RNAseq of SN dopaminergic neurons uncovers upregulation of pathways involved in axon guidance, calcium signalling and neuroactive ligand-receptor interaction in K320E/K320E^DaN mice. (A) Schematic of the range of midbrain sections used for laser capture microscopy [top and middle, substantia nigra (SN)-containing brain area highlighted in blue; images modified from Paxinos and Franklin³²]. Immunohistochemical image showing the SN after laser dissection of tyrosine hydroxylase (TH)-positive neurons (bottom). Scale bar = 500 μm. (B) Heat map showing the amount of total read counts for genes expressed by distinct cell types in laser-captured SN neurons at 5 and 20 months. (C) Bar graph illustrating enriched upregulated pathways in SN dopaminergic neurons of 20-month-old K320E/K320E^DaN mice. The top 20 most statistically significant clusters are shown; −log(10)P is the P-value in negative log base 10. (D) Network visualization of enriched protein-protein interaction for upregulated genes in 20-month-old K320E/K320E^DaN mice. The four networks with strongest interaction are illustrated. (E) Schematic of the range of striatal sections used for RNA isolation (striatum-containing brain area highlighted in blue; images modified from Paxinos and Franklin³²). (F) mRNA quantification by qPCR of axon guidance molecules in the striatum of 20-month-old K320E/K320E^DaN and control mice. Values were normalized to Gapdh mRNA (n = 4 mice per group). P-values were calculated using unpaired two-tailed Student’s t-test. Data are presented as mean ± standard error of the mean (SEM).