title: Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium.
abstract: OBJECTIVE
  Phenotypic transformation of retinal pigment epithelial (RPE) cells contributes to the onset and progression of ocular proliferative disorders such as proliferative vitreoretinopathy (PVR). The formation of epiretinal membranes in PVR may involve an epithelial-mesenchymal transformation (EMT) of RPE cells as part of an aberrant wound healing response. While the underlying mechanism remains unclear, this likely involves changes in RPE cell gene expression under the control of specific transcription factors (TFs). Thus, the purpose of the present study was to identify TFs that may play a role in this process.
  
  
  METHODS
  Regulatory regions of genes that are differentially regulated during phenotypic transformation of ARPE-19 cells, a human RPE cell line, were subjected to computational analysis using the promoter analysis and interaction network toolset (PAINT). The PAINT analysis was used to identify transcription response elements (TREs) statistically overrepresented in the promoter and first intron regions of two reciprocally regulated RPE gene clusters, across four species including the human genome. These TREs were then used to construct transcriptional regulatory network models of the two RPE gene clusters. The validity of these models was then tested using RT-PCR to detect differential expression of the corresponding TF mRNAs during RPE differentiation in both undifferentiated and differentiated ARPE-19 and primary chicken RPE cell cultures.
  
  
  RESULTS
  The computational analysis resulted in the successful identification of specific transcription response elements (TREs) and their cognate TFs that are candidates for serving as nodes in a transcriptional regulatory network regulating EMT in RPE cells. The models predicted TFs whose differential expression during RPE EMT was successfully verified by reverse transcriptase polymerase chain reaction (RT-PCR) analysis, including Oct-1, hepatocyte nuclear factor 1 (HNF-1), similar to mothers against decapentaplegic 3 (SMAD3), transcription factor E (TFE), core binding factor, erythroid transcription factor-1 (GATA-1), interferon regulatory factor-1 (IRF), natural killer homeobox 3A (NKX3A), Sterol regulatory element binding protein-1 (SREBP-1), and lymphocyte enhancer factor-1 (LEF-1).
  
  
  CONCLUSIONS
  These studies successfully applied computational modeling and biochemical verification to identify biologically relevant transcription factors that are likely to regulate RPE cell phenotype and pathological changes in RPE in response to diseases or trauma. These TFs may provide potential therapeutic targets for the prevention and treatment of ocular proliferative disorders such as PVR.
authors.affiliation: Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Craig H
authors.initials: CH
authors.lastname: Pratt
authors.forename: Rajanikanth
authors.initials: R
authors.lastname: Vadigepalli
authors.forename: Praveen
authors.initials: P
authors.lastname: Chakravarthula
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Gonye
authors.forename: Nancy J
authors.initials: NJ
authors.lastname: Philp
authors.forename: Gerald B
authors.initials: GB
authors.lastname: Grunwald
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D002461:Cell Line, Transformed; D002645:Chickens; D017124:Conserved Sequence; D004847:Epithelial Cells / Q000166:cytology / Q000378:metabolism; D004848:Epithelium / Q000378:metabolism*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D008648:Mesoderm / Q000378:metabolism*; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D010857:Pigment Epithelium of Eye / Q000166:cytology / Q000378:metabolism*; D015203:Reproducibility of Results; D020218:Response Elements / Q000235:genetics; D013045:Species Specificity; D014157:Transcription Factors; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors