DNA methylation downregulated mir-10b acts as a tumor suppressor in gastric cancer

LncRNA SNHG6 Promotes Wilms' Tumor Progression Through Regulating miR-429/FRS2 Axis

Background: Long noncoding RNA (lncRNA) small nucleolar RNA host gene 6 (SNHG6) has been reported to be an oncogene in a variety of cancers. However, the role of SNHG6 and its associated mechanisms in Wilms' tumor progression remain largely unknown. Methods: The expression of SNHG6, microRNA-429 (miR-429), and FGF receptor substrates 2 (FRS2) messenger RNA (mRNA) was detected by quantitative real-time polymerase chain reaction. Cell proliferation was analyzed through 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and plate colony assay. The apoptosis was assessed by flow cytometry. Cell glycolytic metabolism was analyzed through detecting the lactate dehydrogenase activity, glucose uptake, lactate production, and ATP level. The target relationship between miR-429 and SNHG6 or FRS2 was predicted by miRcode or Starbase and then validated by dual-luciferase reporter assay and RNA pull-down assay. Murine xenograft model was established to validate the function of SNHG6 in vivo. Results: The level of SNHG6 was elevated in Wilms' tumor tissues and cells, and SNHG6 played an oncogenic role to promote the proliferation and glycolysis and restrain the apoptosis of Wilms' tumor cells. MiR-429 was identified as a target of SNHG6, and miR-429 interference partly reversed the inhibitory effects induced by SNHG6 silencing on the malignant behaviors of Wilms' tumor cells. FRS2 mRNA bound to miR-429 in Wilms' tumor cells. SNHG6 upregulated the expression of FRS2 through acting as a sponge of miR-429. MiR-429-induced influences in Wilms' tumor cells were largely counteracted by the overexpression of FRS2. SNHG6 silencing suppressed the Wilms' tumor growth through miR-429/FRS2 axis in vivo. Conclusion: SNHG6 accelerated Wilms' tumor progression through regulating miR-429/FRS2 signaling in vitro and in vivo.

"Salivary LINC00657 and miRNA-106a as diagnostic biomarkers for oral squamous cell carcinoma, an observational diagnostic study"

BACKGROUND

Early detection and diagnosis of malignant tumors is critical for improving the survival rate and treatment outcomes of oral cancer. Thus, the current prospective investigation was designed to verify the role, sensitivity, and specificity of salivary LINC00657 and miRNA-106a as diagnostic markers in oral squamous cell carcinoma patients as compared to oral lichen planus (as an example of oral potentially malignant disorders) and normal individuals, and to show LINC00657 relation to miR-106a.

METHODS

A total of 36 participants were included, subdivided into 3 groups: Group I: 12 patients diagnosed with oral squamous cell carcinoma (OSCC). Group II: 12 patients diagnosed with oral lichen planus (OLP). Group III: 12 systemically free individuals with no oral mucosal lesions. Unstimulated salivary samples were collected from all participants to evaluate level of LINC00657 and miR-106a in different groups using quantitative real-time PCR.

RESULTS

OSCC showed the highest LINC00657 and lowest miR-106a fold change among included groups. Receiver Operating Characteristic (ROC) curve analysis of the two biomarkers for detecting OSCC revealed that LINC00657 had higher diagnostic accuracy (DA) (83.3%) compared to miR-106a (80.4%). As for detecting OLP, ROC analysis showed that miR-106a had higher (DA) (61%) compared to LINC00657 (52.5%). To discriminate OSCC from OLP, the diagnostic accuracy of both markers is the same (75%). Moreover, differentiating OSCC grades II and III, ROC analysis showed that miR-106a had lower (DA) (60%) compared to LINC00657 (DA) (83.3%).

CONCLUSIONS

Salivary LINC00657 and miR-106a could be promising diagnostic markers for oral squamous cell carcinoma. Salivary LINC00657 may differentiate oral squamous cell carcinoma from oral potentially malignant disorders with considerable diagnostic accuracy. Moreover, low levels of salivary miR-106a could have the potential to indicate malignancy.

TRIAL REGISTRATION

The study was retrospectively registered on clinicaltrial.gov with NCT05821179 (first trial registration in 26/3/2023), date of registration: 19/4/2023.

Research hotspots and trends of microRNAs in intervertebral disc degeneration: a comprehensive bibliometric analysis

BACKGROUND

MicroRNAs (miRNAs) are involved in various pathological processes, such as proliferation, growth, and apoptosis, of intervertebral disc (IVD) cells and play an important role in the development of intervertebral disc degeneration (IDD). Although some studies have reported the role of miRNAs in IDD, scientific econometric analysis in this field is not available.

OBJECTIVES

We designed this study to describe the current research trends and potential mechanisms associated with the role of miRNAs in IDD and to provide new ideas for future research in this field.

METHODS

We conducted a bibliometric analysis of the publications on the role of miRNAs in IDD included in the Web of Science core collection database to elucidate the current research trends in this field. The potential mechanisms were constructed using the Arrowsmith project.

RESULTS

We found that the number of miRNAs and IDD-related publications increased over the years. China was the most important contributor to research in this field. The top three institutions in terms of number of articles published were Huazhong University of Science and Technology, Shanghai Jiao Tong University, and Xi'an Jiao Tong University. Shanghai Jiao Tong University had the highest number of citations. Experimental and thermal medicine had the maximum number of documents, and Cell promotion had the most citations. The journal with the most mean times cited per study was Annals of the Rheumatic Diseases. The author Wang K had the highest number of publications, and Wang HQ had the highest number of citations. These two authors made important contributions to the research in this field. The keyword analysis showed that recent studies have focused on miRNAs regulating nucleus pulposus cell apoptosis and proliferation. Moreover, we revealed the potential mechanisms of miRNAs associated with IDD, including miRNAs regulating the extracellular matrix (ECM) degradation, mediating cartilage endplate (CEP) degeneration, and participating in inflammatory responses.

CONCLUSION

We demonstrated the knowledge map of miRNAs and IDD-related research through bibliometric analysis and elucidated the current research status and hotspots in this field. The mechanisms by which miRNAs regulate the apoptosis and proliferation of degenerated IVDs, promote ECM degradation, mediate CEP degeneration, and participate in inflammatory responses should be explored in further studies.

KAT7 promoted gastric cancer progression through promoting YAP1 activation

Lysine acetyltransferase 7 (KAT7) was upregulated in gastric cancer (GC) patient tissues, and associated with poor prognosis and metastasis. However, its specific role in GC remains unclear. This study aimed to annotate the role of KAT7 in GC cells. The results showed that the overexpression of KAT7 promoted cell growth, migration, and invasion, while KAT7 inhibition has the opposite effect. Besides, KAT7 participated in cell cycle phase distribution and epithelial-mesenchymal transition (EMT) process of GC cells. In addition, KAT7 promoted the transcription and nuclear translocation of Yes-associated protein 1 (YAP1) in MKN45 cells. Silence of YAP1 partly reversed the promoting effect of KAT7 on GC cells progression. In summary, this study indicates that KAT7 promoted GC cells progression through promoting YAP1 activation, contributes to understand the specific role of KAT7 in GC.

The Role, Significance, and Association of MicroRNA-10a/b in Physiology of Cancer

MicroRNAs (miRNAs) are small non-coding RNAs that regulate the translation of mRNA and protein, mainly at the posttranscriptional level. Global expression profiling of miRNAs has demonstrated a broad spectrum of aberrations that correlated with several diseases, and miRNA- 10a and miRNA-10b were the first examined miRNAs to be involved in abnormal activities upon dysregulation, including many types of cancers and progressive diseases. It is expected that the same miRNAs behave inconsistently within different types of cancer. This review aims to provide a set of information about our updated understanding of miRNA-10a and miRNA-10b and their clinical significance, molecular targets, current research gaps, and possible future applications of such potent regulators.

