US20060275897A1 - HIV vaccines based on Env of multiple clades of HIV - Google Patents

HIV vaccines based on Env of multiple clades of HIV Download PDF

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US20060275897A1
US20060275897A1 US11/376,484 US37648406A US2006275897A1 US 20060275897 A1 US20060275897 A1 US 20060275897A1 US 37648406 A US37648406 A US 37648406A US 2006275897 A1 US2006275897 A1 US 2006275897A1
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env
clade
hiv
gag
pol
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Gary Nabel
Bimal Chakrabarti
Wing-pui Kong
Yue Huang
Zengguang Wang
Zhi-Yong Yang
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DEPARTMENT OF HEALTH AND HUMAN SERVICES GOVERNMENT OF United States, AS REPRESENTED BY SECRETARY
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DEPARTMENT OF HEALTH AND HUMAN SERVICES GOVERNMENT OF United States, AS REPRESENTED BY SECRETARY
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Priority to US11/376,484 priority Critical patent/US20060275897A1/en
Assigned to DEPARTMENT OF HEALTH AND HUMAN SERVICES, THE GOVERNMENT OF THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY reassignment DEPARTMENT OF HEALTH AND HUMAN SERVICES, THE GOVERNMENT OF THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CHAKRABARTI, BIMAL, KONG, WING-PUI, YANG, ZHI-YONG, NABEL, GARY J., HUANG, YUE
Publication of US20060275897A1 publication Critical patent/US20060275897A1/en
Priority to US11/818,113 priority patent/US7666427B2/en
Priority to US12/683,844 priority patent/US7947822B2/en
Priority to US13/086,884 priority patent/US8323961B2/en
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    • A61K39/00—Medicinal preparations containing antigens or antibodies
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    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/525—Virus
    • A61K2039/5256—Virus expressing foreign proteins
    • A—HUMAN NECESSITIES
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    • A61K39/00—Medicinal preparations containing antigens or antibodies
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    • A61K2039/53—DNA (RNA) vaccination
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    • C12N2710/10011—Adenoviridae
    • C12N2710/10311—Mastadenovirus, e.g. human or simian adenoviruses
    • C12N2710/10341—Use of virus, viral particle or viral elements as a vector
    • C12N2710/10343—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
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    • C12N2740/16111—Human Immunodeficiency Virus, HIV concerning HIV env
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    • C12N2740/16011—Human Immunodeficiency Virus, HIV
    • C12N2740/16111—Human Immunodeficiency Virus, HIV concerning HIV env
    • C12N2740/16134—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
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    • C12N2740/16211—Human Immunodeficiency Virus, HIV concerning HIV gagpol
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    • C12N2740/10011—Retroviridae
    • C12N2740/16011—Human Immunodeficiency Virus, HIV
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    • C12N2740/16234—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Definitions

  • This invention is related to the field of vaccines against HIV.
  • HIV Human Immunodeficiency Virus
  • the invention provides a multiclade HIV plasmid DNA or viral vector vaccine including components from different clades of Env (optionally Env chimeras) and Gag-Pol-(optionally)Nef from a single clade.
  • the vaccine of the invention may further include V1, V2, V3, or V4 deletions or combinations thereof.
  • the invention provides a multiclade HIV envelope immunogen.
  • FIG. 1 Schematic representation of HIV Env vectors with V3 region replacements.
  • A The CXCR4-tropic HIV HXB2, a clade B gp140 ⁇ CFI, was made as described previously (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-5368). Most divergent region including the V3 regions, from HIV HXB2 was replaced by the similar region of HIV BaL to make R5 tropic clade B HIV HXB/BaL.
  • the gp140 ⁇ CFI of both clade A and clade C were also made as described in the Materials and Methods (see PART I).
  • B. Expression of the indicated vectors was confirmed by transfection in 293 cells and Western blot analysis. The Env was detected by Western blot with polyclonal antibody against gp160 (Intracel, Rockville, Md.) at a dilution of 1:3000.
  • FIG. 2 Induction of neutralizing antibodies by chimeric Env with V3 region substitutions.
  • A Neutralizing antibody activity from guinea pigs immunized with HIV HXB2/BaL gp140 ⁇ CFI. Immune sera were tested for their ability to inhibit HIV IIIB (open bars) and HIV MN (filled bars). The neutralizing antibody titer is defined as the dilution of sera yielding 50% virus neutralization in the MT2 assay killing (Montefiori, D. C. et al. 1988 J Clin Microbiol 26:231-5).
  • B The same sera shown in FIG. 2A were tested against HIV BaL. The data represent the % neutralization of the HIV BaL by these sera at 1:4 dilution.
  • FIG. 3 Titer and specificity of neutralizing antibodies generated in guinea pigs after immunization with gp145/140 ⁇ CFI Envs.
  • A V3-specific neutralization of HIV BaL was measured in peripheral blood mononuclear cells (PBMC) using serum samples that were pre-incubated in the presence and absence of different V3 peptides as described previously (Bures, R. et al. 2000 AIDS Res Hum Retroviruses 16:2019-35). Sera were tested at 1:5 dilution in the PBMC assay.
  • PBMC peripheral blood mononuclear cells
  • V3 peptide-specific neutralizing activity induced by gp145/140 ⁇ CFI of HIV BAL was detected by a reduction in the titer of HIV MN-specific neutralizing antibodies in the presence of either HIV IIIB or HIV BAL V3 peptides compared to the untreated control.
  • Assays were performed in MT2 cells as described in Materials and Methods section of PART I (Montefiori, D. C. et al. 1988 J Clin Microbiol 26:231-5). The dashed line corresponds to a 50% cut-off considered positive for neutralization.
  • FIG. 4 Schematic representation and expression of different 2F5/V3 mutations in HIV HXB/BaL ⁇ CFI Envs.
  • A Schematic representation of gp145 ⁇ CFI derived from clade B HIV HXB/BaL with 2F5 epitopes expressed in V3. Functional domains and major structural motifs are indicated, as previously described (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-5368).
  • V1, V2, V3, and V4 refer to the respective variable regions, and the sequences of the relevant V3 loops are shown.
  • Heptad repeat-2 (HR-2), the coiled-coil peptide sequence upstream of the transmembrane domain in R5/clade B envelope, was replaced by the similar region from the clade C Env.
  • the nucleotide sequence corresponding to the amino acids at the tip of V3 (GPGRA, SEQ ID NO: 12) was replaced by nucleotide sequences corresponding to the polypeptide containing either the minimal 2F5 epitope or by nucleotide sequences corresponding to the polypeptide containing the extended 2F5 epitope.
  • CTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHC (SEQ ID NO: 1); CTRPNNNTRKAIHIFYTTGEIIGDIRQAHC (SEQ ID NO: 2); LELDKWAS (SEQ ID NO: 3); KNEQELLELDKWAS (SEQ ID NO: 4); KNEKDLLALDSWRN (SEQ ID NO: 5).
  • FIG. 5 Antibody response to 2F5 peptide in immunized guinea pigs. Comparison of the antibody response by ELISA in guinea pigs immunized with designated expression vectors. Sera collected 2 weeks after DNA (A.) and ADV boosting (B.) were used to detect the antibody that could bind with 2F5 peptide. Serum from an animal immunized with the control vector alone served as a negative control.
  • C Percent neutralization of the 2F5/V3 mutants in HIV HXB/BaL ⁇ CFI Envs is shown against a panel of HIV-1 clade B strains at 1:5 antibody titer. Four individual sera from 2F5/V3 mutants immunized guinea pigs were screened against HIV BaL, HIV IIIB, and HIV SF162 viruses. Percent neutralization (compared with corresponding pre-immune sera) is indicated.
  • FIG. 6 Interaction of gp140 ⁇ CFI with different monoclonal antibodies or CD4 of gp140 ⁇ CFI from different clades.
  • A Analysis of the antigenic structure of soluble gp140 ⁇ CFI with monoclonal antibodies. Env glycoproteins from the supernatants of 293 cells transfected with the indicated vector expressing gp140 ⁇ CFI were immunoprecipitated with either monoclonal antibodies (5 ⁇ g) 2F5, 2G12, F105, and IgG1b12 or with 5 ⁇ g of HIV-1 IgG. The proteins were analyzed by SDS-PAGE and detected by Western blotting using the IgG from the pooled sera of the patient (HIV-1 IgG).
  • FIG. 7 Comparison of breadth and potency of the neutralizing antibody response induced by ⁇ CFI envelope from clade B (HXB/BaL) and from a combination of clades A, B, and C.
  • A, B Neutralization assays of indicated viruses at a 1:5 dilution of four individual guinea pig sera. The percent neutralization was calculated by direct comparison of immune sera to the corresponding animals pre-immune sera. The single-round intracellular p24-antigen flow cytometric HIV-1 neutralization assay has been described previously (Mascola, J. R. et al. 2002 J Virol 76:4810-21).
  • Panel A shows the results from four guinea pigs immunized with the clade B Env immunogen.
  • C V3 peptide competition analysis of the neutralization of clade B HIV 89.6 and BR07.
  • Panel D shows sera from two representative guinea pigs; one immunized with the clade B Env immunogen (monoclade) and one immunized with the clade A, B, C Env immunogen (multiclade). Sera were tested at a 1:5 dilution and incubated with increasing concentrations of the 23mer V3 peptide based on the HIV BaL sequence. Note that neutralization by the monoclade sera, but not the multiclade sera, was completely inhibited by the HIV BaL V3 peptide. The control values show that the scrambled V3 peptide had no effect on serum neutralization.
  • the bar graph E displays data from neutralization of the HIV SF162 by the same multiclade guinea pig serum, also at a 1:5 dilution.
  • the serum was incubated with 20 ⁇ g/ml of either the clade A, B or C V3 peptide, or with 60 ⁇ g/ml of a combination of all three peptides (panel E).
  • a combination of all three V3 peptides did not reverse the majority of the serum-mediated neutralization of SF162.
  • Error bars are the mean ( ⁇ SEM) of two independent experiments. Both experiments shown in panel C were done with a single serum, but all four sera in each group (monoclade or multiclade) gave similar results.
  • FIG. 8 Comparison of immune response of multivalent multi-plasmids with single gene approaches.
  • Four groups of mice with 5 mice per group were immunized with the control vector alone (50 ⁇ g), Env (25 ⁇ g) with control vector (25 ⁇ g) as filler DNA, Gag-Pol-Nef (25 ⁇ g) with control vector (25 ⁇ g) as filler DNA, or Env (25 ⁇ g) with Gag-Pol-Nef (25 ⁇ g).
  • FIG. 8A mouse sera were collected to detect antibody against Env using ELISA.
  • ELISA plates were prepared and coated as described in Materials and Methods section of PART II with supernatant from cells transfected with pVRC2801 (R5 gp140 ⁇ CFI-Clade-B) from Clade B. Mouse sera from different groups were diluted starting from 1:100 to 1:2700 before testing.
  • the ELISA titers are shown for the group immunized with pVR1012 ( ⁇ ), with pVR1012-B-Gag-Pol-Nef and filler DNA ( ⁇ ),with pVR1012-B-gp145 ⁇ CFI and filler DNA( ⁇ ), or with 1012-B-gp145 ⁇ CFI+1012-B-Gag-Pol-Nef ( ⁇ ). Each point represents the average OD reading from the five animals per group.
  • FIG. 9 T cell and antibody responses in mice immunized Gag-Pol-Nef and clade B Env compared to Gag-Pol-Nef and clade A, B, C Env proteins.
  • A Ten days after the final immunization, splenic cells were harvested and sensitized with a B-Env peptide pool (158 peptide pool of Clade B Env protein).
  • Ebola glycoprotein peptide pool 22 peptides
  • unstimulated cells served as a negative controls
  • PMA was used as the positive control.
  • the cells were fixed, stained with monoclonal antibodies, and analyzed by FACS to detect the IFN- ⁇ and TNF- ⁇ positive cells in the CD4 (left panel) and CD8 (right panel) positive populations.
  • the symbols depict the individual results for the ten mice in each group.
  • the thin horizontal bar represents the average of the ten data points with a standard deviation error bar.
  • Sera from the three groups of animals were collected 10 days after the third immunization, and ELISA was performed to detect the antibody against the respective clade Env's as described in Materials and Methods section of PART II.
  • Mouse sera from different groups were diluted from 1:200 to 1:800 for testing. Each bar represents the average OD reading from the three mice per group.
  • FIG. 10 CD8+ T cell responses to different clade and gene combination vaccine candidates by intracellular cytokine analysis.
  • Three groups of mice were immunized with a control vector (VR1012), ABC ( ⁇ 4) or ABC ( ⁇ 6) as described in Table 1.
  • Ten days after the final immunization splenic cells were harvested and sensitized with the following peptide pools: A-Gag (125 peptides), B-Gag (122 peptides), C-Gag (105 peptides), A-Env (154 peptides), B-Env (158 peptides), C-Env (154 peptides), B-Pol-1 (120 peptides from the first half of Clade B Pol), or B-Pol-2 (128 peptides from the second half of clade B Pol).
  • FIG. 11 CD4+ T cell and antibody responses to combination gene and clade vaccine candidates by intracellular flow cytometry and ELISA.
  • Three groups of mice were immunized with the indicated control or combination vaccines as shown in Table 1.
  • (A) Ten days after the final immunization, splenic cells were harvested and sensitized with the indicated peptide pools as described in the legend to FIG. 9 . Individual responses are shown with the symbols, and the thin horizontal bar depicts the average of the ten data points with a standard deviation error bar.
  • B Sera from the three groups of animals were collected 10 days after the third immunization, and ELISA was performed to detect the antibody against envelope as described in Materials and Methods section of PART II. Mouse sera from different groups were diluted starting from 1:100 to 1:2,700 for testing. Each bar represents the average OD reading from the ten mice per group.
  • FIG. 12 Schematic representation of Envelope mutations.
  • A. The major structural motifs in HIV Env are shown, together with the selected expression vectors used in these studies.
  • V1, V2, V3, and V4 indicate the respective variable regions and the sequence of the relevant V3 loops are indicated (SEQ ID NO: 1).
  • B. Schematic structure of the V3 loop and V3 (1AB) stem-shortening mutations are indicated (SEQ ID NO: 1).
  • FIG. 13 Mutation in the stem of the V3 loop and protein expression of various gp145 ⁇ CFI (HXB2/BaL chimera) V3 deletion mutants.
  • A Sequences of progressive V3 stem deletion mutations in Env from HXB2/BaL chimera.
  • B Protein expression of gp145 ⁇ CFI (HXB2/BaL chimera) V3 deletion mutant expression vectors. The indicated mutations in the gp145 ⁇ CFI constructs, described previously (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-5368), were prepared and analyzed by SDS-PAGE followed by Western blot analysis with human monoclonal antibody 2F5.
  • Plasmid expression vectors encoding the indicated mutants were transfected into 293 cells by use of calcium phosphate. Cell lysates were collected 48 hours later.
  • FIG. 14 Effects of mutations in the stem of the V3 loop on tropism of the 89.6P Env.
  • A B. Buoyant density sedimentation analysis of indicated V3 mutants in lentiviral vector particles, performed as described in Materials and Methods section of PART III.
  • C Effects of V3 mutations in strain 89.6P Env on infection of a CXCR4-tropic cell line, MT-2 (left), and a CCR-5 tropic indicator cell line, MAGI-CCR5 (right), using a liciferase reporter gene.
  • the positions of the indicated V3 mutations in strain 89.6P Env are the same as shown for the HXB2/BaL chimera ( FIG. 13A ). Both codon-modified and wild-type (wt) 89.6P Envs were used as positive controls.
  • FIG. 15 Expression of different HIV gp145 (HXB2/BaL chimera) V region mutants and induction of neutralizing antibodies.
  • FIG. 16 Characterization of antibody response induced by gp145 (HXB2/BaL chimera) ⁇ V1V2 and selected V3 region mutants.
  • A Neutralization activity against BaL induced by immunization of guinea pigs with the indicated mutants, including the ⁇ V1V2 deletion mutants and the ⁇ V1V2V3(1AB) stem-shortening mutants. Sera were tested at 1:5 dilution. Results are the means ( ⁇ SD) for four guinea pig sera for each construct. Results from one of two independent experiments are shown. The sera tested were independent from the sera tested for FIG. 15B .
  • B Total ELISA titers in the same guinea pig sera are shown and are comparable between the different mutants.
  • FIG. 17 Comparison of breadth and potency of the antibody response induced by selected V region mutants.
  • B Four individual sera from ⁇ V1V2V3(1AB) immunized guinea pigs were screened against a panel of 10 primary viruses. Sera were tested at a 1:5 dilution. Percentages of neutralization (compared with corresponding pre-immune sera) are indicated. Data shown are an average of two experiments.
  • FIG. 18 In vitro expression of HXB2/BaL and 89.6P Env by both plasmids and rADV vaccine constructs.
  • the plasmid Env [gp145 ⁇ CFI(R5) and gp145 ⁇ CFI(89.6P)] and rADV [ADV-gp140 ⁇ CFI(R5) and ADV-gp140 ⁇ CFI(89.6P)] vaccine constructs were expressed in vitro, and protein expression was assessed by Western blotting with human anti-HIV IgG.
