Expression of versican 3'-untranslated region modulates endogenous microRNA functions

Coding, or non-coding, that is the question

The advent of high-throughput sequencing uncovered that our genome is pervasively transcribed into RNAs that are seemingly not translated into proteins. It was also found that non-coding RNA transcripts outnumber canonical protein-coding genes. This mindboggling discovery prompted a surge in non-coding RNA research that started unraveling the functional relevance of these new genetic units, shaking the classic definition of "gene". While the non-coding RNA revolution was still taking place, polysome/ribosome profiling and mass spectrometry analyses revealed that peptides can be translated from non-canonical open reading frames. Therefore, it is becoming evident that the coding vs non-coding dichotomy is way blurrier than anticipated. In this review, we focus on several examples in which the binary classification of coding vs non-coding genes is outdated, since the same bifunctional gene expresses both coding and non-coding products. We discuss the implications of this intricate usage of transcripts in terms of molecular mechanisms of gene expression and biological outputs, which are often concordant, but can also surprisingly be discordant. Finally, we discuss the methodological caveats that are associated with the study of bifunctional genes, and we highlight the opportunities and challenges of therapeutic exploitation of this intricacy towards the development of anticancer therapies.

Evaluation of expression level of BANCR, MALAT1 and FER1L4 and their target genes in coumarin-treated AGS cell line

Because long non-coding RNAs (lncRNAs) can affect several interconnected processes, its value as a predictive marker for gastric cancer has been demonstrated. Coumarin - a natural compound known to contain some beneficial antitumor qualities - was tested for its effects on AGS gastric cancer cells. In this study, we investigated the expression level of selected cellular lncRNAs (BANCR, MALAT1 and FER1L4) and their target genes (PTEN, p-PI3K and p-AKT) in coumarin-treated AGS cell line. The expressions of the three lncRNAs: BANCR, MALAT1 and FER1L4, as well as their specified targets, PTEN, PI3K and AKT, were measured by qRT-PCR. To gauge the impact of coumarin on the AGS cells, a MTT assay was utilized. A Western blot has been employed to assess variations in PTEN, p-PI3K, and p-AKT expression. The experiment's results showed that AGS viability diminished with increasing doses of coumarin. Compared to the control cells, the cells exposed to coumarin had showed reduced levels of mRNAs which are known targets of the lncRNA BANCR. At the same time, levels of lncRNAs MALAT1 and FER1L4 within coumarin group have been higher comparing to those within control group. Additionally, the Western blot analysis revealed that the coumarin-treated cells expressed lower levels of p-PI3K, PTEN as well as p-AKT compared to control group. This information points to coumarin being a possible option in a treatment regimen for gastric cancer due to its ability to affect lncRNAs and the molecules they target.

MicroRNA -21 expression as an auxiliary diagnostic biomarker of acute brucellosis

BACKGROUND

This study aimed to measure the expression levels of peripheral blood miRNAs in brucellosis and their involvement in the different phases of the brucellosis.

METHODS

The expression levels of miRNAs including miR-210, miR-155, miR-150, miR-146a, miR-139-3p, miR-125a-5p, miR-29 and miR-21 were quantified in 57 brucellosis patients subgrouped into acute, under treatment & relapse phase and 30 healthy controls (HCs) using real-time polymerase chain reaction (RT-PCR). The receiver operating characteristic (ROC) analysis curve analysis was performed to find a biomarker for discrimination of different phases of brucellosis.

RESULTS

The expression of miR-155, miR-146a, miR-125a-5p, miR-29, and miR-21 was found to be elevated in the acute brucellosis patients compared to HCs. miR-29 changed in under-treatment patients, while miR-139-3p and miR-125a-5p showed alterations in relapse cases. The ROC curve analysis depicted the potential involvement of miR-21 in the pathogenesis of acute brucellosis.

CONCLUSION

The expression level of miR-21 is significantly augmented in acute brucellosis and has the potential to be a contributing diagnostic factor for acute infection.

RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases

The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.

