Figure 6. CXCR5⁻PD-1⁺ICOS⁺ T Cells from HIV-Infected LNs Exhibit a Distinct Gene Expression Profile.

(A) Principal-component analysis of RNA-seq data from different CD4⁺ T cell subsets.

(B) A list of Gene Ontologies based on significantly variant genes compared between CXCR5⁻PD-1⁺/CXCR5⁺PD-1⁺ T cells called by both GSEA and GOrilla. Normalized enrichment score (NES) and false discovery rate (FDR) were generated from GSEA. A positive enrichment score indicates gene set enrichment in CXCR5⁻PD-1⁺ICOS⁺ T cells.

(C) Volcano plot for comparison between T_FH cells and CXCR5⁻PD-1⁺ICOS⁺ cells. The differentially expressed genes were defined with cutoff adjusted p value < 0.05, log₂ |foldchange| > 1.5.

(D) Heatmap representing differentially expressed trafficking-related receptors in 4 cell subsets. Gene expression values were normalized and scaled with DESeq2.

Also see Figure S7.