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WO1997048370A2 - Vaccins comprenant des genes de synthese - Google Patents

Vaccins comprenant des genes de synthese Download PDF

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Publication number
WO1997048370A2
WO1997048370A2 PCT/US1997/010517 US9710517W WO9748370A2 WO 1997048370 A2 WO1997048370 A2 WO 1997048370A2 US 9710517 W US9710517 W US 9710517W WO 9748370 A2 WO9748370 A2 WO 9748370A2
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WIPO (PCT)
Prior art keywords
tpa
hiv
opt
gene
jns
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PCT/US1997/010517
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English (en)
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WO1997048370A3 (fr
Inventor
John W. Shiver
Mary Ellen Davies
Daniel C. Freed
Margaret A. Liu
Helen C. Perry
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Merck & Co., Inc.
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Publication date
Priority claimed from GBGB9614942.2A external-priority patent/GB9614942D0/en
Priority claimed from GBGB9614943.0A external-priority patent/GB9614943D0/en
Application filed by Merck & Co., Inc. filed Critical Merck & Co., Inc.
Priority to AU34918/97A priority Critical patent/AU728422B2/en
Priority to JP10503267A priority patent/JP2000516445A/ja
Priority to EP97931230A priority patent/EP0912607A2/fr
Publication of WO1997048370A2 publication Critical patent/WO1997048370A2/fr
Publication of WO1997048370A3 publication Critical patent/WO1997048370A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/67—General methods for enhancing the expression
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/16011—Human Immunodeficiency Virus, HIV
    • C12N2740/16111—Human Immunodeficiency Virus, HIV concerning HIV env
    • C12N2740/16122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes

Definitions

  • HIV-1 Human Immunodeficiency Virus- 1
  • HIV-1 is the etiological agent of acquired human immune deficiency syndrome (AIDS) and related disorders. HIV-1 is an RNA virus of the Retroviridae family and exhibits the 5'LTR-gag-pol-env-LTR3' organization of all retroviruses. In addition, HIV-1 comprises a handful of genes with regulatory or unknown functions, including the tat and rev genes.
  • the env gene encodes the viral envelope glycoprotein that is translated as a 160-kilodalton (kDa) precursor (gpl60) and then cleaved by a cellular protease to yield the external 120-kDa envelope glycoprotein (gpl20) and the transmembrane 41 -kDa envelope glycoprotein (gp41).
  • Gpl20 and gp41 remain associated and are displayed on the viral particles and the surface of HiV-infected cells.
  • Gpl20 binds to the CD4 receptor present on the surface of helper T- lymphocytes, macrophages and other target cells. After gpl20 binds to CD4, gp41 mediates the fusion event responsible for virus entry.
  • Infection begins when gpl20 on the viral particle binds to the CD4 receptor on the surface of T4 lymphocytes or other target cells.
  • the bound virus merges with the target cell and reverse transcribes its RNA genome into the double-stranded DNA of the cell.
  • the viral DNA is inco ⁇ orated into the genetic material in the cell's nucleus, where the viral DNA directs the production of new viral RNA, viral proteins, and new virus particles.
  • the new particles bud from the target cell membrane and infect other cells.
  • T4 lymphocytes which are critical to immune defense, is a major cause of the progressive immune dysfunction that is the hallmark of HIV infection.
  • the loss of target cells seriously impairs the body's ability to fight most invaders, but it has a particularly severe impact on the defenses against viruses, fungi, parasites and certain bacteria, including mycobacteria.
  • HIV-1 kills the cells it infects by replicating, budding from them and damaging the cell membrane. HIV-1 may kill target cells indirectly by means of the viral gpl20 that is displayed on an infected cell's surface.
  • CD4 receptor on T cells has a strong affinity for gpl20, healthy cells expressing CD4 receptor can bind to gpl20 and fuse with infected cells to form a syncytium. A syncytium cannot survive.
  • HIV-1 can also elicit normal cellular immune defenses against infected cells. With or without the help of antibodies, cytotoxic defensive cells can destroy an infected cell that displays viral proteins on its surface. Finally, free gpl20 may circulate in the blood of individuals infected with HIV-1. The free protein may bind to the CD4 receptor of uninfected cells, making them appear to be infected and evoking an immune response. Infection with HIV-1 is almost always fatal, and at present there are no cures for HIV-1 infection. Effective vaccines for prevention of HIV-1 infection are not yet available. Because of the danger of reversion or infection, live attenuated virus probably cannot be used as a vaccine. Most subunit vaccine approaches have not been successful at preventing HIV infection. Treatments for HIV-1 infection, while prolonging the lives of some infected persons, have serious side effects. There is thus a great need for effective treatments and vaccines to combat this lethal infection.
  • Vaccination is an effective form of disease prevention and has proven successful against several types of viral infection. Determining ways to present HIV- 1 antigens to the human immune system in order to evoke protective humoral and cellular immunity, is a difficult task. To date, attempts to generate an effective HIV vaccine have not been successful. In AIDS patients, free virus is present in low levels only. Transmission of HIV-1 is enhanced by cell-to-cell interaction via fusion and syncytia formation. Hence, antibodies generated against free virus or viral subunits are generally ineffective in eliminating virus-infected cells.
  • Vaccines exploit the body's ability to "remember" an antigen. After first encounters with a given antigen the immune system generates cells that retain an immunological memory of the antigen for an individual's lifetime. Subsequent exposure to the antigen stimulates the immune response and results in elimination or inactivation of the pathogen.
  • the immune system deals with pathogens in two ways: by humoral and by cell-mediated responses.
  • lymphocytes generate specific antibodies that bind to the antigen thus inactivating the pathogen.
  • the cell-mediated response involves cytotoxic and helper T lymphocytes that specifically attack and destroy infected cells.
  • Vaccine development with HIV-1 virus presents problems because HIV-1 infects some of the same cells the vaccine needs to activate in the immune system (i.e., T4 lymphocytes). It would be advantageous to develop a vaccine which inactivates HIV before impairment of the immune system occurs.
  • a particularly suitable type of HIV vaccine would generate an anti-HIV immune response which recognizes HIV variants and which works in HIV-positive individuals who are at the beginning of their infection.
  • CTLs cytotoxic T-lymphocytes
  • the viral peptides are derived from endogenously synthesized viral proteins, regardless of the protein's location or function within the virus. Thus, by recognition of epitopes from conserved viral proteins, CTLs may provide cross-strain protection. Peptides capable of associating with MHC class I for CTL recognition originate from proteins that are present in or pass through the cytoplasm or endoplasmic reticulum. In general, exogenous proteins, which enter the endosomal processing pathway (as in the case of antigens presented by MHC class II molecules), are not effective at generating CD8+ CTL responses.
  • Retroviral vectors have restrictions on the size and structure of polypeptides that can be expressed as fusion proteins while maintaining the ability of the recombinant virus to replicate, and the effectiveness of vectors such as vaccinia for subsequent immunizations may be compromised by immune responses against the vectors themselves. Also, viral vectors and modified pathogens have inherent risks that may hinder their use in humans. Furthermore, the selection of peptide epitopes to be presented is dependent upon the structure of an individual's MHC antigens and, therefore, peptide vaccines may have limited effectiveness due to the diversity of MHC haplotypes in outbred populations.
  • WO 93/17706 describes a method for vaccinating an animal against a virus, wherein carrier particles were coated with a gene construct and the coated particles are accelerated into cells of an animal.
  • HIV essentially the entire genome, minus the long terminal repeats, was proposed to be used. That method represents substantial risks for recipients. It is generally believed that constructs of HIV should contain less than about 50% of the HIV genome to ensure safety of the vaccine; this ensures that enzymatic moieties and viral regulatory proteins, many of which have unknown or poorly understood functions have been eliminated. Thus, a number of problems remain if a useful human HIV vaccine is to emerge from the gene-delivery technology.
  • the instant invention contemplates any of the known methods for introducing polynucleotides into living tissue to induce expression of proteins.
  • this invention provides a novel immunogen for introducing HIV and other proteins into the antigen processing pathway to efficiently generate HIV-specific CTLs and antibodies.
  • the pharmaceutical is effective as a vaccine to induce both cellular and humoral anti-HIV and HIV neutralizing immune responses.
  • the problems noted above are addressed and solved by the provision of polynucleotide immunogens which, when introduced into an animal, direct the efficient expression of HIV proteins and epitopes without the attendant risks associated with those methods.
  • the immune responses thus generated are effective at recognizing HIV, at inhibiting replication of HIV, at identifying and killing cells infected with HIV, and are cross-reactive against many HIV strains.
  • the codon pairings of organisms are highly nonrandom, and differ from organism to organism. This information is used to construct and express altered or synthetic genes having desired levels of translational efficiency, to determine which regions in a genome are protein coding regions, to introduce translational pause sites into heterologous genes, and to ascertain relationship or ancestral origin of nucleotide sequences.
  • the expression of foreign heterologous genes in transformed organisms is now commonplace. A large number of mammalian genes, including, for example, murine and human genes, have been successfully inserted into single celled organisms. Standard techniques in this regard include introduction of the foreign gene to be expressed into a vector such as a plasmid or a phage and utilizing that vector to insert the gene into an organism.
  • the native promoters for such genes are commonly replaced with strong promoters compatible with the host into which the gene is inserted.
  • Protein sequencing machinery permits elucidation of the amino acid sequences of even minute quantities of native protein. From these amino acid sequences, DNA sequences coding for those proteins can be inferred. DNA synthesis is also a rapidly developing art, and synthetic genes corresponding to those inferred DNA sequences can be readily constructed.
  • Many native, active proteins for example, are glycosylated in a manner different from that which occurs when they are expressed in a foreign host. For this reason, eukaryotic hosts such as yeast may be preferred to bacterial hosts for expressing many mammalian genes. The glycosylation problem is the subject of continuing research.
  • the problems related to translational efficiency are believed to be related to codon context effects.
  • the protein coding regions of genes in all organisms are subject to a wide variety of functional constraints, some of which depend on the requirement for encoding a properly functioning protein, as well as appropriate translational start and stop signals.
  • several features of protein coding regions have been discerned which are not readily understood in terms of these constraints. Two important classes of such features are those involving codon usage and codon context. It is known that codon utilization is highly biased and varies considerably between different organisms. Codon usage patterns have been shown to be related to the relative abundance of tRNA isoacceptors. Genes encoding proteins of high versus low abundance show differences in their codon preferences.
  • codon context Apart from the non-random use of codons, considerable evidence has accumulated that codon/anticodon recognition is influenced by sequences outside the codon itself, a phenomenon termed "codon context.” There exists a strong influence of nearby nucleotides on the efficiency of suppression of nonsense codons as well as missense codons. Clearly, the abundance of suppressor activity in natural bacterial populations, as well as the use of "termination" codons to encode selenocysteine and phosphoserine require that termination be context- dependent. Similar context effects have been shown to influence the fidelity of translation, as well as the efficiency of translation initiation.
