino acids that are related in their side chains. Specifically, amino acids are generally divided into four families: (1) acidic ~ aspartate and glutamate; (2) basic — lysine, arginine, histidine; (3) non-polar ~ alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar — glycine, asparagine, glutamine, cysteine, serine threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified as aromatic amino acids. For example, it is reasonably predictable that an isolated replacement of leucine with isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar conservative replacement of an amino acid with a structurally related amino acid, will not have a major effect on the biological activity. For example, the polypeptide of interest, such as an E1E2 polypeptide, may include up to about 5-10 conservative or non-conservative amino acid substitutions, or even up to about 15-25 or 50 conservative or non-conservative amino acid substitutions, or any integer between 5-50, so long as the desired function of the molecule remains intact. One of skill in the art can readily determine regions of the molecule of interest that can tolerate change by reference to Hopp/Woods and Kyte-Doolittle plots, well known in the art. By "fragment" is intended a polypeptide consisting of only a part of the intact full-length polypeptide sequence and structure. The fragment can include a
C-terminal deletion an N-terminal deletion, and/or an internal deletion of the native polypeptide. An "immunogenic fragment" of a particular HCV protein will generally include at least about 5-10 contiguous amino acid residues of the full-length molecule, preferably at least about 15-25 contiguous amino acid residues of the full-length molecule, and most preferably at least about 20-50 or more contiguous amino acid residues of the full-length molecule, that define an epitope, or any integer between 5 amino acids and the full-length sequence, provided that the fragment in question retains the ability to elicit an immunological response as defined herein. For a description of known immunogenic fragments of HCV El and E2, see, e.g., Chien et al., International Publication No. WO 93/00365.
The term "epitope" as used herein refers to a sequence of at least about 3 to 5, preferably about 5 to 10 or 15, and not more than about 500 amino acids (or any integer therebetween), which define a sequence that by itself or as part of a larger sequence, elicits an immunological response in the subject to which it is administered. Often, an epitope will bind to an antibody generated in response to such sequence. There is no critical upper limit to the length of the fragment, which may comprise nearly the full-length of the protein sequence, or even a fusion protein comprising two or more epitopes from the HCV polyprotein. An epitope for use in the subject invention is not limited to a polypeptide having the exact sequence of the portion of the parent protein from which it is derived. Indeed, viral genomes are in a state of constant flux and contain several variable domains which exhibit relatively high degrees of variability between isolates. Thus the term "epitope" encompasses sequences identical to the native sequence, as well as modifications to the native sequence, such as deletions, additions and substitutions (generally conservative in nature).
Regions of a given polypeptide that include an epitope can be identified using any number of epitope mapping techniques, well known in the art. See, e.g., Epitope Mapping Protocols in Methods in Molecular Biology, Vol. 66 (Glenn E. Morris, Ed., 1996) Humana Press, Totowa, New Jersey. For example, linear epitopes may be determined by e.g., concurrently synthesizing large numbers of peptides on solid supports, the peptides corresponding to portions of the protein molecule, and reacting the peptides with antibodies while the peptides are still attached to the supports. Such techniques are known in the art and described in, e.g., U.S. Patent No. 4,708,871 ; Geysen et al. (1984) Proc. Natl. Acad. ScI USA 81:3998-4002; Geysen et al. (1985) Proc. Natl. Acad. Set USA 82:178-182; Geysen et al. (1986) Molec. Immunol. 23:709-715, all incorporated herein by reference in their entireties. Using such techniques, a number of epitopes of HCV have been identified. See, e.g., Chien et al., Viral Hepatitis and Liver Disease (1994) pp. 320-324, and further below. Similarly, conformational epitopes are readily identified by determining spatial conformation of amino acids such as by, e.g., x-ray crystallography and 2-dimensional nuclear magnetic resonance. See, e.g., Epitope Mapping Protocols, supra. Antigenic regions of proteins can also be identified using standard antigenicity and hydropathy plots, such as those calculated using, e.g., the Omiga version 1.0 software program available from the Oxford Molecular Group. This computer program employs the Hopp/ Woods method, Hopp et al., Proc. Natl. Acad. Sd USA (1981) 78:3824-3828 for determining antigenicity profiles, and the Kyte-Doolittle technique, Kyte et al., J. MoI. Biol. (1982) 157:105-132 for hydropathy plots. As used herein, the term "conformational epitope" refers to a portion of a full-length protein, or an analog or mutein thereof, having structural features native to the amino acid sequence encoding the epitope within the full-length natural protein. Native structural features include, but are not limited to, glycosylation and three dimensional structure. The length of the epitope defining sequence can be subject to wide variations as these epitopes are believed to be formed by the three-dimensional shape of the antigen (e.g., folding). Thus, amino acids defining the epitope can be relatively few in number, but widely dispersed along the length of the molecule (or even on different molecules in the case of dimers, etc.), being brought into correct epitope conformation via folding. The portions of the antigen between the residues defining the epitope may not be critical to the conformational structure of the epitope. For example, deletion or substitution of these intervening sequences may not affect the conformational epitope provided sequences critical to epitope conformation are maintained (e.g., cysteines involved in disulfide bonding, glycosylation sites, etc.). Conformational epitopes are readily identified using methods discussed above. Moreover, the presence or absence of a conformational epitope in a given polypeptide can be readily determined through screening the antigen of interest with an antibody (polyclonal serum or monoclonal to the conformational epitope) and comparing its reactivity to that of a denatured version of the antigen which retains only linear epitopes (if any). In such screening using polyclonal antibodies, it may be advantageous to absorb the polyclonal serum first with the denatured antigen and see if it retains antibodies to the antigen of interest. Conformational epitopes derived from the El and E2 regions are described in, e.g., International Publication No. WO 94/01778.
An "immunological response" to an HCV antigen or composition is the development in a subject of a humoral and/or a cellular immune response to molecules present in the composition of interest. For purposes of the present invention, a "humoral immune response" refers to an immune response mediated by antibody molecules, while a "cellular immune response" is one mediated by T-lymphocytes and/or other white blood cells. One important aspect of cellular immunity involves an antigen-specific response by cytolytic T-cells ("CTLs"). CTLs have specificity for peptide antigens that are presented in association with proteins encoded by the major histocompatibility complex (MHC) and expressed on the surfaces of cells. CTLs help induce and promote the intracellular destruction of intracellular microbes, or the lysis of cells infected with such microbes. Another aspect of cellular immunity involves an antigen-specific response by helper T-cells. Helper T-cells act to help stimulate the function, and focus the activity of, nonspecific effector cells against cells displaying peptide antigens in association with MHC molecules on their surface. A "cellular immune response" also refers to the production of cytokines, chemokines and other such molecules produced by activated T-cells and/or other white blood cells, including those derived from CD4+ and CD8+ T-cells. A composition or vaccine that elicits a cellular immune response may serve to sensitize a vertebrate subject by the presentation of antigen in association with MHC molecules at the cell surface. The cell-mediated immune response is directed at, or near, cells presenting antigen at their surface. In addition, antigen-specific T-lymphocytes can be generated to allow for the future protection of an immunized host. The ability of a particular antigen to stimulate a cell-mediated immunological response may be determined by a number of assays, such as by lymphoproliferation (lymphocyte activation) assays, CTL cytotoxic cell assays, or by assaying for T-lymphocytes specific for the antigen in a sensitized subject. Such assays are well known in the art. See, e.g., Erickson et al., J. Immunol. (1993) 151:4189-4199; Doe et al., Eur. J. Immunol. (1994) 24:2369-2376.
Thus, an immunological response as used herein may be one which stimulates the production of CTLs, and/or the production or activation of helper T- cells. The antigen of interest may also elicit an antibody-mediated immune response, including, or example, neutralization of binding (NOB) antibodies. The presence of an NOB antibody response is readily determined by the techniques described in, e.g., Rosa et al., Proc. Natl. Acad. Set USA (1996) 93_:1759. Hence, an immunological response may include one or more of the following effects: the production of antibodies by B-cells; and/or the activation of suppressor T-cells and/or γδT-cells directed specifically to an antigen or antigens present in the composition or vaccine of interest. These responses may serve to neutralize infectivity, and/or mediate antibody-complement, or antibody dependent cell cytotoxicity (ADCC) to provide protection or alleviation of symptoms to an immunized host. Such responses can be determined using standard immunoassays and neutralization assays, well known in the art. By "isolated" is meant, when referring to a polypeptide, that the indicated molecule is separate and discrete from the whole organism with which the molecule is found in nature or is present in the substantial absence of other biological macro-molecules of the same type. The term "isolated" with respect to a polynucleotide is a nucleic acid molecule devoid, in whole or part, of sequences normally associated with it in nature; or a sequence, as it exists in nature, but having heterologous sequences in association therewith; or a molecule disassociated from the chromosome.
By "equivalent antigenic determinant" is meant an antigenic determinant from different sub-species or strains of HCV, such as from strains 1, 2, 3, etc., of HCV which antigenic determinants are not necessarily identical due to sequence variation, but which occur in equivalent positions in the HCV sequence in question. In general the amino acid sequences of equivalent antigenic determinants will have a high degree of sequence homology, e.g., amino acid sequence homology of more than 30%, usually more than 40%, such as more than 60%, and even more than 80-90% homology, when the two sequences are aligned.
"Homology" refers to the percent identity between two polynucleotide or two polypeptide moieties. Two DNA, or two polypeptide sequences are "substantially homologous" to each other when the sequences exhibit at least about 50% , preferably at least about 75%, more preferably at least about 80%-85%, preferably at least about 90%, and most preferably at least about 95%-98% sequence identity over a defined length of the molecules. As used herein, substantially homologous also refers to sequences showing complete identity to the specified DNA or polypeptide sequence. In general, "identity" refers to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Percent identity can be determined by a direct comparison of the sequence information between two molecules by aligning the sequences, counting the exact number of matches between the two aligned sequences, dividing by the length of the shorter sequence, and multiplying the result by 100. Readily available computer programs can be used to aid in the analysis, such as ALIGN, Dayhoff, M.O. in Atlas of Protein Sequence and Structure M.O. Dayhoff ed., 5 Suppl. 3:353-358, National biomedical Research Foundation, Washington, DC, which adapts the local homology algorithm of Smith and Wateπnan Advances in Appl. Math. 2:482-489, 1981 for peptide analysis. Programs for determining nucleotide sequence identity are available in the Wisconsin Sequence Analysis Package, Version 8 (available from Genetics Computer Group, Madison, WI) for example, the BESTFIT, FASTA and GAP programs, which also rely on the Smith and Waterman algorithm. These programs are readily utilized with the default parameters recommended by the manufacturer and described in the Wisconsin Sequence Analysis Package referred to above. For example, percent identity of a particular nucleotide sequence to a reference sequence can be determined using the homology algorithm of Smith and Waterman with a default scoring table and a gap penalty of six nucleotide positions. Another method of establishing percent identity in the context of the present invention is to use the MPSRCH package of programs copyrighted by the University of Edinburgh, developed by John F. Collins and Shane S. Sturrok, and distributed by IntelliGenetics, Inc. (Mountain View, CA). From this suite of packages the Smith- Waterman algorithm can be employed where default parameters are used for the scoring table (for example, gap open penalty of 12, gap extension penalty of one, and a gap of six). From the data generated the "Match" value reflects "sequence identity." Other suitable programs for calculating the percent identity or similarity between sequences are generally known in the art, for example, another alignment program is BLAST, used with default parameters. For example, BLASTN and
BLASTP can be used using the following default parameters: genetic code = standard; filter = none; strand = both; cutoff = 60; expect = 10; Matrix = BLOSUM62; Descriptions = 50 sequences; sort by = HIGH SCORE; Databases = non-redundant, GenBank + EMBL + DDBJ + PDB + GenBank CDS translations + Swiss protein + Spupdate + PIR. Details of these programs can be found at the following internet address: http://www.ncbi.nlm.gov/cgi-bin/BLAST.
