# Patent

## Title
Chimeric adenoviral vectors

## Abstract

The present invention provides chimeric adenoviral vectors and methods for using the vectors to elicit an immune response to an antigen of interest.

## Background
CROSS-REFERENCES TO RELATED APPLICATIONS
The present application claims priority to U.S. Provisional Patent Application No. 60/778,026, filed Feb. 28, 2006, U.S. Provisional Patent Application No. 60/801,645, filed May 19, 2006, U.S. Provisional Patent Application No. 60/802,992, filed May 22, 2006, U.S. Provisional Patent Application No. 60/821,492, filed Aug. 4, 2006, U.S. Provisional Patent Application No. 60/846,658, filed Sep. 22, 2006, and U.S. Provisional Patent Application No. 60/848,195, filed Sep. 28, 2006), the disclosures of which are hereby incorporated by reference in their entirety for all purposes.


STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
Not applicable.
BACKGROUND OF THE INVENTION
Vaccines are an important means for preventing and/or treating a number of diseases and disorders (e.g., viral infection, bacterial infection, and cancer). Nucleic acid-based vaccines have several advantages over protein or attenuated-live vaccines. Introduction of a nucleic acid that expresses an antigen into a target cell allows for rapid development of vaccine that generates and immune response against an antigen of interest. For protein vaccines, an effective and efficient method of protein purification needs to be developed each time a new vaccine is created. For live vaccines, a method of attenuation needs to be identified that doesn't completely stop the growth of the pathogen, yet proven to be completely safe in humans. Development of protein purification and attenuation methodologies are extremely time-consuming processes. In contrast, most nucleic acid-based vaccines can be manufactured very quickly using the same manufacturing techniques each time with just a quick change in the nucleic acid encoding the antigen of interest. Replication incompetent adenovirus is one nucleic acid-based vaccine system which is rapidly, predictably, and inexpensively made at high titer [Polo, J. M. and Dubensky, T. W., Jr., Drug Discov Today, 7(13), 719-727 (2002)]. However, the efficiency of the antigen-specific response following administration of adenoviral vectors known in the art is low. Thus, there is a need in the art for new adenoviral vectors that can be used to efficientlyt elicit an immune response against an antigen of interest. The present invention satisfies these and other needs.
SUMMARY OF THE INVENTION
The present invention provides chimeric adenoviral vectors comprising nucleic acids encoding a heterologous polypeptide and methods for eliciting an immune response against the heterologous polypeptide.
One embodiment of the invention provideschimeric adenoviral expression vectors comprising an expression cassette comprising: (a) first promoter operably linked to a nucleic acid encoding a toll-like receptor (TLR)-3 agonist; and (b) a second promoter operably linked to a nucleic acid encoding a heterologous polypeptide. In some embodiments, the TLR-3 agonist is dsRNA. In some embodiments, the nucleic acid encoding the TLR agonist comprises a sequence selected from SEQ ID NOS: 3, 7, 8, 9, 10, 11, and 12. In some embodiments, the heterologous polypeptide is selected from an HIV envelope polypeptide (e.g., gp41, gp120 or gp160) and influenza HA polypeptide. In some embodiments, the first and second promoters are the same. In some embodiments, the first and second embodiments are different. In some embodiments, the promoters are selected from the beta actin promoter and the CMV promoter. The invention also provides immunogenic compositions comprising the expression vector.
A further embodiment of the invention provides methods of eliciting an immune response against the heterologous polypeptide by administering an immunogenically effective amount of the compositions to a mammalian subject (e.g., a rodent such as a mouse, a rat, or a guinea pig or a primate such as a chimpanzee, a rhesus macaque, or a human). In some embodiments, the vector is administered via any non-parenteral route (e.g., orally, intranasally, or mucosally). In some embodiments, the heterologous polypeptide is expressed in a cell selected from a dendritic cell, a microfold cell, and an intestinal epithelial cell.
A further embodiment of the invention provides immunogenic compositions comprising: (a) a chimeric adenoviral expression vector comprising a promoter operably linked to a nucleic acid encoding a heterologous polypeptide; and (b) a TLR-3 agonist (e.g., a dsRNA). In some embodiments, the TLR-3 agonist is encoded by a nucleic acid. The invention also provides methods of eliciting an immune response by administering the compositions to a mammalian subject (e.g., a rodent such as a mouse, a rat, or a guinea pig or a primate such as a chimpanzee, a rhesus macaque, or a human) via any non-parenteral route (e.g., oral, intranasal, or mucosal).
Another embodiment of the invention provides an isolated nucleic acid comprising the sequence set forth in SEQ ID NOS:1, 2, 6, 7, 13, 14, 15, 16, or 17.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 illustrates data demonstrating that a chimeric adnenoviral vector of the invention (i.e., DS1) in combination with a TLR-3 agonist is more effective than a standard adenoviral vector (i.e., rAd5) at inducing an antigen specific immune response following oral vector delivery. FIG. 1A illustrates data depicting the antibody titer to HIV envelope protein (i.e., gp120) at 3 weeks following oral delivery of the adenoviral vectors. FIG. 1B illustrates data depicting the antibody titer to HIV envelope protein (i.e., gp120) at 6 weeks following oral delivery of the adenoviral vectors.
FIG. 2 illustrates data demonstrating that a chimeric adenoviral vector of the invention (i.e., DS1b or DS1c) in combination with a TLR-3 agonist is more effective at inducing an antigen specific immune response than a standard adenoviral vector (i.e., rAd5). FIG. 2A illustrates data depicting the anti-GFP IgG titer at 3 weeks following oral administration of the vectors. FIG. 2B illustrates data depicting the CD8+ T cell response to GFP at 10 weeks following administration of the vector at 0, 4, and 8 weeks. FIG. 2C illustrates data depicting the anti-HA antibody titer at 3 weeks following oral administration of the vectors.
FIG. 3 illustrates data demonstrating that the chimeric adenoviral vectors of the invention are superior for eliciting immune responses when administered non-parenterally. FIG. 3A illustrates data depicting the anti-gp120 antibody titer 3 weeks following intramuscular administration of DS1. FIG. 3B illustrates data depicting the anti-HA antibody titer three weeks following intransal administration of DS1c.
FIG. 4 illustrates data demonstrating that the expressed TLR-3 ligand agonists can induce activation of antigen presenting cells. FIG. 4A illustrates data depicting dendritic cell activation by the expressed dsRNA TLR-3 agonist luc1. FIG. 4B illustrates data depicting dendritic cell activation by the expressed dsRNA TLR-3 agonists luc1 and m1.
FIG. 5 is a graphic illustration of the chimeric adenoviral vectors of the invention, i.e., chimeric adenoviral vectors comprising nucleic acids encoding expressed ds RNA TLR-3 agonists.
FIG. 6 illustrates data demonstrating that the chimeric adenoviral vectors of the invention are effective at inducing an antigen-specific immune response following oral delivery. FIG. 6 illustrates data depicting anti-gp120 antibody titer 3 weeks following oral administration of a chimeric adenoviral comprising a nucleic acid sequence encoding the dsRNA TLR-3 agonist luc1.
FIG. 7 illustrates data demonstrating that TLR-7/8 agonists have poor effectiveness in inducing an antigen-specific immune response.
FIG. 8 illustrates data demonstrating that chimeric adenoviral vectors of the invention are effective at inducing an antigen-specific immune response following oral delivery. FIG. 8A illustrates data depicting the anti-HA antibody titer 4 weeks following oral administration of a chimeric adenoviral comprising a nucleic acid sequence encoding the dsRNA TLR-3 agonist luc1. FIG. 8B illustrates data depicting the anti-HA antibody titer 4 weeks or 7 weeks following administration of a chimeric adenoviral comprising a nucleic acid sequence encoding the dsRNA TLR-3 agonist luc1. FIG. 8C illustrates data depicting the anti-HA antibody titer 3 weeks following oral or intranasal administration of a chimeric adenoviral comprising a nucleic acid sequence encoding the dsRNA TLR-3 agonist luc1.



