title: Expression profiling of the RPE in zebrafish smarca4 mutant revealed altered signals that potentially affect RPE and retinal differentiation.
abstract: OBJECTIVE
  The purpose of this study was to develop a framework for analyzing retinal pigment epithelium (RPE) expression profiles from zebrafish eye mutants.
  
  
  METHODS
  The fish model we used was SWI/SNF-related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (smarca4), a retinal dystrophic mutant with a previously described retinal phenotype and expression profiles. Histological and Affymetrix GeneChip analyses were conducted to characterize the RPE defects and underlying differential expression, respectively.
  
  
  RESULTS
  Histological analysis revealed that smarca4 RPE was formed, but its differentiation was abnormal. In particular, ultrastructural analysis of smarca4 RPE by transmission electron microscopy demonstrated several defects in melanogenesis. The nature of these defects also suggests that the cytoskeletal dynamics, which are tightly linked with melanogenesis, were impaired in smarca4 RPE. To compare the expression profile of normal wild-type (WT) and smarca4 RPE, the gene expression profiles of microdissected retinas and RPE-attached retinas were measured with Affymetrix GeneChip analysis. The RPE expression values were then estimated from these samples by subtracting the retinal expression values from the expression values of the RPE-attached retinas. A factorial analysis was conducted using the expression values of the RPE, retinal, and whole-embryo samples. Specific rules (contrasts) were built using the coefficients of the resulting fitted models to select for three groups of genes: 1) smarca4-regulated RPE genes, 2) smarca4-regulated retinal genes, and 3) smarca4-regulated RPE genes that are not differentially expressed in the retina. Interestingly, the third group consists of 39 genes that are highly related to cytoskeletal dynamics, melanogenesis, and paracrine and intracellular signal transduction.
  
  
  CONCLUSIONS
  Our analytical framework provides an experimental approach to identify differentially-regulated genes in the retina and the RPE of zebrafish mutants in which both of these tissues are affected by the underlying mutation. Specifically, we have used the method to identify a group of 39 genes that can potentially explain the melanogenesis defect in the smarca4 RPE. In addition, several genes in this group are secreted signaling molecules. Thus, this observation further implicates that the smarca4 RPE might play a role in the retinal dystrophic phenotype in smarca4.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN.
authors.forename: Liyun
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Statistics, University of Georgia, Athens, GA.
authors.forename: Ping
authors.initials: P
authors.lastname: Ma
authors.affiliation: Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI.
authors.forename: Ross
authors.initials: R
authors.lastname: Collery
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA.
authors.forename: Sara
authors.initials: S
authors.lastname: Trowbridge
authors.affiliation: Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China.
authors.forename: Mingzhi
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Department of Statistics, University of Georgia, Athens, GA.
authors.forename: Wenxuan
authors.initials: W
authors.lastname: Zhong
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN ; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Lafayette, West Lafayette, IN.
authors.forename: Yuk Fai
authors.initials: YF
authors.lastname: Leung
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics*; D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D020460:Melanosomes / Q000378:metabolism; D009154:Mutation / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D055213:Retinal Pigment Epithelium / Q000196:embryology / Q000378:metabolism / Q000473:pathology* / Q000648:ultrastructure; D015398:Signal Transduction / Q000235:genetics; D015027:Zebrafish / Q000196:embryology* / Q000235:genetics*; D029961:Zebrafish Proteins / Q000235:genetics*
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D029961:Zebrafish Proteins; C516328:smarca4a protein, zebrafish