Dataset DOI: 10.5061/dryad.v41ns1s2b

Description of the data and file structure

HIV-specific CD8+ T cell responses in HIV vaccine recipients are compared with those of chronically infected long-term nonprogressors / elite controllers (LTNP/EC) and progressors specifically as they relate to the response to HIV-infected autologous primary CD4+ T cell targets. LTNP/ECs represent a rare population of people living with HIV who maintain durable control over HIV replication without antiretroviral therapy. A variety of experimental assays employing subject derived peripheral blood mononuclear cells (PBMCs) were used in these investigations. Relative to chronically infected patients, we found that the CD8+ T cells induced by HIV vaccines exhibited lower cytotoxic capacity due to impaired degranulation and perforin polarization to the immunologic synapse. This was associated with reduced functional avidity and a polyclonal T-cell receptor (TCR) repertoire. Vaccinee-derived TCRs transduced into primary PBMCs had the same reduced functions, localizing the cause of low avidity to the antigen receptor.

Files and variables

File: EC_Sequences_VB_Summary.fas.txt

Description: "EC Sequences VB Summary" contains the full TCR beta and alpha chain, Variable region DNA sequences derived from the sorted immunodominant HLA class I/HIV Gag tetramer+ CD8+ T cells of seven LTNP/EC. The HIV tetramers used in these experiments include: A02-SLYNTVATL (A2-SL9), A0301-RLRPGGKKK (A3-RK9), B0801-EIYKRWII (B8-EI8), B2705-KRWIILGLNK (B27-KK10), B5701-KAFSPEVIPMF (B57-KF11), and B5701-QASQEVKNW (B57-QW9). Identifiers preceding nucleotide sequences include LTNP/EC subject number (e.g., EC01 refers to sequences derived from LTNP/EC subject 1), abbreviated peptide name corresponding to the epitope specificity recognized by the TCR (e.g., KK10 refers to the B27-KK10 specificity), clonotype number, and BV or AV to distinguish beta from alpha chain sequences, respectively.

File: Fig1AB_FigS4AB.csv

Description: "Fig1AB_FigS4AB" contains CD8+ T cell responses pre-HIV infection (Pre, n=34) and post-HIV infection (Post, n=14) in Adenovirus serotype 5 (Ad5) HIV vaccinees from the Step study compared with LTNP/EC (LTNP) and progressors (Prog). The 14 vaccinees, from whom postinfection PBMC samples were available, were divided into two subgroups based on either low (Low VL, <10,000 copies/ml, n=6) or high (High VL, >10,000 copies/ml, n=8) set point HIV-1 RNA levels (Log Viral Load or VL). A confocal microscopy bioimaging platform, called BD Pathway, was used to measure the ability of multi-day restimulated CD8+ T cells to eliminate HIV-infected CD4+ T cell targets (infected CD4 elimination, ICE) after a 40-minute incubation. Frequencies of CD107a+ and/or IFN-gamma+ CD8+ T cells were also quantified with cells from the same subjects by flow cytometry, expressed as percentages of “CD107 and/or IFN” positive cells. Background responses to uninfected CD4+ T cell targets were subtracted. Post-infection set point HIV-1 RNA levels and experimental results for the 14 “high VL” and “low VL” vaccinees are summarized in columns J-O. Results were compared among the groups by the Wilcoxon two-sample test.

Variables

• LTNP Path ICE: measurement of cytotoxic capacity of CD8+ T cells from long-term nonprogressor (LTNP) using infected CD4 T cell elimination (ICE) measured using the BD Pathways
• Prog Path ICE: measurement of cytotoxic capacity of CD8+ T cells from progressors (prog) using infected CD4 T cell elimination (ICE) measured using the BD Pathways
• Step Path ICE: measurement of cytotoxic capacity of CD8+ T cells from STEP vaccinees (STEP) using infected CD4 T cell elimination (ICE) measured using the BD Pathways
• Step : participants who received Merck replication defective trivalent adenovirus (Ad) serotype 5 gag/pol/nef subtype B vaccine

File: Fig1C_FigS3D_FigS4CD.csv

Description: "Fig1C_FigS3D_FigS4CD" contains data for CD8+ T cell cytotoxic capacity (also presented in “Fig1AB_FigS4AB”) expressed on a per cell basis in LTNP/EC (LTNP), progressors (Prog), and Step study vaccinees (Step). ICE responses were measured at a 10:1 (columns B through E) or 5:1 (columns F and G) plated effector:target (E:T) ratios and then plotted as curves against the true E:T ratios (column A), which were determined by flow cytometric measurement of CD107a+ and/or IFN-gamma+ CD8+ T cell frequencies after 5-hour stimulation (for effectors) and baseline confocal imaging percentages of green fluorescent protein (GFP+) CD4+ T cell targets (for targets). Group differences were quantified by regression analysis.

