Parkinson's disease (PD) genetic asymmetry in SNCA PFF injected mouse model

We measured gene expression in neuronal nuclei from cortex derived from both hemispheres (injected and noninjected side) of mice (16 male, 16 female) intected with either PBS or SNCA PFFs. Mice were sacrificied at either 1 or 3 month post injection. This was a preliminary experiment done to examine a mouse model of asymmetry in a PD-like condition. RNA-sequencing was used to measure gene expression differences resulting from injecting PBS or alpha-synuclein pre-formed fibrils (PFFs), an inducer of PD like neuropathy, in the right olfactory bulb of 32 (C57BL/6J) mice, 16 male and 16 female. Cortex was then isolated for RNA extraction from both right and left hemispherical cortex in all mice at either 1 month or 3-months post-injection. The overall conclusion was that expression changes were found but were too modest to warrant further focus using mice. Greater detail is given below. While the model has some value and the results may be useful for comparison with human data, nuisance variables were found to induce changes of similar magnitude to treatment conditions. The small magnitude in differential expression levels, coupled with strong effects by confounds, primarily cage to cage variation, resulted in less robust results than desirable. Thus, while this pilot experiment indicates that a few dozen to a few hundred genes may show hemispherical asymmetry in the mouse model across sex and timepoint, further experiments will focus on human data. Within the experiment the features conferring the greatest difference in overall gene expression levels between the mice were sex, followed by time post injection (1-month vs. 3-month) (figure 1,2). The conditions of interest, treatment: PBS or PFF, and hemisphere: injected vs non-injected, do not confer obvious structure to overall gene expression patterns. Rather differences between individual mice as well as between cage mates outweigh overall differences for the latter 2 experimental conditions. However, some individual genes do show significant treatment or hemispherical differential expression. This is truer when treatment or hemisphere are considered while holding sex and/or timepoint constant (Table 1). Overall, across 16 statistical comparisons, 1038 statistically significant (FDR < 0.05) and high fold change (>40% change in expression) genes. Of these, excluding simple male vs. female, 342 genes are unique. These 342 genes show enrichment in processes related to neurotransmitter function, especially dopamine, cell signaling, drug binding, complement activation of the immune system, and others. Individual comparisons are expected to be most relevant for elucidating PD asymmetry. For instance, 23 genes are significant (adj. p.value < 0.5 and logFC > 0.5) for differences between injected and non-injected hemispheres regardless of sex or timepoint. These 23 genes show some GO enrichment for axonogenesis and dopaminergic systems, among other things. It is somewhat surprising that such PD-relevant categories show differential expression in this comparison, as the PBS condition should not induce a disease like state. However, the sensitivity of the analysis may be misleading. 2/3 of the significant DE genes were also