Alternatively, homology can be determined by hybridization of polynucleotides under conditions which form stable duplexes between homologous regions, followed by digestion with single-stranded-specific nuclease(s), and size determination of the digested fragments. DNA sequences that are substantially homologous can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art. See, e.g., Sambrook et al., supra; DNA Cloning, supra; Nucleic Acid Hybridization, supra. "Recombinant" as used herein to describe a nucleic acid molecule means a polynucleotide of genomic, RNA, DNA, cDNA, viral, semisynthetic, or synthetic origin which, by virtue of its origin or manipulation is not associated with all or a portion of the polynucleotide with which it is associated in nature. The term "recombinant" as used with respect to a protein or polypeptide means a polypeptide produced by expression of a recombinant polynucleotide. In general, the gene of interest is cloned and then expressed in transformed organisms, as described further below. The host organism expresses the foreign gene to produce the protein under expression conditions.
The terms "effective amount" or "pharmaceutically effective amount" of an immunogenic composition, as provided herein, refer to a nontoxic but sufficient amount of the composition to provide the desired response, such as an immunological response, and optionally, a corresponding therapeutic effect. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the condition being treated, and the particular macromolecule of interest, mode of administration, and the like. An appropriate "effective" amount in any individual case may be determined by one of ordinary skill in the art using routine experimentation. By "vertebrate subject" is meant any member of the subphylum chordata, including, without limitation, humans and other primates, including non-human primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs; birds, including domestic, wild and game birds such as chickens, turkeys and other gallinaceous birds, ducks, geese, and the like. The term does not denote a particular age. Thus, both adult and newborn individuals are intended to be covered. The invention described herein is intended for use in any of the above vertebrate species, since the immune systems of all of these vertebrates operate similarly. The term "treatment" as used herein refers to either (1) the prevention of infection or reinfection (prophylaxis), or (2) the reduction or elimination of symptoms of the disease of interest (therapy).
2. MODES OF CARRYING OUT THE INVENTION Before describing the present invention in detail, it is to be understood that this invention is not limited to particular formulations or process parameters as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments of the invention only, and is not intended to be limiting. Although a number of methods and materials similar or equivalent to those described herein can be used in the practice of the present invention, the preferred materials and methods are described herein.
Central to the present invention is the use of HCV envelope polypeptides from HCV genotypes capable of cross-neutralizing multiple HCV genotypes. For example, it has been found that neutralizing antibodies produced by infection with HCV-Ia are capable of cross-neutralizing HCV genotypes 4a, 5a and 6a. See, Meunier et al., Proc. Natl. Acad. ScL USA (2005) 102:4560-4565. Thus, the use of envelope polypeptides from one or more of HCV genotypes 1, 4, 5 and 6, when combined with the use of envelope polypeptides from HCV-2 and/or 3, may provide broad-based protection and/or treatment against multiple HCV genotypes. In fact, it is expected that when envelope polypeptides from any one of HCV genotypes 1, 4, 5 and 6, are combined with envelope polypeptides from both HCV-2 and 3, protection against, or treatment for, all six of these HCV genotypes will be achieved.
Thus, as described in more detail below, subjects can be administered envelope polypeptides from all of these genotypes, or envelope polypeptides from some of the genotypes, such as from two, three, four, five or all six of these genotypes, so long as neutralizing antibodies are produced that are directed against more than one of the six genotypes. The HCV envelope polypeptides can be administered together, in the same composition, or can be administered in separate compositions. If delivered in separate compositions, administration can be, but need not be, concurrent. For example, an HCV envelope polypeptide from an HCV genotype selected from one or more of HCV-I, HCV-4, HCV-5 and HCV-6, can be delivered prior to, subsequent to, or concurrent with an HCV envelope polypeptide from an HCV genotype selected from HCV-2 and/or HCV-3.
Subjects can subsequently be boosted with either protein or DNA compositions that deliver HCV envelope polypeptides, such as HCV E1E2 protein complexes. The molecules used for boosting can be either the same as initially administered, or can be different HCV envelope polypeptides, as described further below, so long as an immune response is generated. Additionally, the compositions above can be used alone, or in combination with other compositions, such as compositions comprising other HCV proteins, compositions comprising DNA encoding other HCV proteins, as well as compositions comprising ancillary substances. If used in combination with other compositions, such compositions can be administered prior to, concurrent with, or subsequent to the HCV envelope compositions.
In order to further an understanding of the invention, a more detailed discussion is provided below regarding HCV polypeptides and compositions for use in the subject methods. HCV Envelope Polypeptides and Polynucleotides
As explained above, the compositions of the invention include HCV envelope polypeptides from more than one HCV genotype. For ease of discussion, the amino acid positions discussed below are generally with reference to HCV-Ia. However, the corresponding region for other HCV genotypes and subtypes are known and readily determined by comparison to the HCV-Ia polyprotein. It is to be understood that polypeptides and polynucleotides from any of the various HCV genotypes, such as HCV-2, HCV-3, HCV-4, HCV-5 and HCV-6 and subtypes thereof, including but not limited to HCV-2a, HCV-3a, HCV-4a, HCV-5a and HCV-6a, are also intended. For example, the complete sequences for several HCV-I isolates are reported.
See, e.g., NCBI accession nos. ABO 16785, AB049087, AB049088, AB049089, AB049090, AB049091, AB049092, AB049093, AB049094, AB049095, AB049096, AB049097, AB049098, AB049099, AB0490100, AB0490101, AB080299, AB119282, AB154177, AB154178, AB154179, AB154180, AB154181, AB154182, AB154183, AB154184, AB154185, AB154186, AB154187, AB154188, AB154189, AB154190, AB154191, AB154192, AB154193, AB154194, AB154195, AB154196, AB154197, AB154198, AB154199, AB154200, AB 154201, AB154202, AB154203, AB154204, AB154205, AB154206, AB19133, AF009606, AFOl 1751, AFOl 1752, AFOl 1753, AF054247, AF054248, AF054249, AF054250, AF139594, AF165045, AF165046, AF165047, AF165048, AF165049, AF165050, AF165051, AF165052, AF165053, AF165054, AF165055, AF165056, AF165057, AF165058, AF165059, AF165060, AF165061, AF165062, AF165063, AF165064, AF176573, AF207752, AF207753, AF207754, AF207755, AF207756, AF207757, AF207758, AF207759, AF207760, AF207761, AF207762, AF207763, AF207764, AF207765, AF207766, AF207767, AF207768, AF207769, AF207770, AF207771, AF207772, AF207773, AF207774, AF208024, AF271632, AF290978, AF313916, AF333324, AF356827, AF483269, AF511948, AF511949, AF511950, AJ000009, AJ132996, AJ132997, AJ238799, AJ238800, AJ278830, AY045702, AY051292, AY460204, AY587016, D10934, D11168, D11355, D13558, D14484, D14853, D30613, D45172, D50480, D50481, D50482, D50483, D50484, D50485, D63857, D85516, D89815, D89872, D90208, L02836, M58335, M62321, M67463, M84754, M96362, NC_004102, S62220, U01214, U16362, U45476, U89019, X61596. Similarly, the complete sequences for several HCV-2 isolates are reported. See, e.g., NCBI accession nos. AB030907, AB031663, AB047639, AB047640, AB047641, AB047642, AB047643, AB047644, AB047645, AP169002, AF169003, AF169004, AF169005, AF177036, AF238481, AF238482, AF238483, AF238484, AF238485, AF238486, AY232730, AY232731, AY232732, AY232733, AY232734, AY232735, AY232736, AY232737, AY232738, AY232739, AY232740, AY232741, AY232742, AY232743, AY232744, AY232745, AY232746, AY232747, AY232748, AY232749, AY587845, AY746460, D00944, D10988, D50409.
The complete sequences for several HCV-3 isolates are also reported. See, e.g., NCBI accession nos. AF046866, D17763, D28917, D49374, D63821, X76918. The complete sequences for HCV-4 isolates are also known. See, e.g., NCBI accession no. Yl 1604. The complete sequences for several HCV-5 isolates are known. See, e.g., NCBI accession nos. AF064490 and Y13184. The complete sequences for several HCV-6 isolates are also known. See, e.g., NCBI accession nos. AY859526, AY878650, D63822, D84262, D84263, D84264, D84265, Y12083.
Additional sequences are as follows. Isolate HCV Jl.1 is described in Kubo et al. (1989) Japan. Nucl. Acids Res. 17:10367-10372; Takeuchi et al.(1990) Gene 91:287-291; Takeuchi et al. (1990) J. Gen. Virol. 71:3027-3033; and Takeuchi et al. (1990) Nucl. Acids Res.18:4626. The complete coding sequences of two independent isolates, HCV-J and BK, are described by Kato et al., (1990) Proc. Natl. Acad. ScL USA 87:9524-9528 and Takamizawa et al., (1991) J. Virol. 65:1105-1113, respectively. HCV-I isolates are described by Choo et al. (1990) Brit. Med. Bull. 46:423-441; Choo et al. (1991) Proc. Natl. Acad. Sci. USA 88:2451-2455 and Han et al. (1991) Proc. Natl. Acad. Sci. USA 88:1711-1715. HCV isolates HC-Jl and HC-J4 are described in Okamoto et al. (1991) Japan J. Exp. Med. 60: 167-177. HCV isolates HCT 18, HCT 23, Th, HCT 27, ECl and EClO are described in Weiner et al. (1991) Virol. 180:842-848. HCV isolates Pt-I, HCV-Kl and HCV-K2 are described in Enomoto et al. (1990) Biochem. Biophys. Res. Commun. 170:1021-1025. HCV isolates A, C, D & E are described in Tsukiyama-Kohara et al. (1991) Virus Genes 5:243-254.
The HCV El polypeptide is a glycoprotein and extends from approximately amino acid 192 to amino acid 383, numbered relative to the polyprotein of HCV-Ia. See, Choo et al., Proc. Natl. Acad. Sci. USA (1991) 88:2451-2455. Amino acids at around 173 through approximately 191 represent a signal sequence for El. The HCV E2 polypeptide is also a glycoprotein and extends from approximately amino acid 383 or 384 to amino acid 746. A signal peptide for E2 begins at approximately amino acid 364 of the polyprotein. Thus, the term "full-length" El or "not truncated" El as used herein refers to polypeptides that include, at least, amino acids 192-383 of an HCV polyprotein (numbered relative to HCV-Ia). With respect to E2, the term "full-length" or "not truncated" as used herein refers to polypeptides that include, at least, amino acids 383 or 384 to amino acid 746 of an HCV polyprotein (numbered relative to HCV-Ia). As will be evident from this disclosure, E2 polypeptides for use with the present invention may include additional amino acids from the p7 region, such as amino acids 747-809, numbered relative to HCV-Ia.
E2 exists as multiple species (Spaete et al., Virol. (1992) .188:819-830; Selby et al., J. Virol. (1996) 70:5177-5182; Grakoui et al., J. Virol. (1993) 67:1385-1395; Tomei et al., J. Virol. (1993) 67:4017-4026) and clipping and proteolysis may occur at the N- and C-termini of the El and E2 polypeptides. Thus, an E2 polypeptide for use herein may comprise at least amino acids 405-661, e.g., 400, 401, 402... to 661, such as 383 or 384-661, 383 or 384-715, 383 or 384-746, 383 or 384-749 or 383 or 384-809, or 383 or 384 to any C-terminus between 661-809, of an HCV polyprotein, numbered relative to the full-length HCV-I polyprotein. Similarly, preferable El polypeptides for use herein can comprise amino acids 192-326, 192-330, 192-333, 192-360, 192-363, 192-383, or 192 to any C-terminus between 326-383, of an HCV polyprotein.
El and E2 polypeptides for use in the subject compositions and methods also include immunogenic fragments of El and E2 which comprise epitopes. For example, fragments of El polypeptides can comprise from about 5 to nearly the full-length of the molecule, such as 6, 10, 25, 50, 75, 100, 125, 150, 175, 185 or more amino acids of an El polypeptide, or any integer between the stated numbers. Similarly, fragments of E2 polypeptides can comprise 6, 10, 25, 50, 75, 100, 150, 200, 250, 300, or 350 amino acids of an E2 polypeptide, or any integer between the stated numbers. The El and E2 polypeptides may be from the same or different HCV strains.
