FOXA2 binding is redistributed in NAFLD patients. (A) Heatmap of results of FOXA2 ChIP-seq showing that binding increases in livers of mice on WD (6623 sites in normal, 4578 in mild steatosis, 9664 in NAFLD). (B) PscanChIP motif analysis identified highly enriched forkhead consensus sites for FOXA2 in both conditions. (C) Western blot analysis of protein nuclear extracts from the livers of three normal and six NAFLD patients with antibodies to FOXA2 and histone H3 (loading control). FOXA2 protein levels decrease in NAFLD patients. (D) Lamin B1 ChIP-seq signal (RPKM) calculated in the overlap of lamin B1 domains in normal patients with FOXA2-binding sites in NAFLD patients with severe steatosis is considerably reduced in NAFLD patients to the same extent in mild and severe steatosis. (E) Enrichr analysis identified overrepresented pathways “bile acid and bile salt biosynthesis,” “FOXA2 pathway,” and “nuclear receptors in lipid metabolism” for FOXA2 sites in normal patients. Pathways consistent with the phenotype, including “oxysterol pathway,” “PPAR pathway,” and “telomere attrition/genomic instability,” were overrepresented in FOXA2-bound regions in NAFLD livers.
