Hepatocellular carcinoma: molecular and genomic guideline for the clinician

Expression and prognostic signatures of m6A-related lncRNAs in hepatocellular carcinoma

BACKGROUND

N6-methyladenosine (m6A) is a common modification and plays an important role in various biological processes, but m6A-related lncRNA functions in hepatocellular carcinoma (HCC) have not been systematically clarified.

METHODS

The clinical data and RNA-seq transcriptome of 375 cases of HCC and 50 cases of normal tissues were obtained from the Cancer Gene Atlas database. Co-expression analysis was used to obtain m6A-related lncRNA. The independent prognostic factors were identified by univariate and multivariate Cox regression models. Kaplan-Meier method was used in survival analysis. The core gene of the mRNA-mRNA interaction network is related to m6A-related lncRNAs obtained by the CytoHubba plugin of Cytoscape. Gene ontology and Kyoto Gene Encyclopedia were analyzed to find out the potential mechanism. CIBERSORT algorithm was used to calculate the relative proportion of immune infiltrating cells.

RESULTS

We identified two subgroups (cluster 1 and cluster 2) according to the expression level. The survival analysis curve and receiver operating characteristic curve proved that this model could predict the prognosis of HCC patients. The univariate and multivariate Cox regression analyses showed the independent prognostic value. UBE2C was screened as the pivotal gene. The expression level of m6A-related lncRNAs causes changes in the tumor immune microenvironment.

CONCLUSION

The expression levels of m6A-related lncRNAs were significantly different and the prognostic value of m6A-related lncRNAs was confirmed. The m6A-related lncRNAs are expected to be prognostic signatures in HCC.

Identification of a novel anti-EGFR nanobody by phage display and its distinct paratope and epitope via homology modeling and molecular docking

Since EGFR is an important and effective target for tumor therapy in the clinic. Several monoclonal antibodies and nanobodies were proved to target domain III of EGFR. Regarding the increased attention on nanobodies, the present study aimed to generate nanobodies specifically against domain III. After camel immunization, a gene repertoire of sdAb fragments with a diversity of 3×10⁹ clones was produced. Following the construction of two sdAb phage display libraries, the successful epitope binning was carried out to identify the nanobody with the designated epitope. Modelling of the identified nanobody and molecular docking studies illustrated the paratope and epitope. Docking analysis revealed that the paratope focused on CDR2 loop of the identified nanobody. The identified nanobody potently cover part of the epitope of Matuzumab and Nb 9G8, which indicated that it blocked EGFR by preventing dimerization of the receptors.

Expression Pattern and Prognostic Value of Key Regulators for m6A RNA Modification in Hepatocellular Carcinoma

As the most prevalent type of mRNA modification in mammals, N6-methyladenosine (m6A) is involved in various biological processes. Accumulating studies have indicated that the deregulation of m6A RNA modification is linked to cancer and other diseases. However, its implications in hepatocellular carcinoma (HCC) remain poorly characterized. Herein, we sought to investigate the expression pattern of 13 key regulators for m6A RNA modification and to evaluate their prognostic value in HCC. First, we systematically analyzed data from The Cancer Genome Atlas (TCGA) database pertaining to patient clinical information and mRNA gene expression data. We found that 11 out of 13 key regulators for m6A RNA modification showed significantly higher expression levels in HCC. Subsequently, we identified two subgroups (clusters 1 and 2) via consensus clustering based on the expression of 13 m6A RNA methylation regulators. Cluster 2 had a worse prognosis and was also significantly correlated with higher histological grade and pathological stage when compared with cluster 1. Moreover, cluster 2 was remarkedly enriched for cancer-related pathways. We further constructed a robust risk signature of five regulators for m6A RNA modification. Further analysis indicated that this risk signature could be an independent prognostic factor for HCC, and the prognostic relevance of this five-gene risk signature was successfully validated using the Gene Expression Omnibus (GEO) dataset. Finally, we established a novel prognostic nomogram on the basis of age, gender, histological grade, pathological stage, and risk score to precisely predict the prognosis of patients with HCC. In summary, we herein uncovered the vital role of regulators for m6A RNA modification in HCC and developed a risk signature as a promising prognostic marker in HCC patients.

