Fig 2: Active NK cells with a unique transcriptome profile. a Top two enriched gene sets (ranked by normalized enrichment score) of five different datasets from GSEA of the “Inflamed NK” cluster compared to the rest of the cells were plotted. b The expression of CD69 in the BM sample was shown as a violin plot. The y-axis represents log-normalized expression value. c Module score was calculated using up-regulated DEGs of “Active NK” (left) or “Inflamed NK” (right) cluster from BM sample and plotted via violin plots. d Up-regulated IEGs from “Active NK” cluster were plotted using heatmap of the BM sample. e The expression of CXCR4 in the BM sample was shown as a violin plot. The y-axis represents log-normalized expression value. f Percentage of CXCR4+ NK cells (gated on Lin−CD56+ cells) was evaluated via flow cytometry. g The expression of CXCR4 in CD57+/−, CD62L+/−, or NKG2A+/− CD56dim NK populations from BM was assessed via flow cytometry (top). Percentage of CXCR4+ cells within each population were quantified (bottom). n ≥ 6 from two to five independent experiments. Paired Student’s t test was used for the statistical analysis. *P < 0.05; **p < 0.01; ***p < 0.001; n.s. stands for “not significant.” Source data for f and g are provided as a Source Data file. See also Supplementary Fig. 5

Fig 3: Derivation and characterization of H9-NCCs differentiated from H9-hESCs. (A) Phase-contrast images of H9 hESCs at passage 56 (P56) and H9-NCCs and passage 0 (P0) and passage 4 (P4). (B) Flow cytometry analysis of H9-NCCs. (C) Immunocytochemistry analysis showed that H9 hESC-derived H9-NCCs were positive for HNK1, FOXD3, AP2α, p75, SOX9, SOX10 and were negative for neural progenitor marker PAX6 and undifferentiated hESCs markers SOX2 and OCT4. (D) Real-time PCR data showed the expression of OCT4, NANOG, SOX9, SOX10, P75, PAX3, ZIC1 and AP2α in H9-NCCs relative to H9 hESCs. Data were shown as the means ± SEM of three independent experiments. Unpaired two-tailed Student's t test. *p < 0.05, **p < 0.01. Scale bars, 100 μm.

Fig 4: T cell phenotype and senescence/exhaustion markers in MDD(A–D) PBMCs from patients with MDD and matched HC were examined by flow cytometry. CD4+ (upper panel) and CD8+ T cell subpopulations (lower panel) were analyzed for the expression of markers classifying differentiation (CD45RA, CCR7; n = 25) (A), chemokine receptors (CXCR3, CCR6, CCR4; n = 25) or regulatory T cell markers (CD25, CD127; n = 22) (B), markers indicative of exhaustion or senescence (PD-1, KLRG1, CD57; n = 19–20) (C) or inhibitory receptors (CTLA-4, LAG-3, Tim-3; n = 20) (D). Naive/Memory subpopulations were defined as TNaive (CCR7+/CD45RA+), TEM (CCR7-/CD45RA-), TCM (CCR7+/CD45RA-), and TEMRA (CCR7-/CD45RA+). T helper cell subsets were defined as Th1 (CXCR3+/CCR6-), Th2 (CXCR3-/CCR6-/CCR4+), Th17 (CXCR3-/CCR6+/CCR4+), and Th1/Th17 cells (CXCR3+/CCR6+) (n = 25). For the analysis of inhibitory receptors, PBMCs were stimulated with 10 µg/mL of a-CD3 and 1 µg/mL a-CD28 for 48 h. Median and interquartile ranges are shown. Wilcoxon signed-rank test was used to compare groups. All p values > 0.1 if not otherwise indicated.