Pharmacogenomic profiling of intra-tumor heterogeneity using a large organoid biobank of liver cancer

Inter- and intra-tumor heterogeneity is a major hurdle in primary liver cancer (PLC) precision therapy. Here, we establish a PLC biobank, consisting of 399 tumor organoids derived from 144 patients, which recapitulates histopathology and genomic landscape of parental tumors, and is reliable for drug sensitivity screening, as evidenced by both in vivo models and patient response. Integrative analysis dissects PLC heterogeneity, regarding genomic/transcriptomic characteristics and sensitivity to seven clinically relevant drugs, as well as clinical associations. Pharmacogenomic analysis identifies and validates multi-gene expression signatures predicting drug response for better patient stratification. Furthermore, we reveal c-Jun as a major mediator of lenvatinib resistance through JNK and β-catenin signaling. A compound (PKUF-01) comprising moieties of lenvatinib and veratramine (c-Jun inhibitor) is synthesized and screened, exhibiting a marked synergistic effect. Together, our study characterizes the landscape of PLC heterogeneity, develops predictive biomarker panels, and identifies a lenvatinib-resistant mechanism for combination therapy.

NQO1 Mediates Lenvatinib Resistance by Regulating ROS-induced Apoptosis in Hepatocellular Carcinoma

OBJECTIVE

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-associated death worldwide. As a first-line drug for advanced HCC treatment, lenvatinib faces a significant hurdle due to the development of both intrinsic and acquired resistance among patients, and the underlying mechanism remains largely unknown. The present study aims to identify the pivotal gene responsible for lenvatinib resistance in HCC, explore the potential molecular mechanism, and propose combinatorial therapeutic targets for HCC management.

METHODS

Cell viability and colony formation assays were conducted to evaluate the sensitivity of cells to lenvatinib and dicoumarol. RNA-Seq was used to determine the differences in transcriptome between parental cells and lenvatinib-resistant (LR) cells. The upregulated genes were analyzed by GO and KEGG analyses. Then, qPCR and Western blotting were employed to determine the relative gene expression levels. Afterwards, the intracellular reactive oxygen species (ROS) and apoptosis were detected by flow cytometry.

RESULTS

PLC-LR and Hep3B-LR were established. There was a total of 116 significantly upregulated genes common to both LR cell lines. The GO and KEGG analyses indicated that these genes were involved in oxidoreductase and dehydrogenase activities, and reactive oxygen species pathways. Notably, NAD(P)H:quinone oxidoreductase 1 (NQO1) was highly expressed in LR cells, and was involved in the lenvatinib resistance. The high expression of NQO1 decreased the production of ROS induced by lenvatinib, and subsequently suppressed the apoptosis. The combination of lenvatinib and NQO1 inhibitor, dicoumarol, reversed the resistance of LR cells.

CONCLUSION

The high NQO1 expression in HCC cells impedes the lenvatinib-induced apoptosis by regulating the ROS levels, thereby promoting lenvatinib resistance in HCC cells.

Focal adhesion kinase confers lenvatinib resistance in hepatocellular carcinoma via the regulation of lysine-deficient kinase 1

Lenvatinib is a clinically effective multikinase inhibitor approved for first-line therapy of advanced hepatocellular carcinoma (HCC). Although resistance against lenvatinib often emerges and limits its antitumor activity, the underlying molecular mechanisms involved in endogenous and acquired resistance remain elusive. In this study, we identified focal adhesion kinase (FAK) as a critical contributor to lenvatinib resistance in HCC. The elevated expression and phosphorylation of FAK were observed in both acquired and endogenous lenvatinib-resistant (LR) HCC cells. Furthermore, inhibition of FAK reversed lenvatinib resistance in vitro and in vivo. Mechanistically, FAK promoted lenvatinib resistance through regulating lysine-deficient kinase 1 (WNK1). Phosphorylation of WNK1 was significantly increased in LR-HCC cells. Further, WNK1 inhibitor WNK463 resensitized either established or endogenous LR-HCC cells to lenvatinib treatment. In addition, overexpression of WNK1 desensitized parental HCC cells to lenvatinib treatment. Conclusively, our results establish a crucial role and novel mechanism of FAK in lenvatinib resistance and suggest that targeting the FAK/WNK1 axis is a promising therapeutic strategy in HCC patients showing lenvatinib resistance.

AKR1C1 overexpression leads to lenvatinib resistance in hepatocellular carcinoma

Background

Lenvatinib is an orally administered drug that works as a multi-targeted tyrosine kinase inhibitor. It has been approved as a first-line drug after sorafenib in hepatocellular carcinoma (HCC). However, little is currently known about its treatment, targets, and possible resistance in HCC.

