Journal: Nature Immunology

Article Title: Autologous neutralizing antibodies and polyfunctional T cells contribute to long-term HIV-1 post-intervention control

doi: 10.1038/s41590-026-02448-z

Figure Lengend Snippet: ( A ) Spectral flow cytometric assessment of cytokine production by memory CD8 T cells (top panel) and memory CD4 T cells (bottom panel) (see Methods and ) in response to stimulation with HIV-1 Gag, Pol, Env or Nef peptide pools in ART-suppressed individuals. For ID104 and ID112, the viral rebound timepoint was also included. Color denotes positivity for cytokines and degranulation (CD107a), and the eight dominant responses are highlighted in bold in the legend. Each bar represents a single experiment per individual and timepoint, utilizing a minimum of 0.8 x 106 PBMCs per stimulation. The frequency of cells expressing each combination of cytokines is calculated by subtracting the value of responding cells to the specific stimulation by that within the negative control (stimulation of cells with DMSO). * denotes excluded data due to insufficient number of cells in the PBMC vials. ( B-C ) HIV-1-specific CD8 T cell responses over time on- and off-ART for ( B ) ID107 and ( C ) ID142 as characterized by lymphocyte proliferation assay (column graphs; left y-axis) and IFN-γ ELISpot assay (symbols; right y-axis) in response to stimulation with HIV-1 Gag, Pol and Nef peptide pools. Each datapoint represents a single experiment per stimulation and timepoint. ( D-E ) HIV-1-specific CD4 T cell responses over time on- and off-ART for ID107 ( D ) and ID142 ( E ) as characterized by lymphocyte proliferation assay in response to stimulation with HIV-1 Gag, Pol and Nef peptide pools. Each datapoint represents a single experiment per stimulation and timepoint. Analyzed samples are color-coded according to timepoint. Gray shading indicates time on ART.

Article Snippet: After stimulation and staining, T cells were enriched using the Pan T cell Isolation kit (Miltenyi Biotec, 130-096-535) and sorted on a MACSQuant Tyto.

Techniques: Expressing, Negative Control, Lymphocyte Proliferation Assay, Enzyme-linked Immunospot

Journal: Nature Immunology

Article Title: Autologous neutralizing antibodies and polyfunctional T cells contribute to long-term HIV-1 post-intervention control

doi: 10.1038/s41590-026-02448-z

Figure Lengend Snippet: Spectral flow cytometric assessment of cytokine production by memory CD8 + T cells (top) and memory CD4 + T cells (bottom) in response to stimulation with HIV-1 Gag, Pol, Env or Nef peptide pools in PICs and ART-suppressed individuals. Asterisk denotes excluded data due to insufficient number of cells in the PBMC vials. a , b , Direct comparison of the percentage of memory CD4 + and CD8 + T cells responding to stimulation with a monofunctional response or a polyfunctional response at the ART-suppressed, pre-ART interruption timepoint, for Gag, Pol and Nef (as cells from some ART-suppressed individuals were not stimulated with Env peptides) stimulation combined ( a ) or stratified by HIV-1 peptide pool stimulation ( b ). Cells with a polyfunctional response were defined as those positive for two or more of the markers IFNγ, TNF, IL-2 and CD107a. Center line of box plots represents the median, edges of the box plot represent first and third quartiles, whiskers represent ±1.5 × IQR. To compare the frequencies of mono- and polyfunctional memory CD4 + and CD8 + T cells between PICs and ART controls ( n = 3 and 6 biological replicates, respectively), two-sided, unpaired, nonparametric Wilcoxon signed-rank tests with a Bonferroni correction for multiple comparisons were used. Each data point represents a single experiment per individual and time point, utilizing a minimum of 0.8 × 10 6 PBMCs per stimulation. Each data point is calculated by subtracting the value of responding cells to the specific stimulation by that within the negative control (stimulation of cells with dimethylsulfoxide (DMSO)). c , Specific cytokine production by responding CD8 + and CD4 + T cells in PICs ID107, ID9254 and ID142 at multiple time points before and after ART interruption. Color denotes positivity for cytokines and degranulation (CD107a), and the eight dominant responses are highlighted in bold in the legend.

Article Snippet: After stimulation and staining, T cells were enriched using the Pan T cell Isolation kit (Miltenyi Biotec, 130-096-535) and sorted on a MACSQuant Tyto.

