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Series GSE9025 Query DataSets for GSE9025
Status Public on Apr 01, 2011
Title A novel approach to investigate tissue-specific trinucleotide repeat instability - A validation set of prediction model
Organism Mus musculus
Experiment type Expression profiling by array
Summary In Huntington’s disease (HD), an expanded CAG repeat produces characteristic striatal neurodegeneration. Interestingly, the HD CAG repeat, whose length determines age at onset, undergoes tissue-specific somatic instability, predominant in the striatum, suggesting that tissue-specific CAG length changes could modify the disease process. Therefore, understanding the mechanisms underlying the tissue specificity of somatic instability may provide novel routes to therapies. However progress in this area has been hampered by the lack of sensitive high-throughput instability quantification methods and global approaches to identify the underlying factors.
Here we describe a novel approach to gain insight into the factors responsible for the tissue specificity of somatic instability. Using accurate genetic knock-in mouse models of HD, we developed a reliable, high-throughput method to quantify tissue HD CAG instability and integrated this with genome-wide bioinformatic approaches. Using tissue instability quantified in 16 tissues as a phenotype and tissue microarray gene expression as a predictor, we built a mathematical model and identified a gene expression signature that accurately predicted tissue instability. Using the predictive ability of this signature we found that somatic instability was not a consequence of pathogenesis. In support of this, genetic crosses with models of accelerated neuropathology failed to induce somatic instability. In addition, we searched for genes and pathways that correlated with tissue instability. We found that expression levels of DNA repair genes did not explain the tissue specificity of somatic instability. Instead, our data implicate other pathways, particularly cell cycle, metabolism and neurotransmitter pathways, acting in combination to generate tissue-specific patterns of instability.
Our study clearly demonstrates that multiple tissue factors reflect the level of somatic instability in different tissues. In addition, our quantitative, genome-wide approach is readily applicable to high-throughput assays and opens the door to widespread applications with the potential to accelerate the discovery of drugs that alter tissue instability.
 
Overall design Mouse striatum and cerebellum, 5 months old, Affymetrix MG430 2.0 arrays, gcRMA.

 
Contributor(s) Lee J
Citation(s) 20302627
Submission date Sep 12, 2007
Last update date Feb 11, 2019
Contact name Jong-Min Lee
E-mail(s) jlee51@partners.org
Phone 617-726-5726
Organization name Massachusetts General Hospital
Department Center for Human Genetic Reseaarch
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (2)
GSM228967 HdhQ111/Hdh+ striatum at 5 months
GSM228968 HdhQ111/Hdh+ cerebellum at 5 months
Relations
BioProject PRJNA102523

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9025_RAW.tar 7.4 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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