Epigenetic biomarkers in liver cancer

circRNA_PTPRA functions as a sponge of miR-582-3p to regulate hepatocellular carcinoma cell proliferation, migration, invasion and apoptosis

Hepatocellular carcinoma (HCC) is a lethal disease and one of the most common types of cancer. HCC is associated with exponentially increasing morbidity and mortality rates. Accumulating evidence has identified circular RNAs (circRNAs) to be regulators of cancer progression. However, to the best of our knowledge, the potential effect of circRNA protein tyrosine phosphatase receptor type A (circRNA_PTPRA) in HCC and its mechanism remain unknown. The present study aimed to assess the effects and underlying mechanism of circRNA_PTPRA in a HCC Huh-7 cells model. The sites of interaction between circRNA_PTPRA and microRNA (miR)-582-3p were predicted using the StarBase software and verified using dual luciferase reporter and RNA immunoprecipitation (RIP) assays in Huh-7 cells. HCC cell viability, apoptosis, migration and invasion were measured using MTT, flow cytometry and Transwell assays, respectively. The expression levels of circRNA_PTPRA, miR-582-3p, cyclin D1, MMP-9, Bcl-2 and Bax were analyzed using reverse transcription-quantitative PCR and western blotting. The results of the dual luciferase reporter and RIP assays demonstrated that miR-582-3p directly targeted circRNA_PTPRA. Compared with the human normal hepatocyte cell line, THLE-2, the expression levels of circRNA_PTPRA were upregulated, which were found to be inversely correlated with those of miR-582-3p expression in Huh-7 and HCCLM3 cells. miR-582-3p overexpression using mimics suppressed cell proliferation, migration and invasion, whilst downregulating cyclin D1 and MMP-9 expression in Huh-7 cells. In addition, transfection of HCC cells with the miR-582-3p mimic promoted apoptosis by downregulating Bcl-2 expression and upregulating Bax expression in Huh-7 cells. Knocking down circRNA_PTPRA expression using small interfering RNA (siRNA) markedly downregulated circRNA_PTPRA expression levels and upregulated miR-582-3p expression, but was reversed by co-transfection with the miR-582-3p inhibitor. Furthermore, reduced HCC cell proliferation, migration and invasion, increased levels of cell apoptosis, upregulated Bax expression and downregulated cyclin D1, MMP-9 and Bcl-2 expression were all observed after knocking down circRNA_PTPRA. All these effects aforementioned were reversed by co-transfection with the miR-582-3p inhibitor. In conclusion, findings from the present study suggested that circRNA_PTPRA may regulate HCC cell proliferation, invasion, apoptosis and migration by sponging miR-582-3p. This indicates that the circRNA_PTPRA/miR-582-3p axis may represent a potential target for HCC diagnosis and treatment.

Long non-coding RNA-based signature for predicting prognosis of hepatocellular carcinoma

Long non-coding RNAs (lncRNAs), as one common type of non-coding RNAs, play a critical role in the tumorigenesis and development of hepatocellular carcinoma (HCC). In the current study, we aimed to assess the correlation between lncRNAs expression levels and prognosis of HCC patients. A lncRNA-based signature was also developed to predict the prognosis of HCC in this work. The lncRNAs expression profiles in tissues of tumor and para-carcinoma were obtained from The Cancer Genome Atlas (TCGA) database. The lncRNA-based prognostic model was established by least absolute shrinkage and selection operator (LASSO). The multivariate Cox-regression analysis was applied to identify the independent risk factors and subsequently developed a prognostic nomogram. Based on the co-expression analyses, we identified the lncRNA-related mRNAs and performed the biological function analysis. Between HCC and para-carcinoma tissues, 220 differentially expressed lncRNAs were filtered. Among these lncRNAs, 19 lncRNAs were identified as prognostic factors and were used to build a prognostic signature of overall survival (OS). Furthermore, a nomogram with high performance for predicting the OS of HCC patients (C-index: 0.779) by combining the 19-lncRNA signature (P < 0.001) and clinicopathologic factors including HBV (P = 0.005) and stage (P =0.017) was established. Functional enrichment analysis revealed that 19 lncRNAs had potential effects on tumor cell proliferation in HCC. In summary, we established a 19-lncRNA signature to predict the prognosis of HCC patients, which may perform a crucial role in guiding the management of HCC.

A signature of 13 autophagy‑related gene pairs predicts prognosis in hepatocellular carcinoma

Growing evidences suggest that autophagy plays a momentous part in the tumorigenesis and development of hepatocellular carcinoma (HCC). However, there are not many researches to predict the prognosis of HCC using autophagy-related genes. Therefore, based on the clinical information and RNA-Seq data of The Cancer Genome Atlas data portal (TCGA), 13 autophagy‑related gene pairs were screened to build the autophagy‑related signature to predict the prognosis by least absolute shrinkage and selection operator (LASSO) regression analysis. Besides, the International Cancer Genome Consortium (ICGC) cohort was further applied to verify the autophagy‑related prognostic signature. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA) were also used to predict the relevant function of the autophagy-related gene pairs signature. As shown in the results, the autophagy-related gene pairs were mainly involved in process utilizing autophagic mechanism, autophagy, macroautophagy and cellular response to oxidative stress. The immune cell levels in the high-risk and low-risk group were explored, which showed that the three immune cells were obviously increased in the high-risk group, while the five immune cells were obviously increased in the low-risk group. In conclusion, an autophagy‑related prognostic signature was established to predict the prognosis of HCC patients with great accuracy and we found that autophagy‑related prognostic signature was related to infiltrating immune cells.