Variables

• E:T effector:CD4 target ratio
• LTNP 10:1 ICE measurement after plating LTNP effectors:CD4 targets at a ratio of 10:1
• Progressor 10:1 ICE measurement after plating progressor effectors:CD4 targets at a ratio of 10:1
• Step 10:1 ICE measurement after plating STEP vaccinee effectors:CD4 targets at a ratio of 10:1
  • Step Post Inf 10:1  ICE measurement after plating effectors:CD4 targets at a ratio of 10:1 for the subset of STEP vaccinees who acquired HIV
• LTNP 5:1 ICE measurement after plating LTNP effectors:CD4 targets at a ratio of 5:1
• Prog 5:1: ICE measurement after plating progressor effectors:CD4 targets at a ratio of 5:1

File: Fig1DE_FigS3EF_FigS5AG.csv

Description:  "Fig1DE_FigS3EF_FigS5AG" contains data of Step vaccinees (Step Vx, column A), including  set point HIV-1 RNA levels (Log Viral L), preinfection ICE (Pre ICE), preinfection frequencies of CD107a+ and/or IFN-gamma+ CD8+ T cells (Pre CD107a and/or IFN), CD107a+ CD8+ T cells (Pre CD107a), IFN-gamma+ CD8+ T cells (Pre IFN), and IL2+ and/or IFN-gamma+ CD8+ T cells, as well as the fold change of HIV-specific CD8+ T cell frequency, calculated by dividing frequencies of “Pre CD107a+ and/or IFN” (column D, that had been expanded for 6 days and then restimulated for 5 hours) by “IL2+ and/or IFN-gamma+ CD8+ T cells” (column G, that had only been restimulated for 6 hours). Measurements made on postinfection samples from 14 vaccinees are shown in columns I through L. Correlations were calculated with the Spearman rank method. Cells labeled N/A represent vaccinees who did not acquire HIV after vaccination. For row 14, this vaccinee did not have IL-2 and/or IFN-gamma measured from CD8+ T cells by HVTN.

Variables

• Step Vx: STEP vaccinees, participants who received Merck replication defective trivalent adenovirus (Ad) serotype 5 gag/pol/nef subtype B vaccine
• Log Viral L: set point HIV-1 RNA levels reported on a logarithmic scale
• Pre ICE: ICE measured before HIV acquisition 
• Pre CD107a and/or IFN: CD107a and/or IFN measured before HIV acquisition
• Pre CD107a: CD107a measured before HIV acquisition
• Pre IFN: IFN  measured before HIV acquisition
• IL2 and/or IFN-+CD8+ T Cells (%):  IL2 and/or IFN  measured from CD8+ cells
• Fold Change: the fold change of HIV-specific CD8+ T cell frequency, calculated by dividing frequencies of “Pre CD107a+ and/or IFN” (column D, that had been expanded for 6 days and then restimulated for 5 hours) by “IL2+ and/or IFN-gamma+ CD8+ T cells” (column G, that had only been restimulated for 6 hours).
• Post ICE: ICE measured before HIV acquisition 
• Post CD107a and/or IFN: CD107a and/or IFN measured before HIV acquisition 
• Post CD107a: CD107a measured before HIV acquisition 
• Post IFN: IFN measured before HIV acquisition 

File: Fig2AB_FigS6A.csv

Description:  "Fig2AB_FigS6A" contains HIV-specific CD8+ T cell responses against autologous primary HIV-infected CD4+ T cell targets derived from LTNP/EC (LTNP), progressors (Prog), and Ad5/HIV vaccinees from the HVTN 071 study (“HVTN 071” or simply “071”). Higher PBMC numbers were available from 12 Ad5/HIV vaccinees who had undergone leukaphereses as part of HVTN 071. Flow cytometric measurements include infected CD4 elimination (ICE) and percentages of CD107a+ and/or IFN-gamma+ CD8+ T cells (CD107a and/or IFN), CD107a+ CD8+ T cells (CD107a+), IFN-gamma+ CD8+ T cells (IFN+), perforin+ CD8+ T cells (PRF Freq), and granzyme B+ CD8+ T cells (GrB Freq). Also shown are PRF and GrB expression as mean fluorescence intensity (MFI). Results were compared among the groups by the Wilcoxon two-sample test. Correlations were calculated by the Spearman rank method. N/A indicates an individual with progressive HIV who did not have enough cells for replicate wells needed to measure CD107a and/or IFN-gamma.

