Establishment of tumor organoids and patient-derived xenograft (PDX) models
Tumor organoids were cultured using surgically removed primary tumor tissues of 160 patients (131 with HCC, 17 with ICC, five with CHC, one with hepatoblastoma, one with hepatocellular adenoma, one with B cell lymphoma, one with hepatocellular carcinoma with bile duct epithelial differentiation, one with hepatic sarcoma; one with angiomyolipoma and one with metastatic carcinoma) from January 2018 to January 2019, from which we successfully constructed organoids from the tissues of 38 patients with HCC (29.0%), nine with ICC (52.9%), five with CHC, one with hepatoblastoma, one with hepatocellular adenoma, one with angiomyolipoma, and one with metastatic carcinoma (Figure S1A). The organoids from HCC and ICC were frozen in liquid nitrogen and then thawed for in vitro culture for several (3–5) cycles. This process lasted for up to 3.5 years, which did not alter their histological features. We also successfully developed PDX models using these tissues from 31 patients with HCC (23.7%), seven with ICC (41.2%), three with CHC, one with hepatoblastoma, one with hepatocellular adenoma, and one with metastatic carcinoma (Figure S1B). The duration of HCC organoids’ culture from tissue separation to the first passage was significantly shorter than that of PDX development from the first tumor implantation to the second implantation (13.0±4.7 vs. 25.1±5.4 days, P=2.28×10−13) (Figure S1C,1D).
The factors affecting the success rate of developing organoids and PDX models
To identify factors influencing the success rate of constructing HCC organoids, we compared the clinical data of patients whose tissues were successfully developed to organoids with those whose tissues failed. It was found that larger tumor size (P=0.030), microvascular invasion (MVI) (P=0.014), macrovascular invasion (P<0.001), advanced TNM stage (P=0.006), and advanced Barcelona Clinic Liver Cancer (BCLC) stage (P=0.010) were associated with successful development of HCC organoids (Table 1). Larger tumor size (P=0.005), MVI (P=0.014), macrovascular invasion (P=0.001), advanced TNM stage (P=0.004), and advanced BCLC stage (P=0.010) were also associated with successful PDX establishment (Table S1).
PLC organoids and PDX recapitulate the histopathological features of the original PLC types in vitro and in animal models
We confirmed that tumor organoids recapitulate histological features of the original tumors. HCC organoids mostly displayed solid structures. ICC organoids formed compact spheroids and irregularly shaped cyst-like structures. To assess if tumor organoids retained the histological characteristics of the corresponding PLC subtypes in vivo, we subcutaneously transplanted the organoids of HCC, ICC, and CHC into nude mice to establish organoids-derived xenograft (ODX). It was shown that ODX retained the histological characteristics of the corresponding PLC subtypes in nude mice. Moreover, PDX in nude mice also well recapitulated the histology of the corresponding PLC subtypes. These data are shown in Figure 1.
Tumor organoids enriched the aggressive cell types of the original PLC subtypes, but retain the heterogeneity
Immunohistochemistry demonstrated that α-fetoprotein (AFP) was highly expressed in HCC organoids, rather than in ICC and CHC organoids, which was consistent with the expression pattern of the original tumors (Figure S2A). The expression of cytokeratin 19 (CK19), a marker of HCC stem cells, was higher in tumor organoids than in the corresponding tumor tissues of HCC-25 (immunoreactive score: 12.0 vs. 1.2, P=8.1×10−9), ICC-6 (12 vs. 7.5, P=0.015), and CHC-3 (10.2 vs. 2.8, P=3.0×10−5), rather than in that from HCC-118. The expression of CK19 was higher in ODX than in the corresponding tumor tissues of HCC-25 (9.2 vs. 1.2, P=4.0×10−4) and CHC-3 (8.2 vs. 2.8, P=0.001), rather than in those from HCC-118 and ICC-6. The expression of CK19 was not statistically different in the primary tumors and PDX of HCC-25, HCC-118, ICC-6, and CHC-3 (Figure S2B). The expression of epithelial cell adhesion molecule (EpCAM), another epithelial stem marker, was higher in tumor organoids of HCC-25 (8.8 vs. 2.8, P=2.8×10−6) and CHC-3 (3.7 vs. 1.7, P=0.023) as well as the ODX from HCC-25 (8.3 vs. 2.8, P=9.8×10−6) than in the corresponding tumor tissues. No difference was found between the organoids and primary tumors of HCC-118 and ICC-6 as well as between PDX and the corresponding tumor tissues from HCC-25, HCC-118, ICC-6, and CHC-3 (Figure S2C). These results indicate that tumor organoids enriched the aggressive cell types of the corresponding PLC subtypes; however, the heterogeneity is evident.
