FIGURE 4 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Single-cell analysis of IsoPlexis data for CD4 cells (left) and CD8 cells (right). A, UMAP visualization colored by sample location (orange for PB, purple for BM). B, UMAP colored by time point (green for baseline, pink for post-therapy). C, Neighborhood graph depicting differential abundance testing results obtained from miloR. Colors represent the log fold-change between baseline (red) and post-IO (blue) cells. White neighborhoods are nondifferential (FDR 10%). The edges depict links between cells shared by neighborhoods. D, Beeswarm plot of the distribution of neighborhoods by timepoint. E, Beeswarm plot of the distribution of neighborhoods by UMAP-based cluster.</p

FIGURE 1 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Integrative analysis approach and clinical characteristic profile of patient cohort. A, Clinical characteristics of RelRef AML cohort for 21 patients involved in the phase II clinical trial. Among the 21 patients enrolled, 20 had baseline PB samples, 16 had baseline BM samples, 10 had posttreatment PB samples, and 6 had posttreatment BM samples. Four patients had prior allogeneic stem cell transplantation (all-SCT) therapy; 11 patients had prior HMA therapy; 11 patients had Secondary AML; 10 patients had CR to Aza/Nivo immunotherapy in the phase II clinical trial; Karyotype and molecular diagnostics at baseline for all 21 patients are included. B, Venn diagram visualizing the patient cohort.</p

FIGURE 3 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Exploratory analysis of CR and NR patients at baseline. CRs have significantly higher CD4 effector cytokine expression than NRs in the BM. No significant difference in functional group expression from CD8 cells in either PB and BM between CR and NR.</p

Supplementary Figure 2 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Baseline correlation analysis of age with individual cytokines and functional groups.</p

Supplementary Figure 1 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Exploratory analysis of baseline T cell cytokine dynamics in PB and BM.</p

FIGURE 2 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Baseline T-cell functional activity in PB and BM. A, Heat map of T-cell cytokine expression values in PB (n = 20) and BM (n = 16) samples at baseline split by cell subset and scaled by row with clinical characteristic and functional group annotations. ComplexHeatmap was used for data analysis and visualization. B, ComplexHeatmap comparing cytokine expression based on functional groups of CD4 and CD8 cells between TMEs at baseline in the PB and BM. C, Bar plot representation of the significant functional groups from B. Pairwise analysis using ggpaired shows differences based on functional group expression compared between TMEs (P < 0.05).</p

Supplementary Figure 3 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Baseline T cell individual cytokine activity in PB and BM.</p

Supplementary Figure 4 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Baseline and post-therapy T cell functional activity within PB and BM.</p

FIGURE 5 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

Single-cell cytokine and polyfunctional group analysis at baseline. Heat map of cytokine expression by cluster for A. CD4 T cells. Annotation bars show cluster breakdown by sample location and timepoint. Hierarchical clustering was used to create new polyfunctional groups (CD4-G1-5), which are highlighted by black boxes. B, Boxplots for CD4 T cells show the comparison of complete responders (CR, brown) and nonresponders (NR, blue) at baseline by sample location in these newly defined polyfunctional groups for T cells. C, Heat map of cytokine expression by cluster for CD8 T cells with hierarchical clustering creating new polyfunctional groups (CD8-G1-6). D, Boxplots for CD8 T cells show comparison of CR (brown) and NR (blue) at baseline.</p

Supplementary Figure 5 from Single-Cell CD4 and CD8 T-Cell Secretome Profiling Reveals Temporal and Niche Differences in Acute Myeloid Leukemia Following Immune Checkpoint Blockade Therapy

UMAP visualization depicting batch-corrected Seurat defined clusters.</p