BRIEF DESCRIPTION OF THE SEQUENCES
SEQ ID NO:1 sets forth the nucleotide sequence for the chimeric adenoviral vector DS1.
SEQ ID NO:2 sets forth the nucleotide sequence for the chimeric adenoviral vector DS2.
SEQ ID NO:3 sets forth a nucleotide sequence encoding a TLR-3 agonist.
SEQ ID NO:4 sets forth a nucleotide sequence encoding a TLR-3 agonist.
SEQ ID NO:5 sets forth a nucleotide sequence encoding a TLR-3 agonist.
SEQ ID NO:6 sets forth a nucleotide sequence for a chimeric adenoviral vector comprising a nucleic acid encoding influenza HA and a nucleic acid encoding a TLR-3 agonist (luc), wherein the influenza HA and the TLR-3 agonist are in the same orientation.
SEQ ID NO: 7 sets forth a nucleotide sequence for a chimeric adenoviral vector comprising a nucleic acid encoding influenza HA and a nucleic acid encoding a TLR-3 agonist (luc), wherein the influenza HA and the TLR-3 agonist are in the opposite orientation.
SEQ ID NO:8 sets forth a nucleotide sequence encoding a short hairpin RNA TLR-3 agonist. Complementary portions of the sequence are shown in capital letters and the linker sequence is shown in lower case letters.
SEQ ID NO: 9 sets forth a nucleotide sequence encoding a short hairpin RNA TLR-3 agonist (g1). Complementary portions of the sequence are shown in capital letters and the linker sequence is shown in lower case letters.
SEQ ID NO: 10 sets forth a nucleotide sequence encoding a short hairpin RNA TLR-3 agonist (luc). Complementary portions of the sequence are shown in capital letters and the linker sequence is shown in lower case letters.
SEQ ID NO: 11 sets forth a nucleotide sequence encoding a short hairpin RNA TLR-3 agonist (m1). Complementary portions of the sequence are shown in capital letters and the linker sequence is shown in lower case letters.
SEQ ID NO: 12 sets forth a nucleotide sequence encoding a short hairpin RNA TLR-3 agonist. Complementary portions of the sequence are shown in capital letters and the linker sequence is shown in lower case letters.
SEQ ID NO: 13 sets forth the nucleotide sequence for the chimeric adenoviral vector DS1c. The sequence comprises a nucleotide encoding HA(PR8/34).
SEQ ID NO: 14 sets forth the nucleotide sequence for the chimeric adenoviral vector DS2beta-luc. The vector comprises a sequence encoding the TLR-3 agonist luc under the control of the beta actin promoter. The vector also comprises open cloning sites for insertion of nucleic acid sequence(s) encoding an antigen of interest.
SEQ ID NO: 15 sets forth the nucleotide sequence for the chimeric adenoviral vector DS2C-luc The vector comprises a sequence encoding the TLR-3 agonist luc under the control of the CMV promoter. The vector also comprises open cloning sites for insertion of nucleic acid sequence(s) encoding an antigen of interest.
SEQ ID NO: 16 sets forth the nucleotide sequence for the pShuttle vector comprising a nucleic acid sequence encoding the TLR-3 agonist luc under the control of the CMV promoter and a nucleic acid sequence encoding HA (avian flu) under the control of a separate CMV promoter.
SEQ ID NO: 17 sets forth the nucleotide sequence for the chimeric adenoviral vector ND1.1 214. The nucleic acid encoding the heterologous antigen is in bold text and is flanked by a Cla I recognition site on the 5′ end and a Not 1 recognition site on the 3′end. The nucleic acid sequence encoding the TLR-3 agonists is in italic, with the linker sequence in bold.
DETAILED DESCRIPTION OF THE INVENTION
I. Introduction
The present invention provides novel chimeric adenoviral vectors that can be administered non-parenterally to elicit an immune response against an antigen of interest. The chimeric adenoviral vectors of the invention comprise a nucleic acid encoding a heterologous polypeptide and a nucleic acid encoding a TLR-3 agonist. The chimeric adenoviral vectors elicit strong and effective immune responses specific for the heterologous polypeptide, particularly when administered via a non-parenteral route (e.g., orally, intranasally, or mucosally).
The invention is based on the suprising discovery that administration of dsRNA TLR-3 agonists are effective adjuvants when administered in conjunction with viral vectors. In fact, the use of dsRNA as an adjuvant for viral vectors would be counterintuitive considering that the major proposed utility of the dsRNA mimetic poly I:C was as an antiviral agent [Nemes, et al., Proc Soc Exp Biol Med. (1969) 132:776; Schafer, et al, Nature. (1970) 226:449; Fenje, et al, Nature (1970) 226:171.].
II. Definitions
The term “chimeric” or “recombinant” as used herein with reference, e.g., to a nucleic acid, protein, or vector, indicates that the nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein. Thus, for example, chimeric and and recombinant vectors include nucleic acid sequences that are not found within the native (non-chimeric or non-recombinant) form of the vector. A chimeric adenoviral expression vector refers to an adenoviral expression vector comprising a nucleic acid sequence encoding a heterologous polypeptide.
An “expression vector” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell. The expression vector can be part of a plasmid, virus, or nucleic acid fragment. Typically, the expression vector includes a nucleic acid to be transcribed operably linked to a promoter.
The terms “promoter” and “expression control sequence” are used herein to refer to an array of nucleic acid control sequences that direct transcription of a nucleic acid. As used herein, a promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element. A promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. Promoters include constitutive and inducible promoters. A “constitutive” promoter is a promoter that is active under most environmental and developmental conditions. An “inducible” promoter is a promoter that is active under environmental or developmental regulation. The term “operably linked” refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.
The terms “TLR agonist” or “Toll-like receptor agonist” as used herein refers to a compound that binds and stimulates a Toll-like receptor including, e.g., TLR-2, TLR-3, TLR-6, TLR-7, or TLR-8. TLR agonists are reviewed in MacKichan, IAVI Report. 9:1-5 (2005) and Abreu et al., J Immunol, 174(8), 4453-4460 (2005). Agonists induce signa transduction following binding to their receptor.
The terms “TLR-3 agonist” or “Toll-like receptor 3 agonist” as used herein refers to a compound that binds and stimulates the TLR-3. TLR-3 agonists have been identified including double-stranded RNA, virally derived dsRNA, several chemically synthesized analogs to double-stranded RNA including polyinosine-polycytidylic acid (poly I:C)—polyadenylic-polyuridylic acid (poly A:U) and poly I:poly C, and antibodies (or cross-linking of antibodies) to TLR-3 that lead to IFN-beta production [Matsumoto, M, et al, Biochem Biophys Res Commun 24:1364 (2002), de Bouteiller, et al, J Biol Chem 18:38133-45 (2005)]. TLR-3 agonists also include expressed dsRNA (e.g., dsRNA encoded by a nucleic acid comprising a sequence set forth in SEQ ID NOS: 3, 7, 8, 9, 10, 11, or 12).
The terms “TLR-7/8 agonist” or “Toll-like receptor 7/8 agonist” as used herein refers to a compound that binds and stimulates either the TLR-7 or TLR-8 receptors; these receptors recognize several of same ligands. Several TLR-7/8 agonists have been identified such as viral single-stranded RNA, imiquimod, loxoribine, polyuridylic acid, or resiquimod.
The term “heterologous” when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).
The terms “nucleic acid” and “polynucleotide” are used interchangeably herein to refer to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).
Unless otherwise indicated, a particular nucleic acid sequence also encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide.
Antigen—refers to a protein or part of a polypeptide chain that can be recognized by T cell receptors and/or antibodies. Typically, antigens are derived from bacterial, viral, or fungal proteins.
An “immunogenically effective dose or amount” of the of the compositions of the present invention is an amount that elicits or modulates an immune response specific for the heterologous polypeptide. Immune responses include humoral immune responses and cell-mediated immune responses. An immunogenic composition can be used therapeutically or prophylactically to treat or prevent disease at any stage.
“Humoral immune responses” are mediated by cell free components of the blood, i.e., plasma or serum; transfer of the serum or plasma from one individual to another transfers immunity.
“Cell mediated immune responses” are mediated by antigen specific lymphocytes; transfer of the antigen specific lymphocytes from one individual to another transfers immunity.
A “therapeutic dose” or “therapeutically effective amount” or “effective amount” of a chimeric adenoviral vector or a composition comprising a chimeric adenoviral vector is an amount of the vector or composition comprising the vector which prevents, alleviates, abates, or reduces the severity of symptoms of diseases and disorders associated with the source of the heterologous polypeptide (e.g., a virus, bacteria, a parasite, or a cancer).
Antibody—refers to a polypeptide encoded by an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.
T cells—refer to a particular class of lymphocytes that express a specific receptor (T cell receptor) encoded by a family of genes. The recognized T cell receptor genes include alpha, beta, delta, and gamma loci, and the T cell receptors typically (but not universally) recognize a combination of MHC plus a short peptide.
Adaptive immune response—refers to T cell and/or antibody recognition of antigen.
Antigen presenting cells (APCs)—as used herein refers to cells that are able to present immunogenic peptides or fragments thereof to T cells to activate or enhance an immune response. APCs include dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered to be efficient APCs. Such cells may, but need not, be genetically modified to increase the capacity for presenting the antigen, to improve activation and/or maintenance of the T cell response, to have anti-tumor effects per se and/or to be immunologically compatible with the receiver (i.e., matched HLA haplotype). APCs may be isolated from any of a variety of biological fluids and organs including bone marrow, peripheral blood, tumor and peritumoral tissues, and may be autologous, allogeneic, syngeneic or xenogeneic cells. APCs typically utilize a receptor from the major histocompatability (MHC) locus to present short polypeptides to T cells.
Adjuvant—is a non-specific immune response enhancer. Suitable adjuvants include, for example, cholera toxin, monophosphoryl lipid A (MPL), Freund's Complete Adjuvant, Freund's Incomplete Adjuvant, Quil A, and Al(OH). Adjuvants can also be those substances that cause APC activation and enhanced presentation of T cells through secondary signaling molecules like Toll-like receptors. Examples of Toll-like receptors include the receptors that recognize double-stranded RNA, bacterial flagella, LPS, CpG DNA, and bacterial lipopeptide (Reviewed recently in [Abreu et al., J Immunol, 174(8), 4453-4460 (2005)]).
The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.
The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, {umlaut over (γ)}-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an {umlaut over (γ)} carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
“Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.
As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.
The following eight groups each contain amino acids that are conservative substitutions for one another:

    
    
        1) Alanine (A), Glycine (G);
        2) Aspartic acid (D), Glutamic acid (E);
        3) Asparagine (N), Glutamine (Q);
        4) Arginine I, Lysine (K);
        5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);
        6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);
        7) Serine (S), Threonine (T); and
        8) Cysteine (C), Methionine (M)
        (see, e.g., Creighton, Proteins (1984)).
    
