Identifying hepatocellular carcinoma-related genes and pathways by system biology analysis

Novel Insights into MEG3/miR664a-3p/ADH4 Axis and Its Possible Role in Hepatocellular Carcinoma from an in Silico Perspective

Hepatocellular carcinoma (HCC) is a complex disease involving altered interactomes of transcripts and proteins. MicroRNAs (miRNAs) are small-noncoding RNAs that can interact with specific gene transcripts and an array of other vital endogenous non-coding RNAs (lncRNAs) that can influence gene expression. Maternally Expressed Gene 3 (MEG3) is an imprinted lncRNA that is reported to be downregulated in HCC (in both cell lines and tumors). Alcohol Dehydrogenase 4 (ADH4) is a well-known prognostic protein biomarker for predicting the survival outcomes of patients with hepatocellular carcinoma whose expression is regulated by miR-664a-3p, which is upregulated in HCC. In this study, we performed a battery of robust and systematic in silico analyses to predicate the possible lncRNA-miRNA interactions between MEG3, miR-664a-3p, and ADH4. miRNA-mRNA and lncRNA-miRNA hybrid structures were primarily obtained, and the minimum free energies (MFEs) for the 3'UTR (Untranslated Regions) of ADH4-miR-664a-3p and the 3'UTR of MEG3-miR-664a-3p interactions were assessed to predict the stability of the obtained RNA heteroduplex hybrids. The hybrid with the least minimum free energy (MFE) was considered to be the most favorable. The MFEs were around -28.1 kcal/mol and -31.3 kCal/mol for the ADH4-miR-664a-3p and MEG3-miR-66a-3p RNA hybrids, respectively. This demonstrated that lncRNA-MEG3 might be a competitive endogenous RNA that acts as a molecular sponge for miR-664a-3p. In summary, our interaction analyses results predict the significance of the MEG3/miR-664a-3p/ADH4 axis, where MEG3 downregulation results in miR-664a-3p overexpression and the subsequential underexpression of ADH4 in HCC, as a novel axis of interest that demands further validation.

LncRNA HOTAIR: A Potential Prognostic Factor and Therapeutic Target in Human Cancers

Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of gene expression and physiological processes. LncRNAs are a class of ncRNAs of 200 nucleotides in length. HOX transcript antisense RNA (HOTAIR), a trans-acting lncRNA with regulatory function on transcription, can repress gene expression by recruiting chromatin modifiers. HOTAIR is an oncogenic lncRNA, and numerous studies have determined that HOTAIR is highly upregulated in a wide variety of human cancers. In this review, we briefly summarize the impact of lncRNA HOTAIR expression and functions on different human solid tumors, and emphasize the potential of HOTAIR on tumor prognosis and therapy. Here, we review the recent studies that highlight the prognostic potential of HOTAIR in drug resistance and survival, and the progress of therapies developed to target HOTAIR to date. Furthermore, targeting HOTAIR results in the suppression of HOTAIR expression or function. Thus, HOTAIR knockdown exhibits great therapeutic potential in various cancers, indicating that targeting lncRNA HOTAIR may serve as a promising strategy for cancer therapy. We also propose that preclinical studies involving HOTAIR are required to provide a better understanding of the exact molecular mechanisms underlying the dysregulation of its expression and function in different human cancers and to explore effective methods of targeting HOTAIR and engineering efficient and targeted drug delivery methods in vivo.

Mass Spectrometry as a Clinical Integrative Tool to Evaluate Hepatocellular Carcinoma: Moving to the Mainstream

Introduction: Since the pioneering work of J. J. Thomson on magnetic deflection of charged particles, mass spectrometry (MS) has become the most progressive clinical tool by continuously providing new applications in medical research. In hepatocellular carcinoma (HCC), MS can be used from surveillance in early stages of the disease to constant evaluation of effective treatments. Areas covered: This Special Report highlights the groundbreaking possibilities of mass spectrometry clinical application in the mainstream to evaluate HCC development and progression. Expert opinon: MS has been employed to understand a myriad of liver diseases, such as the identification of early biomarkers in cirrhosis and HVB and HVC, as well as metabolic alterations of lipidic imbalance in HCC due to fatty liver disease. In an integrative point-of-view, researchers worldwide are looking for molecular signatures that may represent more faithfully the complex scenario of the onset and progression of HCC. Following the steps of MELD score (Model of End-stage Liver Disease), which evaluates biochemical dysfunction of end-stage liver diseases, the necessity to use innovative attempts to pursue a molecular-MEaLD (mMEaLD - molecular Model for Early Liver Disease), shifting MS to the upstream and from the lab facilities into the mainstream, inside the surgery room.