Heterogeneity of inherent drug response in tumor organoids
To evaluate if tumor organoids are suitable for drug selection in vitro, we treated PLC organoids with different concentrations of sorafenib, regorafenib, lenvatinib, and mTOR inhibitor compound RAD001/TAK228 /phenformin (RTP) and then examined cell viability. It was found that sorafenib and regorafenib inhibited the growth of HCC organoids; however, this effect was not observed in nearly all the ICC and CHC organoids. RTP decreased the growth of PLC organoids in a dose-dependent manner. However, the majority of the PLC organoids showed resistance to lenvatinib treatment, with an half-maximal inhibitory concentration (IC50) value higher than the maximum screening concentration (Figure 2A,B).
To explore the therapeutic potentials of targeted therapeutics including RTP on PLC of each histotype, we examined their effects on the growth of tumor ODX models. The results show that the anti-tumor effect of RTP was comparable to that of sorafenib in HCC, while RTP inhibited ICC and CHC more effectively than did sorafenib. In contrast to the resistance to the majority of PLC organoids, lenvatinib was effective in all the tested ODX models (Figure 2C,D).
Acquired sorafenib-resistant HCC organoids and gene expression profiles
To explore the evolution of the resistance to sorafenib in HCC organoids, four HCC organoids (HCC-10, HCC-25, HCC-52, and HCC-118) were randomly selected. HCC-10 was derived from a female HBV-positive HCC patient with lymph node metastasis. HCC-25 was an invasive tumor organoid derived from a female HBV-positive HCC (HBV-HCC) patient. HCC-52 was an invasive tumor organoid derived from a male HBsAg-negative HCC patient. HCC-118 was a non-invasive tumor organoid derived from a male HBV-positive HCC patient who had received long-term antiviral treatment before surgery. After approximately 3–5 months of culture, the IC50 values of drug-resistant HCC-10, HCC-25, HCC-52, and HCC-118 strains increased 1.59-, 4.11-, 2.01-, and 2.31-fold, respectively (Table S2).
RNA sequencing was applied to assess the expression profiles of mRNA between sorafenib-resistant and parental tumor organoids from four HCC patients (HCC-10, HCC-25, HCC-52, and HCC-118). Combining the data from the four organoids, we identified that a group of genes including MCM6 and RRS1 were upregulated while most genes including TP53INP2 and MYH14 were downregulated in acquired sorafenib-resistant HCC organoids (Table S3). GSEA identified a group of gene sets enriched in acquired sorafenib-resistant organoids (Table S4). Importantly, cancer stemness-related gene sets including Myc- and EGFR-related gene sets were enriched in the sorafenib-resistant organoids; epithelial–mesenchymal transition (EMT)-related gene sets including TGFβ1- and E2F-related gene sets were also enriched in the sorafenib-resistant organoids (Figure 3A,B). Importantly, liver development- and liver specific gene-related gene sets were often downregulated, whereas undifferentiated cancer- and proliferation-related gene sets were upregulated in the sorafenib-resistant organoids (Figure 3C,D).
