Non-Coding RNA Pvt1 Promotes Cancer Stem Cell-Like Traits in Nasopharyngeal Cancer via Inhibiting miR-1207

Impact of MICA 3'UTR allelic variability on miRNA binding prediction, a bioinformatic approach

MicroRNAs (miRNAs) are small non-coding RNAs that participate as powerful genetic regulators. MiRNAs can interfere with cellular processes by interacting with a broad spectrum of target genes under physiological and pathological states, including cancer development and progression. Major histocompatibility complex major histocompatibility complex class I-related chain A (MICA) belongs to a family of proteins that bind the natural-killer group 2, member D (NKG2D) receptor on Natural Killer cells and other cytotoxic lymphocytes. MICA plays a crucial role in the host's innate immune response to several disease settings, including cancer. MICA harbors various single nucleotide polymorphisms (SNPs) located in its 3'-untranslated region (3'UTR), a characteristic that increases the complexity of MICA regulation, favoring its post-transcriptional modulation by miRNAs under physiological and pathological conditions. Here, we conducted an in-depth analysis of MICA 3'UTR sequences according to each MICA allele described to date using NCBI database. We also systematically evaluated interactions between miRNAs and their putative targets on MICA 3'UTR containing SNPs using in silico analysis. Our in silico results showed that MICA SNPs rs9266829, rs 1880, and rs9266825, located in the target sequence of miRNAs hsa-miR-106a-5p, hsa-miR-17-5p, hsa-miR-20a-5p, hsa-miR-20b-5p, hsa-miR-93, hsa-miR-1207.5p, and hsa-miR-711 could modify the binding free energy between -8.62 and -18.14 kcal/mol, which may affect the regulation of MICA expression. We believe that our results may provide a starting point for further exploration of miRNA regulatory effects depending on MICA allelic variability; they may also be a guide to conduct miRNA in silico analysis for other highly polymorphic genes.

A Mouse Systems Genetics Approach Reveals Common and Uncommon Genetic Modifiers of Hepatic Lysosomal Enzyme Activities and Glycosphingolipids

Identification of genetic modulators of lysosomal enzyme activities and glycosphingolipids (GSLs) may facilitate the development of therapeutics for diseases in which they participate, including Lysosomal Storage Disorders (LSDs). To this end, we used a systems genetics approach: we measured 11 hepatic lysosomal enzymes and many of their natural substrates (GSLs), followed by modifier gene mapping by GWAS and transcriptomics associations in a panel of inbred strains. Unexpectedly, most GSLs showed no association between their levels and the enzyme activity that catabolizes them. Genomic mapping identified 30 shared predicted modifier genes between the enzymes and GSLs, which are clustered in three pathways and are associated with other diseases. Surprisingly, they are regulated by ten common transcription factors, and their majority by miRNA-340p. In conclusion, we have identified novel regulators of GSL metabolism, which may serve as therapeutic targets for LSDs and may suggest the involvement of GSL metabolism in other pathologies.

Profiling of circRNA expressions in radiation-treated head and neck cancer cells and the potential role of circPVT1

OBJECTIVE

Radiotherapy is an indispensable treatment modality for head and neck cancers (HNCs). Due to their stable structure, circular RNAs (circRNA) have been implicated as potential biomarkers for clinical use in cancers. The purpose of this study was profiling the circRNA in radiation-treated head and neck cancer cells to identify potential differentially expressed circRNAs.

DESIGN

The effects of radiation on the expression level of circRNAs were investigated in HNCs cells, compared to healthy cell lines. To predict the potential role of circRNAs in HNC patients, tissue expression levels, survival analyses of circRNAs, and circRNA-miRNA network were evaluated using TCGA/CPTAC datasets. Based on expression level in irradiated cells, circPVT1 (plasmacytoma variant translocation 1) was further investigated by sequence analysis.

RESULTS

The study revealed the characterization of differentially expressed circRNAs in cancer cells and that irradiation made significant changes in the expression of circRNAs. These findings suggest that certain circRNAs, especially circPVT1, may be potential biomarkers to monitor radiotherapy effects in patients with HNCs.

