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. 2021 Feb 20;1(1):100003. doi: 10.1016/j.xjidi.2021.100003

Figure 3.

Figure 3

Single-cell RNA-seq analysis of sorted CD4+ T cells and ILCs from human peripheral blood. (a) Th2 cells are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-seq data of 6,402 CD4+ T cells combined from six samples (before [Pre] and 16 weeks after [Post] dupilumab treatment from patient IDs 895, 918, and 939). Hierarchical clustering based on gene expression profiles was performed, and the T cells split into four clusters: naive T, Th1/17, Th2, and Treg. (b) Heatmaps of the representative genes from each cluster, naive T, Th1/17, Th2, and Treg. (c) Single-gene expression t-SNE plots of the single-cell RNA-Seq data. CCR7, CCL5, PTGDR2 (CRTH2), and FOXP3 are markers of naive T cells, Th1/17 cells, Th2 cells, and Treg cells, respectively. (d) Heatmaps of the representative genes (selected by differential expression analysis) gated on the Th2 cluster using the BD DataView software (n = 3, patient IDs 895, 918, and 939). (e) ILC2s are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-Seq data of 638 ILCs combined from six samples (patient IDs 924 Pre/Post, 938 Pre/Post, 1049 Post, and 1062 Post). Hierarchical clustering based on gene expression profiles was performed, and the ILCs split into three clusters: NK/ILC1, ILC2, and ILC3. (f) Heatmaps of the representative genes from each cluster, NK/ILC1, ILC2, and ILC3. (g) Single-gene expression t-SNE plots of the single-cell RNA-seq data. PTGDR2 (CRTH2), KIT, and GZMK are markers of naive ILC2s, ILC3s, and NK/ILC1, respectively. (h) Heatmaps of the representative genes (selected by differential expression analysis) gated on ILC2 cluster using the BD DataView software (n = 2, patient IDs 924 and 938). ID, identification; ILC, innate lymphoid cell; max, maximum; min, minimum; RNA-seq, RNA sequencing; Th, T helper type; Treg, regulatory T cell; t-SNE, t-distributed stochastic neighbor embedding.