For example, epitopes derived from, e.g., the hypervariable region of E2, such as a region spanning amino acids 384-410 or 390-410, can be included in the E2 polypeptide. A particularly effective E2 epitope to incorporate into the E2 sequence is one which includes a consensus sequence derived from this region, such as the consensus sequence
Gly-Ser-Ala-Ala-Arg-Thr-Thr-Ser-Gly-Phe-Val-Ser-Leu-Phe-Ala-Pro-Gly-Ala-Lys- Gln-Asn (SEQ ID NO:3), which represents a consensus sequence for amino acids 390-410 of the HCV type 1 genome. Additional epitopes of El and E2 are known and described in, e.g., Chien et al., International Publication No. WO 93/00365.
Moreover, the El and E2 polypeptides may lack all or a portion of the membrane spanning domain. The membrane anchor sequence functions to associate the polypeptide to the endoplasmic reticulum. Normally, such polypeptides are capable of secretion into growth medium in which an organism expressing the protein is cultured. However, as described in International Publication No. WO 98/50556, such polypeptides may also be recovered intracellularly. Secretion into growth medium is readily determined using a number of detection techniques, including, e.g., polyacrylamide gel electrophoresis and the like, and immunological techniques such as immunoprecipitation assays as described in, e.g., International Publication No. WO 96/04301, published February 15, 1996. With El, generally polypeptides terminating with about amino acid position 370 and higher (based on the numbering of HCV-I El) will be retained by the ER and hence not secreted into growth media. With E2, polypeptides terminating with about amino acid position 731 and higher (also based on the numbering of the HCV-I E2 sequence) will be retained by the ER and not secreted. (See, e.g., International Publication No. WO 96/04301, published February 15, 1996). It should be noted that these amino acid positions are not absolute and may vary to some degree. Thus, the present invention contemplates the use of El and E2 polypeptides which retain the transmembrane binding domain, as well as polypeptides which lack all or a portion of the transmembrane binding domain, including El polypeptides terminating at about amino acids 369 and lower, and E2 polypeptides, terminating at about amino acids 730 and lower, are intended to be captured by the present invention. Furthermore, the C-terminal truncation can extend beyond the transmembrane spanning domain towards the N-terminus. Thus, for example, El truncations occurring at positions lower than, e.g., 360 and E2 truncations occurring at positions lower than, e.g., 715, are also encompassed by the present invention. All that is necessary is that the truncated El and E2 polypeptides remain functional for their intended purpose. However, particularly preferred truncated El constructs are those that do not extend beyond about amino acid 300. Most preferred are those terminating at position 360. Preferred truncated E2 constructs are those with C-terminal truncations that do not extend beyond about amino acid position 715. Particularly preferred E2 truncations are those molecules truncated after any of amino acids 715-730, such as 725. If truncated molecules are used, it is preferable to use El and E2 molecules that are both truncated.
Also contemplated for use in the compositions and methods of the invention are complexes of El and E2 polypeptides as described above. The El and E2 polypeptides in such complexes can be associated either through non-covalent or covalent interactions. Such complexes may also include all or a portion of the p7 region which occurs immediately adjacent to the C-terminus of E2. Representative HCV E1E2 complexes are described in PCT Publication No. WO 03/002065, incorporated herein by reference in its entirety. The El and E2 polypeptides and complexes thereof may also be present as asialoglycoproteins. Such asialoglycoproteins are produced by methods known in the art, such as by using cells in which terminal glycosylation is blocked. When these proteins are expressed in such cells and isolated by GNA lectin affinity chromatography, the El and E2 proteins aggregate spontaneously. Detailed methods for producing these E1E2 aggregates are described in, e.g., U.S. Patent No. 6,074,852, incorporated herein by reference in its entirety.
Moreover, the E1E2 complexes may comprise a heterogeneous mixture of molecules, due to clipping and proteolytic cleavage, as described above. Thus, a composition including E1E2 complexes may include multiple species of E1E2, such as E1E2 terminating at amino acid 746 (EIE2746), E1E2 terminating at amino acid 809 (ElE2gQ9), or any of the other various El and E2 molecules described above, such as E2 molecules with N-terminal truncations of from 1-20 amino acids, such as E2 species beginning at amino acid 387, amino acid 402, amino acid 403, etc. As explained above, the mode of association of El and E2 in an E1E2 complex is immaterial. The El and E2 polypeptides may be associated through non-covalent interactions such as through electrostatic forces, or by covalent bonds. Typically, E1E2 complexes form spontaneously by mixing El and E2 proteins which have been produced individually. Similarly, when co-expressed and secreted into media, the El and E2 proteins can form a complex spontaneously. Thus, E1E2 complexes (also called aggregates) may include one or more El monomers in association with one or more E2 monomers. The number of El and E2 monomers present need not be equal so long as at least one El monomer and one E2 monomer are present.
The El, E2 and E1E2 complexes are readily produced recombinantly. If E1E2 complexes are desired, they can be produced either as fusion proteins or by e.g., cotransfecting host cells with constructs encoding for the El and E2 polypeptides of interest. Cotransfection can be accomplished either in trans or cis, i.e., by using separate vectors or by using a single vector which bears both of the El and E2 genes. If done using a single vector, both genes can be driven by a single set of control elements or, alternatively, the genes can be present on the vector in individual expression cassettes, driven by individual control elements. Following expression, the El or E2 proteins will spontaneously associate. Alternatively, the complexes can be formed by mixing the individual proteins together which have been produced separately, either in purified or semi-purified form, or even by mixing culture media in which host cells expressing the proteins, have been cultured, if the proteins are secreted. Finally, the E1E2 complexes of may be expressed as a fusion protein wherein the desired portion of El is fused to the desired portion of E2. Methods for producing E1E2 complexes from full-length, truncated El and E2 proteins which are secreted into media, as well as intracellularly produced truncated proteins, are known in the art. For example, such complexes may be produced recombinantly, as described in U.S. Patent No. 6,121,020; Ralston et al., J. Virol. (1993) 67:6753-6761, Grakoui et al., J. Virol. (1993) 67:1385-1395; and Lanford et al., Virology (1993) 197:225-235.
Polynucleotides encoding HCV El and E2 polypeptides, to be used for expressing El and E2 polypeptides for use either alone or in complexes, can be made using standard techniques of molecular biology. For example, polynucleotide sequences coding for the above-described molecules can be obtained using recombinant methods, such as by screening cDNA and genomic libraries from cells expressing the gene, or by deriving the gene from a vector known to include the same. Furthermore, the desired gene can be isolated directly from viral nucleic acid molecules, using techniques described in the art, such as in Houghton et al., U.S. Patent No. 5,350,671. The gene of interest can also be produced synthetically, rather than cloned. The molecules can be designed with appropriate codons for the particular sequence. The complete sequence is then assembled from overlapping oligonucleotides prepared by standard methods and assembled into a complete coding sequence. See, e.g., Edge (1981) Nature 292:756; Nambair et al. (1984) Science 223:1299; and Jay et al. (1984) J. Biol. Chem. 259:6311.
Thus, particular nucleotide sequences can be obtained from vectors harboring the desired sequences or synthesized completely or in part using various oligonucleotide synthesis techniques known in the art, such as site-directed mutagenesis and polymerase chain reaction (PCR) techniques where appropriate. See, e.g., Sambrook, supra. In particular, one method of obtaining nucleotide sequences encoding the desired sequences is by annealing complementary sets of overlapping synthetic oligonucleotides produced in a conventional, automated polynucleotide synthesizer, followed by ligation with an appropriate DNA ligase and amplification of the ligated nucleotide sequence via PCR. See, e.g., Jayaraman et al. (1991) Proc. Natl. Acad. ScL USA 88:4084-4088. Additionally, oligonucleotide directed synthesis (Jones et al. (1986) Nature 54:75-82), oligonucleotide directed mutagenesis of preexisting nucleotide regions (Riechmann et al. (1988) Nature 332:323-327 and Verhoeyen et al. (1988) Science 239:1534-1536), and enzymatic filling-in of gapped oligonucleotides using T4 DNA polymerase (Queen et al. (1989)
Proc. Natl. Acad. ScL USA 86"-10029-10033) can be used to provide molecules having altered or enhanced antigen-binding capabilities and immunogenicity.
Once coding sequences have been prepared or isolated, such sequences can be cloned into any suitable vector or replicon. Numerous cloning vectors are known to those of skill in the art, and the selection of an appropriate cloning vector is a matter of choice. Suitable vectors include, but are not limited to, plasmids, phages, transposons, cosmids, chromosomes or viruses which are capable of replication when associated with the proper control elements.
The coding sequence is then placed under the control of suitable control elements, depending on the system to be used for expression. Thus, the coding sequence can be placed under the control of a promoter, ribosome binding site (for bacterial expression) and, optionally, an operator, so that the DNA sequence of interest is transcribed into RNA by a suitable transformant. The coding sequence may or may not contain a signal peptide or leader sequence which can later be removed by the host in post-translational processing. See, e.g., U.S. Patent Nos. 4,431,739; 4,425,437; 4,338,397.
In addition to control sequences, it may be desirable to add regulatory sequences which allow for regulation of the expression of the sequences relative to the growth of the host cell. Regulatory sequences are known to those of skill in the art, and examples include those which cause the expression of a gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. Other types of regulatory elements may also be present in the vector. For example, enhancer elements may be used herein to increase expression levels of the constructs. Examples include the SV40 early gene enhancer (Dijkema et al. (1985) EMBOJ. 4:761), the enhancer/promoter derived from the long terminal repeat (LTR) of the Rous Sarcoma Virus (Gorman et al. (1982) Proc. Natl. Acad. ScL USA 79:6777) and elements derived from human CMV (Boshart et al. (1985) Cell 41:521), such as elements included in the CMV intron A sequence (U.S. Patent No. 5,688,688). The expression cassette may further include an origin of replication for autonomous replication in a suitable host cell, one or more selectable markers, one or more restriction sites, a potential for high copy number and a strong promoter.
An expression vector is constructed so that the particular coding sequence is located in the vector with the appropriate regulatory sequences, the positioning and orientation of the coding sequence with respect to the control sequences being such that the coding sequence is transcribed under the "control" of the control sequences (i.e., RNA polymerase which binds to the DNA molecule at the control sequences transcribes the coding sequence). Modification of the sequences encoding the molecule of interest may be desirable to achieve this end. For example, in some cases it may be necessary to modify the sequence so that it can be attached to the control sequences in the appropriate orientation; i.e., to maintain the reading frame. The control sequences and other regulatory sequences may be ligated to the coding sequence prior to insertion into a vector. Alternatively, the coding sequence can be cloned directly into an expression vector which already contains the control sequences and an appropriate restriction site.
As explained above, it may also be desirable to produce mutants or analogs of the polypeptide of interest. Mutants or analogs of HCV polypeptides for use in the subject compositions may be prepared by the deletion of a portion of the sequence encoding the polypeptide of interest, by insertion of a sequence, and/or by substitution of one or more nucleotides within the sequence. Techniques for modifying nucleotide sequences, such as site-directed mutagenesis, and the like, are well known to those skilled in the art. See, e.g., Sambrook et al., supra; Kunkel, T.A. (1985) Proc. Natl. Acad. Sci. USA (1985) 82:448; Geisselsoder et al. (1987) BioTechniques 5:786; Zoller and Smith (1983) Methods Enzymol. 100:468; Dalbie-McFarland et al. (1982) Proc. Natl. Acad Sci USA 79:6409.
The molecules can be expressed in a wide variety of systems, including insect, mammalian, bacterial, viral and yeast expression systems, all well known in the art. For example, insect cell expression systems, such as baculovirus systems, are known to those of skill in the art and described in, e.g., Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987). Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego CA ("MaxBac" kit). Similarly, bacterial and mammalian cell expression systems are well known in the art and described in, e.g., Sambrook et al., supra. Yeast expression systems are also known in the art and described in, e.g., Yeast Genetic Engineering (Barr et al., eds., 1989) Butterworths, London. A number of appropriate host cells for use with the above systems are also known. For example, mammalian cell lines are known in the art and include immortalized cell lines available from the American Type Culture Collection (ATCC), such as, but not limited to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human embryonic kidney cells, human hepatocellular carcinoma cells (e.g., Hep G2), Madin-Darby bovine kidney ("MDBK") cells, as well as others. Similarly, bacterial hosts such as E. coli, Bacillus subtilis, and Streptococcus spp., will find use with the present expression constructs. Yeast hosts useful in the present invention include inter alia, Saccharomyces cerevisiae, Candida albicans, Candida maltosa, Hansenula polymorpha, Kluyveromyces fragilis, Klύyveromyces lactis, Pichia guillerimondii,
Pichia pastoris, Schizosaccharomyces pombe and Yarrowia lipolytica. Insect cells for use with baculovirus expression vectors include, inter alia, Aedes aegypti, Autographa californica, Bombyx mori, Drosophila melanogaster, Spodoptera frugiperda, and Tήchoplusia ni.