The Advances in Epigenetics for Cancer Radiotherapy

Cancer is an important factor threatening human life and health; in recent years, its morbidity and mortality remain high and demosntrate an upward trend. It is of great significance to study its pathogenesis and targeted therapy. As the complex mechanisms of epigenetic modification has been increasingly discovered, they are more closely related to the occurrence and development of cancer. As a reversible response, epigenetic modification is of great significance for the improvement of classical therapeutic measures and the discovery of new therapeutic targets. It has become a research focusto explore the multi-level mechanisms of RNA, DNA, chromatin and proteins. As an important means of cancer treatment, radiotherapy has made great progress in technology, methods, means and targeted sensitization after years of rapid development, and even research on radiotherapy based on epigenetic modification is rampant. A series of epigenetic effects of radiation on DNA methylation, histone modification, chromosome remodeling, RNA modification and non-coding RNA during radiotherapy affects the therapeutic effects and prognosis. Starting from the epigenetic mechanism of tumorigenesis, this paper reviews the latest progress in the mechanism of interaction between epigenetic modification and cancer radiotherapy and briefly introduces the main types, mechanisms and applications of epigenetic modifiers used for radiotherapy sensitization in order to explore a more individual and dynamic approach of cancer treatment based on epigenetic mechanism. This study strives to make a modest contribution to the progress of human disease research.

Novel biomarkers of microRNAs in gastric cancer; an overview from diagnosis to treatment

The fourth frequent disease in the world and the second cause of cancer-related death is gastric cancer (GC). In this way, over 80% of diagnoses are made in the middle to advanced degrees of the disease, underscoring the requirement for innovative biomarkers that can be identified quickly. Meaningly, biomarkers that can complement endoscopic diagnosis and be used to detect patients with a high risk of GC are desperately needed. These biomarkers will allow for the accurate prediction of therapy response and prognosis in GC patients, as well as the development of an optimal treatment strategy for each individual. Conspicoiusly, microRNAs (miRNAs) and small noncoding RNA regulates the expression of target mRNA and thereby modifies critical biological mechanisms. According to the data, abnormally miRNAs expression in GC is linked to tumor growth, carcinogenesis, aggression and distant metastasis. Importantly, miRNA expression patterns and next-generation sequencing (NGS) can also be applied to analyze kinds of tissues and cancers. Given the high death rates and poor prognosis of GC, and the absence of a clinical diagnostic factor that is adequately sensitive to GC, research into novel sensitive and specific markers for GC diagnosis is critical. In this review,we evaluate the latest research findings that suggest the feasibility and clinical utility of miRNAs in GC.

Sox2 induces glioblastoma cell stemness and tumor propagation by repressing TET2 and deregulating 5hmC and 5mC DNA modifications

DNA methylation is a reversible process catalyzed by the ten–eleven translocation (TET) family of enzymes (TET1, TET2, TET3) that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Altered patterns of 5hmC and 5mC are widely reported in human cancers and loss of 5hmC correlates with poor prognosis. Understanding the mechanisms leading to 5hmC loss and its role in oncogenesis will advance the development of epigenetic-based therapeutics. We show that TET2 loss associates with glioblastoma (GBM) stem cells and correlates with poor survival of GBM patients. We further identify a SOX2:miR-10b-5p:TET2 axis that represses TET2 expression, represses 5hmC, increases 5mC levels, and induces GBM cell stemness and tumor-propagating potential. In vivo delivery of a miR-10b-5p inhibitor that normalizes TET2 expression and 5hmC levels inhibits tumor growth and prolongs survival of animals bearing pre-established orthotopic GBM xenografts. These findings highlight the importance of TET2 and 5hmC loss in Sox2-driven oncogenesis and their potential for therapeutic targeting.

Natural Products Targeting Cancer Stem Cells for Augmenting Cancer Therapeutics

Cancer stem cells (CSC) have been identified in several types of solid tumors. In some cases, CSC may be the source of all the tumor cells, the cause of the tumor's resistance to chemotherapeutic agents, and the source of metastatic cells. Thus, a combination therapy targeting non-CSC tumor cells as well as specifically targeting CSCs holds the potential to be highly effective. Natural products (NPs) have been a historically rich source of biologically active compounds and are known for their ability to influence multiple signaling pathways simultaneously with negligible side effects. In this review, we discuss the potential of NPs in targeting multiple signaling pathways in CSC and their potential to augment the efficacy of standard cancer therapy. Specifically, we focus on the anti-CSC activities of flavonoids, FDA-approved drugs originating from natural sources. Additionally, we emphasize the potential of NPs in targeting microRNA-mediated signaling, given the roles of microRNA in the maintenance of the CSC phenotype.

Propranolol Suppresses Proliferation and Migration of HUVECs through Regulation of the miR-206/VEGFA Axis

Propranolol has been used in the first-line therapy of infantile hemangioma (IH) for a number of years; however, the mechanisms through which propranolol regulates IH are not yet fully understood. In the present study, microRNA (miRNA/miR) sequencing analysis was performed to identify differentially expressed miRNAs in human umbilical vascular endothelial cells (HUVECs) treated with propranolol. Cell viability and apoptosis were detected using CCK-8 assay and flow cytometry, respectively. Cell migration was assessed using wound healing, Transwell, and tube formation assays. Methylation-specific PCR was then used to investigate the promoter methylation status. The levels of oxidative stress indicators, including superoxide dismutase, glutathione, and malondialdehyde were also detected. Finally, cell cycle analysis was performed using flow cytometry and western blotting. It was observed that propranolol induced the upregulation of miR-206 in HUVECs, which was caused by demethylation of the miR-206 promoter. Moreover, propranolol significantly inhibited the proliferation of HUVECs by inducing apoptosis, while these phenomena were reversed by miR-206 antagomir. VEGFA was found to be a target gene of miR-206. In addition, propranolol notably inhibited the migration and induced G1 arrest of the HUVECs, whereas these results were eliminated by miR-206 antagomir. Collectively, the findings of the present study demonstrated that propranolol may inhibit the proliferation and migration in HUVECs via modulating the miR-206/VEGFA axis. These findings suggest a novel mechanism through which propranolol suppresses the progression of IH.

MiR-10b-5p inhibits tumorigenesis in gastric cancer xenograft mice model through down-regulating Tiam1

The miR-10b-5p plays an important role in gastric cancer development but its exact effect on gastric cancer development in vivo has not been fully studied. We showed that miR-10b-5p inhibited the proliferation and migration of gastric cancer cells by down-regulating Tiam1 which was up-regulated in both gastric cancer cells and tissues. Gastric cancer xenograft experiment showed that lenti-miR-10b-5p treatment and agomir-10b-5p injection could significantly retard tumor growth and reduce tumor size and induced apoptosis. Therefore, our results elucidate the tumor suppressor role of miR-10b-5p in gastric cancer in which it acts as a negative regulator of Tiam1 and also provide a molecular mechanism for agomir-10b-5p to treat gastric cancer.

The emerging role of miR-10 family in gastric cancer

Evidence has demonstrated that miRNAs play an irreplaceable role in tumorigenesis and progression of a broad range of cancers, including gastric cancer. Among these miRNAs, miR-10a and miR-10b have been identified to critically participate in gastric carcinogenesis and malignant progression. In this review, we briefly describe the role of miR-10a and miR-10b in gastric cancer, especially in the regulation of cell proliferation, apoptosis, cell cycle, migration, invasion and metastasis, drug resistance, and cancer stem cells. Furthermore, we highlight several compounds that target the miR-10 family and exhibit antitumor activity in cancer cells. Moreover, we conclude that targeting the miR-10 family might be a promising approach for the treatment of gastric cancer.