Variables

• LTNP ICE: HIV-specific CD8+ T cell responses against autologous primary HIV-infected CD4+ T cell targets derived from LTNP/EC (LTNP)

• Prog ICE: HIV-specific CD8+ T cell responses against autologous primary HIV-infected CD4+ T cell targets derived from progressor (prog)

• 071 ICE: CD8+ T cell responses against autologous primary HIV-infected CD4+ T cell targets derived from Ad5/HIV vaccinees from the HVTN 071 study (“HVTN 071” or simply “071”)

• LTNP PRF Freq: percentage of perforin+ CD8+ T cells derived from LTNP/EC (LTNP)

• Prog PRF Freq: percentage of perforin+ CD8+ T cells derived from progressor (progressor)

• 071 PRF Freq: percentage of perforin+ CD8+ T cells derived from Ad5/HIV vaccinees from the HVTN 071 study (“HVTN 071” or simply “071”)

• LTNP PRF+ MFI: perforin expression as mean fluorescence intensity (MFI) derived from LTNP/EC (LTNP)

• Prog PRF+ MFI: perforin expression as mean fluorescence intensity (MFI) derived from progressor (prog)

  071 PRF+ MFI: perforin expression as mean fluorescence intensity (MFI) derived from Ad5/HIV vaccinees from the HVTN 071 study (“HVTN 071” or simply “071”)

File: Fig2GH_FigS6BC.csv

Description:  "Fig2GH_FigS6BC" contains PRF and GrB net extracellular concentrations, measured by ELISA (columns B and E, respectively), and their activities, measured by percentages of PI+ live, infected CD4+ T cell targets (PI+ Tinf, column C) and GrB substrate fluorescence AUC (GrB AUC, column F), respectively, in LTNP/EC (LTNP/EC or LTNP), progressors (Prog), and HVTN 071 vaccinees (also shown in “Fig2CF”). Extracellular PRF and GrB concentrations were correlated with their activities by the Spearman rank method.

Variables

• PRF ELISA Diff: perforin extracellular concentration measured by ELISA
• PI+ Tinf: percentages of PI+ live, infected CD4+ T cell targets
• GrB ELISA Diff: GrB extracellular concentration measured by ELISA
• GrB AUC: GrB substrate concentration measured by a microplate reader as the net area under the curve (AUC) changes in fluorescence of a fluorogenic GrB substrate in cell free supernatants

File: Fig2CF.csv

Description:  "Fig2CF" contains ELISA measurements of PRF and GrB extracellular concentrations in response to uninfected (Tun) or infected (Tinf) CD4+ T cell targets and the differences of Tinf-Tun for LTNP/EC (LTNP), Prog, and HVTN 071 vaccinees (071). Rows 29-42 show PRF and GrB extracellular activities in the same groups, measured by flow cytometry as percentages and MFI of propidium iodide+ live CD4+ T cell targets (PI+ Tinf) or by a microplate reader as the net area under the curve (AUC) changes in fluorescence of a fluorogenic GrB substrate in cell free supernatants, respectively. Results were compared among the groups by the Wilcoxon two-sample test. For cells with N/A, these reflect conditions with cells from two LTNP/ECs where results for GrB ELISA with infected targets were uninterpretable (and could not be repeated) and thus the difference between the GrB measured with uninfected targets compared to infected targets could not be calculated.

Variables

• LTNP PRF ELISA Tun: perforin extracellular concentration in response to uninfected CD4+ T cells targets for LTNP/EC (LTNP)
• LTNP PRF ELISA Tinf: perforin extracellular concentration in response to infected CD4+ T cells targets for LTNP/EC (LTNP)
• LTNP PRF ELISA Diff: differences in extracellular perforin concentrations when comparing response to infected targets and uninfected targets among  LTNP/EC (LTNP)
• Prog PRF ELISA Tun: perforin extracellular concentration in response to uninfected CD4+ T cells targets for progressor (progressor)
• Prog PRF ELISA Tinf: perforin extracellular concentration in response to infected CD4+ T cells targets for progressor (progressor)
• Prog PRF ELISA Diff: differences in extracellular perforin concentrations when comparing response to infected targets and uninfected targets among  progressor (progressor)
• 071 PRF ELISA Tun: perforin extracellular concentration in response to uninfected CD4+ T cells targets for Ad5/HIV vaccinees from the HVTN 071 study (“HVTN 071” or simply “071”)
• 071 PRF ELISA Tinf: perforin extracellular concentration in response to infected CD4+ T cells targets for Ad5/HIV vaccinees from the HVTN 071 study (“HVTN 071” or simply “071”)
• 071 PRF ELISA Diff: differences in extracellular perforin concentrations when comparing response to infected targets and uninfected targets among Ad5/HIV vaccinees from the HVTN 071 study (“HVTN 071” or simply “071”)

