Extended Data Fig. 3: Microglial cluster GO analysis, histology, and validation.
From: Repeated head trauma causes neuron loss and inflammation in young athletes
a,b. snRNAseq fraction of (a) homeostatic and (b) RHI microglia. Statistics performed by ANOVA with Bonferroni correction. Bar represents mean, error bars show SEM. Tests were two-tailed. n = 28 individuals. c. Microglial subtypes across control compared to RHI-exposed individuals. Statistical analysis performed by two-tailed t-test or Mann Whitney U test with Welch correction. Bar represents mean, error bars show SEM. n = 28 individuals. d. UMAPs of SPP1 and HIF1A microglial expression. Dashed lines indicate RHIM2/3. e,f. Volcano plots showing DEGs between RHIM2/3 and homeostatic microglia (e) and RHIM2 and RHIM3 (f). n = 28 individuals g,h. Heatmap of (g) GO analysis of RHI microglia and (h) transcriptional regulatory network analysis of microglial subtype DEGs. Statistics generated with GSEA and single-tailed hypergeometric test with Benjamini-Hochberg multiple hypothesis correction. i. UMAPs depicting microglia module scores of microglial subtypes from Sun et al. j. Heatmap depicting Jaccard score similarity analysis between Sun et al. and current study microglial DEGs. Significance denoted by **p < 0.01, ***p < 0.001. Statistical analysis performed using GeneOverlap package and Jaccard analysis settings. k. Representative images of P2RY12, Iba1. Scale bar, 50 μm. l, m, n. SPP1 + /HIF1A+ microglial fraction in the grey matter (l) crest, (m) L2/3 Sulcus (n) layers 4–6 sulcus colored by pathological group compared to years of football play. Statistical analysis performed by linear regression. Black line represents linear regression, grey shows 95% confidence interval. Test was two-tailed. n = 22 individuals. o. P2RY12 low/Iba1+ microglial densities in the grey matter sulcus compared to years of football play. Statistics with linear regression with age included as a covariate. Test was two-tailed. n = 37 individuals. p. Homeostatic microglial densities compared to Nissl+ neuronal densities in layers 2/3 (left) and layers 4–6 (right). Each dot represents a single individual. Statistical analysis performed by linear regression with age as a covariate. Tests were two-tailed. n = 37. Black line represents linear regression, grey shows 95% confidence interval.