Association of tagSNPs at lncRNA MALAT-1 with HCC Susceptibility in a Southern Chinese Population

As a long non-coding RNA (lncRNA) and a transcriptional regulator, Metastasis associated lung adenocarcioma transcript-1 (MALAT-1) has been reported to be associated with proliferation and metastasis of hepatocellular carcinoma (HCC). However, the effects of MALAT-1 single nucleotide polymorphisms (SNPs) on HCC remains poorly understood. This study, including 624 HCC cases and 618 controls, aimed to explore the potential associations between three common tagSNPs at MALAT-1 and HCC risk in a Southern Chinese population. No significant associations were observed between the three tagSNPs and HCC risk under any genetic models after adjusting for potential confounders. Additionally, there were no any significant associations in the stratified analysis, combined effect analysis, and multifactor dimensionality reduction (MDR) analysis. Unification analysis of mediation and interaction on HCC risk further showed that four decomposition of total effects ((controlled direct effect (CDE), the reference interaction effect (INTref), the mediated interaction effect (INTmed), or the pure indirect effect (PIE)) were also not significant. Neither was the association between the MALAT-1 SNPs and progression factors of HCC, including TNM staging, metastasis, and cancer embolus; Overall, this study suggested that tagSNPs rs11227209, rs619586, and rs3200401 at MALAT-1 were not significantly associated with HCC susceptibility. Nevertheless, large population-based studies are warranted to further explore the role of MALAT-1 SNPs in HCC incidence and development.

LINC00339 promotes growth and invasiveness of hepatocellular carcinoma by the miR-1182/SKA1 pathway

Background: Extensive research has shown that long noncoding RNA (lncRNA) is involved in tumorigenesis, including hepatocellular carcinoma (HCC). The lncRNA LINC00339 was reported to regulate the development of lung cancer or breast cancer. However, whether LINC00339 participates in HCC progression remains unclear. Here, our results showed that LINC00339 was upregulated in HCC.

Methods: qRT-PCR and in situ hybridization (ISH) was used to analyze LINC00339 expression in tumor tissues and cell lines. CCK8 and colony formation assays were used to analyze cell proliferation. Transwell assay was used to analyze cell migration and invasion. Xenograft experiment was used to test tumor growth in vivo.

Results: LINC00339 overexpression was correlated with an advanced stage, metastasis, and bad prognosis in HCC patients. Functional investigation showed that LINC00339 knockdown significantly suppressed HCC cell proliferation, migration, and invasion. Moreover, decreased LINC00339 expression inhibited HCC growth in vivo. Mechanistically, LINC00339 could interact with miR-1182 to promote SKA1 expression. We also demonstrated that SKA1 acted as an oncogene and SKA1 upregulation reversed the effect of LINC00339 silencing.

Conclusion: Our results illustrated that the LINC00339/miR-1182/SKA1 axis plays an essential role in HCC progression.

Increased expression of SLC46A3 to oppose the progression of hepatocellular carcinoma and its effect on sorafenib therapy

Hepatocellular carcinoma (HCC) prognosis remains dismal due to postsurgical recurrence and distant metastasis. Therefore, novel prognostic biomarkers and therapeutic targets for HCC therapy are urgently needed to improve the survival of liver cancer patients. Our evidence suggests that SLC46A3 (the gene solute carrier family 46 (sodium phosphate), member 3) is a member of the SLC46 family and has a potential role in the progression and treatment of HCC. The objective of the present study was to estimate the expression pattern and biological function of SLC46A3 in the progression of HCC, which may serve as a promising biomarker for diagnosis and therapy. In order to determine the expression pattern of SLC46A3 in HCC, several public HCC databases and tissue chips were used to examine 129 sets of primary HCC and non-tumor adjacent tissues from patients who had undergone surgery. The expression of SLC46A3 in 80 sets of HCC and non-tumor adjacent tissues were then compared by RT-PCR and Western Blot. The proliferation, invasion, migration and sphere-forming abilities of SLC46A3 knock-down and overexpressing cell lines were evaluated and the expression of related molecules in the epithelial mesenchymal transition (EMT) were detected by RT-PCR, western blot and immunofluorescence assay. The IC₅₀ value was used to evaluate the effect of SLC46A3 on sorafenib resistance. A lung metastasis model of mice HCC was constructed to test the potential effect of SLC46A3 on cancer metastasis and a subcutaneous xenografted tumor mice model was designed to verify the effect of SLC46A3 on the resistance of HCC cell lines to sorafenib. The expression of SLC46A3 was down-regulated in 83.2% of human HCC tissues compared to non-tumor adjacent tissues. Tumors that expressed low levels of SLC46A3 had more aggressive phenotypes, and patients with these tumors had shorter survival times after surgery compared to patients whose tumors expressed high levels of SLC46A3. Hepatocellular carcinoma cell lines that stably overexpressed SLC46A3 inhibited the levels of migration and invasion compared with control HCC cells, and formed smaller xenograft tumors with more metastases in mice compared with HCC cells that did not overexpress SLC46A3. In addition, overexpression of SLC46A3 obviously inhibited epithelial-to-mesenchymal transition-activating transcription factors such as N-cadherin and Vimentin. Furthermore, descended of IC₅₀ showed that overexpressed SLC46A3 could reduce sorafenib resistance and improve drug response in vivo and in vitro. In conclusion, increased expression of SLC46A3 could favor a better clinical prognosis for patients with HCC, ameliorate sorafenib resistance, and improve drug response. SLC46A3 might serve as a potential prognostic biomarker and therapeutic target in HCC.