  • FIG. 19 Vaccine-elicited PBMC IFN- ⁇ ELISPOT responses to SIVmac Gag-Pol-Nef and HIV-1 Env.
  • Freshly isolated PBMCs were assessed for IFN- ⁇ ELISPOT responses after in vitro exposure to peptide pools spanning the SIVmac Gag-Pol-Nef and HIV-1 Env proteins. All Env-specific responses were assessed by using peptides that were matched to the Env immunogen.
  • the terms “matched” and “mismatched” refer to the relationship between the Env immunogen and the challenge virus. Arrows indicate time of inoculation with either DNA or rADV immunogens. Data are presented as the total antigen-specific SFC responses to Gag-Pol-Nef and HIV-1 Env per 10 6 PBMCs and represent the mean values for six monkeys ⁇ standard error.
  • FIG. 20A and B Vaccine-elicited PBMC IFN- ⁇ ELISPOT responses to individual viral proteins assessed 2 weeks following rADV boosting. ELISPOT responses to SIVmac239 Gag and Pol and HIV-1 Env antigens were assessed. Env-specific responses were assessed with peptides that were matched to the Env immunogen, and mock Env-vaccinated monkeys were assayed with 89.6P peptide pools. ELISPOT assays were performed on whole PBMCs (A) or PBMCs depleted of CD8 + T lymphocytes (B). Data are presented as the mean SFC responses to individual viral proteins per 10 6 PBMCs and represent the mean values for six experimentally vaccinated monkeys ⁇ standard error.
  • FIG. 21 Postchallenge peripheral blood CD4 + T-lymphocyte counts. These values represent the mean percentage of CD3 + CD4 + lymphocytes assessed prospectively on all experimental monkeys through day 168 postchallenge.
  • FIG. 22 Postchallenge plasma viral RNA levels. These values were determined by an ultrasensitive bDNA amplification assay with a detection limit of 50 copies/ml. The values plotted represent the geometric mean ⁇ standard error at each sampling time for each experimental group of monkeys.
  • FIG. 23 Plasma SHIV-89.6P neutralization titers determined from plasma samples obtained from the monkeys following SHIV-89.6P challenge. Neutralization was determined with an MT-2 dye exclusion assay.
  • FIG. 24 89.6P Env-specific PBMC IFN- ⁇ ELISPOT responses assessed 1 week following rADV boost and both 3 and 10 weeks following SHIV-89.6P challenge. ELISPOT responses were determined after in vitro exposure of PBMCs (peripheral blood lymphocytes, PBL) to peptide pools spanning the HIV-1 89.6P Env protein. The bars represent the mean values for six monkeys with the standard error shown.
  • FIG. 25A , B and C Vaccine-elicited cellular immune responses to HIV-1 clade A, clade B, clade C, and 89.6P Env antigens by PBL of rhesus monkeys following DNA prime and rAd boost immunizations.
  • PBL were freshly isolated at weeks 12 (post-DNA prime) (A), 27 (post-rAd boost) (B) and 42 (day of challenge) (C) post-immunization and assessed for IFN- ⁇ ELISPOT responses following stimulation with peptide pools spanning the indicated HIV-1 Env proteins. Data are presented as the mean number of antigen-specific spot forming cells (SFC) per 10 6 PBL ⁇ SEM from 6 monkeys per group.
  • SFC spot forming cells
  • FIG. 26 Vaccine-elicited cellular immune responses to SIV Gag and Pol by PBL of rhesus monkeys following DNA prime/rAd boost immunizations. PBL were freshly isolated at week 27 post-immunization (1 week following rAd boost) and assessed for IFN- ⁇ ELISPOT responses following stimulation with peptide pools spanning the SIV Gag and Pol proteins. Data are presented as the mean number of antigen-specific spot forming cells (SFC) per 10 6 PBL ⁇ SEM from 6 monkeys per group.
  • SFC spot forming cells
  • FIG. 27 Antibody titers to HIV-1 clade A, clade B, or clade C Env proteins in plasma from rhesus monkeys following DNA prime/rAd boost immunizations. Plasma samples were obtained at week 28 post-immunization (2 weeks following rAd boost) and anti-gp145 antibody titers to the indicated HIV-1 Env proteins were determined by ELISA. Data are presented as the mean geometric titer from 6 monkeys per group.
  • FIG. 28A , B and C Antibody neutralizing activity in plasma of rhesus monkeys following DNA prime/rAd boost immunizations. Plasma samples were obtained from vaccinated and control monkeys at week 28 post-immunization (2 weeks following rAd boost), and tested for neutralizing activity against panels of lade A, lade B, and clade C HIV-1 isolates. The dashed line represents a reference point of 20% neutralization, as noted in the results section. Data are presented as the mean percent neutralizing activity ⁇ SEM from 6 monkeys per group. Note that the top panel of clade A viruses also includes a control MuLV Env pseudovirus.
  • FIG. 29A and B Cellular immune responses to HIV-1 Env and SIV Gag and Pol by PBL of vaccinated and control rhesus monkeys following SHIV-89.6P challenge.
  • PBL were freshly isolated two weeks following challenge and assessed for IFN- ⁇ ELISPOT responses following stimulation with peptide pools spanning the indicated HIV-1 Env proteins (A) or the SIV Gag and Pol (B) proteins.
  • Data are presented as the mean number of antigen-specific spot forming cells (SFC) per 10 6 PBL ⁇ SEM from 6 monkeys per group.
  • SFC spot forming cells
  • FIG. 30A and B Plasma viral RNA levels following SHIV-89.6P challenge.
  • the peak plasma viral RNA level (A) for each monkey was measured on day 16 post-challenge.
  • the set point plasma viral RNA level (B) for each monkey was calculated as the median of values detected between days 85 and 169 post-challenge. Log viral copies/ml from individual monkeys are indicated, with bars indicating the median value of the 6 monkeys per experimental group.
  • the detection limit of the assay, 125 copies/ml, is shown with a dashed line.
  • FIG. 31 Peripheral blood CD4 + T lymphocytes post-SHIV-89.6P challenge. The percentage of CD3 + CD4 + T lymphocytes in the peripheral blood of the rhesus monkeys was assessed by flow cytometry through day 169 following SHIV-89.6P infection. Data are presented as the mean percent of peripheral blood CD4 + T lymphocytes from 6 monkeys per group ⁇ SEM.
  • FIG. 32 VRC-4306 DNA construct.
  • This plasmid DNA is designed to express the HIV-1 Gag, Pol, and Nef polyproteins with modifications to reduce potential toxicity (deletions in the regions which affect protease, RT and integrase) and increase expression in human cells, together with a strong, constitutive CMV promoter. It contains the gene for kanamycin resistance incorporated into the bacterial vector backbone as a selectable marker.
  • FIG. 33 VRC-5305 DNA Construct.
  • This plasmid DNA is designed to express the HIV-1 Clade A Env protein with modifications to reduce potential toxicity (deletions of fusion and cleavage domains and the interspace between heptad (H) 1 and 2) and increase expression in human cells, together with a strong, constitutive CMV promoter. It contains the gene for kanamycin resistance incorporated into the bacterial vector backbone as a selectable marker.
  • FIG. 34 VRC-2805 DNA Construct.
  • This plasmid DNA is designed to express the HIV-1 clade B Env glycoprotein with modifications to reduce potential toxicity (deletions of fusion and cleavage domains and the interspace between heptad (H) 1 and 2) and increase expression in human cells, together with a strong, constitutive CMV promoter. It contains the gene for kanamycin resistance incorporated into the bacterial vector backbone as a selectable marker.
  • FIG. 35 VRC-5309 DNA Construct.
  • This plasmid DNA is designed to express the HIV-1 Clade C Env glycoprotein with modifications to reduce potential toxicity (deletions of fusion and cleavage domains and the interspace between heptad (H) 1 and 2) and increase expression in human cells, together with a strong, constitutive CMV promoter. It contains the gene for kanamycin resistance incorporated into the bacterial vector backbone as a selectable marker.
  • FIG. 36 Plasmid map for HIV-1 Clade B Gag (VRC-4401).
  • FIG. 37 Plasmid map for HIV-1 Clade B Pol (VRC-4409).
  • FIG. 38 Plasmid map for HIV-1 Clade B Nef (VRC-4404).
  • FIG. 39 Plasmid map for HIV-1 Clade A Env (VRC-5736).
  • FIG. 40 Plasmid map for HIV-1 Clade B Env (VRC-5737).
  • FIG. 41 Plasmid map for HIV-1 Clade C Env (VRC-5738).
  • FIG. 42 Adgp 140(A).11D adenoviral vector map.
  • FIG. 43 Adgp 140(C).11D adenoviral vector map.
  • FIG. 44 B287-B Adt.gp140dv12(B).11D adenoviral vector map.
  • FIG. 45 GV326A Adt.GagPol(B).11D adenoviral vector map.
  • FIG. 46 Plasmid map for VRC 5747.
  • FIG. 47 Plasmid map for VRC5753.
  • FIG. 48 Plasmid map for VRC 5754.
  • FIG. 49 Plasmid map for VRC 5755.
  • FIG. 50 Plasmid map for VRC 5766.
  • FIG. 51 Plasmid map for VRC 5767.
  • FIG. 52 Plasmid map for VRC 5768.
  • FIG. 53 Plasmid map for VRC 5769.
  • FIG. 54 Plasmid map for VRC 5770.
  • FIG. 55 Plasmid map for VRC 5771.
  • FIG. 56 Plasmid map for VRC 5772.
  • FIG. 57 Plasmid map for VRC 5773.
  • FIG. 58 Plasmid map for CMVR-gp145 ⁇ CFI ⁇ V1(V2 ⁇ LR)(V3-1AB)(Bal).
  • FIG. 59 Plasmid map for CMVR-gp145 ⁇ CFI(V1V2 ⁇ G)(V3-1AB)(Bal).
  • FIG. 60 Plasmid map for CMVR-gp145 ⁇ CFI(V1 ⁇ G)(V2 ⁇ LR)(V3-1AB)(Bal).
  • FIG. 61 Plasmid map for CMVR-gp145 ⁇ CFI(V1 ⁇ G)(V2 ⁇ M)(V3-1AB)(Bal).
  • FIG. 62 Plasmid map for CMVR-gp145 ⁇ CFI(V1 ⁇ G) ⁇ V2(V3-1AB)(Bal).
  • FIG. 63 Plasmid map for CMVR-gp145 ⁇ CFI(V1 ⁇ LR)(V2 ⁇ G)(V3-1AB)(Bal).
  • FIG. 64 Plasmid map for CMVR-gp145 ⁇ CFI(V1 ⁇ LR) ⁇ V2(V3-1AB)(Bal).
  • FIG. 65 Plasmid map for CMVR-gp145 ⁇ CFI(V1 ⁇ M)(V2 ⁇ G)(V3-1AB)(Bal).
  • FIG. 66 Plasmid map for CMVR-gp145 ⁇ CFI(V1 ⁇ M) ⁇ V2(V3-1AB)(Bal).
  • FIG. 67 Plasmid map for CMVR-gp145 ⁇ CFI(V3-1AB)(Bal).
  • FIG. 68 Plasmid map for CMVR-gp145 ⁇ CFI ⁇ V1(V2 ⁇ G)(V3-1AB)(Bal).
  • FIG. 69 Plasmid map for CMVR-gp145 ⁇ CFI ⁇ V1(V2 ⁇ M)(V3-1AB)(Bal).
  • FIG. 70 Plasmid map for CMVR-gp145 ⁇ CFI ⁇ V1(V3-1AB)(Bal).
  • FIG. 71 Plasmid map for CMVR-gp145 ⁇ CFI ⁇ V1V2(V3-1AB)(Bal).
  • FIG. 72 Plasmid map for CMVR-gp145 ⁇ CFI ⁇ V2(V3-1AB)(Bal).
  • FIG. 73 Adenoviral vector map for VRC 5781.
  • FIG. 74 Plasmid map for VRC 5782.
  • FIG. 75 Adenoviral vector map for VRC 5783.
  • FIG. 76 Plasmid map for VRC 5784.
  • FIG. 77 Adenoviral vector map for VRC 5785.
  • FIG. 78 Plasmid map for VRC 5786.
  • FIG. 79 Adenoviral vector map for VRC 5787.
  • FIG. 80 Plasmid map for CMVR-gp145 ⁇ CFI(BBBB).
  • FIG. 81 Adenoviral vector map for VRC 5789.
  • FIG. 82 Plasmid map for VRC 5790.
  • FIG. 83 Adenoviral vector map for VRC 5791.
  • FIG. 84 Plasmid map for VRC 5792.
  • FIG. 85 Adenoviral vector map for VRC 5793.
  • FIG. 86 Plasmid map for VRC 5794.
  • V3 loop of the human immunodeficiency virus type 1 (HIV-1) envelope (Env) effectively elicits potent neutralizing antibody responses
  • the specificity of the antibody response is often restricted to T cell line adapted (TCLA) strains and a small subset of primary isolates, limiting its utility for an AIDS vaccine.
  • TCLA T cell line adapted
  • Env immunogens with substituted V3 regions to combinations of strains from different clades and evaluated their ability to expand the breadth of the neutralizing antibody response.
  • the V3 region from HIV BaL was substituted for HIV HXB2
  • an effective neutralizing antibody response against several clade B primary isolates was elicited, but it remained restricted to neutralization of mostly lade B isolates.
  • V3 2F5 epitope was identified that bound to 2F5 and elicited a potent 2F5 antibody response as an immunogen, but the antisera neutralized only a lab-adapted strain and not primary isolates.
  • combinations of Envs from clades A, B, and C elicited neutralizing antibodies to a more diverse group of primary HIV-1 isolates.
  • the 2F5 epitope is linear in nature and is found in the ectodomain of gp41 (Muster, T. et al. 1993 J Virol 67:6642-7; Purtscher, M. et al. 1994 AIDS Res Hum Retroviruses 10:1651-8; Stiegler, G. et al. 2001 AIDS Res Hum Retroviruses 17:1757-65; Zwick, M. B. et al. 2001 J Virol 75:10892-905).
  • the V3 region is particularly immunogenic and elicits potent, although restricted, antibody responses.
  • Plasmids encoding CCR5-tropic V3 loops from clades A, B and C were built on the backbone of gp145 ⁇ CFI and gp140 ⁇ CFI versions of the CXCR4-tropic strain HIV HXB2 (GenBank accession number K03455) and the CCR5-tropic strain HIV BaL (GenBank accession number K03455) as described previously (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-68).
  • CCR5-tropic version of the envelope glycoprotein (CCR5 gp160/h)
  • the region encoding amino acids 205 to 361 from HIV HXB2 gp160 was replaced with the corresponding region from the HIV BaL strain of HIV-1 (GenBank accession number M68893, with preferred human codon usage) to make it hybrid, HIVHXB/Bal.
  • Synthetic versions of clades A and C gp145 ⁇ CFI and gp140 ⁇ CFI Env glycoprotein were made based on HIV-1 strains 92rw020 (CCR5-tropic, GenBank accession number U51283) and 97ZA012 (GenBank accession number AF286227) following the same approach described above.
  • the fusion domain and the cleavage sequence from amino acids 486-519 and the interspace between H1(heptad 1) and H2 (heptad 2) from amino acids 576-604 were deleted and the protein was terminated after the codons for aa 690 and aa 664 to make gp145 ⁇ CFI and gp140 ⁇ CFI Env respectively.
  • the fusion domain and the cleavage sequence from amino acids 487-520 and the interspace between H1 and H2 from amino acids 577-605 clade C gp160 were deleted.
  • the protein was terminated after the codons for aa 689 and aa 664 to create a synthetic protein clade C gp145 ⁇ CFI/h and clade C gp140 ⁇ CFI/h respectively.
  • a hybrid envelope gp140 ⁇ CFI B(C-HR2), completely lacking 2F5 ( ⁇ 2F5) was made by replacing the sequence of CCR5-tropic gp140 ⁇ CFI of strain of HIVHXB/Bal from aa 592 to 680 that includes the HR2 (heptad repeat 2) and the monoclonal antibody 2F5 binding region with the corresponding region from clade C gp140 ⁇ CFI that lacks 2F5, aa 592 to 688.
  • the hybrid envelope gp140 ⁇ CFI clade B (C-HR2), ⁇ 2F5, in HIVHXB/Bal backbone was further modified by deleting GPGRA (aa 309-313) to generate gp140 ⁇ CFI ⁇ GPGRA B(C-HR2), designated -tip ⁇ 2F5.
  • the minimal and the extended 2F5 epitopes encoding ‘LELDKWAS’ (SEQ ID NO: 3) and ‘KNEQELLELDKWAS’ (SEQ ID NO: 4) respectively were inserted in the place of GPGRA (SEQ ID NO: 12) in the V3 loop of gp140 ⁇ CFI B(C-HR2), ⁇ 2F5, by site-directed mutagenesis to form gp140 ⁇ CFI B(C-HR2) 2F5, termed V3 2F5, and gp140 ⁇ CFI B(C-HR2) ext 2F5 or V3 ext2F5 respectively.
