Methylome and Transcriptome Profiling of Hepatocytes Derived from Human Pluripotent Stem Cells

Abstract: Six hundred million people suffering from liver diseases worldwide of which the lethality is two million. Freshly isolated hepatocytes from the liver have been used for transplantation purposes and are extensively used to recapitulate drug metabolism. However, they lack stem cell ability and therefore cannot multiply, and will vary depending on each donator. Toward this, hepatocytes derived from human pluripotent stem cells (hPSC-HEP) recapitulate many features of their in vivo counterparts. However, the establishment of fully functional mature hepatocytes in vitro is still lacking. Abnormal DNA methylation emerging in in vitro cultured cells may underlie the immature functionality of hPSC-HEP and might explain the observed transcriptional differences between the in vitro generated hepatocytes and their in vivo counterparts. The aim of the thesis was to investigate the transcriptome and methylome of hPSC-HEP to identify their similarities and differences with human adult liver tissues. Interestingly, on the transcriptome level, the results revealed stronger correlation and higher similarity of hPSC-HEP to adult liver than to fetal liver. Moreover, genes important for the functionality of hepatocytes with deviating expression and DNA methylation patterns, including a protein module consisting of seven drug-metabolizing enzymes that were downregulated in hPSC-HEP compared to adult liver, were identified. In conclusion, the thesis shed light on significant deviations in the transcription and methylation of genes that are critical for the hepatic functionality. Further in-depth investigation and manipulation of these genes and their regulators in the differentiation protocol will pave the way for the generation of more functional hepatocytes in vitro.