Techniques: Comparison, Negative Control

Journal: Nature Immunology

Article Title: Autologous neutralizing antibodies and polyfunctional T cells contribute to long-term HIV-1 post-intervention control

doi: 10.1038/s41590-026-02448-z

Figure Lengend Snippet: ( A-B ) Peptide-stratified HIV-1-specific CD8 ( A ) and CD4 ( B ) T cell responses in ID107 were quantified by the AIM assay in response to stimulation with HIV-1 Gag, Pol, Nef and Env peptide pools. ( C-D ) Peptide-stratified HIV-1-specific CD8 ( A ) and CD4 ( B ) T cell responses in ID9254 were quantified by the AIM assay in response to stimulation with HIV-1 Gag, Pol, Nef and Env peptide pools. ( E-F ) Peptide-stratified HIV-1-specific CD8 ( E ) and CD4 ( F ) T cell responses in ID142 before viral rebound were quantified by the AIM assay in response to stimulation with HIV-1 Gag, Pol, Nef and Env peptide pools. ( G-H ) Total HIV-1-specific CD4 and CD8 T cell responses were plotted over time for ID107 ( G ) and ID142 before viral rebound ( H ), calculated as the sum of the responses to HIV-1 Gag, Pol and Nef. Analyzed samples are color-coded according to timepoint. Gray shading indicates time on ART. Each datapoint represents a single experiment per stimulation and timepoint.

Article Snippet: After stimulation and staining, T cells were enriched using the Pan T cell Isolation kit (Miltenyi Biotec, 130-096-535) and sorted on a MACSQuant Tyto.

Techniques:

Journal: Nature Immunology

Article Title: Autologous neutralizing antibodies and polyfunctional T cells contribute to long-term HIV-1 post-intervention control

doi: 10.1038/s41590-026-02448-z

Figure Lengend Snippet: a , Plasma HIV-1 viral load over time following ART interruption for ID142. b , Maximum likelihood phylogenetic tree of pre-rebound and rebound HIV-1 sequences sourced from multiple time points following ATI. Asterisk indicates branch support >70%. Scale bar indicates nucleotide substitutions per site. c , Dose–response neutralization curves for pseudoviruses sourced from post-rebound env sequences ID142.REBOUND1, ID142.REBOUND2 and ID142.REBOUND3. Pseudoviruses were tested against autologous IgG purified from longitudinal time points (see color keys; one IgG sample per time point). Data represent mean ± s.d., based on three replicates of culture wells containing pseudovirus and TZM-bl cells for each IgG concentration. For each experiment, control wells were included containing pseudovirus and TZM-bl cells with no IgG (six wells per experiment) and TZM-bl cells with no pseudovirus or IgG (six wells per experiment). The env sequences used to generate pseudoviruses ID142.REBOUND1, ID142.REBOUND2 and ID142.REBOUND3 are shown in Extended Data Fig. . d , IIP values at 10 mg ml −1 of longitudinally sampled autologous IgG for each pseudovirus from pre-rebound and rebound time points, and these are represented on the right y axis. The dashed line at IIP = 5 represents the threshold for effective suppression of in vivo viral replication. e , Spectral flow cytometric assessment of cytokine production by memory CD8 + T cells (top) and memory CD4 + T cells (bottom) in response to stimulation with HIV-1 Gag, Pol, Env or Nef peptide pools in ID142 between pre-rebound and rebound time points. Time points ATI weeks 135 and 140 are included and highlighted in black boxes. Color denotes positivity for cytokines and degranulation (CD107a), and the eight dominant responses are highlighted in bold in the legend. Each bar represents a single experiment per individual and time point, utilizing a minimum of 0.8 × 10 6 PBMCs per stimulation. The frequency of cells expressing each combination of cytokines is calculated by subtracting the value of responding cells to the specific stimulation by that within the negative control (stimulation of cells with DMSO). f , HIV-1-specific CD8 + T cell responses over time pre- and post-rebound as characterized by lymphocyte proliferation assay (column graphs; left y axis) and IFNγ ELISpot assay (symbols; right y axis) in response to stimulation with HIV-1 Gag, Pol and Nef peptide pools. Each data point represents a single experiment per stimulation and time point. g , HIV-1-specific CD4 + T cell responses over time pre- and post-rebound as characterized by lymphocyte proliferation assay in response to stimulation with HIV-1 Gag, Pol and Nef peptide pools. Each data point represents a single experiment per stimulation and time point. h , i , HIV-1-specific CD8 + ( h ) and CD4 + ( i ) T cell responses as characterized by the AIM assay in response to stimulation with HIV-1 Gag, Pol and Nef peptide pools. Each data point represents a single experiment per stimulation and time point. Gray shading indicates time on ART and blue shading indicates viremic time points during viral rebound. Analyzed samples are color-coded according to time point.

Article Snippet: After stimulation and staining, T cells were enriched using the Pan T cell Isolation kit (Miltenyi Biotec, 130-096-535) and sorted on a MACSQuant Tyto.

Techniques: Clinical Proteomics, Neutralization, Purification, Concentration Assay, Control, In Vivo, Expressing, Negative Control, Lymphocyte Proliferation Assay, Enzyme-linked Immunospot