title: Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells.
abstract: OBJECTIVE
  Age-related macular degeneration (AMD) is a major cause of blindness in developed countries. The molecular pathogenesis of early events in AMD is poorly understood. We investigated differential gene expression in samples of human retinal pigment epithelium (RPE) and choroid from early AMD and control maculas with exon-based arrays.
  
  
  METHODS
  Gene expression levels in nine human donor eyes with early AMD and nine control human donor eyes were assessed using Affymetrix Human Exon ST 1.0 arrays. Two controls did not pass quality control and were removed. Differentially expressed genes were annotated using the Database for Annotation, Visualization and Integrated Discovery (DAVID), and gene set enrichment analysis (GSEA) was performed on RPE-specific and endothelium-associated gene sets. The complement factor H (CFH) genotype was also assessed, and differential expression was analyzed regarding high AMD risk (YH/HH) and low AMD risk (YY) genotypes.
  
  
  RESULTS
  Seventy-five genes were identified as differentially expressed (raw p value <0.01; ≥50% fold change, mean log2 expression level in AMD or control ≥ median of all average gene expression values); however, no genes were significant (adj. p value <0.01) after correction for multiple hypothesis testing. Of 52 genes with decreased expression in AMD (fold change <0.5; raw p value <0.01), 18 genes were identified by DAVID analysis as associated with vision or neurologic processes. The GSEA of the RPE-associated and endothelium-associated genes revealed a significant decrease in genes typically expressed by endothelial cells in the early AMD group compared to controls, consistent with previous histologic and proteomic studies. Analysis of the CFH genotype indicated decreased expression of ADAMTS9 in eyes with high-risk genotypes (fold change = -2.61; raw p value=0.0008).
  
  
  CONCLUSIONS
  GSEA results suggest that RPE transcripts are preserved or elevated in early AMD, concomitant with loss of endothelial cell marker expression. These results are consistent with the notion that choroidal endothelial cell dropout or dedifferentiation occurs early in the pathogenesis of AMD.
authors.affiliation: Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA ; Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA.
authors.forename: S Scott
authors.initials: SS
authors.lastname: Whitmore
authors.forename: Terry A
authors.initials: TA
authors.lastname: Braun
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Skeie
authors.forename: Christine M
authors.initials: CM
authors.lastname: Haas
authors.forename: Elliott H
authors.initials: EH
authors.lastname: Sohn
authors.forename: Edwin M
authors.initials: EM
authors.lastname: Stone
authors.forename: Todd E
authors.initials: TE
authors.lastname: Scheetz
authors.forename: Robert F
authors.initials: RF
authors.lastname: Mullins
mesh_terms: D000369:Aged, 80 and over; D016022:Case-Control Studies; D002829:Choroid / Q000473:pathology*; D017242:Complement Factor H / Q000235:genetics; D019295:Computational Biology; D042783:Endothelial Cells / Q000378:metabolism* / Q000473:pathology*; D004730:Endothelium, Vascular / Q000378:metabolism / Q000473:pathology; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D020022:Genetic Predisposition to Disease; D006801:Humans; D008268:Macular Degeneration / Q000235:genetics* / Q000473:pathology*; D008297:Male; D011786:Quality Control; D055213:Retinal Pigment Epithelium / Q000378:metabolism / Q000473:pathology; D012307:Risk Factors
chemical_list: D017242:Complement Factor H