  • a "triplet" codon of four possible nucleotide bases can exist in 64 variant forms. That these forms provide the message for only 20 different amino acids (as well as transcription initiation and termination) means that some amino acids can be coded for by more than one codon. Indeed, some amino acids have as many as six “redundant", alternative codons while some others have a single, required codon.
  • codons are not at all uniformly present in the endogenous DNA of differing types of cells and there appears to exist a variable natural hierarchy or "preference" for certain codons in certain types of cells.
  • the amino acid leucine is specified by any of six DNA codons including CTA, CTC, CTG, CTT, TTA, and TTG (which correspond, respectively, to the mRNA codons, CUA, CUC, CUG, CUU, UUA and UUG).
  • CTA CTC
  • CTG CTT
  • TTA TTA
  • TTA TTA
  • coli most commonly contains the CTG leucine-specifying codon
  • DNA of yeasts and slime molds most commonly includes a TTA leucine-specifying codon.
  • TTA leucine-specifying codon the DNA of yeasts and slime molds.
  • the likelihood of obtaining high levels of expression of a leucine- rich polypeptide by an E. coli host will depend to some extent on the frequency of codon use. For example, a gene rich in TTA codons will in all probability be poorly expressed in E. coli. whereas a CTG rich gene will probably highly express the polypeptide.
  • yeast cells are the projected transformation host cells for expression of a leucine-rich polypeptide, a preferred codon for use in an inserted DNA would be TTA.
  • codon preference phenomena on recombinant DNA techniques are manifest, and the phenomenon may serve to explain many prior failures to achieve high expression levels of exogenous genes in successfully transformed host organisms-a less "preferred" codon may be repeatedly present in the inserted gene and the host cell machinery for expression may not operate as efficiently.
  • This phenomenon suggests that synthetic genes which have been designed to include a projected host cell's preferred codons provide a preferred form of foreign genetic material for practice of recombinant DNA techniques.
  • the diversity of function that typifies eukaryote cells depends upon the structural differentiation of their membrane boundaries. To generate and maintain these structures, proteins must be transported from their site of synthesis in the endoplasmic reticulum to predetermined destinations throughout the cell. This requires that the trafficking proteins display sorting signals that are recognized by the molecular machinery responsible for route selection located at the access points to the main trafficking pathways. Sorting decisions for most proteins need to be made only once as they traverse their bio synthetic pathways since their final destination, the cellular location at which they perform their function, becomes their permanent residence.
  • Synthetic polynucleotides comprising a DNA sequence encoding a peptide or protein are provided.
  • the DNA sequence of the synthetic polynucleotides comprise codons optimized for expression in a nonhomologous host.
  • the invention is exemplified by synthetic DNA molecules encoding HIV env as well as modifications of HIV env.
  • the codons of the synthetic molecules include the projected host cell's preferred codons.
  • the synthetic molecules provide preferred forms of foreign genetic material.
  • the synthetic molecules may be used as a poly nucleotide vaccine which provides effective immunoprophylaxis against HIV infection through neutralizing antibody and cell-mediated immunity.
  • This invention provides polynucleotides which, when directly introduced into a vertebrate in vivo, including mammals such as primates and humans, induces the expression of encoded proteins within the animal.
  • Figure 1 shows HIV env cassette-based expression strategies.
  • Figure 2 shows DNA vaccine mediated anti-gpl20 responses.
  • Figure 3 shows anti-gpl20 ELISA titers of murine DNA vaccinee sera.
  • Figure 4 shows the relative expression of gpl20 after HIV env PNV cell culture transfection.
  • Figure 5 shows the mean anti-gpl20 ELISA responses following tPA-gpl43/optA vs. optB DNA vaccination.
  • Figure 6 shows the neutralization of HIV by murine DNA vaccinee sera.
  • Figure 7 shows HIV neutralization by sera from murine HIV env DNA vaccinees.
  • Figure 8 is an immunoblot analysis of optimized HIV env DNA constructs.
  • Figure 9 shows anti-gpl20 ELISA responses in rhesus monkeys following final vaccination with gpl40 DNA and o-gpl60 protein.
  • Figure 10 shows SHIV neutralizing antibody responses of rhesus monkeys following final vaccination.
  • Synthetic polynucleotides comprising a DNA sequence encoding a peptide or protein are provided.
  • the DNA sequence of the synthetic polynucleotides comprise codons optimized for expression in a nonhomologous host.
  • the invention is exemplified by synthetic DNA molecules encoding HIV env as well as modifications of HIV env are provided.
  • the codons of the synthetic molecules include the projected host cell's preferred codons.
  • the synthetic molecules provide preferred forms of foreign genetic material.
  • the synthetic molecules may be used as a polynucleotide vaccine which provides immunoprophylaxis against HIV infection through neutralizing antibody and cell-mediated immunity.
  • This invention provides polynucleotides which, when directly introduced into a vertebrate in vivo, including mammals such as primates and humans, induces the expression of encoded proteins within the animal.
  • synthetic DNA molecules encoding HIV env and synthetic DNA molecules encoding modified forms of HIV env are provided.
  • the codons of the synthetic molecules are designed so as to use the codons preferred by the projected host cell.
  • the synthetic molecules of this portion of the invention may be used as a polynucleotide vaccine which provides effective immunoprophylaxis against HIV infection through neutralizing antibody and cell-mediated immunity.
  • the synthetic molecules may be used as an immunogenic composition.
  • This portion of the invention also provides polynucleotides which, when directly introduced into a vertebrate in vivo, including mammals such as primates and humans, induces the expression of encoded proteins within the animal.
  • a polynucleotide is a nucleic acid which contains essential regulatory elements such that upon introduction into a living, vertebrate cell, it is able to direct the cellular machinery to produce translation products encoded by the genes comprising the polynucleotide.
  • the polynucleotide is a polydeoxyribonucleic acid comprising at least one HIV gene operatively linked to a transcriptional promoter.
  • the polynucleotide vaccine (PNV) comprises polyribonucleic acid encoding at least one HIV gene which is amenable to translation by the eukaryotic cellular machinery (ribosomes, tRNAs, and other translation factors).
  • the protein encoded by the polynucleotide is one which does not normally occur in that animal except in pathological conditions, (i.e., a heterologous protein) such as proteins associated with human immunodeficiency vims, (HIV), the etiologic agent of acquired immune deficiency syndrome, (AIDS), the animals' immune system is activated to launch a protective immune response. Because these exogenous proteins are produced by the animals' tissues, the expressed proteins are processed by the major histocompatibility system, MHC, in a fashion analogous to when an actual infection with the related organism (HIV) occurs.
  • MHC major histocompatibility system
  • the instant inventors have prepared nucleic acids which, when introduced into the biological system induce the expression of HIV proteins and epitopes.
  • the induced antibody response is both specific for the expressed HIV protein, and neutralizes HIV.
  • cytotoxic T-lymphocytes which specifically recognize and destroy HIV infected cells are induced.
  • the instant invention provides a method for using a polynucleotide which, upon introduction into mammalian tissue, induces the expression in a single cell, in vivo, of discrete gene products.
  • the instant invention provides a different solution which does not require multiple manipulations of rev dependent HIV genes to obtain rev- independent genes.
  • the rev-independent expression system described herein is useful in its own right and is a system for demonstrating the expression in a single cell m vivo of a single desired gene-product.
  • polynucleotide vaccine a polynucleotide vaccine
  • PNV polynucleotide vaccine
  • a gene encoding an HIV gene product is inco ⁇ orated in an expression vector.
  • the vector contains a transcriptional promoter recognized by an eukaryotic RNA polymerase, and a transcriptional terminator at the end of the HIV gene coding sequence.
  • the promoter is the cytomegalovirus promoter with the intron A sequence (CMV-intA), although those skilled in the art will recognize that any of a number of other known promoters such as the strong immunoglobulin, or other eukaryotic gene promoters may be used.
  • a preferred transcriptional terminator is the bovine growth hormone terminator. The combination of CMVintA-BGH terminator is particularly preferred.
  • an antibiotic resistance marker is also preferably included in the expression vector under transcriptional control of a prokaryotic promoter so that expression of the antibiotic does not occur in eukaryotic cells.
  • Ampicillin resistance genes, neomycin resistance genes and other pharmaceutically acceptable antibiotic resistance markers may be used.
  • the vector it is advantageous for the vector to contain a prokaryotic origin of replication and be of high copy number. A number of commercially available prokaryotic cloning vectors provide these benefits. It is desirable to remove non-essential DNA sequences.
  • the vectors not be able to replicate in eukaryotic cells. This minimizes the risk of integration of polynucleotide vaccine sequences into the recipients' genome.
  • Tissue-specific promoters or enhancers may be used whenever it is desirable to limit expression of the polynucleotide to a particular tissue type.
  • the expression vector pnRSV is used, wherein the Rous Sarcoma Virus (RSV) long terminal repeat (LTR) is used as the promoter.
  • RSV Rous Sarcoma Virus
  • LTR Rous Sarcoma Virus
  • VI a mutated pBR322 vector into which the CMV promoter and the BGH transcriptional terminator were cloned is used.
  • the elements of V 1 and pUC 19 have been combined to produce an expression vector named V1J.
  • an HIV gene such as gpl20, gp41 , gpl60, gag, pol, env, or any other HIV gene which can induce anti-HIV immune responses.
  • the ampicillin resistance gene is removed from VI J and replaced with a neomycin resistance gene, to generate VlJ-neo into different HIV genes have been cloned for use according to this invention.
  • the vector is VlJns, which is the same as VUneo except that a unique Sfil restriction site has been engineered into the single Kpnl site at position 2114 of VlJ-neo.
  • the incidence of Sfil sites in human genomic DNA is very low (approximately 1 site per 100,000 bases).
  • this vector allows careful monitoring for expression vector integration into host DNA, simply by Sfil digestion of extracted genomic DNA.
  • the vector is VI R.
  • This vector is a derivative of VlJns. This vector allows larger inserts to be used, with less concern that undesirable sequences are encoded and optimizes uptake by cells.
  • One embodiment of this invention inco ⁇ orates genes encoding HIV g ⁇ l60, gpl20, gag and other gene products from laboratory adapted strains of HIV such as SF2, IIIB or MN. Those skilled in the art will recognize that the use of genes from HIV-2 strains having analogous function to the genes from HIV-1 would be expected to generate immune responses analogous to those described herein for HIV-1 constructs. The cloning and manipulation methods for obtaining these genes are known to those skilled in the art.