File: Fig3AC.csv

Description: "Fig3AC" contains data for each subject on HLA class I A and B genotype (columns B and C), HLA class I/HIV tetramers used to stain expanded CD8+ T cells (column D), the numbers of tetramers used (column E), the expression of various markers on the HIV tetramer+ CD8+ T cells after stimulation with HIV-infected autologous CD4+ T cell targets (columns F through M), and cytotoxic responses expressed as infected CD4 elimination (ICE) when sufficient PBMCs were available from LTNP/EC, Progressors, and vaccinees in the HVTN 071, VRC_006, VRC_008 and HVTN 087 trials. VRC_006 refers to healthy subjects who received one dose of the VRC-replication-defective Ad5/HIV vaccine administered as a single intramuscular injection whereas VRC_008 refers to a boost after priming with three multi-antigen DNA vaccinations. Vaccinees in HVTN 087 were primed with three multiantigen DNA vaccinations (ProfectusVax) plus high-dose (1500 μg) Interleukin-12 before boosting with a live, attenuated vesicular stomatitis virus expressing HIV-1 Gag (VSV-Gag) Details of abbreviated names of the HIV tetramers (column D) are included in table S4. Responses to uninfected CD4+ T cell targets after 6-hour restimulation are subtracted from responses to infected CD4+ T cell targets (net results in columns H and I). Tetramer+ GrB delta (column L) is calculated by subtracting GrB MFI of tetramer+ cells in response to uninfected CD4+ T cell targets (column J) from GrB MFI of tetramer+ cells in response to infected CD4+ T cell targets (column K). Percent tetramer+ GrB delta MFI (column M) is derived from dividing tetramer+ GrB delta MFI (column L) by GrB MFI of tetramer+ cells in response to uninfected CD4+ T cell targets (column J). Group comparisons were determined by the Wilcoxon two-sample test and correlations were measured by the Spearman rank method. N/A data in the LTNP/EC and progressor groups indicates subjects where certain markers were not measured. N/A among the vaccinees reflects samples where low small cell numbers precluded measurement of ICE. 

Variables

• Subject ID: unique identifier for each study participant
• HLA A: major histocompatibility complex, class I, A
• HLA B: major histocompatibility complex, class I, B
• HLA Class I/HIV Tetramers: artificial, fluorescently labeled complex that mimics natural HLA-peptide complex, assembled into a four-part structure, and used to detect and quantify human T cells that specifically recognize HIV antigen
• Number of Tetramers: number of tetramers used for a given participant
• Tetramer+ PRF+: expression of perforin on the HIV tetramer+ CD8+ T cells after stimulation with HIV-infected autologous CD4+ T cell targets
• Tetramer+ GrB+: expression of Granzyme B on the HIV tetramer+ CD8+ T cells after stimulation with HIV-infected autologous CD4+ T cell targets
• Tetramer+ CD107a+: expression of CD107a on the HIV tetramer+ CD8+ T cells after stimulation with HIV-infected autologous CD4+ T cell targets
• Tetramer+ IFN-g+: expression of interferon gamma on the HIV tetramer+ CD8+ T cells after stimulation with HIV-infected autologous CD4+ T cell targets
• Tetramer+ GrB MFI (T Uninf): granzyme B MFI of tetramer+ cells in response to uninfected CD4+ T cell targets
• Tetramer+ GrB MFI (T Inf): granzyme B MFI of tetramer+ cells in response to infected CD4+ T cell targets
• Tetramer+ GrB DMFI : Tetramer+ GrB delta is calculated by subtracting GrB MFI of tetramer+ cells in response to uninfected CD4+ T cell targets from GrB MFI of tetramer+ cells in response to infected CD4+ T cell targets
• %GrB DMFI: percent tetramer+ GrB delta MFI is derived from dividing tetramer+ GrB delta MFI by GrB MFI of tetramer+ cells in response to uninfected CD4+ T cell targets
• ICE: infected CD4+ T cell elimination assay measured by change in intracellular p24 expression after the addition of effectors

