Fig. 3: Single-cell transcriptional profiling of nasal mucosal cells in HIV infection.
Nasal cells from HIV-uninfected adults (HIV-adults, n = 3), PLHIV on ART for <3 months (PLHIV-ART < 3 months, n = 3) and PLHIV on ART for >1 year (PLHIV-ART > 1 year, n = 5) were processed for single-cell RNA sequencing using the 10x Genomics 5′ platform. After quality control and normalisation, 22,119 cells were analysed using the Seurat pipeline with Harmony integration. a UMAP visualisation of all nasal cells coloured by major cell types. b Distribution of major cell clusters across study groups. c Violin plots showing expression of canonical marker genes used for broad cell-type identification. d UMAP visualisation of 4099 immune cells coloured by fine-grained immune cell annotations. e Bar plot showing the distribution of immune cell subsets across study groups. f Box plots comparing neutrophil abundance among HIV–, PLHIV-ART < 3 months and PLHIV-ART > 1 year groups. Box plots show the interquartile range (25th–75th percentiles). The bold horizontal line inside each boxplot indicates the median. Whiskers extend to the smallest and largest values within 1.5× the interquartile range (IQR) from the lower and upper quartiles, respectively. Individual points beyond the whiskers denote outliers. Cell type: NK natural killer cells; Mono monocytes; Mac macrophages; DCs dendritic cells. Statistical significance was determined using the two-sided Wilcoxon rank-sum test; P < 0.05 was considered significant.
