title: Identification and functional clustering of global gene expression differences between human age-related cataract and clear lenses.
abstract: OBJECTIVE
  Age-related cataract is a multi-factorial disease with a poorly understood etiology. Numerous studies provide evidence that the human eye lens has evolved specific regulatory and protective systems to ameliorate lens damage associated with cataract. Other studies suggest that the presence of cataract is associated with the altered expression of specific genes including metallothionein IIa, osteonectin, transglutaminase 2, betaig-h3, multiple ribosomal proteins, ADAM9, and protein phosphatase 2A. Here, we sought to identify further gene expression changes that are associated with cataract and to cluster the identified genes into specific biological pathways.
  
  
  METHODS
  Oligonucleotide microarray hybridization was used to analyze the full complement of gene expression differences between lens epithelia isolated from human age-related cataract relative to clear lenses. The expression levels of a subset of the identified genes were further evaluated by semi-quantitative RT-PCR. The identified genes were functionally clustered into specific categories and the probability of over-representation of each category was determined using the computer program EASE.
  
  
  RESULTS
  412 transcripts were observed to be increased and 919 transcripts were observed to be decreased by 2 fold or more in lens epithelia isolated from age-related cataract relative to clear lenses. Of these, 74 were increased and 241 were decreased at the 5 fold level or greater. Seventeen genes selected for further confirmation exhibited similar trends in expression when examined by RT-PCR using both the original and separately prepared clear and cataract RNA populations. Functional clustering of the identified genes using the EASE bioinformatics software package revealed that, among others, transcripts increased in cataract are associated with transcriptional control, chromosomal organization, ionic and cytoplasmic transport, and extracellular matrix components while transcripts decreased in cataract are associated with protein synthesis, defense against oxidative stress, heat-shock/chaperone activity, structural components of the lens, and cell cycle control.
  
  
  CONCLUSIONS
  These data suggest that cataract is associated with multiple previously identified and novel changes in lens epithelial gene expression and they point to numerous pathways likely to play important roles in lens protection, maintenance, and age-related cataract.
authors.affiliation: Biomedical Sciences, Florida Atlantic University, Boca Raton, FL 33431-0991, USA.
authors.forename: John R
authors.initials: JR
authors.lastname: Hawse
authors.forename: James F
authors.initials: JF
authors.lastname: Hejtmancik
authors.forename: Quingling
authors.initials: Q
authors.lastname: Huang
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Sheets
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Hosack
authors.forename: Richard A
authors.initials: RA
authors.lastname: Lempicki
authors.forename: Joseph
authors.initials: J
authors.lastname: Horwitz
authors.forename: Marc
authors.initials: M
authors.lastname: Kantorow
mesh_terms: D000368:Aged; D000375:Aging / Q000502:physiology*; D002386:Cataract / Q000378:metabolism*; D017931:DNA Primers / Q000737:chemistry; D004847:Epithelial Cells / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D007908:Lens, Crystalline / Q000378:metabolism*; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015854:Up-Regulation
chemical_list: D017931:DNA Primers