LncRNA TUG1 Contributes to Hypoxia-Induced Myocardial Cell Injury Through Downregulating miR-29a-3p in AC16 Cells

Myocardial ischemia is a common reason that causes human death globally. Long noncoding RNA taurine upregulated 1 (TUG1) serves as an oncogene in a variety of cancers. In this article, we aimed to investigate the role of TUG1 and its underlying signal pathway in hypoxia-induced myocardial cell injury. Cell viability, apoptosis, and lactate dehydrogenase (LDH) release were detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, flow cytometry, western blot assay, and LDH cytotoxicity assay. Quantitative real-time polymerase chain reaction was applied to measure the enrichment of TUG1 and miR-29a-3p. MiR-29a-3p was predicted as a target of TUG1 by StarBase bioinformatic software, and the target relationship between TUG1 and miR-29a-3p was verified by dual-luciferase reporter assay. Hypoxia treatment induced the apoptosis and LDH release while inhibited the viability of AC16 cells. TUG1 was markedly upregulated while the level of miR-29a-3p was notably decreased in hypoxia-stimulated AC16 cells. TUG1 contributed to hypoxia-induced AC16 injury. MiR-29a-3p depletion intensified hypoxia-induced AC16 damage. TUG1 negatively regulated the expression of miR-29a-3p through their direct interaction in AC16 cells. TUG1 silencing-mediated influences in hypoxia-induced AC16 cells were partly reversed by the interference of miR-29a-3p. In conclusion, TUG1 accelerated hypoxia-induced AC16 injury through inversely modulating the level of miR-29a-3p. TUG1/miR-29a-3p axis might be an underlying therapeutic target for myocardial ischemia.

Role of microRNAs in intervertebral disc degeneration (Review)

The incidence of lower back pain caused by intervertebral disc degeneration (IDD) is gradually increasing. IDD not only affects the quality of life of the patients, but also poses a major socioeconomic burden. There is currently no optimal method for delaying or reversing IDD, mainly due to its unknown pathogenesis. MicroRNAs (miRNAs/miRs) participate in the development of a number of diseases, including IDD. Abnormal expression of miRNAs in the intervertebral disc is implicated in various pathological processes underlying the development of IDD, including nucleus pulposus (NP) cell (NPC) proliferation, NPC apoptosis, extracellular matrix remodeling, inflammation and cartilaginous endplate changes, among others. The focus of the present review was the advances in research on the involvement of miRNAs in the mechanism underlying IDD. Further research is expected to identify markers for early diagnosis of IDD and new targets for delaying or reversing IDD.

Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer

BACKGROUND

The recent discovery of cancer/tissue specificity of miRNA has indicated its great potential as a therapeutic target. In Epstein-Barr virus-associated gastric cancer (EBVaGC), host genes are affected by extensive DNA methylation, including miRNAs. However, the role of methylated miRNA in the development of EBVaGC and immune cell infiltration has largely remained elusive.

RESULTS

After crossmatching the DNA methylation and expression profile of miRNA and mRNA in the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas Research Network (TCGA), we discovered that miR-129-2-3p was significantly suppressed due to hypermethylation on its enhancer in EBVaGC. The differentially expressed genes (DEGs) added up to 30, among which AKAP12 and LARP6 were predicted to be the target genes of miR-129-2-3p and negatively correlated with patients' survival. Accordingly, miR-129-2-3p was significantly down-regulated in tumor samples in 26 (65%) out of 40 cases in our cohort (P < 0.0001). The proliferation, migration and invasion functions of GC cells were significantly promoted when transfected with miR-129-2-3p inhibitor and suppressed when transfected with mimics or treated with 5-aza-2'-deoxycytidine. Moreover, a comprehensive regulation network was established by combining the putative transcription factors, miRNA-mRNA and protein-protein interaction (PPI) analysis. Pathway enrichment analysis showed that cytokine activity, especially CCL20, was the most prominent biological process in EBVaGC development. Immune cell infiltration analysis demonstrated CD4+ T cell, macrophage and dendritic cell infiltrates were significantly enriched for the prognostic-indicated hub genes.

CONCLUSION

This study has provided a comprehensive analysis of differentially expressed miRNAs and mRNAs associated with genome-wide DNA methylation by integrating multi-source data including transcriptome, methylome and clinical data from GEO and TCGA, QPCR of tumor samples and cell function assays. It also gives a hint on the relationships between methylated miRNA, DEGs and the immune infiltration. Further experimental and clinical investigations are warranted to explore the underlying mechanism and validate our findings.

CircDDX42 Accelerates the Development of Pancreatic Cancer via miR-613/ID4/PI3K/AKT Axis

Background

Pancreatic cancer (PC) is one of the fatal cancers globally. CircDEAD-box helicase 42 (circDDX42) has been reported to play an oncogenic role in many cancers. The purpose of our study was to explore the relationship between circDDX42 and PC development and the potential mechanism by which circDDX42 modulating the progression of PC.

Methods

The enrichment of circDDX42, miR-613 and inhibitor of DNA binding 4 (ID4) was determined by quantitative real-time polymerase chain reaction (qRT-PCR) in PC tissues and cells. The proliferation, apoptosis and metastasis of PC cells were examined by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), Western blot, flow cytometry and transwell migration and invasion assays, respectively. The binding sites between miR-613 and circDDX42 or ID4 were predicted by Starbase bioinformatic software, and dual-luciferase reporter assay was conducted to verify the combination between miR-613 and circDDX42 or ID4. Western blot was carried out to detect the abundance of ID4, p-phosphatidylinositol 3-kinase (p-PI3K), PI3K, p-AKT serine/threonine kinase (p-AKT) and AKT in PC cells. The in vivo role of circDDX42 was verified through using murine xenograft model.

Results

The level of circDDX42 was enhanced in PC tissues and cells compared with that in matching normal tissues and HPDE cells. CircDDX42 promoted the proliferation and metastasis and suppressed the apoptosis of PC cells. CircDDX42 could sponge miR-613, and miR-613 was negatively regulated by circDDX42 in PC cells. MiR-613 suppressed the progression of PC. ID4 was a direct target of miR-613. ID4 was inversely modulated by miR-613 and positively regulated by circDDX42 in PC cells. ID4 played an oncogenic role in the tumorigenesis of PC. CircDDX42/miR-613/ID4 axis regulated the activation of PI3K/AKT pathway in PC cells. ID4 facilitated the progression of PC via activating PI3K/AKT signal pathway. CircDDX42 promoted the tumor growth of PC in vivo.

Conclusion

CircDDX42 accelerated the proliferation and metastasis while impeded the apoptosis of PC cells via circDDX42/miR-613/ID4/PI3K/AKT axis. This axis might be a promising target for PC therapy.

Systematic Elucidation of the Mechanism of Quercetin against Gastric Cancer via Network Pharmacology Approach

This study was aimed at elucidating the potential mechanisms of quercetin in the treatment of gastric cancer (GC). A network pharmacology approach was used to analyze the targets and pathways of quercetin in treating GC. The predicted targets of quercetin against GC were obtained through database mining, and the correlation of these targets with GC was analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Next, the protein-protein interaction (PPI) network was constructed, and overall survival (OS) analysis of hub targets was performed using the Kaplan–Meier Plotter online tool. Finally, the mechanism was further analyzed via molecular docking of quercetin with the hub targets. Thirty-six quercetin-related genes were identified, 15 of which overlapped with GC-related targets. These targets were further mapped to 319 GO biological process terms and 10 remarkable pathways. In the PPI network analysis, six hub targets were identified, including AKT1, EGFR, SRC, IGF1R, PTK2, and KDR. The high expression of these targets was related to poor OS in GC patients. Molecular docking analysis confirmed that quercetin can bind to these hub targets. In conclusion, this study provided a novel approach to reveal the therapeutic mechanisms of quercetin on GC, which will ease the future clinical application of quercetin in the treatment of GC.

