Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

• DOI: 10.18632/oncotarget.4925
• Publication Date: 2015-09-29T17:43:03Z
• Authors: Adil El Taghdouini; Anita L. Sørensen; Andrew H. Reiner; Mar Coll; Stefaan Verhulst; Inge Mannaerts; Cristina I. Øie; Bård Smedsrød; Mustapha Najimi; Etienne Sokal; Aernout Luttun; Pau Sancho-Bru; Philippe Collas; Leo A. van Grunsven
• Keywords: Liver Cirrhosis; Male; 0301 basic medicine; 570; Chromatin Immunoprecipitation; Adolescent; 610; HEPATOCYTES; FIBROGENESIS; Epigenesis, Genetic; Mice; 03 medical and health sciences; epigenetic modification; Hepatic Stellate Cells; FIBROSIS; Animals; Humans; TRANSCRIPTION; SINUSOIDAL ENDOTHELIAL-CELLS; Child; VDP::Medical disciplines: 700::Basic medical, dental and veterinary science disciplines: 710::Medical molecular biology: 711; Cells, Cultured; hepatic stellate cell; liver fibrosis; Aged; Science & Technology; DNA methylation; epigenetics; Gene Expression Profiling; BINDING PROTEINS; Infant, Newborn; Infant; Cell Biology; IN-VITRO; DNA Methylation; Pathology section; 3. Good health; DIFFERENTIATION; Oncology; Liver; Hepatocytes; 5-HYDROXYMETHYLCYTOSINE; Female; hepatic stellate cells; EMBRYONIC STEM-CELLS; Life Sciences & Biomedicine; VDP::Medisinske Fag: 700::Basale medisinske, odontologiske og veterinærmedisinske fag: 710::Medisinsk molekylærbiologi: 711; Genome-Wide Association Study

Liver fibrogenesis - scarring of the liver that can lead to cirrhosis and liver cancer - is characterized by hepatocyte impairment, capillarization of liver sinusoidal endothelial cells (LSECs) and hepatic stellate cell (HSC) activation. To date, the molecular determinants of a healthy human liver cell phenotype remain largely uncharacterized. Here, we assess the transcriptome and the genome-wide promoter methylome specific for purified, non-cultured human hepatocytes, LSECs and HSCs, and investigate the nature of epigenetic changes accompanying transcriptional changes associated with activation of HSCs.Gene expression profile and promoter methylome of purified, uncultured human liver cells and culture-activated HSCs were respectively determined using Affymetrix HG-U219 genechips and by methylated DNA immunoprecipitation coupled to promoter array hybridization. Histone modification patterns were assessed at the single-gene level by chromatin immunoprecipitation and quantitative PCR.We unveil a DNA-methylation-based epigenetic relationship between hepatocytes, LSECs and HSCs despite their distinct ontogeny. We show that liver cell type-specific DNA methylation targets early developmental and differentiation-associated functions. Integrative analysis of promoter methylome and transcriptome reveals partial concordance between DNA methylation and transcriptional changes associated with human HSC activation. Further, we identify concordant histone methylation and acetylation changes in the promoter and putative novel enhancer elements of genes involved in liver fibrosis.Our study provides the first epigenetic blueprint of three distinct freshly isolated, human hepatic cell types and of epigenetic changes elicited upon HSC activation.