Expression and significance of the novel tumor-suppressor gene SMG-1 in hepatocellular carcinoma

DNA and RNA Binding Proteins: From Motifs to Roles in Cancer

DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.

Discovery of new therapeutic targets in ovarian cancer through identifying significantly non-mutated genes

BACKGROUND

Mutated and non-mutated genes interact to drive cancer growth and metastasis. While research has focused on understanding the impact of mutated genes on cancer biology, understanding non-mutated genes that are essential to tumor development could lead to new therapeutic strategies. The recent advent of high-throughput whole genome sequencing being applied to many different samples has made it possible to calculate if genes are significantly non-mutated in a specific cancer patient cohort.

METHODS

We carried out random mutagenesis simulations of the human genome approximating the regions sequenced in the publicly available Cancer Growth Atlas Project for ovarian cancer (TCGA-OV). Simulated mutations were compared to the observed mutations in the TCGA-OV cohort and genes with the largest deviations from simulation were identified. Pathway analysis was performed on the non-mutated genes to better understand their biological function. We then compared gene expression, methylation and copy number distributions of non-mutated and mutated genes in cell lines and patient data from the TCGA-OV project. To directly test if non-mutated genes can affect cell proliferation, we carried out proof-of-concept RNAi silencing experiments of a panel of nine selected non-mutated genes in three ovarian cancer cell lines and one primary ovarian epithelial cell line.

RESULTS

We identified a set of genes that were mutated less than expected (non-mutated genes) and mutated more than expected (mutated genes). Pathway analysis revealed that non-mutated genes interact in cancer associated pathways. We found that non-mutated genes are expressed significantly more than mutated genes while also having lower methylation and higher copy number states indicating that they could be functionally important. RNAi silencing of the panel of non-mutated genes resulted in a greater significant reduction of cell viability in the cancer cell lines than in the non-cancer cell line. Finally, as a test case, silencing ANKLE2, a significantly non-mutated gene, affected the morphology, reduced migration, and increased the chemotherapeutic response of SKOV3 cells.

CONCLUSION

We show that we can identify significantly non-mutated genes in a large ovarian cancer cohort that are well-expressed in patient and cell line data and whose RNAi-induced silencing reduces viability in three ovarian cancer cell lines. Targeting non-mutated genes that are important for tumor growth and metastasis is a promising approach to expand cancer therapeutic options.

Non-coding RNA-associated competitive endogenous RNA regulatory networks: Novel diagnostic and therapeutic opportunities for hepatocellular carcinoma

Hepatocellular carcinoma (HCC), as the most prevalent liver malignancy, is annually diagnosed in more than half a million people worldwide. HCC is strongly associated with hepatitis B and C viral infections as well as alcohol abuse. Obesity and nonalcoholic fatty liver disease (NAFLD) also significantly enhance the risk of liver cancer. Despite recent improvements in therapeutic approaches, patients diagnosed in advanced stages show poor prognosis. Accumulating evidence provides support for the regulatory role of non-coding RNAs (ncRNAs) in cancer. There are a variety of reports indicating the regulatory role of microRNAs (miRNAs) in different stages of HCC. Long non-coding RNAs (LncRNAs) exert their effects by sponging miRNAs and controlling the expression of miRNA-targeted genes. Circular RNAs (circRNAs) perform their biological functions by acting as transcriptional regulators, miRNA sponges and protein templates. Diverse studies have illustrated that dysregulation of competing endogenous RNA networks (ceRNETs) is remarkably correlated with HCC-causing diseases such as chronic viral infections, nonalcoholic steatohepatitis and liver fibrosis/cirrhosis. The aim of the current article was to provide an overview of the role and molecular mechanisms underlying the function of ceRNETs that modulate the characteristics of HCC such as uncontrolled cell proliferation, resistance to cell death, metabolic reprogramming, immune escape, angiogenesis and metastasis. The current knowledge highlights the potential of these regulatory RNA molecules as novel diagnostic biomarkers and therapeutic targets in HCC.

