Transcriptome variations in human CaCo-2 cells: a model for enterocyte differentiation and its link to iron absorption He ´le `ne Be ´drine-Ferran, a Nolwenn Le Meur, b Isabelle Gicquel, a Martine Le Cunff, b Nicolas Soriano, a Isabelle Guisle, b Ste ´phanie Mottier, a Annabelle Monnier, a Raluca Teusan, b Patricia Fergelot, a Jean-Yves Le Gall, a Jean Le ´ger, b and Jean Mosser a, * a UMR-6061 CNRS, IFR 97, Faculte ´ de Me ´decine, CS 34317-35043 Rennes, France b U533 INSERM, 44035 Nantes, France Received 25 September 2003; accepted 19 November 2003 Abstract Complete clinical expression of the HFE1 hemochromatosis is very likely modulated by genes linked to duodenal iron absorption, whose level is conditioned by unknown processes taking place during enterocyte differentiation. We carried out a transcriptomic study on CaCo-2 cells used as a model of enterocyte differentiation in vitro. Of the 720 genes on the microarrays, 80, 50, and 56 were significantly down- regulated, up-regulated, and invariant during differentiation. With regard to iron metabolism, we showed that HEPH, SLC11A2, SLC11A3, and TF are significantly up-regulated, while ATP7B and SLC39A1 (and SFT) are down-regulated and ACO1, dCYTb, FECH, and FTH1 show constant expression. Ontological annotations highlight the decrease in the expression of cell cycle and DNA metabolism associated genes as well as transcription, protein metabolism, signal transduction, and nucleocytoplasmic transport associated genes, whereas there are increases in the expression of genes linked to cell adhesion, lipid and xenobiotic metabolism, iron transport and homeostasis, and immune response. D 2004 Elsevier Inc. All rights reserved. Keywords: Iron overload; Enterocytes; Microarray analysis of gene expression; CaCo-2 cells; Cell differentiation; Ontological annotations Introduction Primary iron overload or hemochromatosis (HHC) is a frequently encountered human disease characterized by excessive iron absorption. This disorder appears to be genetically heterogeneous. Although HFE1 [1] accounts for most of the cases, it has recently been demonstrated that other genes are involved in either hemochromatosis (for those coding TfR2, Ireg-1, H-Ferritin, and Hepcidin, respectively designated HFE3 [2], HFE4 [3], HFE5 [4] and HFE6 [5]) or its juvenile form for the HFE2 locus [6]. Not all of these genes account for all of the primary iron overload disorders, and others are still to be identi- fied. Despite this genetic heterogeneity, more than 90% of patients from Northern Europe are homozygous for the C282Y mutation in HFE1 [7]. Nevertheless, the incom- plete penetrance of this mutation [8] strongly suggests that its clinical expression is modulated by other factors, some of which are genetic in nature. Among these factors, those regulating intestinal iron absorption are certainly determin- ing since hemochromatosis is due to excessive iron absorption [9]. Intestinal iron absorption is certainly a critical step for the regulation of the total amount of iron in the organism. It takes place almost exclusively in the duodenum, where apical iron uptake and basolateral transfer are performed by SLC11A2 (solute carrier family 11 member 2, also known as iron uptake transporter DMT1/DCT1/Nramp2) and SLC11A3 (solute carrier family 11 member 3, also known as iron export transporter IREG1/ferroportin1/ MTP1). In the duodenum, it is known that the HFE protein can form a complex with the transferrin receptor (TfR) [10] and that these two proteins are expressed in crypt cells, exclusively for HFE and predominantly for TfR [10]. Since crypt cells are mostly undifferentiated, this localization 0888-7543/$ - see front matter D 2004 Elsevier Inc. All rights reserved. doi:10.1016/j.ygeno.2003.11.014 * Corresponding author. UMR6061 CNRS, Faculte ´ de Me ´decine, 2 av du Prof L. Bernard, 35043 Rennes Cedex, France. Fax: +33-2-23-23-44-78. E-mail address: Jean.Mosser@univ-rennes1.fr (J. Mosser). www.elsevier.com/locate/ygeno Genomics 83 (2004) 772 – 789