File: Fig4AC_FigS11B.csv

Description:  contains functional avidity data on CD107a expression measured by flow cytometry of virus tetramer/multimer-labelled (column B) CD8+ T cells of LTNP/EC, progressors, Ad5/HIV vaccinees and individuals with “other specificities”, including controlled cytomegalovirus (CMV) infection, convalesced influenza virus (Flu) or respiratory syncytial virus (RSV) infections and SARS-CoV-2 mRNA vaccine recipients (SARS-CoV-2 Vx) in response to 10-fold serial dilutions of viral peptide (column B), ranging from 10e-9 M (-9) to 10e-5 M (-5) (columns D through H). Details of abbreviated names of the viral multimers (column B) are included in table S4. Cells from some patients were used in experiments in which CD8+ T cell responses to HIV-infected CD4+ T cell targets (Inf T, column I) were plotted on the peptide-response curves (derived from the same CD8 effectors) to interpolate the peptide concentration that would yield the same degranulation response from stimulation with infected targets. Individuals where this was not done have N/A. Half-maximal effective concentrations (EC50) inducing CD107a expression in HIV tetramer+ CD8+ T cells from LTNP/EC, progressors and Ad5/HIV vaccinees were estimated by a non-linear fit model (column J). One LTNP/EC had measurements done with two HIV viral multimers and thus the half-maximal concentration was only reported for one multimer (and the other shows N/A). The half-maximal concentration was not calculated for non-HIV specificities and instead curve analysis was performed (corresponding cells show N/A). Responses were compared across all dilutions by the GEE method and pairwise comparisons were analyzed by the Wilcoxon two-sample test. 

File: Fig4E_FigS11C.csv

Description:  “Fig4E_FigS11C” contains data on the formation of conjugates after a 15-minute incubation between CD8+ T cells and CD8- (CD4+) T cell targets of LTNP/EC (LTNP/EC or EC) and vaccinees that had been pulsed with single optimal epitope peptides at high concentration (10e-5 M, High OE) or low concentration (10e-8 M, Low OE), as measured with a fluorescent microscopy platform. The numbers of CD8+ cells conjugated to targets and containing bright perforin above a pre-determined threshold intensity were classified as polarized or nonpolarized by two blinded observers according to pre-determined criteria. Image numbers (column B), frequencies of HIV tetramer+ CD8+ T cells measured by flow cytometry (HIV-specific freq, column C), absolute numbers of CD8+ cells detected by the bioimager (# CD8s, column D), calculated numbers of HIV-specific CD8+ T cells by multiplying frequencies of HIV tetramer+ CD8+ T cells by the absolute numbers of CD8+ T cells (# HIV-specific CD8s, column E), conjugate numbers (# Conjugates, column F), perforin+ conjugate numbers (# Perf+ conjugates, column G), conjugate numbers containing polarized perforin determined by blinded observers (# Polarized, column H), calculated percentages of perforin+ conjugates containing polarized perforin (# Polarized divided by # Perf+ conjugates, column I) and calculated percentages of HIV-specific CD8+ T cells forming conjugates (# Conjugates divided by # HIV-specific CD8+ T cell numbers, column J) are shown for each subject. The latter parameters are also summarized in rows 1-9. Comparisons were made using the Wilcoxon two-sample test.

Variables

• Conjugates/HIV-specific 8s: formation of conjugates after a 15-minute incubation between CD8+ T cells and CD8- (CD4+) T cell targets of LTNP/EC (LTNP/EC or EC) and vaccinees that had been pulsed with single optimal epitope peptides at high concentration (10e-5 M, High OE) or low concentration (10e-8 M, Low OE), as measured with a fluorescent microscopy platform
• LTNP/EC 1: LTNP/EC participant #1
• LTNP/EC 2: LTNP/EC participant #2
• LTNP/EC 3: LTNP/EC participant #3
• LTNP/EC 4: LTNP/EC participant #4
• LTNP/EC 5: LTNP/EC participant #5
• LTNP/EC 6: LTNP/EC participant #6
• LTNP/EC 7: LTNP/EC participant #7
• Ad5/HIV Vx 1: Ad5/HIV vaccinee #1
• Ad5/HIV Vx 2: Ad5/HIV vaccinee #2
• Ad5/HIV Vx 3: Ad5/HIV vaccinee #3
• Ad5/HIV Vx 4: Ad5/HIV vaccinee #4
• Ad5/HIV Vx 5: Ad5/HIV vaccinee #5
• Ad5/HIV Vx 6: Ad5/HIV vaccinee #6

File: Fig5A.csv

Description:  "Fig5A" contains CD107a expression in HIV tetramer+ CD8+ T cells of LTNP/EC (EC, rows 3 through 10) and Ad5/HIV vaccinees from the Step, HVTN 071 and VRC_008 studies (Ad5/HIV Vx, rows 13 through 20) after restimulation with plate-bound anti-CD3 (clone OKT3) at multiple dilutions (unstim and 10e0 through 10e-6, denoted as 0 through -6), measured by flow cytometry. Unstim values were subtracted as background from the values for the OKT3 dilutions. Comparisons were made by the GEE method.