CONCLUSIONS

CircRNAs may be promising molecules for improving and understanding radiotherapy efficacy in HNCs.

lncRNA PVT1: a novel oncogene in multiple cancers

Long noncoding RNAs are involved in epigenetic gene modification, including binding to the chromatin rearrangement complex in pre-transcriptional regulation and to gene promoters in gene expression regulation, as well as acting as microRNA sponges to control messenger RNA levels in post-transcriptional regulation. An increasing number of studies have found that long noncoding RNA plasmacytoma variant translocation 1 (PVT1) plays an important role in cancer development. In this review of a large number of studies on PVT1, we found that PVT1 is closely related to tumor onset, proliferation, invasion, epithelial–mesenchymal transformation, and apoptosis, as well as poor prognosis and radiotherapy and chemotherapy resistance in some cancers. This review comprehensively describes PVT1 expression in various cancers and presents novel approaches to the diagnosis and treatment of cancer.

Long non-coding RNA PVT1: A promising chemotherapy and radiotherapy sensitizer

The long non-coding RNA (lncRNA) PVT1 was first found to activate variant translocations in the plasmacytoma of mice. Human lncPVT1 is located on chromosome 8q24.21, at the same locus as the well-known MYC oncogene. LncPVT1 has been found to promote the progression of various malignancies. Chemoresistance and radioresistance seriously affect tumor treatment efficacy and are associated with the dysregulation of physiological processes in cancer cells, including apoptosis, autophagy, stemness (for cancer stem cells, CSC), hypoxia, epithelial–mesenchymal transition (EMT), and DNA damage repair. Previous studies have also implicated lncPVT1 in the regulation of these physiological mechanisms. In recent years, lncPVT1 was found to modulate chemoresistance and radioresistance in some cancers. In this review, we discuss the mechanisms of lncPVT1-mediated regulation of cellular chemoresistance and radioresistance. Due to its high expression in malignant tumors and sensitization effect in chemotherapy and radiotherapy, lncPVT1 is expected to become an effective antitumor target and chemotherapy and radiotherapy sensitizer, which requires further study.

CircPVT1: a pivotal circular node intersecting Long Non-Coding-PVT1 and c-MYC oncogenic signals

The role of circular RNAs in oncogenesis has begun to be widely studied in recent years, due to the significant impact that these molecules have in disease pathogenesis, as well as their potential for the future of innovative therapies. Moreover, due to their characteristically circular shape, circular RNAs are very resistant molecules to RNA degradation whose levels are easily assessed in body fluids. Accordingly, they represent an opportunity for the discovery of new diagnostic and prognostic markers in a wide range of diseases. Among circular RNAs, circPVT1 is a rather peculiar one that originates from the circularization of the exon 2 of the PVT1 gene that encodes a pro-tumorigenic long non-coding RNA named lncPVT1. There are a few examples of circular RNAs that derive from a locus producing another non-coding RNA. Despite their apparent transcriptional independence, which occurs using two different promoters, a possible synergistic effect in tumorigenesis cannot be excluded considering that both have been reported to correlate with the oncogenic phenotype. This complex mechanism of regulation appears to also be controlled by c-MYC. Indeed, the PVT1 locus is located only 53 Kb downstream c-MYC gene, a well-known oncogene that regulates the expression levels of about 15% of all genes. Here, we review circPVT1 origin and biogenesis highlighting the most important mechanisms through which it plays a fundamental role in oncogenesis, such as the well-known sponge activity on microRNAs, as well as its paradigmatic interactome link with lncPVT1 and c-MYC expression.

