Extended Data Fig. 3: Longitudinal HIV reservoir measurements and HIV-specific T cell responses.
From: Correlates of HIV-1 control after combination immunotherapy
a) Cell-associated 3′ and 5′ defective HIV DNA in peripheral blood CD4+ T cells by IPDA. b) Longitudinal cell-associated HIV RNA transcript measurements. c) IPDA measurements from gut tissue in select participants (ND, not detected). All sampled post-ATI. All participants were aviremic at the time of sampling. On ART: 35933, 10227, 71190. Off ART: 60610. d) Intracellular cytokine staining (ICS) gating scheme. e) Longitudinal phenotypes of HIV Gag/CE-specific (IFNγ+) CD8+ T cells. Missing points reflect timepoints with no or too few (<50) CE-specific CD8+ T cells to phenotype. f) Frequency of Nef-specific (IFNγ+) CD4+ and CD8+ T cells. g) PD-1 expression on Nef-specific CD8+ T cells. h) Frequency of total (IFNγ+) HIV-specific CD4+ T cells by ICS (sum: Gag+Pol+Nef+Env). IPDA, intact proviral DNA assay. Timepoints (applies to all figures): BL, baseline prior to interventions (i.e., on ART); Post-prime, day of MVA vaccination (>6 weeks after last DNA vaccination); Post-boost, 2 weeks after MVA vaccination; pre-LEF, prior to lefitolimod dosing; pre-ATI, prior to ATI; pre-R, last PBMC sampling timepoint available prior to rebound (sampled within 1-4 weeks prior to HIV rebound). Note: for PID 60610 (aviremic controller), the data shown at the “pre-R” timepoint was evaluated 44 weeks into the ATI. IFNγ, interferon gamma. ICS, intracellular cytokine staining.