Mutational signatures representative transcriptomic perturbations in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a primary malignancy with increasing incidence and poor prognosis. Heterogeneity originating from genomic instability is one of the critical reasons of poor outcomes. However, the studies of underlying mechanisms and pathways affected by mutations are still not intelligible. Currently, integrative molecular-level studies using multiomics approaches enable comprehensive analysis for cancers, which is pivotal for personalized therapy and mortality reduction. In this study, genomic and transcriptomic data of HCC are obtained from The Cancer Genome Atlas (TCGA) to investigate the affected coding and non-coding RNAs, as well as their regulatory network due to certain mutational signatures of HCC. Different types of RNAs have their specific enriched biological functions in mutational signature-specific HCCs, upregulated coding RNAs are predominantly associated with lipid metabolism-related pathways, and downregulated coding RNAs are enriched in axonogenesis for tumor microenvironment generation. Additionally, differentially expressed miRNAs are inclined to concentrate in cancer-related signaling pathways. Some of these RNAs also serve as prognostic factors that help predict the survival outcome of HCCs with certain mutational signatures. Furthermore, deregulation of competing endogenous RNA (ceRNA) regulatory network is identified, which suggests a potential therapy via interference of miRNA activity for mutational signature-specific HCC. This study proposes a projection approach to reduce therapeutic complexity from genomic mutations to transcriptomic alterations. Through this method, we identify genes and pathways critical for mutational signature-specific HCC and further discover a series of prognostic markers indicating patient survival outcome.

Identification of lncRNA Biomarkers and LINC01198 Promotes Progression of Chronic Rhinosinusitis with Nasal Polyps through Sponge miR-6776-5p

Background

Chronic sinusitis (CRS) was a chronic inflammation that originated in the nasal mucosa and affected the health of most people around the world. Chronic rhinosinusitis with nasal polyps (CRSwNP) was one kind of chronic sinusitis. Emerging research had suggested that long noncoding RNAs (lncRNAs) played vital parts in inflammatories and inflammation development.

Methods

We acquired GEO data to analyze the differential expression between the miRNA, immune genes, TF, and lncRNA data in CRSWNP and the corresponding control tissues. Bioinformatic analysis by coexpression of endogenous RNA network and competitive way enrichment, analysis, and forecasting functions of these noncoding RNA. The different pathway expressions in CRSwNP patients were confirmed using GSVA to analyze the differentially expressed immune genes and TF data sets in CRSwNP patients. The differential immune gene and transcription factor data set in CRSwNP perform functional notes and protein-protein interaction (PPI) network structure. We predicted the potential genes and RNAs related to CRSWNP by constructing a ceRNA network. In addition, we also used 19 hub immune genes to predict the potential drugs of CRSWNP. lncRNA biomarkers in CRSwNP were identified by lncRNAs LASSO regression. The CIBERSORT algorithm was used to contrast the divergence in immune infiltrations between CRSwNP and usual inferior turbinate organizations in 22 immunocyte subgroups.

Results

We identified a total of 48 miRNAs, 304 lncRNAs, 92 TFs, and 525 immune genes as CRSwNP-specific RNAs. GO and KEGG pathways both analyzed differentially expressed immune genes and transcription factor data sets. We predicted the potential genes GNG7, TUSC8, LINC01198, and has-miR-6776-5p by constructing ceRNA and PPI networks. At the same time, we found that the above genes were involved in two important pathways: chemokine signal path and PI3K/AKT signal path. In addition, we predicted 5 small molecule drugs to treat CRSwNP by analyzing 19 central immune genes, namely, danazol, ikarugamycin, semustine, cefamandole, and molindone. Finally, we identified 5 biomarkers in CRSwNP, namely, LINC01198, LINC01094, LINC01798, LINC01829, and LINC01320.

Conclusions

We had identified CRSwNP-related miRNAs, lncRNAs, TFs, and immune genes, which may be making use of latent therapeutic target for CRSwNP. At the same time, we identified 5 lncRNA biomarkers in CRSwNP. The results of this study showed that LINC01198 promoted the progression of CRSwNPs through spongy miR-6776-5p. Our studies provide a new way for further analyses of the pathogenesis of CRSwNP.

