Skip to main content
. Author manuscript; available in PMC: 2020 Jan 15.
Published in final edited form as: Nat Immunol. 2019 Jul 15;20(8):1059–1070. doi: 10.1038/s41590-019-0418-x

Figure 2. HIV-specific CD4+ T cell polarization is associated with level of viral control.

Figure 2.

(a-d) Barcode plots of enriched Thelper polarization and exhaustion gene sets by CAMERA in CP (n=11) vs EC (n=12) people. Red and blue lines denote positive and negative enrichment of CP genes vs. EC, respectively. (A) TH1 signature: GSE59295 (TH1 vs TH2), (B) TH17 signature: GSE49703 (TH17 vs TH1), (C) TFH signature: GSE50391 (CXCR5high CD45RO vs CXCR5-tonsil samples), (d) LCMV exhaustion signature GSE41866 (LCMV Clone 13 D30 vs Armstrong D30-Exhausted vs Memory). Two sided p-value by CAMERA and FDR by Benjamini-Hochberg method. The arrows beneath the barcode plots depict the orientation of the enrichment between CP and EC. (e-h) Heatmaps of mRNA expression of the top 50 significant genes of each CD4+ T cell signature in CPs and ECs. Red and blue font of gene names denote upregulated and downregulated mRNA expression in CPs vs ECs, respectively. (i) PCA representation of CPs (n=11), VCs (n=9) and ECs (n=12) based on transcriptional expression of 90 genes associated with CD4+ T cell differentiation, effector functions and exhaustion. Transcriptional expression (-ΔCt values) was evaluated by qRT-PCR (Fluidigm). The top 35 contributing genes are displayed and color-coded according to their contribution. Bigger dots represent the mean PC coordinates for each group. The numbers in parenthesis stand for the percentage of variance that the PC accounts for. (j) Correlation of PC1 values for each individual with viral load by two-tailed Spearman correlation (n= 11CPs, 9 VCs, 12 ECs).