  • genes from virulent, primary field isolates of HIV are inco ⁇ orated in the polynucleotide immunogen. This is accomplished by preparing cDNA copies of the viral genes and then subcloning the individual genes into the polynucleotide immunogen.
  • one of the utilities of the instant invention is to provide a system for in vivo as well as in vitro testing and analysis so that a correlation of HIV sequence diversity with serology of HIV neutralization, as well as other parameters can be made.
  • Inco ⁇ oration of genes from primary isolates of HIV strains provides an immunogen which induces immune responses against clinical isolates of the virus and thus meets a need as yet unmet in the field.
  • the immunogen may be modified to reflect new sequences as necessary.
  • the following convention is followed herein for describing polynucleotide immunogen constructs: "Vector name-HIV strain-gene-additional elements".
  • VUneo-MN- gpl60 a construct wherein the gpl60 gene of the MN strain is cloned into the expression vector VUneo, the name it is given herein is: "VUneo-MN- gpl60".
  • VUneo-MN- gpl60 the name it is given herein is: "VUneo-MN- gpl60”.
  • the additional elements that are added to the construct are described in further detail below.
  • the etiologic strain of the virus changes, the precise gene which is optimal for inco ⁇ oration in the pharmaceutical may be changed.
  • the strain variability is less critical in the immunogen and vaccines of this invention, as compared with the whole virus or subunit polypeptide based vaccines.
  • the pharmaceutical is easily manipulated to insert a new gene, this is an adjustment which is easily made by the standard techniques of molecular biology.
  • promoter refers to a recognition site on a DNA strand to which the RNA polymerase binds.
  • the promoter forms an initiation complex with RNA polymerase to initiate and drive transcriptional activity.
  • the complex can be modified by activating sequences termed “enhancers” or inhibiting sequences termed “silencers.”
  • leader refers to a DNA sequence at the 5' end of a structural gene which is transcribed along with the gene.
  • the leader usually results in the protein having an N -terminal peptide extension sometimes called a pro-sequence.
  • this signal sequence which is generally hydrophobic, directs the protein into endoplasmic reticulum from which it is discharged to the appropriate destination.
  • intron refers to a section of DNA occurring in the middle of a gene which does not code for an amino acid in the gene product.
  • the precursor RNA of the intron is excised and is therefore not transcribed into mRNA nor translated into protein.
  • cassette refers to the sequence of the present invention which contains the nucleic acid sequence which is to be expressed.
  • the cassette is similar in concept to a cassette tape. Each cassette will have its own sequence. Thus by interchanging the cassette the vector will express a different sequence. Because of the restrictions sites at the 5' and 3' ends, the cassette can be easily inserted, removed or replaced with another cassette.
  • the term "3' untranslated region” or “3' UTR” refers to the sequence at the 3' end of a structural gene which is usually transcribed with the gene. This 3' UTR region usually contains the poly A sequence. Although the 3' UTR is transcribed from the DNA it is excised before translation into the protein.
  • Non-Coding Region or “NCR” refers to the region which is contiguous to the 3' UTR region of the structural gene. The NCR region contains a transcriptional termination signal.
  • restriction site refers to a sequence specific cleavage site of restriction endonucleases.
  • vector refers to some means by which DNA fragments can be introduced into a host organism or host tissue. There are various types of vectors including plasmid, bacteriophages and cosmids.
  • the term "effective amount” means sufficient PNV is injected to produce the adequate levels of the polypeptide. One skilled in the art recognizes that this level may vary.
  • the human immunodeficiency virus has a ribonucleic acid (RNA) genome.
  • RNA ribonucleic acid
  • This RNA genome must be reverse transcribed according to methods known in the art in order to produce a cDNA copy for cloning and manipulation according to the methods taught herein.
  • a long terminal repeat which acts as a promoter.
  • gag-pol- env As the major gene products: gag is the group specific antigen; pol is the reverse transcriptase, or polymerase; also encoded by this region, in an alternate reading frame, is the viral protease which is responsible for post-translational processing, for example, of gpl60 into gpl20 and gp41 ; env is the envelope protein; vif is the virion infectivity factor; rev is the regulator of virion protein expression; neg is the negative regulatory factor; vpu is the virion productivity factor "u"; tat is the trans-activator of transcription; vpr is the viral protein r. The function of each of these elements has been described. In one embodiment of this invention, a gene encoding an antigen; pol is the reverse transcriptase, or polymerase; also encoded by this region, in an alternate reading frame, is the viral protease which is responsible for post-translational processing, for example, of gpl60 into gpl20 and g
  • HIV or SrV protein is directly linked to a transcriptional promoter.
  • the env gene encodes a large, membrane bound protein, gpl60, which is post-translationally modified to gp41 and gpl20.
  • the gpl20 gene may be placed under the control of the cytomegalovirus promoter for expression.
  • gpl20 is not membrane bound and therefore, upon expression, it may be secreted from the cell.
  • immune responses directed at cell-bound HIV epitopes also be generated.
  • a vaccine produce membrane bound, oligomeric ENV antigen similar in structure to that produced by viral infection in order to generate the most efficacious antibody responses for viral neutralization.
  • This goal is accomplished herein by expression in vivo of a secreted gpl40 epitope (gpl40 > gpl20 + ectodomain of gp41) or the cell-membrane associated epitope, gpl60, to prime the immune system.
  • expression of gp 160 is repressed in the absence of rev due to non-export from the nucleus of non-spliced genes.
  • HIV RNA genome is reverse-transcribed into a proviral DNA which integrates into host genomic DNA as a single transcriptional unit.
  • the LTR provides the promoter which transcribes HIV genes from the 5' to 3' direction (gag, pol, env), to form an unspliced transcript of the entire genome.
  • the unspliced transcript functions as the mRNA from which gag and pol are translated, while limited splicing must occur for translation of env encoded genes.
  • For the regulatory gene product rev to be expressed more than one splicing event must occur because in the genomic setting, rev and env overlap. In order for transcription of env to occur, rev transcription must stop, and vice versa.
  • rev is required for export of unspliced RNA from the nucleus.
  • a rev responsive element RRE must be present on the transcript [Malim et al., Nature 338:254-257 (1989)].
  • the obligatory splicing of certain HIV genes is eliminated by providing fully spliced genes (i.e.: the provision of a complete open reading frame for the desired gene product without the need for switches in the reading frame or elimination of noncoding regions; those of ordinary skill in the art would recognize that when splicing a particular gene, there is some latitude in the precise sequence that results; however so long as a functional coding sequence is obtained, this is acceptable).
  • the entire coding sequence for gpl60 is spliced such that no intermittent expression of each gene product is required.
  • the dual humoral and cellular immune responses generated according to this invention are particularly significant to inhibiting HIV infection, given the propensity of HIV to mutate within the population, as well as in infected individuals.
  • an effective protective vaccine for HIV it is desirable to generate both a multivalent antibody response for example to gpl60 (env is approximately 80% conserved across various HIV-1 , clade B strains, which are the prevalent strains in US human populations), the principal neutralization target on HIV, as well as cytotoxic T cells reactive to the conserved portions of gpl60 and, internal viral proteins encoded by gag.
  • HIV vaccine comprising gpl60 genes selected from common laboratory strains; from predominant, primary viral isolates found within the infected population; from mutated gpl60s designed to unmask cross- strain, neutralizing antibody epitopes; and from other representative HIV genes such as the gag and pol genes (-95% conserved across HIV isolates.
  • Mice also provide the most facile animal model suitable for testing CTL induction by our constructs and are therefore used to evaluate whether a particular construct is able to generate such activity.
  • Monkeys African green, rhesus, chimpanzees
  • Monkeys provide additional species including primates for antibody evaluation in larger, non-rodent animals. These species are also preferred to mice for antisera neutralization assays due to high levels of endogenous neutralizing activities against retroviruses observed in mouse sera.
  • gp 160 and gpl20 An ELISA assay is used to determine whether vaccine vectors expressing either secreted gpl20 or membrane-bound gpl60 are efficacious for production of env-specific antibodies.
  • Initial in vitro characterization of env expression by our vaccination vectors is provided by immunoblot analysis of gpl60 transfected cell lysates. These data confirm and quantitate gpl60 expression using anti-gp41 and anti-gpl20 monoclonal antibodies to visualize transfectant cell gpl60 expression.
  • gp 160 is preferred to gp 120 for the following reasons: (1) an initial gpl20 vector gave inconsistent immunogenicity in mice and was very poorly or non-responsive in African green Monkeys; (2) gpl60 contributes additional neutralizing antibody as well as CTL epitopes by providing the addition of approximately 190 amino acid residues due to the inclusion of gp41; (3) gpl60 expression is more similar to viral env with respect to tetramer assembly and overall conformation, which may provide oligomer-dependent neutralization epitopes; and (4) we find that, like the success of membrane-bound, influenza HA constructs for producing neutralizing antibody responses in mice, ferrets, and nonhuman primates [see Ulmer et al., Science 259:1745-1749, 1993; Montgomery, D., et al., DNA and Cell Biol. 12:777-783, 1993] anti-gpl60 antibody generation is superior to anti- gpl20 antibody generation. Selection of which type of en
  • Antibodies to this domain are polyclonal and more broadly cross-neutralizing probably due to restraints on mutations imposed by the need for the virus to bind its cellular ligand.
  • An in vitro assay is used to test for blocking gpl20 binding to CD4 immobilized on 96 well plates by sera from immunized animals.
  • a second in vitro assay detects direct antibody binding to synthetic peptides representing selected V3 domains immobilized on plastic. These assays are compatible for antisera from any of the animal types used in our studies and define the types of neutralizing antibodies our vaccines have generated as well as provide an in vitro correlate to virus neutralization. b.
  • gp41 harbors at least one major neutralization determinant, corresponding to the highly conserved linear epitope recognized by the broadly neutralizing 2F5 monoclonal antibody (commercially available from Viral Testing Systems Co ⁇ ., Texas Commerce Tower, 600 Travis Street, Suite 4750, Houston, TX 77002- 3005(USA), or Waldheim Pharmazeutika GmbH, Boltzmangasse 1 1, A- 1091 Wien, Austria), as well as other potential sites including the well- conserved "fusion peptide" domain located at the N-terminus of gp41.
  • an m vitro assay test is used for antibodies which bind to synthetic peptides representing these domains immobilized on plastic.
  • the neutralizing antibody responses progress from chiefly anti-V3 to include more broadly neutralizing antibodies comprising the structural gpl20 domain epitopes described above (#3), including gp41 epitopes. These types of antibody responses are monitored over the course of both time and subsequent vaccinations.
  • syngeneic tumor lines such as the murine mastocytoma P815, transfected with these genes to provide targets for CTL as well as for in vitro antigen specific restimulation.