LncRNA HOTAIR contributes to the malignancy of hepatocellular carcinoma by enhancing epithelial-mesenchymal transition via sponging miR-23b-3p from ZEB1

Hepatocellular carcinoma (HCC) is the fifth most common cancer around the world, along with high mortality and metastasis rate. Our present study aimed to explore the role of LncRNA HOTAIR in the progression of HCC. Our data showed that HOTAIR was overexpressed in HCC tissues and cell lines (Huh7, Hep3B, HepG2, MHCC97H). Overexpressed HOTAIR promoted invasion and migration of HCC cells (Huh7) by enhancing epithelial-mesenchymal transition (EMT). Besides that, miR-23b-3p was predicted to be a target of HOTAIR and decreased expression of miR-23b-3p was observed in HCC tissues and cell lines. The up-regulation of HOTAIR strongly decreased the expression of miR-23b-3p. The further luciferase report confirmed the targeting reaction between HOTAIR and miR-23b-3p, suggesting that the expression of miR-23b-3p was negatively regulated by HOTAIR. Moreover, the zinc-finger E-box-binding homeobox 1 (ZEB1) protein was predicted to be a target of miR-23b-3p. The expression of ZEB1 was negatively regulated by miR-23b-3p while positively regulated by HOTAIR. Besides that, transfection with miR-23b-3p mimic counteracted the promoting effects of HOTAIR on invasion, migration and EMT of HCC cells. Our in vitro experiments suggested that HOTAIR promoted invasion and migration of HCC cells through enhancing EMT via sponging miR-23b-3p from ZEB1. Finally, the in vivo experiments indicated that HOTAIR could promote metastasis of HCC by enhancing EMT in vivo. Taken together, our study demonstrated that the HOTAIR-miR-23b-3p-ZEB1 axis may provide a new perspective for treatment of HCC.

HOTAIR, a long non-coding RNA driver of malignancy whose expression is activated by FOXC1, negatively regulates miRNA-1 in hepatocellular carcinoma

Evidence is rapidly accumulating that long non-coding RNAs (lncRNAs) are involved in human tumorigenesis and are dysregulated in multiple cancers, including hepatocellular carcinoma (HCC). lncRNAs can regulate essential pathways that contribute to tumor initiation and progression with tissue specificity, which suggests that lncRNAs may be valuable biomarkers and therapeutic targets. HOX transcript antisense intergenic RNA (HOTAIR) has previously been demonstrated to be an oncogene and a negative prognostic factor in a variety of cancers; however, the factors that contribute to the upregulation of HOTAIR and the interaction between HOTAIR and microRNAs (miRNAs or miRs) are largely unknown. In the present study, the expression levels of HOTAIR, forkhead box C1 (FOXC1) and miRNA-1 were examined in 50 matched pairs of HCC and HCC cells. The effects of HOTAIR on HCC cell proliferation were tested using trypan blue exclusion assay. The effect of HOTAIR on HCC growth in vivo was determined in a (nu/nu) mouse model. A computational screening of HOTAIR promoter was conducted to search for transcription factor-binding sites. FOXC1 binding to the promoter region of HOTAIR was confirmed using a chromatin immunoprecipitation assay. A search for miRNAs that had complementary base paring with HOTAIR was performed utilizing an online software program. The interaction between miR-1 and HOTAIR was examined using a luciferase reporter assay. Gain and loss of function approaches were used to determine the changes of HOTAIR or miR-1 expression. The relative levels of FOXC1 and HOTAIR expression in HCC tissues and HepG2 cells were significantly higher than those in normal liver LO2 cells and adjacent carcinoma tissues; the relative expression of miR-1 exhibited the opposite pattern. Overexpression of HOTAIR promoted HCC cell proliferation and progression of tumor xenografts. The present authors have demonstrated that FOXC1 binds to the upstream region of HOTAIR in HCC cells and that FOXC1 activates lncRNA HOTAIR expression in HCC HepG2 cells, which suggests that HOTAIR harbors a miRNA-1 binding site. The present data revealed that this binding site is vital for the regulation of miRNA-1 by HOTAIR. Furthermore, HOTAIR negatively regulated the expression of miRNA-1 in HepG2 cells. Additionally, the present study demonstrated that the oncogenic activity of HOTAIR is in part based on the negative regulation of miR-1. Taken together, these results suggest that HOTAIR is a FOXC1-activated driver of malignancy, which acts in part through the repression of miR-1.