The long noncoding RNA FOXCUT promotes proliferation and migration by targeting FOXC1 in nasopharyngeal carcinoma

FOXCUT regulates the malignant phenotype of triple-negative breast Cancer via the miR-337-3p/ANP32E Axis

BACKGROUND

The lack of specific molecular targets and the rapid spread lead to a worse prognosis of triple-negative breast cancer (TNBC). Therefore, identifying new therapeutic and prognostic biomarkers helps to develop effective treatment strategies for TNBC.

METHODS

Through preliminary bioinformatics analysis, FOXCUT was found to be significantly overexpressed in breast cancer, especially in TNBC. Tissue samples were collected from 15 TNBC patients, and qRT-PCR was employed to validate the expression of FOXCUT in both TNBC patient tissues and TNBC cell lines. We also carried out the GSEA analysis and KEGG enrichment analysis of FOXCUT. Additionally, the effects of FOXCUT knockdown on TNBC cell malignant behaviors, and aerobic glycolysis were assessed by methods including CCK-8, Transwell, western blot, and Seahorse XF 96 analyses. Moreover, utilizing databases predicting interactions between ceRNAs, corresponding lncRNA-miRNA binding relationships, and miRNA-mRNA interactions were predicted. These predictions were subsequently validated through RNA immunoprecipitation and dual-luciferase reporter assays.

RESULTS

FOXCUT exhibited high expression in both TNBC tissues and cell lines, fostering cell malignant behaviors and glycolysis. FOXCUT was found to sponge miR-337-3p, while miR-337-3p negatively regulated the expression of ANP32E. Consequently, FOXCUT ultimately facilitated the malignant phenotype of TNBC by upregulating ANP32E expression.

CONCLUSION

This study elucidated the role of FOXCUT in elevating aerobic glycolysis levels in TNBC and driving malignant cancer cell development via the miR-337-3p/ANP32E regulatory axis.

Noncoding RNA landscape and their emerging roles as biomarkers and therapeutic targets in meningioma

Meningiomas are among the most prevalent primary CNS tumors in adults, accounting for nearly 38% of all brain neoplasms. The World Health Organization (WHO) grade assigned to meningiomas guides medical care in patients and is primarily based on tumor histology and malignancy potential. Although often considered benign, meningiomas with complicated histology, limited accessibility for surgical resection, and/or higher malignancy potential (WHO grade 2 and WHO grade 3) are harder to combat, resulting in significant morbidity. With limited treatment options and no systemic therapies, it is imperative to understand meningioma tumorigenesis at the molecular level and identify novel therapeutic targets. The last decade witnessed considerable progress in understanding the noncoding RNA landscape of meningioma, with microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) emerging as molecular entities of interest. This review aims to highlight the commonly dysregulated miRNAs and lncRNAs in meningioma and their correlation with meningioma progression, malignancy, recurrence, and radioresistance. The role of "key" miRNAs as biomarkers and their therapeutic potential has also been reviewed in detail. Furthermore, current and emerging therapeutic modalities for meningioma have been discussed, with emphasis on the need to identify and subsequently employ clinically relevant miRNAs and lncRNAs as novel therapeutic targets and biomarkers.

Serum lncRNAs, NBAT-1, and FOXCUT signature in hepatocellular carcinoma developed on top of chronic hepatitis C

BACKGROUND

Hepatocellular Carcinoma (HCC) is a universal health problem responsible for 8.2% of all cancer deaths. Numerous risk factors were documented to be contributed to HCC development with viral hepatitis C ranking as the major predisposing factor in Egypt. The presence of a detectable amount of long noncoding RNAs (lncRNAs) in the circulation is linked to the development and spread of tumors. LncRNAs NBAT-1 and FOXCUT expression levels were used as genetic markers for the detection of gastrointestinal tract cancers. We hypothesized that serum expression levels of NBAT-1 and FOXCUT are new biomarkers for HCC that are related to laboratory and pathological markers.

PATIENTS AND METHODS

This study included 165 hepatitis C virus (HCV)-related HCC Egyptian patients, 180 HCV-infected noncancer patients, and 180 healthy controls, the serum expression levels of NBAT-1 and FOXCUT were measured by using quantitative real-time polymerase chain reaction.

RESULTS

This study's results include that medians (inter-quartile range [IQRs]) of NBAT-1 in HCC and HCV patients were (1.9 [0.87-4.94], 10.01 [7.34-13.29] respectively) which exhibited significantly higher expression than controls, while the medians (IQRs) of FOXCUT in HCC and HCV patients were (0.15 [0.04-0.52], 6.42 [2.49-10.10], respectively) that exhibited significantly lower expression than controls regarding HCC patients but significantly higher expression than controls regarding HCV patients. In comparing serum fold changes of NBAT-1 and FOXCUT between HCC patients and HCV patients; we obtained significantly higher levels of target genes in HCV patients (p < 0.001) than in HCC patients. Also, a positive correlation was detected between NBAT-1 and FOXCUT in HCC group (r = 0.262, p = 0.001) and in HCV group (r = 0.937, p < 0.001). Higher serum NBAT-1 and FOXCUT were significantly associated with better clinical and laboratory data of the disease. Multivariate regression analysis showed that FOXCUT was an independent predictor for HCC among HCV patients (p < 0.001).

CONCLUSION

Our study cited that NBAT-1 and FOXCUT could be considered new diagnostic serum biomarkers for HCC on top of HCV.

Epigenetic dysregulation in meningiomas

Background

Meningiomas are the most common primary brain tumor. Though typically benign with a low mutational burden, tumors with benign histology may behave aggressively and there are no proven chemotherapies. Although DNA methylation patterns distinguish subgroups of meningiomas and have higher predictive value for tumor behavior than histologic classification, little is known about differences in DNA methylation between meningiomas and surrounding normal dura tissue.

Methods

Whole-exome sequencing and methylation array profiling were performed on 12 dura/meningioma pairs (11 WHO grade I and 1 WHO grade II). Single-nucleotide polymorphism (SNP) genotyping and methylation array profiling were performed on an additional 19 meningiomas (9 WHO grade I, 5 WHO grade II, 4 WHO grade III).