High expression of the TEFM gene predicts poor prognosis in hepatocellular carcinoma

BACKGROUND

Mitochondrial transcription elongation factor (TEFM) is an essential molecule that regulates the replication-transcription switch of mitochondrial DNA. TEFM modulates both transcription elongation and RNA processing in mitochondria. The purpose of the present study was to determine the association of TEFM with tumor progression and prognosis in hepatocellular carcinoma (HCC) patients.

METHODS

The different protein expression level of TEFM among HCC cell lines was detected by Western blotting. The gene expression profiling interactive analysis (GEPIA) was used to dynamically analyze the mRNA expression of TEFM gene in different stages of HCC. The protein and mRNA expression levels of TEFM were detected by immunohistochemistry, Western blotting and qRT-PCR. The mRNA-SeqV2 expression of TEFM and clinical information of HCC patients were downloaded from the TCGA database by using R3.6.3 software. Next, the relationships between the expression level of TEFM and clinicopathological characteristics and the prognostic value of TEFM were analyzed. A Cox regression model was used for multivariate analysis of the factors that affected the prognosis of HCC. Finally, the association between the expression levels of TEFM and other mitochondrial regulatory genes and HCC biomarker genes was analyzed by GEPIA.

RESULTS

TEFM is upregulated in HCC cell lines compared to noncancerous liver cell line. TEFM protein and mRNA expression levels in HCC tissues were significantly upregulated compared with those in noncancerous liver tissues. In addition, the mRNA expression level of TEFM was significantly correlated with sex, serum AFP level, and vascular invasion (P<0.05). Further analysis showed that high expression level of TEFM was unfavorable in terms of the prognosis of patients with HCC. Cox multivariate regression analysis showed that patient age, vascular invasion, and TEFM expression were independent factors affecting the prognosis of HCC patients (P<0.05). The expression level of the TEFM gene was significantly positively correlated with the expression of multiple mitochondrial regulatory genes and biomarker genes of HCC (P<0.01, R>0).

CONCLUSIONS

Our findings reveal that TEFM may play an important role in the progression of HCC. More importantly, the elevated expression of TEFM may potentially predict poor overall survival (OS) and disease-free survival (DFS) in patients with HCC.

MicroRNAs alteration as early biomarkers for cancer and neurodegenerative diseases: New challenges in pesticides exposure

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Current knowledge linking pesticide exposure, cancer and neuro-degenerative diseases to dysregulation of microRNA network was summarized.

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Literature indicates differential miRNA expression targeting biomolecules and pathways involved in cancer and neurodegenerative diseases.

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Evaluation of miRNA expression may be used to develop new non-invasive strategies for the prediction and prognosis of diseases including cancer.

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The application of miRNAs as diagnostic and therapeutic biomarkers in the clinical field is extremely challenging.

This review summarizes the current knowledge linking cancer and neuro-degenerative diseases to dysregulation of microRNA network following pesticide exposure. Most findings revealed differential miRNA expression targeting biomolecules and pathways involved in various neoplastic localizations and neurodegenerative diseases.

A growing body of evidence in recent literature indicates that alteration of specific miRNAs can represent an early biomarker of disease following exposure to chemical agents, including pesticides. Different miRNAs seem to regulate cell proliferation, apoptosis, migration, invasion, and metastasis via many biological pathways through modulation of the expression of target mRNAs.

The evaluation of miRNA expression levels may be used to develop new non-invasive strategies for the prediction and prognosis of many diseases, including cancer. However, the application of miRNAs as diagnostic and therapeutic biomarkers in the clinical field is extremely challenging.

Inhibiting effect of MicroRNA-3619-5p/PSMD10 axis on liver cancer cell growth in vivo and in vitro

AIMS

Liver cancer is one of the leading causes of cancer death worldwide owing to its delayed diagnosis and absence of efficient treatment at advanced TNM stages. Increasing evidence demonstrated that microRNAs are implicated in tumorgenesis and cancer development by regulating cancer-related proteins. This study aimed to explore the effect of miR-3619-5p on cell growth in liver cancer.

MAIN METHODS

The effect of miR-3619-5p on cell proliferation was measured by quantitative real-time PCR, MTT assay, flow cytometry, and Immunofluorescence assay. The interaction between miR-3619-5p and PSMD10 was validated using dual-luciferase. The expression of PSMD10 and Ki67 was further determined by immunohistochemistry.