Nucleic acid molecules comprising nucleotide sequences of interest can be stably integrated into a host cell genome or maintained on a stable episomal element in a suitable host cell using various gene delivery techniques well known in the art. See, e.g., U.S. Patent No. 5,399,346.
Depending on the expression system and host selected, the molecules are produced by growing host cells transformed by an expression vector described above under conditions whereby the protein is expressed. The expressed protein is then isolated from the host cells and purified. If the expression system secretes the protein into growth media, the product can be purified directly from the media. If it is not secreted, it can be isolated from cell lysates. The selection of the appropriate growth conditions and recovery methods are within the skill of the art.
The above methods of recombinant production can be used to obtain other polypeptides, such as other HCV polypeptides described below, for administration with the HCV envelope compositions.
Other HCV Polypeptides and Polynucleotides
As explained above, the methods of the present invention may employ other compositions comprising HCV immunogens or DNA encoding such immunogens. Such compositions can be delivered prior to, subsequent to, or concurrent with the above envelope compositions, as well as prior to, subsequent to, or concurrent with compositions for boosting the immune response, if used.
In particular, the genome of the hepatitis C virus typically contains a single open reading frame of approximately 9,600 nucleotides, which is transcribed into a polyprotein. The full-length sequence of the polyprotein is disclosed in European Publication No. 388,232 and U.S. Patent No. 6,150,087, incorporated herein by reference in their entireties. As shown in Table 1 and Figure 1, An HCV polyprotein, upon cleavage, produces at least ten distinct products, in the order of NH2_Core-El-E2-p7-NS2-NS3-NS4a-NS4b-NS5a-NS5b-COOH. The core polypeptide occurs at positions 1-191, numbered relative to HCV-Ia (see, Choo et al. (1991) Proc. Natl. Acad Sci. USA 88:2451-2455, for the HCV-I genome). This polypeptide is further processed to produce an HCV polypeptide with approximately amino acids 1-173. The envelope polypeptides, El and E2, occur at about positions 192-383 and 384-746, respectively. The P7 domain is found at about positions 747-809. NS2 is an integral membrane protein with proteolytic activity and is found at about positions 810-1026 of the polyprotein. NS2, either alone or in combination with NS3 (found at about positions 1027- 1657), cleaves the NS2-NS3 sissle bond which in turn generates the NS3 N-terminus and releases a large polyprotein that includes both serine protease and RNA helicase activities. The NS3 protease, found at about positions 1027-1207, serves to process the remaining polyprotein. The helicase activity is found at about positions 1193-1657. Completion of polyprotein maturation is initiated by autocatalytic cleavage at the NS3-NS4a junction, catalyzed by the NS3 serine protease. Subsequent NS3-mediated cleavages of the HCV polyprotein appear to involve recognition of polyprotein cleavage junctions by an NS3 molecule of another polypeptide. In these reactions, NS3 liberates anNS3 cofactor (NS4a, found about positions 1658-1711), two proteins (NS4b found at about positions 1712-1972, and NS5a found at about positions 1973-2420), and an RNA-dependent RNA polymerase (NS5b found at about positions 2421-3011).
Figure imgf000031_0001
*Numbered relative to HCV-Ia. See, Choo et al. (1991) Proc. Natl. Acad. ScL USA 88:2451-2455.
Sequences for the above HCV polyprotein products, DNA encoding the same and immunogenic polypeptides derived therefrom, are known (see, e.g., U.S. Patent No. 5,350,671, incorporated herein by reference in its entirety). For example, a number of general and specific immunogenic polypeptides, derived from the HCV polyprotein, have been described. See, e.g., Houghton et al., European Publ. Nos. 318,216 and 388,232; Choo et al. Science (1989) 244:359-362; Kuo et al. Science (1989) 244:362-364; Houghton et al. Hepatology (1991) .14:381-388; Chien et al. Proc. Natl. Acad. ScL USA (1992) 89:10011-10015; Chien et al. J. Gastroent. Hepatol. (1993) 8:S33-39; Chien et al., International Publ. No. WO 93/00365; Chien, D.Y., International Publ. No. WO 94/01778. These publications provide an extensive background on HCV generally, as well as on the manufacture and uses of HCV polypeptide immunological reagents. For brevity, therefore, the disclosure of these publications is incorporated herein by reference.
Any desired immunogenic HCV polypeptide or DNA encoding the same can be utilized with the present invention. For example, HCV polypeptides derived from the Core region, such as polypeptides derived from the region found between amino acids 1-191; amino acids 10-53; amino acids 10-45; amino acids 67-88; amino acids 86-100; 81-130; amino acids 121-135; amino acids 120-130; amino acids 121-170; and any of the Core epitopes identified in, e.g., Houghton et al., U.S. Patent No. 5,350,671; Chien et al. Proc. Natl. Acad. ScL USA (1992) 89:10011-10015; Chien et al. J. Gastroent. Hepatol. (1993) 8:S33-39; Chien et al., International Publ. No. WO 93/00365; Chien, D.Y., International Publ. No. WO 94/01778; and U.S. Patent No. 6,150,087, the disclosures of which are incorporated herein by reference in their entireties, will find use with the subject compositions and methods.
Additionally, polypeptides derived from the nonstructural regions of the virus will also find use herein. The NS3/4a region of the HCV polyprotein has been described and the amino acid sequence and overall structure of the protein are disclosed in Yao et al. Structure (November 1999) 7:1353-1363. See, also, Dasmahapatra et al., U.S. Patent No. 5,843,752, incorporated herein by reference in its entirety. As explained above, either the native sequence or immunogenic analogs can be used in the subject formulations. Dasmahapatra et al., U.S. Patent No. 5,843,752 and Zhang et al., U.S. Patent No. 5,990,276, both describe analogs of NS3/4a and methods of making the same.
Moreover, polypeptides for use in the subject compositions and methods may be derived from the NS3 region of the HCV polyprotein. A number of such polypeptides are known, including, but not limited to polypeptides derived from the c33c and clOO regions, as well as fusion proteins comprising an NS3 epitope, such as c25. These and other NS3 polypeptides are useful in the present compositions and are known in the art and described in, e.g., Houghton et al, U.S. Patent No. 5,350,671; Chien et al. Proc. Natl. Acad. ScL USA (1992) 89:10011-10015; Chien et al. J. Gastroent. Hepatol. (1993) 8:S33-39; Chien et al., International Publ. No. WO 93/00365; Chien, D.Y., International Publ. No. WO 94/01778; and U.S. Patent No. 6,150,087, the disclosures of which are incorporated herein by reference in their entireties. Additionally, multiple epitope fusion antigens (termed "MEFAs"), as described in, e.g., U.S. Patent Nos. 6,514,731 and 6,428,792, incorporated herein by reference in their entireties, may be used in the subject compositions. Such MEFAs include multiple epitopes derived from two or more of the various viral regions. The epitopes are preferably from more than one HCV strain, thus providing the added ability to protect against multiple strains of HCV in a single vaccine.
As explained above, for convenience, the various HCV regions have been defined with respect to the amino acid number relative to the polyprotein encoded by the genome of HCV-Ia, as described in Choo et al. (1991) Proc Natl Acad Sci USA 88 :2451, with the initiator methionine being designated position 1. However, HCV polypeptides and polynucleotides for use with the present invention are not limited to those derived from the HCV-Ia sequence and any strain or isolate of HCV can serve as the basis for providing antigenic sequences for use with the invention. In this regard, the corresponding regions in another HCV isolate can be readily determined by aligning sequences from the two isolates in a manner that brings the sequences into maximum alignment.
Various strains and isolates of HCV are known in the art, which differ from one another by changes in nucleotide and amino acid sequence. Accession numbers for polyprotein sequences from several of the HCV genotypes and subtypes are described above. Additional sequences are as follows. Isolate HCV J 1.1 is described in Kubo et al. (1989) Japan. Nucl. Acids Res. 17:10367-10372; Takeuchi et al.(1990) Gene 91:287-291; Takeuchi et al. (1990) J. Gen. Virol. 71:3027-3033; and Takeuchi et al. (1990) Nucl. Acids Res.18:4626. The complete coding sequences of two independent isolates, HCV-J and BK, are described by Kato et al., (1990) Proc. Natl. Acad. ScL USA 87:9524-9528 and Takamizawa et al., (1991) J. Virol. 65:1105-1113, respectively. HCV-I isolates are described by Choo et al. (1990) Brit. Med. Bull. 46:423-441; Choo et al. (1991) Proc. Natl. Acad. Sci. USA 88:2451-2455 and Han et al. (1991) Proc. Natl. Acad. Sci. USA 88:1711-1715. HCV isolates HC-Jl and HC-J4 are described in Okamoto et al. (1991) Japan J. Exp. Med. 60:167-177. HCV isolates HCT 18, HCT 23, Th, HCT 27, ECl and EClO are described in Weiner et al. (1991) Virol. 180:842-848. HCV isolates Pt-I, HCV-Kl and HCV-K2 are described in Enomoto et al. (1990) Biochem. Biophys. Res. Commun. 170:1021-1025. HCV isolates A, C, D & E are described in Tsukiyama-Kohara et al. (1991) Virus Genes 5:243-254. HCV E1E2 polynucleotides and polypeptides for use in the compositions and methods of the invention can be obtained from any of the above cited strains of HCV or from newly discovered isolates isolated from tissues or fluids of infected patients.
Immunogenic Compositions and Administration
A. Compositions
Once produced, the envelope polypeptides or other immunogens may be provided in immunogenic compositions, in e.g., prophylactic (i.e., to prevent infection) or therapeutic (to treat HCV following infection) vaccine compositions. As explained above, the compositions can comprise mixtures of more than one envelope polypeptide, at least one of the polypeptides derived from any one of HCV genotypes 1, 4, 5 and/or 6, and at least one of the polypeptides derived from HCV genotype 2 and/or 3. In fact, HCV envelope polypeptides from all of these genotypes can be present, if desired. Typically, the compositions will include at least an envelope polypeptide from HCV genotype 1, 4, 5 or 6, such as from HCV-Ia, 4a, 5a or 6a, and at least an envelope polypeptide from HCV genotype 2 or 3, preferably both of 2 and 3 such as HCV-2a and 3a. Alternatively, two or more compositions can be provided, one including at least one envelope polypeptides derived from HCV genotypes 1, 4, 5 and/or 6, such as from HCV-Ia, 4a, 5a and/or 6a, and another composition including at least one envelope polypeptide derived from HCV genotype 2 and/or 3, such as HCV-2a and/or 3 a. In fact, separate compositions, each with an HCV envelope polypeptide from each of these six genotypes, can be provided, if desired.
The compositions will generally include one or more "pharmaceutically acceptable excipients or vehicles" such as water, saline, glycerol, ethanol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.
A carrier is optionally present which is a molecule that does not itself induce the production of antibodies harmful to the individual receiving the composition. Suitable carriers are typically large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycollic acids, polymeric amino acids, amino acid copolymers, lipid aggregates (such as oil droplets or liposomes), and inactive virus particles. Such carriers are well known to those of ordinary skill in the art. Furthermore, the HCV polypeptide may be conjugated to a bacterial toxoid, such as toxoid from diphtheria, tetanus, cholera, etc.