  • Antibody (5 ⁇ g) was used to immunoprecipitate gp140 ⁇ CFI from 100 ⁇ l of membrane-free supernatant from 293 cells transfected with the expression vector expressing clade A, lade B or clade C gp140 ⁇ CFI. The same volume of supernatant from cells transfected with empty vector was used as a control. Antibodies were obtained from the AIDS Research and Reference Reagent Program, National Institutes of Health. The binding of HIV-1 IgG to either R5/B 140 ⁇ CFI or different mutants was measured by ELISA.
  • Immulon 2HB ELISA plates (Thermo Labsystems, Franklin, Mass.) were coated with 100 ⁇ l/well of Lectin Galanthus Nivalis (Sigma, St. Louis, Mo.) (10 ⁇ g/ml in PBS) overnight at 4° C. The plates were blocked with 200 ⁇ l of PBS containing 10% FBS for 2 hours at room temperature, and washed twice with PBS containing 0.2% TWEENTM-20 (PBS-T). Samples were added and developed as described in PART II below.
  • ELISA plates were coated with either 100 ⁇ l of 2F5 peptide, KNEQELLELDKWAS (10 ⁇ g/ml) (SEQ ID NO: 4), or 100 ⁇ l of V3 peptide, ‘TRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAH’ (SEQ ID NO: 13), overnight at 4° C.
  • the peptide solution was removed from the wells and blocked with 200 ⁇ l of PBS containing 10% FBS for 2 hours at room temperature.
  • the plates were washed twice with PBS containing 0.2% TWEENTM 20 (PBS-T), and then the sera from immunized guinea pigs from different groups were added with 3-fold dilutions for 1 hour.
  • the guinea pigs received a boost with replication-defective recombinant adenovirus (ADV) encoding the gp140 ⁇ CFI form of the same immunogen as described previously (Sullivan, N. J. et al. 2000 Nature 408:605-9; Xu, L. et al. 1998 Nat Med 4:37-42; Yang, Z. et al. 1998 Science 279:1034-7) and were bled 2 weeks after ADV injection.
  • ADV replication-defective recombinant adenovirus
  • HIV-1 Viruses HIV-1 primary isolates, and the T-cell line adapted HIV MN and HIV IIIB, were obtained from NIH AIDS Research and Reference Reagent Program except as noted below.
  • Primary isolates 6101 (previously called P15) and 1168 are CCR5 using clade B HIV-1 strains described previously (Bures, R. et al. 2000 AIDS Res Hum Retroviruses 16:2019-35).
  • DU151, DU123 and S007 are clade C viruses that have also been previously described (Bures R et al. 2002 J Virol 76:2233-44).
  • TV1 (clade C) was provided by Estrelita Janse Van Rensburg (University of Why Willbosch, South Africa).
  • DJ263 is a clade A virus that was provided by investigators from the U.S. Military HIV Research Program. All primary viral stocks were prepared and titrated in PHA and IL-2 stimulated human peripheral blood mononuclear cells (PBMC). Viruses BL01 and BR07 were provided by Dana Gabuzda of the Dana-Farber Cancer Institute (Ohagen, A. et al. 2003 J Virol 77:12336-45). Both are chimeric infectious molecular clones of NL4-3 that contain the near full-length env genes from HIV-1 strains indicated. After initial plasmid transfection of 293 cells, these viruses were expanded in PBMC as described above.
  • Neutralizing antibody assays Two assays for neutralization were used. Neutralization of a BaL isolate was measured in PBMC by using a reduction in p24 Gag antigen synthesis as described previously (Bures, R. et al. 2000 AIDS Res Hum Retroviruses 16:2019-35). Briefly, 500 50% tissue culture infective doses of virus were incubated with various dilutions of test samples (serum) in triplicate for 1 h at 37° C. in 96-well U-bottom culture plates. PHA-PBMC were added and incubated for one day. The cells were then washed three times with growth medium and resuspended in 200 ⁇ l of fresh growth medium.
  • Culture supernatants (25 ⁇ l) were collected twice daily thereafter and mixed with 225 ⁇ l of 0.5% Triton X-100. The 25 ⁇ l of culture fluid removed each day was replaced with an equal volume of fresh growth medium. Concentrations of p24 Gag antigen were measured in an antigen capture ELISA as described by the supplier (DuPont/NEN Life Sciences, Boston, Mass.). Concentrations of p24 in virus control wells (virus plus cells but no test serum) were determined for each harvest day. Concentrations in all remaining wells were determined for a harvest day that corresponded to a time when p24 production in virus control wells was in an early linear phase of increase that exceeded 3 ng/ml, which is when optimum sensitivity is achieved in this assay (Zhou, J.
  • a 50% reduction in cell killing corresponds to an approximate 90% reduction in p24 Gag antigen synthesis in this assay (Bures, R. et al. 2000 AIDS Res Hum Retroviruses 16:2019-35).
  • Each set of assays included a positive control serum that had been assayed multiple times and had a known average titer.
  • V3-specific neutralizing antibodies were assessed by incubating diluted serum samples (diluted with an equal volume of phosphate-buffered saline, pH 7.4) for 1 h at 37° C. in the presence and absence of V3 peptide (50 ⁇ g/ml). Titers of neutralizing antibodies were then determined in either the PBMC assay (in the case of primary isolates) or the MT-2 cell assay (in the case of HIV IIIB and HIV MN) by using neutral red as described above.
  • the alternative assay used a single round intracellular p24-antigen flow cytometric HIV-1 neutralization assay has been described previously (Mascola, J. R. et al. 2002 J Virol 76:4810-21). Briefly, 40 ⁇ l of virus stock (multiplicity of infection, approximately 0.1) was incubated with 10 ⁇ l of heated inactivated guinea pig serum, or with 10 ⁇ l of control antibody. After incubation for 30 min at 37° C., 20 ⁇ l of mitogen stimulated CD8 depleted PBMC (1.5 ⁇ 10 5 cells) were added to each well.
  • T-cells were maintained in IL-2 culture medium containing 1 ⁇ M indinavir, and the cells were fed on day 1 with 150 ⁇ l of IL-2 culture medium.
  • IL-2 culture medium containing 1 ⁇ M indinavir
  • cells were stained for intracellular p24-Ag using the KC57 (Beckman Coulter, Inc.) anti-p24 antibody, followed by quantitation of HIV-1 infected cells by flow cytometry. Live cells initially gated by forward and side scatter were analyzed for p24-Ag positive cells. After forward and side scatter gating, 50,000 events were counted. Final quantitation of p24 positive PBMC was done by subtraction of background events in mock-infected cells (typically less than 10 cells per 50,000 events counted).
  • the percent neutralization was derived by calculating the reduction in the number of p24-Ag positive cells in the test wells with immune sera, compared to the number of p24-Ag positive cells in wells containing pre-immune sera from the corresponding animal. All assays included additional control wells with commercial pooled guinea pig sera (Gemini Bio-Products, Woodland, Calif.), as well as positive control wells containing well characterized monoclonal or polyclonal neutralizing antibodies. Standard operating procedures prescribed the acceptable positive and negative control values, and all data shown are from assays that met these criteria.
  • V3 peptide competition assays were done in the same assay format, except that the V3 peptide was added to the serum 30 minutes before virus was added. The concentration of peptide reported was that present when peptide, serum and virus were incubated together.
  • the V3 peptides based on HIV-1 strains BaL, ZA12 and RW20 (matching the vaccine strains), and a scrambled V3 peptide, was made as a 23mer (IGPGRATRPNNNFYTTGTRKSIH) (SEQ ID NO: 14) by SynPep (Dublin, Calif.).
  • the HIV IIIB V3 peptide (a 24 mer) was purchased from Sigma-Aldrich.
  • V3 peptide was included as a control in all assays. Additional controls, a mixture of 22 peptides (15 mers overlapping by nine spanning the Ebola (Zaire) viral glycoprotein sequence), were used to confirm specificity of V3 peptide inhibition.
  • V3 loop Modified Env Immunogens To develop HIV Env vaccines with alternative V3 specificities, modifications of a previous clade B HIV-1 prototype strain (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-68) containing ⁇ CFI mutations were made. Replacements of the V3 loop were made at the junction of highly conserved sites at the base of C2 and C4. Specifically, the V3 loop of HIV HXB2 was replaced with that of a CCR5-tropic strain, HIV BaL ( FIG. 1A ). Expression of these envelope glycoproteins was confirmed in transfected 293 cells as visualized by Western blot analysis ( FIG. 1B ). As with earlier prototypes (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-68), the gp140 ⁇ CFI, which lacks the transmembrane domain, was readily detected in the supernatant, indicating that it could give rise to soluble antigen.
  • HIV HXB/Bal Induction of neutralizing antibody responses by Env immunogen, HIV HXB/Bal. Sera from guinea pigs immunized with the HIV HXB/BaL gp140 ⁇ CFI immunogen were able to neutralize laboratory-adapted strains HIV MN, to a lesser extent, HIV IIIB ( FIG. 2A ) and CCR5-tropic HIV-1 BaL ( FIG. 2B ). In contrast, sera from guinea pigs immunized with the parental HIV HXB gp140 ⁇ CFI were not able to neutralize these viruses. It was therefore possible to generate neutralizing antibodies against HIV BaL by inserting the V3 loop of this virus in place of the HIV HXB2 V3 loop that existed in the gp140 ⁇ CFI immunogen.
  • V3 2F5 A mutant V3 loop sequence was prepared in which the sequence for 2F5 epitope replaced native V3 sequence at the tip of the V3 loop, designated V3 2F5.
  • the tip of V3, GPGRA (SEQ ID NO: 8) was deleted in another version, -tip ⁇ 2F5, as a negative control ( FIG. 4A ).
  • the minimal peptide that is recognized by 2F5 antibody defined previously (Muster T et al. 1994 J Virol 68:4031-4), as well as an extended amino acid sequence more recently recognized (Zwick M B et al.
  • Plasmid expression vectors encoding clade A and clade C gp140/145 ⁇ CFI proteins were synthesized using the same modified codon preferences and mutations applied to the clade B vectors. Their expression was confirmed in transfected 293 cells by immunoprecipitation with well-defined broadly neutralizing monoclonal antibodies such as 2F5, 2G12, F105, and IgG1b12, followed by Western blot analysis ( FIG. 6A ). Reactivity of these antibodies with clades A, B, and C varied in terms of recognition and specificity ( FIG. 6A ) as expected from previous analyses with these antibodies across clades (Moore, J. P. et al.
  • the gp140 ⁇ CFI forms that lack the transmembrane domain were readily detected in the supernatant ( FIG. 6A , B), indicating that they gave rise to soluble antigen.
  • CD4 To further assess whether these glycoproteins retained conformational structures relevant to Env function, their ability to interact specifically with its receptor, CD4, was assessed. Compared to negative control supernatants, these Envs readily bound to soluble CD4 produced from transfected 293 cells ( FIG. 6B ), as previously described for clade B (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-68), confirming that the CD4 binding site determinants were intact.
  • Immunization with the multiclade Env vaccine candidate increases the breadth of the neutralizing antibody response.
  • the ability of the multiclade Env vaccine candidate to elicit neutralizing antibodies was analyzed by immunization with an equal mixture of these vectors and compared to antibodies elicited by the single clade B Env immunogen (monoclade) vaccination as described in Materials and Methods.
  • ELISAs were done using clade-specific envelope captured on lectin-coated plates, or by using V3 peptides. Our data showed that the antibody response after HxB2/BaL immunization was directed preferentially to clade B Env and clade B V3.
  • HIV SF162 To determine the contribution of anti-V3 antibodies specificity to virus neutralization, competition studies were also performed using HIV SF162. This clade B virus was chosen because it is a fairly sensitive primary isolate that was neutralized by sera from both the clade B and multiclade immune sera. The HIV BaL V3 peptide was able to block essentially all neutralization of the clade B immune sera. Thus, anti-V3 antibodies largely mediated neutralization of HIV SF162 ( FIG. 7D ).
  • a multiclade immune response is envisioned to help to reduce the likelihood of viral escape, both from CTL and antibodies (Richman, D. D. et al. 2003 PNAS USA 100:4144-9; Wei, X. et al. 2003 Nature 422:307-12).
  • HIV-1 human immunodeficiency virus type 1
  • mice were immunized with a mixture of Env from three clades, A, B, and C, together with Gag-Pol-Nef, the overall potency and balance of CD4+ ⁇ and CD8+ ⁇ T-cell responses to all viral antigens were similar, with only minor differences noted.
  • plasmid mixtures elicited antibody responses comparable to those from individual inoculations.
  • HIV-1 The genetic variation of HIV-1 has created challenges for the development of a preventive AIDS vaccine (van der Groen, G. et al. 1998 AIDS Res Hum Retroviruses 14 Suppl 3:S211-S221). Not only would such a vaccine be expected to be safe and immunogenic, it must also induce immune recognition of a broad spectrum of HIV isolates to prove highly effective (Mascola, J. R. & Nabel, G. J 2001 Curr Opin Immunol 13:489-495). Though progress has been made with subtype-specific and Gag- or Env-based HIV vaccines (Bojak, A. et al. 2002 Vaccine 20:1975-1979; Deml, L. et al.
  • Env is a major target of both humoral and cellular immunity, while the viral genes for Gag, Pol and Nef are potential targets of the CD8 + immune response.
  • a modified form of HIV-1 envelope (Env), gp145 ⁇ CFI, has been shown to improve antibody responses while maintaining its ability to induce cytotoxic T-lymphocyte (CTL) responses (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-5368).
  • a fusion protein of Gag and Pol has also been developed that generates a protein from a single open reading frame that can be processed to present linear epitopes from at least four viral gene products: Gag, protease (PR), reverse transcriptase (RT), and integrase (IN) (Huang, Y. et al. 2001 J Virol 75:4947-4951).
  • PR protease
  • RT reverse transcriptase
  • IN integrase
  • the present study evaluates the immunogenicity of Env and Gag-Pol-Nef vaccine candidates alone or in combination.
  • the ability to combine these immunogens from different clade isolates has also been evaluated.
  • the combination of Gag-Pol-Nef with Env elicited strong CD8 immunity to Env without compromising the CD4 or antibody response.
  • combinations of Env from multiple clades help to expand the immune response to these alternative clades.
  • the combination of multiple HIV genes from different clades is envisioned to facilitate the generation of immune responses to diverse HIV strains.
  • Gag-Pol-Nef Immunogens Plasmids expressing HIV genes were synthesized by reverse translation (Genetics Computer Group, Inc., Madison, Wis.) of published sequences using codons expected for human cells. The methods used to make DNA plasmids expressing HIV-1 Gag-Pol-Nef polyproteins from different clades were similar to those previously described for Gag-Pol (Huang, Y. et al. 2001 J Virol 75:4947-4951). To further inactivate viral proteins, additional inactivating mutations were inserted into protease (PR), reverse transcriptase (RT), and integrase (IN).
  • PR protease
  • RT reverse transcriptase
  • I integrase
  • the amino acid sequence of the Nef protein was not modified, but the NH 2 -terminal myristylation site required for its functional activity was not available, as it is synthesized as a fusion protein.
  • the clade A, B and C Gag-Pol-Nef plasmids were 9783, 9790 and 9786 nucleotides in length, respectively, and the clade A, B, and C Env plasmids are 6836, 6869 and 6829 nucleotides.
  • each Gag polyprotein from the appropriate HIV-1 clade was used to create a synthetic version of the gag gene (gag/h) using codons preferred for expression in human cells.
  • the synthetic gag/h gene contained all mature Gag proteins except for p1 and p6 (amino acids 433-500).
  • the synthetic gag/h gene from clade A, B, or C was ligated in frame with codon-modified pol (pol/h) encoding amino acids 3-1003 from NL4-3 (GenBank accession number M19921).
  • a protease (PR) mutation (Arg to Gly) was inserted at aa 553, a reverse transcriptase (RT) mutation (Asp to His) at aa 771, and an integrase (IN) mutation (Asp to Ala) at aa 1209.
  • PR protease
  • RT reverse transcriptase
  • IN integrase
  • a synthetic nef gene (nef/h) based on aa 1 to 206 from NL4-3 was fused to the 3′ end of pol/h by PCR to generate the appropriate Gag-Pol-Nef expression vector.
  • Gag-Pol-Nef fusion protein amino acids 1 to 432 from a CCR5-tropic clade A (GenBank accession number AF004885) were used and fused to the pol/h gene described above. In all three Gag-Pol-Nef plasmids, the same pol sequence was inserted, as this viral gene product is more than 90% conserved at the amino acid level among disparate clades.
  • clade A nef/h (GenBank accession number: AF069670) was fused to the 3′ end of pol/h by PCR to generate the clade A plasmid, pVRC-4313.
  • sequence encoding amino acids 1 to 432 from a CCR5-tropic clade B (GenBank accession number K03455) was used and fused to the pol/h described above.
  • the stop codon from Pol was removed and fused to a lade B synthetic Nef/h gene (aa 1 to 206) from HIV-1 PV22 (GenBank accession number K02083) to generate the lade B plasmid, pVRC-4306.
  • aa 1 to 206 from HIV-1 PV22 (GenBank accession number K02083)
  • pVRC-4306 amino acids 1 to 432 from a CCR5-tropic clade C (GenBank accession number U52953) were used and fused to the pol/h gene described above.