  • Methods for defining immunogens capable of eliciting MHC class I- restricted cytotoxic T lymphocytes are known [see Calin-Laurens, et al., Vaccine 1 1(91:974-978, 1993; see particularly Eriksson, et al., Vaccine ⁇ (8):859-865, 1993, wherein T-cell activating epitopes on the HIV gpl20 were mapped in primates and several regions, including gpl20 amino acids 142-192, 296-343, 367-400, and 410-453 were each found to induce lymphoproliferation; furthermore, discrete regions 248-269 and 270-295 were lymphoproliferative.
  • a peptide encompassing amino acids 152-176 was also found to induce HIV neutralizing antibodies], and these methods may be used to identify immunogenic epitopes for inclusion in the PNV of this invention.
  • the entire gene encoding gpl60, gpl20, protease, or gag could be used.
  • Shirai et al. J. Immunol 148:1657-1667, 1992; Choppin et al.. J. Immunol 147:569-574. 1991; Choppin et al., J. Immunol 147:575-583, 1991 ; Berzofsky et al., L
  • T-cell effector function is associated with mature T-cell phenotype, for example, cytotoxicity, cytokine secretion for B-cell activation, and/or recruitment or stimulation of macrophages and neutrophils.
  • TH Activities Spleen cell cultures derived from vaccinated animals are tested for recall to specific antigens by addition of either recombinant protein or peptide epitopes. Activation of T cells by such antigens, presented by accompanying splenic antigen presenting cells, APCs, is monitored by proliferation of these cultures or by cytokine production. The pattern of cytokine production also allows classification of TH response as type 1 or type 2. Because dominant TH2 responses appear to correlate with the exclusion of cellular immunity in immunocompromised seropositive patients, it is possible to define the type of response engendered by a given PNV in patients, permitting manipulation of the resulting immune responses.
  • DTH Delayed Type Hypersensitivitv
  • This model allows testing of the human lymphocyte immune system and our vaccine with subsequent HIV challenge in a mouse host.
  • This system is advantageous as it is easily adapted to use with any HIV strain and it provides evidence of protection against multiple strains of primary field isolates of HIV.
  • a third challenge model utilizes hybrid HIV/SI V viruses (SHrV), some of which have been shown to infect rhesus monkeys and lead to immunodeficiency disease resulting in death [see Li, J., et al.. J. AIDS 5:639-646. 1992].
  • Vaccination of rhesus with our polynucleotide vaccine constructs is protective against subsequent challenge with lethal doses of SHIV.
  • HIV and other genes are ligated into an expression vector which has been optimized for polynucleotide vaccinations. Essentially all extraneous DNA is removed, leaving the essential elements of transcriptional promoter, immunogenic epitopes, transcriptional terminator, bacterial origin of replication and antibiotic resistance gene. Expression of HIV late genes such as env and gag is rev- dependent and requires that the rev response element (RRE) be present on the viral gene transcript.
  • RRE rev response element
  • a secreted form of gpl20 can be generated in the absence of rev by substitution of the gpl20 leader peptide with a heterologous leader such as from tPA (tissue-type plasminogen activator), and preferably by a leader peptide such as is found in highly expressed mammalian proteins such as immunoglobulin leader peptides.
  • tPA tissue-type plasminogen activator
  • a leader peptide such as is found in highly expressed mammalian proteins such as immunoglobulin leader peptides.
  • RD transfected cells
  • Monocistronic gpl60 does not produce any protein upon transfection without the addition of a rev expression vector.
  • Construct Components include (but are not restricted to): 1. tPA-gpl20MN; 2. gpl60HIB;
  • gaglim for anti-g ⁇ g CTL
  • tPA-gpl40 6. tPA-gp 160 with structural mutations: VI , V2, and/or V3 loop deletions or substitutions
  • antigens expressed by pathogens other than HIV such as, but not limited to, influenza virus nucleoprotein, hemagglutinin, matrix, neuraminidase, and other antigenic proteins; he ⁇ es simplex virus genes; human papillomavirus genes; tuberculosis antigens; hepatitis A, B, or C vims antigens.
  • the protective efficacy of polynucleotide HIV immunogens against subsequent viral challenge is demonstrated by immunization with the non-replicating plasmid DNA of this invention. This is advantageous since no infectious agent is involved, assembly of virus particles is not required, and determinant selection is permitted. Furthermore, because the sequence of gag and protease and several of the other viral gene products is conserved among various strains of HIV, protection against subsequent challenge by a virulent strain of HIV that is homologous to, as well as strains heterologous to the strain from which the cloned gene is obtained, is enabled. The i.m. injection of a DNA expression vector encoding gpl60 results in the generation of significant protective immunity against subsequent viral challenge.
  • gp 160-specific antibodies and primary CTLs are produced. Immune responses directed against conserved proteins can be effective despite the antigenic shift and drift of the variable envelope proteins. Because each of the HIV gene products exhibit some degree of conservation, and because CTL are generated in response to intracellular expression and MHC processing, it is predictable that many virus genes give rise to responses analogous to that achieved for gpl60. Thus, many of these genes have been cloned, as shown by the cloned and sequenced junctions in the expression vector (see below) such that these constructs are immunogenic agents in available form.
  • the invention offers a means to induce cross -strain protective immunity without the need for self-replicating agents or adjuvants.
  • immunization with the instant polynucleotides offers a number of other advantages.
  • This approach to vaccination should be applicable to tumors as well as infectious agents, since the CD8+ CTL response is important for both pathophysiological processes [K. Tanaka et al, Annu. Rev. Immunol. 6, 359 (1988)]. Therefore, eliciting an immune response against a protein crucial to the transformation process may be an effective means of cancer protection or immunotherapy.
  • DNA constructs compares favorably with traditional methods of protein purification, thus facilitating the generation of combination vaccines. Accordingly, multiple constructs, for example encoding gpl60, gpl20, gp41, or any other HIV gene may be prepared, mixed and co-administered. Because protein expression is maintained following DNA injection, the persistence of B- and T-cell memory may be enhanced, thereby engendering long-lived humoral and cell-mediated immunity.
  • Standard techniques of molecular biology for preparing and purifying DNA constructs enable the preparation of the DNA immunogens of this invention. While standard techniques of molecular biology are therefore sufficient for the production of the products of this invention, the specific constructs disclosed herein provide novel polynucleotide immunogens which su ⁇ risingly produce cross-strain and primary HIV isolate neutralization, a result heretofore unattainable with standard inactivated whole virus or subunit protein vaccines.
  • the amount of expressible DNA or transcribed RNA to be introduced into a vaccine recipient will depend on the strength of the transcriptional and translational promoters used and on the immunogenicity of the expressed gene product.
  • an immunologically or prophylactically effective dose of about 1 ng to 100 mg, and preferably about 10 ⁇ g to 300 ⁇ g is administered directly into muscle tissue.
  • Subcutaneous injection, intradermal introduction, impression through the skin, and other modes of administration such as intraperitoneal, intravenous, or inhalation delivery are also contemplated.
  • booster vaccinations are to be provided.
  • boosting with HIV protein immunogens such as gpl60, gpl20, and gag gene products is also contemplated.
  • Parenteral administration such as intravenous, intramuscular, subcutaneous or other means of administration of interleukin-12 protein or GM-CSF or similar proteins alone or in combination, concurrently with or subsequent to parenteral introduction of the PNV of this invention is also advantageous.
  • the polynucleotide may be naked, that is, unassociated with any proteins, adjuvants or other agents which impact on the recipients' immune system.
  • the DNA may be associated with liposomes, such as lecithin liposomes or other liposomes known in the art, as a DNA-liposome mixture, or the DNA may be associated with an adjuvant known in the art to boost immune responses, such as a protein or other carrier.
  • Agents which assist in the cellular uptake of DNA such as, but not limited to, calcium ions, may also be used to advantage. These agents are generally referred to herein as transfection facilitating reagents and pharmaceutically acceptable carriers. Techniques for coating microprojectiles coated with polynucleotide are known in the art and are also useful in connection with this invention.
  • Vectors pF411 and pF412 were subcloned from vector pSP62 which was constructed in R. Gallo's lab.
  • pSP62 is an available reagent from Biotech Research Laboratories, Inc.
  • pSP62 has a 12.5 kb Xbal fragment of the HXB2 genome subcloned from lambda HXB2. Sail and Xba I digestion of pSP62 yields to HXB2 fragments: 5'-XbaI/SalI, 6.5 kb and 3'- Sall/Xbal, 6 kb.
  • pF411 (5'- Xbal/Sall) and pF412 (3'-XbaI/SalI).
  • pF41 1 contains gaglpol and pF412 contains tat/re v/e/zv/nef.
  • Repligen reagents recombinant rev (IIIB), #RP1024-10 rec. gpl20 (IIIB), #RP1001-10 anti-rev monoclonal antibody, #RP1029-10 anti-gpl20 mAB, #1C1, #RP1010-10
  • the strategies are designed to induce both cytotoxic T lymphocyte (CTL) and neutralizing antibody responses to HIV, principally directed at the HIV gag ( ⁇ 95% conserved) and env (gpl60 or gpl20; 70-80% conserved) gene products.
  • CTL cytotoxic T lymphocyte
  • gpl60 contains the only known neutralizing antibody epitopes on the HrV particle while the importance of anti-env and anti-gag CTL responses are highlighted by the known association of the onset of these cellular immunities with clearance of primary viremia following infection, which occurs prior to the appearance of neutralizing antibodies, as well as a role for CTL in maintaining disease-free status.
  • HIV structural genes such as env and gag require expression of the HIV regulatory gene, rev, in order to efficiently produce full-length proteins.
  • rev-dependent expression of gag yielded low levels of protein and that rev itself may be toxic to cells.
  • this vaccine elicited low levels of antibodies to gpl60 following in vivo immunization with rev/gpl60 DNA. This may result from known cytotoxic effects of rev as well as increased difficulty in obtaining rev function in myotubules containing hundreds of nuclei (rev protein needs to be in the same nucleus as a rev- dependent transcript for gag or env protein expression to occur).
  • rev protein needs to be in the same nucleus as a rev- dependent transcript for gag or env protein expression to occur.
  • VlJns which is comprised of a CMV immediate- early (IE) promoter, BGH polyadenylation site, and a pUC backbone.
  • IE immediate- early
  • tPA tissue-specific plasminogen activator
  • VUns-tPA-gpl60 and VUns-rev/gpl60 were prepared.
  • the tPA-gp!60 vector produced detectable quantities of gpl60 and gpl20, without the addition of rev, as shown by immunoblot analysis of transfected cells, although levels of expression were much lower than that obtained for rev/gpl60, a rev-dependent gpl60-expressing plasmid.
  • inhibitory regions which confer rev dependence upon the gpl60 transcript, occur at multiple sites within gpl60 including at the COOH- terminus of gp41 (see Figure 1 for schematic view of gpl43 construct strategies).
