Effects of insulin-like growth factors-IR and -IIR antisense gene transfection on the biological behaviors of SMMC-7721 human hepatoma cells

Identification and characterization of the lncRNA signature associated with overall survival in patients with neuroblastoma

Neuroblastoma (NB) is a commonly occurring cancer among infants and young children. Recently, long non-coding RNAs (lncRNAs) have been using as prognostic biomarkers for therapeutics and interventions in various cancers. Considering the poor survival of NB, the lncRNA-based therapeutic strategies must be improved. This work proposes an overall survival time estimator called SVR-NB to identify the lncRNA signature that is associated with the overall survival of patients with NB. SVR-NB is an optimized support vector regression (SVR)-based method that uses an inheritable bi-objective combinatorial genetic algorithm for feature selection. The dataset of 231 NB patients that contains overall survival information and expression profiles of 783 lncRNAs was used to design and evaluate SVR-NB from the database of gene expression omnibus accession GSE62564. SVR-NB identified a signature of 35 lncRNAs and achieved a mean squared correlation coefficient of 0.85 and a mean absolute error of 0.56 year between the actual and estimated overall survival time using 10-fold cross-validation. Further, we ranked and characterized the 35 lncRNAs according to their contribution towards the estimation accuracy. Functional annotations and co-expression gene analysis of LOC440896, LINC00632, and IGF2-AS revealed the association of co-expressed genes in Kyoto Encyclopedia of Genes and Genomes pathways.

Long non-coding RNAs: novel prognostic biomarkers for liver metastases in patients with early stage colorectal cancer

Liver metastasis is the primary cause of death for colorectal cancer (CRC) patients. To investigate the prognostic value of long non-coding RNAs (lncRNAs) on colorectal liver metastases, quantitative reverse-transcriptase PCR (quantitative RT-PCR) was performed on 15 lncRNAs in 51 stage IV CRC with liver metastases and 57 stage I/II CRC specimens. The expression levels of four lncRNAs (GAS5, H19, MEG3 and Yiya) were significantly different between liver metastases and primary tumors of stage IV CRC patients. Furthermore, the high expression levels of GAS5 and Yiya were significantly associated with future occurrence of liver metastases in early stage CRC patients. Kaplan-Meier analysis showed that the high expression levels of GAS5 or Yiya were correlated with poor prognosis of early stage CRC patients (p = 0.0206 and 0.0005 for GAS5 and Yiya, respectively). Yiya expression was proved to be an independent prognostic indicator of colorectal liver metastases in a multivariate analysis (relative risk = 10.7; p < 0.0001). Our study revealed that GAS5 and Yiya were promising prognostic biomarkers of liver metastases for early stage CRC patients.

Systemically identifying and prioritizing risk lncRNAs through integration of pan-cancer phenotype associations

LncRNAs have emerged as a major class of regulatory molecules involved in normal cellular physiology and disease, our knowledge of lncRNAs is very limited and it has become a major research challenge in discovering novel disease-related lncRNAs in cancers. Based on the assumption that diverse diseases with similar phenotype associations show similar molecular mechanisms, we presented a pan-cancer network-based prioritization approach to systematically identify disease-specific risk lncRNAs by integrating disease phenotype associations. We applied this strategy to approximately 2800 tumor samples from 14 cancer types for prioritizing disease risk lncRNAs. Our approach yielded an average area under the ROC curve (AUC) of 80.66%, with the highest AUC (98.14%) for medulloblastoma. When evaluated using leave-one-out cross-validation (LOOCV) for prioritization of disease candidate genes, the average AUC score of 97.16% was achieved. Moreover, we demonstrated the robustness as well as the integrative importance of this approach, including disease phenotype associations, known disease genes and the numbers of cancer types. Taking glioblastoma multiforme as a case study, we identified a candidate lncRNA gene SNHG1 as a novel disease risk factor for disease diagnosis and prognosis. In summary, we provided a novel lncRNA prioritization approach by integrating pan-cancer phenotype associations that could help researchers better understand the important roles of lncRNAs in human cancers.

