The diagnosis of inherited metabolic diseases by microarray gene expression profiling.
BACKGROUND
Inherited metabolic diseases (IMDs) comprise a diverse group of generally progressive genetic metabolic disorders of variable clinical presentations and severity. We have undertaken a study using microarray gene expression profiling of cultured fibroblasts to investigate 68 patients with a broad range of suspected metabolic disorders, including defects of lysosomal, mitochondrial, peroxisomal, fatty acid, carbohydrate, amino acid, molybdenum cofactor, and purine and pyrimidine metabolism. We aimed to define gene expression signatures characteristic of defective metabolic pathways.


METHODS
Total mRNA extracted from cultured fibroblast cell lines was hybridized to Affymetrix U133 Plus 2.0 arrays. Expression data was analyzed for the presence of a gene expression signature characteristic of an inherited metabolic disorder and for genes expressing significantly decreased levels of mRNA.


RESULTS
No characteristic signatures were found. However, in 16% of cases, disease-associated nonsense and frameshift mutations generating premature termination codons resulted in significantly decreased mRNA expression of the defective gene. The microarray assay detected these changes with high sensitivity and specificity.


CONCLUSIONS
In patients with a suspected familial metabolic disorder where initial screening tests have proven uninformative, microarray gene expression profiling may contribute significantly to the identification of the genetic defect, shortcutting the diagnostic cascade.
Purine Research Laboratory, GSTS Pathology, Guy's and St, Thomas' Hospitals, London, UK.
Monica Arenas
MA
Hernandez
Reiner
R
Schulz
Tracy
T
Chaplin
Bryan D
BD
Young
David
D
Perrett
Michael P
MP
Champion
Jan-Willem
JW
Taanman
Anthony
A
Fensom
Anthony M
AM
Marinaki
D002460:Cell Line; D018388:Codon, Terminator / Q000235:genetics; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism*; D020869:Gene Expression Profiling; D006801:Humans; D008659:Metabolic Diseases / Q000175:diagnosis* / Q000235:genetics; D008661:Metabolism, Inborn Errors / Q000235:genetics*; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
D018388:Codon, Terminator; D012333:RNA, Messenger