  • the Pol stop codon was removed and fused to synthetic clade C Nef/h (aa 1 to 206) (GenBank accession number: U52953), designated pVRC-4311.
  • the synthetic protein sequence for the clade A Env polyprotein was derived from 92rw020 (R5-tropic, GenBank accession number U51283) and designated lade A gp145 ⁇ CFI/h.
  • An XbaI site was inserted 18 nucleotides upstream from the ATG, together with a known Kozak sequence, and a BamH1 site created 1,912 nt downstream of the ATG for all Env expression vectors. This fragment was cloned into the XbaI-to-BamH1 sites of pVR1012x/s sites.
  • the fusion and cleavage domains from amino acids 486-519 and the interspace between H1 and H2 from amino acids 576-604 were deleted.
  • the protein sequence of the clade B Env glycoprotein (gp160) from HXB2 was used to create a synthetic version of the gene (X4gp160/h) by alteration of codons for better expression in human cells.
  • the nucleotide sequence X4gp160/h shows little homology to the HXB2 gene, but the protein encoded is the same with the following aa substitutions: aa 53 (Phe ⁇ Leu), aa 94 (Asn ⁇ Asp), aa 192 (Lys ⁇ Ser), aa 215 (Ile ⁇ Asn), aa 224 (Ala ⁇ Thr), aa 346 (Ala ⁇ Asp), and aa 470 (Pro ⁇ Leu).
  • R5-tropic version of the envelope glycoprotein (R5gp160/h)
  • the region encoding HIV-1 envelope glycoprotein amino acids 205 to 361 from X4gp160/h was replaced with the corresponding region from the BaL strain of HIV-1 (GenBank accession number M68893, again using human-preferred codons).
  • the full-length CCR5-tropic version of the envelope gene from pR5gp160/h was terminated after the codon for aa 704 to generate gp145/h.
  • the fusion and cleavage domains from amino acids 503-536 and the interspace between H1 and H2 from amino acids 593-620 were then deleted.
  • mice received two 100- ⁇ l injections intramuscularly in each thigh at days 0, 14 and 42. Ten days after the final injection, mice were bled and sera were collected. Then the mice were sacrificed, spleens were removed, and the spleen cells were analyzed by intracellular cytokine flow cytometry (ICC) for CD4+ and CD8+ T-cell responses.
  • ICC intracellular cytokine flow cytometry
  • CD4+ ⁇ and CD8+ ⁇ T-cell responses were evaluated by using intracellular cytokine flow cytometry (ICC) for gamma interferon (IFN- ⁇ ) and tumor necrosis factor-alpha (TNF- ⁇ ).
  • IFN- ⁇ gamma interferon
  • TNF- ⁇ tumor necrosis factor-alpha
  • Anti-CD28 and anti-CD49d antibodies were added (1 ⁇ g/ml) to the medium for costimulation. After an hour, brefeldin A (Sigma) was added to the medium (10 ⁇ g/ml) for an additional 5 h. After a total of 6 h, cells were washed and incubated with FC block (BD-Pharmingen) for 15 min on ice, fixed, and permeabilized with Cytofix/Cytoperm (BD-Pharmingen) according to manufacturer's instructions.
  • FC block BD-Pharmingen
  • the cells were washed with phosphate-buffered saline (PBS) with 0.1% saponin (Sigma) followed by staining with the indicated fluorescent-labeled monoclonal antibodies against CD3, CD4, CD8, IFN- ⁇ and TNF- ⁇ (BD-Pharmingen) for 20 min on ice. After washing with PBS with 0.1% saponin, the cells were analyzed by fluorescence-activated cell sorting (FACS) to detect the IFN- ⁇ - and TNF- ⁇ -positive cells in the CD4+ and CD8+ cell populations and analyzed with the program FlowJo (Tree Star, Inc.).
  • FACS fluorescence-activated cell sorting
  • ELISA Assays To detect antibodies against Env proteins of different clades, enzyme-linked immunosorbent assay (ELISA) plates were coated with 100 ⁇ l of Galanthus Nivalis lectin (10 ⁇ g/ml) overnight at 4° C. The lectin solution was removed from the wells and blocked with 200 ⁇ l of PBS containing 10% fetal bovine serum (FBS) for 2 h at room temperature.
  • FBS fetal bovine serum
  • the plates were washed twice with PBS containing 0.2% TWEENTM 20 (PBS-T) and then 100 ⁇ l of supernatant from cells transfected with pVRC5304 (R5 gp140 ⁇ CFI-Clade-A), pVRC2801 (R5 gp140 ⁇ CFI-Clade-B), or pVRC5308 (R5 gp140 ⁇ CFI-Clade-C) was added to each well, and wells were incubated for an hour at room temperature. The plates were washed with PBS-T five times, and then the sera from immunized mice from different groups were added with 3-fold dilutions for 1 h.
  • PBS-T PBS containing 0.2% TWEENTM 20
  • HRP horseradish peroxidase
  • mice were sacrificed, and splenocytes were incubated with overlapping Gag peptide pools.
  • Intracellular IFN- ⁇ and TNF- ⁇ expression in stimulated CD4+ or CD8+ lymphocytes were analyzed by flow cytometry, and positive cells were enumerated.
  • Cells from mice immunized with Gag-Pol-Nef alone and those immunized with the combination of Env and Gag-Pol-Nef responded similarly to Gag stimulation ( FIG. 8A , left).
  • lymphocytes from mice vaccinated with Env alone, and those with a combination of Env and Gag-Pol-Nef responded similarly to incubation with Env peptide pools ( FIG.
  • mice were immunized with the control plasmid and two combinations of plasmids (Table 1), including a combination of six plasmids, designated ABC( ⁇ 6), because it covered the Gag, Nef, and Env from Clades A, B and C with Pol from Clade B, or the ABC group with four components, ABC( ⁇ 4), in which the Gag-Pol-Nef fusion protein from Clade B was used alone, rather than with the Gag-Pol-Nef proteins from Clades A and C.
  • Table 1 Table 1
  • Table 1 including a combination of six plasmids, designated ABC( ⁇ 6), because it covered the Gag, Nef, and Env from Clades A, B and C with Pol from Clade B, or the ABC group with four components, ABC( ⁇ 4), in which the Gag-Pol-Nef fusion protein from Clade B was used alone, rather than with the Gag-Pol-Nef proteins from Clades A and C.
  • Both plasmid combination groups had similar CD8 response to Gag, Pol, and Env from Clade B, but not from other clades ( FIG. 10 ) and Table 2.
  • Responses to Gag from Clades A and B were significantly higher than the control (pVR1012) for both ABC( ⁇ 6) and ABC( ⁇ 4), but the differences between the response rates of the two treatment groups were not significantly different for either of these clades.
  • CD8+ responses to Pol-1 and Env from Clade B were significantly higher than the control (pVR1012) responses for both ABC( ⁇ 6) and ABC( ⁇ 4).
  • both ABC( ⁇ 6) and ABC( ⁇ 4) elicited comparable cell-mediated immune responses.
  • AIDS vaccine One requirement of a highly effective AIDS vaccine is the need to induce both neutralizing antibodies and cellular immunity to the many strains of HIV-1 that circulate throughout the world.
  • Env, Gag, Pol and Nef were chosen as targets because they represent the major expressed proteins during viral infection.
  • a mutant Env with deletions in the cleavage site, fusion domain, and a region between the heptad repeats was used for its ability to elicit a more potent humoral immune response while retaining its ability to stimulate Env-specific cytotoxic T lymphocytes (CTL) (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-5368).
  • CTL Env-specific cytotoxic T lymphocytes
  • T cell response is sufficiently robust, it is hoped that these cells will kill HIV-infected cells before the virus can replicate and establish a reservoir of infection in vivo.
  • CTL that react with strains from multiple clades.
  • there may be some cross-clade reactivity after immunization with a single clade e.g., Keating, S. M. et al. 2002 AIDS Res Hum Retroviruses 18:1067-1079
  • there is also evidence of disparities in such immune responses e.g., Dorrell, L. et al. 2001 Eur J Immunol 31:1747-1756).
  • ABC( ⁇ 6) containing the same Env-gp145 ⁇ CFI from different clades as in group ABC( ⁇ 4) plus the Gag-Pol-Nef fusion protein from clades A and C, minor differences in immunogenicity were seen. Analyzing the Gag response, ABC( ⁇ 4) elicited CD4 + and CD8 + responses to clades A and B, while ABC( ⁇ 6) improved the response to clade C Gag peptides.
  • both groups demonstrated CD4 + and CD8 + responses against Pol from Clade B.
  • the ABC( ⁇ 4) group elicited a CD4 + response to both sets of Pol peptides, while ABC( ⁇ 6) stimulated CD4 + response only against one of the two Pol peptide pools (Table 2).
  • Both groups induced CD8 + responses to the first half of the Clade B pol ( FIG. 10B , left panel).
  • For Nef only the ABC( ⁇ 4) group elicited a CD4+ response against Nef from clade B (Table 2).
  • the poor anti-Nef response also may be due to the inability of Balb/c mice to recognize Nef epitopes, as other groups have reported that Nef is highly immunogenic in other strains of mice (Kjerrstrom, A. et al. 2001 Virology 284:46-61).
  • the ABC( ⁇ 4) vaccine regimen was able to induce substantial and balanced CD4 + and CD8 + T cell responses to the viral antigens from different clades.
  • the results here indicate that a multi-gene HIV-1 DNA vaccine is feasible because the immune responses to individual genes do not cause interference when combined with one another.
  • the concern about virus variability becomes increasingly problematic.
  • a few subtypes of HIV-1 predominate in different regions of the world a rising number of recombinant strains have been reported lately (Kuiken, C. et al. 2000. Human Retroviruses and AIDS 1999. Los Alamos National Laboratory, Los Alamos, N. Mex.).
  • Such viruses continually mutate and escape (Barouch, D. H.
  • each of these domains contains a subset of sequences that remain conserved.
  • the V3 loop has been much studied for its ability to elicit neutralizing antibodies, which are often restricted to a limited number of closely related strains, likely because a large number of antigenic structures are generated from the diverse amino acid sequences in this region.
  • subregions of V3 are highly conserved, and the effect of different portions of the V3 loop on Env tropism and immunogenicity has not been well delineated.
  • selective deletions in V3 have been introduced by shortening the stem of the V3 loop. These mutations were explored in combination with deletions of selected V regions.
  • V3 Progressive shortening of the stem of V3 abolished the immunogenicity as well as the functional activity of HIV Env; however, two small deletions on both arms of the V3 stem altered the tropism of the dual-tropic 89.6P viral strain so that it infected only CXCR4 + cells. When this smaller deletion was combined with removal of the V1 and V2 loops and used as an immunogen in guinea pigs, the antisera were able to neutralize multiple independent clade B isolates with higher potency.
  • the envelope protein utilizes a variety of mechanisms to evade detection, including carbohydrate modification, conformational flexibility, and genetic variability between isolates (Burns, D. P. & Desrosiers, R. C. 1994 Curr Top Microbiol Immunol 188:185-219; Burton, D. R. 2002 Nat Rev Immunol 2:706-713; Chakrabarti, B. K. et al. 2002 J Virol 76:5357-5368; Gorny, M. K. et al. 2002 J Virol 76:9035-9045; Kwong, P. D. et al.
  • variable regions have been defined by their genetic differences among alternative isolates, it is clear that there are subregions within the V loops that show some degree of conservation. This sequence homology is particularly evident in such regions as the tip of the V3 loop (Korber, B. T. et al. 1994 J Virol 68:7467-7481). Other motifs can also be identified in various virus strains. For example, specific N-linked glycosylation sites and sequences near the base of the V3 loop are well conserved (Korber, B. T. et al. 1994 J Virol 68:7467-7481). In this study, the fine specificity of the variable regions was explored in further detail.
  • V3 loop has been examined with regard to the contribution of the putative stem structures to viral tropism and immunogenicity.
  • a specific mutation that shortens the stem of the V3 loop can alter the tropism of HIV envelope.
  • This mutation in combination with deletion of the V1 and V2 loops, further enhances the ability of the envelope to elicit a neutralizing antibody response.
  • Anti-HIV-1 human monoclonal antibody 2F5 Purtscher, M. et al. 1996 AIDS 10:587-593
  • human HIV immunoglobulin G IgG
  • NIH National Institutes of Health
  • Anti-HIV p24 antibody KC57-RD1 was obtained from Beckman Coulter, Inc.
  • Human embryonic kidney cell 293 was purchased from ATCC, and maintained in Dulbecco's modified Eagle's media (Invitrogen, Carlsbad, Calif.) containing 10% fetal bovine serum (FBS) and 100 ⁇ g/ml of penicillin/streptomycin.
  • the human T-cell leukemia cell line MT-2 and the HeLa-derived cell line MAGI-CCR5 were obtained from the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH.
  • HIV-1 isolates (ADA, JRCSF, JRFL, Bal, SF162 and 89.6) were obtained from the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH.
  • the viruses were expanded by two or three cycles of growth on phytohemagglutinin (PHA)- and interleukin (IL-2)-stimulated peripheral blood mononuclear cells (PBMC).
  • PHA phytohemagglutinin
  • IL-2 interleukin
  • PBMC peripheral blood mononuclear cells
  • IL-2 culture medium was added to bring the concentration to 10 6 cells/ml.
  • the IL-2 culture medium was changed every 2 days, and supernatants were collected during the peak of p24 expression, usually 5-10 days after infection.
  • Virus stocks were made cell free centrifugation at 1,000 ⁇ g and filtration through a 0.45- ⁇ m-pore-size filter. In some cases, viral stocks were concentrated by as much as 10-fold using a 100-kDa cutoff polyethersulfone filter (Centricon Plus Biomax filter, Millipore, Bedford, Mass.), according to manufacturer's instructions. Virus aliquots were stored in the vapor phase of liquid nitrogen.
  • Viruses BL01 and BR07 were provided by Dana Gabuzda of the Dana-Farber Cancer Institute.
  • Buoyant density gradient analysis of lentiviral vectors 293T cells (3 ⁇ 10 6 ) were transfected with 3 ⁇ g each of the relevant Gag and Env ecpression vectors in a 100-mm-diameter tissue culture dish with Dulbecco's modified Eagle's medium. Three days later, the cell supernatants were collected and mixed with 60% OptiPrep (iodixanol) medium (Invitrogen); the final concentration of OptiPrep was adjusted to a 30% density gradient formed by centrifugation at 45,000 ⁇ g for 6 h in a VTI50 rotor (used according to the manufacturer's instructions; Invitrogen); and each fraction was collected according to the indicated density.
  • OptiPrep iodixanol
  • Lentiviral vector proteins were separated in a sodium dodecyl sulphate-4 to 15% polyacrylamide gel electrophoresis (SDS-4 to 15% PAGE) gel, transferred onto an Immobilon-P membrane, and plotted for the expression of Gag (human HIV IgG, used at 1:5,000) and Env (human HIV IgG, used at 1:5,000).
  • Adenovirus type 5 (Ad5)-based first-generation ( ⁇ E1, ⁇ E3) recombinant adenoviruses expressing different V loop deletions of gp140( ⁇ CFI) were constructed as described previously (Aoki, K. et al. 1999 Mol Med 5:224-231).
  • PacI-linearized shuttle vectors containing V loop deletions of gp140( ⁇ CFI) were recombined with the right side of Ad5 genomic DNA carried in cosmid by useof Cre recombinase (Novagen, Madison, Wis.).
  • telomeres were ethanol precipitated, dissolved in Tris-EDTA, and transfected into 293 cells. Recombinant adenoviruses were observed based on plaque formation 10 to 14 days after transfection. Viruses were amplified, purified two times through a CsCl gradient, and stored in PBS+15% glycerol at ⁇ 20° C.
  • HIV-Luc pseudotyped with HIV gp160(89.6P) and its V3 deletion mutants were prepared according to published methods (Naldini, L .et al. 1996 Science 272:263-267). Briefly, the packaging vector pMD 8.2, pHR-Luciferase, and the envelope-expressing vector were transiently cotransfected into 293T cells by use of calcium phosphate. Supernatants were harvested 48 and 72 h after transfection, filtered, and stored at ⁇ 80° C. Virus concentrations were determined by an ELISA assay for the p24 antigen (Coulter).
  • MT-2 X4 tropic
  • MAGI-CCR5 R5 tropic
  • the same amount of virus was added onto MT-2 (X4 tropic) and MAGI-CCR5 (R5 tropic) cells, and the cells were incubated for 2 h at 37° C.
  • the cells were harvested 48 h after infection and lysed in cell culture lysis buffer (Promega, Madison, Wis.).
  • the luciferase assay was performed according to the manufacturer's recommendation (Promega, Madison, Wis.).
  • Plasmid construction Plasmid pVRC1012-gp140( ⁇ CFI) (HXB2/BaL chimera) and pVRC1012-gp145( ⁇ CFI) (HXB2/BaL chimera) have been described previously (Chakrabarti B K et al. 2002 J Virol 76:5357-5368).