Imaging biomarkers for well and moderate hepatocellular carcinoma: preoperative magnetic resonance image and histopathological correlation

Background

Our aim of the study is to investigate the feasibility of preoperative prediction for hepatocellular carcinoma (HCC) histological grading using gadoxetic acid-enhanced magnetic resonance imaging (MRI).

Methods

This study included one hundred and fifty-six patients with solitary HCC. Preoperative gadoxetic acid-enhanced MRI findings were retrospectively analyzed. MRI qualitative features such as tumor size, margin, capsule status, signal homogeneity, intratumoral vessels, peritumoral enhancement during mid-arterial phase, peritumoral hypointensity during the hepatobiliary phase (HBP) were investigated. Apparent diffusion coefficients (ADCs), T1 reduction ratio of pre- and post-contrast enhanced images of the tumors were calculated. HCC histological grading in surgical specimens were confirmed by Edmonson’s criteria. Correlations between these MRI features and HCC histological grading were analyzed using multivariate logistic regression. The receiver operating characteristic (ROC) curve was used to assess the predictive efficacy of the model.

Results

Univariate analysis showed that maximum tumor diameter (p = 0.004), tumor margin (p = 0.006), intratumoral vessels (p = 0.001) and peritumoral hypointensity during HBP (p = 0.000), were significantly correlated with HCC histological grading. There was no relationship between capsule, tumor signal, venous thrombosis, peritumoral enhancement during mid-arterial phase, ADC value, T1 reduction ratio, and HCC histological grading. Multivariate logistic regression analysis demonstrated that the maximum tumor diameter (p = 0.012, odds ratio = 1.002, 95% confidence interval: 1.007–1.046)) was an independent risk factor for high grade HCC.

Conclusions

Greater tumor size, a more irregular margin, presence of intratumoral vessels, and peritumoral hypointensity during HBP were indicators for high grade HCC. The maximum tumor diameter was an independent risk factor for high grade HCC.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-5574-8) contains supplementary material, which is available to authorized users.

The different expression of tumor suppressors, RASSF1A, RUNX3, and GSTP1, in patients with alcoholic steatohepatitis (ASH) vs non-alcoholic steatohepatitis (NASH)

As the fifth most common cancer and the second leading cause of cancer related deaths worldwide, hepatocellular carcinoma (HCC) causes up to one million deaths annually. Alcoholic steatohepatitis (ASH) and non-alcoholic steatohepatitis (NASH) are becoming the two major risk factors because both may develop liver fibrosis and hepatocellular carcinoma (HCC) if left untreated. However, compared with 3-10% of patients with ASH may progress to HCC annually, about only 0.5% NASH patients may progress to HCC annually. The present study is to clarify the protein expression differences of tumor suppressor genes (TSGs) between ASH and NASH. In liver biopsied specimens from NASH and ASH patients, using an immunofluorescence method and morphometrically quantitating the fluorescence intensity, we studied the protein expression within hepatocytes cytoplasm of candidate TSGs including RUNX3, GSTP1, and RASSF1A. Compared with the control group of patients, the expression levels of all three proteins were upregulated in the ASH group of patients (p < .001 in all molecules). While RUNX3 was upregulated, GSTP1 and RASSF1 did not change in the NASH group of patients. The most important finding is that compared with the ASH group of patients, the expression levels of all three TSG proteins, RUNX3, GSTP1, and RASSF1, were significantly lower in the NASH group of patients (p < .001 in all three molecules). These results confirmed our previous finding that there are significant differences of many molecules including TSGs that changed in NASH compared to ASH. Thus, we conclude that there are significantly different TSGs and pathways involved during the pathogenesis of HCC development in NASH compared to ASH that may help to develop different strategies for prevention and treatment of NASH and ASH patients.

Novel approaches for molecular targeted therapy against hepatocellular carcinoma

Systemic chemotherapy using a multitargeted tyrosine kinase inhibitor is an established treatment for advanced-stage tumors in various organs. Comprehensive genomic analyses using next-generation sequencing technology revealed the intra- and intertumor heterogeneity of human hepatocellular carcinomas (HCCs), and provided evidence for the use of therapeutic agents effective against multiple targets in tumor cells. Recently, the efficacy and safety of a multitargeted tyrosine kinase inhibitor, lenvatinib, was confirmed by a randomized global phase III trial; thus, lenvatinib was approved as first-line therapy for HCC, providing a new therapeutic option for patients at an advanced stage. In this article, we introduce the application of molecular targeted therapy using lenvatinib and discuss future aspects of therapeutic options for advanced HCC.