LncRNA DDX11-AS1: a novel oncogene in human cancer

Long noncoding RNA (lncRNA) is a newly identified type of noncoding RNA with a length of more than 200 nucleotides. The latest research shows that lncRNAs play important roles in the occurrence and development of human tumours by acting both as carcinogenic genes and as tumour suppressor genes. LncRNAs plays a role in various biological processes, such as cell growth, apoptosis, migration and invasion. The newly discovered lncRNA DDX11-AS1 is abnormally highly expressed in various malignant tumours, such as hepatocellular carcinoma, colorectal cancer, osteosarcoma, bladder cancer, NSCLC and gastric cancer. DDX11-AS1 mainly regulates the expression of related genes through direct or indirect ways to perform its functions in carcinogenicity. These results indicate that DDX11-AS1 may be a marker or therapeutic target of tumours. This review summarizes the biological function and mechanism of DDX11-AS1 in the process of tumour development.

Expression of ASAP1 and FAK in gastric cancer and its clinicopathological significance

The present study aimed to analyze the expression levels of adenosine diphosphate ribosylation factor guanylate kinase 1 (ASAP1) and focal adhesion kinase (FAK) in gastric cancer (GC) tissues in order to explore their association with clinicopathological features and prognosis. A total of 32 patients with GC were enrolled in the present study. All patients had complete clinical follow-up data and paraffin-embedded normal gastric mucosal tissues. The expression levels of ASAP1 and FAK in these tissues were measured by immunohistochemistry. The associations of ASAP1 and FAK expression with clinicopathological factors and the survival of patients with GC were subsequently analyzed. The expression levels of ASAP1 (59.4%) and FAK (68.8%) in GC tissues were significantly higher than those in normal gastric mucosal tissues (28.1 and 40.6%, P<0.05). The expression levels of ASAP1 and FAK were associated with depth of invasion, lymph node metastasis and pathological stage (P<0.05). ASAP1 expression was positively associated with FAK expression (P<0.001). In addition, ASAP1 and FAK expression levels were negatively associated with disease-free survival time and overall survival time (P<0.05). The 5-year overall survival rate was significantly higher in patients with negative ASAP1 or FAK expression compared with that in patients with positive ASAP1 or FAK expression (P<0.05). In conclusion, ASAP1 and FAK were highly expressed in human GC tissues and may serve a synergistic role in promoting tumorigenesis, progression, invasion and metastasis in patients with GC. ASAP1 and FAK expression in GC were associated with patient's survival. Therefore, ASAP1 and FAK may represent novel molecular markers for the pathophysiology and prognosis of GC.

MicroRNA Regulation of the Small Rho GTPase Regulators-Complexities and Opportunities in Targeting Cancer Metastasis

The small Rho GTPases regulate important cellular processes that affect cancer metastasis, such as cell survival and proliferation, actin dynamics, adhesion, migration, invasion and transcriptional activation. The Rho GTPases function as molecular switches cycling between an active GTP-bound and inactive guanosine diphosphate (GDP)-bound conformation. It is known that Rho GTPase activities are mainly regulated by guanine nucleotide exchange factors (RhoGEFs), GTPase-activating proteins (RhoGAPs), GDP dissociation inhibitors (RhoGDIs) and guanine nucleotide exchange modifiers (GEMs). These Rho GTPase regulators are often dysregulated in cancer; however, the underlying mechanisms are not well understood. MicroRNAs (miRNAs), a large family of small non-coding RNAs that negatively regulate protein-coding gene expression, have been shown to play important roles in cancer metastasis. Recent studies showed that miRNAs are capable of directly targeting RhoGAPs, RhoGEFs, and RhoGDIs, and regulate the activities of Rho GTPases. This not only provides new evidence for the critical role of miRNA dysregulation in cancer metastasis, it also reveals novel mechanisms for Rho GTPase regulation. This review summarizes recent exciting findings showing that miRNAs play important roles in regulating Rho GTPase regulators (RhoGEFs, RhoGAPs, RhoGDIs), thus affecting Rho GTPase activities and cancer metastasis. The potential opportunities and challenges for targeting miRNAs and Rho GTPase regulators in treating cancer metastasis are also discussed. A comprehensive list of the currently validated miRNA-targeting of small Rho GTPase regulators is presented as a reference resource.

Identification of key microRNAs involved in tumorigenesis and prognostic microRNAs in breast cancer

Breast cancer is a commonly diagnosed cancer in women, and one of the leading causes of cancer-related death among female patients However, the key microRNAs involved in its tumorigenesis and microRNAs of prognostic values have not been fully understood. In the present study, we aimed to perform a systematic analysis of microRNA expression profiles to identify some key microRNAs associated with tumor initiation and prognosis. Using TCGA breast cancer datasets, we identified 110 differentially expressed microRNAs. The functional enrichment analysis of the upregulated microRNAs revealed signaling transduction pathways, such as Notch and Wnt signaling pathway, and metabolism-related pathways such as sugar and nucleotide sugar metabolism, and oxidative stress response. Moreover, multivariable Cox model based on three variables of hsa-mir-130a, hsa-mir-3677, and hsa-mir-1247 stratified patients into high-risk and low-risk groups, which showed significant prognostic difference. In addition, we also tested the performance of this model in patient cohorts of any specific breast cancer subtypes or different TNM stages. The high performance in risk prediction was also observed in all of breast cancer subtypes and TNM stages. We also observed that there were highly possible interactions between hsa-mir-130a and seven target genes. Among these target genes, VAV3 and ESR1 were predicted as the target genes of hsa-mir-130a, suggesting that hsa-mir-130a may function by regulating the expression of VAV3 and ESR1 in breast cancer. In conclusion, the stratification based on the multivariable Cox model showed high performance in risk prediction. The dysregulated microRNAs and prognostic microRNAs greatly improved our understanding of the microRNA-related molecular mechanism underlying breast cancer.

Circ-ABCB10 Contributes to Paclitaxel Resistance in Breast Cancer Through Let-7a-5p/DUSP7 Axis

Background

Paclitaxel (PTX) is one of the widely used chemotherapy drugs in breast cancer (BC) treatment. Unfortunately, the survival rate of metastatic BC patients remains poor due to PTX resistance. Therefore, uncovering the underlying mechanism behind the PTX resistance of BC cells is crucial for BC therapy.

Methods

The enrichment of circular RNA ATP binding cassette subfamily B member 10 (circ-ABCB10), let-7a-5p and dual specificity phosphatase 7 (DUSP7) was measured by quantitative real time polymerase chain reaction (qRT-PCR) in PTX-resistant and PTX-sensitive BC tissues and cells. Chemoresistance, apoptosis, invasion and autophagy of BC cells were measured by 3-(4, 5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), flow cytometry, transwell invasion assay and Western blot assay, respectively. The binding sites between let-7a-5p and circ-ABCB10 or DUSP7 were predicted by Starbase bioinformatic software, and the combination was confirmed by dual-luciferase reporter assay. The protein expression of DUSP7 was examined by Western blot assay. Murine xenograft model was established to confirm the role of circ-ABCB10 in vivo.

Results

Circ-ABCB10 depletion promoted the PTX sensitivity and apoptosis while suppressed the invasion and autophagy of PTX-resistant BC cells. Circ-ABCB10 could bind to let-7a-5p in BC cells, and circ-ABCB10 contributed to PTX resistance of BC cells via let-7a-5p. DUSP7 is a direct target of let-7a-5p in BC cells, and the accumulation of DUSP7 reversed the promoting effects of let-7a-5p overexpression on the PTX sensitivity and apoptosis and the inhibitory impact on the invasion and autophagy of PTX-resistant BC cells. Circ-ABCB10 interference suppressed the growth of BC tumors in vivo.

Conclusion

Circ-ABCB10 mediated PTX resistance, apoptosis, invasion and autophagy of BC cells via let-7a-5p/DUSP7 axis.

Accumulation of DNA methylation alterations in paediatric glioma stem cells following fractionated dose irradiation

BACKGROUND

Radiation is an important therapeutic tool. However, radiotherapy has the potential to promote co-evolution of genetic and epigenetic changes that can drive tumour heterogeneity, formation of radioresistant cells and tumour relapse. There is a clinical need for a better understanding of DNA methylation alterations that may follow radiotherapy to be able to prevent the development of radiation-resistant cells.

