Figure 2.

Activated PD-1^highCXCR5^– 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-1^highCXCR5^– Tph cells compared with five subsets.

(B) Heatmap of PD-1^highCXCR5^– Tph cell-related genes (selected in A).

(C) Heatmap of PD-1^highCXCR5^– 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-1^highCXCR5^– Tph cells between non-ICU and ICU patients (left). The proportions of activated PD-1^highCXCR5^– 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 CD27^highCD138⁺ plasma cells after co-culture (F, left) and the proportion of plasma cells (F, right). IgG concentrations in supernatants were evaluated (G). PD-1^int/−CXCR5^– T cells indicate both PD-1^intCXCR5^– T cells (subset iii) and PD-1⁻CXCR5^– T cells (v).

Data are represented as mean ± SEM (D–G).

See also Figure S4.