  • a vector was prepared for a COOH-terminally truncated form of tPA-gpl60, tPA-gpl43, which was designed to increase the overall expression levels of env by elimination of these inhibitory sequences.
  • the gpl43 vector also eliminates intracellular gp41 regions containing peptide motifs (such as leu-leu) known to cause diversion of membrane proteins to the lysosomes rather than the cell surface.
  • gpl43 may be expected to increase both expression of the env protein (by decreasing rev-dependence) and the efficiency of transport of protein to the cell surface compared to full-length gpl60 where these proteins may be better able to elicit anti-gpl60 antibodies following DNA vaccination.
  • tPA-gpl43 was further modified by extensive silent mutagenesis of the rev response element (RRE) sequence (350 bp) to eliminate additional inhibitory sequences for expression.
  • RRE rev response element
  • This constmct, gpl43/mutRRE was prepared in two forms: either eliminating (form A) or retaining (form B) proteolytic cleavage sites for gp 120/41. Both forms were prepared because of literature reports that vaccination of mice using uncleavable gpl60 expressed in vaccinia elicited much higher levels of antibodies to gpl60 than did cleavable forms.
  • tPA-gpl20 vector derived from a primary HIV isolate (containing the North American consensus V3 peptide loop; macrophage-tropic and nonsyncytia-inducing phenotypes). This vector gave high expression/secretion of gpl20 with transfected 293 cells and elicited anti-gpl20 antibodies in mice demonstrating that it was cloned in a functional form.
  • Primary isolate gpl60 genes will also be used for expression in the same way as for gpl60 derived from laboratory strains.
  • African green (AGM) and Rhesus (RHM) monkeys which received gpl20 DNA vaccines showed low levels of neutralizing antibodies following 2-3 vaccinations, which could not be increased by additional vaccination.
  • gpl20 DNA vaccination produced potent helper T cell responses in all lymphatic compartments tested (spleen, blood, inguinal, mesenteric, and iliac nodes) with THl-like cytokine secretion profiles (i.e., g-interferon and IL-2 production with little or no IL-4).
  • cytokines generally promote strong cellular immunity and have been associated with maintenance of a disease-free state for HIV-seropositive patients.
  • Lymph nodes have been shown to be primary sites for HIV replication, harboring large reservoirs of virus even when virus cannot be readily detected in the blood.
  • a vaccine which can elicit anti-HIV immune responses at a variety of lymph sites may help prevent successful colonization of the lymphatics following initial infection.
  • the amp 1* gene from the pUC backbone of VIJ was removed by digestion with Sspl and Eaml 1051 restriction enzymes.
  • the remaining plasmid was purified by agarose gel electrophoresis, blunt-ended with T4 DNA polymerase, and then treated with calf intestinal alkaline phosphatase.
  • VUneo #'s 1 and 3 plasmids with the kan r gene in either orientation were derived which were designated as VUneo #'s 1 and 3.
  • VUneo #'s 1 and 3 plasmids with the kan r gene in either orientation were derived which were designated as VUneo #'s 1 and 3.
  • Each of these plasmids was confirmed by restriction enzyme digestion analysis, DNA sequencing of the junction regions, and was shown to produce similar quantities of plasmid as VIJ. Expression of heterologous gene products was also comparable to VIJ for these VUneo vectors.
  • VUneo#3 referred to as VUneo hereafter (SEQ ID: 1), which contains the kan r gene in the same orientation as the amp r gene in VIJ as the expression constmct.
  • VlJns Expression Vector An Sfi I site was added to VUneo to facilitate integration studies. A commercially available 13 base pair Sfi I linker (New England BioLabs) was added at the Kpn I site within the BGH sequence of the vector. VUneo was linearized with Kpn I, gel purified, blunted by T4 DNA polymerase, and ligated to the blunt Sfi I linker. Clonal isolates were chosen by restriction mapping and verified by sequencing through the linker. The new vector was designated VlJns. Expression of heterologous genes in VlJns (with Sfi I) was comparable to expression of the same genes in VUneo (with Kpn I).
  • VlJn was modified to include the human tissue-specific plasminogen activator (tPA) leader.
  • tPA tissue-specific plasminogen activator
  • the sense and antisense oligomers were 5'-GATC ACC ATG GAT GCA ATG AAG AGA GGG CTC TGC TGT GTG CTG CTG CTG TGT GGA GCA GTC TTC GTT TCG CCC AGC GA-3' (SEQ.TD:2), and 5'-GAT CTC GCT GGG CGA AAC GAA GAC TGC TCC ACA CAG CAG CAG CAC ACA GCA GAG CCC TCT CTT CAT TGC ATC CAT GGT-3' (SEQ. ID:3).
  • the Kozak sequence is underlined in the sense oligomer. These oligomers have overhanging bases compatible for ligation to Bglll-cleaved sequences.
  • Vaccines Producing Secreted ewv-derived Antigen (gp!20 and gp!40): Expression of the rev -dependent env gene as gpl20 was conducted as follows: gpl20 was PCR-cloned from the MN strain of HIV with either the native leader peptide sequence (VUns-gpl20), or as a fusion with the tissue-plasminogen activator (tPA) leader peptide replacing the native leader peptide (VUns-tPA-gpl20). tPA-gpl20 expression has been shown to be rev-independent [B.S. Chapman et al., Nuc. Acids Res. 19, 3979 (1991); it should be noted that other leader sequences would provide a similar function in rendering the gpl20 gene rev independent]. This was accomplished by preparing the following gpl20 constructs utilizing the above described vectors.
  • HIVMN gpl20 gene (Medimmune) was PCR amplified using oligomers designed to remove the first 30 amino acids of the peptide leader sequence and to facilitate cloning into VUns-tPA creating a chimeric protein consisting of the tPA leader peptide followed by the remaining gpl20 sequence following amino acid residue 30.
  • This design allows for rev -independent gpl20 expression and secretion of soluble gpl20 from cells harboring this plasmid.
  • the sense and antisense PCR oligomers used were 5'-CCC CGG ATC CTG ATC ACA GAA AAA TTG TGGGTC ACA GTC-3' (SEQ.
  • oligomers contain BamHI restriction enzyme sites at either end of the translation open reading frame with a Bell site located 3' to the BamHI of the sense oligomer.
  • the PCR product was sequentially digested with Bell followed by BamHI and ligated into VUns-tPA which had been Bglll digested followed by calf intestinal alkaline phosphatase treatment.
  • the resulting vector was sequenced to confirm in-frame fusion between the tPA leader and gpl20 coding sequence, and gpl20 expression and secretion was verified by immunoblot analysis of transfected RB cells.
  • VUns-tPA-HrVjTTB gp!20 This vector is analogous to I. A. except that the HIV HUB strain was used for gpl20 sequence.
  • the sense and antisense PCR oligomers used were: 5'-GGT ACA TGA TCA CA GAA AAA TTG TGG GTC ACA GTC-3' (SEQ.ID:6), and 5'-CCA CAT TGA TCA GAT ATC TTA TCT TTT TTC TCT CTG CAC CAC TCT TC-3' (SEQ.ID:7), respectively.
  • These oligomers provide Bell sites at either end of the insert as well as an EcoRV just upstream of the Bell site at the 3'-end.
  • the 5'-terminal Bell site allows ligation into the Bglll site of VUns-tPA to create a chimeric tPA-gpl20 gene encoding the tPA leader sequence and gpl20 without its native leader sequence. Ligation products were verified by restriction digestion and DNA sequencing.
  • gpl40 constructs should produce oligomeric antigen and retain known gp41 -contained antibody neutralization epitopes such as ELDKWA (SEQ.ID:53) defined by the 2F5 monoclonal antibody.
  • VUns-tPA-gpl40/mutRRE-A/SRV-l 3'-UTR (based on HIV- lIIIBl: This constmct was obtained by PCR using the following sense and antisense PCR oligomers: 5'-CT GAA AGA CCA GCA ACT CCT AGG GAAT TTG GGG TTG CTC TGG-3' (SEQ.ID: 11 ) :, and 5 - CGC AGG GGA GGT GGT CTA GAT ATC TTA TTA TTT TAT ATA CCA CAG CCA ATT TGT TAT G-3' (SEQ ID: 12) to obtain an Avrll/EcoRV segment from vector IVB (containing the optimized RRE- A segment).
  • the 3'-UTR prepared as a synthetic gene segment, that is derived from the Simian Retrovirus-1 (SRV-1 , see below) was inserted into an Srfl restriction enzyme site introduced immediately 3'- of the gpl40 open reading frame. This UTR sequence has been described previously as facilitating rev-independent expression of HIV env and gag.
  • VUns-tPA-gpl40/mutRRE-B/SRV-l 3'-UTR (based on HIV- 1IIIB): This construct is similar to IIA except that the env proteolytic cleavage sites have been retained by using constmct IVC as starting material.
  • VUns-tPA-gpl40/opt30-A (based on HIV-I TTJR): This construct was derived from IVB by Avrll and Srfl restriction enzyme digestion followed by ligation of a synthetic DNA segment corresponding to gp30 but comprised of optimal codons for translation (see gp32-opt below).
  • the gp30-opt DNA was obtained from gp32-opt by PCR amplification using the following sense and anti- sense oligomers: 5'-GGT ACA CCT AGG CAT CTG GGG CTG CTC TGG-3 * , (SEQ ID: 13) and, 5'-CCA CAT GAT ATC G CCC GGG C TTA TTA TTT GAT GTA CCA CAG CCA GTT GGT GAT G-3', (SEQ ID: 14), respectively.
  • This DNA segment was digested with Avrll and EcoRV restriction enzymes and ligated into VUns-tPA- gpl43/opt32-A (IVD) that had been digested with Avrll and Srfl to remove the corresponding DNA segment.
  • IVD VUns-tPA- gpl43/opt32-A
  • This construct is similar to IIC except that the env proteolytic cleavage sites have been retained.
  • the env gene of this construct is comprised completely of optimal codons.
  • the constant regions (Cl , C5, gp32) are those described in IVB,D,H with an additional synthetic DNA segment corresponding to variable regions 1 -5 is inserted using a synthetic DNA segment comprised of optimal codons for translation (see example below based on HIV-1 MN VI -V5).
  • This constmct is similar to HE except that the env proteolytic cleavage sites have been retained.
  • This constmct is similar to ITE above except that env amino acid sequences from strains other than IIIB are used to determine optimum codon usage throughout the variable (V1-V5) regions.
  • Constructs were prepared in two forms (A or B) depending upon whether the gpl60 proteolytic cleavage sites as described above.
  • This vector is a variation of the one described in section D above except that the entire tat coding region in exon 1 is deleted up to the beginning of the rev open reading frame.