METHODS

We examined radiation-induced changes in DNA methylation profiles of paediatric glioma stem cells (GSCs) in vitro. Five GSC cultures were irradiated in vitro with repeated doses of 2 or 4 Gy. Radiation was given in 3 or 15 fractions. DNA methylation profiling using Illumina DNA methylation arrays was performed at 14 days post-radiation. The cellular characteristics were studied in parallel.

RESULTS

Few fractions of radiation did not result in significant accumulation of DNA methylation alterations. However, extended dose fractionations changed DNA methylation profiles and induced thousands of differentially methylated positions, specifically in enhancer regions, sites involved in alternative splicing and in repetitive regions. Radiation induced dose-dependent morphological and proliferative alterations of the cells as a consequence of the radiation exposure.

CONCLUSIONS

DNA methylation alterations of sites with regulatory functions in proliferation and differentiation were identified, which may reflect cellular response to radiation stress through epigenetic reprogramming and differentiation cues.

A novel risk score model for stomach adenocarcinoma based on the expression levels of 10 genes

Stomach adenocarcinoma (STAD) accounts for 95% of cases of malignant gastric cancer, which is the third leading cause of cancer-associated mortality worldwide. The pathogenesis and effective diagnosis of STAD have become popular topics for research in the previous decade. In the present study, high-throughput RNA sequencing expression profiles and clinical data from patients with STAD were obtained from The Cancer Genome Atlas database and were used as a training dataset to screen differentially expressed genes (DEGs). Prognostic DEGs were identified using univariate Cox regression analysis and were further screened by the least absolute shrinkage and selection operator regularization regression algorithm. The resulting genes were used to construct a risk score model, the validation and effectiveness evaluation of which were performed on an independent dataset downloaded from the Gene Expression Omnibus database. Stratified and functional pathway (gene set enrichment) analyses were performed on groups with different estimated prognosis. A total of 92 genes significantly associated with STAD prognosis were obtained by univariate Cox regression analysis, and 10 prognosis-associated DEGs; hemoglobin b, chromosome 4 open reading frame 48, Dickkopf WNT signaling pathway inhibitor 1, coagulation factor V, serpin family E member 1, transmembrane protein 200A, NADPH oxidase organizer 1, C-X-C motif chemokine ligand 3, mannosidase endo-α-like and tripartite motif-containing 31; were selected for the development of the risk score model. The reliability of this prognostic method was verified using a validation set, and the results of multivariate Cox analysis indicated that the risk score may serve as an independent prognostic factor. In functional DEG analysis, eight Kyoto Encyclopedia of Genes and Genomes pathways were identified to be significantly associated with STAD risk factors. Thus, the 10-gene risk score model established in the present study was regarded as credible. This risk assessment tool may help identify patients with a high risk of STAD, and the proposed prognostic mRNAs may be useful in elucidating STAD pathogenesis.

DNA hypomethylation promotes invasion and metastasis of gastric cancer cells by regulating the binding of SP1 to the CDCA3 promoter

BACKGROUND

Cell division cycle associated protein-3 (CDCA3) has been reported frequently upregulated in various cancers. It has been progressively realized that changed DNA methylations occur in diverse carcinomas. However, the concrete involvement of CDCA3 and DNA methylation in gastric cancer (GC) still needs to be further elucidated.

METHODS

In this study, quantitative reverse-transcription polymerase chain reaction (PCR) was utilized to determine the relative expressions of CDCA3 in GC and normal tissue samples. The methylation condition of CDCA3 was determined by bisulfite-sequencing PCR (BSP) and methylation-specific PCR (MSP). A chromatin immunoprecipitation (ChIP) assay and luciferase activity assay was used for the interaction between transcription factors and promoters and binding site determination, respectively. The effects of knockdown or overexpression of specificity protein 1 (SP1) or CDCA3 on GC cells in vitro were further assessed via wound healing assay, colony formation assay, and matrigel invasion assay.

RESULTS

In comparison to paired normal tissues, CDCA3 expressions were significantly increased in the GC tissues. The CDCA3 expression was regulated by DNA methylation, with the CpG island hypomethylation responsible for CDCA3 upregulation of GC. ChIP assays verified that the activity of SP1 binding to the CDCA3 promoter was dramatically increased. When the CDCA3 expression was downregulated in MKN45 cells by knockdown SP1, the proliferation ability, healing ability, and invasive ability were significantly suppressed.

CONCLUSION

The process by which SP1 bound to the nearest promoter region was expedited in GC cells, by which DNA was hypomethylated and CDCA3 expression was promoted. The effect on cell proliferation and invasion by CDCA3 was under the regulation of SP1 and also affected by hypomethylation of DNA.

Emerging roles of non-coding RNAs in scoliosis

Scoliosis, a complex three‐dimensional deformity of the spine with the Cobb angle (a measure of the spinal lateral curvature) >10 degree, encompasses a spectrum of pathologies, including congenital, idiopathic, syndromic and neuromuscular aetiologies. The pathogenesis is multifactorial involving both environmental and genetic factors but the exact cellular and molecular mechanisms of disease development remain largely unknown. Emerging evidence showed that non‐coding RNAs (ncRNAs), namely microRNAs, long ncRNAs and circular RNAs, are deregulated in many orthopaedic diseases, including scoliosis. Importantly, these deregulated ncRNAs functionally participate in the initiation and progression of scoliosis. Here, we review recent progress in ncRNA research on scoliosis.

MiR-338 regulates NFATc1 expression and inhibits the proliferation and epithelial-mesenchymal transition of human non-small-cell lung cancer cells

BACKGROUND

It is well known that nuclear factor of activated T cells c1 (NFATc1) expression is closely associated with progression of many cancers. And we found that miR-338 could directly target the NFATc1. However, the precise mechanisms of miR-338 in non-small-cell lung cancer (NSCLC) have not been well clarified. Our study aimed to explore the interaction between NFATc1 and miR-338 in NSCLC.

METHODS

Quantitative RT-PCR was utilized to determine the expressions of NFATc1 and miR-338 in NSCLC tissues and cell lines. And the cell proliferation and epithelial-mesenchymal transition (EMT) were assessed to determine the functional roles of miR-338 and NFATc1 in NSCLC cells. NFATc1 expression was detected using quantitative RT-PCR and western blotting, respectively. Luciferase reporter assays were performed to validate NFATc1 as a target of miR-338 in NSCLC cells.

RESULTS

In this study, our results showed that NFATc1 expression was significantly up-regulated in NSCLC tissues and cell lines, and the miR-338 level was dramatically down-regulated. Moreover high NFATc1 expression was closely associated with low miR-338 level in NSCLC tissues. Moreover introduction of miR-338 significantly inhibited proliferation and EMT of NSCLC cells. Bioinformatics analysis predicted that the NFATc1 was a potential target gene of miR-338. We demonstrated that miR-338 could directly target NFATc1 by using luciferase reporter assay. Besides, knockdown of NFATc1 had the similar effects with miR-338 overexpression on NSCLC cells. Up-regulation of NFATc1 in NSCLC cells partially abolished the inhibitory effects of miR-338 mimic.

CONCLUSIONS

Overexpression of miR-338 inhibited cell proliferation and EMT of NSCLC cells by directly down-regulating NFATc1 expression.

MicroRNA-320a suppresses tumor progression by targeting PBX3 in gastric cancer and is downregulated by DNA methylation

BACKGROUND

Ectopic expression of miRNAs promotes tumor development and progression. miRNA (miR)-320a is downregulated in many cancers, including gastric cancer (GC). However, the mechanism underlying its downregulation and the role of miR-320a in GC are unknown.

AIM

To determine expression and biological functions of miR-320a in GC and investigate the underlying molecular mechanisms.

