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From: TSS ()
Subject: Gene expression alterations in brains of mice infected with three strains of Scrapie
Date: May 22, 2006 at 2:33 pm PST

Gene expression alterations in brains of mice infected with three strains of scrapie
Pamela J Skinner , Hayet Abbassi , Bruce Chesebro , Richard E Race , Cavan Reilly and Ashley T Haase

BMC Genomics 2006, 7:114 doi:10.1186/1471-2164-7-114

Published 16 May 2006

Abstract (provisional)


Transmissible spongiform encephalopathies (TSEs) or prion diseases are fatal neurodegenerative disorders which occur in humans and various animal species. Examples include Creutzfeldt-Jakob disease (CJD) in humans, bovine spongiform encephalopathy (BSE) in cattle, chronic wasting disease (CWD) in deer and elk, and scrapie in sheep, and experimental mice. To gain insights into TSE pathogenesis, we made and used cDNA microarrays to identify disease-associated alterations in gene expression. Brain gene expression in scrapie-infected mice was compared to mock-infected mice at pre-symptomatic and symptomatic time points. Three strains of mouse scrapie that show striking differences in neuropathology were studied: ME7, 22L, and Chandler/RML.


In symptomatic mice, over 400 significant gene expression alterations were identified. In contrast, only 22 genes showed significant alteration in the pre-symptomatic animals. We also identified genes that showed significant differences in alterations in gene expression between strains. Genes identified in this study encode proteins that are involved in many cellular processes including protein folding, endosome/lysosome function, immunity, synapse function, metal ion binding, calcium regulation and cytoskeletal function.


These studies shed light on the complex molecular events that occur during prion disease, and identify genes whose further study may yield new insights into strain specific neuropathogenesis and ante-mortem tests for TSEs.

full text concusions;


We identified alterations in gene expression that occur in the brains of mice infected with

scrapie strains ME7, 22L, and RML-Chandler at two times post infection. While it is difficult to

compare our results with other previously performed gene expression studies in related TSE

systems, because of the multiple differences in the methodologies used, the considerable overlap

in the genes identified in our study and those identified in previous studies validate the

importance of these alterations in gene expression in scrapie and suggest that these genes may

generally play important roles in TSEs.

We identified for the first time novel scrapie-associated alterations in expression in

numerous genes with known and as of yet unknown function. Many of the identified alterations

in brain gene expression are likely important contributors to disease. In support of this notion,

Klein et al., showed that complement gene knock out mice are resistant to intraperitoneal but not

intracerebral inoculation of scrapie indicating that a single gene can be important to early events

in peripheral transmission, propagation, and dissemination of scrapie in mice [33].

There are several genes identified in our studies that stand out as likely cofactors in TSE

pathogenesis. For example, a large percentage of the genes we identified function in the

endosome/lysosome system. These genes are of particular interest because the conversion of

PrPc to PrPsc is thought to occur on the cell membrane or in the endosome/lysosome system and

PrPsc accumulates in endosomes and lysosomes of brain cells [34-37]. Over twenty percent of

the scrapie-associated alterations identified in our study encode proteins that function in protein

folding, protein degradation or localize to the endosomes/lysosomes system. We hypothesize

that many of these genes are cofactors in prion protein misfolding and accumulation.

Other important scrapie-associated alterations identified in this study include genes that

function in immunity, neuronal synapses, metal ion binding, calcium regulation, mitochondria

and the cytoskeleton. Alterations in immunity genes are likely largely associated with microglial

and astrocyte activation. Alterations in synapse genes may be important factors in the

degeneration of neuronal dendrites. Many of the genes identified in this study bind metal ions,

consistent with a role for disruption of metal ion homeostasis in scrapie neuropathogenesis.

Alterations in genes that function in calcium homoeostasis and the mitochondria may be

important factors in the degeneration of neurons, as maintenance of calcium homeostasis and

energy production is critical for neuronal survival. Cytoskeleton gene alterations are likely

reflective of migration of microglia, but may also be factors in other changes in cellular activity

important to prion diseases such as vacuole formation in neurons.