  • VUns-gpl60lHB (see section A. above) was digested with Pstl and Kpnl restriction enzymes to remove the 5'-region of the gpl60 gene. PCR amplification was used to obtain a DNA segment encoding the first REV exon up to the Kpnl site in gpl60 from the HXB2 genomic clone.
  • the sense and antisense PCR oligomers were 5'-GGT ACA CTG CAG TCA CCG TCC T ATG GCA GGA AGA AGC GGA GAC-3' (SEQ.ID: 15) and 5'-CCA CAT CA GGT ACC CCA TAA TAG ACT GTG ACC-3" (SEQ.ID:16) respectively. These oligomers provide Pstl and Kpnl restriction enzyme sites at the 5'- and 3'- termini of the DNA fragment, respectively.
  • the resulting DNA was digested with Pstl and Kpnl, purified from an agarose electrophoretic gel, and ligated with VUns- gpl60(PstI/KpnI). The resulting plasmid was verified by restriction enzyme digestion.
  • VUns-gpl60 HlVi ⁇ b gpl60 was cloned by PCR amplification from plasmid pF412 which contains the 3'-terminal half of the HIVi ⁇ b genome derived from HIV ⁇ ib clone HXB2.
  • the PCR sense and antisense oligomers were 5'-GGT ACA TGA TCA ACC ATG AGA GTG AAG GAG AAA TAT CAG C-3' (SEQ. ID:17), and 5'-CCA CAT TGA TCA GAT ATC CCC ATC TTA TAG CAA AAT CCT TTC C-3' (SEQ. ID: 18), respectively.
  • the Kozak sequence and translation stop codon are underlined.
  • oligomers provide Bell restriction enzyme sites outside of the translation open reading frame at both ends of the env gene.
  • Bell was chosen for PCR-cloning gpl60 because this gene contains internal Bglll and as well as BamHI sites).
  • the antisense oligomer also inserts an EcoRV site just prior to the Bell site as described above for other PCR-derived genes.
  • the amplified gpl60 gene was agarose gel-purified, digested with Bell, and ligated to VlJns which had been digested with Bgi ⁇ and treated with calf intestinal alkaline phosphatase.
  • the cloned gene was about 2.6 kb in size and each junction of gp!60 with VlJns was confirmed by DNA sequencing.
  • This vector is similar to Example 1 (C) above, except that the full-length gpl60, without the native leader sequence, was obtained by PCR.
  • the sense oligomer was the same as used in I.C. and the antisense oligomer was 5 * -CCA CAT TGA TCA GAT ATC CCC ATC TTA TAG CAA AAT CCT TTC C-3' (SEQ.ID: 19). These oligomers provide Bell sites at either end of the insert as well as an EcoRV just upstream of the Bell site at the 3'-end.
  • the 5'-terminal Bell site allows ligation into the Bglll site of VUns-tPA to create a chimeric tPA-gpl60 gene encoding the tPA leader sequence and gpl60 without its native leader sequence. Ligation products were verified by restriction digestion and DNA sequencing.
  • VUns-tPA-gpl60/opt Cl/opt41 -A (based on HIV-lTTTB): This constmct was based on IVH, having a complete optimized codon segment for C5 and gp41 , rather than gp32, with an additional optimized codon segment (see below) replacing Cl at the amino terminus of gpl20 following the tPA leader.
  • the new Cl segment was joined to the remaining gpl43 segment via SOE PCR using the following oligomers for PCR to synthesize the joined C 1/143 segment: 5 -CCT GTG TGT GAG TTT AAA C TGC ACT GAT TTG AAG AAT GAT ACT AAT AC-3' (SEQ ID:20).
  • the resulting gpl43 gene contains optimal codon usage except for V 1 - V5 regions and has a unique Pmel restriction enzyme site placed at the junction of Cl and VI for insertion of variable regions from other HIV genes.
  • VUns-tPA-gpl60/opt Cl/opt41-B (based on HIV-IJT ⁇ R): This constmct is similar to HID except that the env proteolytic cleavage sites have been retained.
  • the env gene of this construct is comprised completely of optimal codons as described above.
  • the constant regions (Cl , C5, gp32) are those described in IIID,E which is used as a cassette
  • variable regions, VI -V5 are derived from a synthetic DNA segment comprised of optimal codons.
  • This constmct is similar to IIIF except that the env proteolytic cleavage sites have been retained.
  • This constmct was designed with the pu ⁇ ose of combining the increased expression of env accompanying tPA introduction and minimizing the possibility that a transcript or peptide region corresponding to the intracellular portion of env might negatively impact expression or protein stability/transport to the cell surface.
  • Constmcts were prepared in two forms (A or B) depending upon whether the gp 160 proteolytic cleavage sites were removed or retained as described above.
  • the residual gp41 fragment resulting from tmncation to gpl43 is referred to as gp32.
  • This constmct was prepared by PCR using plasmid pF412 with the following sense and antisense PCR oligomers: 5'-GGT ACA TGA TCA CA GAA AAA TTG TGG GTC ACA GTC-3' (SEQ.ID:21):, and 5'- CCA CAT TGA TCA G CCC GGG C TTA GGG TGA ATA GCC CTG CCT CAC TCT GTT CAC-3' (SEQ.ID:22).
  • the resulting DNA segment contains Bell restriction sites at either end for cloning into VUns-tPA/Bglll-digested with an Srfl site located immediately 3'- to the env open reading frame. Constmcts were verified by DNA sequencing of ligation junctions and immunoblot analysis of transfected cells (Figure 8).
  • V 1 Jns-tP A-gp 143/mutRRE- A V 1 Jns-tP A-gp 143/mutRRE- A :
  • This constmct was based on IVA by excising the DNA segment using the unique Muni restriction enzyme site and the downstream Srfl site described above.
  • This segment corresponds to a portion of the gpl20 C5 domain and the entirety of gp32.
  • RRE A rev response element
  • PCR reactions were performed using the following sense and antisense PCR oligomers for generating the gp32-containing domain: 5'-CT GAA AGA CCA GCA ACT CCT AGG GAT TTG GGG TTG CTG TGG-3' (SEQ ID:23) and 5'-CCA CAT TGA TCA G CCC GGG C TTA GGG TGA ATA GCC CTG CCT CAC TCT GTT CAC-3' [SEQ ID:24] (which was used as the antisense oligomer for IVA), respectively.
  • the mutated RRE (mutRRE-A) segment was joined to the wild type sequence of gp32 by SOE PCR using the following sense oligomer, 5'-GGT ACA CAA TTG GAG GAG CGA GTT ATA TAA ATA TAA G-3' (SEQ ID:25), and the antisense oligomer used to make the gp32 segment.
  • the resulting joined DNA segment was digested with Muni and Srfl restriction enzymes and ligated into the parent gpl43/MunI/SrfI digested plasmid. The resulting constmct was verified by DNA sequencing of ligation and SOE PCR junctions and immunoblot analysis of transfected cells (Figure 8).
  • V 1 Jns-tPA-gp 143/mutRRE-B V 1 Jns-tPA-gp 143/mutRRE-B :
  • This constmct is similar to IVB except that the env proteolytic cleavage sites have been retained by using the mutRRE-B synthetic gene segment in place of mutRRE-A.
  • This constmct is similar to IVD except that the env proteolytic cleavage sites have been retained by using IVC as the initial plasmid.
  • This constmct is similar to IVA except that the 3'-UTR derived from the Simian Retrovims-1 (SRV-1 , see below) was inserted into the Srfl restriction enzyme site introduced immediately 3'- of the gpl43 open reading frame.
  • This UTR sequence has been described previously as facilitating rev-independent expression of HIV env and gag-
  • VI Jns-tPA-gp 143/opt Cl/opt32A This constmct was based on IVD, having a complete optimized codon segment for C5 and gp32 with an additional optimized codon segment (see below) replacing Cl at the amino terminus of gpl20 following the tPA leader.
  • the new Cl segment was joined to the remaining gpl43 segment via SOE PCR using the following oligomers for PCR to synthesize the joined Cl/143 segment: 5'-CCT GTG TGT GAG TTT AAA C TGC ACT GAT TTG AAG AAT GAT ACT AAT AC-3' (SEQ ID:26).
  • the resulting gpl43 gene contains optimal codon useage except for VI -V5 regions and has a unique Pmel restriction enzyme site placed at the junction of Cl and VI for insertion of variable regions from other HIV genes.
  • the env gene of this constmct is comprised completely of optimal codons.
  • the constant regions (Cl , C5, gp32) are those described in 4B,D,H with an additional synthetic DNA segment corresponding to variable regions VI -V5 is inserted using a synthetic DNA segment comprised of optimal codons for translation.
  • constmcts were prepared by PCR similarly as other tPA-containing constmcts described above (tPA-gpl20, tPA-gpl40, tPA-gpl43 and tPA-gpl60), with the tPA leader in place of the native leader, but designed to produce COOH -terminated, membrane -bound env as with gpl43.
  • V 1 Jns-tPA-gp 143/opt32- A/glvB
  • This constmct is the same as IVD except that the following antisense PCR oligomer was used to replace the intracellular peptide domain of gpl43 with that of glycophorin B as described above: 5'- CCA CAT GAT ATC G CCC GGG C TTA TTA GGC CTT GAT CAG CCG GTT CAC AAT GGA CAG CAC AGC-3' (SEQ ID:28).
  • VUns-tPA-gpl43/opt32-B/glvB This constmct is similar to VA except that the env proteolytic cleavage sites have been retained.
  • This constmct is the same as VA except that the first constant region (Cl) of gpl20 is replaced by optimal codons for translation as with IVH.
  • This constmct is similar to VC except that the env proteolytic cleavage sites have been retained.
  • This constmct is similar to VE except that the env proteolytic cleavage sites have been retained.
  • This constmct is similar to VG except that the env proteolytic cleavage sites have been retained.
  • HIV env Vaccine Constmcts with Variable Loop Deletions HIV env Vaccine Constmcts with Variable Loop Deletions:
  • constmcts may include all env forms listed above (gpl20, gpl40, gpl43, gpl60, gpl43/glyB) but have had variable loops within the gpl20 region deleted during preparation (e.g., VI , V2, and/or V3).
  • the pu ⁇ ose of these modifications is to eliminate peptide segments which may occlude exposure of conserved neutralization epitopes such as the CD4 binding site.
  • oligomer was used in a PCR reaction to create a V1/V2 deletion resulting in adjoining THE Cl and C2 segments: 5'-CTG ACC CCC CTG TGT GTG GGG GCT GGC AGT TGT AAC ACC TCA GTC ATT ACA CAG-3' (SEQ ID:29).