The microRNA-cell surface proteoglycan axis in cancer progression

Proteoglycans consist one of the major extracellular matrix class of biomolecules that demonstrate nodal roles in cancer progression. Μodern diagnostic and therapeutic approaches include proteoglycan detection and pharmacological targeting in various cancers. Proteoglycans orchestrate critical signaling pathways for cancer development and progression through dynamic interactions with matrix components. It is well established that the epigenetic signatures of cancer cells play critical role in guiding their functional properties and metastatic potential. Secreted microRNAs (miRNAs) reside in a complex network with matrix proteoglycans, thus affecting cell-cell and cell-matrix communication. This mini-review aims to highlight current knowledge on the proteoglycan-mediated signaling cascades that regulate miRNA biogenesis in cancer. Moreover, the miRNA-mediated proteoglycan regulation during cancer progression and mechanistic aspects on the way that proteoglycans affect miRNA expression are presented. Recent advances on the role of cell surface proteoglycans in exosome biogenesis and miRNA packaging and expression are also discussed.

Endogenous miRNA Sponges

MicroRNAs (miRNAs) are a class of noncoding RNAs of 17-22 nucleotides in length with a critical function in posttranscriptional gene regulation. These master regulators are themselves subject to regulation both transcriptionally and posttranscriptionally. Recently, miRNA function has been shown to be modulated by exogenous RNA molecules that function as miRNA sponges. Interestingly, endogenous transcripts such as transcribed pseudogenes, long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and mRNAs may serve as natural miRNA sponges. These transcripts, which bind to miRNAs and competitively sequester them away from their targets, are naturally existing endogenous miRNA sponges, called competing endogenous RNAs (ceRNAs). Here we present a historical background of miRNAs, exogenous and endogenous miRNA sponges as well as some examples of endogenous miRNA sponges involved in regulatory mechanisms associated with various diseases, developmental stages, and other cellular processes.

A novel mechanism of the lncRNA PTTG3P/miR-142-5p/JAG1 axis modulating tongue cancer cell phenotypes through the Notch1 signaling

Tongue cancer is the most prevalent type of oral cancer. Our previous study revealed that JAG1 exerted an oncogenic effect on tongue carcinoma through the JAG1/Notch pathway. In this study, a lncRNA PTTG3P which was upregulated in tongue cancer, was found to be positively correlated with JAG1. In CAL-27 and SCC4 cells, PTTG3P silencing significantly decreased JAG1 proteins and the ability of tongue tumor cells to proliferate and migrate. PTTG3P overexpression exhibited the opposite effect on CAL-27 and SCC4 cells. PPTG3P directly bound miR-142-5p, and miR-142-5p directly bound 3'UTR of JAG1 and inhibited the expression levels of JAG1. As opposed to PTTG3P silencing, miR-142-5p inhibition increased JAG1 protein levels and tongue cancer cell proliferation and migration; moreover, miR-142-5p inhibition substantially reversed the effects of PTTG3P silencing. Finally, the PPTG3P/miR-142-5p axis regulated the level of NICD, Notch downstream c-myc, and cyclin D1, as well as EMT markers Snail, Twist, and Vimentin. In conclusion, the PTTG3P/miR-142-5p axis modulates tongue cancer aggressiveness through JAG1, potentially through a JAG1/Notch signaling pathway.

A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide-Induced Acute Lung Injury in Mice

