Distinct Gene Expression and Epigenetic Signatures in Hepatocyte-like Cells Produced by Different Strategies from the Same Donor

Abstract

SummaryHepatocyte-like cells (HLCs) can be generated through directed differentiation or transdifferentiation. Employing two strategies, we generated induced pluripotent stem cell (iPSC)-HLCs and hiHeps from the same donor cell line. Both types of HLCs clustered distinctly from each other during gene expression profiling. In particular, differences existed in gene expression for phase II drug metabolism and lipid accumulation, underpinned by H3K27 acetylation status in iPSC-HLCs and hiHeps. While distinct phenotypes were achieved in vitro, both types of HLCs demonstrated similar phenotypes following transplantation into Fah-deficient mice. In conclusion, functional HLCs can be obtained from the same donor using two strategies. Global gene expression defined the differences between those populations in vitro. Importantly, both HLCs displayed partial but markedly improved hepatic function following transplantation in vivo, demonstrating plasticity and the potential for cell-based modeling in the dish and cell-based therapy in the future.

Analysis of differentially expressed genes among human hair follicle–derived iPSCs, induced hepatocyte-like cells, and primary hepatocytes

“…Downregulated DEGs were associated with cell cycle, systemic lupus erythematosus, alcoholism, DNA replication, and viral carcinogenesis pathways, indicating that differentiation reduced the cell proliferation and tumorigenicity risk. Additionally, from the enriched KEGG pathways of upregulated DEGs in HLCs/hHF-iPSCs and HLCs/PHHs groups, we found that the induced HLCs further repressed the downregulated pathways, consistent with the PHHs/hHF-iPSCs group; however, the pathways of alcoholism, cell cycle, and systemic lupus erythematosus continued to be downregulated, and the complement and coagulation cascades, metabolic pathways, drug metabolism-cytochrome P450, and steroid hormone biosynthetic pathway-associated DEGs needed to be increased [ 8 ]. Although our experiments confirmed that the HLCs we obtained mimicked the synthesis and metabolism functions of the liver, our data analysis supported that they needed to be further improved.…”

In Vitro Expansion of Primary Human Hepatocytes with Efficient Liver Repopulation Capacity

“…We further compared the global gene expression between freshly thawed PHHs and ProliHHs cultured in normoxia by RNA sequencing analysis. To verify the extent to which ProliHHs maintained hepatic gene expression, we used HLCs derived from human pluripotent stem cells (hiPSC-Hep) or from human somatic cells by direct transdifferentiation (hiHep) as controls (Gao et al, 2017). Notably, principal-component analysis (PCA) and hierarchical clustering revealed that ProliHHs formed an associated group and were distinct from other cells ( Figures 2C and S4A).…”

“…This method was able to generate large numbers of functional HLCs capable of rescuing liver failure in mice after transplantation. Nevertheless, human HLCs showed limited engraftment capability in mouse livers (Gao et al, 2017;Ji et al, 2013). The repopulation efficiency of HLCs, which is around 2%, is far lower than that of PHHs, which is around 70% (Ji et al, 2013;Rezvani et al, 2016;Sampaziotis et al, 2015).…”

Art of Making Artificial Liver: Depicting Human Liver Biology and Diseases in Mice

“…Accordingly, protocols to differentiate ES/iPS cells into hepatocytes, hereafter iHep, has also evolved substantially over time; however, the degree of maturity is still far from that of freshly isolated PHH. [284][285][286][287] For example, transcriptome analysis of iHep demonstrated a highly distinctive gene expression profile compared with that of PHH. 284 These important observations collectively indicate that there remains a significant gap in terms of the degree of differen-tiation/maturation between genuine hepatocytes and iHeps.…”

“…[284][285][286][287] For example, transcriptome analysis of iHep demonstrated a highly distinctive gene expression profile compared with that of PHH. 284 These important observations collectively indicate that there remains a significant gap in terms of the degree of differen-tiation/maturation between genuine hepatocytes and iHeps. Of great interest, it has been shown that the implantation of iHep into the liver of HLCM prompted engraftment, proliferation, and further maturation.…”