Results

Using multimodal studies of meningioma/dura pairs, we identified 4 distinct DNA methylation patterns. Diffuse DNA hypomethylation of malignant meningiomas readily facilitated their identification from lower-grade tumors by unsupervised clustering. All clusters and 12/12 meningioma-dura pairs exhibited hypomethylation of the gene promoters of a module associated with the craniofacial patterning transcription factor FOXC1 and its upstream lncRNA FOXCUT. Furthermore, we identified an epigenetic continuum of increasing hypermethylation of polycomb repressive complex target promoters with increasing histopathologic grade.

Conclusion

These findings support future investigations of the role of epigenetic dysregulation of FOXC1 and cranial patterning genes in meningioma formation as well as studies of the utility of polycomb inhibitors for the treatment of malignant meningiomas.

The role of FOXC1/FOXCUT/DANCR axis in triple negative breast cancer: a bioinformatics and experimental approach

BACKGROUND

Triple-negative breast cancer (TNBC) is the most challenging subtype of breast cancer and does not benefit from the existing targeted therapies. In the present study, we used bioinformatics and experimental approaches to assess the genes that are somehow involved in the epithelial-mesenchymal transition (EMT) pathway which may explain the invasive features of TNBC.

METHOD AND RESULTS

We analyzed five GEO datasets consisting of 657 breast tumors by GEO2R online software to achieve common differentially expressed genes (DEGs) between TNBC and non-TNBC tumors. The expression of the selected coding and non-coding genes was validated in 100 breast tumors, including fifty TNBC and fifty non-TNBC samples, using quantitative Real-Time PCR (qRT-PCR). The bioinformatics approach resulted in a final DEG list consisting of ten upregulated and seventeen downregulated genes (logFC ≥|1| and P < 0.05). Co-expression network construction indicated the FOXC1 transcription factor as a central hub node. Considering the notable role of FOXC1 in EMT, the expression levels of FOXC1-related lncRNAs, lnc-FOXCUT and lnc-DANCR, were also evaluated in the studied tumors. The results of qRT-PCR confirmed notable upregulation of FOXC1, lnc-FOXCUT, and lnc-DANCR in TNBC tissues compared to non-TNBC samples (P < 0.0001, P = 0.0005, and P = 0.0008, respectively). Moreover, ROC curve analysis revealed the potential biomarker role of FOXC1 in TNBC samples.

CONCLUSION

Present study suggested that the deregulation of FOXC1/lnc-FOXCUT/lnc-DANCR axis may contribute to the aggressive features of triple-negative breast tumors. Therefore, this axis may be considered as a new probable therapeutic target in the treatment of TNBC.

miR-149 Suppresses the Proliferation and Metastasis of Human Gastric Cancer Cells by Targeting FOXC1

Purpose

Gastric cancer is one of the most common cancers in the world. miRNAs play an important role in regulating gene expression by binding with 3'-UTR of the target gene. The aim of this study was to investigate the function of miRNA-149 and FOXC1 in gastric cancer. Patients and Methods. qRT-PCR was used to detect the expression of miRNA-149 and FOXC1 in gastric cancer tissues and cells. Human gastric cancer cell lines AGS and MKN28 were cultured and transfected with miR-149 overexpression plasmid and its control or FOXC1 siRNA and its control. The MTT, colony formation, flow cytometry, wound healing, transwell, and western blotting were performed to examine the function of miRNA-149 and FOXC1 in the development of gastric cancer. What is more, dual-luciferase assay and western blotting were used to demonstrated the relationship between miRNA-149 and FOXC1.

Results

miRNA-149 was underexpressed in gastric cancer tissues and cells, while overexpression of miRNA-149 promoted cell apoptosis, retarded cell cycle, and inhibited proliferation and migration in AGS and MKN28 cells. In addition, we showed that miRNA-149 targeted FOXC1. What is more, FOXC1 was highly expressed in gastric cancer tissues and cells; the silencing of FOXC1 inhibited the biological function of AGS and MKN28 cells.

Conclusion

miRNA-149 inhibits the biological behavior of gastric cancer by targeting FOXC1, providing a promising target in the treatment of human gastric cancer.

[Interference of long noncoding RNA FOXCUT inhibits epithelial-mesenchymal transformation and induces mitochondrial injury in nasopharyngeal carcinoma cells]

OBJECTIVE

To investigate the effects of RNA interference of long noncoding RNA FOXCUT on epithelial mesenchymal transformation and mitochondrial function in nasopharyngeal carcinoma (NPC) cells.

METHODS

FOXCUT expression levels were detected by RT-PCR in tumor tissues and adjacent tissues from 50 patients with NPC and in NP69, CNE1, CNE2, SUNE2, HER2 and 5-8F cell lines. CNE1 cells were transfected with a short hairpin RNA (shRNA) targeting FOXCUT or a negative control RNA construct (shRNA-NC), and the changes in cell proliferation and morphology were assessed with CCK8 assay, clone formation assay and microscopic observation. An immunofluorescence assay was used to examine the vimentin-positive cells, and the levels of SOD, MDA and LDH in the cells were detected. The changes of mitochondrial membrane potential were detected with flow cytometry, and the expression levels of E-cad, N-cad, vimentin, Bax, Bcl-2, caspase-3 and c-Myc in the cells were detected with Western blotting.

RESULTS

The expression level of FOXCUT was significantly increased in NPC tissues as compared with the adjacent tissues (P < 0.001). Compared with NP69 cells, CNE1, CNE2, SUNE2, HER2 and 5-8F cells all exhibited significantly increased expressions of FOXCUT (P < 0.001). In CNE1 cells, transfection with FOXCUT shRNA significantly inhibited cell proliferation and clone formation (P < 0.001), and caused obvious changes in cell morphology. FOXCUT knockdown significantly decreased the expressions of N-cad and vimentin, increased E- cad expression and the contents of MDA and LDH (P < 0.05), reduced vimentin- positive cells and the activity of SOD, and caused a shift of red fluorescent cells to green fluorescent cells and an increased percentage of green fluorescent cells. FOXCUT knockdown also resulted in significantly increased expressions of Bax/Bcl2 and cleaved Cas3/Cas3 and a lowered expression of c-Myc.