Epigenetic silencing of PRSS3 provides growth and metastasis advantage for human hepatocellular carcinoma

Protease, serine, 3 (PRSS3), a member of the trypsin family of serine proteases, has been shown to be aberrantly expressed in several cancer types and to play important roles in tumor progression and metastasis. However, the expression and function of PRSS3 gene in hepatocellular carcinoma (HCC) remain unclear. Here we found that PRSS3 expression was decreased in human HCC cell lines and HCC surgical specimens. This was associated with intragenic methylation of PRSS3 gene. Treatment with DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine and/or histone deacetylase inhibitor trichostatin A restored PRSS3 expression in HCC cell lines. Ectopic overexpression of PRSS3 gene in HCC cell lines significantly suppressed cell proliferation and colony formation and arrested cell cycle at G1/S phase, accompanied with downregulation of cyclin D1 (CCND1)/CDK4 and cyclin E1 (CCNE1)/CDK2 complexes. Moreover, PRSS3 overexpression in HCC cells inhibited HCC cell migration and invasion with downregulation of matrix metallopeptidase 2 (MMP2). Further study showed that PRSS3 overexpression diminished the phosphorylation of mitogen-activated protein kinase/extracellular-signal-regulated kinase signaling protein, mitogen-activated protein kinase kinase 1 (MEK1)/mitogen-activated protein kinase kinase 2 (MEK2) and extracellular-signal related kinase 1 (ERK1)/extracellular-signal related kinase 2 (ERK2), in HCC cells. In contrast, knockdown of PRSS3 by small interfering RNA resulted in opposite effects on an HCC cell line SNU-387 which constitutively expresses PRSS3. These results demonstrate that downregulation of PRSS3 by intragenic hypermethylation provides growth and metastasis advantage to HCC cells. The clinical relevance of PRSS3 to human HCC was shown by the intragenic methylation of PRSS3 in HCC specimens and its association with poor tumor differentiation in patients with HCC. Thus, PRSS3 is a potential prognostic biomarker and an epigenetic target for intervention of human HCC.

KEY MESSAGES

• PRSS3 is downregulated by intragenic hypermethylation in HCC. • Epigenetic silencing of PRSS3 facilitates growth, migration, and invasion of HCC. • PRSS3 intragenic methylation has implication in diagnosis of HCC.

Biomarkers for Hepatocellular Carcinoma (HCC): An Update

The past decades have witnessed increased use of biomarkers in disease management. A biomarker is any characteristic that can be objectively measured and evaluated as an indicator of normal biological process, pathogenic process, or pharmacological response to a therapeutic intervention. The clinical measurements of biomarkers can be carried out in vivo using imaging modalities like ultrasound (US), computed tomography (CT), and magnetic resonance imaging (MRI), as well as in vitro utilizing serum or plasma or other body fluids as specimens. In contrast to the imaging modalities, a prominent value of serum biomarkers is that they could be biologically relevant and disease-specific to pathophysiologic or pathologic process of disease development. This article provides an update of serum biomarkers for hepatocellular carcinoma (HCC) in risk assessment for early detection through surveillance.

CT and MR imaging diagnosis and staging of hepatocellular carcinoma: part I. Development, growth, and spread: key pathologic and imaging aspects

Computed tomography (CT) and magnetic resonance (MR) imaging play critical roles in the diagnosis and staging of hepatocellular carcinoma (HCC). The first article of this two-part review discusses key concepts of HCC development, growth, and spread, emphasizing those features with imaging correlates and hence most relevant to radiologists; state-of-the-art CT and MR imaging technique with extracellular and hepatobiliary contrast agents; and the imaging appearance of precursor nodules that eventually may transform into overt HCC.

