Peroxisome proliferator-activated receptor-gamma (PPAR gamma) is expressed in the intestinal epithelium, yet little is known about the physiological role of PPAR gamma in the small bowel or the effects of PPAR gamma on small intestinal epithelial cells. The present studies investigate cellular and genomic effects of PPAR gamma in nontransformed rat intestinal epithelial cells (RIE). These cells were engineered to express mouse PPAR gamma 1, and thereby to model the molecular phenotype that obtains upon induction of PPAR gamma at the crypt/villus junction in the small intestine. In these studies, we have used a novel third generation thiazolidinedione derivative, RS5444, which activates PPAR gamma with an EC50 about 1/50th that of rosiglitazone and has no effect on RIE cells that do not express PPAR gamma. We used Affymetrix oligonucleotide microarrays to identify potential PPAR gamma-regulated processes in RIE cells, including lipid metabolism, cell proliferation and differentiation, remodeling of the extracellular matrix, cell morphology, cell-cell adhesion, and motility. The genomic profile reflects cellular events that occur following PPAR gamma activation: RS5444 inhibited culture growth and caused. irreversible G1 arrest, but did not induce apoptosis. In addition, RS5444 caused dramatic changes in cellular morphology which were associated with increased motility and diminished cellular adherence, but no increase in the ability of such cells to digest and invade Matrigel. Inhibition of proliferation, cell cycle arrest, increased motility, and altered adherence are aspects of the differentiated phenotype of villus epithelial cells, which withdraw from the cell cycle at the crypt/villus interface, migrate to the villus tips, and are subsequently shed by loss of contact with the epithelium and the underlying extracellular matrix. Our results are consistent with the hypothesis that PPAR gamma regulates critical aspects of differentiation in the small intestinal epithelium. Many nuclear receptors regulate differentiation. However, our results point to novel effects of PPAR gamma on cell-cell and cell-matrix interactions, which are not typical of other nuclear receptors. (c) 2006 Elsevier Ireland Ltd. All rights reserved.