Figure 5.

Observation of SIV-specific cellular responses and tissue reorganization

(A) LDA was performed on the collective markers for each of the 14 CNs within each of the six animals. Each dot represents a single CN from a single animal. CNs are colored by the animal infection status and the animal of origin. Dotted lines indicate animal infection status: uninfected control (cyan), acute infection (purple), and chronic infection (orange). The variances accounted for by each of the two linear discriminants, LD1 and LD2, are plotted on the x and y axes, respectively.

(B) The rank plot of the markers that account for LD1 (top) and LD2 (bottom) colored based on enrichment (orange) or depletion (green) in individual CNs of infected animals versus uninfected animals.

(C) Pairwise Pearson’s correlations of selected immune markers across each individual cell from healthy (top; teal) and SIV-infected (bottom; orange) animals. Representative infection-related processes are highlighted: (1) macrophage immunosuppression as indicated by a M2 switch via CD163 and FoxO1 (blue boxes), (2) increased CD8 T cell infiltration (black boxes), (3) B and T cell proliferation via elevated Ki-67 correlation (yellow boxes), and (4) FDC activation and antigen presentation via increased CD169 and CD11b presence (green boxes).

(D) Pairwise Pearson’s correlations of selected immune markers across each individual cell within CN8, separated by healthy (top; teal) and SIV-infected (bottom; orange) animals. The colored boxes are as above in (C).

(E and F) The pairwise cell distances for (E) each cell type and (F) each CN over 1,000 iterations of randomized background permutations are plotted as colored shapes for infected (orange, triangle) and healthy (teal, square) animals. Only interactions that passed a correlation test (p < 0.05) for both infection conditions are shown. Shapes that are toward the left indicate cell-cell or CN-CN interactions that are closer than expected, and those toward the right indicate interactions that are further apart than expected. Pairs of cells are given in text form (left) and colored heatmaps (right). In (E), purple arrows indicate B cell-macrophage interactions, and green arrows indicate NK cell-T cell interactions that are closer in infected than uninfected tissues. In (F), the green arrow indicates CN8-CN4 interactions that are closer in uninfected than infected tissues, whereas purple and red arrows indicate interactions that are closer in infected tissues than uninfected tissues.

See also Figure S5.