    


The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).
The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point I for the specific sequence at a defined ionic strength Ph. The Tm is the temperature (under defined ionic strength, Ph, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at Ph 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, optionally 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50% formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C.
Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately stringent hybridization conditions” include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1×SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.
“Antibody” refers to a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.
An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chains respectively.
The phrase “specifically (or selectively) binds” to an antibody or “specifically (or selectively) immunoreactive with,” when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein in a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two times the background and do not substantially bind in a significant amount to other proteins present in the sample. Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein. For example, polyclonal antibodies raised to fusion proteins can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with fusion protein and not with individual components of the fusion proteins. This selection may be achieved by subtracting out antibodies that cross-react with the individual antigens. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow & Lane, Antibodies, A Laboratory Manual (1988), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity). Typically a specific or selective reaction will be at least twice background signal or noise and more typically more than 10 to 100 times background.
Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes an individual polypeptide or dsRNA or a portion thereof) or may comprise a variant of such a sequence. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the biological activity of the encoded polypeptide is not diminished, relative to a polypeptide comprising native antigens. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the TLR-3 agonist activity of the encoded dsRNA is not diminished, relative to a dsRNA that does not contain the substitutions, additions, deletions and/or insertions. Variants preferably exhibit at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, to a polynucleotide sequence that encodes a native polypeptide or a portion thereof or to a polynucleotide sequence that encodes a dsRNA with TLR-3 agonist activity.
The terms “identical” or percent “identity,” in the context of two or more nucleic acids (e.g., a dsRNA that is a TLR-3 agonist) or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identity over a specified region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.” This definition also refers to the compliment of a test sequence. Optionally, the identity exists over a region that is at least about 10 to about 100, about 20 to about 75, about 30 to about 50 amino acids or nucleotides in length.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions from about 10 to about 500, about 25 to about 200, 50 to about 150, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)).
One example of a useful algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments to show relationship and percent sequence identity. It also plots a tree or dendogram showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351-360 (1987). The method used is similar to the method described by Higgins & Sharp, CABIOS 5:151-153 (1989). The program can align up to 300 sequences, each of a maximum length of 5,000 nucleotides or amino acids. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster is then aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences are aligned by a simple extension of the pairwise alignment of two individual sequences. The final alignment is achieved by a series of progressive, pairwise alignments. The program is run by designating specific sequences and their amino acid or nucleotide coordinates for regions of sequence comparison and by designating the program parameters. Using PILEUP, a reference sequence is compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted end gaps. PILEUP can be obtained from the GCG sequence analysis software package, e.g., version 7.0 (Devereaux et al., Nuc. Acids Res. 12:387-395 (1984).
Another example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) or 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands.
The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.
III. Compositions of the Present Invention
The invention provides compositions comprising chimerical adenoviral vectors. In some embodiments, the chimeric adenoviral vectors of the invention comprise a first promoter operably linked to a nucleic acid encoding a heterologous polypeptide and a second promoter operably linked to a nucleic acid encoding a TLR3 agonist. The first and second promoters may be the same or different. In some embodiments, the first and second promoters are independently selected from: the beta actin promoter and the CMV promoter.
In some embodiments, the chimeric adenoviral vector comprises the adenoviral genome (minus the E1 and E3 genes) and a nucleic acid encoding a a gene that activates IRF-3 and other signaling molecules downstream of TLR-3. The chimeric vector can be administered to a cell that expresses Ad's E1 gene such that recombinant adenovirus (rAd) is produced by the cell. This rAd can be harvested and is capable of a single round of infection that will deliver the transgenic compostion to another cell within a mammal in order to elicit immune responses to the heterologous polypeptide.
A. Suitable Adenoviral Vectors
In some embodiments, the adenoviral vector is adenovirus 5, including, for example, Ad5 with deletions of the E1/E3 regions and Ad5 with a deletion of the E4 region. Other suitable adenoviral vectors include strains 2, orally tested strains 4 and 7, enteric adenoviruses 40 and 41, and other strains (e.g. Ad34) that are sufficient for delivering an antigen and eliciting an adaptive immune response to the transgene antigen [Lubeck et al., Proc Natl Acad Sci USA, 86(17), 6763-6767 (1989); Shen et al., J Virol, 75(9), 4297-4307 (2001); Bailey et al., Virology, 202(2), 695-706 (1994)]. In some embodiments, the adenoviral vector is a live, replication incompetent adenoviral vector (such as E1 and E3 deleted rAd5), live and attenuated adenoviral vector (such as the E1B55K deletion viruses), or a live adenoviral vector with wild-type replication.
The transcriptional and translational control sequences in expression vectors to be used in transforming vertebrate cells in vivo may be provided by viral sources. For example, commonly used promoters and enhancers are derived, e.g., from beta actin, adenovirus, simian virus (SV40), and human cytomegalovirus (CMV). For example, vectors allowing expression of proteins under the direction of the CMV promoter, SV40 early promoter, SV40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, transducer promoter, or other promoters shown effective for expression in mammalian cells are suitable. Further viral genomic promoter, control and/or signal sequences may be used, provided such control sequences are compatible with the host cell chosen.
B. Heterologous Polypeptides
Nucleic acids encoding suitable heterologous polypeptides may be derived from antigens, such as, for example, viral antigens, bacterial antigens, cancer antigens, fungal antigens, or parasite antigens.
Viral antigens may be derived from, for example, human immunodeficiency virus (e.g., gag (p55 and p160), pol, env (gp120 and gp41) as set forth in Shiver et al. Nature 415(6869):331 (2002); the HIV genomic sequences set forth in Genbank Accession Nos. EF363127; EF363126; EF363125; EF363124; EF363123; EF363122; EF192592; and EF192591; the HIV gag sequences set forth in Genbank Accession Nos. EF396891; EF396890; EF396889; EF396888; EF396887; EF396886; EF396885; EF396884; EF396883; EF396882; EF396881; EF396880; EF396879; EF396878; EF396877; EF396876; EF39687; EF396874; EF396873; and EF396872; the HIV pol sequences set forth in Genbank Accession Nos. EF396810; EF396809; EF396808; EF396807; EF396806; EF396805; EF396804; EF396803; EF396802; EF396801; EF396800; EF396799; EF396798; EF396797; EF396796; EF396795; EF396794; EF396793; EF396792; and EF396791; and the HIV env sequences set forth in Genbank Accession Nos. 9: EF367234; EF367233; EF367232; EF367231; EF367230; EF367229; EF367228; EF367227; EF367226; EF367225; EF367224; and EF367223, human papilloma virus (e.g., capsid protein L1 as described in, e.g., Donnelly et al. J Infect Dis. 173:314 (1996) and the sequences set forth in Genbank Accession Nos. EF362755; EF362754; NC—001694; NC—001693; NC—001691; NC—001690; NC—005134; NC—001458; NC—001457; NC—001354; NC—001352; NC—001526; and X94164), Epstein Barr virus, herpes simplex virus, human herpes virus, rhinoviruses, cocksackieviruses, enteroviruses, hepatitis A, B, C, and E (e.g., hepatitis B surface antigen as described in e.g., Lubeck et al, PNAS USA 86:6763 (1989) and the sequences set forth in GenBank Accession Nos. AB236481; AB236471; AB206501; AB206489; AB206487; AB221788; AB221777; AB221773; AR933671;AR933670; AB236514; AB236513; AB236512; AB236511; AB236510; AB236509; AB236508; AB236507); hepatitis C NS5 (see, e.g., Genbank Accession Nos. X59609; DQ911563; S71627; S70787; S70786; S70341; S62220; S70790; S70789; S70788; and AB204642)), mumps virus, rubella virus, measles virus, poliovirus, smallpox virus, rabies virus, and Variella-zoster virus. Influenza antigens include, e.g., hemagluttinin (HA), matrix protein 1 (M1), and nucleoprotein (NP) (see, e.g., Donnelly, et al, Vaccine 15:865 (1997) and the influenza HA sequences set forth in Genbank Accession Nos. AB294219; AB294217; AB294215; AB294213; EF102944; EF102943; EF102942; EF102941; EF102940; EF102939; EF102938; EF102937; EF102936; EF102935; EF102934; EF102933; DQ643982; DQ464354; CY019432; CY019424; CY019416; CY019408; CY019400; CY019392; CY019384; CY019376; CY019368; CY019360; CY019352; EF124794;EF110519; EF110518; EF165066; EF165065; EF165064; and EF165063; the influenza M1 sequences set forth in Genbank Accession Nos. AB292791; CY019980; CY019972; CY019964; CY019956; CY019948; CY019940; CY019628; CY019652; CY019644; CY019932; CY019924; CY019916; CY019908; CY019900; CY019892; CY019884; CY019876; CY019868; CY019860; and the influenza NP sequences set forth in Genbank Accession Nos. AB292790; CY019461; CY019974; CY019966; CY019958; CY019950; CY019942; CY019630; CY019654; CY019646; CY019934; CY019926; CY019918 CY019910; CY019902; CY019894; CY019886; CY019878; CY019870; and CY019862.
Suitable viral antigens also include, e.g., viral nonstructural proteins. The term “Viral nonstructural protein” as used herein refers to proteins encoded by viral nucleic acid that do not encode for structural polypeptides, such as those that make capsid or the protein surrounding a virus. Non-structural proteins include those proteins that promote viral nucleic acid replication and viral gene expression such as, for example, Nonstructural proteins 1, 2, 3, and 4 (NS1, NS2, NS3, and NS4, respectively) from Venezuelan Equine encephalitis (VEE), EEE, or Semliki Forest virus [Dubensky et al., J Virol, 70(1), 508-519 (1996); Petrakova et al J Virol 2005 79(12): 7597-608; U.S. Pat. Nos. 5,185,440; 5,739,026; 6,566,093; and 5,814,482. Several representative examples of suitable alphaviruses include Aura (ATCC VR-368), Bebaru virus (ATCC VR-600, ATCC VR-1240), Cabassou (Genbank Accession Nos. AF398387, ATCC VR-922), Chikungunya virus (ATCC VR-64, ATCC VR-1241), Eastern equine encephalomyelitis virus (Genbank Accession Nos. AY705241, AY705240, ATCC VR-65, ATCC VR-1242), Fort Morgan (ATCC VR-924), Getah virus (ATCC VR-369, ATCC VR-1243), Kyzylagach (ATCC VR-927), Mayaro (ATCC VR-66), Mayaro virus (ATCC VR-1277), Middleburg (ATCC VR-370), Mucambo virus (ATCC VR-580, ATCC VR-1244), Ndumu (ATCC VR-371), Pixuna virus (ATCC VR-372, ATCC VR-1245), Ross River virus (ATCC VR-373, ATCC VR-1246), Semliki Forest (Genbank Accession Nos. AJ251359, ATCC VR-67, ATCC VR-1247), Sindbis virus (Genbank Accession Nos. J02363, ATCC VR-68, ATCC VR-1248), Tonate (ATCC VR-925), Triniti (ATCC VR-469), Una (ATCC VR-374), Venezuelan equine encephalomyelitis (ATCC VR-69), Venezuelan equine encephalomyelitis virus (Genbank Accession Nos. AY986475, AY973944, NC 001449, ATCC VR-923, ATCC VR-1250 ATCC VR-1249, ATCC VR-532), Western equine encephalomyelitis (ATCC VR-70, ATCC VR-1251, ATCC VR-622, ATCC VR-1252), Whataroa (ATCC VR-926), and Y-62-33 (ATCC VR-375).
