Figure 7

Systematic analysis of data of immunosenescence, disease progression and host response. (a) The correlation network of immunophenotype and gene expression data was constructed by using the qgraph package with R. The 4 groups of nodes are colored on the basis of data types. The groups include genes expressed higher in the young group (IFNB1, CCL2 and SOCS1), genes elevated in only the old group (TLR7, IFI16 and CCL5), other genes significantly correlated with immunophenotype (OAS3, CXCL10, MX2, IRF7, STAT1, IRF9, AIM2, LY96, TLR8 and IFNG) and an immunophenotype that differed between the young and old groups (CD4T, CD4⁺ T cell number; Ratio, CD4/CD8; CD4TN, naïve CD4⁺ T cell number; CD8 TN, naïve CD8⁺ T cell number; CD4Ki67, % of Ki67⁺CD4⁺ T cells; CD4TNKi67, % of Ki67⁺CD4⁺ T cells; CD8TNKi67, % of Ki67⁺CD8⁺ T cells; BN, naïve B cell number; BNKi67, % of Ki67⁺ naïve B cells). The node size indicates the relative strength value according to a centrality analysis. The thicker lines indicate more correlated genes. The green lines represent significantly positive Pearson correlation coefficients ≥ 0.40, and the red lines represent significantly negative Pearson correlation coefficients ≤ −0.40. (b) Model of immunosenescence, disease progression and host response in ChRM that demonstrates their variation differences during early SIV infection as detailed in the text. Immunosenescence is shown by the numbers of naïve CD4⁺ T cells and the percentage of Ki67⁺ naïve T cells. The plasma viral loads and CD4⁺ T cell numbers represent the level of disease progression. The innate host response is defined by the fold-changes of differentially expressed genes. The smooth curves were constructed by a spline fit method using GraphPad Prism 6 software.