CONCLUSIONS

Interference of FOXCUT can inhibit the proliferation and epithelial-mesenchymal transformation, enhance oxidative stress, induce mitochondrial function injury, and promote apoptosis in NPC cells, suggesting the potential of FOXCUT interference for targeted treatment of NPC.

LncRNA TCONS_00041002 improves neurological outcomes in neonatal rats with hypoxic-ischemic encephalopathy by inhibiting apoptosis and promoting neuron survival

It has been reported that Neonatal hypoxic-ischemic encephalopathy (HIE) could induce apoptosis in neonates and result in cognitive and sensory impairments, which are associated with poor developmental outcomes. Despite the improvement in neonatology, there is still no clinically effective treatment for HIE presently. Long non-coding RNAs (lncRNAs) play important roles in cellular homeostasis. Nevertheless, their effects in developing rat brains with HI is little known. Here, we established HIE model in neonate rats and explored the expression and function of lncRNAs in HI, and found the expression of 19 lncRNAs was remarkably changed in the brains of HI rats, compared to the sham group. Among them, three lncRNAs (TCONS_00041002, TCONS_00070547, TCONS_00045572) were enriched in the apoptotic process via gene ontology (GO) and pathway analysis, which were selected for the further qRT-PCR verification. Through lentivirus-mediated overexpression of these three lncRNAs, we found that overexpression of TCONS_00041002 attenuated the cell apoptosis, and increased the vitality of neurons after oxygen-glucose deprivation (OGD), therefore reduced the brain infarction and further promoted the neuron survival as well as improved the neurological disorders in the rats subjected to HIE. What's more, ceRNA network prediction and co-expression verification showed that the expression of TCONS_00041002 was positively associated with Foxe1, Pawr and Nfkbiz. Altogether, this study has exhibited that lncRNA TCONS_00041002 participates in the cell apoptosis and neuronal survival of HIE and represents a potential new target for the treatment of HIE.

Long non-coding RNAs orchestrate various molecular and cellular processes by modulating epithelial-mesenchymal transition in head and neck squamous cell carcinoma

Long noncoding RNAs (lncRNAs) regulate various hallmarks associated with the progression of human cancers through their binding with RNA, DNA, and proteins. Epithelial-Mesenchymal Transition (EMT) is a cardinal and multi-stage process where epithelial cells acquire a mesenchymal-like phenotype that is instrumental for tumor cells to initiate invasion and metastasis. LncRNAs can potentially promote tumor onset and progression as well as drug resistance by directly or indirectly altering the EMT program. Head and neck squamous cell carcinoma (HNSCC) are a dreadful malignancy affecting public health globally. The past few years have provided a better insight into the mechanism of EMT in HNSCC. The differential expression of the lncRNAs that can act either as promoters or suppressors in the process of EMT is of great importance. In this review, we aim to sum up, the highly structured mechanism with the diverse role of lncRNAs and their interaction with different molecules in the regulation of EMT. Moreover, discussing principal EMT pathways modulated by lncRNAs and their prospective potential value as therapeutic targets.

An Immune-Related Long Non-Coding RNA Signature to Predict the Prognosis of Ewing's Sarcoma Based on a Machine Learning Iterative Lasso Regression

The aim of this study was to construct a new immune-associated long non-coding RNA (lncRNA) signature to predict the prognosis of Ewing sarcoma (ES) and explore its molecular mechanisms. We downloaded transcriptome and clinical prognosis data from the Gene Expression Omnibus (GSE17679, which included 88 ES samples and 18 matched normal skeletal muscle samples), and used it as a training set to identify immune-related lncRNAs with different expression levels in ES. Univariable Cox regression was used to screen immune-related lncRNAs related to ES prognosis, and an immune-related lncRNA signature was constructed based on machine learning iterative lasso regression. An external verification set was used to confirm the predictive ability of the signature. Clinical feature subgroup analysis was used to explore whether the signature was an independent prognostic factor. In addition, CIBERSORT was used to explore immune cell infiltration in the high- and low-risk groups, and to analyze the correlations between the lncRNA signature and immune cell levels. Gene set enrichment and variation analyses were used to explore the possible regulatory mechanisms of the immune-related lncRNAs in ES. We also analyzed the expression of 17 common immunotherapy targets in the high- and low-risk groups to identify any that may be regulated by immune-related lncRNAs. We screened 35 immune-related lncRNAs by univariate Cox regression. Based on this, an immune-related 11-lncRNA signature was generated by machine learning iterative lasso regression. Analysis of the external validation set confirmed its high predictive ability. DPP10 antisense RNA 3 was negatively correlated with resting dendritic cell, neutrophil, and γδ T cell infiltration, and long intergenic non-protein coding RNA 1398 was positively correlated with resting dendritic cells and M2 macrophages. These lncRNAs may affect ES prognosis by regulating GSE17721_CTRL_VS_PAM3CSK4_12H_BMDC_UP, GSE2770_IL4_ACT_VS_ACT_CD4_TCELL_48H_UP, GSE29615_CTRL_VS_DAY3_ LAIV_IFLU_VACCINE_PBMC_UP, complement signaling, interleukin 2-signal transducer and activator of transcription 5 signaling, and protein secretion. The immune-related 11-lncRNA signature may also have regulatory effects on the immunotherapy targets CD40 molecule, CD70 molecule, and CD276 molecule. In conclusion, we constructed a new immune-related 11-lncRNA signature that can stratify the prognoses of patients with ES.

The contributory role of long non-coding RNAs (lncRNAs) in head and neck cancers: Possible biomarkers and therapeutic targets?

Along with the developments in techniques for genome study, our understanding of its sequences has completely changed. The non-coding sequences of the human genome are no longer considered as "junk" but are rather known to be the source of high-functioning molecules. Some of the most fascinating transcripts in this regard are long non-coding RNAs (lncRNAs) ^___RNA molecules that exceed 200 nucleotides and are not transcribed from protein-coding regions of the genome. These transcripts are capable of gene regulation by various mechanisms, from epigenetic changes and chromosomal arrangements to post-transcription modulation of messenger RNAs. Furthermore, lncRNAs interact with other non-coding transcripts such as microRNAs that further affects gene expression. Considering the fact that cancer is a disease of deregulated expression, recent studies have identified lncRNAs acting as either oncogene or tumor suppressor in a wide range of human malignancies. Head and neck cancer (HNC), with a high incidence rate and unfavorable survival, is no exception in this matter and many investigations have introduced lncRNAs involved in its tumor progression and drug response, as well as those acting as promising diagnostic or prognostic markers. The present study reviews the vital regulatory roles of lncRNAs and further introduces their role in progression of HNC subtypes.