Bacterial antigens may be derived from, for example, Staphylococcus aureus, Staphylococcus epidermis, Helicobacter pylori, Streptococcus bovis, Streptococcus pyogenes, Streptococcus pneumoniae, Listeria monocytogenes, Mycobacterium tuberculosis, Mycobacterium leprae, Corynebacterium diphtheriae, Borrelia burgdorferi, Bacillus anthracis, Bacillus cereus, Clostridium botulinum, Clostridium difficile, Salmonella typhi, Vibrio chloerae, Haemophilus influenzae, Bordetella pertussis, Yersinia pestis, Neisseria gonorrhoeae, Treponema pallidum, Mycoplasm sp., Neisseria □ransducer□s, Legionella pneumophila, Rickettsia typhi, Chlamydia trachomatis, and Shigella dysenteriae, Vibrio cholera(e.g., Cholera toxin subunit B as set forth in Genbank Accession Nos. U25679; A09803; EF158842; X76391; AF390572; cholera toxin-coregulated pilus (TCP) as described in Wu et al., Infection and Immunity Vol. 69(12):7695 (2001) and as set forth in Genbank Accession Nos. NC—002505 and AE004169); Helicobacter pylorii (VacA as set forth in Genbank Accession Nos. AY848858; AF042737; AF042736; AF042735; AF042734; NC—000921; CagA as set forth in Genbank Accession Nos. AF043490; AF043489; AF043488; AF043487; NAP as set forth in Genbank Accession Nos. AF284121; AF284120; AF284119; AF284118; AF284117; AF284116; AB045143; AB045142; AF227081; AF227080; AF227079; AF227078; AF227077; AF227076; AF227075; AF227074; Hsp or catalase as set forth in Genbank Accession No. NC—000921; urease as set forth in Genbank Accession Nos. AM417610; AM417609; AM417608; AM417607; AM417606; AM417605; AM417604; AM417603; AM417602; AM417601; and AM417600; E. coli antigens as set forth in Genbank Accession Nos. NC—000913; U00096; NC—002655; BA000007; AE014075; including E. coli fimbrial antigens as set forth in Genbank Accession Nos. AB214865; AB214864; AB214863; AB214862; E. coli heat-labile enterotoxin as set forth in Genbank Accession Nos. X83966; V00275; X83966; J01646; V00275; M35581; M17873; M17874; K01995; M61015; M17894; M17101; K00433.
Parasite antigens may be derived from, for example, Giardia lamblia, Leishmania sp., Trypanosoma sp., Trichomonas sp., Plasmodium sp. (e.g., P. faciparum surface protein antigens such as pfs25 sequences as set forth in Genbank Accession Nos. XM—001347551; X07802; AF193769; AF179423; AF154117; and AF030628, pfs28 sequences as set forth in Genbank Accession No. L25843, pfs45 sequences as set forth in Genbank Accession Nos. EF158081; EF158079; EF158078; EF158076; EF158075; and EF158085, pfs84, pfs 48/45 sequences as set forth in Genbank Accession Nos. AF356146; AF356145; AF356144; AF356143; AF356142; AF356141; AF356140; AF356139; AF356138; AF356137; AF356136; AF356135; AF356134; AF356133; AF356132; AF356131; AF356130; AF356129; AF356128; AF356127, pfs 230 sequences as set forth in Genbank Accession Nos. NC—000910; XM—001349564; AE001393; L22219; L08135; and AF269242, P. vivax antigens such as Pvs25 sequences as set forth in Genbank Accession Nos. DQ641509; DQ641508; DQ641507; AY639972; AY639971; AY639970; AY639969; AY639968; AY639967; AY639966; and AY639965; and Pvs28 sequences as set forth in Genbank Accession Nos. AB033364; AB033363; AB033362; AB033361; AB033360; AB033359; AB033358; AB033357; AB033356; B033355; AB033354; AB033353; AB033352; AB033351; AB033350; AB033349; AB033348; AB033347; AB033346; and AB033345), Schistosoma sp., Mycobacterium tuberculosis (e.g., Ag85 sequences as set forth in Genbank Accession Nos. AX253506; AX253504; AX253502; and AX211309; MPT64, ESAT-6, CFP10, R8307, MTB-32 MTB-39, CSP, LSA-1, LSA-3, EXP1, SSP-2, SALSA, STARP, GLURP, MSP-1, MSP-2, MSP-3, MSP-4, MSP-5, MSP-8, MSP-9, AMA-1, Type 1 integral membrane protein, RESA, EBA-175, and DBA sequences as set forth in Genbank Accession Nos. BX842572; BX842573; BX842574; BX842575; BX842576; BX842577; BX842578; BX842579; BX842580; BX842581; BX842582;BX842583; BX842584 and NC—000962, HSP65 sequences as set forth in Genbank Accession Nos. AY299175; AY299174; AY299144; AF547886; and AF547885).
Cancer antigens include, for example, antigens expressed, for example, in colon cancer, stomach cancer, pancreatic cancer, lung cancer, ovarian cancer, prostate cancer, breast cancer, skin cancer (e.g., melanoma), leukemia, lymphoma, or myeloma, exemplary cancer antigens include, for example, HPV L1, HPV L2, HPV E1, HPV E2, placental alkaline phosphatase, AFP, BRCA1, Her2/neu, CA 15-3, CA 19-9, CA-125, CEA, Hcg, urokinase-type plasminogen activator (Upa), plasminogen activator inhibitor.
Fungal antigens may be derived from, for example, Tinea pedis, Tinea corporus, Tinea cruris, Tinea unguium, Cladosporium carionii, Coccidioides immitis, Candida sp., Aspergillus fumigatus, and Pneumocystis carinii. 
The nucleic acids encoding immunogenic polypeptides, are typically produced by recombinant DNA methods (see, e.g., Ausubel, et al. ed. (2001) Current Protocols in Molecular Biology). For example, the DNA sequences encoding the immunogenic polypeptide can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of oligonucleotides, or amplified from cDNA using appropriate primers to provide a synthetic gene which is capable of being inserted in a recombinant expression vector (i.e., a plasmid vector or a viral vector) and expressed in a recombinant transcriptional unit. Once the nucleic acid encoding an immunogenic polypeptide is produced, it may be inserted into a recombinant expression vector that is suitable for in vivo or ex-vivo expression.
Recombinant expression vectors contain a DNA sequence encoding an immunogenic polypeptide operably linked to suitable transcriptional or translational regulatory elements derived from mammalian or viral genes. Such regulatory elements include a transcriptional promoter, an optional operator sequence to control transcription, a sequence encoding suitable mRNA ribosomal binding sites, and sequences which control the termination of transcription and translation. An origin of replication and a selectable marker to facilitate recognition of transformants may additionally be incorporated. The genes utilized in the recombinant expression vectors may be divided between more than one virus such that the gene products are on two different vectors, and the vectors are used for co-transduction to provide all the gene products in trans. There may be reasons to divide up the gene products such as size limitations for insertions, or toxicity of the combined gene products to the virus produce cell-lines.
C. TLR Agonists
According to the methods of the invention, TLR agonists are used to enhance the immune response to the heterologous polypeptide. In some embodiments, TLR-3 agonists are used. In other embodiments, TLR 7/8 agonists are used. The TLR agonists described herein can be delivered simultaneously with the expression vector encoding an antigen of interest or delivered separately (i.e., temporally or spatially) from the expression vector encoding an antigen of interest. For example, the expression vector may be administered via a non-parenteral route (e.g., orally, intranasally, or mucosally), while the TLR-agonist is delivered by a parenteral route (e.g., intramuscularly, intraperitoneally, or subcutaneously).
1. TLR-3 Agonists
In a preferred embodiment of the present invention, a TLR-3 agonist is used to stimulate immune recognition of an antigen of interest. TLR-3 agonists include, for example, short hairpin RNA, virally derived RNA, short segments of RNA that can form double-strands or short hairpin RNA, and short interfering RNA (siRNA). In one embodiment of the invention, the TLR-3 agonist is virally derived dsRNA, such as for example, a dsRNA derived from a Sindbis virus or dsRNA viral intermediates [Alexopoulou et al, Nature 413:732-8 (2001)]. In some embodiments, the TLR-3 agonists is a short hairpin RNA. Short hairpin RNA sequences typically comprise two complementary sequences joined by a linker sequence. The particular linker sequence is not a critical aspect of the invention. Any appropriate linker sequence can be used so long as it does not interfere with the binding of the two complementary sequences to form a dsRNA.
In some embodiments, the short hairpin RNA comprises a sequence set forth in SEQ ID NOS: 3, 4, 5, 8, 9, 10, 11, or 12, a sequence with substantial identity to a sequence set forth in SEQ ID NOS: 3, 4, 5, 8, 9, 10, 11, or 12, or a variant of a sequence set forth in SEQ ID NOS: 3, 4, 5, 8, 9, 10, 11, or 12. In certain embodiments, dsRNA that is a TLR-3 agonist does not encode a particular polypeptide, but produces a pro-inflammatory cytokine (e.g. IL-6, IL-8, TNF-alpha, IFN-alpha, IFN-beta) when contacted with a responder cell (e.g., a dendritic cell, a peripheral blood mononuclear cell, or a macrophage) in vitro or in-vivo. In some cases, the nucleic acid encoding the TLR-3 agonist (e.g., an expressed dsRNA) and the chimeric adenoviral vector comprising a nucleic acid encoding a heterologous antigen are administered in the same formulation. In other cases the nucleic acid encoding the TLR-3 agonist and the chimeric adenoviral vector comprising a nucleic acid encoding a heterologous polypeptide are administered in different formulations. When the nucleic acid encoding the TLR-3 agonist and the adenoviral vector comprising a nucleic acid encoding a heterologous antigen are administered in different formulations, their administration may be simultaneous or sequential. For example, the nucleic acid encoding the TLR-3 agonist may be administered first, followed by the chimeric adenoviral vector (e.g., 1, 2, 4, 8, 12, 16, 20, or 24 hours, 2, 4, 6, 8, or 10 days later). Alternatively, the adenoviral vector may be administered first, followed by the nucleic acid encoding the TLR-3 agonist (e.g., 1, 2, 4, 8, 12, 16, 20, or 24 hours, 2, 4, 6, 8, or 10 days later). In some embodiment, the nucleic acid encoding the TLR-3 agonist and the nucleic acid encoding the heterologous antigen are under the control of the same promoter. In other embodiments, the nucleic acid encoding the TLR-3 agonist and the nucleic acid encoding the heterologous antigen are under the control of different promoters.
Several chemically synthesized analogs to double-stranded RNA are commercially available. These include polyinosine-polycytidylic acid (poly I:C), polyadenylic:polyuridylic acid (poly A:U), and poly I:poly C. Antibodies (or cross-linking of antibodies) to TLR-3 can also lead to IFN- beta or pro-inflammatory cytokine production [Matsumoto et al, Biochem. Biophys. Res. Commun. 24:1364 (2002), de Bouteiller et al, J Biol. Chem. 18:38133-45 (2005)]. Commercially available siRNA segments of any sequence can also be obtained through sources such as Invitrogen.
2. TLR7/8 Agonists
In some embodiments, the TLR agonists are TLR7/8 agonists. TLR7/8 ligands are typically single-stranded, virally derived RNA. Because the receptors are expressed in intracellular compartments such as the endosome, not all short segments of RNA will trigger the TLR7/8 signaling cascade because they need to reach the correct compartment. Some ligands that have been shown to trigger this through exogenous addition are polyuridylic acid, resiquimod, and imiquimod [Westwood, et al, Vaccine 24:1736-1745(2006)].
IV. Pharmaceutical Compositions
