Research ArticleHIV

Immune correlates of the Thai RV144 HIV vaccine regimen in South Africa

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Science Translational Medicine  18 Sep 2019:
Vol. 11, Issue 510, eaax1880
DOI: 10.1126/scitranslmed.aax1880
  • Fig. 2 T cell responses in vaccinees and placebo recipients in the HVTN 097 and RV144 per-protocol cohorts at the peak immunogenicity time point.

    T cell responses were measured by intracellular cytokine staining. (A) 92TH023-Env–specific IL-2 and/or IFN-γ CD4+ T cell responses among vaccinees in the HVTN 097 and RV144 per-protocol cohorts. Boxplots are based on positive responders only, with negative responders shown as gray triangles and response rates above the boxes. A response is considered positive if the number of CD4+ or CD8+ T cells positive for IL-2 and/or IFN-γ is higher in the peptide-stimulated samples than in the negative control samples for at least one peptide pool (as determined by one-sided Fisher’s exact test, P < 0.00001 after a discrete Bonferroni adjustment for testing against multiple peptide pools). Fisher’s exact test P values comparing response rates (p.rate) and Wilcoxon rank sum test P values comparing magnitudes (p.mag) among positive responders between HVTN 097 and RV144 vaccine recipients are provided. (B) Functionality and polyfunctionality scores of 92TH023-Env–specific CD4+ T cell subsets among vaccinees in the HVTN 097 and RV144 per-protocol cohorts. P values compare functionality or polyfunctionality scores between HVTN 097 and RV144 vaccinees. (C) Heatmap of COMPASS posterior probabilities for 92TH023-Env–specific CD4+ T cell responses among vaccine and placebo recipients in the HVTN 097 and RV144 per-protocol cohorts. White indicates that the cytokine subset is not expressed, and purple indicates that it is expressed, ordered by degree of functionality. Rows correspond to participants, ordered by treatment group and by functionality score within each group. Each cell shows the probability [ranging from white (zero) to purple (one)] that the corresponding cell subset (column) demonstrates an antigen-specific response in the corresponding participant (row).

  • Fig. 3 IL-2 and/or IFN-γ CD4+ T cell responses to Env among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.

    (A) Stratified by BMI. (B) Stratified by sex. (C) Stratified by age.

  • Fig. 4 IgG binding antibody responses in vaccine recipients to Env gp120 vaccine-insert antigens in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.

    IgG BAMA responses to Env gp120 vaccine-insert antigens (92TH023.AE and A244.AE) at the 1:50 dilution among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 2 weeks after the second ALVAC/AIDSVAX vaccination are shown by boxplot (A) and histogram (B). The net response magnitude (MFI-blank) is background-subtracted mean fluorescent intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate). A post-enrollment sample is considered to be positive if the net magnitude is greater than or equal to an antigen-specific cutoff, the net magnitude is more than three times the baseline net magnitude, and the MFI is more than three times the baseline MFI. Fisher’s exact test P values comparing response rates (p.rate) and Wilcoxon rank sum test P values comparing magnitudes (p.mag) among positive responders between HVTN 097 and RV144 vaccine recipients are provided in (A). (C) Geometric mean IgG binding antibody responses among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point. Fisher’s exact test P values comparing response rates (p.rate) and Wilcoxon rank sum test P values comparing magnitudes (p.mag) among positive responders between HVTN 097 and RV144 vaccine recipients are provided. Boxplots are based on positive responders only represented by the green and blue circles for HVTN 097 and RV144, respectively; negative responders are shown as gray triangles.

  • Fig. 5 IgG and IgG3 binding antibody responses to V1V2 antigens and magnitude-breadth plot of IgG binding antibody responses to clade C V1V2 antigens among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.

    (A) IgG binding antibody responses to V1V2 antigens among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 2 weeks after the second ALVAC/AIDSVAX vaccination. (B) Magnitude-breadth plot of IgG binding antibody responses to clade C V1V2 antigens among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 2 weeks after the second ALVAC/AIDSVAX vaccination. Solid curves are average breadth across individuals for HVTN 097 and RV144 vaccine recipients, with breadth defined by the proportion of antigens in the panel with log10 (MFI-blank) greater than the threshold on the x axis. Clade C V1V2 antigens = gp70-001428_2_42 V1V2.C, gp70–7060101641 V1V2.C, gp70-96ZM651_02 V1v2.C, gp70-BF1266_431a_V1V2.C, gp70-CAP210_2_00_E8 V1V2.C, and gp70-TV1_21 V1V2.C. (C) Binding to peptides in V1V2 region of three vaccine strains. Magnitude of binding to overlapping peptides in V1V2 region of vaccine strains by serum IgG at 2 weeks after the second ALVAC/AIDSVAX vaccination. Thin lines represent individual participants. Thick lines represent weighted means. (D) IgG3 binding antibody responses to V1V2 antigens among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 2 weeks after the second ALVAC/AIDSVAX vaccination. Boxplots are based on positive responders only, with negative responders shown as gray triangles with positive response rates above the boxes. Fisher’s exact test P values comparing response rates (p.rate) and Wilcoxon rank sum test P values comparing magnitudes (p.mag) among positive responders between HVTN 097 and RV144 vaccine recipients are provided.