Downregulation of lncRNA ZFAS1 inhibits the hallmarks of thyroid carcinoma via the regulation of miR‑302‑3p on cyclin&nbsp;D1

At present, treatment options for thyroid carcinoma remain limited. The present study aimed to investigate the role of ZFAS1 in various major hallmarks of cancer and the underlying mechanisms in thyroid carcinoma cells. The interactions between long non‑coding RNAs (lncRNAs), microRNAs (miRs) and target genes were predicted by bioinformatics and confirmed by performing dual‑luciferase assays. The mRNA and protein expressions were determined by reverse transcription‑quantitative PCR and western blotting. Cell invasion, migration, and viability were evaluated via Transwell, wound‑healing and Cell Counting Kit‑8 assays, respectively. The results demonstrated that lncRNA ZFAS1 expression was upregulated in thyroid carcinoma tissues, TT and SW579 cells, and was associated with the proliferation of these two cell lines. Notably, downregulation ZFAS1 reduced migration and invasion, and reversed the promotive effects of miR‑302a‑3p inhibitor on the proliferation, migration and invasion of TT and SW579 cells. Moreover, cyclin D1 (CCND1) is targeted by miR‑302a‑3p, and was regulated by ZFAS1. In addition, the downregulation of ZFAS1 not only reversed the promotive effects of miR‑302a‑3p inhibitor on CCND1 expression and the epithelial‑mesenchymal transition (EMT) of TT and SW579 cells, but also targeted and increased the expression of miR‑302a‑3p, and further reduced the expression of CCND1, resulting in suppression of the proliferation, migration, invasion and EMT of thyroid carcinoma cells.

Screening key lncRNAs with diagnostic and prognostic value for head and neck squamous cell carcinoma based on machine learning and mRNA-lncRNA co-expression network analysis

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) is the seventh most common type of cancer around the world. The aim of this study was to seek the long non-coding RNAs (lncRNAs) acting as diagnostic and prognostic biomarker of HNSCC.

METHODS

Base on TCGA dataset, the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were identified between HNSCC and normal tissue. The machine learning and survival analysis were performed to estimate the potential diagnostic and prognostic value of lncRNAs for HNSCC. We also build the co-expression network and functional annotation. The expression of selected candidate mRNAs and lncRNAs were validated by Quantitative real time polymerase chain reaction (qRT-PCR).

RESULTS

A total of 3363 DEmRNAs (1822 down-regulated and 1541 up-regulated mRNAs) and 32 DElncRNAs (13 down-regulated and 19 up-regulated lncRNAs) between HNSCC and normal tissue were obtained. A total of 13 lncRNAs (IL12A.AS1, RP11.159F24.6, RP11.863P13.3, LINC00941, FOXCUT, RNF144A.AS1, RP11.218E20.3, HCG22, HAGLROS, LINC01615, RP11.351J23.1, AC024592.9 and MIR9.3HG) were defined as optimal diagnostic lncRNAs biomarkers for HNSCC. The area under curve (AUC) of the support vector machine (SVM) model, decision tree model and random forests model and were 0.983, 0.842 and 0.983, and the specificity and sensitivity of the three model were 95.5% and 96.2%, 77.3% and 97.6% and 93.2% and 97.8%, respectively. Among them, AC024592.9, LINC00941, LINC01615 and MIR9-3HG was not only an optimal diagnostic lncRNAs biomarkers, but also related to survival time. The focal adhesion, ECM-receptor interaction, pathways in cancer and cytokine-cytokine receptor interaction were four significantly enriched pathways in DEmRNAs co-expressed with the identified optimal diagnostic lncRNAs. But for most of the selected DEmRNAs and DElncRNAs, the expression was consistent with our integrated analysis results, including LINC00941, LINC01615, FOXCUT, TGA6 and MMP13.

CONCLUSION

AC024592.9, LINC00941, LINC01615 and MIR9-3HG was not only an optimal diagnostic lncRNAs biomarkers, but also were a prognostic lncRNAs biomarkers.

FOXCUT Promotes the Proliferation and Invasion by Activating FOXC1/PI3K/AKT Pathway in Colorectal Cancer

Introduction

Colorectal cancer (CRC) is the third most commonly diagnosed world cancer. Long noncoding RNAs (lncRNAs) serve important regulatory roles in tumorigenesis. However, the contributions of lncRNAs to human CRC remain largely unknown.

Material and Methods

FOXC1 and FOXCUT lncRNA expression levels were detected in a panel of paired specimens obtained from 48 patients’ tissues and cell lines with CRC using RT-qPCR. RNA interference was used to investigate potential correlations between FOXC1 and FOXCUT expression in HT29. Cell proliferation was assessed by MTT assay and EdU incorporation assay. The migration and invasion of CRC cells were detected by transwell assay. Western blot was applied to assess the protein expression and PI3K/AKT signaling pathway.

Results

In this study, a novel long noncoding RNA (FOXCUT) was frequently overexpressed in CRC tissues and cell lines. In addition, the expressions of FOXCUT and FOXC1 were positively correlated. When the expression of FOXCUT was downregulated by small interfering RNA (siRNA), the expression of FOXC1 was also decreased. Moreover, knockdown of FOXCUT significantly inhibited proliferation and invasion of CRC cell lines and resulted in downregulated expression of the matrix metalloproteinase 1 (MMP-1). Mechanistically, FOXCUT promotes the expression of FOXC1 to activate PI3K/AKT signaling pathway for its regulation of cell growth and proliferation.

Conclusion

In summary, our findings indicate that FOXCUT plays an important oncogenic role and may serve as a novel biomarker and therapeutic target in CRC progression.