METHODS

Quantitative real-time polymerase chain reaction (PCR) was used to determine expression of miR-320a in GC cell lines and tissues. TargetScanHuman7.1, miRDB, and microRNA.org were used to predict the possible targets of miR-320a, and a dual luciferase assay was used to confirm the findings. Western blotting was used to detect the protein levels of pre-B-cell leukemia homeobox 3 (PBX3) in GC cells and tissue samples. Cell Counting Kit-8 proliferation, Transwell, wound healing, and apoptosis assays were performed to analyze the biological functions of miR-320a in GC cells. Methylation-specific PCR was used to analyze the methylation level of the miR-320a promoter CpG islands. 5-Aza-2’-deoxycytidine (5-Aza-CdR) and trichostatin A (TSA) were used to treat GC cells.

RESULTS

miR-320a expression was lower in GC cell lines and tissues than in the normal gastric mucosa cell line GES-1 and matched adjacent normal tissues. miR-320a overexpression suppressed GC cell proliferation, invasion and migration, and induced apoptosis. PBX3 was a target of miR-320a in GC. The methylation level of the miR-320a promoter CpG islands was elevated and this was partly reversed by 5-Aza-CdR and TSA.

CONCLUSION

miR-320a acts as a tumor suppressor and inhibits malignant behavior of GC cells, partly by targeting PBX3. DNA methylation is an important mechanism associated with low expression of miR-320a.

microRNA arm-imbalance in part from complementary targets mediated decay promotes gastric cancer progression

Strand-selection is the final step of microRNA biogenesis in which functional mature miRNAs are generated from one or both arms of precursor. The preference of strand-selection is diverse during development and tissue formation, however, its pathological effect is still unknown. Here we find that two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, are inversely expressed and play exactly opposite roles in gastric cancer progression. Higher-5p with lower-3p expression pattern is significantly correlated with higher TNM stages and poor prognosis of gastric cancer patients. The increase of miR-574-5p/-3p ratio, named miR-574 arm-imbalance is partially due to the dynamic expression of their highly complementary targets in gastric carcinogenesis, moreover, the arm-imbalance of miR-574 is in turn involved and further promotes gastric cancer progression. Our results indicate that miR-574 arm-imbalance contribute to gastric cancer progression and re-modification of the miR-574-targets homeostasis may represent a promising strategy for gastric cancer therapy.

Functional miRNAs derived from the 5p or 3p arm of some miRNA duplexes have opposite roles in cancer progression. Here, the authors show that oncogenic miR-574-5p has greater preference in aggressive gastric cancer as compared with miR-574-3p and this arm preference is partly dependent on complementary targets mediated miRNA decay.

Downregulation of microRNA-3934-5p induces apoptosis and inhibits the proliferation of neuroblastoma cells by targeting TP53INP1

Neuroblastoma is the most common pediatric extracranial solid tumour in the world. miRNAs are a group of endogenous small non-coding RNAs that act on target genes to serve critical roles in many biological processes. Presently, the expression and role of miR-3934-5p in neuroblastoma remains unclear. Therefore, the aim of the present study was to investigate the expression of miR-3934-5p in neuroblastoma tissues and cell lines and to assess the role of miR-3934-5p in neuroblastoma. In the current study, the results revealed that miR-3934-5p was significantly upregulated in neuroblastoma tissues and cell lines. The data also identified TP53INP1 as a direct target gene of miR-3934-5p, which was negatively regulated by miR-3934-5p. The present study further demonstrated that TP53INP1 was downregulated in both neuroblastoma tissues and cell lines. Furthermore, the results of the current study indicate that miR-3934-5p downregulation may induce apoptosis and inhibit neuroblastoma cell viability. However, these effects were reversed via TP53INP1-siRNA. Data from the current study indicates that the miR-3934-5p/TP53INP1 axis may be a novel therapeutic target for neuroblastoma treatment.

Gastric Cancer MicroRNAs Meta-signature

Gastric cancer (GC) is one of the most common types of cancer and the second leading cause of cancer-associated mortality. Identification of novel biomarkers is critical to prolonging patient survival. MicroRNAs (miRNAs) proved to play diverse roles in the physiological and pathological state in cancers including GC. Herein we aimed at performing a meta-analysis on miRNA profiling studies that used microarray platforms. Relevant studies were retrieved from PubMed and GEO databases. We used the robust rank aggregation to perform the meta-analysis. Moreover, for meta-signature miRNAs target genes, we performed pathway enrichment and GO molecular function enrichment analysis. A total of 19 upregulated miRNAs and seven downregulated miRNAs in GC samples were identified. However, only three upregulated and one downregulated miRNA reached statistical significance after multiple test correction. Here we showed that hsa-miR-21-5p, hsa-miR-93-5p, hsa-miR-25-3p, and hsa-miR-375 are differentially expressed in GC samples.

Deregulation of CSMD1 targeted by microRNA-10b drives gastric cancer progression through the NF-κB pathway

Aim: This study aimed to investigate the oncogenic activity of microRNA-10b by targeting CUB and sushi multiple domains protein 1 (CSMD1) in human gastric cancer (GC) and the underlying mechanisms.

Methods: The expression of CSMD1 in human GC tissues was evaluated by real-time reverse transcription polymerase chain reaction (RT-PCR), immunoblotting, and immunohistochemical analysis. The expressive abundance of microRNA-10b was detected by stem-loop RT-PCR. Molecular and cellular techniques, including lentiviral vector-mediated knockdown or overexpression, were used to elucidate the effect of microRNA-10b on the expression of CSMD1.

Results: CSMD1 was targeted and downregulated by microRNA-10b in human GC tissues and cells, and the down-regulated expression of CSMD1 contributed to poor survival. The knockdown of microRNA-10b expression inhibited cell proliferation in GC cells in vitro and tumor growth in vivo. The inhibition of microRNA-10b expression repressed invasion and migration of HGC27 cells and retarded GC cells metastasis to the liver in Balb/c nude mice. The up-regulated expression of microRNA-10b promoted the proliferation and metastasis of MKN74 cell in vitro. Intratumoral injection of microRNA-10b mimic also promoted the growth and metastasis of tumor xenografts in Balb/c nude mice. Mechanistically, microRNA-10b promoted the invasion and metastasis of human GC cells through inhibiting the expression of CSMD1, leading to the activation of the nuclear factor-κB (NF-κB) pathway that links inflammation to carcinogenesis, subsequently resulting in the upregulation of c-Myc, cyclin D1 (CCND1), and epithelial-mesenchymal transition (EMT) markers.

Conclusions: The findings established that microRNA-10b is an oncomiR that drives metastasis. Moreover, a set of critical tumor suppressor mechanisms was defined that microRNA-10b overcame to drive human GC progression.

Long non-coding RNA CHRF promotes proliferation and mesenchymal transition (EMT) in prostate cancer cell line PC3 requiring up-regulating microRNA-10b

Despite the advance of diagnosis and treatment for prostate cancer, the prognosis of metastatic prostate cancer is poor. We aimed to explore the functional role of long non-coding RNA cardiac hypertrophy-related factor (lncRNA CHRF) in prostate cancer cells (PC3) as well as the molecular mechanisms. LncRNA CHRF silence repressed cell number (%), down-regulated expression of cyclinD1, CDK4 and CDK6, and promoted apoptosis along with activation of the casapse-3 and caspase-9. LncRNA CHRF promoted mesenchymal transition (EMT), showing down-regulation of E-cadherin and up-regulation of N-cadherin, vimentin and ZEB1. Afterwards, we found miR-10b expression was positively correlated with lncRNA CHRF expression, and miR-10b inhibition could reverse the effects of lncRNA CHRF on PC3 and LNCaP cell proliferation and EMT. Finally, lncRNA CHRF was found to activate the GSK3β/AKT and NF-κB pathways via up-regulation of miR-10b. LncRNA CHRF silence repressed proliferation and EMT while promoted apoptosis in PC3 cells via positive regulation of miR-10b. The GSK3β/AKT and NF-κB pathways were activated by lncRNA CHRF, possibly through up-regulation of miR-10b.