  • EXAMPLE 1 1 Design of Synthetic Gene Segments for Increased env Gene Expression: Gene segments were converted to sequences having identical translated sequences (except where noted) but with altemative codon usage as defined by R. Lathe in a research article from J. Molec. Biol. Vol. 183, pp. 1-12 (1985) entitled "Synthetic Oligonucleotide Probes Deduced from Amino Acid Sequence Data: Theoretical and Practical Considerations". The methodology described below to increase rev-independent expression of HIV env gene segments was based on our hypothesis that the known inability to express this gene efficiently in mammalian cells is a consequence of the overall transcript composition.
  • gp120-C1 This is a gpl20 constant region 1 (Cl) gene segment from the mature N-terminus to the beginning of V 1 designed to have optimal codon usage for expression.
  • the "A” form also has removed the known proteolytic cleavage sites at the gpl20/gp41 junction by using the nucleotides indicated in boldface.
  • the "B” form retains the known proteolytic cleavage sites at the gpl20/gp41 junction.
  • This synthetic gene segment is identical to SRV-1 CTE (A) shown above except that a single nucleotide mutation was used (indicated by boldface) to eliminate an ATTTA sequence. This sequence has been associated with increased mRNA turnover.
  • VI Jns-tPA-gp 120MN PNV-induced Class II MHC- restricted T lymphocyte gp!20 specific antigen reactivities.
  • Balb/c mice which had been vaccinated two times with 200 ⁇ g VI Jns-tPA-gp 120MN were sacrificed and their spleens extracted for in vitro determinations of helper T lymphocyte reactivities to recombinant gpl20.
  • T cell proliferation assays were performed with PBMC (peripheral blood mononuclear cells) using recombinant gpl20lHB (Repligen, catalogue #RP1016-20) at 5 ⁇ g/ml with 4 x 10 5 cells/ml.
  • Basal levels of 3 H- thymidine uptake by these cells were obtained by culturing the cells in media alone, while maximum proliferation was induced using ConA stimulation at 2 ⁇ g/ml.
  • ConA-induced reactivities peak at -3 days and were harvested at that time point with media control samples while antigen-treated samples were harvested at 5 days with an additional media control.
  • Vaccinated mice responses were compared with naive, age-matched syngeneic mice. ConA positive controls gave very high proliferation for both naive and immunized mice as expected.
  • constmcts for full-length, membrane-bound gpl60.
  • the rationales for a gpl60 constmct, in addition to gpl20, are (1) more epitopes are available both for both CTL stimulation as well as neutralizing antibody production including gp41, against which a potent HIV neutralizing monoclonal antibody (2F5, see above) is directed; (2) a more native protein stmcture may be obtained relative to virus- produced gpl60; and, (3) the success of membrane-bound influenza HA constmcts for immunogenicity [Ulmer et al., Science 259: 1745-1749.
  • gpl60 retains substantial rev dependence even with a heterologous leader peptide sequence so that further constmcts were made to increase expression in the absence of rev.
  • mice The methods described in this section illustrate the assay as used for vaccinated mice.
  • An essentially similar assay can be used with primates except that autologous B cell lines must be established for use as target cells for each animal. This can be accomplished for humans using the Epstein-Barr vims and for rhesus monkey using the he ⁇ es B virus.
  • PBMC Peripheral blood mononuclear cells
  • IL-2 20 U/ml
  • concanavalin A 2 ⁇ g/ml
  • Specific antigen can consist of either synthetic peptides (9-15 amino acids usually) that are known epitopes for CTL recognition for the MHC haplotype of the animals used, or vaccinia vims constmcts engineered to express appropriate antigen.
  • Target cells may be either syngeneic or MHC haplotype-matched cell lines which have been treated to present appropriate antigen as described for in vitro stimulation of the CTLs.
  • Antigen-sensitized target cells are loaded with Na ⁇ 1 Cr ⁇ 4, which is released from the interior of the target cells upon killing by CTL, by incubation of targets for 1-2 hours at 37°C (0.2 mCi for -5 x 106 cells) followed by several washings of the target cells.
  • CTL populations are mixed with target cells at varying ratios of effectors to targets such as 100:1 , 50:1, 25:1, etc., pelleted together, and incubated 4-6 hours at 37°C before harvest of the supematants which are then assayed for release of radioactivity using a gamma counter. Cytotoxicity is calculated as a percentage of total releasable counts from the target cells (obtained using 0.2% Triton X-100 treatment) from which spontaneous release from target cells has been subtracted.
  • ELISA ELISA were designed to detect antibodies generated against HIV using either specific recombinant protein or synthetic peptides as substrate antigens.
  • 96 well microtiter plates were coated at 4°C overnight with recombinant antigen at 2 ⁇ g/ml in PBS (phosphate buffered saline) solution using 50 ⁇ l/well on a rocking platform.
  • PBS phosphate buffered saline
  • Antigens consisted of either recombinant protein (gpl20, rev: Repligen Co ⁇ .; gpl60, gp41 : American Bio-Technologies, Inc.) or synthetic peptide (V3 peptide corresponding to vims isolate sequences from IIIB, etc.: American Bio-Technologies, Inc.; gp41 epitope for monoclonal antibody 2F5). Plates were rinsed four times using wash buffer (PBS/0.05% Tween 20) followed by addition of 200 ⁇ l/well of blocking buffer (1 % Carnation milk solution in PBS/0.05% Tween-20) for 1 hr at room temperature with rocking.
  • wash buffer PBS/0.05% Tween 20
  • blocking buffer 1 % Carnation milk solution in PBS/0.05% Tween-20
  • Pre-sera and immune sera were diluted in blocking buffer at the desired range of dilutions and 100 ⁇ l added per well. Plates were incubated for 1 hr at room temperature with rocking and then washed four times with wash buffer. Secondary antibodies conjugated with horse radish peroxidase, (anti-rhesus Ig, Southern Biotechnology Associates; anti- mouse and anti-rabbit Igs,
  • o-PD o-phenylenediamine
  • HIV viral genes were cloned from infected PBMC's which had been activated by ConA treatment.
  • the preferred method for obtaining the viral genes was by PCR amplification from infected cellular genome using specific oligomers flanking the desired genes.
  • a second method for obtaining viral genes was by purification of viral RNA from the supematants of infected cells and preparing cDNA from this material with subsequent PCR. This method was very analogous to that described above for cloning of the murine B7 gene except for the PCR oligomers used and random hexamers used to make cDNA rather than specific priming oligomers.
  • Genomic DNA was purified from infected cell pellets by lysis in STE solution (10 mM NaCl, 10 mM EDTA, 10 mM Tris-HCl, pH 8.0) to which Proteinase K and SDS were added to 0.1 mg/ml and 0.5% final concentrations, respectively. This mixture was incubated overnight at 56°C and extracted with 0.5 volumes of phenol :chloroform:isoamyl alcohol (25:24:1). The aqueous phase was then precipitated by addition of sodium acetate to 0.3 M final concentration and two volumes of cold ethanol.
  • PCR was performed using the Perkin-Elmer Cetus kit and procedure using the following sense and antisense oligomers for gpl60: 5'-GA AAG AGC AGA AGA CAG TGG CAA TGA -3' (SEQ.ID:38) and 5'-GGG CTT TGC TAA ATG GGT GGC AAG TGG CCC GGG C ATG TGG-3' (SEQ.LD:39), respectively.
  • These oligomers add an Srfl site at the 3'-terminus of the resulting DNA fragment.
  • PCR-derived segments are cloned into either the VlJns or VI R vaccination vectors and V3 regions as well as ligation junction sites confirmed by DNA sequencing.
  • EXAMPLE 17 T Cell Proliferation Assays PBMCs are obtained and tested for recall responses to specific antigen as determined by proliferation within the PBMC population. Proliferation is monitored using - ⁇ H-thymidine which is added to the cell cultures for the last 18-24 hours of incubation before harvest. Cell harvesters retain isotope-containing DNA on filters if proliferation has occurred while quiescent cells do not inco ⁇ orate the isotope which is not retained on the filter in free form. For either rodent or primate species 4 X 10 ⁇ cells are plated in 96 well microtiter plates in a total of 200 ⁇ l of complete media (RPMI/10% fetal calf semm).
  • Background proliferation responses are determined using PBMCs and media alone while nonspecific responses are generated by using lectins such as phytohaemagglutin (PHA) or concanavalin A (ConA) at 1- 5 ⁇ g/ml concentrations to serve as a positive control.
  • PHA phytohaemagglutin
  • ConA concanavalin A
  • Specific antigen consists of either known peptide epitopes, purified protein, or inactivated vims. Antigen concentrations range from 1 - 10 ⁇ M for peptides and 1-10 ⁇ g/ml for protein.
  • Lectin-induced proliferation peaks at 3-5 days of cell culture incubation while antigen- specific responses peak at 5-7 days. Specific proliferation occurs when radiation counts are obtained which are at least three-fold over the media background and is often given as a ratio to background, or
  • HIV gpl60 is known to contain several peptides known to cause T cell proliferation of gpl60/gpl20 immunized or HIV- infected individuals. The most commonly used of these are: Tl (LysGlnllelleAsnMetT ⁇ GlnGluValGlyLysAlaMetTyrAla [SEQ.LD:40]); T2 (HisGluAspIlelleSerLeuT ⁇ AspGlnSerLeuLys
  • V1R a derivative of VlJns which was designated as V1R.
  • the pu ⁇ ose for this vector constmction was to obtain a minimum-sized vaccine vector, i.e., without unnecessary DNA sequences, which still retained the overall optimized heterologous gene expression characteristics and high plasmid yields that VIJ and VlJns afford.
  • coli origin of replication could be removed without affecting plasmid yield from bacteria; (2) the 3'-region of the kan ⁇ gene following the kanamycin open reading frame could be removed if a bacterial terminator was inserted in its stead; and, (3) -300 bp from the 3'- half of the BGH terminator could be removed without affecting its regulatory function (following the original Kpnl restriction enzyme site within the BGH element).
  • V1R was constmcted by using PCR to synthesize three segments of DNA from VlJns representing the CMVintA promoter/BGH terminator, origin of replication, and kanamycin resistance elements, respectively. Restriction enzymes unique for each segment were added to each segment end using the PCR oligomers: Sspl and Xhol for CMVintA/BGH; EcoRV and BamHI for the kan r gene; and, Bell and Sail for the ori r .
  • Ligation junctions were sequenced for VI R using the following oligomers:
  • HIV structural genes such as env and gag require expression of the HIV regulatory gene, rev, in order to efficiently produce full-length proteins.
  • rev the HIV regulatory gene
  • rev-dependent expression of gag yielded low levels of protein and that rev itself may be toxic to cells.
  • this vaccine elicited low levels of antibodies to gpl60 following in vivo immunization with rev/gpl60 DNA. This may result from known cytotoxic effects of rev as well as increased difficulty in obtaining rev function in myotubules containing hundreds of nuclei (rev protein needs to be in the same nucleus as a rev- dependent transcript in order for gag or env protein expression to occur).