Guadecitabine (SGI-110) priming sensitizes hepatocellular carcinoma cells to oxaliplatin

Promoter DNA hypermethylation is an important biomarker of hepatocellular carcinoma (HCC), supporting the potential utility of demethylating agents in this disease. Guadecitabine (SGI-110) is a second-generation hypomethylating agent formulated as a dinucleotide of decitabine and deoxyguanosine that yields longer half-life and more extended decitabine exposure than decitabine IV infusion. Here we performed preclinical evaluation of SGI-110 in HCC models to guide the design of a phase I/II clinical trial. HCC cell lines and xenograft models were used to determine the antitumor activity of SGI-110 as a single agent and in combination with oxaliplatin. Pretreatment with low doses of SGI-110 significantly synergized with oxaliplatin yielding enhanced cytotoxicity. The combination of SGI-110 and oxaliplatin was well tolerated and significantly delayed tumor growth in mice compared to oxaliplatin alone. Bromouridine-labeled RNA sequencing (Bru-seq) was employed to elucidate the effects of SGI-110 and/or oxaliplatin on genome-wide transcription. SGI-110 and the combination treatment inhibited the expression of genes involved in WNT/EGF/IGF signaling. DNMT1 and survivin were identified as novel PD markers to monitor the efficacy of the combination treatment. In conclusion, SGI-110 priming sensitizes HCC cells to oxaliplatin by inhibiting distinct signaling pathways. We expect that this combination treatment will show low toxicity and high efficacy in patients. Our study supports the use of the combination of low doses of SGI-110 and oxaliplatin in HCC patients.

Molecular therapies in hepatocellular carcinoma: what can we target?

Numerous signaling pathways, such as Ras/Raf/MAPK, have been implicated in hepatic carcinogenesis. There are at least 35 combination therapy studies for advanced stage hepatocellular carcinoma (HCC) ongoing, and numerous reagents are being tested targeting novel signaling cascades. The management of HCC has changed substantially in recent times, and the successful development of sorafenib has prompted further expansion on molecular targeted therapies to potentially inhibit different pathways in hepatocarcinogenesis.

In silico regulatory analysis for exploring human disease progression

Background

An important goal in bioinformatics is to unravel the network of transcription factors (TFs) and their targets. This is important in the human genome, where many TFs are involved in disease progression. Here, classification methods are applied to identify new targets for 152 transcriptional regulators using publicly-available targets as training examples. Three types of sequence information are used: composition, conservation, and overrepresentation.

Results

Starting with 8817 TF-target interactions we predict an additional 9333 targets for 152 TFs. Randomized classifiers make few predictions (~2/18660) indicating that our predictions for many TFs are significantly enriched for true targets. An enrichment score is calculated and used to filter new predictions.

Two case-studies for the TFs OCT4 and WT1 illustrate the usefulness of our predictions:

• Many predicted OCT4 targets fall into the Wnt-pathway. This is consistent with known biology as OCT4 is developmentally related and Wnt pathway plays a role in early development.

• Beginning with 15 known targets, 354 predictions are made for WT1. WT1 has a role in formation of Wilms' tumor. Chromosomal regions previously implicated in Wilms' tumor by cytological evidence are statistically enriched in predicted WT1 targets. These findings may shed light on Wilms' tumor progression, suggesting that the tumor progresses either by loss of WT1 or by loss of regions harbouring its targets.

• Targets of WT1 are statistically enriched for cancer related functions including metastasis and apoptosis. Among new targets are BAX and PDE4B, which may help mediate the established anti-apoptotic effects of WT1.

• Of the thirteen TFs found which co-regulate genes with WT1 (p ≤ 0.02), 8 have been previously implicated in cancer. The regulatory-network for WT1 targets in genomic regions relevant to Wilms' tumor is provided.

Conclusion

We have assembled a set of features for the targets of human TFs and used them to develop classifiers for the determination of new regulatory targets. Many predicted targets are consistent with the known biology of their regulators, and new targets for the Wilms' tumor regulator, WT1, are proposed. We speculate that Wilms' tumor development is mediated by chromosomal rearrangements in the location of WT1 targets.

Reviewers

This article was reviewed by Trey Ideker, Vladimir A. Kuznetsov(nominated by Frank Eisenhaber), and Tzachi Pilpel.

KAI1 gene suppresses invasion and metastasis of hepatocellular carcinoma MHCC97-H cells in vitro and in animal models

BACKGROUND

Downregulation of KAI1 gene expression has been found in many types of cancer cells and is closely related to cancer invasion and metastasis. This study was aimed at investigating the effects and possible underlying mechanisms of KAI1 gene on invasion and metastasis of human hepatocellular carcinoma (HCC).

METHODS

The invasive ability, visco-elastic properties and cell adhesion forces were analysed in different HCC cells originating from the MHCC97-H cell line transfected with either the sense or the antisense KAI1 expression plasmid. Tumuorigenicity, metastatic abilities, extracellular matrix (ECM) and intercellular adhesion molecule-1 (ICAM-1) expression were also evaluated in the nude mouse models of the xenografted and orthotopic liver cancer cells.