MicroRNAs regulating SOX2 in cancer progression and therapy response

The proliferation, metastasis and therapy response of tumour cells are tightly regulated by interaction among various signalling networks. The microRNAs (miRNAs) can bind to 3'-UTR of mRNA and down-regulate expression of target gene. The miRNAs target various molecular pathways in regulating biological events such as apoptosis, differentiation, angiogenesis and migration. The aberrant expression of miRNAs occurs in cancers and they have both tumour-suppressor and tumour-promoting functions. On the contrary, SOX proteins are capable of binding to DNA and regulating gene expression. SOX2 is a well-known member of SOX family that its overexpression in different cancers to ensure progression and stemness. The present review focuses on modulatory impact of miRNAs on SOX2 in affecting growth, migration and therapy response of cancers. The lncRNAs and circRNAs can function as upstream mediators of miRNA/SOX2 axis in cancers. In addition, NF-κB, TNF-α and SOX17 are among other molecular pathways regulating miRNA/SOX2 axis in cancer. Noteworthy, anti-cancer compounds including bufalin and ovatodiolide are suggested to regulate miRNA/SOX2 axis in cancers. The translation of current findings to clinical course can pave the way to effective treatment of cancer patients and improve their prognosis.

The Impact of lncRNAs and miRNAs in Regulation of Function of Cancer Stem Cells and Progression of Cancer

Stem cells have two important features, namely the ability for self-renewal and the capacity to differentiate into some cell kinds with specialized functions. These two features are also present in cancer stem cells (CSCs). These cells have been detected in almost all kinds of cancers facilitating their tumorigenicity. Molecular cascades that control self-renewal of stem cells, namely the Wnt, Notch, and Hedgehog pathways have been suggested to influence CSCs functions as well. Moreover, non-coding RNAs can regulate function of CSCs. Function of miRNAs in the regulation of CSCs has been mostly assessed in breast cancer and hepatocellular carcinoma. miR-130a-3p, miR-600, miR-590-5p, miR-142-3p, miR-221, miR-222, miR-638, miR-375, miR-31, and miR-210 are among those regulating this feature in breast cancer. Moreover, miR-206, miR-192-5p, miR-500a-3p, miR-125, miR-125b, miR-613, miR-217, miR-194, and miR-494 regulate function of CSCs in hepatocellular carcinoma. DILC, lncTCF7, MUF, HAND2-AS1, MALAT1, DLX6-AS1, HOTAIR, and XIST are among lncRNAs that regulate function of CSCs. In the present paper, we explain the effects of these two classes of non-coding RNAs in the regulation of activity of CSCs.

FBXL19‑AS1 promotes the progression of nasopharyngeal carcinoma by acting as a competing endogenous RNA to sponge miR‑431 and upregulate PBOV1

Long non‑coding RNAs (lncRNAs) have been shown to function as crucial regulators in the progression of various types of cancer, including nasopharyngeal carcinoma (NPC). The aim of the present study was to investigate the mechanisms underlying the role of the FBXL19‑AS1/microRNA (miR)‑431/prostate and breast cancer overexpressed 1 (PBOV1) axis in the progression of NPC. The expression levels of FBXL19‑AS1, miR‑431 and PBOV1 were assessed by reverse transcription‑quantitative PCR. The Cell Counting Kit‑8 assay was utilized to detect cell viability. Cell migration and invasion were determined using a Transwell assay. The associations between FBXL19‑AS1 and miR‑431 or miR‑431 and PBOV1 were verified via bioinformatics analysis, dual‑luciferase and RNA‑binding protein immunoprecipitation assays. It was demonstrated that the expression levels of FBXL19‑AS1 and PBOV1 were upregulated in NPC tissues and cells, whereas miR‑431 expression was downregulated. FBXL19‑AS1 directly interacted with miR‑431. FBXL19‑AS1 silencing inhibited the viability, migration and invasion of C666‑1 and SUNE1 cells, whereas these effects could be alleviated by suppressing miR‑431. miR‑431 could target the 3'‑untranslated region of PBOV1. Overexpression of PBOV1 neutralized the miR‑431‑mediated suppression of NPC progression. Moreover, FBXL19‑AS1 could regulate PBOV1 by sponging miR‑431 in NPC cells. In conclusion, the lncRNA FBXL19‑AS1 accelerated NPC progression via the miR‑431/PBOV1 axis, suggesting that it may serve as a potential therapeutic target for patients with NPC.