  • Fig. 6 Antibody responses in vaccine recipients in HVTN 097 and RV144.

    (A) ADCC responses were evaluated against subtype AE 92TH023_gD-neg and A244_gD-neg recombinant gp120–coated CEM.NKRCCR5 target cells for the HVTN 097 (n = 73) and RV144 (n = 195) samples collected at the peak immunogenicity time point (2 weeks after the second ALVAC/AIDSVAX vaccination), as indicated on the x axis. Peripheral blood mononuclear cells from one normal healthy HIV-seronegative donor were used as source of effector cells. The y axis represents the values of the area under the curve (AUC) to represent the magnitude of responses. Boxplots are based on positive responders only represented by the green and blue circles for HVTN 097 and RV144, respectively; negative responders are shown as gray triangles. Response rates and number of responders over total are reported above each group boxplot. P value comparing response rates among positive responders between HVTN 097 and RV144 vaccine recipients is provided. (B) IgG-mediated ADCP was tested at study baseline and 2 weeks after the second ALVAC/AIDSVAX vaccination for a subset of per-protocol participants, with 63 vaccine recipients (46 in group T1 and 17 in group T2) and 5 placebo recipients. ADCP score using the human THP-1 cell line is shown. (C) Neutralizing antibody responses (magnitude-breadth curves) to tier 1 viruses among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 2 weeks after the second ALVAC/AIDSVAX vaccination. Solid curves are average breadth across individuals for HVTN 097 and RV144 vaccine recipients, with breadth defined by the proportion of antigens in the panel with log10 ID50 titer greater than the threshold on the x axis.

  • Fig. 7 Association between percent of CD4+ T cells expressing CD40L reactive to HIV-1 Env vaccine strain 92TH023 and binding antibodies at the peak immunogenicity time point.

    (A) IgG response to A244.AE gp120. (B) IgG3 response to A244.AE gp120. (C) IgG response (AUC) to clade C V1V2 panel. (D) IgG3 response (AUC) to clade C V1V2 panel. X axis is percent of CD4+ T cells expressing CD40L reactive to 92TH023-ENV, and a histogram of that distribution is shown in green. Along the y axis, a histogram of the corresponding y variable is shown in red.

  • Fig. 8 Multi-assay PCA.

    (A) Biplot and (B) Spearman correlation heatmap for vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point (2 weeks after second ALVAC/AIDSVAX vaccination). In (A), the x axis is the value from the first principal component, and the y axis is the second principal component, where each axis label includes the percentage of variation in the total set of readouts captured by the principal component. Points on the plot represent the values of the principal components of each observation. Points that are close together correspond to observations that have similar values on the components displayed in the plot. The top axis is the first principal component loadings, and the right axis is the second principal component loadings, where loadings are the weights by which each original immunogenicity endpoint score should be multiplied to get the value of the first or second principal component. An arrow (vector) is drawn for each immunogenicity endpoint from the origin to the point defined by its first two principal component loadings. Vectors that point in the same direction correspond to endpoints that have similar response profiles on the basis of the first two principal components. The points that project furthest in the direction in which the vector points are the observations that have the most weight of whatever the endpoint measures. Those points that project at the other end have the least weight of whatever the endpoint measures. The angle between two arrows conveys information about the correlation of the two endpoint scores, with a 0° angle denoting perfect correlation and a 90° angle denoting no correlation. In (A), gp120_IgG3 stands for 92TH023_gp120_IgG3 and A244_gp120_IgG3, gp120_IgG stands for 92TH023_gp120_IgG and A244_gp120_IgG, and PFS(FS) stands for polyfunctionality score (functionality score).

  • Table 1 Demographics of participants in HVTN 097 and RV144.

    BMI was not measured in RV144. NA, not applicable.

