Transcriptome analysis using RNA sequencing of the dorsal root ganglia (DRGs) of Pink1SNCA double mutant Parkinsonian mice versus wildtype control mice

Parkinsons's Diseases causes early pre-motor somatosensory manifestations of the disease, leading to a sensory polyneuropathy with sensory loss and chronic pain. We assessed gene gene regulation in the dorsal root ganglia (DRGs) of aged-old Pink1SNCA double mutant mice by comparing RNA-seq expression profiles. Pink1SNCA mice are a model for Parkinsons's Disease (PD) carrying a Pink1 deletion plus transgene overexpression of human mutant alpha-synuclein. Homozygous Pink1-/-,SNCA A53T double mutant mice were generated by crossing Pink1-/- mice (background: 129/SvEv) with A53T-SNCA-overexpressing mice (background: FVB/N) and then, interbreeding the littermates. They contain 129/SvEv and FVB/N genetic backgrounds approximately in a 50:50 distribution. Wildtype control mice (FVBSv) are hybrids from a crossbreeding of 129/SvEv and FVB/N mice, which were descended from littermates of double mutant mice. RNAseq was performed in two sequential experiments with 4/4 old and 4/5 aged wildytpe and Pink1SNCA mice, respectively. The alignment was done consecutively. For analysis both sets were combined. A total number of 25702 genes was reliably detected in both datasets, and 22784 passed the filtering criteria of >7 valid samples in total. GSEA gene set enrichment analysis was used for gene ranking and identication of top up- and downregulated genes and evaluation of their functions based on P-value, Q-value, fold change and abundance. Apart from the knockout of Pink1, a prominent down-regulated gene was acidic fibroblast growth factor, Fgf1, which is known to restore the survival of dopaminergic neurons in PD models. Up-regulated genes included DNase1l3, CCL27 and CCL25, IFI44 and IL31ra, and pointed to increased DNAse activity and activation of the immune system. RNA from the dorsal root ganglia from middle aged to old Pink1SNCA versus WT mice was analyzed by RNA sequencing of 9 and 8 biological replicates using an Illumina Next Geneneration system, NextSeq500