Cell Proliferation and Apoptosis-Related Genes Affect the Development of Human Nasopharyngeal Carcinoma Through PI3K/AKT Signaling Pathway

Nasopharyngeal carcinoma (NPC) is one of the common malignant tumors in China, which occurs on the top and sidewalls of the nasopharyngeal cavity. The incidence of malignant tumors of the ear, nose and throat is the highest. However, little is known about the growth of the cells. Therefore, this study constructed a multi-regulator-driven NPC cell growth-related module, aiming to explore the mechanism of functional pathways regulating the proliferation of NPC cells in an all-round way. Firstly, differential expression analysis, co-expression analysis, enrichment analysis and connectivity analysis were synthesized to identify the intrinsic genes of expression disorder module. Subsequently, we analyzed the module by crosstalk, and observed the interaction between modules intuitively. Finally, based on hypergeometric test, the significance of multi-regulators on the regulation of potential modules is calculated. We obtained 17 cell growth-related expression disorder modules by 2148 gene modules focusing. These modules are mainly involved in the growth cycle of NPC cells, including cell proliferation, migration and apoptosis. At the same time, they mainly affect the proliferation and apoptosis of NPC cells through PI3K-AKT signaling pathway, NF-kappa B signaling pathway and Wnt signaling pathway. Based on the growth-related modules of NPC cells, we have obtained a series of non-coding RNAs (ncRNAs) including microRNA-92a-3p, microRNA-19a-3p and microRNA-130a-3p, play an important role in regulating the growth of NPC cells. Similarly, we also predicted transcription factors (involving E2F1, NFKB1, SP1, etc.) that may play a key role in cell growth-related modules. This study is based on cell growth-related expression disorder module to explore the regulatory role of its functional pathway on cell proliferation mechanism, which will help researchers to have a deeper understanding of the potential pathogenesis of NPC.

Oncogenic Role of PVT1 and Therapeutic Implications

PVT1, a long non-coding RNA has been implicated in a variety of human cancers. Recent advancements have led to increasing discovery of the critical roles of PVT1 in cancer initiation and progression. Novel insight is emerging about PVT1's mechanism of action in different cancers. Identifying and understanding the variety of activities of PVT1 involved in cancers is a necessity for the development of PVT1 as a diagnostic biomarker or therapeutic target in cancers where PVT1 is dysregulated. PVT1's varied activities include overexpression, modulation of miRNA expression, protein interactions, targeting of regulatory genes, formation of fusion genes, functioning as a competing endogenous RNA (ceRNA), and interactions with MYC, among many others. Furthermore, bioinformatic analysis of PVT1 interactions in cancers has aided understanding of the numerous pathways involved in PVT1 contribution to carcinogenesis in a cancer type-specific manner. However, these recent findings show that there is much more to be learned to be able to fully exploit PVT1 for cancer prognostication and therapy. In this review, we summarize some of the latest findings on PVT1's oncogenic activities, signaling networks and how targeting these networks can be a strategy for cancer therapy.

Long Non-coding RNA PVT1 as a Prognostic and Therapeutic Target in Pediatric Cancer

In recent decades, biomedical research has focused on understanding the functionality of the human translated genome, which represents a minor part of all genetic information transcribed from the human genome. However, researchers have become aware of the importance of non-coding RNA species that constitute the vast majority of the transcriptome. In addition to their crucial role in tissue development and homeostasis, mounting evidence shows non-coding RNA to be deregulated and functionally contributing to the development and progression of different types of human disease including cancer both in adults and children. Small non-coding RNAs (i.e., microRNA) are in the vanguard of clinical research which revealed that RNA could be used as disease biomarkers or new therapeutic targets. Furthermore, many more expectations have been raised for long non-coding RNAs, by far the largest fraction of non-coding transcripts, and still fewer findings have been translated into clinical applications. In this review, we center on PVT1, a large and complex long non-coding RNA that usually confers oncogenic properties on different tumor types. We focus on the compilation of early advances in the field of pediatric tumors which often lags behind clinical improvements in adult tumors, and provide a rationale to continue studying PVT1 as a possible functional contributor to pediatric malignancies and as a potential prognostic marker or therapeutic target.

