A hepatocyte differentiation model reveals two subtypes of liver cancer with different oncofetal properties and therapeutic targets

Abstract

Clinical observation of the association between cancer aggressiveness and embryonic development stage implies the importance of developmental signals in cancer initiation and therapeutic resistance. However, the dynamic gene expression during organogenesis and the master oncofetal drivers are still unclear, which impeded the efficient elimination of poor prognostic tumors, including human hepatocellular carcinoma (HCC). In this study, human embryonic stem cells were induced to differentiate into adult hepatocytes along hepatic lineages to mimic liver development in vitro. Combining transcriptomic data from liver cancer patients with the hepatocyte differentiation model, the active genes derived from different hepatic developmental stages and the tumor tissues were selected. Bioinformatic analysis followed by experimental assays was used to validate the tumor subtype-specific oncofetal signatures and potential therapeutic values. Hierarchical clustering analysis revealed the existence of two subtypes of liver cancer with different oncofetal properties. The gene signatures and their clinical significance were further validated in an independent clinical cohort and The Cancer Genome Atlas database. Upstream activator analysis and functional screening further identified E2F1 and SMAD3 as master transcriptional regulators. Small-molecule inhibitors specifically targeting the oncofetal drivers extensively down-regulated subtype-specific developmental signaling and inhibited tumorigenicity. Liver cancer cells and primary HCC tumors with different oncofetal properties also showed selective vulnerability to their specific inhibitors. Further precise targeting of the tumor initiating steps and driving events according to subtype-specific biomarkers might eliminate tumor progression and provide novel therapeutic strategy.

Alternative Splicing in Hepatocellular Carcinoma

“…For example, the production of catalytically impaired splice variants of the nucleotide-regulating enzymes ecto-5 0nucleotidase (NT5E) 35 and kynurenine formamidase (AFMID) 36 occurs only in humans. In light of that, the most effective strategies for identifying tumor-promoting oncofetal splice variants and mechanisms can come out of integrating data from human HCC cell-based models 64,65 and tissue specimens 66 with the most appropriate animal models. [67][68][69] Up-regulation of the Oncofetal Splicing Factor Muscleblind-Like 3 in HCC Muscleblind-like (MBNL) proteins are encoded by 3 genes (MBNL1-3) and regulate RNA splicing in a tissuespecific manner.…”

RALYL increases hepatocellular carcinoma stemness by sustaining the mRNA stability of TGF-β2

“…Some studies have attempted to induce hepatocytes from several sources, such as embryonic, fetal, and somatic stem cells, by recapitulating the pathways controlling liver development 15,16 . Here, we reported that definitive endoderm (DE), liver progenitor (LP) cells, and premature hepatocytes (PH) could be induced from human embryonic stem (ES) cells by treating cell cultures with certain concentrations of factors 17 . By deep RNA sequencing, we characterized molecular signatures of liver progenitor cells and premature hepatocytes, which may be important to HCC development.…”

PARP inhibitor Olaparib overcomes Sorafenib resistance through reshaping the pluripotent transcriptome in hepatocellular carcinoma

“…Increasing evidences suggested that the hierarchy of cancer stem cells and their differentiated progenies contributed substantially to the heterogeneous tumor and therapeutic failure [ 4 , 5 ]. To better understand the dynamic transcriptomic change during liver development, we have recently established a hepatocyte differentiation model, which specifically induced human embryonic stem cells (hESCs) to differentiate into mature hepatocytes along hepatic lineages [ 6 ]. Meanwhile, liver tumors were inoculated into immune deficient mice and treated with Sorafenib to establish a drug resistant model.…”