Non-coding RNAs in regulating gastric cancer metastasis

Gastric cancer is one of the leading causes of cancer-related deaths worldwide, and mortality remains high, especially in East Asia. At present, the main method to diagnose gastric cancer is pathological biopsy. At the time of diagnosis, most patients have been diagnosed with advanced cancer and metastasis. The treatment of gastric cancer patients is mainly radical surgical resection and chemoradiotherapy, while patients with metastatic tumor have great challenges to radical surgery and are prone to drug resistance. Metastasis is an important factor affecting tumor development. In addition, evidence accumulated in the literature indicates that non-coding RNA plays a key role in tumor metastasis. This article reviews the role of ncRNAs in gastric cancer metastasis and discusses the regulatory mechanism in the development and treatment of gastric cancer.

Upregulated miR-154 promotes ECM degradation in intervertebral disc degeneration

Intervertebral disc degeneration (IDD), a common global health issue, is a major cause for low back pain (LBP). Given the complex etiology of IDD, micro RNA (miRNA) recently has been demonstrated to play essential roles in the progression of IDD. Therefore, this study aims to investigate functions of the miR-154, which is well-documented in a series of cell activities, IDD, and other relevant mechanisms. Lumbar nucleus pulposus (NP) samples were collected from patients with IDD and the control group. After solexa sequencing and bioinformatical analysis, the results showed that miR-154 was increased in NP cells of patients with IDD. Inhibition of miR-154 increased type II collagen and aggrecan and decreased mRNA expressions of collagenase-3 (MMP13) and aggrecanase-1 (ADAMTS4), whereas overexpression of miR-154 reversed such effects in NP cells. In addition, the luciferase reporter assay revealed that fibroblast growth factor 14 (FGF14) is a direct target of miR-154 and that the overexpression of FGF14 leads to similar effects as inhibition of miR-154 did. In conclusion, the results suggested that miR-154 participates in the development of IDD and its effects are mediated via targeting FGF14. Thus, miR-154 may be thought as a potential etiological factor for IDD and may provide insights into a therapeutic target to treat IDD.

Up-regulation of microRNA-496 suppresses proliferation, invasion, migration and in vivo tumorigenicity of human osteosarcoma cells by targeting eIF4E

Osteosarcoma is an aggressive bone tumor characterized by a high level of genetic instability and recurring DNA deletions and amplifications. This study aims to investigate how microRNA-496 (miR-496) affects proliferation, invasion, and migration of human osteosarcoma (OS) cells and in vivo tumorigenicity by targeting eukaryotic translation initiation factor 4E (eIF4E). Microarray-based gene expression profiling involving OS was used in order to identify differentially expressed genes. After that, the interaction between miR-496 expression and OS patients' survival rate was determined. The expression pattern of miR-496 and eIF4E was determined in OS tissues and cells, and their potential relationship was further analyzed by using the dual luciferase reporter gene assay. With the purpose of identifying the functional role miR-496 in OS, cell proliferation, migration, and invasion were measured in cells treated with miR-496 mimic or inhibitor. A nude mouse model was constructed in order to investigate the regulatory effects of miR-496 on tumor growth in vivo by regulating eIF4E. OS cells exhibited a down-regulated expression of miR-496 and an up-regulated expression of eIF4E. miR-496 expression was positively correlated to OS patients' survival rate. Bioinformatics analysis suggested eIF4E would be a direct target of miR-496, and the expression of eIF4E was inhibited by overexpression of miR-496. miR-496 elevation was found to exert suppressive effects on OS cell proliferation, migration and invasion in vitro and tumor growth in vivo, with the effects being reversed using miR-496 depletion. Altogether, the above findings support a conclusion that miR-496 could work as a tumor suppressor in OS through down-regulation of eIF4E. This study may provide a novel target for treatment of OS.

Melatonin protected against the detrimental effects of microRNA-363 in a rat model of vitamin A-associated congenital spinal deformities: Involvement of Notch signaling

Congenital spinal deformities are a result of defective somitogenesis and are associated with vitamin A deficiency (VAD). However, the molecular mechanisms of VAD-associated congenital spinal deformities remain largely unknown. Increasing number of studies suggested that microRNAs and melatonin played important roles in the development of congenital spinal deformities. In this study, we showed that the whole-embryo expression of miR-363 was upregulated in VAD rats. Furthermore, we demonstrated that miR-363 inhibited the proliferation and neuronal differentiation of primary cultured NSCs, accompanied by downregulation of Notch1. To this end, melatonin suppressed miR-363 expression and rescued the effects of miR-363 on NSC proliferation and neuronal differentiation together with restoration of Notch signaling. The present study provided new insights into the mechanism of VAD-associated spinal deformities and the therapeutic effect of melatonin that may lead to novel understanding of the molecular mechanisms of congenital spinal deformities.

MiR-106a directly targets LIMK1 to inhibit proliferation and EMT of oral carcinoma cells

Background

LIM kinase 1 (LIMK1) expression levels are closely associated with microRNA (miRNA) processing. Higher levels of LIMK1 are reported during the progression of many cancers. Our study explored the interaction between LIMK1 and miR-106a in oral squamous cell carcinoma (OSCC).

Methods

Quantitative RT-PCR was performed to detect the levels of LIMK1 and miR-106a in OSCC tissues and cell lines. The rates of cell proliferation and epithelial-mesenchymal transition (EMT) were assessed to determine the biological functions of miR-106a and LIMK1 in OSCC cells. The mRNA and protein levels of LIMK1 were measured using quantitative RT-PCR and western blotting. Luciferase assays were performed to validate LIMK1 as an miR-106a target in OSCC cells.

Results

We found that the level of miR-106a significantly decreased and the expression of LIMK1 significantly increased in OSCC tissues and cell lines. There was a close association between these changes. Knockdown of LIMK1 significantly inhibited the proliferation and EMT of OSCC cells. The bioinformatics analysis predicted that LIMK1 is a potential target gene of miR-106a and the luciferase reporter assay confirmed that miR-106a could directly target LIMK1. Introduction of miR-106a to OSCC cells had similar effects to LIMK1 silencing. Overexpression of LIMK1 in OSCC cells partially reversed the inhibitory effects of the miR-106a mimic.

Conclusion

MiR-106a inhibited the cell proliferation and EMT of OSCC cells by directly decreasing LIMK1 expression.

miR-202 modulates the progression of neuropathic pain through targeting RAP1A

Neuropathic pain is a somatosensory disorder which is caused by disease or nerve injury that affects the nervous system. microRNAs (miRNAs) are proved to play crucial roles in the development of neuropathic pain. However, the role of miR-202 in neuropathic pain is still unknown. Sprague-Dawley rats were used for constructing the neuropathic pain model. The expression of miR-202 was determined by quantitative real-time polymerase chain reaction. Potential target gene for miR-202 was measured using bioinformatics methods and Western blot analysis. In this study, we used rats to establish a neuropathic pain model and measured the effect of miR-202 in neuropathic pain. We demonstrated that miR-202 expression was downregulated in the spinal dorsal horn of bilateral sciatic nerve chronic constriction injury (bCCI) rat. However, miR-202 expression was not changed in the dorsal root ganglion, hippocampus, and anterior cingulated cortex of bCCI rat. We identified that RAP1A was a direct target gene of miR-202 in the PC12 cell. RAP1A expression was upregulated in the spinal dorsal horn of bCCI rat. Overexpression of miR-202 could improve the pain threshold for bCCI rats in both hindpaws, indicating that miR-202 overexpression could lighten the pain threshold for model rats. Moreover, RAP1A overexpression increased the pain threshold effect of miR-202 overexpression treated bCCI rats, indicating that miR-202 could lighten the pain threshold through inhibiting RAP1A expression. These data suggested that miR-202 acted pivotal roles in the development of neuropathic pain partly through targeting RAP1A gene.

