Genome-wide mapping of 5-hydroxymethylcytosine enrichment in a novel model of 'NAFLD in a Dish'

Human pluriopotent H9 cells were differentiated to hepatocyte-like cells and exposed to a cocktail of lactate, pyruvate and octanoic acid (LPO) for 48 hours. This stimulated development of macrovesicular steatosis, which has previously been reported to impact on mitochondrial metabolism. Under our experimental conditions, we identified rewiring of the TCA cycle linked to macrovesicular steatosis. As key TCA cycle metabolites, alpha-ketoglutarate, succinate and fumarate impact on ten-eleven translocation (TET) enzyme activity, we hypothesised that this rewiring would impact on levels of 5-hydroxymethylcytosine (5hmC) enrichment across the genome. To this end, we performed DNA immunoprecipitation sequencing (DIPseq) to map any changes that occurred. Using IonTorrent, we sequenced our samples and generated bam files aligned to Homo sapiens Hg19. We used the MACS2 pipeline to compare our control and steatosis group, and identified a large number of changes in 5hmC enrichment in response to LPO exposure, indicating that TCA cycle wiring may impact on TET activity. Overall design: 5hmC profiles were generated for ES-derived hepatocyte-like cells following treatment with lactate (10 mM), pyruvate (1 mM) and octanoate (2 mM) to induce intracellular lipid accumulation, resulting in a NAFLD-like phenotype