Emerging Contribution of PancRNAs in Cancer

“Cancer” includes a heterogeneous group of diseases characterized by abnormal growth beyond natural boundaries. Neoplastic transformation of cells is orchestrated by multiple molecular players, including oncogenic transcription factors, epigenetic modifiers, RNA binding proteins, and coding and noncoding transcripts. The use of computational methods for global and quantitative analysis of RNA processing regulation provides new insights into the genomic and epigenomic features of the cancer transcriptome. In particular, noncoding RNAs are emerging as key molecular players in oncogenesis. Among them, the promoter-associated noncoding RNAs (pancRNAs) are noncoding transcripts acting in cis to regulate their host genes, including tumor suppressors and oncogenes. In this review, we will illustrate the role played by pancRNAs in cancer biology and will discuss the latest findings that connect pancRNAs with cancer risk and progression. The molecular mechanisms involved in the function of pancRNAs may open the path to novel therapeutic opportunities, thus expanding the repertoire of targets to be tested as anticancer agents in the near future.

Dissecting the transcriptional regulatory networks of promoter-associated noncoding RNAs in development and cancer

In-depth analysis of global RNA sequencing has enabled a comprehensive overview of cellular transcriptomes and revealed the pervasive transcription of divergent RNAs from promoter regions across eukaryotic genomes. These studies disclosed that genomes encode a vast repertoire of RNAs beyond the well-known protein-coding messenger RNAs. Furthermore, they have provided novel insights into the regulation of eukaryotic epigenomes, and transcriptomes, including the identification of novel classes of noncoding transcripts, such as the promoter-associated noncoding RNAs (pancRNAs).

PancRNAs are defined as transcripts transcribed within few hundred bases from the transcription start sites (TSSs) of protein-coding or non-coding genes. Unlike the long trans-acting ncRNAs that regulate expression of target genes located in different chromosomal domains and displaying their function both in the nucleus and in the cytoplasm, the pancRNAs operate as cis-acting elements in the transcriptional regulation of neighboring genes. PancRNAs are very recently emerging as key players in the epigenetic regulation of gene expression programs in development and diseases.

Herein, we review the complex epigenetic network driven by pancRNAs in eukaryotic cells, their impact on physiological and pathological states, which render them promising targets for novel therapeutic strategies.

lncRNA SNHG7 promotes tumorigenesis of nasopharyngeal carcinoma via epithelial-to-mesenchymal transition

Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors. Studies have indicated that long noncoding RNAs (lncRNAs) function as important regulators in progression of tumorigenesis. In this study, lncRNA small nucleolar RNA host gene 7 (SNHG7) was selected to identify how it functioned in the development of NPC. Real-time quantitative polymerase chain reaction (RT-qPCR) was performed to detect SNHG7 expression in paired NPC patient tissue samples and cell lines. The role of SNHG7 in the metastasis of NPC was detected through scratch wound assay and Transwell assay. RT-qPCR and western blot assay were used to discover the function of SNHG7 in epithelial-to-mesenchymal transition (EMT) process. Tumor metastasis assay was also performed in vivo. In this study, RT-qPCR results showed that SNHG7 expression in NPC samples was remarkably higher when compared with that in adjacent ones. Cell invasion and cell migration of NPC were inhibited due to silence of SNHG7 and were promoted due to overexpression of SNHG7. Moreover, results of further experiments revealed that the EMT-related proteins were regulated via knockdown or overexpression of SNHG7 in NPC. Furthermore, tumor metastasis of NPC was inhibited via knockdown of SNHG7 and was enhanced via overexpression of SNHG7 in nude mice. These results indicate that SNHG7 enhances NPC cell invasion and cell migration by eliciting the EMT process.

Biological and clinical relevance of metastasis-associated long noncoding RNAs in esophageal squamous cell carcinoma: A systematic review

Esophageal squamous cell carcinoma (ESCC) is a foremost cancer-related death worldwide owing to rapid metastasis and poor prognosis. Metastasis, as the most important reason for death, is biologically a multifaceted process involving a range of cell signaling pathways. Long noncoding RNAs (lncRNAs), as transcriptional regulators, can regulate numerous genomic processes and cellular processes such as cell proliferation, migration, and invasion. LncRNAs have also been shown to involve in/regulate the cancer metastasis-related signaling pathways. Hence, they have increasingly been brought to international attention in molecular oncology research. A number of researchers have attempted to reveal the biological and clinical relevance of lncRNAs in ESCC tumourigenesis and metastasis. The aberrant expression of these molecules in ESCC has regularly been reported to involve in various cellular processes and clinical features, including diagnosis, prognosis, and therapeutic responses. Here, we especially consider the pathways in which lncRNAs act as metastasis-mediated effectors, mainly by interacting with epithelial-mesenchymal transition-associated factors. We review the biological roles of lncRNAs through involving in ESCC metastasis as well as the clinical significance of the metastasis-related lncRNAs in cancer diagnosis and prognosis.

Long noncoding RNA ZFAS1 promotes tumorigenesis and metastasis in nasopharyngeal carcinoma by sponging miR-892b to up-regulate LPAR1 expression

OBJECTIVE

In this study, we explored the NPC-specific expression of ZFAS1 and the mechanism of ZFAS1-mediated growth, aggressiveness and tumorigenesis in NPC.

METHODS

The expression profile of lncRNAs was detected in NPC tissues and matching para-carcinoma tissues using microarray analysis. LncRNA-miRNA and miRNA-mRNA interaction networks were constructed using the miRcode v11 and TargetScanHuman v7.2 web server and then validated using dual-luciferase assay. Western blot and RT-qPCR were performed to detect protein and RNA expression. The effects of ZFAS1, miR-892b and LPAR1 dysregulation on the proliferative, migratory and invasive abilities of NPC cells were observed using colony formation, cell counting kit-8 (CCK-8) and transwell assays in vitro. In vivo, a xenograft nude mouse model was established to detect the impact of ZFAS1 dysregulation on the tumorigenicity of NPC cells.

RESULTS

The expression of multiple lncRNAs, of which ZFAS1 was up-regulated, was dysregulated in NPC tissues. ZFAS1 directly targeted miR-892b, and miR-892b negatively regulated the expression of downstream LPAR1. The proliferation, migration and invasion of NPC cells could be largely enhanced by the downregulation of miR-892b as well as the up-regulation of ZFAS1 and LPAR1, while the overexpression of miR-892b and the downregulation of ZFAS1 and LPAR1 decreased these abilities. In nude mice, the growth of tumour xenografts formed by HONE1 cells was significantly suppressed when ZFAS1 was silenced.

