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


METHODS
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.


RESULTS
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.


CONCLUSIONS
Our study provides the first epigenetic blueprint of three distinct freshly isolated, human hepatic cell types and of epigenetic changes elicited upon HSC activation.
Liver Cell Biology Lab, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
Adil
A
El Taghdouini
Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
Anita L
AL
Sørensen
Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
Andrew H
AH
Reiner
Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Mar
M
Coll
Liver Cell Biology Lab, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
Stefaan
S
Verhulst
Liver Cell Biology Lab, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
Inge
I
Mannaerts
Department of Medical Biology, Vascular Biology Research Group, UiT, The Arctic University of Norway, Tromsø, Norway.
Cristina I
CI
Øie
Department of Medical Biology, Vascular Biology Research Group, UiT, The Arctic University of Norway, Tromsø, Norway.
Bård
B
Smedsrød
Université Catholique de Louvain, Institut de Recherche Expérimentale et Clinique (IREC), Laboratory of Pediatric Hepatology and Cell Therapy, Brussels, Belgium.
Mustapha
M
Najimi
Université Catholique de Louvain, Institut de Recherche Expérimentale et Clinique (IREC), Laboratory of Pediatric Hepatology and Cell Therapy, Brussels, Belgium.
Etienne
E
Sokal
Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.
Aernout
A
Luttun
Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Pau
P
Sancho-Bru
Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
Philippe
P
Collas
Liver Cell Biology Lab, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
Leo A
LA
van Grunsven
D000293:Adolescent; D000368:Aged; D000818:Animals; D002478:Cells, Cultured; D002648:Child; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D055166:Hepatic Stellate Cells / Q000166:cytology*; D022781:Hepatocytes / Q000166:cytology; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008099:Liver / Q000166:cytology*; D008103:Liver Cirrhosis / Q000473:pathology; D008297:Male; D051379:Mice; D008807:Mice, Inbred BALB C; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic; D059467:Transcriptome
DNA methylation; Pathology Section; epigenetics; hepatic stellate cells; liver fibrosis