Pharmaceutically acceptable salts can also be used in compositions of the invention, for example, mineral salts such as hydrochlorides, hydrobromides, phosphates, or sulfates, as well as salts of organic acids such as acetates, proprionates, malonates, or benzoates. Especially useful protein substrates are serum albumins, keyhole limpet hemocyanin, immunoglobulin molecules, thyroglobulin, ovalbumin, tetanus toxoid, and other proteins well known to those of skill in the art. Compositions of the invention can also contain liquids or excipients, such as water, saline, glycerol, dextrose, ethanol, or the like, singly or in combination, as well as substances such as wetting agents, emulsifying agents, or pH buffering agents. The proteins or polynucleotides of the invention can also be adsorbed to, entrapped within or otherwise associated with liposomes and particulate carriers such as PLG. Liposomes and other particulate carriers are described above.
If desired, co-stimulatory molecules which improve immunogen presentation to lymphocytes, such as B7-1 or B7-2, or cytokines, lymphokines, and chemokines, including but not limited to cytokines such as IL-2, modified IL-2 (cysl25 to serl25), GM-CSF, IL-12, γ- interferon, IP-IO, MlPlβ, FLP-3, ribavirin and RANTES, may be included in the composition. Optionally, adjuvants can also be included in a composition. Adjuvants which can be used include, but are not limited to: (1) aluminum salts (alum), such as aluminum hydroxide, aluminum phosphate, aluminum sulfate, etc; (2) oil-in-water emulsion formulations (with or without other specific immunostimulating agents such as muramyl peptides (see below) or bacterial cell wall components), such as for example (a) MF59 (PCT Publ. No. WO 90/14837), containing 5% Squalene, 0.5% TWEEN 80, and 0.5% SPAN 85 (optionally containing various amounts of MTP-PE ), formulated into submicron particles using a microfluidizer such as Model HOY microfluidizer (Microfluidics, Newton, MA), (b) SAF, containing 10% Squalane, 0.4% TWEEN 80, 5% pluronic-blocked polymer L 121, and thr-MDP (see below) either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion, and (c) RibiTM adjuvant system (RAS), (Ribi Immunochem, Hamilton, MT) containing 2% Squalene, 0.2% TWEEN 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton
(CWS), preferably MPL + CWS (Detox™); (3) saponin adjuvants, such as QS21 or Stimulon™ (Cambridge Bioscience, Worcester, MA) may be used or particles generated therefrom such as ISCOMs (immunostimulating complexes), which ISCOMs may be devoid of additional detergent (see, e.g., International Publication No. WO 00/07621); (4) Complete Freunds Adjuvant (CFA) and Incomplete Freunds Adjuvant (IFA); (5) cytokines, such as interleukins, such as IL-I, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 etc. (see, e.g., International Publication No. WO 99/44636), interferons, such as gamma interferon, macrophage colony stimulating factor (M-CSF), tumor necrosis factor (TNF), etc.; (6) detoxified mutants of a bacterial ADP-ribosylating toxin such as a cholera toxin (CT), a pertussis toxin (PT), or an E. coli heat-labile toxin (LT), particularly LT-K63 (where lysine is substituted for the wild-type amino acid at position 63) LT-R72 (where arginine is substituted for the wild-type amino acid at position 72), CT-S 109 (where serine is substituted for the wild-type amino acid at position 109), and PT-K9/G129 (where lysine is substituted for the wild-type amino acid at position 9 and glycine substituted at position 129) (see, e.g., International Publication Nos. W093/13202 and W092/19265); (7) monophosporyl lipid A (MPL) or 3-O-deacylated MPL (3dMPL) (see, e.g., GB 2220221; EPA 0689454), optionally in the substantial absence of alum (see, e.g., International Publication No. WO 00/56358); (8) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulations (see, e.g., EPA 0835318; EPA 0735898; EPA 0761231); (9) a polyoxyethylene ether or a polyoxyethylene ester (see, e.g., International Publication No. WO 99/52549); (10) an immunostimulatory oligonucleotide such as a CpG oligonucleotide, or a saponin and an immunostimulatory oligonucleotide, such as a CpG oligonucleotide (see, e.g., International Publication No. WO 00/62800); (11) an immunostimulant and a particle of a metal salt (see, e.g., International Publication No. WO 00/23105); (12) a saponin and an oil-in-water emulsion (see, e.g., International Publication No. WO 99/11241 ; (13) a saponin (e.g., QS21) + 3dMPL + IL-12 (optionally + a sterol) (see, e.g., International Publication No. WO 98/57659); (14) the MPL derivative RC529; and (15) other substances that act as immunostimulating agents to enhance the effectiveness of the composition. Alum and MF59 are preferred. As mentioned above, muramyl peptides include, but are not limited to,
N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), - acetyl-normuramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(l'-2'-dipalmitoyl-Λ'«-glycero- 3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE), etc. Moreover, the HCV polypeptides can be adsorbed to, or entrapped within, an
ISCOM. Classic ISCOMs are formed by combination of cholesterol, saponin, phospholipid, and immunogens. Generally, immunogens (usually with a hydrophobic region) are solubilized in detergent and added to the reaction mixture, whereby ISCOMs are formed with the immunogen incorporated therein. ISCOM matrix compositions are formed identically, but without viral proteins. Proteins with high positive charge may be electrostatically bound in the ISCOM particles, rather than through hydrophobic forces. For a more detailed general discussion of saponins and ISCOMs, and methods of formulating ISCOMs, see Barr et al. (1998) Adv. Drug Delivery Reviews 32:247-271 (1998). ISCOMs for use with the present invention are produced using standard techniques, well known in the art, and are described in e.g., U.S. Patent Nos. 4,981,684, 5,178,860, 5,679,354 and 6,027,732; European Publ. Nos. EPA 109,942; 180,564 and 231,039; Coulter et al. (1998) Vaccine 16:1243. Typically, the term "ISCOM" refers to immunogenic complexes formed between glycosides, such as triterpenoid saponins (particularly Quil A), and antigens which contain a hydrophobic region. See, e.g., European Publ. Nos. EPA 109,942 and 180,564. In this embodiment, the HCV polypeptides (usually with a hydrophobic region) are solubilized in detergent and added to the reaction mixture, whereby ISCOMs are formed with the polypeptides incorporated therein. The HCV polypeptide ISCOMs are readily made with HCV polypeptides which show amphipathic properties. However, proteins and peptides which lack the desirable hydrophobic properties may be incorporated into the immunogenic complexes after coupling with peptides having hydrophobic amino acids, fatty acid radicals, alkyl radicals and the like.
As explained in European Publ. No. EPA 231,039, the presence of antigen is not necessary in order to form the basic ISCOM structure (referred to as a matrix or ISCOMATRIX), which may be formed from a sterol, such as cholesterol, a phospholipid, such as phosphatidylethanolamine, and a glycoside, such as Quil A. Thus, the HCV polypeptide of interest, rather than being incorporated into the matrix, is present on the outside of the matrix, for example adsorbed to the matrix via electrostatic interactions. For example, HCV polypeptides with high positive charge may be electrostatically bound to the ISCOM particles, rather than through hydrophobic forces. For a more detailed general discussion of saponins and ISCOMs, and methods of formulating ISCOMs, see Barr et al. (1998) Adv. Drug Delivery Reviews 32:247-271 (1998).
The ISCOM matrix may be prepared, for example, by mixing together solubilized sterol, glycoside and (optionally) phospholipid. If phospholipids are not used, two dimensional structures are formed. See, e.g., European Publ. No. EPA 231 ,039. The term "ISCOM matrix" is used to refer to both the 3-dimensional and 2- dimensional structures. The glycosides to be used are generally glycosides which display amphipathic properties and comprise hydrophobic and hydrophilic regions in the molecule. Preferably saponins are used, such as the saponin extract from Quillaja saponaria Molina and Quil A. Other preferred saponins are aescine from Aesculus hippocastanum (Part et al. (1960) Arzneimittelforschung JO:273-275 and sapoalbin from Gypsophilla struthium (Vochten et al. (1968) J. Pharm. BeIg. 42:213-226. In order to prepare the ISCOMs, glycosides are used in at least a critical micelle-forming concentration. In the case of Quil A, this concentration is about 0.03% by weight. The sterols used to produce ISCOMs may be known sterols of animal or vegetable origin, such as cholesterol, lanosterol, lumisterol, stigmasterol and sitosterol. Suitable phospholipids include phosphatidylcholine and phosphatidylethanolamine. Generally, the molar ratio of glycoside (especially when it is Quil A) to sterol (especially when it is cholesterol) to phospholipid is 1:1:0-1, + 20% (preferably not more than +10%) for each figure. This is equivalent to a weight ratio of about 5:1 for the Quil Axholesterol.
A solubilizing agent may also be present and may be, for example a detergent, urea or guanidine. Generally, a non-ionic, ionic or zwitter-ionic detergent or a cholic acid based detergent, such as sodium desoxycholate, cholate and CTAB
(cetyltriammonium bromide), can be used for this purpose. Examples of suitable detergents include, but are not limited to, octylglucoside, nonyl N-methyl glucamide or decanoyl N-methyl glucamide, alkylphenyl polyoxyethylene ethers such as a polyethylene glycol p-isooctyl-phenylether having 9 to 10 oxyethylene groups (commercialized under the trade name TRITON X- 100RTM)5 acylpolyoxy ethylene esters such as acylpolyoxyethylene sorbitane esters (commercialized under the trade name TWEEN 2θTM , TWEEN 80™ and the like). The solubilizing agent is generally removed for formation of the ISCOMs, such as by ultrafiltration, dialysis, ultracentrifugation or chromatography, however, in certain methods, this step is unnecessary. (See, e.g., U.S. Patent No. 4,981,684).
Generally, the ratio of glycoside, such as QuilA, to HCV fusion by weight is in the range of 5:1 to 0.5:1. Preferably the ratio by weight is approximately 3:1 to 1:1, and more preferably the ratio is 2:1.
Once the ISCOMs are formed, they may be formulated into compositions and administered to animals, as described herein. If desired, the solutions of the immunogenic complexes obtained may be lyophilized and then reconstituted before use.
For example, if HCV envelope polypeptides, including E1E2 complexes, can be provided in compositions that include a submicron oil-in-water emulsion such as MF59 and/or oligonucleotides containing immunostimulatory nucleic acid sequences (ISS), such as CpY, CpR and unmethylated CpG motifs (a cytosine followed by guanosine and linked by a phosphate bond). Such compositions are described in detail in PCT Publication No. WO 03/002065, incorporated herein by reference in its entirety.
Compositions including the HCV envelope polypeptides or polynucleotides described above, can be used in combination with other HCV immunogenic proteins, and/or compositions comprising the same. For example, the HCV envelope proteins can be used in combination with any of the various HCV immunogenic proteins derived from one or more of the regions of the HCV polyprotein described in Table 1. The additional HCV immunogenic proteins can be provided in compositions with excipients, adjuvants, immunstimulatory molecules and the like, as described above. Thus, it is readily apparent that the compositions of the present invention may be administered in conjunction with a number of immunoregulatory agents and will usually include an adjuvant. Such agents and adjuvants for use with the compositions include, but are not limited to, any of those substances described above, as well as one or more of the following set forth below.
A. Mineral Containing Compositions
Mineral containing compositions suitable for use as adjuvants in the invention include mineral salts, such as aluminum salts and calcium salts. The invention includes mineral salts such as hydroxides (e.g. oxyhydroxides), phosphates (e.g. hydroxyphosphates, orthophosphates), sulfates, etc. (e.g. see chapters 8 & 9 of Vaccine Design (1995) eds. Powell & Newman. ISBN: 030644867X. Plenum), or mixtures of different mineral compounds (e.g. a mixture of a phosphate and a hydroxide adjuvant, optionally with an excess of the phosphate), with the compounds taking any suitable form (e.g. gel, crystalline, amorphous, etc.), and with adsorption to the salt(s) being preferred. The mineral containing compositions may also be formulated as a particle of metal salt (PCT Publication No. WO00/23105).