CONCLUSION

The study demonstrated that lncRNA ZFAS1 may act as a promoter of tumorigenesis and metastasis in nasopharyngeal carcinoma, by up-regulating the expression of LPAR1 in a miR-892b-dependent manner.

Silencing of long noncoding RNA SRRM2-AS exerts suppressive effects on angiogenesis in nasopharyngeal carcinoma via activating MYLK-mediated cGMP-PKG signaling pathway

Long noncoding RNAs (lncRNAs) play a crucial role in several malignances, involving nasopharyngeal carcinoma (NPC), a heterogeneous disease. This study investigated mechanism of serine/arginine repetitive matrix protein 2-alternative splicing (SRRM2-AS) in NPC cell proliferation, differentiation, and angiogenesis. Initially, differentially expressed lncRNAs were screened out via microarray analysis. Vascular endothelial growth factor (VEGF) protein positive rate and microvessel density (MVD) were determined in NPC and adjacent tissues. NPC CNE-2 cells were treated with a series of vector and small interfering RNA to explore the effect of SRRM2-AS in NPC. The target relationship between myosin light chain kinase (MYLK) and SRRM2-AS was verified. Levels of SRRM2-AS, MYLK, cGMP, PKG, VEGF, PCNA, Ki-67, B-cell lymphoma-2 (Bcl-2), Bcl-2-associated X protein (Bax), and Caspase 3 were determined after transfection. Finally, the effect of SRRM2-AS on cell proliferation, colony formation, angiogenesis, cell cycle, and apoptosis in NPC was evaluated. SRRM2-AS was highly expressed and MYLK was poorly expressed in NPC tissues. VEGF protein positive rate and MVD were elevated in NPC tissues. MYLK was confirmed to be a target gene of SRRM2-AS. Silencing of SRRM2-AS elevated levels of MYLK, cGMP, PKG, Bax, and Caspase 3, but decreased levels of VEGF, PCNA, Ki-67, and Bcl-2. Especially, silencing of SRRM2-AS suppressed cell proliferation, colony formation and angiogenesis, blocked cell cycle, and enhanced cell apoptosis in NPC. Our results suggested that silencing of SRRM2-AS protected against angiogenesis of NPC cells by upregulating MYLK and activating the cGMP-PKG signaling pathway, which provides a new target for NPC treatment.

Forkhead box C1 promotes metastasis and invasion of non-small cell lung cancer by binding directly to the lysyl oxidase promoter

Increasing evidence indicates that human forkhead box C1 (FOXC1) plays important roles in tumor development and metastasis. However, the underlying molecular mechanism of FOXC1 in non–small cell lung cancer (NSCLC) metastasis remains unclear. Here, we identified FOXC1 as an independent prognostic factor in NSCLC and showed clear biological implications in invasion and metastasis. FOXC1 overexpression enhanced the proliferation, migration and invasion of NSCLC cells, whereas FOXC1 silencing impaired the effects both in vitro and in vivo. Importantly, we found a positive correlation between FOXC1 expression and lysyl oxidase (LOX) expression in NSCLC cells and patient samples. Downregulation of LOX or LOX activity inhibition in NSCLC cells inhibited the FOXC1‐driven effects on cellular migration and invasion. Xenograft models showed that inhibition of LOX activity by β‐aminopropionitrile monofumarate decreased the number of lung metastases. Mechanistically, we demonstrated a novel FOXC1‐LOX mechanism that was involved in the invasion and metastasis of NSCLC. Dual‐luciferase assay and ChIP identified that FOXC1 bound directly in the LOX promoter region and activated its transcription. Collectively, the present study offered new insight into FOXC1 in the mediation of NSCLC metastasis through interaction with the LOX promoter and further revealed that targeted inhibition of LOX protein activity could prevent lung metastasis in murine xenograft models. These data implicated FOXC1 as a potential therapeutic strategy for the treatment of NSCLC metastasis.

LINC00958 Promotes The Malignancy Of Nasopharyngeal Carcinoma By Sponging microRNA-625 And Thus Upregulating NUAK1

Purpose

The aberrant expression of long noncoding RNAs (lncRNAs) indicates progression of various diseases. LINC00958 has been well studied in several types of human cancer; however, the expression profile, functions, and potential mechanism of action of this lncRNA in nasopharyngeal carcinoma (NPC) remain largely unclear and still need to be elucidated. In the present study, we aimed to measure LINC00958 expression in NPC, determine its clinical value, and explore its roles in NPC progression as well as the mechanisms behind these processes.

Methods

The expression profile of LINC00958 in NPC was evaluated by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). A series of functional assays, including the Cell Counting Kit-8 assay, flow cytometry, a Transwell assay, and an in vivo nude mouse model, were utilized to determine the participation of LINC00958 in the malignancy of NPC.

Results

LINC00958 was found to be upregulated in NPC tissue specimens and cell lines. The LINC00958 overexpression significantly correlated with tumor size, lymph node status, TNM stage, and worse overall survival among NPC patients. Downregulation of LINC00958 suppressed NPC cell proliferation, migration, and invasion and induced apoptosis in vitro. Additionally, the LINC00958 knockdown impaired tumor growth in vivo. Mechanistically, LINC00958 was found to serve as a molecular sponge of microRNA-625 (miR-625), thereby upregulating NUAK family SNF1-like kinase 1 (NUAK1) in NPC cells. Lastly, rescue experiments validated the involvement of the miR-625–NUAK1 axis in LINC00958-mediated biological functions in NPC.

Conclusion

Our results demonstrated that LINC00958 works as an oncogene in NPC and plays a key role in the malignant phenotype of NPC cells by sponging miR-625 and increasing NUAK1 expression. The LINC00958–miR-625–NUAK1 pathway might be a target for anticancer therapy in patients with NPC.

Inhibitory Traits of Dendrosome Curcumin (DNC) on Breast Cancer Compared to Curcumin Single Compound

PURPOSE

Vast therapeutic traits and very low toxicity of curcumin compound have made it and related formulations promising for treatment purposes. The aim of this study was the assessment of dendrosome curcumin (DNC) inhibitory effects on breast cancer therapy compared to single curcumin compound.

