title: Gene expression profiles in developing nephrons using Lim1 metanephric mesenchyme-specific conditional mutant mice.
abstract: BACKGROUND
  Lim1 is a homeobox gene that is essential for nephrogenesis. During metanephric kidney development, Lim1 is expressed in the nephric duct, ureteric buds, and the induced metanephric mesenchyme. Conditional ablation of Lim1 in the metanephric mesenchyme blocks the formation of nephrons at the nephric vesicle stage, leading to the production of small, non-functional kidneys that lack nephrons.
  
  
  METHODS
  In the present study, we used Affymetrix probe arrays to screen for nephron-specific genes by comparing the expression profiles of control and Lim1 conditional mutant kidneys. Kidneys from two developmental stages, embryonic day 14.5 (E14.5) and 18.5 (E18.5), were examined.
  
  
  RESULTS
  Comparison of E18.5 kidney expression profiles generated a list of 465 nephron-specific gene candidates that showed a more than 2-fold increase in their expression level in control kidney versus the Lim1 conditional mutant kidney. Computational analysis confirmed that this screen enriched for kidney-specific genes. Furthermore, at least twenty-eight of the top fifty (56%) candidates (or their vertebrate orthologs) were previously reported to have a nephron-specific expression pattern. Our analysis of E14.5 expression data yielded 41 candidate genes that are up-regulated in the control kidneys compared to the conditional mutants. Three of them are related to the Notch signaling pathway that is known to be important in cell fate determination and nephron patterning.
  
  
  CONCLUSIONS
  Therefore, we demonstrate that Lim1 conditional mutant kidneys serve as a novel tissue source for comprehensive expression studies and provide a means to identify nephron-specific genes.
authors.affiliation: Department of Molecular Genetics, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA. ytchen@mdanderson.org
authors.forename: You-Tzung
authors.initials: YT
authors.lastname: Chen
authors.forename: Akio
authors.initials: A
authors.lastname: Kobayashi
authors.forename: Kin Ming
authors.initials: KM
authors.lastname: Kwan
authors.forename: Randy L
authors.initials: RL
authors.lastname: Johnson
authors.forename: Richard R
authors.initials: RR
authors.lastname: Behringer
mesh_terms: D000818:Animals; D004622:Embryo, Mammalian / Q000378:metabolism; D047108:Embryonic Development; D020869:Gene Expression Profiling; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism*; D060850:LIM-Homeodomain Proteins; D051379:Mice; D008817:Mice, Mutant Strains; D009399:Nephrons / Q000196:embryology*; D020411:Oligonucleotide Array Sequence Analysis; D051880:Receptors, Notch / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors; D015854:Up-Regulation
chemical_list: D018398:Homeodomain Proteins; D060850:LIM-Homeodomain Proteins; C499523:Lhx1 protein, mouse; D051880:Receptors, Notch; D014157:Transcription Factors