Fig 2: Effector Functions of CD56neg NK CellsPseudocolor graphs representing degranulation capability (CD107a) and production of IFN? and TNF of CD56neg NK cells in the IL-15 primed non-stimulated and K562 conditions and IL-12+IL-15+IL-18 condition of the functional assay. The percentage of cells positive for each marker is shown. Data from a representative cART HIV-1 infected subject is shown.

Fig 3: Diverse subsets within HLA-DRhigh macrophages(A) UMAP highlighting diverse subsets of macrophages within HLA-DRhigh macrophages when analyzed under a higher resolution. Arrows point in the direction of pseudo temporal trajectory predicted by Monocle.(B) Trajectory of cells ordered by predicted pseudo time colored by pseudotime (top) or by the cluster of origin (bottom).(C) Heatmap of top 100 genes that define the trajectory originating from HLA-DRlow macrophages, through clusters 1, 2, and 3 of HLA-DRhigh macrophages. Low and high gene expression is indicated by blue and red, respectively.(D) Violin plots comparing the expression of the top eight markers from each of the HLA-DRhigh macrophages across all three clusters.(E) Violin plot comparing aggregate score for modules of genes highly expressed in macrophages stimulated with TPP (TNF+Pam3CSK4+PGE2), an in vitro model for chronic inflammation.(F) Gating strategy for flow cytometry-based identification of HLA-DRhigh macrophage clusters based on markers discovered from differential gene analyses.(G) Three-way functional enrichment of top genes expressed by each HLA-DRhigh subset performed in Metascape. The size of the bubble denotes the number of genes mapping to each gene ontology (GO) term, and the intensity of color denotes the statistical strength of prediction.