Variables

• [OKT3 Log]:  plate-bound anti-CD3 (clone OKT3) at multiple dilutions expressed on log scale
• LTNP/EC: long-term nonprogressor/elite controller

File: Fig5CD_FigS14BC.csv

Description:  "Fig5CD_FigS14BC" contains measures of clonotypic diversity of the TCRs of LTNP/EC and Ad5/HIV vaccinees (Ad5/HIV Vx), calculated by Simpson's diversity index (SDI), after excluding low-sequence number repertoires and standardizing for sampling differences (columns A and B). Also listed are data on the TCR-peptide/MHC dissociation or off rates (Koff) measured by flow cytometry on Jurkat cells transduced with TCRs from LTNP/EC or Ad5/HIV vaccinees. Comparisons include differences between all TCRs tested (columns D and E) or just the dominant (“Dom”, columns F and G) TCRs. Flow cytometric analysis of CD107a expression in HIV tetramer+ cells of an HIV-negative donor transduced with single TCRs from LTNP/EC or Ad5/HIV vaccinees and restimulated for 6 hours with HIV-infected heterologous targets matched at the restricting HLA class I protein are shown for all TCR transductants (columns I and J) and just those transduced with dominant (Dom) TCR clonotypes (columns K and L). Lastly, TCR transduction success is shown, based on flow cytometry-determined percentages of HIV tetramer+ Jurkat cells (all transductants, columns B and D; transductants used in Koff experiments, column G) or primary PBMC TCR transductants used in CD107a experiments (column J). Comparisons were made using the Wilcoxon two-sample test. Cells with N/A represent results mediated by non-dominant TCR clonotypes.

Variables

• LTNP/EC SDI: measures of clonotypic diversity of the TCRs of LTNP/EC calculated by Simpson's diversity index (SDI)
• Ad5/HIV Vx SDI: measures of clonotypic diversity of the TCRs of Ad5/HIV vaccinees calculated by Simpson's diversity index (SDI)
• LTNP/EC Koff: TCR-peptide/MHC dissociation or off rates (Koff) measured by flow cytometry on Jurkat cells transduced with TCRs from LTNP/EC 
• Ad5/HIV Vx Koff: TCR-peptide/MHC dissociation or off rates (Koff) measured by flow cytometry on Jurkat cells transduced with TCRs from Ad5/HIV vaccinees
• LTNP/EC Dom Koff: TCR-peptide/MHC dissociation or off rates (Koff) measured by flow cytometry on Jurkat cells transduced with just the dominant LTNP/EC TCRs
• Ad5/HIV Vx Dom Koff: TCR-peptide/MHC dissociation or off rates (Koff) measured by flow cytometry on Jurkat cells transduced with just the dominant Ad5/HIV vaccinee TCRs
• LTNP/EC TCR CD107a: Flow cytometric analysis of CD107a expression in HIV tetramer+ cells of an HIV-negative donor transduced with single TCRs from LTNP/EC and restimulated for 6 hours with HIV-infected heterologous targets matched at the restricting HLA class I protein for all TCR transductants
• Ad5/HIV Vx TCR CD107a: Flow cytometric analysis of CD107a expression in HIV tetramer+ cells of an HIV-negative donor transduced with single TCRs from Ad5/HIV vaccinee and restimulated for 6 hours with HIV-infected heterologous targets matched at the restricting HLA class I protein for all TCR transductants
• LTNP/EC Dom TCR CD107a: Flow cytometric analysis of CD107a expression in HIV tetramer+ cells of an HIV-negative donor transduced with single TCRs from LTNP/EC and restimulated for 6 hours with HIV-infected heterologous targets matched at the restricting HLA class I protein for just dominant TCR clonotypes
• Ad5/HIV Vaccinees Dom TCR CD107a: Flow cytometric analysis of CD107a expression in HIV tetramer+ cells of an HIV-negative donor transduced with single TCRs from Ad5/HIV vaccinee and restimulated for 6 hours with HIV-infected heterologous targets matched at the restricting HLA class I protein for just dominant TCR clonotypes

File: FigS3AB.csv

**Description: **"FigS3AB" contains CD8+ T cell cytotoxic responses expressed as infected CD4 elimination (ICE), measured by BD Pathway or by flow cytometry (FACS), with cells from chronic progressors (CP), LTNP/EC (EC), a healthy, HIV-negative donor (NL) and two Ad5/HIV vaccinees (V). Correlations were measured by the Spearman rank method. Pathway ICE responses in four replicates with cells from four chronically infected subjects are also shown.