METHODS

DNC was synthesized and MCF-7 cells were prepared. The cultured cells were treated with 20 μg/ml and 25 μg/ml of DNC. Real-time quantitative PCR (RT-qPCR) was performed to measure the expression of FOXCUT and MEG3 genes. Additionally, flow cytometry was applied to measure cell death rate and apoptosis.

RESULTS

The results outlined that DNC enhanced the MEG3 gene expression significantly higher than the control. Furthermore, DNC was associated with a significant decrease in the expression of FOXCUT gene as compared to the control. The application of DNC in the MCF7 cell line enhanced cell death and reduced necrosis.

CONCLUSIONS

The rate of apoptosis (programmed cell death) was enhanced, but necrosis was decreased in treated cancer cells compared to those treated with single curcumin. Accordingly, the DNC can be applied to hinder the growth and dissemination of cancer cells as a preferred approach to reduce the complications of other strategies such as chemotherapy and radiation therapy. Indeed, we concluded that DNC enhanced the expression of MEG3, a tumor suppressor, at 25 μm dose, but reduced the expression of the FOXCUT gene, possibly via the methylation of the gene. Thereby, DNC exerted a promising tumor inhibitory growth potential for the eradication of cancer cells.

The functions and oncogenic roles of CCAT1 in human cancer

In various human cancers, long non-coding RNAs (lncRNAs), a novel class of RNAs longer than 200 nucleotides without protein-coding potential, are implicated in a variety of biological processes, such as cell proliferation, invasion, metastasis, and apoptosis through regulation of gene expression at various levels including chromatin, splicing, transcriptional and post-transcriptional levels. However, the mechanisms underlying these are still elusive. Colon cancer-associated transcript 1(CCAT1) has received increased attention among those lncRNAs. Studies have shown high expression pattern and oncogenic role of CCAT1 in different types of cancer, and aberrant expression of CCAT1 has been involved in tumor-genesis, progression, metastasis, and patient survival via regulating different target genes and signaling pathways. In this review, we first introduce the concept, identification, and biological function of CCAT1; we then describe the mechanisms by which CCAT1 regulate the cancer proliferation and progression. In the last, we discuss emerging insights into the role of CCAT1 as potential biomarker and therapeutic target for novel treatment paradigms in cancer.

Inactivation of Stat3 and crosstalk of miRNA155-5p and FOXO3a contribute to the induction of IGFBP1 expression by beta-elemene in human lung cancer

β-Elemene, an active component of natural plants, has been shown to exhibit anticancer properties. However, the detailed mechanism underlying these effects has yet to be determined. In this study, we show that β-elemene inhibits the growth of lung cancer cells. Mechanistically, we found that β-elemene decreased the phosphorylation of signal transducer and activator of transcription 3 (Stat3) and miRNA155-5p mRNA but induced the protein expression of human forkhead box class O (FOXO)3a; the latter two were abrogated in cells with overexpressed Stat3. Notably, miRNA155-5p mimics reduced FOXO3a luciferase reporter activity in the 3-UTR region and protein expression, whereas overexpressed FOXO3a countered the reduction of the miRNA155-5p levels by β-elemene. Moreover, β-elemene increased the mRNA and protein expression levels as well as promoter activity of insulin-like growth factor-binding protein 1 (IGFBP1); this finding was not observed in cells with a silenced FOXO3a gene and miRNA155-5p mimics. Finally, silencing of IGFBP1 blocked β-elemene-inhibited cell growth. Similar findings were observed in vivo. In summary, our results indicate that β-elemene increases IGFBP1 gene expression via inactivation of Stat3 followed by a reciprocal interaction between miRNA155-5p and FOXO3a. This effect leads to inhibition of human lung cancer cell growth. These findings reveal a novel molecular mechanism underlying the inhibitory effects of β-elemene on lung cancer cells.

A compound found in one Chinese medicinal herb inhibits the growth of lung cancer cells by indirectly activating a protein with anti-proliferative properties. Hann and colleagues from the Guangzhou University of Chinese Medicine, China, uncovered the molecular pathways by which β-elemene, a natural compound isolated from the Curcuma wenyujin plant, mediates the anti-cancer effects. They showed that β-elemene inactivates the two important regulatory molecules, one protein and another small RNA, while also inducing the expression of one protein that promotes in killing cancer cells. These changes lead to elevated levels of the protein that prevents cell invasion and spread. Collectively, this altered signaling inside the lung cancer cell lead to reduced growth, in both cell-based culture and mouse model. The findings help explain why β-elemene has potential as a therapeutic agent in lung cancer.

Comprehensive analysis of novel three-long noncoding RNA signatures as a diagnostic and prognostic biomarkers of human triple-negative breast cancer

Currently, traditional predictors of prognosis (tumor size, nodal status, progesterone receptor [PR], estrogen receptor [ER], or human epidermal growth factor receptor-2 [HER2]) are insufficient for precise survival prediction for triple-negative breast cancer (TNBC). Long noncoding RNAs (lncRNAs) have been observed to exert critical functions in cancer, including in TNBC. Nevertheless, systematically tracking expression-based lncRNA biomarkers based on the sequence data for the prediction of prognosis in TNBC has not yet been investigated. To ascertain whether biomarkers exist that can distinguish TNBC from adjacent normal tissue or nTNBC, we implemented a comprehensive analysis of lncRNA expression profiles and clinical data of 1097 BC samples from The Cancer Genome Atlas database. A total of 1510 differentially expressed lncRNAs in normal and TNBC samples were extracted. Similarly, 672 differentially expressed lncRNAs between nTNBC and TNBC samples were detected. The receiver operating characteristic curve analysis indicated that three upregulated lncRNAs (AC091043.1, AP000924.1, and FOXCUT) may be of strong diagnostic value for predicting the existence of TNBC in the training and validation sets (area under the curve (AUC > 0.85). Kaplan-Meier analysis demonstrated that the other three lncRNAs (AC010343.3, AL354793.1, and FGF10-AS1) were associated with the prognosis of TNBC patients (P < 0.05). We used the three overall survival (OS)-related lncRNAs to establish a three-lncRNA signature. Multivariate Cox regression analysis suggested that the three-lncRNA signature was a prognostic factor independent of other clinical variables ( P < 0.01) for predicting OS in TNBC patients that could be utilized to classify patients into high- or low-risk subgroups. Our results might provide efficient signatures for clinical diagnosis and prognostic evaluation of TNBC.