    Modified intention to treat cohortPer-protocol cohort*
    MeasureHVTN 097RV144
    contemporaneous
    cohort (2015)
    RV144
    case-control
    study (2010)
    HVTN 097RV144
    contemporaneous
    cohort (2015)
    RV144
    case-control
    study (2010)
    TreatmentPlacebo202420182420
    Vaccine8021220573201195
    Age (years)18–2037 (37%)66 (28%)52 (23.1%)34 (37.4%)60 (26.7%)47 (21.9%)
    21–2541 (41%)112 (47.5%)122 (54.2%)37 (40.7%)111 (49.3%)118 (54.9%)
    ≥2622 (22%)58 (24.6%)51 (22.7%)20 (22%)54 (24%)50 (23.3%)
    SexFemale49 (49%)98 (41.5%)85 (37.8%)42 (46.2%)91 (40.4%)75 (34.9%)
    Male51 (51%)138 (58.5%)140 (62.2%)49 (53.8%)134 (59.6%)140 (65.1%)
    BMI<2566 (66%)NANA61 (67%)NANA
    25–3019 (19%)NANA18 (19.8%)NANA
    ≥3115 (15%)NANA12 (13.2%)NANA

    *Per-protocol for HVTN 097 is defined as receiving all four HIV vaccinations, regardless of tetanus and HBV vaccination status.

    †RV144—Thai subjects enrolled in RV144 selected in 2015 matched on sex and vaccine schedule to South Africans enrolled in HVTN 100. The 2015 cohort was used for the main analyses (BAMA, intracellular cytokine staining).

    ‡RV144—Original case-control cohort selected in 2010 used for the neutralizing antibody comparison.

    • Table 2 Durability of immune responses among vaccine recipients in the per-protocol cohort of HVTN 097.

      MFI-Blank, background-subtracted MFI, where background refers to a plate level control (i.e., a blank well run on each plate).

      Measure*Peak time
      point (V14)
      response
      rate
      Durability
      time point
      (V17)
      response rate
      McNemar’s test
      P value V14
      versus V17
      (response rate)
      Peak time point
      (V14) median
      magnitude
      (among V14
      responders)
      Durability time
      point (V17)
      median
      magnitude
      (among V14
      responders)
      Durability time
      point median/
      peak time point
      median
      Wilcoxon
      signed-rank test
      P value V14
      versus V17
      (magnitude)
      CD4+ Env.92TH023.AE§70.8%36.1%<0.0010.15% T cells expr.
      IL-2/IFN-γ
      0.07% T cells expr.
      IL-2/IFN-γ
      46.7%<0.001
      BAMA IgG
      92TH023_D11gp120.AE
      100%51.5%<0.00117713.4 MFI-Blank176.1 MFI-Blank1.0%<0.001
      BAMA IgG A244
      D11gp120_avi.AE
      100%98.5%120274.8 MFI-Blank1098.8 MFI-Blank5.4%<0.001
      BAMA IgG Con 6
      gp120/B
      100%62.7%<0.00115022.3 MFI-Blank372.4 MFI-Blank2.5%<0.001
      BAMA IgG MN
      gp120
      gDneg/293F.B
      100%20.9%<0.0019507.4 MFI-Blank208.2 MFI-Blank2.2%<0.001
      BAMA IgG con_
      env03 140 CF.A1
      100%7.0%<0.0011453 MFI-Blank17.9 MFI-Blank1.2%<0.001
      BAMA IgG 01_con
      _env03
      gp140CF_avi.AE
      100%67.2%<0.00114395.1 MFI-Blank251.5 MFI-Blank1.8%<0.001
      BAMA IgG Con S
      gp140 CFI
      100%33.3%<0.00117069.3 MFI-Blank449 MFI-Blank2.6%<0.001
      BAMA IgG A244 V1V2
      Tags/293F.AE
      100%62.7%<0.00125793.7 MFI-Blank680.5 MFI-Blank2.6%<0.001
      BAMA IgG
      CaseA2_gp70_
      V1V2.B
      96.8%19.1%<0.0014145.6 MFI-Blank23.5 MFI-Blank0.6%<0.001
      BAMA IgG3
      92TH023 gp120.
      AE
      66.7%1.4%<0.001475.8 MFI-Blank1.8 MFI-Blank0.4%<0.001
      BAMA IgG3 A244
      D11gp120_avi.
      AE
      72.2%2.8%<0.001412 MFI-Blank5.1 MFI-Blank1.2%<0.001
      BAMA IgG3 Con 6
      gp120/B
      62.5%0%<0.001246.9 MFI-Blank4.1 MFI-Blank1.7%<0.001
      BAMA IgG3 MN
      gp120
      gDneg/293F.B
      70.8%1.4%<0.001741.4 MFI-Blank2.8 MFI-Blank0.4%<0.001
      BAMA IgG3 con_
      env03 140 CF.A1
      9.7%0%0.016172 MFI-Blank3.8 MFI-Blank2.2%0.016
      BAMA IgG3 01_
      con_env03
      gp140CF_avi.AE
      45.8%1.4%<0.001295 MFI-Blank3.6 MFI-Blank1.2%<0.001
      BAMA IgG3 Con S
      gp140 CFI
      75.0%0%<0.001348.7 MFI-Blank2.1 MFI-Blank0.6%<0.001
      BAMA IgG3 A244
      V1V2 Tags/293F.
      AE
      88.9%4.2%<0.0011464.8 MFI-Blank6.5 MFI-Blank0.4%<0.001
      BAMA IgG3 1086
      V2 tags/293F.C
      29.2%1.4%<0.001241.1 MFI-Blank9.2 MFI-Blank3.8%<0.001
      BAMA IgG3
      1086_V1V2_
      Tags.C
      72.2%1.4%<0.001727 MFI-Blank6.6 MFI-Blank0.9%<0.001
      BAMA IgG3
      CaseA2_gp70_
      V1V2.B
      28.6%0%<0.001400.9 MFI-Blank2.1 MFI-Blank0.5%<0.001
      BAMA IgG3 MN V3
      gp70.B
      74.3%0%<0.001491.8 MFI-Blank1 MFI-Blank0.2%<0.001
      BAMA IgG3 gp415.6%5.6%1286.6 MFI-Blank62 MFI-Blank21.6%0.125
      BAMA IgG3 p2470.8%33.8%<0.0013013.3 MFI-Blank177 MFI-Blank5.9%<0.001

