Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE

Invest Ophthalmol Vis Sci. 2006 Jun;47(6):2305-16. doi: 10.1167/iovs.05-1437.

Abstract

Purpose: To develop large-scale, high-throughput annotation of the human macula transcriptome and to identify and prioritize candidate genes for inherited retinal dystrophies, based on ocular-expression profiles using serial analysis of gene expression (SAGE).

Methods: Two human retina and two retinal pigment epithelium (RPE)/choroid SAGE libraries made from matched macula or midperipheral retina and adjacent RPE/choroid of morphologically normal 28- to 66-year-old donors and a human central retina longSAGE library made from 41- to 66-year-old donors were generated. Their transcription profiles were entered into a relational database, EyeSAGE, including microarray expression profiles of retina and publicly available normal human tissue SAGE libraries. EyeSAGE was used to identify retina- and RPE-specific and -associated genes, and candidate genes for retina and RPE disease loci. Differential and/or cell-type specific expression was validated by quantitative and single-cell RT-PCR.

Results: Cone photoreceptor-associated gene expression was elevated in the macula transcription profiles. Analysis of the longSAGE retina tags enhanced tag-to-gene mapping and revealed alternatively spliced genes. Analysis of candidate gene expression tables for the identified Bardet-Biedl syndrome disease gene (BBS5) in the BBS5 disease region table yielded BBS5 as the top candidate. Compelling candidates for inherited retina diseases were identified.

Conclusions: The EyeSAGE database, combining three different gene-profiling platforms including the authors' multidonor-derived retina/RPE SAGE libraries and existing single-donor retina/RPE libraries, is a powerful resource for definition of the retina and RPE transcriptomes. It can be used to identify retina-specific genes, including alternatively spliced transcripts and to prioritize candidate genes within mapped retinal disease regions.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Databases, Factual
  • Female
  • Gene Expression Profiling
  • Gene Expression Regulation / physiology*
  • Gene Library
  • Humans
  • Macula Lutea / metabolism*
  • Male
  • Middle Aged
  • Oligonucleotide Array Sequence Analysis
  • Photoreceptor Cells, Vertebrate / metabolism
  • Pigment Epithelium of Eye / metabolism
  • RNA, Messenger / metabolism
  • Retinal Degeneration / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Transcription, Genetic*

Substances

  • RNA, Messenger