Gene expression profiling identifies regulatory pathways involved in the late stage of rat fetal lung development

• Published in: American journal of physiology. Lung cellular and molecular physiology 2006-11, Vol.291 (5), p.L1027-L1037
• Main Authors: Weng, Tingting, Chen, Zhongming, Jin, Nili, Gao, Li, Liu, Lin
• Format: Article
• Language: English
• Subjects: Animals; Blood vessels; Carrier Proteins - genetics; Cluster Analysis; Cytokines - genetics; Deoxyribonucleic acid; DNA; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Genes; Homeodomain Proteins - genetics; LIM-Homeodomain Proteins; Lung - embryology; Lung - physiology; Oligonucleotide Array Sequence Analysis; Prenatal development; Rats; Reverse Transcriptase Polymerase Chain Reaction; RNA, Messenger - genetics; Signal Transduction - genetics; Transcription Factors
• ISSN: 1040-0605; 1522-1504
• DOI: 10.1152/ajplung.00435.2005

Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma Submitted 11 October 2005 ; accepted in final form 11 June 2006 Fetal lung development is a complex biological process that involves temporal and spatial regulations of many genes. To understand the molecular mechanisms of this process, we investigated gene expression profiles of fetal lungs on gestational days 18, 19, 20 , and 21 , as well as newborn and adult rat lungs. For this analysis, we used an in-house rat DNA microarray containing 6,000 known genes and 4,000 expressed sequence tags (ESTs). Of these, 1,512 genes passed the statistical significance analysis of microarray (SAM) test; an at least twofold change was shown for 583 genes (402 known genes and 181 ESTs) between at least two time points. K -means cluster analysis revealed seven major expression patterns. In one of the clusters, gene expression increased from day 18 to day 20 and then decreased. In this cluster, which contained 10 known genes and 5 ESTs, 8 genes are associated with development. These genes can be integrated into regulatory pathways, including growth factors, plasma membrane receptors, adhesion molecules, intracellular signaling molecules, and transcription factors. Real-time PCR analysis of these 10 genes showed an 88% consistency with the microarray data. The mRNA of LIM homeodomain protein 3a (Lhx3), a transcription factor, was enriched in fetal type II cells. In contrast, pleiotrophin, a growth factor, had a much higher expression in fetal lung tissues than in fetal type II cells. Immunohistochemistry revealed that Lhx3 was localized in fetal lung epithelial cells and pleiotrophin in the mesenchymal cells adjacent to the developing epithelium and blood vessel. Using GenMAPP, we identified four regulatory pathways: transforming growth factor- signaling, inflammatory response, cell cycle, and G protein signaling. We also identified two metabolic pathways: glycolysis-gluconeogenesis and proteasome degradation. Our results may provide new insights into the complex regulatory pathways that control fetal lung development. DNA microarray; cell differentiation Address for reprint requests and other correspondence: L. Liu, Dept. of Physiological Sciences, Oklahoma State Univ., 264 McElroy Hall, Stillwater, OK 74078 (e-mail: lin.liu{at}okstate.edu )