C57Bl mice infected intracerebrally with scrapie strains ME7, 22L and RML-Chandler

have similar time courses of disease and develop clinical symptoms within a week of each other

at approximately 140 dpi. However, mice infected with these three strains of scrapie differ in the

extent and localization of vacuolization and plaque formation. The intensity of vacuolation is

highest in the anterior of the brain in mice infected with ME7, similar in various brain regions

with RML-Chandler, and highest in the posterior of the brain with strain 22L. Strain 22L also

shows a unique brain pathology in that it induces vacuolation in the cerebellar cortex and the

vacuoles are larger in size compared to those induced by other strains of scrapie [29, 31, 32].

Strain specific alterations in gene expression detected in this study may indicate genes that

contribute to the molecular mechanisms underlying strain specific neuropathology. However,

from this study we canít distinguish alterations in gene expression between strains that are due to

differences in neuropathology and those due to mice being at slightly differently stages of

infection. In future experiments we hope to better understand the process of vacuolization by the

analysis of regional expression of genes identified as strain-specific in our studies at multiple

time-points post infection using in situ hybridization and immunohistochemical approaches.

Analysis of the cellular localization of the known genes showed that over 40 genes

encode extracellular proteins (indicated with an asterisk in Table 1, Table 2 and additional file

1). If in future studies these proteins show TSE-specific differential accumulation in the

cerebrospinal fluid or other accessible tissues, they could provide novel ante-mortem diagnostic

markers for TSEs using simple antibody based or enzyme detection assays.

The studies reported here add to the handful of previously reported gene profiling studies

of TSE pathogenesis using DNA microarrays. Our study included analysis of scrapie strain 22L

which has not previously been reported in gene expression profiling studies, and implemented

refined microarray analysis methodologies that allowed for identification of significant diseaseassociated

alterations in gene expression using minimal numbers of mice. These studies are

important because they shed light on the molecular mechanisms underlying TSE pathogenesis,

identify potential surrogate markers for TSE diagnosis, and identify potential targets for drug

treatment for TSEs. However, information gleaned from these studies represents just the tip of

the iceberg of all of the genomic and other cellular and molecular changes that occur during

TSEs. Additional studies are needed in order to unravel the rest of the mystery. The strain

specific as well as strain non-specific alterations in gene expression identified in this study need

to be evaluated using in situ hybridization and immunohistochemical approaches at multiple

times post infection in order to determine the cell types in which alterations occur, the precise

time post infection that they occur, and to determine whether specific TSE pathology including

PrPsc accumulation is associated with cellular populations showing alterations in gene

expression. In addition, studies are needed to investigate gene expression changes in animals

and humans infected with TSEs that have different genetic backgrounds including different

alleles of PrP. Indeed Booth et al., found differences in alterations in gene expression in

C57Bl/6 mice compared to VM mice infected with scrapie strain 22A [10]. Genomic studies in

TSEs have thus far been confined to brain and need to be expanded to other tissues such as

spleen and blood. Gene knock-out studies are needed to determine the extent to which each of

the TSE-associated alterations in gene expression contributes to PrPsc formation, and disease

pathogenesis and progression. Cross-species studies are needed to determine alterations that are

species specific and species non-specific. A comparison to other infectious and

neurodegenerative diseases is needed to establish TSE-specific alterations from non-specific

alterations. Studies are also needed to evaluate the use of genomic changes as surrogate markers

for disease diagnosis, as well as the targeting genomic changes for potential drug therapies to

treat TSEs. Thus, the scrapie-associated alterations in gene expression identified in the studies

presented here and in those previously described have taken an important step in furthering our

understanding the molecular mechanisms underlying TSE disease pathogenesis and disease

progression. These discoveries provide a foundation for future studies that will take the next

steps towards fully understanding TSEs, developing novel genomic based diagnostic assays for

TSEs, and identifying targets for drug therapies to treat TSEs.

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