Fig. 1

Study design and characterization of major immune cell subsets from PBMCs. (A) Overview of workflow. PBMCs were isolated from healthy individuals (n = 10) and individuals infected with HIV-1 including TN individuals (n = 20), INRs (n = 20) and IRs (n = 20). PBMCs were stained using metal-labeled antibodies to simultaneously quantitate the levels of 43 different surface and intracellular proteins followed by acquisition using CyTOF2 (Fluidigm) and analysis using t-Distributed Stochastic Neighbor Embedding (t-SNE). (B) T-SNE projection of PBMCs showing major cell clusters based on expression of cell type-specific makers. Each dot corresponds to a single cell and colored according to PhenoGraph clustering (left); groups are each colored as indicated (right). (C) Heatmap showing the median metal intensity of individual markers for each cluster as indicated. (D) Frequency of major immune cell subsets including CD4⁺ T cells, CD8⁺ T cells, γδT cells, NK cells, B cells, DCs, and monocytes from individuals with chronic HIV-1 infection and healthy individuals. Groups are shown in different colors. Horizontal lines represent mean values, and each dot represents one sample. Significant differences are indicated by *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001. Differences between each group were analyzed using a two-sided unpaired Mann–Whitney U-test. (E) Donut chart showing the composition of CD45⁺ cells colored according to major cell types from each cohort. TNs: treatment-naïve HIV-1-infected individuals; INRs: immune non-responders to antiretroviral therapy; IRs: immune responders to antiretroviral therapy; HCs: healthy controls