Regulatory Mechanisms and Clinical Applications of the Long Non-coding RNA PVT1 in Cancer Treatment

Cancer is the second leading cause of death worldwide, and no obvious decline in incidence and mortality has occurred in recent years. It is imperative to further investigate the mechanisms underlying tumor progression. Long non-coding RNAs have received considerable attention in recent years because of their major regulatory roles in gene expression. Among them, PVT1 is well-studied, and substantial evidence indicates that PVT1 plays critical roles in the onset and development of cancers. Normally, PVT1 acts as an oncogenic factor by promoting cancer cell proliferation, invasion, metastasis, and drug resistance. Herein, we summarize current knowledge regarding the regulatory effects of PVT1 in cancer progression, as well as the related underlying mechanisms, such as interaction with Myc, modulation of miRNAs, and regulation of gene transcription and protein expression. In extracellular fluid, PVT1 mainly promotes cancer initiation, and it normally enhances cellular cancer characteristics in the cytoplasm and cell nucleus. Regarding clinical applications, its role in drug resistance and its potential use as a diagnostic and prognostic marker have received increasing attention. We hope that this review will contribute to a better understanding of the regulatory role of PVT1 in cancer progression, paving the way for the development of PVT1-based therapeutic approaches in cancer treatment.

The lncRNA PVT1 regulates nasopharyngeal carcinoma cell proliferation via activating the KAT2A acetyltransferase and stabilizing HIF-1α

Long noncoding RNAs (lncRNAs) play important roles in regulating the development and progression of many cancers. However, the clinical significance of specific lncRNAs in the context of nasopharyngeal carcinoma (NPC) and the molecular mechanisms by which they regulate this form of cancer remain largely unclear. In this study we found that the lncRNA PVT1 was upregulated in NPC, and that in patients this upregulation was associated with reduced survival. RNA sequencing revealed that PVT1 was responsible for regulating NPC cell proliferation and for controlling a hypoxia-related phenotype in these cells. PVT1 knockdown reduced NPC cell proliferation, colony formation, and tumorigenesis in a subcutaneous mouse xenograft model systems. We further found that PVT1 serves as a scaffold for the chromatin modification factor KAT2A, which mediates histone 3 lysine 9 acetylation (H3K9), recruiting the nuclear receptor binding protein TIF1β to activate NF90 transcription, thereby increasing HIF-1α stability and promoting a malignant phenotype in NPC cells. Overexpression of NF90 or HIF-1α restored the proliferation in cells that had ceased proliferating due to PVT1 or KAT2A depletion. Conversely, overexpression of active KAT2A or TIF1β, but not of KAT2A acetyltransferase activity-deficient mutants or TIF1β isoforms lacking H3K9ac binding sites, promoted a PVT1-mediated increase in NF90 transcription, as well as increased HIF-1α stability and cell proliferation. PVT1 knockdown enhanced the radiosensitization effect in NPC cells via inhibiting binding between H3K9ac and TIF1β in a manner. Taken together, our results demonstrate that PVT1 serves an oncogenic role and plays an important role in radiosensitivity in malignant NPC via activating the KAT2A acetyltransferase and stabilizing HIF-1α.

PVT1 Promotes Cancer Progression via MicroRNAs

Non-coding RNA (ncRNA) plays a regulatory role in a variety of cellular activities. And long non-coding RNA (lncRNA) is one of the important kinds of ncRNA. Previous studies have shown that various lncRNAs are involved in the progression of cancer. LncRNA plasmacytoma variant translocation 1 (PVT1) is a newly discovered oncogenic factor that has been confirmed to be overexpressed in many cancer cells. Moreover, the role of PVT1 in cancer development is closely linked to microRNAs (miRNAs). PVT1 can act as a "sponge" for miRNAs to inhibit their activities, thereby affecting proliferation, invasion, and angiogenesis of cancer. In addition, PVT1 itself can be spliced and processed into several miRNAs such as miR-1204 and miR-1207, which can also regulate the development of cancer. This review summarizes various pathways through which PVT1 regulates the progression of cancer via miRNAs. We also propose additional regulatory mechanisms of PVT1 and their potential clinical applications.