  • PCR was performed to amplify an XbaI/NheI fragment covering ATG and the boundary of V1 loop using primers 5′CCTCTAGACACCATGCGCGTGAAGGAGAAG3′ (SEQ ID NO: 15) and 5′CCGCTAGCGTCGGTGCACTTCAGGCTCACGCACAGGGG3′ (SEQ ID NO: 16) and an NheI/ApaI fragment covering the 3′ boundary of the V2 loop and the C3 region using primers 5′CCGCTAGCACCAGCTGCAACACCAGCGTGATCACCCAG3′ (SEQ ID NO: 17) and 5′GGTGCAGGGGCCCTTGCCGTTGAACTTCTT3′ (SEQ ID NO: 18).
  • the XbaI/NheI- and NheI/ApaI-digested PCR fragments were cloned into XbaI/ApaI-digested pVRC1012-gp140( ⁇ CFI) and pVRC1012-gp145( ⁇ CFI).
  • the resulting plasmids pVRC1012-gp140( ⁇ V 1 V 2 ) and pVRC1012-gp145( ⁇ CFI)( ⁇ V 1 V 2 ) have deletions of the V1 and V2 loops as follows: CTDASTSC (SEQ ID NO: 19). Two extra amino acids (AS) were introduced due to introduction of NheI site.
  • V loop deletion mutants of gp145DCFI (HXB2/BaL chimera) and gp140 ⁇ CFI (HXB2/BaL chimera).
  • the amino acid sequences of deleted V loops are as follows: ⁇ V 1 , CTDASKNC (SEQ ID NO: 34); ⁇ V 2 , CSFASTSC (SEQ ID NO: 35); ⁇ V 3 , CTRASAHC (SEQ ID NO: 36); and ⁇ V 4 , CNSASLPC (SEQ ID NO: 37).
  • V3 deletion mutants were made using the PCR-based Quickchange (Stratagene, La Jolla, Calif.) method according to the manufacturer's instructions. Each mutant was confirmed by double strain sequencing. An ApaI/SexAI fragment containing each confirmed V3 deletion was swapped with a corresponding fragment in pVRC1012-gp140( ⁇ CFI)( ⁇ V 1 V 2 ) and pVRC 1012-gp145( ⁇ CFI)( ⁇ V 1 V 2 ). The cDNA encoding gp160(89.6P)(KB9) (Karlsson, G. B. et al. 1997 J Virol 71:4218-4225) was synthesized by using human preferred codons. Plasmids expressing different V3 deletion mutants of gp160(89.6P) were made similarly and are shown in FIG. 12 . The details for each V3 mutant are listed in FIG. 13A .
  • Guinea pig anti-HIV gp140( ⁇ CFI) ELISA titer was measured by using a modified lectin capture method. Briefly, Immunon 2HB ELISA plates (Thermo Labsystems, Franklin, Mass.) were coated with 100 ⁇ l of Galanthus Nivalis lectin (Sigma, St. Louis, Mo.) (10 ⁇ g/ml in PBS)/well overnight at 4° C. The plates were blocked with 200 ⁇ l of PBS containing 10% FBS for 2 h at room temperature, and washed twice with PBS containing 0.2% TWEENTM-20 (PBS-T).
  • PBS-T TWEENTM-20
  • tissue culture supernatant from pVRC 1012-gp140( ⁇ CFI)-transfected 293 cells was added in each well and incubated at room temperature for 1 h. The plates were washed 5 times with PBS-T. One hundred microliter serial dilutions of guinea pig immune serum in PBS containing 1% FBS were then added in triplicate and incubated for 1 h at room temperature.
  • HRP horseradish peroxidase
  • F(ab)′2 donkey anti-guinea pig IgG 1:5,000
  • PBS+1% FBS horseradish peroxidase
  • the plates were washed 5 times with PBS-T, developed by the addition of 100 ⁇ l of o-phenylenediamine dihydrochloride (Sigma, St. Louis, Mo.) (one gold and one silver tablet in 20 ml of water) and incubated at room temperature for 30 min.
  • the reaction was stopped by the addition of 100 ⁇ l of 1 N H 2 SO 4 to each well.
  • the readout was measured at 450 nm by a SPECTRAmax plate reader (Molecular Devices, Sunnyvale, Calif.).
  • the endpoint dilution was calculated by picking the dilution for which the readout was above that of 1:100 dilution of preimmune serum.
  • IC 50 50% inhibitory concentration
  • IC 80 50% inhibitory concentration
  • serial dilutions of anti-serum were incubated with virus as described above.
  • Antiserum dose-response curves were fit with a nonlinear function, and the inhibitory dilutions that neutralized 50 and 80% (IC 50 and IC 80 respectively) of virus were calculated by a least-squares regression analysis.
  • Statistical analysis of IC 50 titers was performed using the non-parametric Mann-Whitney rank-order test (GraphPad Prism software package V3.0, GraphPad Software Inc., San Diego, Calif.).
  • Guinea pigs were immunized intramuscularly with 500 ⁇ g (in 400 ⁇ l PBS) of gp145 version of plasmid DNA at weeks 0, 2, and 6. At week 14, the guinea pigs were boosted with 10 11 (in 400 ⁇ l PBS) particles of recombinant adenovirus expressing the corresponding gp140 version of the protein. Sera were collected at weeks -2 and 16, divided into aliquots, and frozen at ⁇ 20° C.
  • sample loading buffer 100 mM Tris, 4% SDS, 20% glycerol, 5% 2-mercaptoethanol, 0.2% bromophenol blue
  • sample loading buffer 100 mM Tris, 4% SDS, 20% glycerol, 5% 2-mercaptoethanol, 0.2% bromophenol blue
  • the sample was then resolved by 4 to 15% gradient SDS-PAGE and transferred onto a nitrocellulose membrane (Bio-Rad, Hercules, Calif.).
  • TBS Tris-buffered saline
  • BSA bovene serum albumin
  • the membrane was washed twice with 100 ml TBS containing 0.3% TWEENTM-20, followed by incubation with HRP-conjugated goat anti-human IgG (Chemicon, Temecula, Calif.) (1:5,000) for 30 min at room temperature. Following two washes with 100 ml of washing buffer, the membrane was developed using ECL Western blotting detection reagents (Amersham, Piscataway, N.J.), and exposed on Hyperfilm ECL (Amersham, Piscataway, N.J.).
  • V region mutants Modifications of three regions of the HIV envelope, the cleavage site, fusion peptide, and interhelical coiled-coil domain ( ⁇ CFI) were shown previously to enhance the ability of Env to elicit an antibody response (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-5368). We evaluated additional mutations either in different V regions or through selective modifications of V3 ( FIG. 12 ).
  • the internal V3 loop deletions were made both in gp145 ⁇ CFI (HXB2/BaL chimera), which was inserted into DNA expression vectors for primary immunization, and in gp140 ⁇ CFI (HXB2/BaL chimera), which was placed into an adenoviral vector for boosting. These series of mutations were also introduced into the strain 89.6P Env ( FIG. 13A ), a dual-tropic virus that was analyzed initially in functional pseudotyping assays for effects on tropism of different chemokine receptors. The expression of these progressive deletions of the V3 region was assessed by Western blot analysis.
  • Immunoreactive proteins of the expected molecular weight were detected in cell lysates from 293T cells transfected with these expression vectors ( FIG. 13B ). These same mutations were also introduced into the gp145 ⁇ CFI (HXB2/BaL chimera) with V1 and V2 regions deleted, and protein expression was also confirmed ( FIG. 13C ).
  • V region mutations on immunogenicity. To evaluate the effect of these and other V region mutations on the elicitation of a neutralizing antibody response, deletions of different V regions in gp145 ⁇ CFI (HXB2/BaL chimera) and gp140 ⁇ CFI (HXB2/BaL chimera), individually or with combinations of V1 to V4, were made. Expression of the mutants revealed similar levels of protein by Western blotting ( FIG. 15A ). These V region mutants were assessed for their ability to elicit neutralizing antibodies using DNA/ADV immunization of guinea pigs. The elimination of specific V regions, particularly the combination of V1 and V3, or V1 and V4, markedly reduced their ability to induce a neutralizing antibody response.
  • vectors with specific combined deletions increased the neutralizing antibody response to HIV BaL (FIG. 15 B).
  • the increased potency of the V1V2 deletion construct was confirmed in further experiments using nine additional primary HIV-1 isolates; these data strongly indicated that this deletion construct provided better immunogenicity than the other constructs shown in FIG. 15B .
  • additional V3 region mutations were made in the V 1 V 2 deletion construct and the gp145 ⁇ CFI envelope mutant.
  • gp145 ⁇ CFI immunogen elicited slightly increased neutralization compared to wild-type gp145, but it did not reach statistical significance ( FIGS. 15B and 16A ).
  • V 1 V 2 gp145 ⁇ CFI ⁇ seen in FIG. 16A was due to a single nonresponder in a group of four animals.
  • the actual values in FIG. 16A for gp145 ⁇ CFI were 47, 60, 51, and 53, and those for V 1 V 2 gp145 ⁇ CFI ⁇ were 16, 71, 62, and 77%.
  • a further increment was suggested when the 1AB mutation was included in the V 1 V 2 gp145 ⁇ CFI ⁇ immmunogen.
  • larger deletions of the V3 region were made, they became successively less able to elicit a neutralizing antibody response.
  • all mutants were able to elicit comparable antibody responses, as determined by ELISA end-point limiting dilution analysis ( FIG. 16B ).
  • the ⁇ V 1 V 2 V 3 (1AB) ⁇ CFI mutant was most effective in inhibiting these four isolates.
  • Antisera elicited by this optimal immunogen, ⁇ V 1 V 2 V 3 (1AB) ⁇ CFI, were examined against a panel of ten primary HIV-1 isolates. The antisera displayed reactivities against a number of unrelated HIV-1 strains.
  • the breadth of the optimal candidate was determined against ten representative lade B viral isolates.
  • the breadth of this antisera was increased, with a higher IC 50 titer and increased reactivity against different HIV isolates ( FIG. 17 ).
  • V3 may be conserved among various isolates and affect Env function. This conservation is evident in specific sequences in this region, for example, the tip of the V3 (Korber, B. T. et al. 1994 J Virol 68:7467-7481). Though the V3 region has been shown to affect the tropism of HIV for the chemokine receptor (Briggs, D. R. et al. 2000 AIDS 14:2937-2939), the effects of progressive deletions in the V3 loop and its selective effect on CXCR4 targeting have not been previously appreciated. Recently, it has been suggested that conserved conformational determinants are present in the V3 loop of diverse isolates that show similar sensitivity to neutralizing antibodies (Gorny, M. K.
  • V1V2 mutations The enhanced immunogenicity of the V1V2 mutations in this study indicates that there may be masking of the V3 loop by V1 and V2 in HIVBal. Deletion of the V2 region has been suggested in previous studies to improve the antibody response (Srivastava, I. K. et al. 2003 J Virol 77:2310-2320), but it is not certain whether similar mechanisms are responsible for those effects and the observations noted here in a different strain in combination with V3 partial deletions, since the additional V1 deletion and the 1AB mutation in V3 further enhances its immunogenicity.
  • the increased breadth of this response indicates that common antigenic determinants are shared by many, though not all, clade B viruses. Taken together, these conserved regions reflect underlying functional requirements and structural homologies between different viruses. Therefore, the families of V3 determinants are envisioned as targets for expansion of the breadth of the neutralizing antibody response.
  • HIV-1 Env immunogen genetically disparate from the Env of the challenge virus can contribute to protective immunity.
  • the vaccine regimen included a plasmid DNA prime and replication-defective adenoviral vector boost.
  • Vaccine regimens that included the matched or mismatched Env immunogens conferred better protection against CD4 + T-lymphocyte loss than that seen with comparable regimens that did not include Env immunogens.
  • This increment in protective immunity was associated with anamnestic Env-specific cellular immunity that developed in the early days following viral challenge.
  • Env envelope (Env) proteins in human immunodeficiency virus (HIV) isolates worldwide poses a challenge for the development of an effective AIDS vaccine.
  • the failure of traditional vaccine strategies to provide protection against HIV infection is attributable, at least in part, to the genetic heterogeneity of Env (Letvin, N. L. et al. 2002 Annu Rev Immunol 20:73-99).
  • Env diversity underlies many of the problems associated with eliciting antibody responses that neutralize a variety of HIV isolates (Mascola, J. R. 2003 Curr Mol Med 3:209-216). This diversity also poses difficulties for generating T-lymphocyte responses through vaccination that recognize genetically varied viruses (Letvin, N. L. et al. 2002 Annu Rev Immunol 20:73-99).
  • the problems associated with Env diversity have raised questions about the utility of including an Env immunogen in candidate HIV vaccines.
  • Nonhuman primates have been powerful models for evaluating HIV vaccine strategies. Studies with macaques have provided evidence for the critical contribution of cellular immunity in controlling AIDS virus replication (Jin, X. et al. 1999 J Exp Med 189:991-998; Schmitz, J. E. et al. 1999 Science 283:857-860) and have illustrated the ability of vaccines to modify the clinical course of disease even when such vaccines cannot confer frank protection against infection with an AIDS virus isolate (Barouch, D. H. et al. 2000 Science 290:486-492; Amara, R. R. et al. 2001 Science 292:69-74).
  • HIV-1 gp120-specific binding antibodies were quantified by enzyme-linked immunosorbent assay as described previously (Crawford, J. M. et al. 1999 J Virol 73:10199-10207). Immunoplates (MaxiSorb F96) (Nunc, Roskilde, Denmark) were coated with BaL-gp120 (Quality Biological, Inc., Gaithersburg, Md.), IIIB-gp120 (Advanced Biotechnologies, Inc., Columbia, Md.), or KB9-gp120 (kindly provided by Patricia Earl, National Institutes of Allergy and Infectious Diseases, Bethesda, Md.).
  • Antibody detection was accomplished with alkaline phosphate-conjugated, goat anti-monkey immunoglobulin G (IgG) (whole molecule; Sigma Chemical Co, St. Louis, Mo.). Neutralizing antibodies were measured in MT-2 cells as described previously (Crawford, J. M. et al. 1999 J Virol 73:10199-10207). Briefly, 50 ⁇ l of cell-free SHIV-89.6P virus containing 500 50% tissue culture infective doses and grown in human peripheral blood mononuclear cells (PBMCs) was added to multiple dilutions of test plasma in 150 ⁇ l of growth medium in triplicate. These mixtures were incubated for 1 h before the addition of 5 ⁇ 10 4 MT-2 cells.
  • IgG immunoglobulin G
  • Neutralizing titers were calculated as the reciprocal dilution of plasma required to protect 50% of cells from virus-induced killing as measured by neutral red uptake.
  • the synthetic SIVmac239 gag-pol-nef gene was prepared by using a strategy similar to that used to construct a previously described HIV vaccine vector (Huang, Y. et al. 2001 J Virol 75:4947-4951). Briefly, the protein sequences of Gag, Pol, and Nef from SIVmac239 (GenBank accession no. M33262) were reverse translated with the GCG package (Genetics Computer Group, Inc., Madison, Wis.) with codons typically utilized in human cells.
  • Oligonucleotides covering 5169 DNA bp of the theoretical gene with 5′ SalI and 3′ BamHI sites and a consensus Kozak sequence were synthesized (GIBCO Life Technologies) from multiple fragments, each 75 bp long with 25 nucleotides (nt) of overlap.
  • the codon-modified gag-pol-nef gene was assembled by PCR with Pwo (Boehringer Mannheim) and Turbo Pfu (Stratagene) high-fidelity DNA polymerase. The PCR conditions were optimized with a PCR optimization kit (Stratagene) on a gradient Robocycler (Stratagene). The full-length synthetic gag-pol-nef gene was cloned into the SalI and BamHI site of the mammalian expression vector, pVR1012, and confirmed by DNA sequencing.
  • a synthetic 89.6P gp145 ⁇ CFI Env gene was made analogously to a previous HIV vector (Huang, Y. et al. 2001 J Virol 75:4947-4951; Xu, L. et al. 1998 Nat Med 4:37-42). Briefly, the protein sequence of the 89.6P envelope (GenBank accession no. U89134) was reverse translated as described above. Oligonucleotides covering 1,950 DNA bp of the theoretical gene, with a 5′ XbaI, a consensus Kozak sequence, and 3′ BamHI site, were synthesized (GIBCO Life Technologies): each fragment was 60 bp in length with 20 nt of overlap.
  • nt 1501 amino acids [aa] 501, R) to 1602 (aa 534, T) and nt 1771 (aa 591, M) to 1851 (aa 617, V) with respect to start codon ATG (A as nt 1) were deleted.
  • This deletion removes the cleavage site and fusion peptide for the envelope as well as part of the interspace between the two heptad repeats.
  • the protein was terminated at nt 2124 (aa 702, I).
  • the amino acid at 617 was changed to E from D due to the creation of XhoI cloning sites.
  • the codon-modified gp145 ⁇ CFI gene was assembled by PCR as described above.
  • the synthetic gp145 ⁇ CFI gene was cloned into the XbaI and BamHI sites of the mammalian expression vector pVR1012, and the sequence was confirmed by DNA sequencing.
  • the synthetic 89.6Pgp140 ⁇ CFI gene was derived from the gp145 ⁇ CFI plasmid with introduction of a termination codon after nt 2046 (aa 676, W).
  • the synthetic CCR-5-tropic clade B immunogen was derived from both HXB2 and Bal strain envelopes.