Pharmaceutical compositions comprising the vectors described herein may also contain other compounds, which may be biologically active or inactive. Polypeptides may, but need not, be conjugated to other macromolecules as described, for example, in U.S. Pat. Nos. 4,372,945 and 4,474,757. Pharmaceutical compositions may generally be used for prophylactic and therapeutic purposes. Pharmaceutical compositions may be composed of methods to protect against stomach degradation such that the administered chimeric adenoviral vector may reach the desired locations. For the oral environment, several of these are available including the Eudragit and the TimeClock release systems as well as other methods specifically designed for adenovirus [Lubeck et al., Proc Natl Acad Sci USA, 86(17), 6763-6767 (1989); Chourasia and Jain, J Pharm Pharm Sci, 6(1), 33-66 (2003)]. There are also several methods already described for microencapsulation of DNA and drugs for oral delivery (see, e.g., U.S. Patent Publication No. 2004043952). In some embodiments, the Eudragit system will be used to to deliver the chimeric adenoviral vecto to the lower small intestine. However, delivery to other locations of the small intestine should also work.
As noted above, the chimeric adenoviral vectors on the invention may be delivered using any delivery systems known to those of ordinary skill in the art. Numerous gene delivery techniques are well known in the art, such as those described by Rolland (1998) Crit. Rev. Therap. Drug Carrier Systems 15:143-198, and references cited therein.
It will be apparent that an immunogenic compostions may contain pharmaceutically acceptable salts of the polynucleotides encoding the heterologous polypeptides (e.g., immunogenic polypeptides). Such salts may be prepared from pharmaceutically acceptable non-toxic bases, including organic bases (e.g., salts of primary, secondary and tertiary amines and basic amino acids) and inorganic bases (e.g., sodium, potassium, lithium, ammonium, calcium and magnesium salts). Some particular examples of salts include phosphate buffered saline and saline for injection.
Any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of this invention. Suitable carriers include, for example, water, saline, alcohol, a fat, a wax, a buffer, a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, or biodegradable microspheres (e.g., polylactate polyglycolate). Suitable biodegradable microspheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268; 5,075,109; 5,928,647; 5,811,128; 5,820,883. The immunogenic polypeptide and/or carrier virus may be encapsulated within the biodegradable microsphere or associated with the surface of the microsphere.
Such compositions may also comprise buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide), solutes that render the formulation isotonic, hypotonic or weakly hypertonic with the blood of a recipient, suspending agents, thickening agents and/or preservatives. Alternatively, compositions of the present invention may be formulated as a lyophilizate. Compounds may also be encapsulated within liposomes using well known technology.
In some embodiments of the present invention, the compositions further comprise an adjuvant. Suitable adjuvants include, for example, the lipids and non-lipid compounds, cholera toxin (CT), CT subunit B, CT derivative CTK63, E. coli heat labile enterotoxin (LT), LT derivative LTK63, Al(OH)3, and polyionic organic acids as described in e.g., WO 04/020592, Anderson and Crowle, Infect. Immun. 31(1):413-418 (1981), Roterman et al., J. Physiol. Pharmacol., 44(3):213-32 (1993), Arora and Crowle, J. Reticuloendothel. 24(3):271-86 (1978), and Crowle and May, Infect. Immun. 38(3):932-7 (1982)). Suitable polyionic organic acids include for example, 6,6′-[3,3′-demithyl[1,1′-biphenyl]-4,4′-diyl]bis(azo)bis[4-amino-5-hydroxy-1,3-naphthalene-disulfonic acid] (Evans Blue) and 3,3′-[1,1′biphenyl]-4,4′-diylbis(azo)bis[4-amino-1-naphthalenesulfonic acid] (Congo Red). It will be appreciated by those of skill in the art that the polyionic organic acids may be used for any genetic vaccination method in conjunction with any type of administration.
Other suitable adjuvants include topical immunomodulators such as, members of the imidazoquinoline family such as, for example, imiquimod and resiquimod (see, e.g., Hengge et al., Lancet Infect. Dis. 1(3):189-98 (2001). Expressed TLR-3 agonists (e.g., dsRNA) and TLR-7 agonists (e.g., ssRNA) could also be used with the invention
Additional suitable adjuvants are commercially available as, for example, additional alum-based adjuvants (e.g., Alhydrogel, Rehydragel, aluminum phosphate, Algammulin); oil based adjuvants (Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.), Specol, RIBI, TiterMax, Montanide ISA50 or Seppic MONTANIDE ISA 720); nonionic block copolymer-based adjuvants, cytokines (e.g., GM-CSF or Flat3-ligand); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2 (SmithKline Beecham, Philadelphia, Pa.); salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and Quil A. Cytokines, such as GM-CSF or interleukin-2, -7, or -12, are also suitable adjuvants. Hemocyanins (e.g., keyhole limpet hemocyanin) and hemoerythrins may also be used in the invention. Polysaccharide adjuvants such as, for example, chitin, chitosan, and deacetylated chitin are also suitable as adjuvants. Other suitable adjuvants include muramyl dipeptide (MDP, N acetylmuramyl L alanyl D isoglutamine) bacterial peptidoglycans and their derivatives (e.g., threonyl-MDP, and MTPPE). BCG and BCG cell wall skeleton (CWS) may also be used as adjuvants in the invention, with or without trehalose dimycolate. Trehalose dimycolate may be used itself (see, e.g., U.S. Pat. No. 4,579,945). Detoxified endotoxins are also useful as adjuvants alone or in combination with other adjuvants (see, e.g., U.S. Pat. Nos. 4,866,034; 4,435,386; 4,505,899; 4,436,727; 4,436,728; 4,505,900; and 4,520,019. The saponins QS21, QS17, QS7 are also useful as adjuvants (see, e.g., U.S. Pat. No. 5,057,540; EP 0362 279; WO 96/33739; and WO 96/11711). Other suitable adjuvants include Montanide ISA 720 (Seppic, France), SAF (Chiron, Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2, SBAS-4 or SBAS-6 or variants thereof, available from SmithKline Beecham, Rixensart, Belgium), Detox (Corixa, Hamilton, Mont.), and RC-529 (Corixa, Hamilton, Mont.).
Superantigens are also contemplated for use as adjuvants in the present invention. Superantigens include Staphylococcus exoproteins, such as the α, β, γ and Δ enterotoxins from S. aureus and S. epidermidis, and the α, β, γ and Δ E. coli exotoxins. Common Staphylococcus enterotoxins are known as staphylococcal enterotoxin A (SEA) and staphylococcal enterotoxin B (SEB), with enterotoxins through E (SEE) being described (Rott et al., 1992). Streptococcus pyogenes B (SEB), Clostridium perfringens enterotoxin (Bowness et al., 1992), cytoplasmic membrane-associated protein (CAP) from S. pyogenes (Sato et al., 1994) and toxic shock syndrome toxin 1 (TSST 1) from S. aureus (Schwab et al., 1993) are further useful superantigens.
Within the pharmaceutical compositions provided herein, the adjuvant composition can be designed to induce, e.g., an immune response predominantly of the Th1 or Th2 type. High levels of Th1-type cytokines (e.g., IFN-gamma, TNF-alpha, IL-2 and IL-12) tend to favor the induction of cell mediated immune responses to an administered antigen. In contrast, high levels of Th2-type cytokines (e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoral immune responses. Following oral delivery of a composition comprising an immunogenic polypeptide as provided herein, an immune response that includes Th1- and Th2-type responses will typically be elicited.
The compositions described herein may be administered as part of a sustained release formulation (i.e., a formulation such as a capsule or sponge that effects a slow release of compound following administration). Such formulations may generally be prepared using well known technology (see, e.g., Coombes et al. (1996) Vaccine 14:1429-1438). Sustained-release formulations may contain a polypeptide, polynucleotide or antibody dispersed in a carrier matrix and/or contained within a reservoir surrounded by a rate controlling membrane.
Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. Such carriers include microparticles of poly(lactide-co-glycolide), as well as polyacrylate, latex, starch, cellulose and dextran. Other delayed-release carriers include supramolecular biovectors, which comprise a non-liquid hydrophilic core (e.g., a cross-linked polysaccharide or oligosaccharide) and, optionally, an external layer comprising an amphiphilic compound (see, e.g., WO 94/20078; WO 94/23701; and WO 96/06638). The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature of the condition to be treated or prevented.
The pharmaceutical compositions may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers are preferably hermetically sealed to preserve sterility of the formulation until use. In general, formulations may be stored as suspensions, solutions or emulsions in oily or aqueous vehicles. Alternatively, a pharmaceutical composition may be stored in a freeze-dried condition requiring only the addition of a sterile liquid carrier immediately prior to use.
V. Therapeutic Uses of the Invention
One aspect of the present invention involves using the immunogenic compositions described herein to elicit an antigen specific immune response from a subject or patient with a disease such as, for example, a viral infection, bacterial infection, a parasitic infection, a fungal infection, or cancer. As used herein, a “subject” or a “patient” refers to any warm-blooded animal, such as, for example, a rodent, a feline, a canine, or a primate, preferably a human. The immunogenic compositions may be used to treat at any stage of the disease, i.e., at the pre-cancer, cancer, or metastatic stages, or to prevent disease. For example, the compositions described herein may be used to treat a viral disease such as HIV or hepatitis or for prevention or treatment of cancer. Within such methods, pharmaceutical compositions are typically administered to a patient. The patient may or may not be afflicted with the disease or disorder (e.g., a viral infection, a bacterial infection, or cancer). Accordingly, the above pharmaceutical compositions may be used to prevent the development of a disease or disorder (e.g., a viral infection, a bacterial infection, or cancer)or to treat a patient afflicted with the disease or disorder (e.g., a viral infection, a bacterial infection, or cancer). The disease or disorder may be diagnosed using criteria generally accepted in the art. For example, viral infection may be diagnosed by the measurement of viral titer in a sample from the patient, bacterial infection may be diagnosed by detecting the bacteria in a sample from the patient, and cancer may be diagnosed by detecting the presence of a malignant tumor. Pharmaceutical compositions may be adminiastered either prior to or following surgical removal of primary tumors and/or treatment such as administration of radiotherapy or conventional chemotherapeutic drugs.
Immunotherapy is typically active immunotherapy, in which treatment relies on the in vivo stimulation of the endogenous host immune system to react against, e.g., tumors or bacterially or virally infected cells, with the administration of immune response-modifying agents (compositions comprising nucleic acids encoding immunogenic polypeptides as provided herein).
Frequency of administration of the prophylactic or therapeutic compositions described herein, as well as dosage, will vary from individual to individual, and may be readily established using standard techniques. Often between 1 and 10 doses may be administered over a 52 week period. Typically 3 doses are administered, at intervals of 1 month, more typically, 2-3 doses are administered every 2-3 months. It is possible that the intervals will be more like once a year for certain therapies. Booster vaccinations may be given periodically thereafter. Alternate protocols may be appropriate for individual patients and particular diseases and disorders. A suitable dose is an amount of a compound that, when administered as described above, is capable of promoting, e.g., an anti-tumor, an anti-viral, or an antibacterial, immune response, and is at least 10-50% above the basal (i.e., untreated) level. Such response can be monitored by measuring the anti-tumor antibodies in a patient or by vaccine-dependent generation of cytolytic T cells capable of killing, e.g., the patient's tumor cells, the patient's virally infected cells, or the patient's bacterially infected cells in vitro. Such vaccines should also be capable of causing an immune response that leads to an improved clinical outcome (e.g., more frequent remissions, complete or partial or longer disease-free survival) in vaccinated patients as compared to non-vaccinated patients. Typically, the amount of the viral titers will be between 1.0×104 pfu/animal and 1.0×1015 pfu/animal. Suitable dose sizes will vary with the size of the patient, but will typically range from about 0.01 ml to about 10 ml, more typically from about 0.025 to about 7.5 ml, most typically from about 0.05 to about 5 ml. Those of skill in the art will appreciate that the dose size may be adjusted based on the particular patient or the particular disease or disorder being treated. For oral administration, the chimeric adenoviral vector can conveniently be formulated in a pill.