Circular RNA CircPPP1CB Suppresses Tumorigenesis by Interacting With the MiR-1307-3p/SMG1 Axis in Human Bladder Cancer

Circular RNA (circRNA) is a newly discovered endogenous non-coding RNA (ncRNA), which is characterized with a closed circular structure. A growing body of evidence has verified the vital roles of circRNAs in human cancer. In this research, we selected circPPP1CB as a study object by circRNA sequencing and quantitative real-time PCR (qRT-PCR) validation in human bladder cancer (BC). CircPPP1CB is downregulated in BC and is negatively correlated with clinical stages and histological grades. Functionally, circPPP1CB modulated cell growth, metastasis, and epithelial-to-mesenchymal transition (EMT) process in vitro and in vivo. Mechanically, we performed various experiments to verify the circPPP1CB/miR-1307-3p/SMG1 regulatory axis. Taken together, our results demonstrated that circPPP1CB participates in tumor growth, metastasis, and EMT process by interacting with the miR-1307-3p/SMG1 axis, and that circPPP1CB might be a novel therapeutic target and diagnostic biomarker in human BC.

Long intergenic noncoding RNA smad7 (Linc-smad7) promotes the epithelial-mesenchymal transition of HCC by targeting the miR-125b/SIRT6 axis

Long intergenic noncoding RNA smad7 (Linc-smad7) has been recently identified as a new long non-coding RNA (lncRNA). However, the role of Linc-smad7 in the tumourigenesis of human cancers remains unknown. This study uncovered that Linc-smad7 was increased in HCC samples and HCC cell lines using RT-qPCR assays. Furthermore, the overexpression of Linc-smad7 indicated poor clinicopathological features and outcomes for HCC patients. In addition, Linc-smad7 promoted HCC cells proliferation, migration, invasion and EMT, as determined by MTT, colony formation, Transwell assays and western blot analysis. Functionally, it was demonstrated that Linc-smad7 could bind with microRNA-125b (miR-125b), and the restoration of miR-125b rescued the promoting effects of Linc-smad7 on HCC cells. Finally, it was observed that sirtuin 6 (SIRT6) was positively regulated by Linc-smad7 in HCC as the direct target of miR-125b, and decreased SIRT6 reversed the effects of Linc-smad7 on promoting HCC. In conclusion, the current study first identified Linc-smad7 is increased in HCC, facilitating HCC cells proliferation, migration, invasion and EMT via regulating the miR-125b/SIRT6 axis.

Serum miR-375 Levels Are Closely Related to Disease Progression from HBV Infection to HBV-Related Hepatocellular Carcinoma

Background

There is an urgent need to identify ideal serological biomarkers that not only are closely related to disease progression from hepatitis B virus (HBV) infection to hepatocellular carcinoma (HCC) but also have high specificity and sensitivity. We conducted this study to analyze whether miR-375 has a potential value in the early prediction of the progression from HBV-related hepatitis or cirrhosis to HCC.

Methods

A total of 177 participants were enrolled. Receiver operating characteristic (ROC) curve was used to evaluate the predictive capability of selected miR-375 for HBV-HCC. We upregulated the miR-375 expression in HepG2, HepG2.2.15, and HepAD38 cells to determine its effect on cellular proliferation and migration, in vitro using Cell Counting Kit-8 (CCK-8) assays.

Results

Serum miR-375 levels decreased in order from healthy controls to chronic hepatitis B (CHB) without cirrhosis, followed by cirrhosis, and finally, HBV-HCC patients. miR-375 levels were significantly lower in HBeAg-positive and HBV DNA-positive patients than negative (P < 0.05) and significantly lower in patients with elevated alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA) than normal levels (P < 0.05). miR-375 might be a biomarker for HBV-HCC, with a high area under the curve (AUC) of 0.838 (95% confidence interval (CI) 0.780 to 0.897; sensitivity: 73.9%; specificity: 93.0%). The AUC (0.768 vs. 0.584) and sensitivity (93.8% vs. 75.0%) for miR-375 were higher than those for AFP. The overexpression of miR-375 noticeably inhibited proliferation and migration in HepG2, HepG2.2.15, and HepAD38, especially in HepG2.2.15 and HepAD38, which are stably infected with HBV.

