Fig. 2: Phenotypic diversity of myeloid cells in the MDD brain.

a The overlaid t-SNE plot of 16 huMG samples (SVZ = 4; THA = 4; GTS = 4; GFM = 4) isolated from four biologically independent donors (CON = 2; MDD = 2) is shown. The 2D t-SNE maps were generated based on expression levels of all markers of Panel A (Supplementary Table 4). The coloring indicates eight defined clusters representing diverse myeloid cell phenotypes. b Heat map and cluster analysis of all samples demonstrates the phenotypes of all eight defined clusters on the basis of the mean expression levels of 36 markers used for the cluster analysis. Identified clusters are indicated by dendrograms. Heat colors show overall marker expression levels (red: high expression; dark blue: no expression). c Heat map cluster demonstrates the expression levels of 36 analyzed markers for all eight clusters of each sample. Samples are indicated by dendrograms. Heat colors show overall expression levels (dark blue: no expression; red: high expression). d Boxplots on the left show the cluster distribution across four different brain regions (SVZ, blue; THA, light blue; GTS, green; GFM, red) and on the right the cluster distribution for the two groups (CON and MDD). Whisker plots show the min (smallest) and max (largest) values. A dot indicates the frequency (%) of an individual sample. The line in the box denotes the median. **P < 0.01, multiple t-test with FDR adjustment (at 10% using the Benjamini–Krieger–Yekutieli procedure). (e–g) Boxplots showing markers with differential expression (arcsinh) between CON and MDD for (e) the main microglia cluster C2, (f) the SVZ-enriched huMG cluster C3, and (g) the P2Y₁₂^lo/− (or TMEM119^lo/−) macrophage cluster C8. A dot indicates the mean expression of an individual sample from all three measurements. *P < 0.05, **P < 0.01, multiple t-test with FDR adjustment (at 10% using the Benjamini-Krieger-Yekutieli procedure). h Boxplots showing selected cytokines and chemokines (IL-6, IL-1β, MIP-1β, TNF, IL-10, CCL2) that are not differentially expressed (arcsinh) between CON and MDD for the clusters C2, C3, and C8. A dot indicates the mean expression of an individual sample from all three measurements. A P value < 0.05 was considered statistically significant (multiple t-test with FDR adjustment at 10% using the Benjamini–Krieger–Yekutieli procedure).