Knockdown of long non-coding RNA PVT1 inhibits the proliferation of Raji cells through cell cycle regulation

Long non-coding RNA plasmacytoma variant translocation 1 (PVT1) has been reported to be associated with oncogenesis. However, the functional role of PVT1 in Burkitt lymphoma has not yet been addressed. The purpose of the present study was to investigate the effect of PVT1 knockdown by small interfering RNA (siRNA) on the proliferation of Burkitt lymphoma Raji cells and to explore its possible mechanism of action. An effective siRNA targeting PVT1 was screened and the corresponding short hairpin RNA (shRNA) was reconstructed into a lentiviral vector. Cell proliferation and cell cycle distribution were assessed by Cell Counting kit-8 assay and flow cytometry, respectively. Protein expression levels of c-Myc, cyclin-dependent kinase inhibitor1A (CDKN1A, P21) and cyclin E1 (CCNE1) were detected by western blotting. A polymerase chain reaction (PCR) array was used to analyse the expression of genes associated with the cell cycle. PVT1 knockdown markedly suppressed proliferation, and induced cell cycle arrest at the G₀/G₁ phase in Raji cells. Protein expression levels of c-Myc and CCNE1 were reduced, whereas P21 protein expression was markedly increased following downregulation of PVT1 in Raji cells. The cell cycle PCR array revealed that 54 genes were upregulated and 26 genes were downregulated in Raji cells following PVT1 knockdown. Reverse transcription-quantitative PCR demonstrated that cyclin G2 (CCNG2), CDKN1A, Retinoblastoma-like 2 (RBL2, p130), HUS1 checkpoint homolog, cyclin dependent kinase inhibitor 3 (CDKN3) and cyclin dependent kinase inhibitor 1B (CDKN1B) expression were upregulated, whereas the expression levels of CCNE1, cyclin D1 (CCND1) and cell division cycle 20 (CDC20) were downregulated in Raji cells with PVT1 knockdown. In conclusion, PVT1 knockdown may inhibit the proliferation of Raji cells by arresting cells in G₀/G₁ phase. Furthermore, inhibition of cell proliferation may be associated with a reduction inc-Myc expression and alterations in the expression levels of cell cycle-associated genes.

Expression of vimentin in nasopharyngeal carcinoma and its possible molecular mechanism: A study based on immunohistochemistry and bioinformatics analysis

BACKGROUND

Although previous researchers have analyzed the expression level of vimentin in nasopharyngeal carcinoma (NPC), the sample size of each study was too small, and there was no further in-depth study utilizing microarray and RNA-sequencing data. More importantly, the role and molecular mechanism of vimentin in NPC have not yet been addressed comprehensively. Accordingly, the aim of the present research was to conduct a full exploration of the clinical significance of vimentin in NPC in a large sample size.

MATERIALS AND METHODS

Immunohistochemistry was used to test the expression of vimentin in clinical samples. Data from relevant microarray and RNA-sequencing datasets were screened and extracted to explore the clinical role of vimentin in NPC. Subsequently, vimentin-related signaling pathways were investigated via in-silico approaches.

RESULTS

The clinical immunohistochemistry detection showed the positive expression ratio of vimentin was 24.6% (14/57) of the NPC specimens, whereas vimentin expression was negative in nasopharyngitis (NPG) tissues (0/20, P = 0.016). The mRNA and protein levels of vimentin were both remarkably up-regulated in NPC based on 196 and 1566 cases, respectively. The protein level of vimentin was also a risky factor for the prognosis prediction of NPC with the hazard ratios (HR) being 3.831. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses, the localization of vimentin was in both the cytoplasm and the cytoskeleton, and vimentin was involved in the regulation of molecular function, the execution phase of apoptosis, and the regulation of cellular component organization.

CONCLUSION

The high expression of vimentin plays a pivotal role in the development and poor progression of NPC, which indicates that vimentin may be an effective predictive indicator for NPC.