Conclusions

Serum miR-375 levels are closely related to disease progression from HBV-related hepatitis or cirrhosis to HCC.

Nonsense-mediated RNA Decay Pathway Inhibition Restores Expression and Function of W1282X CFTR

The recessive genetic disease cystic fibrosis (CF) is caused by loss-of-function mutations in the CFTR (CF transmembrane conductance regulator) gene. Approximately 10% of patients with CF have at least one allele with a nonsense mutation in CFTR. Nonsense mutations generate premature termination codons that can subject mRNA transcripts to rapid degradation through the nonsense-mediated mRNA decay (NMD) pathway. Currently, there are no approved therapies that specifically target nonsense mutations in CFTR. Here, we identified antisense oligonucleotides (ASOs) that target the NMD factor SMG1 to inhibit the NMD pathway, and determined their effects on the W1282X CFTR mutation. First, we developed and validated two in vitro models of the W1282X CFTR mutation. Next, we treated these cells with antisense oligonucleotides to inhibit NMD and measured the effects of these treatments on W1282X expression and function. SMG1-ASO-mediated NMD inhibition upregulated the RNA, protein, and surface-localized protein expression of the truncated W1282X gene product. Additionally, these ASOs increased the CFTR chloride channel function in cells homozygous for the W1282X mutation. Our approach suggests a new therapeutic strategy for patients harboring nonsense mutations and may be beneficial as a single agent in patients with CF and the W1282X mutation.

The RNA-binding protein SORBS2 suppresses hepatocellular carcinoma tumourigenesis and metastasis by stabilizing RORA mRNA

BACKGROUND

Numerous studies have revealed that dysregulation of RNA-binding protein (RBP) expression is causally linked with human cancer tumourigenesis. However, the detailed biological effect and underlying mechanisms of most RBPs remain unclear.

METHODS

Expression of sorbin and SH3 domain-containing 2 (SORBS2) in hepatocellular carcinoma (HCC) was detected by qRT-PCR, immunohistochemistry assay and Western blot assay. Proliferation, migration, invasion and cell cycle progression of HCC cells were measured by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, colony-forming assay, Transwell assay and flow cytometry assay respectively. A xenograft model and metastatic model were established to evaluate the proliferation and metastasis of HCC cells in vivo. Western blot assays were performed to assess the expression of epithelial-mesenchymal transition markers. Luciferase reporter assay, RNA immunoprecipitation and pull-down assay elucidated the effect of SORBS2 on one of its downstream genes.

RESULTS

The expression of SORBS2 was significantly decreased in HCC and was associated with metastasis, advanced TNM clinical stage and poor clinical outcome of HCC patients. Furthermore, our results suggested that SORBS2 inhibited HCC cell proliferation, invasion, migration and EMT both in vivo and in vitro. Mechanistically, we revealed that retinoic acid receptor-related orphan receptor (RORA) was a major target of SORBS2 and was critical to sustaining the antitumour effect of SORBS2 on HCC cells. SORBS2 reduced RORA mRNA degradation by directly binding to the 3'UTR of RORA mRNA.

CONCLUSIONS

In this study, we found for the first time that SORBS2 contributed to the suppression of HCC tumourigenesis and metastasis via post-transcriptional regulation of RORA expression as an RBP.