  • the protein sequence of the clade B Env glycoprotein (gp160) from HXB2 (X4-tropic; GenBank accession no. K03455) was used to create a synthetic version of the gene (X4gp160/h).
  • the nucleotide sequence of X4gp160/h shows little homology to the HXB2 gene, but the protein encoded is the same, with the following amino acid substitutions: aa 53 (phenylalanine ⁇ leucine), aa 94 (asparagine ⁇ aspartic acid), aa 192 (lysine ⁇ serine), aa 215 (isoleucine ⁇ asparagine), aa 224 (alanine ⁇ threonine), aa 346 (alanine ⁇ aspartic acid), and aa 470 (proline ⁇ leucine). These seven amino acid substitutions were present in the Los Alamos sequence database at the time those genes were synthesized.
  • R5gp160/h To produce an R5-tropic version of the envelope glycoprotein (R5gp160/h), the region encoding HIV-1 envelope glycoprotein aa 205 to 361 from X4gp160/h (VRC-3300, described in WO 02/32943) was replaced with the corresponding region from the BaL strain of HIV-1 (GenBank accession no. M68893, again using human preferred codons).
  • the full-length R5-tropic version of the envelope gene from pR5gp160/h (VRC-3000, described in WO 02/32943) was terminated after the codon for aa 704.
  • the truncated envelope glycoprotein contained the entire SU protein and a portion of the TM protein, including the fusion domain, the transmembrane domain, and regions important for oligomer formation. (H1 and H2 and their interspace are required for oligomerization.) Subsequently, the fusion and cleavage domains from aa 503 to 536 were deleted. The interspace between H1 and H2 from aa 593 to 620 was also deleted.
  • the gp140 ⁇ CFI version was derived from this sequence by introduction of a termination codon as previously described (Chakrabarti B K et al. 2002 J Virol 76:5357-5368).
  • rADVs Recombinant ADVs
  • rADVs Recombinant ADVs
  • SIVmac239 gag-pol adapted from the sequence described above (terminated at aa 1451) was cut with SalI, blunted, and then digested with BamHI, after which it was subcloned into the blunted EcoRV and BamHI sites of the shuttle plasmid pAdAdaptCMVmcs.
  • Synthetic HIV-1 gp140 ⁇ CFI adapted from the sequence described above was subcloned into the shuttle vector by using the XbaI and BamHI sites.
  • 293T cells were plated onto six-well plates and cultured to about 30% confluence, and then cotransfected with 2 ⁇ g of twice-cesium chloride-purified and linearized shuttle plasmid with ADV cosmid by the calcium phosphate method. After 7 to 12 days, the supernatant containing recombinant adenovirus was collected from the cell lysate with freezing and thawing at least three times in 0.6 ml of Tris-HCl, pH 8.0.
  • the production of recombinant adenovirus was scaled up by infection of 293T cells with the virus-containing supernatant.
  • the viruses were purified by cesium chloride, aliquoted as 10 12 particles/ml, and stored in phosphate-buffered saline (PBS) with 13% glycerol at ⁇ 20° C. for future use.
  • PBS phosphate-buffered saline
  • Expression of plasmid and rADV Env vaccine constructs Expression of plasmid and rADV Env vaccine constructs. Expression of plasmids encoding gp145 ⁇ CFI(R5) and gp145 ⁇ CFI(89.6P) was measured after transfection of 293T cells (in a six-well-dish) with a calcium phosphate transfection reagent (Invitrogen) with 2 ⁇ g of each plasmid.
  • ELISPOT assays Ninety-six well multiscreen plates were coated overnight with 100 ⁇ l (per well) of 5 ⁇ g/ml anti-human gamma interferon (IFN- ⁇ ) (B27; BD Pharmingen) in endotoxin-free Dulbecco's phosphate-buffered saline (D-PBS). The plates were then washed three times with D-PBS containing 0.25% TWEENTM 20 (D-PBS/Tween), blocked for 2 h with D-PBS containing 10% fetal bovine serum to remove the TWEENTM 20, and incubated with peptide pools and 2 ⁇ 10 5 PBMCs in triplicate in 100- ⁇ l reaction volumes.
  • IFN- ⁇ anti-human gamma interferon
  • D-PBS Dulbecco's phosphate-buffered saline
  • Each pool comprised 15-aa peptides overlapping by 11 aa, except for the HIV-1 89.6P Env pool, which comprised 20-aa peptides overlapping by 10 aa.
  • Each pool contained no more than 130 peptides.
  • Each peptide in a pool was present at a concentration of 1 ⁇ g/ml. Following an 18-h incubation at 37° C., the plates were washed nine times with D-PBS/TWEENTM and once with distilled water.
  • the plates were then incubated with 2 ⁇ g of biotinylated rabbit anti-human IFN- ⁇ /ml (Biosource) for 2 h at room temperature, washed six times with Coulter Wash (Beckman Coulter), and incubated for 2.5 h with a 1:500 dilution of streptavidin-alkaline phosphate (Southern Biotechnology).
  • CD4 + T-lymphocyte counts and viral RNA levels were determined by monoclonal antibody staining and flow cytometry. Plasma viral RNA levels were measured by an ultrasensitive branched DNA (bDNA) amplification assay with a detection limit of 500 copies per ml (Bayer Diagnostics).
  • bDNA ultrasensitive branched DNA
  • the Kruskal-Wallis test for three or four groups was used to compare the CD4 T-lymphocytes, peak viral RNA, set point viral RNA, and ELISPOT counts between vaccine groups.
  • the Wilcoxon test for censored data was used to compare time to detectable neutralizing antibodies between vaccine groups.
  • the Fisher exact test was used to compare the presence of detectable neutralizing antibodies at day 20 or within the first 42 days. Linear regression (ordinary least squares) was used to relate neutralizing antibodies and ELISPOT counts to CD4 T-lymphocyte counts and (separately) to log 10 plasma viral RNA; the Wald test was used to obtain significance levels. Power calculations for the Kruskal-Wallis and Wilcoxon tests were based on the fact that the worst asymptotic relative efficiency of these tests versus Gaussian-based tests is 0.86.
  • the DNA plasmid used in this study encoded a Gag-Pol-Nef fusion protein, but because of the instability of rADV constructs expressing Gag-Pol-Nef, the ADV vectors used in this study expressed only Gag-Pol. All HIV or SIV genes used in these vaccine constructs were codon modified as previously described to optimize expression in mammalian cells (Chakrabarti, B. K. et al. 2002 J Virol 76:5357-5368; Huang, Y. et al. 2001 J Virol 75:4947-4951).
  • the ADV vector contained a deletion in E1 to render the vector replication defective and a partial deletion/substitution in E3 that disrupts the coding sequences for the E3 proteins (Crawford, J. M. et al. 1999 J Virol 73:10199-10207; Ourmanov, I. et al. 2000 J Virol 74:2740-2751).
  • the rADV expressing either the HXB2/BaL or 89.6P gp140 ⁇ CFI was made as described previously (Polacino, P. et al. 1999 J Virol 73:618-630; Polacino, P. S. et al. 1999 J Virol 73:8201-8215).
  • the related gag-pol or identical env cDNA inserts were introduced and matched to the immunogens in the plasmid used for DNA priming as previously described (Amara, R. R. et al. 2002 J Virol 76:6138-6146; Barouch, D. H. et al. 2000 Science 290:486-492).
  • Each plasmid DNA was delivered intramuscularly as a 4-mg inoculum with a needleless Biojector device (Biological; Bioject Medical Technologies, Inc., Beckminister, N.J.) on a schedule of weeks 0, 4, and 8.
  • the levels of in vitro expression of the HXB2/Bal and 89.6P env genes were comparable in both the plasmid and rADV vaccine constructs ( FIG. 18 ).
  • a single inoculation of 10 12 particles of each rADV construct was given intramuscularly to each monkey on week 26.
  • the immunogenicity of these vaccine constructs was assessed by antibody binding, virus neutralization, and pooled-peptide ELISPOT assays. Plasma obtained 2 weeks after the rADV boost was assessed for BaL and 89.6P gp120 binding and for neutralization of the SHIV-89.6P challenge virus. While the Env-immunized monkeys developed high-titer antibodies to the immunizing BaL or 89.6P gp120, plasma from week 28 of the study, the time of peak ELISA titer antibody responses, failed to neutralize the challenge virus SHIV-89.6P.
  • ELISPOT responses by the PBMCs of all monkeys receiving experimental immunogens were robust ( FIG. 19 ).
  • Cellular immunity to SIV Gag, Pol, and Nef was generated in all groups of vaccinated monkeys, and that to HIV-1 89.6P and HXB2/BaL Env was generated in monkeys receiving these respective Env immunogens.
  • Monkeys injected with the mock Env (empty vectors) did not develop Env-specific cellular immunity.
  • SHIV-89.6P infection causes a precipitous decline in peripheral blood CD4 + T lymphocytes in approximately 75% of immunologically naive rhesus monkeys, and selected vaccine strategies can generate immune responses that blunt this CD4 + T-lymphocyte loss (Amara, R. R. et al. 2001 Science 292:69-74; Barouch, D. H. et al. 2000 Science 290:486-492; Reimann, K. A. et al.
  • Viral replication in the SHIV-89.6P-challenged monkeys was assessed by quantitating viral RNA in their plasma by using a bDNA assay ( FIG. 22 ). Since only 15% of immunologically na ⁇ ve rhesus monkeys control this virus to undetectable levels following infection, the plasma viral RNA levels at both peak and steady state or set point in experimental animals provide a measure of vaccine-mediated containment of virus. The medians of peak viral loads in the four groups of monkeys were 1 ⁇ 10 8 (control), 6 ⁇ 10 6 (mock Env), 4 ⁇ 10 6 (matched Env), and 1 ⁇ 10 6 (mismatched Env).
  • the group of monkeys that received SIV Gag-Pol-Nef plus mismatched Env immunogens also demonstrated better containment of virus at set point than the monkeys receiving SIV Gag-Pol-Nef plus mock Env immunogens.
  • the antiviral humoral immune response was evaluated.
  • Anti-Env antibody could potentially contribute to protection by neutralizing infectious virus at the time of challenge.
  • a rapidly evolving anamnestic neutralizing antibody response after infection could contribute to the control of viral spread.
  • None of the vaccinated monkeys had detectable plasma neutralizing antibodies at the time of challenge, indicating that vaccine-elicited preexisting neutralizing antibody did not contribute to viral containment.
  • the evolution of an antibody response that neutralized the challenge virus SHIV-89.6P was monitored on a weekly basis in vaccinated monkeys after viral challenge ( FIG. 23 ).
  • PBMC cellular immune responses from the four groups of experimental monkeys were assessed 1 week following rADV boosting for cellular immunity to a pool of HIV-1 89.6P Env peptides in an ELISPOT assay ( FIG. 24 , top panel).
  • the mean responses were 449 ⁇ 122 SFC (mean ⁇ standard error) in the matched Env group, 730 ⁇ 306 SFC in the mismatched Env group, and 13 ⁇ 8 SFC in the mock Env group.
  • the apparent higher PBMC SFC response in the HXB2/Bal Env-vaccinated monkeys to 89.6P Env than to HXB2/BaL Env does not achieve statistical significance.
  • Multiclade HIV-1 Envelope Immunogens Elicit Broad Cellular and Humoral Immunity in Rhesus Monkeys
  • HIV-1 vaccine that elicits potent cellular and humoral immune responses that recognize divergent strains of HIV-1 will be critical for combating the global AIDS epidemic.
  • the present studies were initiated to examine the magnitude and breadth of envelope (Env)-specific T lymphocyte and antibody responses generated by vaccines containing either a single or multiple genetically distant HIV-1 Env immunogens.
  • Rhesus monkeys were immunized with DNA prime/rAd boost vaccines encoding a Gag/Pol/Nef polyprotein in combination with either a single Env or with a mixture of clade A, clade B, and clade C Envs.
  • HIV-1 envelope The extreme genetic diversity of human immunodeficiency virus type 1 (HIV-1) envelope (Env) poses a daunting challenge for the creation of an effective AIDS vaccine (Letvin, N. L et al. 2002 Annu Rev Immunol 20:73-99). While Env is the principal target for HIV-1-specific antibody responses, it also serves as a potent T cell immunogen (See PART IV). An ideal HIV-1 vaccine should elicit potent cellular and humoral immunity capable of recognizing a diversity of viral isolates (Mascola, J. R., and G. J. Nabel. 2001 Curr Opin Immunol 13:489-95; Nabel, G. J. 2001 Nature 410:1002-7). However, the extraordinary genetic variation of HIV-1 Env worldwide may make it impossible to create an effective vaccine using only a single Env gene product.
  • Env immunogens derived from a single HIV-1 primary isolate (Graham, B. S. 2002 Annu Rev Med 53:207-21)
  • this approach has significant limitations. Although these vaccines generate potent cellular and humoral immune responses against HIV-1 Env, it is likely that the breadth of immunity elicited by a single Env immunogen will not effectively confer protection against divergent strains of HIV-1. It is, however, not feasible to undertake the development of multiple country- or clade-specific vaccines. Moreover, such region-specific vaccines would likely not protect against unrelated strains that might be newly introduced into a population.
  • the present studies utilized the simian human immunodeficiency virus (SHIV)/rhesus monkey model to investigate the breadth and magnitude of immunity elicited by a DNA prime/recombinant adenovirus boost vaccine containing Gag/Pol/Nef and either single lade or multiple clade Env immunogens.
  • SHIV simian human immunodeficiency virus
  • Our findings demonstrate that a multiclade Env vaccine elicits potent cellular and humoral immune responses with greater breadth than can be generated with immunizations performed with a single Env immunogen.
  • Plasmid DNA and recombinant adenovirus (rAd) vaccine vectors were constructed as previously described (see PARTS II and IV), and administered by intramuscular injection using a needle-free Biojector system and a no. 3 syringe (Bioject, Portland, Oreg.) as outlined in Table 3. Each plasmid DNA or rAd vaccine vector was split into two aliquots of 0.5 ml each, and delivered into each quadriceps muscle. Control monkeys were similarly immunized with sham DNA and sham rAd vectors. At week 42, all monkeys received an intravenous challenge with 50 50% monkey infective doses (MID 50 ) of SHIV-89.6P.
  • MID 50 monkey infective doses
  • IFN- ⁇ ELISPOT assays IFN- ⁇ ELISPOT assays. IFN- ⁇ ELISPOT assays were performed as described above in PART IV. Freshly isolated PBL were plated in triplicate at 2+10 5 cells/well in 100 ⁇ l final volume with either medium alone or peptide pools. Peptide pools covered the entire SIVmac239 Gag, Nef, and Pol proteins, and the HIV-1 clade A, clade B, clade C, and 89.6P Env proteins. Each pool was comprised of 15 amino acid peptides overlapping by 11 amino acids, but for the HIV-1 89.6P Env pool, which was comprised of 20 amino acid peptides overlapping by 10 amino acids.
  • Pol and Env peptides were each split into two separate pools such that each pool contained no more than 130 peptides. Each peptide in a pool was present at a concentration of 1 ⁇ g/ml. The mean number of spots from triplicate wells was calculated for each animal and adjusted to represent the mean number of spots per 10 6 PBL. Data are presented as the mean number of antigen-specific spots per 10 6 PBL from 6 monkeys per group.
  • HIV-1 Envelope Antibody ELISA HIV-1 Envelope Antibody ELISA.
  • Vaccine Research Center (VRC) plasmids 5304, 2801, and 5308 (which encode HIV-1 gp145 clade A, clade B, and clade C Env, respectively) (described in WO 02/32943) were expressed in 293 cells and purified for the major protein product.
  • Optimized concentrations of the recombinant antigens (37.5 ng/well) were coated onto Immunol-2 HB microtiter plates (Thermo Labsystems, Milford, Mass.) overnight at 4° C. Serial dilutions of monkey plasma were done in duplicate wells and incubated for 2 hours at 37° C.
  • Biotin labeled anti-monkey IgG/IgA/IgM (Rockland Immunochemicals, Gilbertsville, Pa.) was added for 1 hr at 37° C. Streptavidin-HRPO (KPL, Gaitherburg, Md.) was added to wells for 30 minutes at room temperature, followed by TMB substrate (KPL) for 30 minutes at room temperature. Endpoint titers for each animal were established as the last dilution with a pre-immunization corrected OD>0.2. Data are presented as the geometric mean titer from 6 monkeys per group ⁇ SEM.
  • Virus isolates and neutralization assays A total of 30 HIV-1 isolates were studied: 11 clade B, 11 clade C and 8 clade A. Viruses were obtained from the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH, except as specifically noted below. All clade B viruses were primary isolates except the T-cell line adapted HxB2, which is the molecular clone of HIV-IIIB. BR07 was provided by Dana Gabuzda of the Dana-Farber Cancer Institute.
  • TV1 (clade C) was provided by David Montefiori and Estrelita Janse Van Rensburg (University of Whybosch, South Africa).
  • GS14 is an infectious molecular clone of an Ethiopian clade C virus that was provide by Francine McCutchan and colleagues from the US Military HIV Research program.
  • Clade A viruses DJ263 and 44951 were primary virus isolates provided by researchers from the US Military HIV Research program. The UG29 isolate had been previously passaged into H9 cells, and would therefore be considered a T-cell line adapted virus.