  • rev-independent expression using selected modifications of the env gene.
  • VlJns which is comprised of a CMV immediate- early (IE) promoter, a BGH-derived polyadenylation and transcriptional termination sequence, and a pUC backbone.
  • IE immediate- early
  • tPA tissue-specific plasminogen activator
  • VUns-tPA-gpl60 and VUns- rev/gpl60 were prepared.
  • the tPA-gpl60 vector produced detectable quantities of gpl60 and gpl20, without the addition of rev, as shown by immunoblot analysis of transfected cells, although levels of expression were much lower than that obtained for rev/gpl60, a rev-dependent gpl60- expressing plasmid.
  • tPA- gpl43 COOH-terminally tmncated form of tPA-gp 160
  • the gpl43 vector also eliminates intracellular gp41 regions containing peptide motifs (such as Leu-Leu) known to cause diversion of membrane proteins to the lysosomes rather than the cell surface.
  • gp 143 may be expected to have increased levels of expression of the env protein (by decreasing rev-dependence) and greater efficiency of transport of protein to the cell surface compared to full-length gpl60 where these proteins may be better able to elicit anti-gpl60 antibodies following DNA vaccination.
  • tPA-gpl43 was further modified by extensive silent mutagenesis of the rev response element (RRE) sequence (350 bp) to eliminate additional inhibitory sequences for expression.
  • RRE rev response element
  • This constmct, gpl43/mutRRE was prepared in two forms: either eliminating (form A) or retaining (form B) proteolytic cleavage sites for gpl20/41. Both forms were prepared because of literature reports that vaccination of mice using uncleavable gpl60 expressed in vaccinia elicited much higher levels of antibodies to gpl60 than did cleavable forms.
  • tPA-gpl43 gave 3-6X greater secretion of gpl20 than rev/gpl60 with only low levels of cell-associated gpl43, confirming that the cytoplasmic tail of gpl60 causes intracellular retention of gpl60 which can be overcome by partial deletion of this sequence; and, (3) tPA-gpl43/mutRRE A and B gave -10X greater expression levels of protein than did parental tPA-gpl43 while elimination of proteolytic processing was confirmed for form A.
  • Figures 2-7 present data supporting the use of various constmcts, including but not limited to a gp 143 -based constmct, and preferably a tPA-gpl43 based constmct, as a DNA vaccine against HIV infection.
  • Figure 3 measures and compares anti-gpl20 antibody titers for several DNA vaccines, including gpl43-based constmcts.
  • Figure 4 shows the relative expression of tPA-gpl43 and tPA-143/mutRRE in comparison to the tPA-gpl60 constmct.
  • Figure 5 measures generation of anti-gpl20 antibodies for both the optA and optB forms of tPA-gpl43 constmcts.
  • Figure 6 shows the ability of several DNA vaccines, including tPA- gpl43-optA and tPA-gpl43-optB, to promote generation of neutralizing antibodies against HIV strains subsequent to murine DNA vaccination.
  • Figure 7 also shows HIV neutralization data for various DNA vaccine constmctions, including tPA-gpl43-optA, tPA-gpl43-optB, tPA-gpl43- optA-glyB and tPA-gpl43-optB-glyB.
  • tPA-gpl20 vector derived from a primary HIV isolate (containing the North American concensus V3 peptide loop; macrophage-tropic and nonsyncytia-inducing phenotypes). This vector gave high expression/secretion of gpl20 with transfected 293 cells and elicited anti-gpl20 antibodies in mice thus demonstrating that it was cloned in a functional form.
  • Primary isolate gpl60 genes will also be used for expression in the same way as for gpl60 derived from laboratory strains. 3. Immune Responses to HIV-1 env Polynucleotide Vaccines
  • helper T-cell responses as determined by antigen-specific in vitro proliferation and cytokine secretion, were higher following i.m. vaccination than i.d. We concluded that i.d. vaccination did not offer any advantages compared to i.m. for this vaccine.
  • gp!20 DNA vaccine-mediated helper T cell immunity in mice gpl20 DNA vaccination produced potent helper T-cell responses in all lymphatic compartments tested (spleen, blood, inguinal, mesenteric, and iliac nodes) with THl-like cytokine secretion profiles (i.e., g-interferon and IL-2 production with little or no IL-4). These cytokines generally promote strong cellular immunity and have been associated with maintenance of a disease-free state for HIV-seropositive patients. Lymph nodes have been shown to be primary sites for HIV replication, harboring large reservoirs of vims even when vims cannot be readily detected in the blood. A vaccine which can elicit anti-HIV immune responses at a variety of lymph sites, such as we have shown with our DNA vaccine, may help prevent successful colonization of the lymphatics following initial infection.
  • African green (AGM) and Rhesus (RHM) monkeys which received gpl20 DNA vaccines showed low levels of neutralizing antibodies following 2-3 vaccinations, which could not be increased by additional vaccination. These results, as well as increasing awareness within the HIV vaccine field that oligomeric gpl60 is probably a more relevant target antigen for eliciting neutralizing antibodies than gpl20 monomers, have led us to focus upon obtaining effective expression of gpl60-based vectors (see above). Mice and AGM were also vaccinated with the primary isolate derived tPA-gpl20 vaccine.
  • SIV simian immunodeficiency vims
  • HIV-1 viral isolates the only animal species which can be infected with HIV-1 viral isolates is the chimpanzee.
  • the resulting viremia from this infection is low-level, transient, and no pathogenic effects (e.g., lymphopenia, immunodeficiency-related opportunistic infections, etc.) develop.
  • vimses comprised of SIV and HIV genomes which are also infectious to rhesus monkeys and which can cause infection-related AIDS.
  • An example of this type of vims is SHIV-4 (IIIB) (Li et al., J. of Acquired Immune Deficiency Syndrome, Vol. 5, 639-646 (1992)).
  • This vims contains the SIV (MAC239) genome except for the regulatory genes, tat and rev, and the structural gene, env. Because the principle component of candidate HIV vaccines is based upon env this vims allows testing vaccines developed for human clinical pu ⁇ oses for protective efficacy against infection in an animal model.
  • Vaccines having both a plasmid DNA HIV env component and a recombinant HIV env protein component were tested for their abilities to induce antibody responses in rhesus monkeys.
  • Figure 9 and Figure 10 show the resulting anti-gpl20 ELISA antibody and SHIV-4 (IIIB) vims neutralizing antibody titers, respectively, following vaccination of rhesus with HIV env gene-containing DNA vaccines and recombinant protein (formulated in an appropriate adjuvant). These monkeys developed high titers of env-specific antibodies and neutralizing antibodies.
  • CTCCGCCCCA TTGACGCAAA TGGGCGGTAG GCGTGTACGG TGGGAGGTCT ATATAAGCAG 900
  • CTGCAGTCAC CGTCCTTAGA TCTGCTGTGC CTTCTAGTTG CCAGCCATCT GTTGTTTGCC 1920
  • ATATTTTCAC CTGAATCAGG ATATTCTTCT AATACCTGGA ATGCTGTTTT CCCGGGGATC 4260
  • MOLECULE TYPE DNA (genomic)
  • xi SEQUENCE DESCRIPTION: SEQ ID NO:30:
  • MOLECULE TYPE DNA (genomic)
  • AACTCCAACT CCGAGGGCAC CATCAAGGGG GGGGAGATGA
  • AAGACCATCA TCGTGCACCT GAATGAGTCT GTGCAGATCA ACTGCACCAG GCCCAACTAC 540 AACAAGAGGA AGAGGATCCA CATTGGCCCT GGCAGGGCCT TCTACACCAC CAAGAACATC 600
  • MOLECULE TYPE DNA (genomic) (Xl) SEQUENCE DESCRIPTION: SEQ ID NO:32:
  • MOLECULE TYPE DNA (genomic)
  • CTCCCCCTAA TAAGCCCGGG CGATATC 387
  • MOLECULE TYPE DNA (genomic)
  • GGCTCATGTC CAACATTACC GCCATGTTGA CATTGATTAT TGACTAGTTA TTAATAGTAA 120
  • GTAACTCCCG TTGCGGTGCT GTTAACGGTG GAGGGCAGTG TAGTCTGAGC AGTACTCGTT 1560

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Abstract

L'invention concerne des polynucléotides de synthèse comprenant une séquence d'ADN codant un peptide ou une protéine. La séquence d'ADN des polypeptides de synthèse comprend des codons optimisés pour une expression chez un hôte non homologue. L'invention est illustrées par des molécules d'ADN de synthèse codant env du VIH ainsi que des modifications d'env du VIH. Les codons des molécules de synthèse comprennent les codons préférés des cellules hôtes prévues. Les molécules de synthèse fournissent des formes préférées de matériel génétique étranger. On peut utiliser les molécules de synthèse en tant que vaccins polynucléotidiques procurant une immunoprophylaxie contre une infection à VIH par un anticorps neutralisant et une immunité à médiation cellulaire. Cette invention présente des polynucléotides qui, lorsqu'ils sont introduits directement dans un vertébré in vivo, notamment des mammifères primates et des sujets humains, induisent l'expression de protéines codées chez l'animal.
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US6316253B1 (en) 1999-11-01 2001-11-13 Chiron Corporation Expression vectors, transfection systems, and method of use thereof
WO2002036791A3 (fr) * 2000-10-30 2003-07-24 Geneart Gmbh Systeme reporteur d'exporation de noyau
WO2002098443A3 (fr) * 2001-06-05 2003-11-13 Curevac Gmbh Composition pharmaceutique contenant un arnm stabilise et optimise pour la traduction dans ses regions codantes
WO2003059381A3 (fr) * 2002-01-18 2004-01-22 Curevac Gmbh Préparations immunogènes et vaccins à base d'arn
US6733993B2 (en) 2000-09-15 2004-05-11 Merck & Co., Inc. Enhanced first generation adenovirus vaccines expressing codon optimized HIV1-gag, pol, nef and modifications
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EP1927598A1 (fr) 2000-06-10 2008-06-04 GlaxoSmithKline Biologicals SA Vaccin
US7901690B2 (en) 2002-12-03 2011-03-08 University Of Massachusetts Polyvalent, primary HIV-1 glycoprotein DNA vaccines and vaccination methods
US7943375B2 (en) 1998-12-31 2011-05-17 Novartis Vaccines & Diagnostics, Inc Polynucleotides encoding antigenic HIV type C polypeptides, polypeptides and uses thereof
US8217016B2 (en) 2001-12-19 2012-07-10 Curevac Gmbh Application of mRNA for use as a therapeutic agent for tumorous diseases
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AU728422B2 (en) 2001-01-11
JP2000516445A (ja) 2000-12-12

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