DOI: 10.5061/dryad.v41ns1s2b
title: HIV vaccines induce CD8+ T cells with low antigen receptor sensitivity

description: Current HIV vaccines designed to stimulate CD8+ T cells have failed to
 induce immunologic control upon infection. Functions of vaccine-induced
 HIV-specific CD8+ T cells were investigated here in detail. HIV-specific
 CD8+ T-cell cytotoxic capacity was extremely low and was not a consequence
 of low frequency nor lack of accumulation of functional perforin (PRF) or
 granzyme B (GrB). Low cytotoxic capacity was attributable to impaired
 degranulation in response to the low levels of antigen present on
 HIV-infected CD4+ T cells. The T cell receptor (TCR) repertoire induced by
 these vaccines was polyclonal and transduction of these TCRs conferred the
 same reduced functions. These results define a mechanism accounting for
 the poor antiviral activity induced by these vaccines and suggest that an
 effective CD8+ T-cell response may require more intensive antigenic
 stimulation.
description: # HIV vaccines induce CD8+ T cells with low antigen receptor sensitivity
 Dataset DOI:
 [10.5061/dryad.v41ns1s2b](https://doi.org/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, &lt;10,000
 copies/ml, n=6) or high (High VL, &gt;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