Extended Data Fig. 4: Pathway analysis of transcriptomic changes induced in CD4+ T cells and myeloid cells during LTT.
a, scRNAseq tSNE analysis of PBMCs after a 4-day culture with or without SMX/TMP, color-coded based on origin (n = 5,881 cells). b, Pathways upregulated in CD4(1) cluster (from Fig. 4b–d, n = 1,486) after SMX/TMP treatment. c, Volcano plot of up- (red) and down-regulated (blue) genes differentially expressed in SMX/TMP treated CD4(1) cells (|log fold change| > 0.5), highlighting relevant genes associated with pathways from (b). With SMX-TMP, n = 418 CD4(1) cells; without SMX-TMP, n = 1,068 CD4(1) cells. Full list of differentially expressed genes from the three CD4 T cell clusters (n = 3,869 cells) observed in LTT (see Fig. 4b, c) is provided in Supplementary Table 2. d, Pathways upregulated in myeloid cells after SMX/TMP treatment. e. Volcano plot of differentially expressed genes in myeloid cells (n = 513) by SMX/TMP treatment, labeling relevant genes in pathways from (d). f, Frequencies of top-20 common T cell receptor (TCR) clonotypes in PBMCs after a 4-day culture with or without SMX/TMP as determined by single-cell TCR V(D)J gene sequencing. g, h, scRNAseq tSNE analysis on SMX/TMP-treated PBMCs with or without tofacitinib (n = 2,068 cells) colour-coded based on cluster (g, top) and origin (h). tSNE projections of selected marker genes (g, bottom). i, Pathways downregulated in CD4 lymphocytes of tofacitinib-treated PBMC, and j, Volcano plot with labeling of relevant downregulated genes. Tofacitinib-treated CD4 cells, n = 825; untreated CD4 cells, n = 508. P-values in b,d,i, hypergeometric test; p-values in c, e, j, Wilcoxon rank sum test.
