Extended Data Fig. 6: FIRM-integrated UMAP of atlas immune cells and further characterization of neutrophils and B lymphocytes.
From: Mouse lemur cell atlas informs primate genes, physiology and disease
a-d. UMAP of atlas immune cells as in Fig. 2b but colored by proliferation state (a), scRNA-seq method (b), individual (c), and tissue of origin (d). e. Heatmap showing relative expression along neutrophil trajectory (10x) of lemur orthologues of human neutrophil markers. Colored bar indicates cell type designation as in Fig. 2b inset. For each gene, expression values (ln(UP10K + 1)) were normalized to its maximal value (99.5 percentile) in trajectory. Non-activated neutrophils in plot were uniformly subsampled (10%). Note human-like sequential expression of granulopoiesis marker genes; azurophilic (primary) granules (AZU1, MPO, ELANE) in early stages, followed by specific (secondary) granules (LTF, CAMP, LCN2), gelatinase granules (MMP9, ARG1), and finally secretory vesicles (ALPL, MME) in mature neutrophils. *, genes without a mouse orthologue; +, genes not expressed in mouse neutrophils. [], description of genes identified by NCBI as loci: [CTSG], LOC105866609; [DEFA4L], LOC105881499; [DEFA1], LOC105881500; [CCL8], LOC105885739; [CCL4], LOC105881712. f. UMAPs of lung neutrophils (10x) of the indicated individuals, with cells colored by cell type designation. Note the two subtypes of activated neutrophils (CCL13+ and IL18BP+) cluster separately from the main neutrophil population (non-activated) in both L1 and L2. g. Heatmap showing relative expression of the indicated marker genes for mature and activated neutrophils as well as DEGs for each activated neutrophil subtypes. Bars at top show for each neutrophil, its tissue source (top set of bars), individual lemur source (middle), and cell type designation (bottom). Note both activated neutrophil subtypes were found in more than one individual and from multiple tissues. Expression values for each gene were normalized to the maximal value (99.5 percentile) for the gene across all cells in the neutrophil trajectory. The mature (non-activated) neutrophils are highly abundant so uniformly subsampled (20%) in plot at late stage (>0.7) of the pseudotime trajectory. *, genes without a mouse orthologue. [IFITM3L], LOC105874071; [Uncharacterized 1], LOC105867541; [CCL2L], LOC105859340 and LOC105885684; [CCL13], LOC105859268; [Uncharacterized 2], LOC105856756; [CCL3L], LOC105881608. h. Dot plot showing mean expression in B lymphocyte lineage cells of marker genes for B cells, plasma cells, and top DEGs in the SOX5+ B cell population compared to other B cells (10x, L1-L4). Lemur B cells and plasma cells in the atlas appear relatively homogenous molecularly, except for SOX5+ B cell population identified in L4’s pancreas (with nearby lymph nodes). See Supplementary Note 6 for further analysis.