Aluminum salts may be included in compositions of the invention such that the dose OfAl3+ is between 0.2 and 1.0 mg per dose. In one embodiment, the aluminum- based adjuvant for use in the present compositions is alum' (aluminum potassium sulfate (AlK(SCU)2)), or an alum derivative, such as that formed in situ by mixing an antigen in phosphate buffer with alum, followed by titration and precipitation with a base such as ammonium hydroxide or sodium hydroxide. Another aluminum-based adjuvant for use in vaccine formulations of the present invention is aluminum hydroxide adjuvant (A1(OH)3) or crystalline aluminum oxyhydroxide (AlOOH), which is an excellent adsorbant, having a surface area of approximately 500m2/g. Alternatively, aluminum phosphate adjuvant (AlPO4) or aluminum hydroxyphosphate, which contains phosphate groups in place of some or all of the hydroxyl groups of aluminum hydroxide adjuvant is provided. Preferred aluminum phosphate adjuvants provided herein are amorphous and soluble in acidic, basic and neutral media.
In another embodiment, the adjuvant for use with the present compositions comprises both aluminum phosphate and aluminum hydroxide. In a more particular embodiment thereof, the adjuvant has a greater amount of aluminum phosphate than aluminum hydroxide, such as a ratio of 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1 or greater than 9:1, by weight aluminum phosphate to aluminum hydroxide. More particularly, aluminum salts may be present at 0.4 to 1.0 mg per vaccine dose, or 0.4 to 0.8 mg per vaccine dose, or 0.5 to 0.7 mg per vaccine dose, or about 0.6 mg per vaccine dose.
Generally, the preferred aluminum-based adjuvant(s), or ratio of multiple aluminum-based adjuvants, such as aluminum phosphate to aluminum hydroxide is selected by optimization of electrostatic attraction between molecules such that the antigen carries an opposite charge as the adjuvant at the desired pH. For example, aluminum phosphate adjuvant (iep = 4) adsorbs lysozyme, but not albumin at pH 7.4. Should albumin be the target, aluminum hydroxide adjuvant would be selected (iep 11.4). Alternatively, pretreatment of aluminum hydroxide with phosphate lowers its isoelectric point, making it a preferred adjuvant for more basic antigens.
B. Oil Emulsions
Oil emulsion compositions suitable for use as adjuvants in the compositions include squalene-water emulsions. Particularly preferred adjuvants are submicron oil- in-water emulsions. Preferred submicron oil-in-water emulsions for use herein are squalene/water emulsions optionally containing varying amounts of MTP-PE, such as a submicron oil-in-water emulsion containing 4-5% w/v squalene, 0.25-1.0% w/v Tween 80™ (polyoxyelthylenesorbitan monooleate), and/or 0.25-1.0% Span 85™ (sorbitan trioleate), and, optionally, N-acetylmuramyl-L-alanyl-D-isogluatminyl-L- alanine-2-(l'-2'-dipalmitoyl-5«-glycero-3-huydroxyphosphophoryloxy)-ethylamine (MTP-PE), for example, the submicron oil-in-water emulsion known as "MF59" (International Publication No. WO90/14837; US Patent Nos. 6,299,884 and 6,451,325, and Ott et al., "MF59 - Design and Evaluation of a Safe and Potent Adjuvant for Human Vaccines" in Vaccine Design: The Subunit and Adjuvant Approach (Powell, M.F. and Newman, MJ. eds.) Plenum Press, New York, 1995, pp. 277-296). MF59 contains 4-5% w/v Squalene (e.g. 4.3%), 0.25-0.5% w/v Tween 80™, and 0.5% w/v Span 85™ and optionally contains various amounts of MTP-PE, formulated into submicron particles using a microfluidizer such as Model HOY microfiuidizer (Microfluidics, Newton, MA). For example, MTP-PE may be present in an amount of about 0-500 μg/dose, more preferably 0-250 μg/dose and most preferably, 0-100 μg/dose. As used herein, the term "MF59-0" refers to the above submicron oil-in-water emulsion lacking MTP-PE, while the term MF59-MTP denotes a formulation that contains MTP-PE. For instance, "MF59-100" contains 100 μg MTP-PE per dose, and so on. MF69, another submicron oil-in-water emulsion for use herein, contains 4.3% w/v squalene, 0.25% w/v Tween 80™, and 0.75% w/v Span 85™ and optionally MTP-PE. Yet another submicron oil-in-water emulsion is MF75, also known as SAF, containing 10% squalene, 0.4% Tween 80™, 5% pluronic- blocked polymer L121, and thr-MDP, also microfluidized into a submicron emulsion. MF75-MTP denotes an MF75 formulation that includes MTP, such as from 100-400 μg MTP-PE per dose.
Submicron oil-in-water emulsions, methods of making the same and immunostimulating agents, such as muramyl peptides, for use in the compositions, are described in detail in International Publication No. WO90/14837 and US Patent Nos. 6,299,884 and 6,451,325. Complete Freund's adjuvant (CFA) and incomplete Freund's adjuvant (IFA) may also be used as adjuvants in the subject compositions.
C. Saponin Formulations
Saponin formulations, may also be used as adjuvants in the compositions. Saponins are a heterologous group of sterol glycosides and triterpenoid glycosides that are found in the bark, leaves, stems, roots and even flowers of a wide range of plant species. Saponins isolated from the bark of the Quillaia saponaria Molina tree have been widely studied as adjuvants. Saponins can also be commercially obtained from Smilax ornata (sarsaprilla), Gypsophilla paniculata (brides veil), and Saponaria offidanalis (soap root). Saponin adjuvant formulations include purified formulations, such as QS21, as well as lipid formulations, such as ISCOMs.
Saponin compositions have been purified using High Performance Thin Layer Chromatography (HP-TLC) and Reversed Phase High Performance Liquid
Chromatography (RP-HPLC). Specific purified fractions using these techniques have been identified, including QS7, QS17, QS18, QS21, QH-A, QH-B and QH-C.
Preferably, the saponin is QS21. A method of production of QS21 is disclosed in US
Patent No. 5,057,540. Saponin formulations may also comprise a sterol, such as cholesterol (see, PCT Publication No. WO96/33739).
Combinations of saponins and cholesterols can be used to form unique particles called Immunostimulating Complexes (ISCOMs). ISCOMs typically also include a phospholipid such as phosphatidylethanolamine or phosphatidylcholine.
Any known saponin can be used in ISCOMs. Preferably, the ISCOM includes one or more of Quil A, QHA and QHC. ISCOMs are further described in EP0109942,
WO96/11711 and WO96/33739. Optionally, the ISCOMS may be devoid of (an) additional detergent(s). See WO00/07621.
A review of the development of saponin-based adjuvants can be found in Barr, et al., "ISCOMs and other saponin based adjuvants", Advanced Drug Delivery Reviews (1998) 32:247-271. See also Sjolander, et al., "Uptake and adjuvant activity of orally delivered saponin and ISCOM vaccines", Advanced Drug Delivery Reviews
(1998) 32:321-338.
D. Virosomes and Virus Like Particles (VLPs)
Virosomes and Virus Like Particles (VLPs) can also be used as adjuvants with the present compositions. These structures generally contain one or more proteins from a virus optionally combined or formulated with a phospholipid. They are generally non-pathogenic, non-replicating and generally do not contain any of the native viral genome. The viral proteins may be recombinantly produced or isolated from whole viruses. These viral proteins suitable for use in virosomes or VLPs include proteins derived from influenza virus (such as HA or NA), Hepatitis B virus (such as core or capsid proteins), Hepatitis E virus, measles virus, Sindbis virus, Rotavirus, Foot-and-Mouth Disease virus, Retrovirus, Norwalk virus, human Papilloma virus, HIV, RNA-phages, Qβ-phage (such as coat proteins), GA-phage, fr- phage, AP205 phage, and Ty (such as retrotransposon Ty protein pi). VLPs are discussed further in WO03/024480, WO03/024481, and Niikura et al., "Chimeric Recombinant Hepatitis E Virus-Like Particles as an Oral Vaccine Vehicle Presenting Foreign Epitopes", Virology (2002) 293:273-280; Lenz et al., "Papillomarivurs-Like Particles Induce Acute Activation of Dendritic Cells", Journal of Immunology (2001) 5246-5355; Pinto, et al., "Cellular Immune Responses to Human Papillomavirus (HPV)-16 Ll Healthy Volunteers Immunized with Recombinant HPV-16 Ll Virus- Like Particles", Journal of Infectious Diseases (2003) 188:327-338; and Gerber et al., "Human Papillomavrisu Virus-Like Particles Are Efficient Oral Immunogens when Coadministered with Escherichia coli Heat-Labile Entertoxin Mutant R192G or CpG", Journal of Virology (2001) 75(10):4752-4760. Virosomes are discussed further in, for example, Gluck et al., "New Technology Platforms in the Development of Vaccines for the Future", Vaccine (2002) 20:B10 -B16. Immunopotentiating reconstituted influenza virosomes (IRIV) are used as the subunit antigen delivery system in the intranasal trivalent INFLEXAL™ product (Mischler & Metcalfe (2002) Vaccine 20 Suppl 5:B17-23) and the INFLUVAC PLUS™ product.
E. Bacterial or Microbial Derivatives
Adjuvants suitable for use in the present compositions include bacterial or microbial derivatives such as: (1) Non-toxic derivatives of enterobacterial lipopolysaccharide (LPS)
Such derivatives include Monophosphoryl lipid A (MPL) and 3-O-deacylated MPL (3dMPL). 3dMPL is a mixture of 3 De-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains. A preferred "small particle" form of 3 De-O-acylated monophosphoryl lipid A is disclosed in EP 0 689454. Such "small particles" of 3dMPL are small enough to be sterile filtered through a 0.22 micron membrane (see EP 0 689 454). Other non-toxic LPS derivatives include monophosphoryl lipid A mimics, such as aminoalkyl glucosaminide phosphate derivatives e.g. RC-529. See Johnson et al. (1999) BioorgMed Chem Lett 9:2273-2278.
(2) Lipid A Derivatives Lipid A derivatives include derivatives of lipid A from Escherichia coli such as OM-174. OM-174 is described for example in Meraldi et al., "OM-174, a New Adjuvant with a Potential for Human Use, Induces a Protective Response with Administered with the Synthetic C-Terminal Fragment 242-310 from the circumsporozoite protein of Plasmodium berghei", Vaccine (2003) 21:2485-2491; and Pajak, et al., "The Adjuvant OM-174 induces both the migration and maturation of murine dendritic cells in vivo", Vaccine (2003) 21:836-842. (3) Immunostimulatory oligonucleotides
Immunostimulatory oligonucleotides suitable for use as adjuvants include nucleotide sequences containing a CpG motif (a sequence containing an unmethylated cytosine followed by guanosine and linked by a phosphate bond). Bacterial double stranded RNA or oligonucleotides containing palindromic or poly(dG) sequences have also been shown to be immunostimulatory.
The CpG' s can include nucleotide modifications/analogs such as phosphorothioate modifications and can be double-stranded or single-stranded. Optionally, the guanosine may be replaced with an analog such as 2'-deoxy-7- deazaguanosine. See, Kandimalla, et al., "Divergent synthetic nucleotide motif recognition pattern: design and development of potent immunomodulatory oligodeoxyribonucleotide agents with distinct cytokine induction profiles", Nucleic Acids Research (2003) 3_1(9): 2393-2400; WO02/26757 and WO99/62923 for examples of possible analog substitutions. The adjuvant effect of CpG oligonucleotides is further discussed in Krieg, "CpG motifs: the active ingredient in bacterial extracts?", Nature Medicine (2003) 9(7): 831-835; McCluskie, et al.,
"Parenteral and mucosal prime-boost immunization strategies in mice with hepatitis B surface antigen and CpG DNA", FEMS Immunology and Medical Microbiology (2002) 32:179-185; WO98/40100; US Patent No. 6,207,646; US Patent No. 6,239,116 and US Patent No. 6,429,199. The CpG sequence may be directed to TLR9, such as the motif GTCGTT or
TTCGTT. See, Kandimalla, et al., "Toll-like receptor 9: modulation of recognition and cytokine induction by novel synthetic CpG DNAs", Biochemical Society Transactions (2003) 3J, (part 3): 654-658. The CpG sequence may be specific for inducing a ThI immune response, such as a CpG-A ODN, or it may be more specific for inducing a B cell response, such a CpG-B ODN. CpG-A and CpG-B ODNs are discussed in Blackwell, et al., "CpG-A-Induced Monocyte IFN-gamma-Inducible Protein- 10 Production is Regulated by Plasmacytoid Dendritic Cell Derived IFN- alpha", J. Immunol. (2003) 170(8):4061-4068; Krieg, "From A to Z on CpG", TRENDS in Immunology (2002) 23(2): 64-65 and WO01/95935. Preferably, the CpG is a CpG-A ODN.