Prognostic significance of the long noncoding RNAs in nasopharyngeal carcinoma: a systematic review and meta-analysis

Background and objective

Nasopharyngeal carcinoma (NPC) is a common head and neck malignancy. Despite recent advances in treatment, the prognosis, particularly for those at the advanced stages, remains poor. Moreover, the underlying genetic and molecular events have remained obscure so far. Recently, increasing evidence has demonstrated that long noncoding RNAs (lncRNAs) could act as either oncogenes or tumor suppressor genes in various cancers depending on their targets. And some lncRNAs have been shown to be aberrantly expressed in NPC. In this meta-analysis, we try to elucidate the possible role of lncRNAs and their expression on prognosis in NPC.

Methods

We searched the databases of PubMed, Embase, and Web of Science for relevant articles ranging from January 2000 to December 2017. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were used to evaluate the prognostic value of lncRNAs in NPC. Odds ratios (ORs) were used to assess the association between lncRNAs and clinicopathological characteristics.

Results

A total of 14 eligible publications including 14 on prognosis and eight on clinicopathological characteristics were identified. Our results demonstrated that the high expression of lncRNAs was related to poor overall survival (OS; HR =1.55; 95% CI =1.01, 2.40; P=0.05) and disease-free survival (DFS; HR =1.83; 95% CI =1.07, 3.13; P=0.03) of NPC. Moreover, the expression of lncRNAs was correlated with male gender (OR =1.42; 95% CI =1.05, 1.91; P=0.02), lymph node status (OR =2.20; 95% CI =1.29, 3.73; P=0.004), and tumor node metastasis (TNM) clinical stage (OR =2.55; 95% CI =1.12, 5.78; P=0.03).

Conclusion

This meta-analysis shows that the level of expression of lncRNAs may be a potential prognostic indicator in NPC.

Long non-coding RNA implicated in the invasion and metastasis of head and neck cancer: possible function and mechanisms

Head and neck cancer (HNC) ranks as the 6th most common malignancy across the world. Metastasis is a hallmark of cancer, primarily contributing to the relapse and poor prognosis of HNC. Recently, long noncoding RNAs (lncRNAs), previously considered as non-functional, are increasingly appreciated by scholars to play crucial roles in mediating HNC metastasis. LncRNAs, which are located in the nucleus and cytoplasm, mainly exert their function via epigenetic modification, transcriptional control and translational regulation. As several lncRNAs are presently demonstrated to participate in HNC metastasis, we make a summary of the functions and mechanisms regarding these lncRNAs. As shown in the literature, most lncRNAs appear to promote the metastasis of HNC. Hence, we primarily discuss the lncRNAs involved in enhancing metastasis. Additionally, more studies are needed to understand those lncRNAs without clear mechanisms. Furthermore, we introduced the upstream regulator for the aberrant expression of lncRNAs in HNC. Finally, we concisely addressed future research prospects of lncRNAs, particularly the interplay between lncRNAs and tumor immunity as well as lncRNA-targeted therapeutic techniques, and we introduced clustered regularly interspaced short palindromic repeats (CRISPR)-Display as a possibly transformative tool to study lncRNAs. Although lncRNA research is still in the initial stage, it holds great promise to be applied as a prognosticator of HNC and a therapeutic target to inhibit HNC metastasis, which could significantly enhance the outcome of HNC patients.

Coordinated targeting of MMP-2/MMP-9 by miR-296-3p/FOXCUT exerts tumor-suppressing effects in choroidal malignant melanoma

Choroidal melanoma is the most common intraocular tumor in adults, and overexpression of matrix metalloproteinase-2 or matrix metalloproteinase-9 (MMP-2/MMP-9) is associated with angiogenesis and tumor metastasis of the choroidal malignant melanoma (CMM). This study aims to investigate the functions and mechanisms of microRNA or long non-coding RNA-targeted MMP-2/MMP-9 in CMM. We demonstrated that expressions of MMP-2/MMP-9 were increased in CMM tissues and C918 cells in comparison with normal choroidal melanocytes. Bio-informatics prediction and our experiments validated that MMP-2 and MMP-9 were simultaneously targeted by miR-296-3p and FOXC1 promoter upstream transcript (FOXCUT); the latter two exerted tumor-suppressing effects on CMM cells by inhibiting cell proliferation, cell cycle progression, migration, invasion, and induction of cell apoptosis. Furthermore, significant downregulations of miR-296-3p and FOXCUT were found in C918 cells compared with choroidal melanocytes from the unaffected eyes, and a positive correlation was observed between their levels in three cases of eye malignant melanomas. Our data indicated that MMP-2/MMP-9 was coordinately targeted by two non-coding RNAs, miR-296-3p and FOXCUT, which were decreased, and tumor-suppressing factors in CMM. Further study will show the possibility of developing them as therapeutic candidates for CMM.

FOXC1 in cancer development and therapy: deciphering its emerging and divergent roles

Forkhead box C1 (FOXC1) is an essential member of the forkhead box transcription factors and has been highlighted as an important transcriptional regulator of crucial proteins associated with a wide variety of carcinomas. FOXC1 regulates tumor-associated genes and is regulated by multiple pathways that control its mRNA expression and protein activity. Aberrant FOXC1 expression is involved in diverse tumorigenic processes, such as abnormal cell proliferation, cancer stem cell maintenance, cancer migration, and angiogenesis. Herein, we review the correlation between the expression of FOXC1 and tumor behaviors. We also summarize the mechanisms of the regulation of FOXC1 expression and activity in physiological and pathological conditions. In particular, we focus on the pathological processes of cancer targeted by FOXC1 and discuss whether FOXC1 is good or detrimental during tumor progression. Moreover, FOXC1 is highlighted as a clinical biomarker for diagnosis or prognosis in various human cancers. The information reviewed here should assist in experimental designs and emphasize the potential of FOXC1 as a therapeutic target for cancer.