MicroRNA-18a promotes cancer progression through SMG1 suppression and mTOR pathway activation in nasopharyngeal carcinoma

miR-18a has been reported to be upregulated in nasopharyngeal carcinoma (NPC) tissues by microarray assays. However, the roles and the underlying mechanisms of miR-18a in NPC remain poorly understood. Here we demonstrated by real-time RT-PCR that miR-18a expression is upregulated in NPC tissues, and positively correlated with tumor size and TNM stage. Moreover, miR-18a expression could be upregulated by NF-κB activation or Epstein-Barr virus encoded latent membrane protein 1 expression. The ectopic expression of miR-18a promoted NPC cell proliferation, migration and invasion, while the repression of miR-18a had opposite effects. Candidate genes under regulation by miR-18a were screened out through a whole-genome microarray assay, further identified by a reporter assay and verified in clinical samples. SMG1, a member of the phosphoinositide 3-kinase-related kinases family and an mTOR antagonist, was identified as functional target of miR-18a. Our results confirmed that miR-18a exerts its oncogenic role through suppression of SMG1 and activation of mTOR pathway in NPC cells. Importantly, in vivo xenograft tumor growth in nude mice was effectively inhibited by intratumor injection of miR-18a antagomir. Our data support an oncogenic role of miR-18a through a novel miR-18a/SMG1/mTOR axis and suggest that the antitumor effects of antagomir-18a may make it suitable for NPC therapy.

NELFE promoted pancreatic cancer metastasis and the epithelial‑to‑mesenchymal transition by decreasing the stabilization of NDRG2 mRNA

Negative elongation factor E (NELFE) has been demonstrated to promote cancer progression as an RNA‑binding protein (RBP). However, the expression patterns, biological role and molecular mechanism of NELFE in pancreatic cancer (PC) remain largely unknown. The expression levels of NELFE in 120 pairs of PC tissues and adjacent non‑tumor clinical samples collected from patients with PC were examined via reverse transcription‑quantitative (RT‑q) PCR and immunohistochemistry. The mRNA expression levels of NELFE, N‑Myc downstream‑regulated gene 2 (NDRG2), c‑Myc, survivin and cyclin D1 were detected via RT‑qPCR. The protein expression levels of NELFE, NDRG2, total β‑catenin, nuclear β‑catenin, cytosolic β‑catenin, E‑cadherin, N‑cadherin and Vimentin were measured by western blotting. NELFE and NDRG2 were then knocked‑down by short hairpin (sh)RNA. PC cell proliferation was detected by MTT and colony formation assays. Invasion and migration were detected by transwell assays. The interaction between NELFE and NDRG2 was detected by luciferase reporter assays, mRNA decay assays and RNA immunoprecipitation. NELFE expression was increased in PC tissues compared with the paired non‑cancerous tissues. NELFE expression was upregulated in PC cells when compared with normal pancreatic cells (HPDE6‑C7). The present study revealed that knockdown of NELFE inhibited the proliferation, invasion and migration of PC cells. In addition, transfection of the sh‑NELFE vector inhibited the epithelial‑to‑mesenchymal transition in PC cells by suppressing the expression and nuclear accumulation of β‑catenin. Further mechanistic studies revealed that NELFE activates the Wnt/β‑catenin signaling pathway by decreasing the stabilization of NDRG2 mRNA in PC. To the best of our knowledge, these results revealed the promotional function of NELFE on PC tumorigenesis and metastasis for the first time, helping to provide a promising strategy for the treatment of patients with PC.