Preferably, the CpG oligonucleotide is constructed so that the 5' end is accessible for receptor recognition. Optionally, two CpG oligonucleotide sequences may be attached at their 3' ends to form "immunomers". See, for example, Kandimalla, et al., "Secondary structures in CpG oligonucleotides affect immunostimulatory activity", BBRC (2003) 306:948-953; Kandimalla, et al., "Toll- like receptor 9: modulation of recognition and cytokine induction by novel synthetic GpG DNAs", Biochemical Society Transactions (2003) 3J,(part 3):664-658; Bhagat et al., "CpG penta- and hexadeoxyribonucleotides as potent immunomodulatory agents" BBRC (2003) 300:853-861 and WO03/035836.
(4) ADP-ribosylating toxins and detoxified derivatives thereof. Bacterial ADP-ribosylating toxins and detoxified derivatives thereof may be used as adjuvants in the compositions. Preferably, the protein is derived from E. coli (i.e., E. coli heat labile enterotoxin "LT), cholera ("CT"), or pertussis ("PT"). The use of detoxified ADP-ribosylating toxins as mucosal adjuvants is described in WO95/17211 and as parenteral adjuvants in WO98/42375. Preferably, the adjuvant is a detoxified LT mutant such as LT-K63, LT-R72, and LTR192G. The use of ADP- ribosylating toxins and detoxified derivatives thereof, particularly LT-K63 and LT- R72, as adjuvants can be found in the following references: Beignon, et al., "The
LTR72 Mutant of Heat-Labile Enterotoxin of Escherichia coli Enhances the Ability of Peptide Antigens to Elicit CD4+ T Cells and Secrete Gamma Interferon after Coapplication onto Bare Skin", Infection and Immunity (2002) 70(6):3012-3019; Pizza, et al., "Mucosal vaccines: non toxic derivatives of LT and CT as mucosal adjuvants", Vaccine (2001) 19:2534-2541; Pizza, et al., "LTK63 and LTR72, two mucosal adjuvants ready for clinical trials" Int. J. Med. Microbiol (2000) 290(4- 5):455-461; Scharton-Kersten et al., "Transcutaneous Immunization with Bacterial ADP-Ribosylating Exotoxins, Subunits and Unrelated Adjuvants", Infection and Immunity (2000) 68(9):5306-5313; Ryan et al., "Mutants of Escherichia coli Heat- Labile Toxin Act as Effective Mucosal Adjuvants for Nasal Delivery of an Acellular Pertussis Vaccine: Differential Effects of the Nontoxic AB Complex and Enzyme Activity on ThI and Th2 Cells" Infection and Immunity (1999) 67(12):6270-6280; Partidos et al., "Heat-labile enterotoxin of Escherichia coli and its site-directed mutant LTK63 enhance the proliferative and cytotoxic T-cell responses to intranasally co- immunized synthetic peptides", Immunol. Lett. (1999) 67(3):209-216; Peppoloni et al., "Mutants of the Escherichia coli heat-labile enterotoxin as safe and strong adjuvants for intranasal delivery of vaccines", Vaccines (2003) 2(2):285-293; and Pine et al., (2002) "Intranasal immunization with influenza vaccine and a detoxified mutant of heat labile enterotoxin from Escherichia coli (LTK63)" J. Control Release (2002) 85(l-3):263-270. Numerical reference for amino acid substitutions is preferably based on the alignments of the A and B subunits of ADP-ribosylating toxins set forth in Domenighini et al., MoI. Microbiol (1995) JJ5(6):1165-1167. F. Bioadhesives and Mucoadhesives
Bioadhesives and mucoadhesives may also be used as adjuvants in the subject compositions. Suitable bioadhesives include esterified hyaluronic acid microspheres (Singh et al. (2001) J. Cont. ReIe. 70:267-276) or mucoadhesives such as cross-linked derivatives of polyacrylic acid, polyvinyl alcohol, polyvinyl pyrollidone, polysaccharides and carboxymethylcellulose. Chitosan and derivatives thereof may also be used as adjuvants in the compositions. See, e.g., WO99/27960.
G. Microparticles
Microparticles may also be used as adjuvants in the compositions. Microparticles (i.e. a particle of ~100 nm to ~150 μm in diameter, more preferably ~200 nm to ~30 μm in diameter, and most preferably ~500 nm to ~10 μm in diameter) formed from materials that are biodegradable and non-toxic (e.g. a poly(α-hydroxy acid), a polyhydroxybutyric acid, a polyorthoester, a polyanhydride, a polycaprolactone, etc.), with poly(lactide-co-glycolide) are preferred, optionally treated to have a negatively-charged surface (e.g. with SDS) or a positively-charged surface (e.g. with a cationic detergent, such as CTAB).
H. Liposomes
Examples of liposome formulations suitable for use as adjuvants are described in US Patent No. 6,090,406, US Patent No. 5,916,588, and EP 0 626 169.
I. Polyoxyethylene ether and Polyoxyethylene Ester Formulations
Adjuvants suitable for use in the compositions include polyoxyethylene ethers and polyoxyethylene esters. See, e.g., WO99/52549. Such formulations further include polyoxyethylene sorbitan ester surfactants in combination with an octoxynol (WO01/21207) as well as polyoxyethylene alkyl ethers or ester surfactants in combination with at least one additional non-ionic surfactant such as an octoxynol (WO01/21152). Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether (laureth 9), polyoxyethylene-9-steoryl ether, polyoxytheylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35- lauryl ether, and polyoxyethylene-23-lauryl ether.
J. Polvphosphazene (PCPP)
PCPP formulations are described, for example, in Andrianov et al., "Preparation of hydrogel microspheres by coacervation of aqueous polyphophazene solutions", Biomaterials (1998) 19(1-3): 109-115 and Payne et al., "Protein Release from Polyphosphazene Matrices", Adv. Drug. Delivery Review (1998) 31(3): 185- 196.
K. Muramyl peptides Examples of muramyl peptides suitable for use as adjuvants include N-acetyl- muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-1-alanyl-d- isoglutamine (nor-MDP), and N~acetylmuramyl-l-alanyl-d-isoglutaminyl-l-alanine-2- ( 1 '-2'-dipalmitoyl-sn-glycero-3 -hydroxyphosphoryloxy)-ethylamine MTP-PE) .
L. Small Molecule Immunopotentiators (SMIPs*) a. Imidazoquinoline Compounds
Examples of imidazoquinoline compounds suitable for use as adjuvants in the compositions include Imiquimod and its analogues, described further in Stanley, "Imiquimod and the imidazoquinolines: mechanism of action and therapeutic potential" Clin Exp Dermatol (2002) 27(7):571-577; Jones, "Resiquimod 3M", Curr Opin Investig Drugs (2003) 4(2):214-218; Wu et al. (2004) Antiviral Res. 64(2):79- 83; Vasilakos et al. (2000) Cell Immunol. 204(l):64-74; and US patents 4689338, 4929624, 5238944, 5266575, 5268376, 5346905, 5352784, 5389640, 5395937, 5482936, 5494916, 5525612, 6083505, 6440992, 6627640, 6656938, 6660735, 6660747, 6664260, 6664264, 6664265, 6667312, 6670372, 6677347, 6677348, 6677349, 6683088, 6703402, 6743920, 6800624, 6809203, 6888000 and 6924293. Preferred SMIPs include:
N2-methyl- 1 -(2-methylpropyl)- lH-imidazo[4,5-c]quinoline-2,4-diamine;
N2,N2-dimethyl-l-(2-methylpropyl)-lH-imidazo[4,5-c]quinoline-2,4- diamine; N2-ethyl-N2-methyl-l-(2-methylpropyl)-lH-imidazo[4,5-c]quinoline-2,4- diamine;
N2-methyl-l-(2-methylpropyl)-N2-propyl-lH-imidazo[4,5-c]quinoline-2,4- diamine; l-(2-methylpropyl)-N2-propyl-lH-imidazo[4,5-c]quinoline-2,4-diamine; N2-butyl- 1 -(2-methylpropyl)- 1 H-imidazo [4, 5 -c]quinoline-2,4-diamine;
N2-butyl-N2-methyl-l-(2-methylpropyl)-lH-imidazo[4,5-c]quinoline-2,4- diamine;
N2-methyl-l-(2-methylpropyl)-N2-pentyl-lH-imidazo[4,5-c]quinoline-2,4- diamine; N2-methyl-l-(2-methylpropyl)-N2-prop-2-enyl-lH-imidazo[4,5-c]quinoline-
2,4-diamine; l-(2-methylpropyl)-2-[(phenylmethyl)thio]-lH-imidazo[4,5-c]quinolin-4- amine; l-(2-methylpropyl)-2-(propylthio)-lH-imidazo[4,5-c]quinolin-4-amine; 2-[[4-amino-l-(2-methylpropyl)-lH-imidazo[4,5-c]quinolin-2- yl](methyl)amino]ethanol;
2-[[4-amino-l-(2-methylpropyl)-lH-imidazo[4,5-c]quinolin-2- yl](methyl)amino]ethyl acetate;
4-amino-l-(2-methylpropyl)-l,3-dihydro-2H-imidazo[4,5-c]quinolin-2-one; N2-butyl-l-(2-methylpropyl)-N4,N4-bis(phenylmethyl)-lH-imidazo[4,5- c]quinoline-2,4-diamine;
N2-butyl-N2-methyl-l-(2-niethylpropyl)-N4,N4-bis(phenylmethyl)-lH- imidazo[4,5-c]quinoline-2,4-diamine;
N2-methyl-l-(2-methylpropyl)-N4,N4-bis(phenylmethyl)-lH-imidazo[4,5- c]quinoline-2,4-diamine;
N2,N2-dimethyl- 1 -(2-methylpropyl)-N4,N4-bis(phenylmethyl)- 1 H- imidazo [4, 5-c] quinoline-2,4-diamine; l-{4-amino-2-[methyl(propyl)amino]-lH-imidazo[4,5-c]quinolin-l-yl}-2- methylpropan-2-ol;
1 -[4-amino-2-(propylamino)- lH-imidazo [4,5 -c] quinolin- 1 -yl] -2- methylpropan-2-ol; N4,N4-dibenzyl-l-(2-methoxy-2-methylpropyl)-N2-propyl-lH-imidazo[4,5- c]quinoline-2,4-diamine. b. Thiosemicarbazone Compounds
Examples of thiosemicarbazone compounds, as well as methods of formulating, manufacturing, and screening for compounds all suitable for use as adjuvants in the compositions include those described in WO04/60308. The thiosemicarbazones are particularly effective in the stimulation of human peripheral blood mononuclear cells for the production of cytokines, such as TNF-α. c. Tryptanthrin Compounds
Examples of tryptanthrin compounds, as well as methods of formulating, manufacturing, and screening for compounds all suitable for use as adjuvants in the compositions include those described in WO04/64759. The tryptanthrin compounds are particularly effective in the stimulation of human peripheral blood mononuclear cells for the production of cytokines, such as TNF-α.