RESULTS

Compared with their parental cells, in the HCC cells transfected with the sense KAI1 gene, the invasive ability in vitro was significantly decreased (P<0.01); the cellular elastic coefficients K(1), K(2) and mu were significantly higher (P<0.05); the cells adhesion forces to fibronectin were significantly lower (P<0.01). The sense KAI1 gene transfection into the cancer cells also inhibited their invasion and lung metastasis in the orthotopic liver cancer nude mice. However, the opposite changes were observed in the HCC cells transfected with the antisense KAI1 gene. KAI1 gene transfection also affected ECM and ICAM-1 expression in the transplanted liver cancer.

CONCLUSION

The KAI1 gene plays an important role in the invasion and metastasis of human HCC and its upregulation in HCC cells suppresses their invasive and metastatic abilities. KAI1 gene functioned as a metastasis inhibitor by regulating the HCC cell biophysical behaviours including aggregation, adhesion, motility and visco-elastic properties.

Inhibition of hepatocellular carcinoma growth by antisense oligonucleotides to type I insulin-like growth factor receptor in vitro and in an orthotopic model

AIM

The type I insulin-like growth factor receptor (IGF-IR) is overexpressed in many tumors including human hepatocellular carcinoma (HCC). It is a critical signaling molecule for tumor cell proliferation and survival. In the present study, IGF-IR expression was down-regulated by phosphorothioate antisense oligonucleotides (AS[S]ODN) to evaluate their specific effects on growth of hepatoma cells in vitro and in vivo.

METHODS

HepG2 cells were transfected with different doses of AS[S]ODN, sense [S]ODN, mismatch [S]ODN, or Lipofectin for 72 h, and cell proliferation was analyzed by MTS assay. In vivo, an orthotopic transplant model of HCC was established in nude mice, which were then injected with AS[S]ODN, sense [S]ODN, 5-fluorouracil or saline. At the endpoint of treatment, the tumors were excised and evaluated.

RESULTS

Compared to sense and mismatched oligonucleotides, AS[S]ODN targeting to IGF-IR mRNA significantly inhibited hepatoma cell lines HepG2 proliferation and IGF-IR expression at both mRNA and protein levels. The in vivo results showed that systemic treatment also resulted in significant inhibition in tumor growth. Tumor growth in mice treated with AS[S]ODN (50 and 75 mg/kg per day) was significantly inhibited (71.81% and 61.74%, respectively) compared to the saline-treated group (P < 0.01) in a dose-dependent manner. The antitumor effect of IGF-IR AS[S]ODN was associated with down-regulation of IGF-IR in tumor xenografts. Furthermore, IGF-IR AS[S]ODN prevented liver recurrence tumor growth and metastasis in the lung, showing a dose-dependent response. The level of serum alpha-fetoprotein in AS[S]ODN-treated groups was also decreased in a dose-dependent manner, and a good correlation was observed between tumor volume and serum alpha-fetoprotein concentration.

CONCLUSIONS

These data suggest that IGF-IR AS[S]ODN can effectively and specifically inhibit HCC growth in vitro and in vivo. Blockage of IGF-IR expression could be a promising therapeutic approach for the management of patients with HCC.

An evaluation of the role of insulin-like growth factors (IGF) and of type-I IGF receptor signalling in hepatocarcinogenesis and in the resistance of hepatocarcinoma cells against drug-induced apoptosis

Strong evidence emphasizes the role of the insulin-like growth factor (IGF) system and of type-I IGF receptor (IGF-IR) signalling in tumourigenesis. In this connection: (i) changes in the expression pattern of components of the IGF system (autocrine/paracrine expression of IGF-I and -II, overexpression of IGF-IR, decreased expression of IGF-binding proteins (IGFBPs) and of type-II IGF receptor/cation-independent mannose-6-phosphate receptor (IGF-II/M6PR) and (ii) increased serum concentrations of proteases that cleave the IGFBPs (e.g., cathepsin D) were observed in patients with hepatocellular carcinomas (HCC), in human hepatoma cell lines and in their conditioned culture medium, as well as in rodent models of hepatocarcinogenesis. Accordingly, studies carried out with animal models do suggest that the IGF system and IGF-IR signalling may play a role in hepatocarcinogenesis and in deregulated proliferation and apoptosis of HCC cells. Finally the instrumental role of Raf/MEK/ERK, one of the signalling cascades stimulated by IGF-IR, in anthracycline-induced apoptosis of HepG2 and Huh-7 human hepatoma cell lines emphasizes that care must be taken when designing combinations of antitumoural molecules for antineoplastic treatment. This review addresses the putative roles of the IGF system in primary HCC, with a special focus on the underlying molecular mechanisms. In a second part it emphasizes the putative interference of IGF-IR signalling with chemotherapeutic drug-induced apoptosis in human hepatoma cells.