Sirtuin6 (SIRT6) Promotes the EMT of Hepatocellular Carcinoma by Stimulating Autophagic Degradation of E-Cadherin

EMT is a pivotal mechanism involved in tumor metastasis, which is the leading cause of poor prognosis for hepatocellular carcinoma (HCC). Sirtuin family members function as NAD⁺-dependent deacetylases that are essential for tumor metastasis and epithelial-mesenchymal transition (EMT). However, no causal association has been established between Sirtuin6 (SIRT6) and HCC metastasis. SIRT6 expression pattern and its association with HCC metastasis were investigated by informatic analysis, and verified by qRT-PCR and immunochemistry in HCC tissues. Transwell assay, qRT-PCR, and immunofluorescence assay were utilized to assess the effects of SIRT6 on metastasis and E-cadherin expression in vitro and in vivo. Immunoprecipitation assay was performed to observe whether SIRT6 deacetylated Beclin-1 in HCC cells. Immunofluorescence assay and inhibitor treatment rescue experiments were used to clarify the mechanism by which SIRT6 facilitated EMT and metastasis. SIRT6 upregulation was quite prevalent in HCC tissues and closely correlated with worse overall survival, disease-relapse free survival, and HCC metastasis. Furthermore, SIRT6 promoted HCC cell migration, invasion, and EMT. Mechanistically, we found that SIRT6 deacetylated Beclin-1 in HCC cells and this event led to the promotion of the autophagic degradation of E-cadherin. Noticeably, E-cadherin degradation and invasion, migration induced by SIRT6 overexpression could be rescued by dual mutation of Beclin-1 (inhibition of acetylation), CQ (autophagy inhibitor), and knockdown of Atg7. In addition, SIRT6 promoted N-cadherin and Vimentin expression via deacetylating FOXO3a in HCC. These results established a relationship between SIRT6 and HCC EMT and further elucidated the mechanisms underlying HCC metastasis, helping provide a promising approach for the treatment of HCC. IMPLICATIONS: Inhibiting SIRT6 represents a potential therapeutic approach to suppress HCC metastasis partially through reduction of autophagic degradation of E-cadherin.

miR-103 promotes the metastasis and EMT of hepatocellular carcinoma by directly inhibiting LATS2

Improving the long-term survival of patients with hepatocellular carcinoma (HCC) remains a challenge due to metastasis and recurrence. In this study, we demonstrate that the overexpression of miR-103 in HCC cells promotes epithelial-mesenchymal transition (EMT), and is associated with an enhanced metastasis and poor outcomes, as shown by western blot analysis and immunohistochemistry. Mechanistically, using reporter luciferase assay we reveal that the serine/threonine-protein kinase, large tumor suppressor kinase 2 (LATS2), a key component of the Hippo signaling pathway, is a direct target of miR-103 in HCC cells. Transwell assay, MTT assay and western blot analysis were performed to reveal that LATS2 can counteract the functional effects of miR-103 on HCC metastasis, growth and EMT. The analyses of clinical data indicated that a high expression of miR-103 correlated with a high expression of vimentin, but with a low expression of LATS2 and E-cadherin in HCC tissues. miR-103 also reduced yes-associated protein (YAP) phosphorylation. On the whole, the findings of this study suggest that miR-103 promotes HCC metastasis and EMT by directly inhibiting LATS2. Thus, targeting miR-103/LATS2 may prove to be a promising therapeutic strategy for HCC.

SMG-1 inhibition by miR-192/-215 causes epithelial-mesenchymal transition in gastric carcinogenesis via activation of Wnt signaling

SMG‐1,a member of the phosphoinositide kinase‐like kinase family, functioned as a tumor suppressor gene. However, the role of SMG‐1 in GC remain uncharacterized. In this study, regulation of SMG‐1 by miR‐192 and‐215, along with the biological effects of this modulation, were studied in GC. We used gene microarrays to screening and luciferase reporter assays were to verify the potential targets of miR‐192 and‐215. Tissue microarrays analyses were applied to measure the levels of SMG‐1 in GC tissues. Western blot assays were used to assess the signaling pathway of SMG‐1 regulated by miR‐192 and‐215 in GC. SMG‐1 was significantly downregulated in GC tissues.The proliferative and invasive properties of GC cells were decreased by inhibition of miR‐192 and‐215, whereas an SMG‐1siRNA rescued the inhibitory effects. Finally, SMG‐1 inhibition by miR‐192 and‐215 primed Wnt signaling and induced EMT. Wnt signaling pathway proteins were decreased markedly by inhibitors of miR‐192 and‐215, while SMG‐1 siRNA reversed the inhibition apparently. Meanwhile, miR‐192 and‐215 inhitibtors increased E‐cadherin expression and decreased N‐cadherin and cotransfection of SMG‐1 siRNA reversed these effects. In summary, these findings illustrate that SMG‐1 is suppressed by miR‐192 and‐215 and functions as a tumor suppressor in GC by inactivating Wnt signaling and suppressing EMT.

Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution

Nonsense-mediated mRNA decay (NMD) is an essential eukaryotic process regulating transcript quality and abundance, and is involved in diverse processes including brain development and plant defenses. Although some of the NMD machinery is conserved between kingdoms, little is known about its evolution. Phosphorylation of the core NMD component UPF1 is critical for NMD and is regulated in mammals by the SURF complex (UPF1, SMG1 kinase, SMG8, SMG9 and eukaryotic release factors). However, since SMG1 is reportedly missing from the genomes of fungi and the plant Arabidopsis thaliana, it remains unclear how UPF1 is activated outside the metazoa. We used comparative genomics to determine the conservation of the NMD pathway across eukaryotic evolution. We show that SURF components are present in all major eukaryotic lineages, including fungi, suggesting that in addition to UPF1 and SMG1, SMG8 and SMG9 also existed in the last eukaryotic common ancestor, 1.8 billion years ago. However, despite the ancient origins of the SURF complex, we also found that SURF factors have been independently lost across the Eukarya, pointing to genetic buffering within the essential NMD pathway. We infer an ancient role for SURF in regulating UPF1, and the intriguing possibility of undiscovered NMD regulatory pathways.

MicroRNA-107: a novel promoter of tumor progression that targets the CPEB3/EGFR axis in human hepatocellular carcinoma

MicroRNAs (miRNAs) are dysregulated in many types of malignancies, including human hepatocellular carcinoma (HCC). MiR-107 has been implicated in several types of cancer regulation; however, relatively little is known about miR-107 in human HCC. In the present study, we showed that the overexpression of miR-107 accelerates the tumor progression of HCC in vitro and in vivo through its new target gene, CPEB3. Furthermore, our results demonstrated that CPEB3 is a newly discovered tumor suppressor that acts via the EGFR pathway. Therefore, our study demonstrates that the newly discovered miR-107/CPEB3/EGFR axis plays an important role in HCC progression and might represent a new potential therapeutic target for HCC treatment.

Circulating miR-375 and miR-199a-3p as potential biomarkers for the diagnosis of hepatocellular carcinoma

Aiming to find novel non-invasive biomarkers with high accuracy for the detention of early-stage hepatocellular carcinoma (HCC), we examined the predictive power of two microRNAs (miR; miR-375 and miR-199a-3p) as potential biomarkers in early-stage HCC. A total of 234 serum samples (78 samples from HCC patients, 156 samples from healthy controls) were collected. We measured the levels of the two mature microRNAs (miRNAs) (miR-375 and miR-199a-3p) with probe-based stem-loop quantitative reverse-transcriptase PCR (RT-qPCR) in all subjects. In addition, the correlation between the expression levels of two miRs and clinicopathological factors was explored. Receiver operating characteristic curve (ROC) analyses revealed that the two serum miRs could be promising biomarkers for HCC, with relatively high area under the curve (AUC) values as follows: miR-375, 0. 637 with 95 % confidence interval (CI) of 0.560-0.741; miR-199a-3p, 0. 883 with 95 % CI of 0.827-0.938. Stratified analyses indicated that circulating miR-199a-3p showed better predictive value in patients with long-term drinking. Our data suggested that circulating miR-375 and miR-199a-3p could be a novel serum biomarker for HCC. Nevertheless, further validating and improving study with larger sample should be conducted to confirm our results.