KEY FINDINGS

MiR-3619-5p over-expression remarkably inhibited cell proliferation and induced G1 phase arrest, accompanied with reduced expression of proliferating cell nuclear antigen. The expression of miR-3619-5p was negatively correlated to that of PSMD10, and PSMD10 was validated to be a downstream target of miR-3619-5p. Moreover, miR-3619-5p induced suppressed proliferation and G1 phase arrest were abrogated by elevated the expression of PSMD10 in liver cancer cells. PSMD10 over-expression also induced phosphorylation of signal transducer and activator of transcription 3 (STAT3) and retinoblastoma protein (Rb1). Besides, elevated cyclin A, cyclin D1 and cyclin E expression supported that PSMD10 promoted the progress of cell cycle. In addition, miR-3619-5p inhibited tumor growth in vivo by targeting PSMD10, accompanied with blocked cell cycle.

SIGNIFICANCE

In conclusion, our findings revealed that miR-3619-5p inhibits cancer cell proliferation by targeting PSMD10, and miR-3619-5p as a potential therapeutic target for the treatment of liver cancer.

Induction of cancer cell stemness by depletion of macrohistone H2A1 in hepatocellular carcinoma

Hepatocellular carcinomas (HCC) contain a subpopulation of cancer stem cells (CSCs), which exhibit stem cell-like features and are responsible for tumor relapse, metastasis, and chemoresistance. The development of effective treatments for HCC will depend on a molecular-level understanding of the specific pathways driving CSC emergence and stemness. MacroH2A1 is a variant of the histone H2A and an epigenetic regulator of stem-cell function, where it promotes differentiation and, conversely, acts as a barrier to somatic-cell reprogramming. Here, we focused on the role played by the histone variant macroH2A1 as a potential epigenetic factor promoting CSC differentiation. In human HCC sections we uncovered a significant correlation between low frequencies of macroH2A1 staining and advanced, aggressive HCC subtypes with poorly differentiated tumor phenotypes. Using HCC cell lines, we found that short hairpin RNA-mediated macroH2A1 knockdown induces acquisition of CSC-like features, including the growth of significantly larger and less differentiated tumors when injected into nude mice. MacroH2A1-depleted HCC cells also exhibited reduced proliferation, resistance to chemotherapeutic agents, and stem-like metabolic changes consistent with enhanced hypoxic responses and increased glycolysis. The loss of macroH2A1 increased expression of a panel of stemness-associated genes and drove hyperactivation of the nuclear factor kappa B p65 pathway. Blocking phosphorylation of nuclear factor kappa B p65 on Ser536 inhibited the emergence of CSC-like features in HCC cells knocked down for macroH2A1. Conclusion: The absence of histone variant macroH2A1 confers a CSC-like phenotype to HCC cells in vitro and in vivo that depends on Ser536 phosphorylation of nuclear factor kappa B p65; this pathway may hold valuable targets for the development of CSC-focused treatments for HCC. (Hepatology 2018;67:636-650).

Study on the diagnosis of small hepatocellular carcinoma caused by hepatitis B cirrhosis via multi-slice spiral CT and MRI

The present study compared the diagnostic accuracy of multi-slice spiral computed tomography (CT) and magnetic resonance imaging (MRI) on small hepatocellular carcinoma (SHCC) caused by hepatitis B cirrhosis. A total of 160 patients with hepatitis B cirrhosis were selected between January 2012 and April 2016, and 183 SHCC lesions were included in the present retrospective study. Patients were divided into the SHCC group (T stage) and the micro hepatocellular carcinoma (MHCC) group (T1 stage). There were a total of 129 SHCC lesions and 54 MHCC lesions identified. All patients underwent multiphasic CT and MRI imaging. The liver acquisition with volume acquisition (LAVA) technique was utilized for MRI. Furthermore, SPSS 20.0 was used for statistical analyses. LAVA in the arterial phase and CT in the arterial phase revealed significantly higher diagnostic rates for the diagnoses of 183 lesions. In addition, standard CT scan exhibited significantly reduced diagnostic rates in SHCC lesions. Results indicated that LAVA in the equilibrium phase had the lowest diagnostic rate in MHCC lesions, which was statistically significant (P<0.05). Overall, the diagnostic rate of CT (79.63%) for MHCC was significantly lower than that of MRI (96.29%) (P<0.05). However, the diagnostic rate of CT for SHCC (96.12%) was significantly higher than that for MHCC (79.63%) (P<0.05). MRI-LAVA in the arterial phase has the highest diagnostic rate for SHCC and MHCC. However, the diagnostic capability of MRI for MHCC lesions is superior to that of CT.

Radiotherapy for Hepatocellular Carcinoma: New Indications and Directions for Future Study

Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide; its incidence is increasing in the United States. Depending on disease extent and underlying liver status, patients may be treated with local, locoregional, and/or systemic therapy. Recent data indicates that radiotherapy (RT) can play a meaningful role in the management of HCC. Here, we review published experiences using RT for HCC, including the use of radiosensitizers and stereotactic RT. We discuss methods for performing preclinical studies of RT for HCC and biomarkers of response. As a part of the HCC Working Group, an informal committee of the National Cancer Institute's Radiation Research Program, we suggest how RT should be implemented in the management of HCC and identify future directions for the study of RT in HCC.