Fig. 2

scRNA-seq analyses reveal the transcriptional characterization of mucosal-associated invariant T (MAIT) cells in human immunodeficiency virus (HIV)-infected patients. a UMAP projection of 5632 MAIT cells from 5 different sample conditions. Each dot corresponds to a single cell, colored according to different samples. b Heatmap showing selected markers’ relative expression levels in different conditions. Columns denote sample conditions, and rows denote genes. c A dot plot showing the Gene Ontology enrichment results for differentially expressed genes identified by comparing TPs with HCs. The top 30 GO terms with P-value cut-off = 0.01 and Q-value cut-off = 0.05 were shown. d GSEA enrichment results for direct T cell activation. P-values were calculated by GSEA with the Benjamin-Hochberg correction. e Heatmap showing selected markers’ relative expression levels in different samples. Columns denote samples, and rows denote genes. f A Venn diagram showing the genes shared by four conditions. g Heatmap showing the expression of shared genes of (f) under at least two conditions. h Pooled data showing expression of indicated markers in HC-MAIT, TP-MAIT (n = 9) and TP FLICA caspase-1⁺ MAIT (n = 9) cells. Each symbol represents a single individual. Data are expressed as M (Q₁, Q₃). Mann–Whitney U test (h). ^**P < 0.01, ^***P < 0.001, ^****P < 0.0001. HCs healthy controls, EC elite controller, TPs treatment-naive patients, ART antiretroviral therapy, GSEA gene set enrichment analysis, PD-1 programmed death-1, IFN-γ interferon-γ, TNF-α tumor necrosis factor-α