Fig. 2: Within-cell-type changes are associated with each exposure.
From: Genetics and environment distinctively shape the human immune cell epigenome
a, UMAP of cells in each cell type from FACS using snmC-seq2 data. The cells are colored according to exposure (HIV, exposure to HIV; HIV_pre, before HIV infection from the same donors; Flu_pos, after IAV infection; Flu_pre, before IAV infection from the same donors; COVID_S, severe COVID patient samples; COVID_nS, nonsevere COVID patient samples; MRSA, samples exposed to MRSA; MSSA, samples exposed to MSSA; BA, samples from the donors that have taken anthrax vaccine and work frequently or infrequently in a controlled BSL3 facility handling B. anthracis; OP, samples from the donors that are exposed to OP). b, Bar plots show the proportions of cells from each group and cell type in the Leiden clusters, colored by the FACS cell types. The x axis is the Leiden clusters and the y axis shows the proportions of cells in each Leiden cluster in each group. c, Scatter plot shows the cell proportional changes before and after infection with HIV and IAV in each Leiden cluster. Dots represent clusters with IAV exposures and crosses indicate HIV exposures. Color shows the FACS cell types. d, UMAP of cells from HIV exposure donors in the cell types that have the most cell proportion changes. The three rows are UMAP of cells from NK cell, Tc-mem and Tc-naive, and the columns are the cells from ‘pre’, ‘acu’ and ‘cro’ stages. Cells from the stage are shown in red and cells from other stages are shown in gray. e, The dot plot shows the odds ratio using two-sided Fisher’s exact test on cells from the three HIV infection stages (‘pre’, ‘acu’, ‘cro’) in the Leiden clusters. The heatmap shows the GO enrichment of DMGs of the corresponding Leiden cluster. The dot plot and heatmap have the same x axis. f, Two clusters of monocytes were identified. The bar plot depicts the cell proportions of the two monocyte clusters in controls, severe and nonsevere COVID-19 samples. Statistical tests were done using the two-sided chi-square test. (Asterisk indicates that P = 1.32 × 10−278). g, Gene body methylation levels at classical and nonclassical monocyte markers in the two clusters of monocytes. h, GO enrichment using the hypergeometric test with Benjamini–Hochberg FDR correction (implemented in Metascape) for DMGs between the two clusters of monocytes.