Effects of KAI1 gene on growth and invasion of human hepatocellular carcinoma MHCC97-H cells

AIM: To study the effects of sense and antisense KAI1 genes on the growth and invasion of human hepatocellular carcinoma (HCC) cell line MHCC97-H.

METHODS: KAI1 sense and antisense eukaryotic expression plasmids were constructed using subclone technique and transfected into MHCC97-H cells respectively by DOTAP liposome. After successful transfection was confirmed, in vitro growth curve, cell cycles, plate clone formation efficiency, invasive ability in Boyden Chamber assay and ultrastructural morphology were studied.

RESULTS: KAI1 sense and antisense genes had no significant effects on the cell growth curve and cell cycles. After transfection with sense KAI1 gene, decreased invasive ability in Boyden Chamber assay and decreased amount of mitochondria, but no significant changes of plate clone formation efficiency were observed in MHCC97-H-S cells. The plate clone formation efficiency and invasive ability in Boyden Chamber assay were significantly increased in MHCC97-H-AS cells, after transfection with antisense KAI1 gene. Furthermore, increased amount of mitochondria, rough endoplasmic reticulum, Golgi apparatus and expanded endoplasmic reticulum were also noted in MHCC97-H-AS cells.

CONCLUSION: Changes of KAI1 expression in HCC cells may alter their invasive and metastasis ability of the tumor.

Effects of metastasis-suppressor gene KAI1 on viscoelastic properties of hepatocellular carcinoma MHCC97-H cells with high metastatic potential

AIM: To study the effects of metastasis-suppressor gene KAI1 on viscoelastic properties of hepatocellular carcinoma MHCC97-H cells with high metastatic potential.

METHODS: The viscoelastic properties of MHCC97-H cells with high metastatic potential transfected with sense or antisense KAI1 expression plasmid in our previous experiments were measured by means of micropipette aspiration technique.

RESULTS: The elastic coefficients K1, K2 and m of the MHCC97-H cells were significantly higher after transfected with sense KAI1 expression plasmid (P = 0.007), lower after transfected with antisense KAI1 expression plasmid (P = 0.000), and no significantly different after transfected with its control vector pCI-neo without KAI1 gene (P = 0.444), as compared with their paternal MHCC97-H cells.

CONCLUSION: The metastasis-suppressor gene KAI1 may significantly affect the viscoelastic properties of MHCC97-H cells with high metastatic potential. It offers an important clue to study the mechanisms of invasion and metastasis of the malignant tumor.

Effects of metastasis-suppressor gene KAI1 on tumorigenicity and metastasis of hepatocellular carcinoma MHCC97-H cells with high metastatic potential in nude mice

AIM: To explore the effects of metastasis-suppressor gene KAI1 on tumorigenicity and metastasis of hepatocellular carcinoma cells MHCC97-H with high metastatic potential in nude mice.

METHODS: The MHCC97-H hepatocellular carcinoma cells with high metastatic potential transfected with sense or antisense KAI1 expression plasmid in our previous experiments were inoculated subcutaneously into nude mice. The growth of subcutaneous tumor was observed, then the subcutaneous tumor tissues were harvested and implanted orthotopicly into nude mice liver. The tumor metastasis in lung was carefully examined under microscope. MHCC97-H and the cells transfected with vector pCI-neo, but without KAI1 gene were used as control.

RESULTS: The different cells inoculated subcutaneously all had tumorigenicity. There were no significant differences in the speed of tumor growth among different groups, but the antisense group showed stronger invasion ability than others. The spontaneous metastasis to lung occurred in latency period of six wk via orthotopic implantation of tumor tissue. Immunostaining showed strongly positive for AFP in lung metastatic lesions, which indicated those were lung metastatic lesions from hepatocellular carcinoma. The number of lung metastatic lesions increased dramaticly in antisense group (P = 0.00 158), decreased significantly in sense group (P = 0.00 465) and no significant difference in vector pCI-neo group (P = 0.15 166), as compared with their paternal MHCC97-H group.

CONCLUSION: The metastasis-suppressor gene KAI1 has no significant effects on tumorigenicity and growth of MHCC97-H hepatocellular carcinoma cells, but enhanced KAI1 expression can decrease the invasion ability and inhibit the metastasis, which offers an important clue to investigate the anti-metastasis treatment for hepatocellular carcinoma.