Fig. 3: The transcriptional signature of MAIT cells before and during acute HIV-1 infection.

RNA-Seq was performed on sorted MAIT cells from the PBMC of longitudinal samples corresponding to one pre-infection and three post-infection time points in the acute capture cohort (n = 9). a Volcano plots depict upregulated (red) or downregulated (blue) genes compared to pre-infection at three post-infection time points in acute HIV-1 infection. Individual genes listed in Supplementary Table 4. Highlighted genes have a –Log₁₀ p-value ≥ 3 and a Log₂ fold change of 0.5 or −0.5 (corresponding to p ≤ 0.001, and fold change of 1 or −1, in a generalized linear model). b The temporal dynamics of the upregulated and downregulated genes shown longitudinally in acute HIV-1 infection, together with plasma VL. c Shared and unshared differently expressed genes compared to pre-infection between all three post-infection time points in acute HIV infection are highlighted as a Venn diagram, and listed in Supplementary Table 4. d Gene expression patterns were subjected to Gene Set Enrichment Analysis (GSEA), and upregulated and downregulated pathways in post-infection time points compared to pre-infection are displayed as a Normalized Enrichment Score (NES) heat map. Enrichment plots from three selected post-infection upregulated pathways compared to pre-infection are shown; e, negative regulation of viral entry into host cell, f, regulation of IFNγ production, and g, natural killer cell mediated immunity. Genes contributing to enrichment plots are listed in Supplementary Table 5. PBMC, Peripheral blood mononuclear cells. VL, viral load. MAIT cells are identified as CD161 + + Vα7.2 + cells within CD3 + CD14-CD19- live lymphocytes.