Non-coding RNAs have remarkable roles in acute lung injury (ALI) initiation. Nevertheless, the significance of long non-coding RNAs (lncRNAs) in ALI is still unknown. Herein, we purposed to identify potential key genes in ALI and create a competitive endogenous RNA (ceRNA) modulatory network to uncover possible molecular mechanisms that affect lung injury. We generated a lipopolysaccharide-triggered ALI mouse model, whose lung tissue was subjected to RNA sequencing, and then we conducted bioinformatics analysis to select genes showing differential expression (DE) and to build a lncRNA-miRNA (microRNA)- mRNA (messenger RNA) modulatory network. Besides, GO along with KEGG assessments were conducted to identify major biological processes and pathways, respectively, involved in ALI. Then, RT-qPCR assay was employed to verify levels of major RNAs. A protein-protein interaction (PPI) network was created using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and the hub genes were obtained with the Molecular Complex Detection plugin. Finally, a key ceRNA subnetwork was built from major genes and their docking sites. Overall, a total of 8,610 lncRNAs were identified in the normal and LPS groups. Based on the 308 DE lncRNAs [p-value < 0.05, |log2 (fold change) | > 1] and 3,357 DE mRNAs [p-value < 0.05, |log2 (fold change) | > 1], lncRNA-miRNA and miRNA-mRNA pairs were predicted using miRanda. The lncRNA-miRNA-mRNA network was created from 175 lncRNAs, 22 miRNAs, and 209 mRNAs in ALI. The RT-qPCR data keep in step with the RNA sequencing data. GO along with KEGG analyses illustrated that DE mRNAs in this network were mainly bound up with the inflammatory response, developmental process, cell differentiation, cell proliferation, apoptosis, and the NF-kappa B, PI3K-Akt, HIF-1, MAPK, Jak-STAT, and Notch signaling pathways. A PPI network on the basis of the 209 genes was established, and three hub genes (Nkx2-1, Tbx2, and Atf5) were obtained from the network. Additionally, a lncRNA-miRNA-hub gene subnetwork was built from 15 lncRNAs, 3 miRNAs, and 3 mRNAs. Herein, novel ideas are presented to expand our knowledge on the regulation mechanisms of lncRNA-related ceRNAs in the pathogenesis of ALI.

ceRNAs in Cancer: Mechanism and Functions in a Comprehensive Regulatory Network

Noncoding RNAs have been shown with powerful ability in post-transcriptional regulation, enabling intertwined RNA crosstalk and global molecular interaction in a large amount of dysfunctional conditions including cancer. Competing endogenous RNAs (ceRNAs) are those competitively binding with shared microRNAs (miRNAs), freeing their counterparts from miRNA-induced degradation, thus actively influencing and connecting with each other. Constantly updated analytical approaches boost outstanding advancement achieved in this burgeoning hotspot in multilayered intracellular communication, providing new insights into pathogenesis and clinical treatment. Here, we summarize the mechanisms and correlated factors under this RNA interplay and deregulated transcription profile in neoplasm and tumor progression, underscoring the great significance of ceRNAs for diagnostic values, monitoring biomarkers, and prognosis evaluation in cancer.

Melatonin as a promising modulator of aging related neurodegenerative disorders: Role of microRNAs

One of the host risk factors involved in aging-related diseases is coupled with the reduction of endogenous melatonin (MLT) synthesis in the pineal gland. MLT is considered a well-known pleiotropic regulatory hormone to modulate a multitude of biological processes such as the regulation of circadian rhythm attended by potent anti-oxidant, anti-inflammatory, and anti-cancer properties. It has also been established that the microRNAs family, as non-coding mRNAs regulating post-transcriptional processes, also serve a crucial role to promote MLT-related advantageous effects in both experimental and clinical settings. Moreover, the anti-aging impact of MLT and miRNAs participation jointly are of particular interest, recently. In this review, we aimed to scrutinize recent advances concerning the therapeutic implications of MLT, particularly in the brain tissue in the face of aging. We also assessed the possible interplay between microRNAs and MLT, which could be considered a therapeutic strategy to slow down the aging process in the nervous system.

The Tumorigenic Properties of EZH2 are Mediated by MiR-26a in Uveal Melanoma

Background: The polycomb group protein enhancer of zeste homolog 2 (EZH2) has been found to be highly expressed in various tumors, and microRNA-26a (miR-26a) is often unmodulated in cancers. However, the functions of these two molecules in uveal melanoma (UM) and their relationships have not been reported.