  • Virus neutralization assays were performed using a single round of infection flow cytometric assay using previously described methods (Mascola, J. R. et al. 2002 J Virol 76:4810-21). This assay detects HIV-1 infected T-cells by intracellular staining for HIV-1 p24 Gag antigen (p24-Ag). A protease inhibitor is used to prevent secondary rounds of virus replication. The percent virus neutralization mediated by each immune plasma was derived by calculating the reduction in the number of p24-Ag positive cells in the test wells with immune sera, compared to the number of p24-Ag positive cells in wells containing pre-immune plasma from the corresponding animal.
  • the MuLV reporter viruses encoded green fluorescent protein (GFP) and infected T-cell cells were detected by expression of GFP rather than expression of p24-Ag (Mascola, J. R. et al. 2002 J Virol 76:4810-21).
  • Plasma viral RNA levels were measured by an ultrasensitive branched DNA amplification assay with a lower detection limit of 125 copies per ml (Bayer Diagnostics, Berkeley, Calif.). Peak plasma viral load was measured on day 16 post-SHIV-89.6P challenge in all vaccinated and control monkeys. Set point plasma viral RNA levels were calculated as the median of values measured at six time points between days 85 and 169 post-challenge. The percentage of CD4 + T lymphocytes in the peripheral blood of infected monkeys was determined by monoclonal antibody staining and flow cytometric analysis.
  • the nonparametric Wilcoxon rank sum test was used to compare CD4 + T lymphocytes, peak viral RNA, and set point viral RNA between monkeys in the non-vaccinated and vaccinated groups. All tests were two-sided.
  • Groups 1-4 received three priming immunizations at weeks 0, 4, and 8 with 4.5 mg plasmid DNA vectors expressing an SIVmac239 Gag-Pol-Nef fusion protein and plasmid DNA vectors expressing various HIV-1 Env proteins.
  • Groups 1-3 were immunized with single HIV-1 Env immunogens as follows: 1) 4.5 mg lade B Env (high lade B), 2) 1.5 mg clade B Env (low clade B), and 3) 4.5 mg clade C Env (high clade C).
  • Group 4 monkeys were immunized with a combination of HIV-1 Env immunogens, 1.5 mg each of a lade A Env, clade B Env, and clade C Env (clade A+B+C).
  • monkeys received a single rAd boost immunization (2.0 ⁇ 10 12 total particles) with vectors expressing SIVmac239 Gag-Pol and various HIV-1 Env genes consistent with those delivered during the DNA priming (Table 3).
  • Groups 1-3 received: 1) 1.0 ⁇ 10 12 particles clade B Env (high clade B), 2) 3.3 ⁇ 10 11 particles clade B Env (low clade B), 3) 1.0 ⁇ 10 12 particles clade C Env (high clade C).
  • Group 4 received 3.3 ⁇ 10 11 particles each of clade A, clade B and clade C Env (clade A+B+C).
  • Group 5 monkeys were immunized with sham DNA and sham rAd vectors. DNA prime and rAd boost immunizations were delivered by intramuscular injection. All plasmid DNA and rAd vectors expressed codon-modified SIVmac239 and HIV-1 genes for enhanced expression in mammalian cells. All env genes used in these vectors were ⁇ CFI constructs, containing mutations in the cleavage, fusion, and interhelical domains that have previously been shown to enhance expression and immunogenicity (Chakrabarti, B. K. et al.
  • the monkeys developed responses to the clade A, lade B, clade C, and 89.6P Env peptide pools that were of comparable magnitude ( FIG. 25B ). Furthermore, the magnitudes of each individual clade-specific ELISPOT response in these monkeys were comparable to the optimal clade-specific response elicited in monkeys receiving a single clade Env immunogen. Finally, the vaccine-elicited Env-specific T cell responses in all groups of monkeys were durable, persisting at a high frequency up to the time of viral challenge ( FIG. 25C ).
  • Plasma samples obtained following the rAd boost immunizations were also tested for neutralizing activity against panels of 30 clade A, clade B, and clade C HIV-1 isolates ( FIG. 28 ). While plasmas from all groups of vaccinated monkeys demonstrated modest levels of neutralization against some HIV-1 isolates, the antibodies of monkeys immunized with a single lade Env immunogen exhibited the highest neutralizing activity against viruses of the same clade. Thus, plasma from the clade B immunized animals displayed little activity against clade A or C viruses and plasmas from clade C immunized animals did not neutralize clade B viruses. However, there was some cross-neutralization of clade A viruses by the clade C vaccine plasma.
  • the multiclade Env immunized monkeys developed antibodies with neutralizing activity against some HIV-1 strains from all three clades, and there was no decrement in the potency of neutralization compared to single Env immunization.
  • Two controls were performed to demonstrate that the modest levels of virus neutralization observed were due to HIV-1 specific antibodies.
  • the mean neutralization activity of plasma obtained from sham vaccinated monkeys was consistently less than twenty percent ( FIG. 28 , dashed line).
  • the mean activity of plasma from each of the vaccine groups against a MuLV Env pseudovirus was less than 20% (shown in FIG. 28A ).
  • HIV-1 vaccine must elicit effective immune responses to diverse viral isolates.
  • broadly cross-reactive HIV-1-specific T cell immune responses have been described. HIV-1-infected individuals develop T lymphocyte responses that recognize viral sequences from a diversity of HIV-1 clades (Cao, H. et al 1997 J Virol 71:8615-23). Cross-clade reactive CTL have also been detected in uninfected volunteers who have been vaccinated with recombinant canarypox constructs (Ferrari, G. et al. 2000 AIDS Res Hum Retroviruses 16:1433-43).
  • a concern with a vaccine that includes viral proteins from multiple clades of HIV-1 is that interference between these diverse antigens may diminish immune responses.
  • interference has been observed in vaccines that include proteins of multiple pathogens (Fattom, A et al. 1999 Vaccine 17:126-33; Drei, R. A. 1995 Ann N Y Acad Sci 754:35-47).
  • studies have shown that complex mixtures of plasmid DNA vaccines can lead to decreased protein expression and immunogenicity in vivo (Kjerrstrom, A. et al. 2001 Virology 284:46-61; Sedegah, M. et al. 2004 Gene Ther 11:448-56).
  • the present study demonstrates that the inclusion of viral proteins from multiple clades of HIV-1 is a viable approach for a global HIV-1 vaccine.
  • VRC-HIVDNA-009-00-VP is a vaccine composed of four DNA plasmids encoding proteins from HIV-1 and is intended to prevent HIV-1 infection. The vaccine has been designed to elicit immune responses against several proteins from three HIV-1 clades. Plasmid VRC-4306 (SEQ ID NO: 20) is designed to express HIV-1 polyproteins (structural core protein Gag, viral polymerase Pol, and accessory protein Nef) from clade B and is 50% (by weight) of the vaccine.
  • HIV-1 polyproteins structural core protein Gag, viral polymerase Pol, and accessory protein Nef
  • Plasmids VRC-5305 (SEQ ID NO: 21), VRC-2805 (SEQ ID NO: 22), and VRC-5309 (SEQ ID NO: 23) express the HIV-1 Envelope (Env) glycoproteins from clade A, clade B, and clade C, respectively, and are each 16.67% (by weight) of the vaccine.
  • the DNA plasmid expressing HIV-1 Gag-Pol-Nef polyprotein has been modified to reduce toxicity through the incorporation of deletions into the regions affecting the protease, reverse transcriptase, and integrase activities.
  • the amino acid sequence of the Nef protein was not modified.
  • the amino acid sequence of the Nef protein was fused in frame from the initiator methionine to the pol gene of HIV and is non-functional.
  • the sequences used to create the DNA plasmids encoding Env are derived from three HIV-1 CCR5-tropic strains of virus. Expression of the gene products is controlled by the constitutive cytomegalovirus (CMV) promoter. These DNA plasmids have been produced in bacterial cell cultures under kanamycin selection.
  • CMV constitutive cytomegalovirus
  • bacterial cell growth is dependent upon expression of the kanamycin resistance protein encoded in the plasmid DNA.
  • the plasmid DNA is purified from cellular components.
  • the clade B gag-pol-nef plasmid (VRC-4306) is 9790 nucleotide pairs in length and has an approximate molecular weight of 6.5 MDa;
  • the clade A, B, and C env plasmids (VRC-5305, VRC-2805, and VRC-5309) are 6836, 6869, and 6829 nucleotides in length, respectively, and have an approximate molecular weight of 4.5 MDa.
  • VRC-4306 [pVR1012 Gag-B ( ⁇ FS) Pol ( ⁇ PR ⁇ RT ⁇ IN) Nef/h]
  • DNA plasmid VRC-4306, diagrammed in FIG. 32 the protein sequences of the Gag, Pol, and Nef proteins from an HIV-1 clade B were used to create a synthetic polyprotein version of the gag-pol-nef genes using codons optimized for expression in human cells.
  • the synthetic gag gene is from HIV-1 clade B strain HXB2 (GenBank accession number K03455, amino acids 1-432), the synthetic pol gene (pol/h) is from HIV-1 clade B NL4-3 (GenBank accession number M19921), and the synthetic nef gene (nef/h) is from HIV-1 clade B strain PV22 (GenBank accession number K02083).
  • the nucleotide sequence of the synthetic gag-pol-nef/h gene shows little homology to the HIV-1 gene, but the protein encoded is the same.
  • Plasmid VRC-4306 was constructed by fusion of nef/h to the 3′ terminal of the gag-pol plasmid (VRC-4302), which is described in the WO 02/32943. There were no losses or additions of amino acids created by the fusion between pol and nef. The ATG of nef was preserved. The construct was then inserted into the pVR1012 backbone using SalI and BbvCI restriction sites. The SalI (5 nt upstream from ATG) to BbvCI (4917 nt downstream from ATG) fragment contains the 5′ end and the ATG was cloned into the SalI to BbvCI sites of the pVR1012 backbone.
  • VRC-4306 domains A summary of the predicted VRC-4306 domains is provided in Table 4.
  • the plasmid is 9790 nucleotide pairs (np) in length and has an approximate molecular weight of 6.5 MDa.
  • the kanamycin gene is incorporated into the bacterial vector backbone as a selectable marker.
  • the sequence of VRC-4306 is provided as SEQ ID NO: 20.
  • DNA plasmids are designed to express HIV-1 Env glycoproteins that are modified to reduce potential cellular toxicity by deletion of the fusion domain, the cleavage domains, and a portion of the interspace (IS) between heptad 1 (HI) and heptad 2 (H2).
  • IS interspace
  • VRC-5305 [pVR1012x/s CCR5-tropic gp145 Clade A ( ⁇ CFI)/h]
  • the DNA plasmid, VRC-5305 is diagrammed in FIG. 33 .
  • the protein sequence of the clade A Env polyprotein (gp160) from 92rw020 (CCR5-tropic, GenBank accession number U08794) was used to create a synthetic version of the gene (clade A gp145 ⁇ CFI/h) using codons modified for expression in human cells.
  • the nucleotide sequence of the clade A CCR5-tropic gp145 ⁇ CFI shows little homology to the 92rw020 gene, but the protein encoded is the same (note that GenBank U08794 sequence does contain the MR codons at the start of the sequence, so these were inserted into the synthetic construct).
  • the truncated Env polyprotein contains the entire surface (SU) and transmembrane (TM) proteins, but lacks the fusion and cytoplasmic domains. Regions important for oligomer formation are retained, specifically the two helical coiled coil regions.
  • the fusion and cleavage (F/CL) domains from amino acids 486-519 were deleted.
  • the IS between H1 and H2 from amino acids 576-603 was also deleted.
  • the construct was then inserted into the pVR1012x/s backbone using XbaI and BamH1 restriction sites.
  • the XbaI (17 nt upstream from ATG) to BamH1 (1897 nt downstream from ATG) fragment contains a polylinker at the 5′ end and the ATG was cloned into the XbaI to BamH1 sites of pVR1012x/s backbone.
  • VRC-5305 domains A summary of the predicted VRC-5305 domains is provided in Table 5.
  • the plasmid is 6836 nucleotide pairs (np) in length and has an approximate molecular weight of 4.5 MDa.
  • the sequence of VRC-5305 is provided as SEQ ID NO: 21.
  • VRC-2805 [pVR1012x/s CCR5-tropic gp145( ⁇ F/CL ⁇ H IS)/h]
  • the DNA plasmid, VRC-2805, is diagrammed in FIG. 34 .
  • the protein sequence of the clade B Env glycoprotein (gp160) from HXB2 (CXCR4-tropic, GenBank accession number K03455) was used to create a synthetic version of the gene (CXCR4gp160/h) using codons modified for optimal expression in human cells.
  • the nucleotide sequence X4gp160/h shows little homology to the HXB2 gene, but the protein encoded is the same with the exception of the following amino acid substitutions: F53L, N94D, K192S, P470L, I580T, and Z653H.
  • R5gp160/h To produce a CCR5-tropic version of the Env glycoprotein (R5gp160/h), the region encoding HIV-1 Env polyprotein amino acids 205 to 361 from X4gp160/h (VRC-3300, described in the WO 02/32943) was replaced with the corresponding region from the BaL strain of HIV-1 (GeneBank accession number M68893), again using human preferred codons.
  • the nucleotide sequence R5gp160/h shows little homology to the CCR5 gene, but the protein encoded is the same with the following amino acid (aa) substitutions: I219N, L265V, N266T, and S268N.
  • the full-length CCR5-tropic version of the env gene from pR5gp160/h was terminated after the codon for amino acid 704.
  • the truncated Env glycoprotein (gp145) contains the entire surface (SU) protein and a portion of the transmembrane (TM) protein including the fusion domain, the transmembrane domain, and regions important for oligomer formation, specifically, the two helical coiled coil motifs.
  • the fusion and cleavage (F/CL) domains from amino acids 503-536 were deleted.
  • the IS between H1 and H2 from amino acids 594-619 was also deleted.
  • the construct was then inserted into the pVR1012x/s backbone using XbaI and BamH1 restriction sites.
  • the XbaI (18 nt upstream from ATG) to BamH1 (1937 nt downstream from ATG) fragment that contains a polylinker at the 5′ end and the ATG was cloned into the XbaI to BamH1 sites of the 1012x/s backbone.
  • VRC-2805 domains A summary of the predicted VRC-2805 domains is provided in Table 6.
  • the plasmid is 6869 nucleotide pairs (np) in length and has an approximate molecular weight of 4.5 MDa.
  • the kanamycin gene is incorporated into the bacterial vector backbone as a selectable marker.
  • the sequence of VRC-2805 is provided as SEQ ID NO: 22.
  • VRC-5309 [pVR1012x/s CCR5-tropic gp145 Clade C ( ⁇ CFI)/h]
  • the DNA plasmid, VRC-5309 is diagrammed in FIG. 35 .
  • the protein sequence of the clade C Env polyprotein (gp145 ⁇ CFI) from 97ZA012 was used to create a synthetic version of the gene (clade C gp145 ⁇ CFI/h) using codons modified for optimal expression in human cells.
  • the nucleotide sequence of the clade C CCR5-tropic gp145 ⁇ CFI/h shows little homology to the gene 97ZA012, but the protein encoded is the same except for the following substitution: D605E.
  • the truncated Env polyprotein contains the entire SU protein and the TM domain, but lacks the fusion domain and cytoplasmic domain. Regions important for oligomer formation are retained, specifically the two helical coiled coil motifs.
  • the fusion and cleavage (F/CL) domains from amino acids 487-520 were deleted.
  • the interspace between H1 and H2 from amino acids 577-604 was also deleted.
  • the construct was then inserted into the pVR1012x/s backbone using XbaI and BamH1 restriction sites.
  • the XbaI (17 nt upstream from ATG) to BamH1 (1882 nt downstream from ATG) fragment contains a polylinker at the 5′ end and the ATG was cloned into the XbaI to BamH1 sites of pVR1012x/s backbone.
  • VRC-5309 domains A summary of the predicted VRC-5309 domains is provided in Table 7.
  • the plasmid is 6829 nucleotide pairs (np) in length and has an approximate molecular weight of 4.5 MDa.
  • the kanamycin gene is incorporated into the bacterial vector backbone as a selectable marker.
  • the sequence of VRC-5309 is provided as SEQ ID NO: 23.
  • Plasmids VRC-2805, 4306, 5305, and 5309 were sequenced by Lark Technologies and the sequences subjected to a BLAST search using the BLASTN program searching the human est database.
  • the search was done using parameters that only identified sequence homologies with expected values (E values) of 0.01 or lower. This means that the statistical possibility of a homology occurring by chance alone is only 1/100. Anything at this level or lower (i.e. less than 1/100) will be picked up by the search.
  • the other result shows homology with the bovine growth hormone poly A terminator portion of the plasmid.
  • the sequences detected were 90 to 100% identical to the sequences in the plasmids.
  • the human genes associated with this homology were not related to human growth hormone or related proteins.
  • the description of the clones revealed that they had been excised from expression vectors (e.g., pDNA3) in which the cloning site was immediately adjacent to a bovine growth hormone poly A terminator.
  • expression vectors e.g., pDNA3
  • pUC18 homologies it is believed that these homologies are spurious and represent contamination of the database with plasmid sequence from cloning operations.
