Fig. 1: IFN signaling is induced in PBMCs and LNMCs of combo-treated RMs pre-ATI and is inversely correlated with virological readouts 24 weeks post-ATI.
From: TGF-β mediates epigenetic control of innate antiviral responses and SIV reservoir size
a, Pathways (MSigDB, Hallmark) significantly (P ≤ 0.05) differentiated in combo-treated RMs from control RMs or aIL-10 treated RMs pre-ATI in PBMCs and LNMCs. Heatmap illustrates GSEA NES ranging from high (red) to low (blue). Rows represent gene sets (IFN pathways) and columns represent contrasts in PBMCs and LNMCs. n = 28. b, Network inference (Cytoscape and Genemania) showing leading-edge genes (LEGs) (P < 0.05) of pathways in Fig. 1a upregulated in PBMCs and LNMCs of combo-treated RMs (red circular nodes). Connecting lines Edges: gene–gene interaction, color-coded by network type. c, Heatmap illustrating SLEA scores for significant (P < 0.05) IFN signaling pathways and RFs pre-ATI in LNMCs from control (black), aIL-10 only (red) and combo-treated RMs (blue). Rows represent pathways and columns represent individual RMs. Red-white-blue gradient for SLEA pathway scores from low and high relative levels of expression, respectively. Top annotation: levels of CA-vRNA, CA-vDNA and 2-LTR circles (white to blue, green, purple, respectively) 24 weeks post-ATI. The rectangle outline indicates the subset of combo-treated RMs (n = 10). n = 28. d, Heatmap illustrating gene expression in LNMCs pre-ATI correlated with viral outcomes (log10 SIV CA-vDNA, log10 CA-vRNA and log10 2-LTR circles) 24 weeks post-ATI (false discovery rate (FDR)-adjusted P < 0.05) (left). Two-sided Spearman correlation, P values adjusted for multiple comparisons with Benjamini–Hochberg (BH) procedure. Rows represent genes and columns represent individual RMs: controls (black), aIL-10 only (red), and combo-treated (blue). Standarized gene expression (z-score): blue-white-red gradient, for low to high relative expression, respectively. n = 25 RMs with virological readouts available. Network representing the top ISGs with antiviral capacity negatively correlated (NES = −1.44, P = 0.021) to viral outcomes at week 24 post-ATI (right). Blue nodes represent inverse correlation with viral outcomes. e, IFN and antiviral pathways (P ≤ 0.05) persistently upregulated in CA-vDNAlo RMs pre- and post-ATI. Heatmap illustrates NES for IFN-related pathways. Rows represent pathway sets and columns represent comparisons at both pre- and post-ATI time points in LNMCs. n = 10 combo-treated RMs. f, Network inference (Cytoscape and Genemania) showing common LEGs upregulated at weeks 0 and 24 in CA-vDNAlo RMs. Red nodes represent upregulated genes. Edges highlight gene interactions. g, Network inference (Cytoscape and Genemania) showing the IFN-associated genes upregulated in PBMCs and LNMCs (significant LEGs, P < 0.05). Red circular nodes represent upregulated genes in combo-treated RMs compared to aIL-10-treated RMs edges highlight gene–gene interactions. h, Experimental design. CD4⁺ T cells from healthy donors (n = 6) were pretreated with IFN-β and divided into two pools. Unlabeled cells were infected with HIV by spinoculation, while uninfected cells were labeled with CTV. On day 2, infected and CTV-labeled cells were mixed (1:1) and co-cultured for 4 days in the presence of saquinavir. Intracellular p24 expression was measured by flow cytometry. Figure created in BioRender; Pereira Ribeiro, S. https://biorender.com/qr7isln (2026). i, Frequencies of HIV p24⁺ cells were measured by flow cytometry 4 days post-infection in CTV⁻ and CTV⁺ cells. Gray bars, untreated; blue bars, IFN-β treated. Circles, HIV-infected CD4⁺ T cells; triangles, CTV-labeled bystander CD4⁺ T cells. Comparison of groups means was performed with a nonparametric Friedman test and P values were adjusted for multiple comparisons with a Benjamini, Krieger and Yekutieli (BKY) procedure. Error bars represent mean ± s.e.m. *P < 0.05, **P < 0.005, paired t-test.