Methods

The proliferation of HCC cells was evaluated using colony formation, 5-ethynyl-2'-deoxyuridine (EDU), wound healing, cell counting kit-8 (CCK-8), and xenograft tumor assays. RNA sequencing (RNA-seq) was utilized to comprehensively examine variations in highly metastatic human liver cancer cells (MHCC-97H) cells (treated with various doses of lenvatinib) at the transcriptomic level. Protein interactions and functions were predicted using Cytoscape-generated networks and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, while the proportions of 22 immune cell types were examined with CIBERSORT. Aldo-keto reductase family 1 member C1 (AKR1C1) expression was verified by quantitative real time polymerase chain reaction (qRT-PCR) or immunohistochemistry in HCC cells and liver tissues. Micro ribonucleic acid (miRNAs) were predicted using online tools and potential drugs were screened using the Genomics of Drug Sensitivity in Cancer (GDSC) database.

Results

Lenvatinib inhibited the proliferation of HCC cells. The obtained results suggested that an elevated level of AKR1C1 expression was observed in lenvatinib-resistant (LR) cell lines and HCC tissues, whereas low AKR1C1 expression inhibited the proliferation of HCC cells. Circulating microRNA 4644 (miR-4644) was predicted to serve as a promising biomarker for the early diagnosis of lenvatinib resistance. Online data analysis of LR cells showed significant differences in the immune microenvironment and drug sensitivity compared with their parental counterparts.

Conclusions

Taken together, AKR1C1 may serve as a candidate therapeutic target for LR liver cancer patients.

circRNA circMED27 acts as a prognostic factor and mediator to promote lenvatinib resistance of hepatocellular carcinoma

Circular RNAs (circRNAs) have been proven to play key roles in the development and progression of various types of cancers. However, there were no reported studies on the roles of circRNA mediator complex subunit 27 (circMED27) in tumors including hepatocellular carcinoma (HCC). In this study, we found that circMED27 was significantly increased in HCC serum and that higher levels of circMED27 were correlated with bad clinical characteristics and poor prognoses of patients with HCC. Furthermore, upregulated circMED27 promoted HCC resistance to lenvatinib. Our mechanistic investigations revealed that circMED27 functions as a competing endogenous RNA (ceRNA) for miR-655-3p to upregulate ubiquitin-specific peptidase 28 (USP28) expression. Thus, we are led to conclude that circMED27 acts as a potential therapeutic target for HCC patients receiving lenvatinib therapy and may represent a promising molecular biomarker for forecasting lenvatinib-resistant HCC.

Characterization of Cisplatin Effects in Lenvatinib-resistant Hepatocellular Carcinoma Cells

BACKGROUND/AIM

Drug resistance to molecular targeted agents, such as lenvatinib, is an important issue. The aim of this study was to explore the mechanism of lenvatinib resistance and to investigate potential drugs that may improve the treatment of lenvatinib-resistant (LR) hepatocellular carcinoma (HCC).

MATERIALS AND METHODS

LR cells were developed by long-term culture under lenvatinib exposure. We analyzed the biological characteristics of LR cells in vitro, and investigated the antitumor effects and endogenous mechanisms of cisplatin in LR cells.

RESULTS

The proliferative potential of LR cells was enhanced by activation of ERK signaling and changes in several miRNAs. Cisplatin inhibited cell proliferation of LR cells and induced G2/M cell cycle arrest. Furthermore, cisplatin triggered the DNA damage response, via the ATM/ATR-Chk1/Chk2 signaling pathway.

CONCLUSION

Proliferation of LR cells was induced upon ERK signaling activation. Cisplatin exerted antitumor effects in LR cells and was involved in the regulation of miRNAs associated with drug resistance.

Sophoridine suppresses lenvatinib-resistant hepatocellular carcinoma growth by inhibiting RAS/MEK/ERK axis via decreasing VEGFR2 expression

Hepatocellular carcinoma (HCC) is one of the most lethal cancer types with insufficient approved therapies, among which lenvatinib is a newly approved multi‐targeted tyrosine kinase inhibitor for frontline advanced HCC treatment. However, resistance to lenvatinib has been reported in HCC treatment recently, which limits the clinical benefits of lenvatinib. This study aims to investigate the underlying mechanism of lenvatinib resistance and explore the potential drug to improve the treatment for lenvatinib‐resistant (LR) HCC. Here, we developed two human LR HCC cell lines by culturing with long‐term exposure to lenvatinib. Results showed that the vascular endothelial growth factor receptors (VEGFR)2 expression and its downstream RAS/MEK/ERK signalling were obviously up‐regulated in LR HCC cells, whereas the expression of VEGFR1, VEGFR3, FGFR1‐4 and PDGFRα/β showed no difference. Furthermore, ETS‐1 was identified to be responsible for VEGFR2 mediated lenvatinib resistance. The cell models were further used to explore the potential strategies for restoration of sensitivity of lenvatinib. Sophoridine, an alkaloid extraction, inhibited the proliferation, colony formation, cell migration and increased apoptosis of LR HCC cells. In vivo and in vitro results showed Sophoridine could further sensitize the therapeutic of lenvatinib against LR HCC. Mechanism studies revealed that Sophoridine decreased ETS‐1 expression to down‐regulate VEGFR2 expression along with downstream RAS/MEK/ERK axis in LR HCC cells. Hence, our study revealed that up‐regulated VEGFR2 expression could be a predicator of the resistance of lenvatinib treatment against HCC and provided a potential candidate to restore the sensitivity of lenvatinib for HCC treatment.