Variables

• Patients: chronic progressors (CP), LTNP/EC (EC), a healthy, HIV-negative donor (NL) and two Ad5/HIV vaccinees (V)
• Pathways ICE: infected CD4 elimination (ICE) measured by BD Pathway
• FACS ICE: infected CD4 elimination (ICE) measured by flow cytometry (FACS)

File: FigS7A.csv

Description:  "FigS7A" contains raw data (unthresholded, log transformed relative fluorescence units) from the secretome analysis of 32 immune proteins (columns E through AJ) that were secreted from the CD8+ T cells of two LTNP/EC (LTNP/EC 1, LTNP/EC 3) and two Ad5/HIV vaccinees (HVTN 071-70 and Step 9734) and were used to create the 3D-tSNE with the IsoSpeak software. Each row corresponds to the multiplexed ELISA results derived from a single cell microchamber on an IsoCode Secretome Chip.

Variables

• Donor Group: Sample categorized as either LTNP/EC or Ad5/HIV vaccinees
• External Donor: Identifies the specific sample used under each donor group LTNP/EC (LTNP/EC 1, LTNP/EC 3) and vaccinees (HVTN 071-70 and Step 9734)
• Cell Subset: secretome analysis only performed on proteins secreted from CD8+ T cells
• CCL-11: CC motif chemokine ligand 11
• GM-CSF: Granulocyte-macrophage colony-stimulating factor
• Granzyme B: granzyme B
• IFN-g: Interferon-gamma
• IL-10: interleukin-10
• IL-12: interleukin-12
• IL-13: interleukin-13
• IL-15: interleukin-15
• IL-17A: interleukin-17A
• IL-17F: interleukin-17F
• IL-1b:  Interleukin-1 beta
• IL-2: Interleukin-2
• IL-21: Interleukin-21
• IL-22: Interleukin-22
• IL-4: Interleukin-4
• IL-5: Interleukin-5
• IL-6: Interleukin-6
• IL-7: Interleukin-7
• IL-8: Interleukin-8
• IL-9: Interleukin-9
• IP-10: interferon-gamma-inducible protein 10
• MCP-1: Monocyte Chemoattractant Protein-1
• MCP-4: Monocyte Chemoattractant Protein-4
• MIP-1a: Macrophage Inflammatory Protein 1-alpha
• MIP-1b: Macrophage Inflammatory Protein 1-beta
• Perforin: perforin
• RANTES: regulated on activation, normal T-cell expressed and secreted
• sCD137: soluble CD137
• sCD40L: soluble CD40 ligand
• TGF-b1: transforming growth factor beta 1
• TNF-a: tumor necrosis factor alpha
• TNF-b: tumor necrosis factor beta

File: FigS7CD.csv

Description: "FigS7CD" contains data, related to the results presented in “FigS7A” and "FigS7B", and includes frequencies of CD8+ T cell-derived signaling phosphoproteins (p-IkBa, p-MEK1-2, p-NFkB p65, p-STAT1, p-STAT3, and p-STAT5; rows 2 through 7) measured from the IsoCode Signaling Chips and the frequencies of individual cells expressing PRF, alone or in combination with up to 31 other immune-related proteins, out of the total sample, which were detected from the IsoCode Secretome Chips (“Secreted PRF”, row 9) or the IsoCode Signaling Chips (“Secreted and Intracellular PRF”, row 10). Comparisons were made using the Wilcoxon two-sample test.

File: FigS9.csv

Description:  "FigS9" contains data on CD8+ T cell cytotoxic responses to HIV-infected autologous CD4+ T cell targets, expressed as infected CD4 elimination (ICE), that was measured by flow cytometry for LTNP/EC, progressors, and vaccinees with sufficient numbers of PBMCs from HVTN 071 (071), VRC_006/008, and HVTN 087 (087). Comparisons were made using the Wilcoxon two-sample test.