Methods: We explored the effects of the miR-26a–EZH2 axis in UM by examining the levels of miR-26a and EZH2. The EZH2 levels in various tumor types and the correlations between EZH2 levels and overall survival and disease-free survival were reanalyzed. The binding of miR-26a to the 3′-untranslated region of EZH2 mRNA was measured using the luciferase reporter assay. The regulation of EZH2 gene expression by miR-26a was also identified, and the effect of elevated EZH2 expression on UM cell function was further examined. Results: miR-26a was downregulated and EZH2 was upregulated in UM cells. Overexpression of miR-26a inhibited cell proliferation, and knockdown of EZH2 suppressed cell growth. EZH2 was a direct target of miR-26a in UM cells. The knockout of EZH2 mimicked the tumor inhibition of miR-26a in UM cells, whereas the reintroduction of EZH2 abolished this effect. In addition, a network of EZH2 and its interacting proteins (UBC, CDK1, HDAC1, SUZ12, EED) was found to participate in miR-26a-mediated tumor progression.

Conclusion: The newly identified miR-26a–EZH2 axis may be a potential target for the development of treatment strategies for UM.

Phosphatase and Tensin Homolog in Non-neoplastic Digestive Disease: More Than Just Tumor Suppressor

The Phosphatase and tensin homolog (PTEN) gene is one of the most important tumor suppressor genes, which acts through its unique protein phosphatase and lipid phosphatase activity. PTEN protein is widely distributed and exhibits complex biological functions and regulatory modes. It is involved in the regulation of cell morphology, proliferation, differentiation, adhesion, and migration through a variety of signaling pathways. The role of PTEN in malignant tumors of the digestive system is well documented. Recent studies have indicated that PTEN may be closely related to many other benign processes in digestive organs. Emerging evidence suggests that PTEN is a potential therapeutic target in the context of several non-neoplastic diseases of the digestive tract. The recent discovery of PTEN isoforms is expected to help unravel more biological effects of PTEN in non-neoplastic digestive diseases.

Inhibition of miR-144/199 promote myeloma pathogenesis via upregulation of versican and FAK/STAT3 signaling

The continuous rise in relapse rate and mortality for multiple myeloma (MM) demands an effective treatment option. The microRNAs are emerging nowadays for their promising therapeutic potential. Earlier, we reported involvement of Versican (VCAN) in myeloma pathogenesis which could be inhibited by miR-144 and miR-199 in stroma. However, there is dearth of literature showcasing the direct effect of these miRs in association with VCAN in MM. Expression of miR-144 and miR-199 was determined in myeloma cell lines (RPMI8226 & U266). These miRs were inhibited by small oligos to elucidate changes in expression of VCAN along with variation in parameters such as proliferation, apoptosis, migration and invasion in vitro. Moreover, effect on certain downstream signaling cascades was also evaluated. Lastly, interaction of miRs with VCAN was assessed by reporter luciferase assay. microRNAs expression were found significantly elevated in myeloma cells in comparison to stromal levels reported previously. The antagomirs-mediated inhibition of miR-144 and miR-199 significantly induced VCAN expression in myeloma cells along with alteration in myeloma-associated parameters in favor of myeloma pathogenesis with downstream activation of FAK/STAT3 signaling. Interestingly, miR-144 found to have direct binding with VCAN 3' UTR while miR-199 possess different mechanism. The inhibition of miR-144 and miR-199 contributed in myeloma progression via upregulation of VCAN in vitro affirming the translational significance of VCAN and associated microRNAs in MM. These miRs, hence might be employed for targeting VCAN and might emerge as an effective therapy for the better outcome of MM in clinical settings in future.

CircRNA_104889 promotes lung adenocarcinoma cell invasion via sponging miR4458

Background

Lung adenocarcinoma is metastatic cancer with a high mortality rate. Circular RNAs (circRNAs) are a type of noncoding RNA and play a vital role in cancer progression. However, the expression and function of circRNAs in lung adenocarcinoma are still mostly unknown.