      *The clade of the antigen is indicated by the last letter(s) of the name (e.g., 92TH023_D11gp120.AE is clade AE).

      †Visit 14 (V14) corresponds to the peak immunogenicity time point (2 weeks after second ALVAC/AIDSVAX vaccination).

      ‡Visit 17 (V17) corresponds to the durability immunogenicity time point (6 months after second ALVAC/AIDSVAX vaccination).

      §This analysis uses 12-color flow cytometric panel originally used for the protocol, whereas the comparisons with RV144 elsewhere in this paper used an updated 16-color panel to match contemporaneous RV144 sample studies.

      Supplementary Materials

      • stm.sciencemag.org/cgi/content/full/11/510/eaax1880/DC1

        Materials and Methods

        Fig. S1. Reactogenicity bar charts for HVTN 097.

        Fig. S2. IgG binding antibody responses to cross-clade V1V2 antigens among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.

        Fig. S3. IgG3 binding antibody responses to gp120 antigens among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.

        Fig. S4. Neutralizing antibody responses in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.

        Table S1. Comparison of ICS (IL-2+ and/or IFN-γ+) CD4+ and CD8+ T cell responses to Env at the peak immunogenicity time point among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144.

        Table S2. Details of the BAMA, ICS, neutralizing antibody, ADCC, and ADCP antigens including HIV-1 viral strain information.

        Table S3. Response rates among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 for IgG and IgG3 binding antibody and neutralizing antibody responses at the peak immunogenicity time point.

        Table S4. IgG binding antibody response among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point by age, sex, and BMI.

        References (48, 49)

      • This PDF file includes:

        • Materials and Methods
        • Fig. S1. Reactogenicity bar charts for HVTN 097.
        • Fig. S2. IgG binding antibody responses to cross-clade V1V2 antigens among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.
        • Fig. S3. IgG3 binding antibody responses to gp120 antigens among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.
        • Fig. S4. Neutralizing antibody responses in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point.
        • Table S1. Comparison of ICS (IL-2+ and/or IFN-γ+) CD4+ and CD8+ T cell responses to Env at the peak immunogenicity time point among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144.
        • Table S2. Details of the BAMA, ICS, neutralizing antibody, ADCC, and ADCP antigens including HIV-1 viral strain information.
        • Table S3. Response rates among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 for IgG and IgG3 binding antibody and neutralizing antibody responses at the peak immunogenicity time point.
        • Table S4. IgG binding antibody response among vaccine recipients in the per-protocol cohorts of HVTN 097 and RV144 at the peak immunogenicity time point by age, sex, and BMI.
        • References (48, 49)

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