NAIF1 suppresses osteosarcoma progression and is regulated by miR-128

Nuclear apoptosis-inducing factor 1 (NAIF1) acts as an oncogene and involves in tumorigenesis in several cancers. However, the expression and mechanism of NAIF1 in osteosarcoma remains unclear. In this study, we demonstrated the downregulation of NAIF1 expression in both osteosarcoma tissues and cell lines. We next explored the potential role of NAIF1 in osteosarcoma cell proliferation and migration. The result showed that overexpression of NAIF1 evidently suppressed the cell proliferation and invasion of osteosarcoma. Furthermore, we investigated the potential mechanisms accounting for dysregulation of NAIF1 in osteosarcoma. The bioinformatic prediction and luciferase reporter assay revealed that miR-128 is a direct upstream regulator of NAIF1 and regulates NAIF1 expression by binding the 3'-UTR of NAIF1. Consistent with previous study, we found that miR-128 was upregulated in both osteosarcoma tissues and cell lines. Moreover, miR-128 expression levels were inversely correlated with that of NAIF1 in osteosarcoma tissues. Finally, functional assay showed that miR-128 significantly suppressed osteosarcoma progression partially mediated by inhibiting NAIF1 expression. These data indicate that the miR-128 and its target gene NAIF1 played important roles by regulating OS cell proliferation and migration phenotype. SIGNIFICANCE OF THE STUDY: Osteosarcoma (OS) is the most common malignant bone tumour and the second leading cause of cancer-related death affecting children and adolescents. Nuclear apoptosis-inducing factor 1 (NAIF1) plays an inhibitory role in the initial steps of different carcinomas. However, the expression and mechanism of NAIF1 in osteosarcoma remains unclear. The data of this study indicated that the miR-128 and its target gene NAIF1 played important roles by regulating OS cell proliferation and migration phenotype. It was demonstrated that NAIF1 would demonstrate important regulative effects and may be a promising therapeutic target of OS.

miR-10b-5p regulates 3T3-L1 cells differentiation by targeting Apol6

MicroRNAs (miRNAs) are small, non-coding RNAs that have been proposed to control or fine-tune complex genetic pathways by post-transcriptional regulation of target genes. It was proved that numerous miRNAs have influence on the biology of adipocytes as well as on the function of adipose tissues. This study shows that miR-10b-5p expression was decreased in mice, rats, and human under obesity. In addition, the obtained results indicated that the expression level of miR-10b-5p was increased in 3T3-L1 pre-adipocytes without manifesting a significant role in 3T3-L1 cells proliferation. On the other hand, the downregulation of miR-10b-5p by the inhibitor played a role in 3T3-L1 cells differentiation and adipogenesis. Our results strongly suggest that Apol6 was the target gene of miR-10b-5p. The inhibition of miR-10b-5p promoted the differentiation of 3T3-L1 cells and adipogenesis by upregulating the Apol6 expression. Then, the upregulated Apol6 acted as an oncogene in certain obesity-related cancers. These results indicate that miR-10b-5p may have a therapeutic significance for obesity and obesity-related cancers.

Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction

Background

In the Next Generation Sequencing (NGS) era a large amount of biological data is being sequenced, analyzed, and stored in many public databases, whose interoperability is often required to allow an enhanced accessibility. The combination of heterogeneous NGS genomic data is an open challenge: the analysis of data from different experiments is a fundamental practice for the study of diseases. In this work, we propose to combine DNA methylation and RNA sequencing NGS experiments at gene level for supervised knowledge extraction in cancer.

Methods

We retrieve DNA methylation and RNA sequencing datasets from The Cancer Genome Atlas (TCGA), focusing on the Breast Invasive Carcinoma (BRCA), the Thyroid Carcinoma (THCA), and the Kidney Renal Papillary Cell Carcinoma (KIRP). We combine the RNA sequencing gene expression values with the gene methylation quantity, as a new measure that we define for representing the methylation quantity associated to a gene. Additionally, we propose to analyze the combined data through tree- and rule-based classification algorithms (C4.5, Random Forest, RIPPER, and CAMUR).

Results

We extract more than 15,000 classification models (composed of gene sets), which allow to distinguish the tumoral samples from the normal ones with an average accuracy of 95%. From the integrated experiments we obtain about 5000 classification models that consider both the gene measures related to the RNA sequencing and the DNA methylation experiments.

Conclusions

We compare the sets of genes obtained from the classifications on RNA sequencing and DNA methylation data with the genes obtained from the integration of the two experiments. The comparison results in several genes that are in common among the single experiments and the integrated ones (733 for BRCA, 35 for KIRP, and 861 for THCA) and 509 genes that are in common among the different experiments. Finally, we investigate the possible relationships among the different analyzed tumors by extracting a core set of 13 genes that appear in all tumors. A preliminary functional analysis confirms the relation of part of those genes (5 out of 13 and 279 out of 509) with cancer, suggesting to focus further studies on the new individuated ones.

Electronic supplementary material

The online version of this article (10.1186/s13040-018-0184-6) contains supplementary material, which is available to authorized users.

Proviral insertion in murine lymphomas 2 promotes stomach cancer progression by regulating apoptosis via reactive oxygen species-triggered endoplasmic reticulum stress

Gastric cancer is one of the most fatal cancers worldwide. The incidence and death rates are still increasing for gastric cancer. Increasing studies have shown that proviral insertion in murine lymphomas 2 (PIM2) functions as critical regulator of multiple cancers. However, it remains unknown whether and how PIM2 regulates gastric cancer progression. In this study, PIM2 was increased in the gastric cancer tissues of patients. Patients with high PIM2 expression levels had significantly shorter survival than those with low PIM2 expression. PIM2 knockdown reduced proliferation, migration and invasion in vitro by up-regulating E-cadherin, and down-regulating N-cadherin and Vimentin. Knockdown of PIM2 induced apoptosis in gastric cancer cells, which was regulated by endoplasmic reticulum (ER) stress, as evidenced by the increased expression levels of Activating transcription factor (ATF) 6, ATF4, X-box- binding protein-1 (XBP-1) and C/EBP homologous protein (CHOP). In addition, our data showed that PIM2 silence induced reactive oxygen species (ROS) production, leading to the activation of c-Jun N-terminal kinase (JNK). Importantly, we found that PIM2 knockdown-induced apoptosis and ER stress could be abolished by reducing reactive oxygen species (ROS) generation. In vivo, PIM2 knockdown showed a significant reduction in SGC-7901 xenograft tumor size. In summary, our findings provided experimental evidence that PIM2 might function as an important oncogene in gastric cancer, which supplied promising target for developing new therapeutic strategy in gastric cancer.

Long noncoding RNA NNT-AS1 promotes gastric cancer proliferation and invasion by regulating microRNA-363 expression

Increasing studies showed that long noncoding RNAs (lncRNAs) had crucial regulatory roles in various tumors, including gastric cancer (GC). Recent studies demonstrated that lncRNA nicotinamide nucleotide transhydrogenase-antisense RNA1 (NNT-AS1) played an important role in several tumors. However, the role and expression of NNT-AS1 in GC progression remain unknown. In our study, we indicated that NNT-AS1 expression was upregulated in GC samples compared with the nontumor tissues. We also showed that NNT-AS1 expression was upregulated in the GC cell lines. Ectopic expression of NNT-AS1 promoted GC cell line HGC-27 cell proliferation, cell cycle progression, and invasion. In addition, we showed that NNT-AS1 acted as a sponge competing endogenous RNA for microRNA-363 (miR-363), which was downregulated in the GC samples and cell lines. miR-363 expression was negatively related with NNT-AS1 expression in GC samples. Upregulated expression of miR-363 suppressed GC cell growth, cycle, and invasion. Furthermore, we reported that elevated expression of NNT-AS1 promoted GC cell proliferation, cycle, and invasion partly by suppressing miR-363 expression. These results indicated that lncRNA NNT-AS1 acted as an oncogene in the development of GC partly by inhibiting miR-363 expression.