M. Nucleoside Analogs Examples of useful nucleoside analogs include: (a) Isatorabine (ANA-245; 7- thia-8-oxoguanosine):
Figure imgf000050_0001
and prodrugs thereof;
(b)ANA975;
(c) ANA-025-l;
(d) ANA380; (e) the compounds disclosed in references US 6,924,271 to
US2005/0070556 US 5,658,731;
(f) a compound having the formula:
Figure imgf000051_0001
wherein: Rl and R2 are each independently H, halo, -NRaRb, -OH, C 1 -6 alkoxy, substituted C 1-6 alkoxy, heterocyclyl, substituted heterocyclyl, C6-10 aryl, substituted C6-10 aryl, C 1-6 alkyl, or substituted C 1-6 alkyl;
R3 is absent, H, C 1-6 alkyl, substituted C 1-6 alkyl, C6-10 aryl, substituted C6-
10 aryl, heterocyclyl, or substituted heterocyclyl; R4 and R5 are each independently H, halo, heterocyclyl, substituted heterocyclyl, C(O)-Rd, C 1-6 alkyl, substituted C 1-6 alkyl, or bound together to form a 5 membered ring as in R4-5:
Figure imgf000051_0002
the binding being achieved at the bonds indicated by a -~>~- Xl and X2 are each independently N, C, O, or S;
R8 is H, halo, -OH, Cl-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, -OH, -NRaRb, -(CH2)n- O-Rc, -0-(C 1 -6 alkyl), -S(O)pRe, or -C(O)-Rd; R9 is H, Cl-6 alkyl, substituted Cl-6 alkyl, heterocyclyl, substituted heterocyclyl or R9a, wherein R9a is:
Figure imgf000051_0003
the binding being achieved at the bond indicated by a ^
RlO and RIl are each independently H, halo, Cl-6 alkoxy, substituted Cl-6 alkoxy, -
NRaRb, or -OH; each Ra and Rb is independently H, Cl-6 alkyl, substituted Cl-6 alkyl, -C(O)Rd, C6- 10 aryl; each Rc is independently H, phosphate, diphosphate, triphosphate, Cl-6 alkyl, or substituted Cl-6 alkyl; each Rd is independently H, halo, Cl-6 alkyl, substituted Cl-6 alkyl, Cl-6 alkoxy, substituted Cl-6 alkoxy, -NH2, -NH(Cl-6 alkyl), -NH(substituted Cl-6 alkyl), - N(C 1 -6 alkyl)2, -N(substituted C 1 -6 alkyl)2, C6- 10 aryl, or heterocyclyl; each Re is independently H, Cl-6 alkyl, substituted Cl-6 alkyl, C6-10 aryl, substituted C6-10 aryl, heterocyclyl, or substituted heterocyclyl; each Rf is independently H, Cl-6 alkyl, substituted Cl-6 alkyl, -C(O)Rd, phosphate, diphosphate, or triphosphate; each n is independently 0, 1, 2, or 3; each p is independently 0, 1, or 2; or
(g) a pharmaceutically acceptable salt of any of (a) to (f), a tautomer of any of
(a) to (f), or a pharmaceutically acceptable salt of the tautomer;
Loxoribine (7-allyl-8-oxoguanosine) [US patent 5,011,828].
N. Human Immunomodulators
Human immunomodulators suitable for use as adjuvants in the compositions include cytokines, such as interleukins (e.g. IL-I, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (e.g. interferon-γ), macrophage colony stimulating factor, and tumor necrosis factor. The compositions may also comprise combinations of aspects of one or more of the adjuvants identified above. For example, the following adjuvant compositions may be used in the invention:
(1) a saponin and an oil-in-water emulsion (WO99/11241);
(2) a saponin (e.g.., QS21) + a non-toxic LPS derivative (e.g. 3dMPL) (see WO94/00153);
(3) a saponin (e.g.., QS21) + a non-toxic LPS derivative (e.g. 3dMPL) + a cholesterol; (4) a saponin {e.g. QS21) + 3dMPL + IL-12 (optionally + a sterol) (WO98/57659);
(5) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulsions (See European patent applications 0835318, 0735898 and 0761231); (6) SAF, containing 10% Squalane, 0.4% Tween 80, 5% pluronic-block polymer L121, and thr-MDP, either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion.
(7) Ribi™ adjuvant system (RAS), (Ribi Immunochem) containing 2% Squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphory lipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL + CWS (Detox™); and
(8) one or more mineral salts (such as an aluminum salt) + a non-toxic derivative of LPS (such as 3dPML).
(9) one or more mineral salts (such as an aluminum salt) + an immunostimulatory oligonucleotide (such as a nucleotide sequence including a CpG motif).
Aluminum salts and MF59 are preferred adjuvants for use with injectable vaccines. Bacterial toxins and bioadhesives are preferred adjuvants for use with mucosally-delivered vaccines, such as nasal vaccines. The contents of all of the above cited patents, patent applications and journal articles are incorporated by reference as if set forth fully herein.
B. Administration
Typically, the compositions described above are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Thus, once formulated, the compositions are conventionally administered parenterally, e.g., by injection, either subcutaneously or intramuscularly. Additional formulations suitable for other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Dosage treatment may be a single dose schedule or a multiple dose schedule. Preferably, the effective amount is sufficient to bring about treatment or prevention of disease symptoms. The exact amount necessary will vary depending on the subject being treated; the age and general condition of the individual to be treated; the capacity of the individual's immune system to synthesize antibodies; the degree of protection desired; the severity of the condition being treated; the particular macromolecule selected and its mode of administration, among other factors. An appropriate effective amount can be readily determined by one of skill in the art. A "therapeutically effective amount" will fall in a relatively broad range that can be determined through routine trials using in vitro and in vivo models known in the art.
For example, the composition is preferably injected intramuscularly to a large mammal, such as a primate, for example, a baboon, chimpanzee, or human. The amount of polypeptide administered will generally be about 0.1 μg to about 5.0 mg per dose, or any amount between the stated ranges, such as .5 μg to about 10 mg, 1 μg to about 2 mg, 2.5 μg to about 250 μg, 4 μg to about 200 μg, such as 4, 5, 6, 7, 8, 9, 10...20...30...40...50...60...70...80...90...100, etc., μg per dose. The compositions can be administered either to a mammal that is not infected with an HCV or can be administered to an HCV-infected mammal.
Administration of the HCV polypeptides can elicit a cellular immune response, and/or an anti-El, anti-E2 and/or anti-El E2 antibody titer in the mammal that lasts for at least 1 week, 2 weeks, 1 month, 2 months, 3 months, 4 months, 6 months, 1 year, or longer. The HCV envelope polypeptides can also be administered to provide a memory response. If such a response is achieved, antibody titers may decline over time, however exposure to the HCV virus or immunogen results in the rapid induction of antibodies, e.g., within only a few days. Optionally, antibody titers can be maintained in a mammal by providing one or more booster injections of the polypeptides at 2 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 1 year, or more after the primary injection.
Preferably, an antibody titer of at least 10, 100, 150, 175, 200, 300, 400, 500, 750, 1,000, 1,500, 2,000, 3,000, 5,000, 10,000, 20,000, 30,000, 40,000, 50,000 (geometric mean titer), or higher, is elicited, or any number between the stated titer, as determined using a standard immunoassay, such as the immunoassay described in, e.g., Chien et al., Lancet (1993) 342:933; and Chien et al., Proc. Natl. Acad. ScL USA (1992) 89:10011. In order to determine whether the HCV envelope polypeptides in question are capable of eliciting a neutralizing antibody reaction or capable of cross-neutralizing additional genotypes, neutralization assays can be performed using techniques well known in the art. For example sera can be isolated from an immunized subject and analyzed using an HCV pseudotyped retroviral particle (HCVpp) assay, as described in e.g., Meunier et al., Proc. Natl. Acad. ScL USA (2005) 102:4560-4565; Bartosch et al., J. Exp. Med. (2003) 197:633-642. Additionally, assays to determine the presence of neutralization of binding (NOB) antibodies can be performed as described in, e.g., Rosa et al., Proc. Natl. Acad. ScL USA (1996) 93:1759. Immune responses of the mammal generated by the delivery of the compositions of the invention, can be enhanced by varying the dosage, route of administration, or boosting regimens. Compositions of the invention may be given in a single dose schedule, or preferably in a multiple dose schedule in which a primary course of vaccination includes 1-10 separate doses, followed by other doses given at subsequent time intervals required to maintain and/or reinforce an immune response, for example, at 1-4 months for a second dose, and if needed, a subsequent dose or doses after several months.
3. EXPERIMENTAL Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way.
Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for.
Example 1 Cross-Neutralization of an HCV Ia Pseudoparticle
Sera, collected from patients infected with different type 1 and type 2 strains of HCV, were analyzed for neutralization of binding (NOB) antibody titers against an HCV type Ia pseudoparticle by standard methods (see, e.g., Rosa et al., Proc. Natl. Acad. ScL USA (1996) 93:1759 for a representative NOB assay and Hsu et al., Proc. Natl. Acad. Sd. USA (2003) 100:7271 for a description of the production of pseudotype particles). As shown in Figure 3, the serum of a patient infected with an HCV 2a strain had lower NOB titers against the HCV Ia pseudoparticle than sera from patients infected with different HCV genotype 1 strains. Accordingly, immunogenic compositions comprising HCV immunogenic polypeptides that cross-neutralize the infectivity of multiple HCV genotypes, and methods of using the same, are disclosed. From the foregoing, it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without departing from the spirit and the scope of the invention as defined by the appended claims.

Claims

1. A composition comprising:
(a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV- 5 and HCV-6; and
(b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
2. The composition of claim 1, wherein the composition comprises an HCV envelope polypeptide from HCV-I and an HCV envelope polypeptide from HCV-2.
3. The composition of 2, wherein the composition further comprises an HCV envelope polypeptide from HCV-3.
4. The composition of claim 1, wherein the composition comprises an HCV envelope polypeptide from HCV-4 and an HCV envelope polypeptide from HCV-2.
5. The composition of 4, wherein the composition further comprises an HCV envelope polypeptide from HCV-3.
6. The composition of 1, wherein the composition comprises an HCV envelope polypeptide from HCV-5 and an HCV envelope polypeptide from HCV-2.
7. The composition of 6, wherein the composition further comprises an HCV envelope polypeptide from HCV-3.
8. The composition of 1, wherein the composition comprises an HCV envelope polypeptide from HCV-6 and an HCV envelope polypeptide from HCV-2.
9. The composition of 8, wherein the composition further comprises an HCV envelope polypeptide from HCV-3.
10. The composition of any one of claims 1-9, wherein the envelope polypeptide of (a) is an E2 polypeptide.
11. The composition of any one of claims 1-9, wherein the envelope polypeptide of (b) is an E2 polypeptide.
12. The composition of any one of claims 1-9, wherein the envelope polypeptide of (a) and (b) is an E2 polypeptide.
13. The composition of any one of claims 1-9, wherein the envelope polypeptide of (a) is an HCV E1E2 complex.
14. The composition of any one of claims 1-9, wherein the envelope polypeptide of (b) is an HCV E1E2 complex.
15. The composition of any one of claims 1-9, wherein the envelope polypeptide of (a) and (b) is an E1E2 complex.
16. The composition of any one of claims 13-15, wherein the E1E2 complex is produced by a method comprising expressing a polynucleotide encoding an HCV
El/E2/p7 region.
17. The composition of any one of claims 1-16, wherein the composition further comprises an adjuvant.
18. The composition of any one of claims 1-17, wherein the envelope polypeptide is produced recombinantly in a mammalian host cell.
19. A method of stimulating an immune response in a vertebrate subject which comprises administering to the subject a therapeutically effective amount of a composition according to any one of claims 1-18.
20. A method of stimulating an immune response in a vertebrate subject, said method comprising administering to the subject a therapeutically effective amount of
(a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV- 5 and HCV-6; and
(b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
21. The method of claim 20, wherein (a) is administered prior to (b).
22. The method of claim 20, wherein (b) is administered prior to (a).
23. The method of claim 20, wherein (a) and (b) are administered concurrently.
24. The method of claim 20, wherein (a) and (b) are present in the same composition.
25. The method of any one of claims 20-24, wherein the envelope polypeptide is produced recombinantly in a mammalian host cell.
26. A method of making a composition comprising: combining
(a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV- 5 and HCV-6; with
(b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3.
27. Use of composition according to any one of claims 1-18 in the manufacture of a medicament for stimulating an immune response in a vertebrate subject.
28. Use of a composition comprising (a) an immunogenic hepatitis C virus (HCV) envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-I, HCV-4, HCV-5 and HCV-6; and (b) an immunogenic HCV envelope polypeptide from one or more HCV genotypes selected from the group consisting of HCV-2 and HCV-3, in the manufacture of a medicament for stimulating an immune response in a vertebrate subject.
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