Fig. 5

Integration of human and mouse CSF proteomes identifies consistent mitochondrial protein decrease in Alzheimer’s disease. a Summary of the DE analysis of mouse CSF proteome, and its integration with human CSF proteome. The analysis was carried out in 4 steps. 1) 1056 proteins were quantified in 6 5XFAD and 5 WT groups that were pooled from 32 mice. 2) 85 proteins were identified as DE proteins with a Z score difference > 2 and p value < 0.05. 3) 11 out of these 85 proteins are differentially expressed in both human and mouse CSF samples. 4) 6 out of these 11 DE proteins are mitochondrial proteins. b Volcano plot for quantified mouse CSF proteome. X-axis shows the Z score transformed log2 fold changes comparing AD to Ctl. Y-axis shows the -log10 p value. Top DE proteins in mice CSF are plotted in black and labeled. Proteins that are differentially expressed in both human and mouse CSF are plotted in red, and mitochondrial proteins are further labeled. Red dashed lines indicate the DE cutoff of p value < 0.05 and Z score difference > 2. c Heatmap shows Z score, −log10 FDR value or p value of the 11 DE proteins in mouse CSF, human CSF, and human cortex proteomes. d Expression levels of representative Mitochondrial DE proteins in human cortex, human CSF and mouse CSF. Dot plots overlaid onto boxplots showing expression of representative DE proteins in panel c and d. The p values of the DE analyses between AD and healthy control are displayed on the top of the plots. DE analyses were carried out through the LIMMA R package. X-axis shows sample groups, y-axis indicates Log2 transformed TMT intensity. Boxplot center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, expression levels of each individual samples. e Expression levels of representative top DE proteins in human cortex and mouse CSF. Dot plots overlaid onto boxplots showing expression of representative DE proteins in panel c and d. The p values of the DE analyses between AD and healthy control are displayed on the top of the plots. DE analyses were carried out through the LIMMA R package. X-axis shows sample groups, y-axis indicates Log2 transformed TMT intensity. Boxplot center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, expression levels of each individual samples