Transcriptomic responses to prion disease in rats

Abstract

Background: Prions diseases are fatal neurodegenerative diseases of mammals. While the molecular responses to prion infection have been extensively characterized in the laboratory mouse, little is known in other rodents. To explore these responses and make comparisons, we generated a prion disease in the laboratory rat by successive passage beginning with mouse RML prions.

Results: We describe the accumulation of rat prions, associated pathology and the transcriptional impact throughout the disease course. Comparative transcriptional profiling between laboratory mice and rats suggests that similar molecular and cellular processes are unfolding in response to prion infection. At the level of individual transcripts, however, variability exists between mice and rats and many genes deregulated by prion infection in mice are not affected in rats.

Conclusion: Our findings detail the molecular responses to prion disease in the rat and highlight the usefulness of comparative approaches to understanding neurodegeneration and prion diseases in particular.

Fig. 1

Interspecies transmission of prion disease. Six prion agents were used for initial transmission to rats including transmissible mink encephalopathy (TME), skunk-adapted TME, hamster-adapted TME strain Hyper, Rocky Mountain Laboratories (RML) mouse-adapted scrapie, chronic wasting disease (CWD) from wild-type deer, and CWD from wt/96S deer. After 1 year of incubation, first passage rats were euthanized to determine the extent of PrP-res accumulation. PrP-res was observed solely in rats infected with RML scrapie prions. This agent was serially passaged until becoming rat-adapted, as indicated by the decrease in and stabilization of the incubation period. Third passage rat-adapted scrapie transmitted to mice and hamsters with 100 % penetrance

Fig. 2

Accumulation of PrP-res in rat-adapted scrapie (RAS). Brain homogenates from each passage were assayed for the presence of protease resistant PrPPrP-res by immunoblot. PrP-res was observed following phosphotungstic acid (PTA) enrichment at first passage. Di- and mono- glycosylated bands were the most abundant isoforms of PrP-res. Uninfected age-matched controls are shown for 3^rd and 4^th passage animals. In fourth passage, PrP-res accumulated to substantial levels by 117 days post-infection (dpi)

Fig. 3

Histological analysis of rat-adapted scrapie in the hippocampus at clinical disease. Infected animals showed intense immuno-staining for deposits of PrP-res and GFAP expressing astrocytes. Spongiform change is an abundant feature in rat prion disease. The scale bar represents 250um

Fig. 4

Gene expression profile from rats clinically affected with prion disease. a. The expression levels of individual genes from uninfected and rats clinically affected with prion disease were plotted. The axis is the expression level from uninfected rats and the y-axis is the corresponding expression level of the gene in infected rats. The green lines indicate 2-fold changes in gene expression. Any points outside of these lines are genes whose expression is deregulated greater than 2-fold. b. Cluster of 81 genes whose expression is up-regulated throughout disease. Clustering was performed using 291 genes whose expression was changed more than 2-fold and with a statistical confidence interval of 90 % using a false positive rate approach. Ontological analysis of this gene cluster is consistent with the involvement of these genes in neuroinflammation. Gene expression profiles were obtained from infected and control rats at three time points. Comparisons between uninfected rats at the three time points did not identify statistically significant changes in gene expression

Fig. 5

Comparison of genes upregulated in rat and mouse prion disease. a. Orthologous probe sets differentially regulated by 2-fold were identified in both rat and mouse prion disease and the overlap determined. Duplicate probe sets measuring the same gene were eliminated for simplicity. b. Mouse scrapie induced gene expression changes were regressed onto changes induced by rat scrapie. Expression values are log2 transformed. The grey box indicates those orthologs whose expression is not changed >2-fold. Expression of probe sets that lie along the axes are highly divergent in prion disease between mice and rats. Stricter bioinformatic mapping of orthologous pairs did not meaningfully improve the regression