Fig. 6: Persistent HIV-associated transcriptional alterations in nasal T cells during long-term ART. | Nature Communications

Fig. 6: Persistent HIV-associated transcriptional alterations in nasal T cells during long-term ART.

From: Persistent pneumococcal colonisation in antiretroviral-treated HIV infection is associated with nasal inflammation

Fig. 6: Persistent HIV-associated transcriptional alterations in nasal T cells during long-term ART.

Differential gene expression analysis was performed on nasal T cells using the MAST algorithm via Seurat’s FindMarkers function. Volcano plots showing differentially expressed genes in T cells comparing: a PLHIV-ART > 1 year vs. HIV-uninfected adults (HIV-adults); b PLHIV-ART < 3 months vs. HIV−; c PLHIV-ART > 1 year vs. PLHIV-ART < 3 months. d Dot plot showing co-expression gene modules enriched in T cells across study groups, identified using CEMiTool. Dot size represents −log₁₀(adjusted P value) and colour denotes normalised enrichment score (NES). Bar plots of the top 10 enriched pathways in e Module 1 (M1), overexpressed in PLHIV-ART > 1 year and f Module 2 (M2), overexpressed in PLHIV-ART < 3 months, based on gene set overrepresentation analysis (ORA) using Reactome pathways. Gene module scores for key immunological pathways in nasal T cells, grouped by HIV status: g exhaustion and senescence-associated genes; h activation-related genes; i intrinsic apoptosis genes; and j extrinsic apoptosis genes. Statistical comparisons were performed using a Holm-adjusted two-sided Wilcoxon rank-sum tests; P < 0.05 was considered significant. NES normalised enrichment score; −log10 Adj. p-value, −log10 of Holm-adjusted p-value.

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