  • Gag-Pol-Nef protein encoded by plasmid VRC-4306 is determined by quantitation of the level of Gag-Pol-Nef protein expressed by transfected HEK-293 (human embryonic kidney) cells. For transfection, 10 5 to 10 6 cells are transfected with 1-5 ⁇ g of VRC-4306 plasmid DNA using the calcium phosphate method. Cells are incubated for 14-20 hours to allow for DNA uptake. Following a medium change, cells are grown for an additional 24-48 hours before harvesting. Transfection efficiency is monitored using a human alkaline phosphatase vector in a similar backbone.
  • H1V1 gag- ⁇ -gal fusion protein (Chemicon) is mixed with 10 ⁇ g of cell lysate from non-transfected HEK293 cells and loaded onto the gel.
  • the proteins are transferred to a nitrocellulose membrane (0.45 ⁇ m) for Western Blot analysis. The membrane is blocked with skim milk to prevent non-specific binding interaction prior to incubation with the primary antibody (mouse anti-HIV p24 [ICN Biomedical]) for 30-60 minutes.
  • the membrane is incubated for 30-60 minutes with HRP-sheep anti-mouse IgG. Visualization of the protein bands is achieved by incubating the membrane with chemiluminescent substrates and exposing to X-ray film for 2-30 minutes. For quantitation, the intensity of the Gag-Pol-Nef protein band is compared to the intensity of t of the HIV-1 gag- ⁇ -gal fusion protein bands.
  • Envelope protein expression by plasmids VRC-5305, VRC-2805, and VRC-5309 is determined in an analogous manner to that used for analysis of VRC-4306.
  • cell lysate is harvested and analyzed by Western Blot analysis.
  • the membrane is incubated with human IgG antiserum against gp160 (NIH AIDS Research and Reference Reagent Program). Protein expression levels are quantitated by comparing the intensity of the envelope protein bands to those of the purified gp160 protein standard. Transfection efficiency is monitored using a ⁇ -galactosidase expression vector in a similar backbone.
  • VRC-HIVDNA016-00-VP is a multi-plasmid DNA vaccine intended for use as a preventive vaccine for HIV-1. It is a mixture of six plasmids in equal concentration. It was constructed to produce Gag, Pol, Nef and Env HIV-1 proteins to potentially elicit broad immune responses to multiple HIV-1 subtypes isolated in human infections.
  • VRC-HIVDNA016-00-VP The drug substances for VRC-HIVDNA016-00-VP are six closed circular plasmid DNA macromolecules (VRC-4401, VRC-4409, VRC-4404, VRC-5736, VRC 5737, and VRC-5738) that have been produced in bacterial cell cultures containing a kanamycin selection medium. In all cases, bacterial cell growth is dependent upon the cellular expression of the kanamycin resistance protein encoded by a portion of the plasmid DNA. Following growth of bacterial cells harboring the plasmid, the plasmid DNA is purified from cellular components.
  • Plasmids containing viral gene complementary DNAs were used to subclone the relevant inserts into plasmid DNA expression vectors that use the CMV/R promoter and the bovine growth hormone polyadenylation sequence.
  • the HIV-1 gene inserts have been modified to optimize expression in human cells.
  • the CMV/R promoter consists of translational enhancer region of the CMV immediate early region 1 enhancer (CMV-IE) substituted with the 5′-untranslated HTLV-1 R-U5 region of the human T-cell leukemia virus type 1 (HTLV-1) long terminal repeat (LTR) to optimize gene expression further.
  • CMV-IE CMV immediate early region 1 enhancer
  • HTLV-1 R-U5 region human T-cell leukemia virus type 1
  • LTR long terminal repeat
  • DNA plasmid VRC-4401 diagrammed in FIG. 36 , the protein sequence of the gag polyprotein (Pr55, amino acids 1-432) from HXB2 (GenBank accession number K03455) was used to create a synthetic version of the gag gene using codons optimized for expression in human cells.
  • the nucleotide sequence of the synthetic gag gene shows little homology to the HXB2 gene, but the protein encoded is the same.
  • the SalI/BamHI fragment of Gag (B) was excised from VRC 3900 (described in the WO 02/32943), which contained the same insert in a pVR1012 backbone, and cloned into the SalI/BamHI sites of the CMV/R backbone described above.
  • VRC-4401 domains A summary of predicted VRC-4401 domains is provided in Table 8.
  • the plasmid is 5886 nucleotide base pairs (bp) in length and has an approximate molecular weight of 3.9 MDa.
  • the sequence of VRC-4401 is provided as SEQ ID NO: 24.
  • DNA plasmid VRC-4409 diagrammed in FIG. 37 , the protein sequence of the pol polyprotein (amino acids 3-1003) from NL4-3 (GenBank accession number M19921) was used to create a synthetic version of the pol gene using codons optimized for expression in human cells.
  • a methionine codon was added to the 5′-end of the synthetic polymerase gene to create the Pol/h gene.
  • the Protease (PR) mutation is at amino acid 553 and is AGG ⁇ GGC or amino acids R ⁇ G.
  • the Reverse Transcriptase (RT) mutation is at amino acid 771 and is GAC ⁇ CAC or amino acids D ⁇ H.
  • the Integrase (IN) mutation is at amino acid 1209 and is ACT ⁇ CAT or amino acids D ⁇ A.
  • the gene expressing Pol was inserted into the CMV/R backbone described above.
  • VRC-4409 domains A summary of predicted VRC-4409 domains is provided in Table 9.
  • the plasmid is 7344 nucleotide base pairs (bp) in length and has an approximate molecular weight of 4.8 MDa.
  • the sequence of VRC-4409 is provided as SEQ ID NO: 25.
  • Nef protein sequence from HIV-1 NY5/BRU (LAV-1) clone pNL4-3 (GenBank accession number M19921) was used to create a synthetic version of the Nef gene (Nef/h) using codons optimized for expression in human cells.
  • the nucleotide sequence. Nef/h shows little homology to the viral gene, but the protein encoded is the same.
  • the Myristol site (GGC-Gly, amino acid 2-3) was deleted.
  • the fragment encoding Nef was digested from the pVR1012 backbone in which it was originally inserted, with XbaI/BamHI, and then cloned into the XbaI/BamHI site of the CMV/R backbone described above.
  • VRC-4404 domains A summary of predicted VRC-4404 domains is provided in Table 10.
  • the plasmid is 5039 nucleotide base pairs (bp) in length and has an approximate molecular weight of 3.3 MDa.
  • the sequence of VRC-4404 is provided as SEQ ID NO: 26.
  • DNA plasmid VRC-5736 diagrammed in FIG. 39 , the protein sequence of the envelope polyprotein (gp160) from 92rw020 (R5-tropic, GenBank accession number U08794) was used to create a synthetic version of the gene (Clade-A gp145 ⁇ CFI) using codons altered for expression in human cells. Plasmids expressing the HIV-1 genes were made synthetically with sequences designed to disrupt viral RNA structures that limit protein expression by using codons typically found in human cells. The nucleotide sequence R5gp145 ⁇ CFI shows little homology to the 92rw020 gene, but the protein encoded is the same.
  • the truncated envelope polyprotein contains the entire SU protein and the TM domain, but lacks the fusion domain and cytoplasmic domain. Regions important for oligomer formation may be partially functional. Heptad(H) 1, Heptad 2 and their Interspace(IS) are required for oligomerization.
  • EnvA summary of predicted VRC-5736 domains is provided in Table 11.
  • the plasmid is 6305 nucleotide base pairs (bp) in length and has an approximate molecular weight of 4.2 MDa.
  • the sequence of VRC-5736 is provided as SEQ ID NO: 27.
  • DNA plasmid VRC-5737 diagrammed in FIG. 40 the protein sequence of the envelope polyprotein (gp160) from HXB2 (X4-tropic, GenBank accession number K03455) was used to create a synthetic version of the gene (X4gp160/h) using codons optimized for expression in human cells.
  • the nucleotide sequence X4gp160/h shows little homology to the HXB2 gene, but the protein encoded is the same with the following amino acid substitutions: F53L, N94D, K192S, I215N, A224T, A346D, and P470L.
  • R5gp160/h an R5-tropic version of the envelope protein (R5gp160/h)
  • the region encoding HIV-1 envelope polyprotein amino acids 275 to 361 from X4gp160/h (VRC3300) were replaced with the corresponding region from the BaL strain of HIV-1 (GeneBank accession number M68893, again using human preferred codons).
  • the full-length R5-tropic version of the envelope protein gene from pR5gp160/h (VRC3000, described in the WO 02/32943) was terminated after the codon for amino acid 704.
  • the truncated envelope polyprotein (gp145) contains the entire SU protein and a portion of the TM protein including the fusion domain, the transmembrane domain, and regions important for oligomer formation.
  • Heptad(H) 1, Heptad 2 and their Interspace (IS) are required for oligomerization.
  • the expression vector backbone is CMV/R, described above.
  • VRC-5737 domains A summary of predicted VRC-5737 domains is provided in Table 12.
  • the plasmid is 6338 nucleotide base pairs (bp) in length and has an approximate molecular weight of 4.2 MDa.
  • the sequence of VRC-5737 is provided as SEQ ID NO: 28.
  • DNA plasmid VRC-5738 diagrammed in FIG. 41 , the protein sequence of the envelope polyprotein (gp145 ⁇ CFI) from 97ZA012 (R5-tropic, GenBank accession number AF286227) was used to create a synthetic version of the gene (Clade-C gp145 ⁇ CFI) using codons optimized for expression in human cells.
  • the nucleotide sequence R5gp145 ⁇ CFI shows little homology to the gene 97ZA012, but the protein encoded is the same.
  • the truncated envelope polyprotein contains the entire SU protein and the TM domain, but lacks the fusion domain and cytoplasmic domain. Regions important for oligomer formation may be partially functional.
  • Heptad(H) 1, Heptad 2 and their Interspace(IS) are required for oligomerization.
  • the XbaI (18nt up-stream from ATG) to BamH1 (1914 nt down-stream from ATG) fragment which contains polylinker at the 5′ end, Kozak sequence and ATG was cloned into the XbaI to BamH1 sites of the CMV/R backbone.
  • VRC-5738 domains A summary of predicted VRC-5738 domains is provided in Table 13.
  • the plasmid is 6298 nucleotide base pairs (bp) in length and has an approximate molecular weight of 4.2 MDa.
  • the sequence of VRC-5738 is provided as SEQ ID NO: 29.
  • VRC-4401, 4409, 4404, 5736, 5737 and 5738 plasmids were sequenced by Lark Technologies and the sequences subjected to a BLAST search of the human genome database. The search was done using parameters which only identified sequence homologies with expected values (E values) of 0.01 or lower. This means that the statistical possibility of a homology occurring by chance alone is only 1/100. Anything at this level or lower (i.e. less than 1/100) will be picked up by the search.
  • the proteins are transferred to a nitrocellulose membrane (0.45 ⁇ m) for Western blot analysis.
  • the membrane is blocked with skim milk to prevent non-specific binding interaction prior to incubation with the primary antibody for 60 minutes.
  • the membrane is incubated for 45 minutes with HRP conjugated second antibody.
  • Visualization of the protein bands is achieved by incubating the membrane with chemiluminescent substrates and exposing to X-ray film for 2 minutes or an appropriate time. Expression of protein produced by transfected cells is determined by observing the intensity of expressed protein on the Western blot.
  • the assay is being further developed to allow for semi-quantitative analysis of protein expression by the vaccine plasmids.
  • the recombinant adenoviral vector product VRC-HIVADV014-00-VP (rAd) is a replication-deficient, combination vaccine containing four recombinant serotype 5 adenoviral vectors. These vectors contain gene sequences that code for Clade B HIV-1 Gag and Pol as well as Clade A, Clade B, and Clade C Env protein. In vivo expression by these vectors produces immunogens that induce an immune response against HIV.
  • the envelope genes were chosen as representative primary isolates from each of the three clades.
  • the process for constructing the four VRC-HIVADV014-00-VP recombinant adenoviral vectors is based upon a rapid vector construction system (AdFASTTM, GenVec, Inc.) used to generate adenoviral vectors that express the four HIV antigens gp140(A), gp140(B)dv12, gp140(C) and GagPol(B) driven by the cytomegalovirus (CMV) immediate-early promoter.
  • Manufacturing is based upon production in a 293-ORF6 cell line (Brough, D. E. at al. 1996 J Virol 70:6497-6501), yielding adenoviral vectors that are replication deficient.
  • the vectors are purified using CsCl centrifugation.
  • the product is formulated as a sterile liquid injectable dosage form for intramuscular injection.
  • the protein sequences of the Gag and Pol proteins from an HIV-1 Clade B were used to create a synthetic polyprotein version of the gag-pol genes using codons optimized for expression in human cells.
  • the synthetic gag gene is from HIV-1 Clade B strain HXB2 (GenBank accession number K03455), and the synthetic pol gene (pol/h) is from HIV-1 Clade B NL4-3 (GenBank accession number M19921).
  • the pol gene is nonfunctional because it is present as a fusion protein. Mutations were introduced in the synthetic protease and reverse transcriptase genes. The protease modification prevents processing of the pol gene product, and reduces the potential for functional protease, reverse transcriptase and integrase enzymatic activity.
  • AdtGagPol(B).11D The cDNA used to produce AdtGagPol(B).11D is similar to an HIV-1 DNA vaccine VRC-4302 (described in WO 02/32943) which was tested and shown to have no reverse transcriptase activity. No modifications were made to the gag.
  • VRC-4302 described in WO 02/32943
  • the HIV-1 DNA sequence was subcloned using standard recombinant DNA techniques into an expression cassette in an E1-shuttle plasmid.
  • Adgp140(A).11D (SEQ ID NO: 30)
  • the protein sequence of the envelope polyprotein (gp160) from 92rw020 was used to create a synthetic version of the gene (Clade-A gp140 ⁇ CFI) using codons altered for expression in human cells. Plasmids expressing the HIV-1 genes were made synthetically with sequences designed to disrupt viral RNA structures that limit protein expression by using codons typically found in human cells. To construct the adenoviral vector, the HIV-1 DNA sequence was subcloned using standard recombinant DNA techniques into an expression cassette in an E1-shuttle plasmid. Adtgp140dv12(B).11D (SEQ ID NO: 32)
  • the protein sequence of the envelope polyprotein (gp160) from HXB2 was used to create a synthetic version of the gene (X4gp160/h) using codons optimized for expression in human cells.
  • X4gp160/h The protein sequence of the envelope polyprotein (gp160) from HXB2 (X4-tropic, GenBank accession number K03455) was used to create a synthetic version of the gene (X4gp160/h) using codons optimized for expression in human cells.
  • R5gp160/h CCR5-tropic version of the envelope protein (R5gp160/h)
  • VRC3300 region encoding HIV-1 envelope polyprotein amino acids 275 to 361 from X4gp160/h
  • the full-length CCR5-tropic version of the envelope protein gene from pR5gp160/h (VRC3000) was terminated after the codon for amino acid 680.
  • the truncated Env glycoprotein (gp140) contains the entire surface protein and the ectodomain of gp41 including the fusion domain, and regions important for oligomer formation, specifically two helical coiled coil motifs.
  • the Env V1 and V2 loops were deleted to improve the stability and yield of the vector in the producer cell line. Two additional amino acids were incorporated immediately after the deletion due to creation of a restriction enzyme site.
  • Adgp140(C).11D SEQ ID NO: 31
  • the protein sequence of the envelope polyprotein (gp140 ⁇ CFI) from 97ZA012 was used to create a synthetic version of the gene (Clade-C gp140 ⁇ CFI) using codons optimized for expression in human cells.
  • the HIV-1 DNA sequence was subcloned using standard recombinant DNA techniques into an expression cassette in an E1-shuttle plasmid.
  • the four E1-shuttle plasmid was recombined in Escherichia coli ( E. coli ) BjDE3 bacteria with the GV11 adenovector based AdFASTTM plasmid pAdE1(BN)E3(10)E4(TIS1) to generate the adenoviral vector plasmids.
  • the replication-deficient adenoviral vectors AdtGagPol(B).11D, Adgp140(A).11D, Adtgp140dv12(B).11D, and Adgp140(C).11D were then generated by introducing the adenoviral vector plasmid into the packaging cell line, 293-ORF6.
  • V3 1AB modified envelope constructs Fig. SEQ VRC NO: Construct NO: ID NO: VRC 5747 CMV/R-Clade B gp145( ⁇ CFI)( ⁇ V12)(V3-1AB-clade C- 46 38 SA)/h VRC 5753 CMV/R-gp145( ⁇ CFI)( ⁇ V1-2)( ⁇ V3)(1AB)(Clade A) 47 39 VRC 5754 CMV/R-gp145( ⁇ CFI)( ⁇ V1-2)( ⁇ V3)(1AB)(Clade SA-C) 48 40 VRC 5755 pAdApt LoxP CMV TbGH(+) 49 41 gp140 ⁇ CFI ⁇ V1V2(1AB)(Bal)/h VRC 5766 pAdApt LoxP CMV TbGH(+) gp140( ⁇ CFI)(V3-1AB) 50 42 Clade A/h VRC 5767 pAdApt Lox

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