Gene expression profiling in frataxin deficient mice: microarray evidence for significant expression changes without detectable neurodegeneration

Abstract

Friedreich's ataxia (FRDA) is caused by reduction of frataxin levels to 5-35%. To better understand the biochemical sequelae of frataxin reduction, in absence of the confounding effects of neurodegeneration, we studied the gene expression profile of a mouse model expressing 25-36% of the normal frataxin levels, and not showing a detectable phenotype or neurodegenerative features. Despite having no overt phenotype, a clear microarray gene expression phenotype was observed. This phenotype followed the known regional susceptibility in this disease, most changes occurring in the spinal cord. Additionally, gene ontology analysis identified a clear mitochondrial component, consistent with previous findings. We were able to confirm a subset of changes in fibroblast cell lines from patients. The identification of a core set of genes changing early in the FRDA pathogenesis can be a useful tool in both clarifying the disease process and in evaluating new therapeutic strategies.

Fig. 1

Study design schematic. Four 6-month-old KIKO mice (2 males, 2 females) were compared to age and gender matched WT littermates. RNA extracted from each of three CNS regions was co-hybridized on microarray slides (n = 12, 4 for spinal cord, 4 brainstem, and 4 cerebellum). To control for biological variability, WT samples from the same gender were pooled. To avoid a dye-effect, replicates were performed with dye-swaps, for a total of 24 array hybridizations performed (8 for spinal cord, 8 brainstem, and 8 cerebellum). SC: spinal cord; BS: brainstem; CB: cerebellum.

Fig. 2

Differentially expressed genes in three CNS regions in frataxin deficient mice. 185 genes were identified as differentially expressed across all regions. An additional 105 genes showed expression changes with a regional distribution, following the gradient of known neuropathological involvement in FRDA (spinal cord > brainstem > cerebellum). The majority of these changes were observed in the cervical spinal cord, the most severely affected region in patients, and most of them were towards downregulation.

Fig. 3

Microarray and qRT-PCR data in KIKO mice and FRDA fibroblasts. Microarray data were confirmed through real-time quantitative PCR. Samples from at least 3 distinct animals and controls were tested. A subset of genes was tested on three fibroblast cell lines from FRDA patients. Two genes with regional changes in spinal cord (sc) were also observed to be differentially expressed in human fibroblasts. Frataxin (bottom row) was not present on the array, so we present qRT-PCR data showing its downregulation in both KIKO mice and FRDA fibroblasts. Bars: fold change. Error bars: standard error.