Gene expression profile studies of human keratoconus cornea for NEIBank: a novel cornea-expressed gene and the absence of transcripts for aquaporin 5

Invest Ophthalmol Vis Sci. 2005 Apr;46(4):1239-46. doi: 10.1167/iovs.04-1148.


Purpose: To increase the database of genes expressed in human cornea and to gain insights into the molecular basis of keratoconus (KC).

Methods: A cDNA library was constructed from KC corneas harvested at keratoplasty and used for expressed sequence tag (EST) analysis. Data were analyzed using grouping and identification of sequence tags (GRIST). Expression of selected clones was examined by RT-PCR.

Results: A total of 7680 clones was sequenced from the 5' end. After bioinformatics analysis, 4090 clusters of clones, each potentially representing individual genes, were identified. Of these, 887 genes were represented by more than one clone. The five most abundant transcripts, represented by >60 clones each, were for keratin-12, TGFBI (BIGH3), decorin, ALDH3, and enolase 1, all known markers for cornea. Many other markers for epithelial, stromal, and endothelial genes were also present. One cluster of six clones came from an apparently novel gene (designated KC6) located on chromosome 18 at p12.3. RT-PCR of RNA from several human tissues detected KC6 transcripts only in cornea. In addition, no clones were observed for the usually prominent corneal epithelial cell marker aquaporin 5 (AQP5), a water channel protein. Semiquantitative RT-PCR confirmed that expression of AQP5 is much lower in KC cornea than in non-KC cornea.

Conclusions: This analysis increases the database of genes expressed in the human cornea and provides insights into KC. KC6 is a novel gene of unknown function that shows cornea-preferred expression, whereas the suppression of transcripts for AQP5 provides the first clear evidence of a molecular defect identified in KC.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Aquaporin 5
  • Aquaporins / genetics*
  • Aquaporins / metabolism
  • Chromosomes, Human, Pair 18 / genetics
  • Collagen / genetics
  • Cornea / metabolism*
  • Expressed Sequence Tags
  • Eye Banks
  • Eye Proteins / genetics*
  • Eye Proteins / metabolism
  • Gene Expression Profiling*
  • Gene Expression*
  • Gene Library
  • Humans
  • Keratoconus / metabolism*
  • Membrane Proteins / genetics*
  • Membrane Proteins / metabolism
  • Molecular Sequence Data
  • National Institutes of Health (U.S.)
  • Ophthalmology
  • RNA, Messenger / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Transcription, Genetic
  • United States


  • AQP5 protein, human
  • Aquaporin 5
  • Aquaporins
  • Eye Proteins
  • Membrane Proteins
  • RNA, Messenger
  • Collagen