In general, an appropriate dosage and treatment regimen provides the active compound(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit. Such a response can be monitored by establishing an improved clinical outcome (e.g., more frequent remissions, complete or partial, or longer disease-free survival) in treated patients as compared to non-treated patients. Such immune responses may generally be evaluated using standard proliferation, cytotoxicity or cytokine assays described above, which may be performed using samples obtained from a patient before and after treatment.
For example, detection of immunocomplexes formed between immunogenic polypeptides and antibodies in body fluid which are specific for immunogenic polypeptides may be used to monitor the effectiveness of therapy, which involves a particular immunogenic polypeptide, for a disease or disorder in which the immunogenic polypeptide is associated. Samples of body fluid taken from an individual prior to and subsequent to initiation of therapy may be analyzed for the immunocomplexes by the methodologies described above. Briefly, the number of immunocomplexes detected in both samples are compared. A substantial change in the number of immunocomplexes in the second sample (post-therapy initiation) relative to the first sample (pre-therapy) reflects successful therapy.
A. Administration of the Compositions of the Present Invention
According to the methods of the present invention, a composition comprising the chimeric adenoviral vector is administered by any non-parenteral route (e.g., orally, intranasally, or mucosally via, for example, the vagina, lungs, salivary glands, nasal cavities, small intestine, colon, rectum, tonsils, or Peyer's patches). The composition may be administered alone or with an adjuvant as described above. In some embodiments, the adjuvants are encoded by a nucleic acid sequence (e.g., a nucleic acid encoding IL-2, GM-CSF, IL-12, or bacterial flagellin). In some embodiments of the present invention, the adjuvant is administered at the same time as the composition. In other embodiments of the present invention, the adjuvant is administered after the composition, e.g., 6, 12, 18, 24, 36, 48, 60, or 72 hours after administration of the composition.
B. Detection of an Immune Response to Atigens of Interest
An immune response to the heterologous polypeptide can be detected using any means know in the art including, for example detecting specific activation of CD4+ or CD8+ T cells or by detecting the presence of antibodies that specifically bind to the polypeptide.
Specific activation of CD4+ or CD8+ T cells associated with a mucosal, humoral, or cell-mediated immune response may be detected in a variety of ways. Methods for detecting specific T cell activation include, but are not limited to, detecting the proliferation of T cells, the production of cytokines (e.g., lymphokines), or the generation of cytolytic activity (i.e., generation of cytotoxic T cells specific for the immunogenic polypeptide). For CD4+ T cells, a preferred method for detecting specific T cell activation is the detection of the proliferation of T cells. For CD8+ T cells, a preferred method for detecting specific T cell activation is the detection of the generation of cytolytic activity using 51Cr release assays (see,. e.g., Brossart and Bevan, Blood 90(4): 1594-1599 (1997) and Lenz et al., J. Exp. Med. 192(8):1135-1142 (2000)).
Detection of the proliferation of T cells may be accomplished by a variety of known techniques. For example, T cell proliferation can be detected by measuring the rate of DNA synthesis. T cells which have been stimulated to proliferate exhibit an increased rate of DNA synthesis. A typical way to measure the rate of DNA synthesis is, for example, by pulse-labeling cultures of T cells with tritiated thymidine, a nucleoside precursor which is incorporated into newly synthesized DNA. The amount of tritiated thymidine incorporated can be determined using a liquid scintillation spectrophotometer. Other ways to detect T cell proliferation include measuring increases in interleukin-2 (IL-2) production, Ca2+ flux, or dye uptake, such as 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium. Alternatively, synthesis of lymphokines (e.g., interferon-gamma) can be measured or the relative number of T cells that can respond to the immunogenic polypeptide may be quantified.
Antibody immune responses (aka Humoral immune responses or B cell responses), including mucosal antibody responses can be detected using immunoassays known in the art [Tucker et al., Mol Therapy, 8, 392-399 (2003); Tucker et al., Vaccine, 22, 2500-2504 (2004)]. Suitable immunoassays include the double monoclonal antibody sandwich immunoassay technique of David et al. (U.S. Pat. No. 4,376,110); monoclonal-polyclonal antibody sandwich assays (Wide et al., in Kirkham and Hunter, eds., Radioimmunoassay Methods, E. and S. Livingstone, Edinburgh (1970)); the “western blot” method of Gordon et al. (U.S. Pat. No. 4,452,901); immunoprecipitation of labeled ligand (Brown et al. (1980) J. Biol. Chem. 255:4980-4983); enzyme-linked immunosorbent assays (ELISA) as described, for example, by Raines et al. (1982) J. Biol. Chem. 257:5154-5160; immunocytochemical techniques, including the use of fluorochromes (Brooks et al. (1980) Clin. Exp. Immunol. 39:477); and neutralization of activity (Bowen-Pope et al. (1984) Proc. Natl. Acad Sci. USA 81:2396-2400). In addition to the immunoassays described above, a number of other immunoassays are available, including those described in U.S. Pat. Nos. 3,817,827; 3,850,752; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; and 4,098,876.
EXAMPLES
The following examples are intended to illustrate, but not to limit the present invention.
Example 1
Construction of a Chimeric Adenoviral Vector (DS1)
To demonstrate that TLR-3 agonists can improve adaptive immune responses to expressed antigens of interest, several different chimeric adenoviral vectors were constructed that comprise nucleic acid sequences encoding several different antigens of interest. In this example, the nucleic acid encoding gp120 (from the NIH AIDS Reagent and Reference Reagent Program) was placed under control of a CMV promoter with a small intron just upstream of the start codon in the shuttle vector (pShuttle, Qbiogene). A poly A tail from bGH was placed downstream of the nucleic acid encoding gp120. The vector sequence is set forth in SEQ ID NO: 1. Homologous recombination with the vector pAd (Qbiogene) was performed to generate a vector capable of producing recombinant Ad (E1/E3 deleted) that contained the nucleic acid encoding gp 120. DS1 was generated by transfecting the new pAd-CMV-gp120 expression construct into 293 cells. Titers were measured by standard methods.
Example 2
DS1 (vector plus TLR-3 agonist) is superior to standard rAd5 for inducing an antigen specific immune response
To determine whether the addition of TLR-3 agonist could improve adaptive immune responses, 10×107 PFU of either rAd-CMV-gp120 plus 5 ug/ml poly I:C (DS1) or rAd-CMV-gp120 alone (rAd5) were administered to animals by oral gavage on weeks 0 and 3. Both vectors express HIV gp120 under control of the CMV promoter and use recombinant E1/E3 deleted adenovirus type 5. Antibody titers to gp120 were measured in the plasma 3 and 6 weeks after the initial administration by anti-gp120 IgG ELISA as described in Tucker, et al., Mol Ther 8:392 (2004)). As shown in FIG. 1, DS1 performed significantly better than rAd5 in eliciting antibody responses to the protein gp120 both at 3 and 6 weeks post initial oral administration. In particular, the average antibody titer to gp120 was 100 fold better with the DS1 group than with the rAd5 group at week 6. It also appears that the DS1 group was boosted by readministration at week 4 in that the average titer increased greater than 20 fold between weeks 3 and 6 whereas the rAd5 group showed only a slight increase in mean antibody titer. The results demonstrate that the addition of a TLR-3 agonist can greatly improve Ad5 mediated antibody responses to antigens of interest following oral administration of a chimeric adenoviral vector comprising a nucleic acid encoding the antigen of interest. As a positive control for the assay, sera from an animal injected subcutaneously with gp120 plus Complete Freund's Adjuvant was also measured in the anti-gp120 ELISA at week 3. Untreated animals and animals administered the dsRNA analog alone (dsRNA) served as negative and background controls respectively for the ELISA. Each group contained 6 animals.
Example 3
Construction of a Second Chimeric Adenoviral Vector (DS1b ) and a Third Chimeric Adenoviral Vector (DS1c)
A nucleic acid encoding green fluorescent protein (GFP) was inserted into pShuttle-CMV (Qbiogene) using standard restriction enzyme digests. The plasmid pShuttleCMV-GFP was combined by homologous recombination with the vector pAd (Qbiogene) as described before in order to generate a vector capable of producing recombinant Ad (E1/E3 eleted) comprising a nucleic acid sequence encoding GFP. A nucleic acid encoding hemagluttinin (HA) from influenza A/PR/8/34 was cloned and placed in the pShuttle-CMV vector (Qbiogene) (SEQ ID NO: 13). The plasmid pShuttleCMV-HA (PR/8) was combined by homologous recombination with the vector pAd (Qbiogene) as described before in order to generate a vector capable of producing recombinant Ad (E1/E3 deleted) comprising a nucleic acid sequence encoding HA. Recombinant Ad was generated by transfecting the new pAd-CMV-GFP and pAd-CMV-HA expression construct into 293 cells. Titers were measured by standard methods.
Example 4
DS1b (Ad-CMV-GFP plus TLR-3 agonist) and DS1c (Ad-CMV-HA plus TLR-3 agonist) is superior to standard rAd5 for inducing an antigen specific immune response
1.0×107 PFU of either Ad-CMV-GFP plus 5 ug/ml poly I:C (DS1b) or Ad-CMV-GFP (rAd5) were administered to animals by oral gavage on week 0. Both viruses express the GFP under control of the CMV promoter and use recombinant E1/E3 deleted adenovirus type 5. Antibody titers to GFP were measured in the plasma 3 weeks after the initial virus administration by anti-GFP IgG ELISA. As shown in in FIG. 2, the DS1b group performed significantly better than rAd5 in eliciting antibody responses to the protein GFP at 3 weeks post initial oral administration.
The CD8+T cell responses to GFP were measured by tetramer staining of splenocytes. Animals were vaccinated on weeks 0, 4, 8 and spleens were harvested on week 10. The splenocytes were stained with CD8-FITC and the tetramer which recognizes the immunodominant epitope to GFP in Balb/c mice. Results show that oral administration of the DS1b vector was statistically better than rAd alone in inducing tetramer positive CD8 cells (FIG. 2b).
1.0×107 PFU of either Ad-CMV-HA plus 5 ug/ml poly I:C (DS1c) or Ad-CMV-HA (rAd5) were administered to animals by oral gavage on week 0. Both viruses express HA under control of the CMV promoter and use recombinant E1/E3 deleted adenovirus type 5. Antibody titers to HA were measured in the plasma 3 weeks after the initial virus administration by anti-PR8/34 IgG ELISA. The procedure for measuring antibody responses is similar to that described before with the exception that the ELISA plates were coated with 5 ug/ml of whole A/PR8/34 lysate (Advanced Biotechnology Incorporated, Gaithersburg, Md.). As shown in FIG. 2C, the DS1c group performed significantly better (approximate 100 fold better) than rAd5 in eliciting antibody responses to influenza at 3 weeks post initial oral administration. The results of these studies also demonstrate that the approach of using TLR-3 agonist along with a chimeric recombinant adnoviral vector can be generally applied to multiple different heterologous antigens, with a 100 fold improvement in antibody titer.
