"Our interest in using genomics to study metabolic diseases led us to screen DNA from liver cells that expressed FOXA2 with an assay called ChIP on Chip," explains first author Irina Bochkis, a doctoral student in Genomics and Computational Biology in the Kaestner lab, which resides in the Department of Genetics and the Institute for Diabetes, Obesity, and Metabolism at Penn.
ChIP-on-Chip assay stands for Chromatin ImmunoPrecipitation on a gene Chip.
First, in the two-step assay, chromatin (DNA and protein) was extracted from liver cells and an antibody specific for FOXA2 was used to recognize the protein and immunoprecipitate the FOXA2 protein-DNA complex. The antibody made a sandwich with FOXA2 in the middle and DNA on the sides. Then FOXA2 and its antibody were degraded, but the DNA that was bound to FOXA2 was put on a gene chip. The genes encoded by this DNA were then identified from this remaining DNA.
"We were surprised that a cluster of genes involved in lipid and steroid metabolism was identified by being bound to FOXA2," says Bochkis.
This study also used mice that expressed no FOXA2 in their liver cells. Compared to normal littermates, the mutant mice accumulated bile salts and failed to detoxify them properly, which resulted in liver damage. In addition, liver biopsies from patients with PSC and biliary atresia, had no detectable levels of FOXA2. These findings suggest that low FOXA2 levels exacerbate liver injury.
Drug or DNA therapies that increase the expression of FOXA2 in liver cells may offer a new means of treating PSC and other similar syndromes. "In order to lay the groundwork for developing new treatments, we have to determine how FOXA2 itself is regulated," notes Bochkis.
|Contact: Karen Kreeger|
University of Pennsylvania School of Medicine