Figure 6. Distinct transcriptional imprint with reduction in T_FH-associated gene expression but poor correction of T_H1, T_H17 and T_H22 gene levels after suppression of viremia by ART.

(a) Paired volcano plot comparisons depicting DEGs as measured by microarray analysis of sorted HIV-specific CD4⁺ T cells in 8 CPs before and after ART and 12 ECs. Red, pink and blue dots represent DEG with log₂|FC| >1 and padj<0.05, log₂FC>1 or padj<0.05, respectively. Moderated two-sided t test followed by Benjamini-Hochberg method. (b) Euler diagrams of DEG between each pairwise comparison of the three groups of participants (log₂|FC|> 1, p<0.05); numbers represent DEGs. (c) Significant enriched Gene Ontology terms from the curated C5 MSigDB via CAMERA analysis. Blue, Red and white color denote negative, positive or not significant (as defined by FDR<0.05, respectively. Two sided p-value by CAMERA and FDR by Benjamini-Hochberg method. (d-f) Barcode plots of enriched Thelper polarization gene sets by CAMERA in paired comparisons between the three groups (n= 8 CPpre 8 CPpost and 12 EC). Red and blue lines denote positive and negative enrichment, respectively. T_H1 signature: GSE59295 (T_H1 vs T_H2), T_H17 signature: GSE49703 (T_H17 vs T_H1), T_FH signature: GSE50391 (CXCR5high CD45RO vs CXCR5-tonsil samples). Two sided p-value by CAMERA and FDR by Benjamini-Hochberg method. (g) Differential expression of genes associated with CD4 T cell differentiation and function in HIV-specific CD4⁺ T cells of CPs before and after treatment compared to ECs. Red and purple denote logarithmic fold change for comparisons CPpre. vs EC and CPpost vs EC, respectively, by microarray analysis in 8 CP before/after ART and 12 ECs.