Fig 2: Activated PD-1highCXCR5– Tph cells are significantly increased in non-ICU patients with COVID-19(A) Venn diagrams showing the overlapped genes among those significantly upregulated (log2FC > 1, FDR < 0.05) (left) and downregulated (log2FC < −1, FDR < 0.05) (right) in PD-1highCXCR5– Tph cells compared with five subsets.(B) Heatmap of PD-1highCXCR5– Tph cell-related genes (selected in A).(C) Heatmap of PD-1highCXCR5– Tph cell-related genes (selected in A) among each T cell cluster of our scRNA-seq dataset reported.5(D) Representative data for each T cell subset among HLA-DR+CD38+CD45RA–CD4+ T cells (left), and their proportions were evaluated by one-way ANOVA with Dunn’s multiple comparisons tests (right). COVID-19 samples that have more than 5% of HLA-DR+CD38+ T cells were evaluated (n = 11).(E) Representative data of HLA-DR+CD38+ activated cells in PD-1highCXCR5– Tph cells between non-ICU and ICU patients (left). The proportions of activated PD-1highCXCR5– Tph cells were evaluated (non-ICU; n = 56, ICU; n = 36) by two-tailed unpaired Student’s t test (right).(F and G) Each T cell subset and autologous CD20+CD27+ B cells were co-cultured (n = 7, patients with COVID-19). Representative data of CD27highCD138+ plasma cells after co-culture (F, left) and the proportion of plasma cells (F, right). IgG concentrations in supernatants were evaluated (G). PD-1int/−CXCR5– T cells indicate both PD-1intCXCR5– T cells (subset iii) and PD-1−CXCR5– T cells (v).Data are represented as mean ± SEM (D–G).See also Figure S4.