Although the sorafenib-resistant organoids enriched with gene signatures of stemness and EMT, the heterogeneity among the four HCC organoids was still evident. Sorafenib-resistant HCC-25, HCC-52, and HCC-10 were associated with upregulation of stemness- and EMT-related gene sets, whereas sorafenib-resistant HCC-118 was associated with downregulation of stemness- and EMT-related gene sets (Figure S3). We then evaluated the effect of drug resistance on the expression of stem-related genes in our sorafenib-resistant HCC organoids by either Western blot or immunohistochemistry. Epithelial markers E-cadherin and ZO-1 were downregulated in sorafenib-resistant HCC-25, HCC-10, and HCC-52 compared to their parental counterparts, in contrast to HCC-118, while β-catenin was upregulated in sorafenib-resistant HCC-25 and HCC-10 (Figure 4A). Stem cell markers CD133, CK19, and β-catenin were upregulated in sorafenib-resistant HCC-25 compared to its parental HCC-25 and this was not apparent in HCC-118 (Figure 4B). The expression of ABCG2 was upregulated in sorafenib-resistant HCC-118 and HCC-52 compared to their parental counterparts; the expression of EpCAM was upregulated in sorafenib-resistant HCC-118 and HCC-10 compared to their parental counterparts. Claudin-1 and N-cadherin were upregulated in sorafenib-resistant HCC-10 compared to its parental counterpart, while CD44 was upregulated in sorafenib-resistant HCC-25 compared to its parental counterpart by both Western blot and IHC assays (Figure S4). Immunohistochemistry for other organoids was technically unsuccessful. Thus, induction of sorafenib resistance is related to the process of cancer stemness and EMT/partial EMT. Similarly, the heterogeneity is apparent.
Targeting mTOR signaling pathway was effective in treating acquired sorafenib-resistant HCC organoids
After establishing acquired sorafenib-resistant HCC organoids, we sought to investigate if inhibitors targeting the sorafenib-induced signaling pathways could inhibit the growth of sorafenib-resistant HCC organoids. We tested the effects of available inhibitors on the cell viability of sorafenib-resistant HCC organoids. It was found that RTP was effective in inhibiting sorafenib-resistant HCC-25 and HCC-118 organoids, with IC50 values of 1.918 and 1.828 nM, respectively (Figure 5A,B). However, the expression levels of mTOR signaling molecules were not significantly upregulated in sorafenib-resistant HCC-25 and HCC-118 organoids (Table S3). It was found that phosphorylation of S6, a key downstream target of PI3K/AKT/mTOR pathway13, was apparently upregulated in sorafenib-resistant HCC-25 and HCC-118 organoids (Figure 5C). Thus, phospho-S6 should be predictive in sorafenib-resistant HCC.
As acquired sorafenib-resistant HCC-25 organoids exhibited more stemness than did acquired sorafenib-resistant HCC-118 (Figuire 4B) and the HCC-118 organoids responded to RTP more efficiently than did the HCC-25 (Figure 5A,B), we sought to identify factor related to the difference. Interestingly, we found that the expression of β-actin was apparently downregulated in acquired sorafenib-resistant HCC-25 (Figure 5D). We then removed sorafenib and cultured sorafenib-resistant HCC-25 organoids for an additional two weeks, and the expression of β-actin was restored after sorafenib withdrawal (Figure 5E). However, the expression of β-actin did not differ between the parental and sorafenib-resistant HCC-118 (Figure 5F). These data imply that β-actin protein is not only indispensable for efficient cell migration14, but also has an opposite effect on maintaining cancer stemness.
Molecules upregulated in sorafenib-resistant organoids are often associated with unfavorable prognosis in HCC
The association of the differential expressed genes related to sorafenib-resistance with postoperative prognosis was evaluated using the data from the Cancer Genome Atlas (TCGA) database. The genes whose expressions were dysregulated in the sorafenib-resistant HCC organoids are listed in Table S5. Of the 26 OS-related genes upregulated in the sorafenib-resistant HCC organoids, 21 were significantly associated with unfavorable prognosis. The genes upregulated in the sorafenib-resistant HCC organoids were more related to unfavorable OS than were the downregulated genes (21/26 (86.8%) vs. 61/119 (51.3%), P=0.010); the genes upregulated in the sorafenib-resistant HCC organoids were more related to unfavorable DFS than were the downregulated genes (12/16 (75.0%) vs. 36/95 (37.9%), P=0.012) (Figure S5). These genes might reflect HCC evolution and development during generating drug resistance against sorafenib pressure.