Example 5
Non-Parenteral Routes of Delivery Are Superior to Parenteral Routes
Intramuscular delivery was tested by directly injecting 1.0×107 pfu of pAd-CMV-gp120 (DS10+/ −poly I:C at 5 ug/ml into the quadriceps of animals. Plasma serum IgG titers to GFP were measured as described before. Each group contained 6 animals. As shown in FIG. 3A, significant antibody titers to gp120 were observed at 3 weeks post administration in the group with TLR-3 agonist (i.m. rAd+PI). (FIG. 3a).
Intranasal administration was tested by administering 20 ul of 1.1×106 pfu of DS1c +/ −5 ug/ml of poly I:C into the nasal cavity of mice. The mice were lightly anesthetized with isoflurane before administering the virus formulated in sterile saline. The results show that the rAd-CMV-HA plus poly I:C (DS1c) had slightly higher antibody titers compared to animals given the standard rAd-CMV-HA. Results are plotted as individual animals for the DS1c (N=6) and the rAd (N=5) groups. Untreated animals (N=4) are used for negative controls.
Example 6
Construction of an Expressed TLR3 Agonist
A short 45 bp segment of DNA was synthesized by ordering of DNA oligos that when annealed together formed a 45 bp seqment designed to make a hairpin of double-stranded RNA (GAAACGATATGGGCTGAATACGGATCCGTATTCAGCCCATATCGTTTC) (SEQ ID NO:10). This short segment (called luc1) was cloned into the plasmid pSK-containing the human beta actin promoter and a BGH poly A tail. This plasmid is called pSk-luc1.
Example 7
The pSK-luc 1 Functions in Dendritic Cell Cultures Like Poly I:C, the Effects of Poly I:C and rAd are Additive
To determine whether the expressed TLR-3 agonist of Example 6 above could function as an inducer of pro-inflammatory cytokines and dendritic cell maturation like the TLR-3 ligand poly I:C, an expressed dsRNA TLR-3 agonist was tested in dendritic cell cultures. Bone marrow from the femurs of Balb/c mice were cultured with flt-3 ligand (200 ng/ml), 5% serum, in DMEM media in order to make primary dendritic cell cultures. Five days after primary bone marrow cultures were set-up, 293 cells were transfected with either pSk-luc1, pSK-beta2 (a long seqment of beta galactosidase that forms a 200 bp hairpin), or pcDNA3 (empty expression vector). On day 6, the transfected cells were treated by UV irradiation (20 seconds at 40 kJ/cm2) to cause apoptosis and these cells were given to the dendritic cells. Either poly I:C (1 ug/ml), rAd (1 pfu/cell), rAd+poly I:C, pSK-luc1 transfected cells, pSK-beta2 transfected cells, or pcDNA3 transfected cells were given to the dendritic cells and cultured overnight. As shown in FIG. 4A, pSK-luc1 transfected cells can significantly improve dendritic cell activation as measured by the mouse IL-6 ELISA. The results of this experiment also show that the combination of rAd plus TLR3 ligand (poly I:C) together can greatly improve dendritic cell activity.
Additional ligands were also tested. The TLR-3 agonist set forth in SEQ ID NO: 11 (m1) also forms a dsRNA hairpin of approximately the same size as luc1. These were made by overlapping oligonucleotides and annealing them together before cloning into the pSK-vector under control of the human beta actin promoter. The vectors were transfected into 293 cells and given to primary dendritic cells as described before. As shown in FIG. 4B, these additional ligands can activate dendritic cells similar to that of the ligand luc1 (FIG. 4B).
Example 8
Construction of a Fourth Chimeric Adenoviral Vector (DS2) and Rapid Cloning Vectors (DS2beta-luc and DS2C-luc)
A nucleic acid encoding gp120 (from the NIH AIDS Research and Reference Reagent Program)) was placed under control of a CMV promoter with a small intron just upstream of the start codon in the shuttle vector (pShuttleCMV, Qbiogene). A poly A tail from bGH was placed downstream of the nucleic acid encoding gp120. The dsRNA TLR-3 agonist luc1 under the control of the human beta actin promoter and poly A (described in example 5 above) was inserted into the gp120 pShuttle vector such that both the nucleic acid encoding gp120 and the nucleic acid encoding TLR-3 agonist were contained in a single vector under the control of two separate promoters. The orientation of the expression of the nucleic acid encoding the antigen of interest and the expression of the TLR-3 agonist is illustrated in FIG. 5.
Two generic shuttle vectors called DS2beta-luc (SEQ ID NO: 14) and DS2C-luc (SEQ ID NO: 15) were also constructed such that a nucleic acid encoding any antigen of interest could be inserted under the CMV promoter and either the human beta actin promoter or the CMV promoter is used to drive expression of a dsRNA TLR-3 agonist. In particular, the vector DS2C-luc has a unique Kpn 1 site that a nucleic acid encoding an antigen of interest can easily be cloned into. The purpose of these vectors is to make subsequent vector construction much easier because a nucleic acid encoding any antigen of interest could be inserted into the cloning site to rapidly manufacture a vector capable of eliciting antibody and T cells responses against the antigen of interest. Homologous recombination of DS2 with the vector pAd (Qbiogene) was performed as before in order to generate a vector capable of producing recombinant Ad(E1/E3 deleted) that contained a nucleic acid encoding GFP and a nucleic acid encoding the dsRNA TLR-3 agonist luc 1. Recombinant Ad was generated by transfecting the new pAd-betaactin -luc1-CMV-gp120 expression construct into 293 cells. Titers were measured by standard methods.
Example 9
Induction of an Antigen Specific Immune Response Following Oral Delivery of DS2
1.0×107 PFU of either pAd-CMV-gp120 plus the TLR-3 agonist luc1 (DS2) or pAd-CMV-gp120 (rAd5) were administered to animals by oral gavage on week. Both viruses express the gp120 under control of the CMV promoter and use recombinant E1/E3 deleted adenovirus type 5. Antibody titers to gp120 were measured in the plasma 3 weeks after virus administration by anti-gp120 IgG ELISA. The ELISA protcol has been described before (Tucker, et al, Mol Therapy 8:392 (2004)). Results demonstrate that DS2 can induce approximately a 2 log improvement in antibody titer to gp120, the heterologous antigen used in the experiment. The DS2 vector comprises a nucleic acid sequence encoding expressing gp120 and a nucleic acid sequence expressing a dsRNA TLR-3 agonist. As a positive control for the assay, sera from two animals injected subcutaneously with 10 micrograms gp120 protein plus Complete Freund's Adjuvant was also measured in the anti-gp120 ELISA. Untreated animals served as negative controls for the ELISA. Each group contained 6 animals. The results are illustrated in FIG. 6.
Example 10
Induction of an Antigen Specific Immune Response Following Oral Delivery of DS3
1.0×107 PFU of either pAd-CMV-influenza HA (from A/PR/8/34) plus the TLR7/8 ligand polyuridylic acid (DS3) or pAd-CMV-HA (rAd5) were administered to animals by oral gavage on week 0. Both viruses express influenza HA under control of the CMV promoter and use recombinant E1/E3 deleted adenovirus type 5. Antibody titers to HA were measured in the plasma 3 weeks after virus administration by anti-influenza HA IgG ELISA. Each group contained 6 animals. The results are illustrated in FIG. 7.
Example 11
Construction of a Fifth, Sixth, and Seventh Chimeric Adenoviral Vector (DS2b, DS2b-for and ND1.1 214)
The gene influenza HA (A/Indo/5/2005) was synthesized by CelTek (Nashville, Tenn.) and placed into the vector pShuttleCMV (Qbiogene) which has a CMV promoter with a small intron just upstream of the start codon in the shuttle vector. The luc1 DNA with human beta actin promoter and poly A (described in example 5) were placed into the vector downstream of the antigen, in the orientation shown in FIG. 5 for DS2b. The sequence of luc1 is (GAAACGATATGGGCTGAATACGGATCCGTATTCAGCCCATATCGTTTC) (SEQ ID NO:10) and the completed pShuttle vector is set forth in SEQ ID NO: 6. An alternative orientation of luc1 with promoter in a shuttle vector is described as SEQ ID NO: 7 and is designated DS2b-for. We have also constructed another pShuttle vector (called DS2bC-HA) (SEQ ID NO: 16) that comprises two separate CMV promoters driving expression of the TLR-3 agonist luc1 and influenza HA described above. Homologous recombination with the vector pAd (Qbiogene) was performed as before in order to generate vectors capable of producing recombinant Ad (E1/E3 deleted) that contained the nucleic acid encoding HA and the TLR-3 agonist luc1 under separate promoters. Recombinant Ad was generated by transfecting the new pAd-constructs into 293 cells. Titers were measured by standard methods. The completed pAd vector containing DS2C-luc was named ND1.1 214 and deposited in the ATCC patent depository on Feb. 22, 2007 (Manassus, Va.). The nucleic acid sequence of this chimeric adenoviral vector is set forth in in SEQ ID NO: 17. The nucleic acid encoding the heterologous antigen is in bold text and is flanked by a Cla I recognition site on the 5′ end and a Not 1 recognition site on the 3′end. The nucleic acid sequence encoding the TLR-3 agonists is in italic, with the linker sequence in bold. A nucleic acid sequence encoding any antigen of interest and a nucleic acid sequence encoding any suitable expressed TLR-3 agonist can be inserted into the chimeric adenoviral vector.
Example 12
Induction of an Antigen Specific Immune Response Following Oral Delivery of DS2b.
1.0×107 PFU of either pAd-CMV-HA plus the TLR-3 agonists luc1 in the reverse orientation (DS2b) or forward orientation (DS2b-for), or pAd-CMV-HA (rAd5) were administered to animals by oral gavage on week 0. These viruses express the antigen influenza HA under control of the CMV promoter and use recombinant E1/E3 deleted adenovirus type 5. Antibody titers to HA were measured in the plasma 3 weeks after virus administration by anti-HA IgG ELISA. Results demonstrate that the DS2b vector elicits an antibody responses to the protein HA greater than the standard rAd vector (rAd5). The DS2b vector contains rAd5 expressing HA as well as expresses a toll-like receptor 3 (TLR3) agonist, a hairpin of double-stranded RNA, demonstrating that the use of the encoded dsRNA ligand can improve adaptive immune responses to antigens of interest. As shown in FIG. 8A and FIG. 6, expressed dsRNA can improve adaptive immune responses to multiple different heterologous antigens. Untreated animals served as negative control for the ELISA. Each group contained 6 animals.
Vectors in the opposite orientation (DS2for) were examined for antibody responses following either oral or intramuscular administration of 1.0×107 pfu virus per animal at 0 and 5 weeks. Antibody responses to HA were measured at 4 and 7 weeks post initial administration. As shown in FIG. 8B, the opposite orientation vector can also induce substantial antibody responses to heterologous antigens. The DS1b and DS1bfor vectors induced similar responses to HA at the 4 week time point. Significantly, the effect of boosting of the antibody response was demonstrated with the DS1bfor vector and showed that multiple doses could be used to increase antibody responses to the heterologous antigen.
Another example of potential of the chimeric adenoviral vector approach was demonstrated as well. The vector ND1.1 214 was given to animals by oral (1.0×107 pfu) or intranasal administration (3×106 pfu) and the antibody responses to the heterologous antigen were measured at week 3. As shown in FIG. 8C, substantial antibody responses to HA were measured following oral administration, well beyond the typical values from a single oral administration of rAd vector.
All publications, patent publications, patents, and Genback Accession Nos. applications cited in this specification are herein incorporated by reference in their entirety for all purposes as if each individual publication, patent publication, or patent were specifically and individually indicated to be incorporated by reference.