Variables

• LTNP/EC: long-term nonprogressor
• Progressors: progressor
• 071: 12 Ad5/HIV vaccinees who had undergone leukaphereses as part of HVTN 071
• VRC_006/008: VRC_006 refers to healthy subjects who received one dose of the VRC-replication-defective Ad5/HIV vaccine administered as a single intramuscular injection whereas VRC_008 refers to a boost after priming with three multi-antigen DNA vaccinations
• 087: Vaccinees in HVTN 087 were primed with three multiantigen DNA vaccinations (ProfectusVax) plus high-dose (1500 μg) Interleukin-12 before boosting with a live, attenuated vesicular stomatitis virus expressing HIV-1 Gag (VSV-Gag)

File: FigS7B.csv

Description:  "FigS7B", which is related to “FigS7A”, contains thresholded (signal intensity normalized relative to that of cell-free microchambers), log transformed secretome data for the same patients shown in FigS7A that was then converted into percent frequencies of multifunctional CD8+ T cell subsets, i.e., the percentages of cells significantly secreting a specific profile of immune-based proteins, for the Granzyme B (column E), MIP-1B (column F), Perforin (column G) and RANTES (column H) immune protein profiles shown on the heatmap in fig. S7B. IsoSpeak software was used to analyze and compare single cell functional phenotypes.

Variables

• Donor Group: Sample categorized as either LTNP/EC or Ad5/HIV vaccinees
• External Donor: Identifies the specific sample used under each donor group LTNP/EC (LTNP/EC 1, LTNP/EC 3) and vaccinees (HVTN 071-70 and Step 9734)
• Cell Subset: secretome analysis only performed on proteins secreted from CD8+ T cells
• Granzyme B: granzyme B
• MIP-1b: macrophage inflammatory protein-1beta
• Perforin: perforin
• RANTES: regulated upon activation, Normal T cell expressed and secreted

File: FigS12.csv

Description:  "FigS12" contains mass spectrometry analysis of PBMC targets pulsed with 10-fold serial dilutions, ranging from 1 nanomolar to 10 micromolar, of the EIYKRWII (B8-EI8) or the FLKEKGGL (B8-FL8) “light”/“endogenous” peptides and then spiked with the corresponding “heavy” peptides, which contained one isotope-labeled amino acid. Area-under-the-curve results are provided. Two technical replicates were performed for each condition. 

Variables

• Peptide: short chain of amino acids used to pulsed peripheral blood mononuclear cells at various concentrations
• TYPE: either light/endogenous or heavy. The heavy peptides contained one isotope-labeled amino acid
• 1nM: one nano molar peptide concentration
• 10nM: ten nanomolar peptide concentration
• 100nM: one hundred nano molar peptide concentration
• 1uM: one micro molar peptide concentration
• 10uM: ten micromolar peptide concentration

File: FigS14A.csv

Description:  "FigS14A" contains flow cytometry-measured expression of the activation/costimulatory receptors CD2, CD11a, CD18, and CD8b on Gag peptide-expanded total CD4+ T cells (columns C through F), total CD8+ T cells (columns G through J), and HIV tetramer+ CD8+ T cells (columns K through N) of LTNP/EC (rows 3 through 10) and Ad5/HIV vaccinees (rows 13 through 21). The four HLA class I/HIV tetramers used in these experiments (column B) were: B2705-KRWIILGLNK (B27-KK10), B5701-KAFSPEVIPMF (B57-KF11), A0301-RLRPGGKKK (A3-RK9), and B0801-EIYKRWII (B8-EI8). Data was not available in cells marked with an “X” due to very low HIV tetramer+ CD8+ T cell frequencies. Comparisons were made using the Wilcoxon two-sample test.

Variables

• CD4: Gag peptide-expanded total CD4+ T cells
• CD8: Gag peptide-expanded total CD8+ T cells
• CD8-HIV Tetramer: Gag peptide-expanded HIV-tetramer CD8+ T cells

File: Vx_Sequences_VB_Summary.fas.txt

Description: "Vx Sequences VB Summary" similarly contains the full TCR beta and alpha chain, Variable DNA sequences derived from the sorted immunodominant HLA class I/HIV Gag tetramer+ CD8+ T cells of eight vaccinees from the Step, HVTN 071 (071) or VRC_008 studies (008). HIV tetramers and vaccinee identifiers follow the same conventions described for LTNP/EC sequences.

Code/software

The tabular (.csv) data can be viewed in any statistical software or basic text editor.

Access information

Other publicly accessible locations of the data:

• n/a

Data was derived from the following sources:

• No