Fig. 3: Gene expression patterning in nuclei and mitochondria from Aβ-deposit-exposed SIM-A9 cells in relation to deposit proximity.

a To assess the effect of proximity of microglial cells to peptide deposits, eight genes were selected and their gene products analyzed in either nucleic or mitochondrial material sampled as described in Fig. 2. Three are nucleic encoded and affect mitochondrial homeostasis (green), two are mitochondrially encoded (red) and three genes (yellow) are not fundamentally related to mitochondrial function but have been described to respond to proximity to Aβ deposits. Gapdh and mt-Atp8 served as housekeeping controls. b Quantification of mitochondrial and nucleic mRNAs and mt-DNA. Mean of uncorrected threshold cycles are shown as a heat map. c Respective mt-RNAs were quantified from mitochondrial samples and related to mt-Atp8. The amount of mt-DNA was normalized to Gapdh mRNA values. d, e Nucleic mRNAs were quantified from nucleic samples and related to Gapdh in two independent experiments (n = 3 each; single values were excluded if outlier analysis indicated an outlier (ROUT, Q = 1%)). Values are expressed as mean + SD. Statistical analysis was performed by one-way ANOVA followed by Sidak’s multiple comparison post-test (***p < 0.001; **p < 0.01; *p < 0.05). f Summary of findings regarding mitochondrially and nucleic encoded genes in relation to proximity of amyloid deposits.