Inhibition of Annexin A2 gene transcription is a promising molecular target for hepatoma cell proliferation and metastasis

Hepatocyte Annexin A2 (ANXA2) expression is associated with the progression and metastasis of hepatocellular carcinoma (HCC). Circulating ANXA2 levels in HCC patients are significantly higher compared with that of patients with benign liver disease. ANXA2 levels have been found to correlate with hepatitis B virus infection, extrahepatic metastasis and portal vein thrombus. By contrast, ANXA2 levels do not correlate with tumour size and AFP levels. However, the underlying mechanisms of ANXA2 remain obscure. The results of the current study identified that abnormalities in hepatic ANXA2 expression were localised to the cell membrane and cytoplasm of HCC tissues and mainly in the cytoplasm of para-cancerous tissues. ANXA2 was overexpressed in MHCC97-H cells which have high metastatic potential. Following specific ANXA2-small hairpin RNA (shRNA) transfection in vitro, ANXA-2 was effectively inhibited and the S phase ratio of cells was 27.76%, compared with 36.14% in mock-treated cells. In addition, the invading cell ratio was reduced in the shRNA-treated group (52.16%) compared with the mock-treated group (86.14%). The growth and volume of xenograft tumours in vivo was significantly suppressed (P<0.05) in the shRNA group compared with that of the mock group, indicating that ANXA2 may be a novel and useful target for elucidating molecular mechanisms involving the proliferation and metastasis of HCC.

Beclin 1 and nuclear factor-κBp65 are upregulated in hepatocellular carcinoma

There are no sensitive and specific biomarkers that aid in the clinical diagnosis and prognosis of hepatocellular carcinoma (HCC). The aim of the present study was to determine the mRNA and protein expression levels of beclin 1 (BECN1) and nuclear factor-κB (NF-κB)p65 in patients with HCC, to evaluate their value as potential diagnostic and prognostic biomarkers. Immunohistochemistry and in situ hybridization were used to detect the expression of hepatic BECN1 and NF-kBp65 in patients with HCC, hepatitis B virus (HBV) or cirrhosis, as compared with the expression levels in healthy subjects. The expression level of the BECN1 protein in the HCC tissue was significantly high compared with that in the cirrhotic, hepatitis and normal tissues. The expression of the BECN1 protein in the hepatitis tissue was significantly high compared with that of the cirrhotic and normal tissues. The expression of the BECN1 mRNA in the cancer tissue was significantly high compared with that of the cirrhotic and normal tissues, and the expression of the BECN1 mRNA in the hepatitis tissue was significantly higher than that of the cirrhotic and normal tissues. The expression of the NF-κBp65 protein in the cancer tissue was significantly high compared with that of the cirrhotic, hepatitis and normal tissues. The expression of the NF-κBp65 mRNA in-the cancer tissue was significantly high compared with that of the cirrhotic, hepatitis and normal tissues. BECN1 expression was positively correlated with NF-κBp65 expression in HCC. The abnormal expression of BECN1 and NF-κBp65 was closely associated with the development of HCC. Finally, a search in GeneGo pathway database observed a link between BECN1 and NF-κBp65 through multiple proteins. These results indicate that BECN1 and NF-κBp65 are upregulated in HCC, and that they may serve as useful biomarkers for HCC.

Targeted glypican-3 gene transcription inhibited the proliferation of human hepatoma cells by specific short hairpin RNA

Hepatocellular carcinoma (HCC) is a highly chemoresistant cancer with no effective systemic therapy. Despite of surgical or locoregional therapies, prognosis remains poor because of high tumor recurrence or progression, and currently, there are no well-established effective adjuvant therapies. Glypican-3 (GPC-3) is specifically overexpressed in hepatoma and perhaps is a valuable molecular target for HCC therapy. In this present study, the effect of silencing GPC-3 gene transcription on human HepG2 cell proliferation was investigated by constructing GPC-3 short hairpin RNA (shRNA) plasmid. After HepG2 cells were transfected with the most efficient shRNA, GPC-3 mRNA expression (90.4 %) was inhibited significantly and estimated by fluorescence quantitative reverse transcriptase-polymerase chain reaction, and the result was accordance with downregulation at the protein level. The percentage of the cell proliferation was down to 28.9 % in the shRNA group and 19.9 % in the shRNA plus sorafenib group. The cell cycles were arrested in the G₁ phase (65.6 %) and the apoptosis rate was increasing (66.75 %) in the shRNA1 group with significant alteration compared with that in the negative-shRNA group. Specific shRNA might intervene effectively GPC-3 activation and inhibit tumor cell proliferation, suggesting that GPC-3 gene should be a potential molecular target for HCC therapy.