Clues to Neuro-Degeneration in Niemann-Pick Type C Disease from Global Gene Expression Profiling
Pfeffer SR (2006) Clues to Neuro-Degeneration in Niemann-Pick Type C Disease from Global Gene Expression
Profiling. PLoS ONE 1(1): e19. doi:10.1371/journal.pone.0000019
Clues to Neuro-Degeneration in Niemann-Pick Type C Disease from Global Gene Expression Profiling
Jonathan V. Reddy 0 1
Ian G. Ganley 0 1
Suzanne R. Pfeffer 0 1
0 Academic Editor: Winston Hide, University of the Western Cape , South Africa
1 Department of Biochemistry, Stanford University School of Medicine , Stanford, California , United States of America
Background. Niemann-Pick Type C (NPC) disease is a neurodegenerative disease that is characterized by the accumulation of cholesterol and glycosphingolipids in the late endocytic pathway. The majority of NPC cases are due to mutations in the NPC1 gene. The precise function of this gene is not yet known. Methodology/Principal Findings. Using cDNA microarrays, we analyzed the genome-wide expression patterns of human fibroblasts homozygous for the I1061T NPC1 mutation that is characterized by a severe defect in the intracellular processing of low density lipoprotein-derived cholesterol. A distinct gene expression profile was identified in NPC fibroblasts from different individuals when compared with fibroblasts isolated from normal subjects. As expected, NPC1 mutant cells displayed an inappropriate homeostatic response to accumulated intracellular cholesterol. In addition, a number of striking parallels were observed between NPC disease and Alzheimer's disease. Conclusions/Significance. Many genes involved in the trafficking and processing of amyloid precursor protein and the microtubule binding protein, tau, were more highly expressed. Numerous genes important for membrane traffic and the cellular regulation of calcium, metals and other ions were upregulated. Finally, NPC fibroblasts exhibited a gene expression profile indicative of oxidative stress. These changes are likely contributors to the pathophysiology of Niemann-Pick Type C disease.
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INTRODUCTION
Niemann Pick Type C disease (NPC) is a fatal, autosomal recessive
neurodegenerative disease due to mutations in the NPC1 or NPC2
genes [1,2]. NPC is associated with an inability to process cellular
cholesterol, which accumulates together with glycosphingolipids
within lysosomes of affected individuals. The disease is often
diagnosed in early childhood, with patients typically displaying
cerebellar ataxia, difficulty speaking and swallowing, and
progressive dementia. Mutations in the NPC1 gene account for
approximately 95% of NPC cases.
NPC1 is a 1278 amino acid protein with 13 transmembrane
domains that is important for normal cholesterol homeostasis [3].
NPC1 transmembrane domains 37 comprise a so-called sterol
sensing domain that is related to hydroxymethlyglutaryl CoA
reductase [4], sterol regulatory element-binding protein cleavage
activating protein (SCAP; [5], PATCHED [6,7]) and NPC1-like
protein, NPC1L1 [8]. The NPC1 protein was recently shown to
bind cholesterol [9]. Mutations in the NPC1 sterol sensing domain
can cause disease, as can mutations throughout the protein, the
bulk of which resides within the membrane bilayer or within the
lumen of late endosomes [1].
To begin to understand how loss of NPC1 function leads to
neurodegeneration, we have examined the global pattern of gene
expression in primary fibroblast cells from NPC patients. To avoid
possible phenotypic variation between different mutant alleles, we
designed our analysis using cells from different individuals who
each carried the identical, homozygous mutations within their
NPC1 loci. The most common NPC-1 mutation described is
I1061T, which accounts for 20% of the alleles in the United
Kingdom and France and about 15% in the United States [10,11]
and leads to a severe disruption of cholesterol processing.
Homozygous carriers of the I1061T mutation present with
a relatively mild neurological form of the disease with onset in
juvenile years; importantly, their clinical presentation is
homogeneous. In our experimental design, we hoped that gene expression
differences between any two individuals would be averaged out,
highlighting changes due to this specific mutation at both NPC1
alleles. As shown here, NPC1 fibroblasts showed highly significant
differences when compared with normal fibroblast controls. The
specific gene expression changes observed provide important clues
to the pathophysiology of NPC disease.
RESULTS AND DISCUSSION
Primary skin fibroblasts isolated from four patients homozygous
for the I1061T mutation and four control individuals were
cultured under identical conditions. RNA was isolated from all
samples and hybridized to cDNA microarrays consisting of
approximately 43,000 elements representing approximately
36,000 genes. Analysis of the data using a supervised hierarchical
clustering method identified a gene expression pattern that was
unique and consistent among NPC fibroblasts (Figure 1A). To
identify statistically significant gene express (...truncated)