## Claims

1. A chimeric adenoviral expression vector, said vector comprising an expression cassette comprising the following elements:
(a) a first promoter operably linked to a nucleic acid encoding a toll-like receptor-3 (TLR-3) agonist, wherein the TLR-3 agonist is a double stranded RNA (dsRNA); and
(b) a second promoter operably linked to a nucleic acid encoding a heterologous polypeptide, wherein said heterologous polypeptide is selected from the group consisting of:
influenza virus HA, influenza virus Ml, influenza virus NP, HIV gag, and HIV env.

2. The chimeric adenoviral expression vector of claim 1, wherein the heterologous polypeptide is an HIV env polypeptide.

3. The chimeric adenoviral expression vector of claim 2, wherein the HIV env polypeptide is selected from the group consisting of: gp41, gp120, and gp160.

4. The chimeric adenoviral expression vector of claim 1, wherein the heterologous polypeptide is an influenza HA polypeptide.

5. The chimeric adenoviral expression vector of claim 1, wherein the first promoter and the second promoter are the same.

6. The chimeric adenoviral expression vector of claim 5, wherein the first promoter and the second promoter are each a CMV promoter.

7. An immunogenic composition comprising the expression vector of claim 1 and a pharmaceutically acceptable carrier.

8. A chimeric adenoviral expression vector, said vector comprising an expression cassette comprising the following elements:
(a) a first promoter operably linked to a nucleic acid encoding a toll-like receptor-3 (TLR-3) agonist, wherein the TLR-3 agonist is a double stranded RNA (dsRNA) and wherein the nucleic acid encoding the TLR-3 agonist comprises a sequence selected from the group consisting of: SEQ ID NOS: 8, 9, 10, 11, and 12; and
(b) a second promoter operably linked to a nucleic acid encoding a heterologous polypeptide.

9. The chimeric adenoviral expression vector of claim 8, wherein the nucleic acid encoding the TLR-3 agonist is a sequence selected from the group consisting of: SEQ ID NOs: 8, 9, 10, 11, and 12.

10. A method for eliciting an immune response, said method comprising administering to a mammalian subject an immunogenically effective amount of a chimeric adenoviral expression vector, said vector comprising an expression cassette comprising the following elements:
(a) a first promoter operably linked to a nucleic acid encoding a toll-like receptor-3 (TLR-3) agonist, wherein the TLR-3 agonist is a double stranded RNA (dsRNA); and
(b) a second promoter operably linked to a nucleic acid encoding a heterologous polypeptide,
wherein the immune response is directed against the heterologous polypeptide, and wherein the route of administration is selected from the group consisting of: oral, intranasal, and mucosal.

11. The method of claim 10, wherein the heterologous polypeptide is expressed in a cell selected from the group consisting of: a dendritic cell, a microfold cell, and an intestinal epithelial cell.

12. The method of claim 10, wherein said mammal is a human.

13. The method of claim 10, wherein nucleic acid encoding the TLR-3 agonist comprises a sequence selected from the group consisting of: SEQ ID NOS: 8, 9, 10, 11, and 12.

14. The method of claim 10, wherein said heterologous polypeptide is an influenza HA polypeptide.