Methods

In this study, we screened the differential expression of circRNAs in human bronchial epithelial cells (HBE) and A549 human lung adenocarcinoma cell line (A549) by human circRNA microarray and RT-qPCR. The role of overexpressed circRNA_104889 in A549 cell proliferation, apoptosis, migration, and invasion was studied extensively. Intracellular localization of circRNA_104889 was visualized by FISH assay. MiRNA sponging, ERK1/2 signaling, and caspase-3 expression were analyzed in siRNA-mediated circRNA_104889 knockdowned A549 cells.

Results

CircRNA microarray showed overexpression of circRNA_104889 (> 13-fold) in A459 cells compared to HBE. This finding was further corroborated by the RT-qPCR result. CircRNA_104889 was mainly localized in the cytoplasm of A549 cells. The knockdown of circRNA_104889 in A549 cells by si-RNA mediated RNA interference did not affect cell proliferation and apoptosis but significantly inhibited cell migration and invasion in vitro. Furthermore, knockdown of circRNA_104889 led to an increase of miR4458 expression. Overexpression of miR4458 inhibited A549 cell migration. Both the knockdown of circRNA_104889 and overexpression of miR4458 inhibited the caspase-3 expression and ERK1/2 phosphorylation in A549 cells.

Conclusions

CircRNA_104889 promotes lung adenocarcinoma cell migration and invasion by sponging miR4458 and targeting ERK1/2 signaling and caspase-3 expression.

miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions

BACKGROUND

Non-coding RNAs include different classes of molecules with regulatory functions. The most studied are microRNAs (miRNAs) that act directly inhibiting mRNA expression or protein translation through the interaction with a miRNAs-response element. Other RNA molecules participate in the complex network of gene regulation. They behave as competitive endogenous RNA (ceRNA), acting as natural miRNA sponges to inhibit miRNA functions and modulate the expression of RNA messenger (mRNA). It became evident that understanding the ceRNA-miRNA-mRNA crosstalk would increase the functional information across the transcriptome, contributing to identify new potential biomarkers for translational medicine.

RESULTS

We present miRTissue ce, an improvement of our original miRTissue web service. By introducing a novel computational pipeline, miRTissue ce provides an easy way to search for ceRNA interactions in several cancer tissue types. Moreover it extends the functionalities of previous miRTissue release about miRNA-target interaction in order to provide a complete insight about miRNA mediated regulation processes. miRTissue ce is freely available at http://tblab.pa.icar.cnr.it/mirtissue.html .

CONCLUSIONS

The study of ceRNA networks and its dynamics in cancer tissue could be applied in many fields of translational biology, as the investigation of new cancer biomarker, both diagnostic and prognostic, and also in the investigation of new therapeutic strategies of intervention. In this scenario, miRTissue ce can offer a powerful instrument for the analysis and characterization of ceRNA-ceRNA interactions in different tissue types, representing a fundamental step in order to understand more complex regulation mechanisms.

CircHIPK3 regulates melanoma cell behaviors by binding with miR-215-5p to upregulate YY1

OBJECT

To investigate the role of circHIPK3 in melanoma.

METHODS

Bioinformatics analysis and experiments including RT-qPCR, Pearson's correlation analysis, luciferase reporter, Western blot, and RIP assays were applied to explore the function and mechanism of circHIPK3 in melanoma.

RESULTS

CircHIPK3 expression was strikingly upregulated while miR-215-5p was downregulated in melanoma tissues and cell lines. Pearson's correlation analysis unveiled circHIPK3 expression was positively correlated with Ki-67 (a marker of proliferation), which implied that circHIPK3 may play a vital role in the progression of melanoma. In mechanism, luciferase reporter and RIP assays validated that circHIPK3 was able to bind with miR-215-5p. Moreover, we confirmed that overexpression of circHIPK3 could facilitate cell proliferation and depress cell apoptosis in melanoma while overexpression of miR-215-5p exerted opposite effects. Besides, our findings indicated that miR-215-5p overexpression significantly reversed the circHIPK3 overexpressing-mediated promotive effect on cell proliferation and inhibitory effect on cell apoptosis. Furthermore, we found that miR-215-5p could directly target YY1. Upregulation of YY1 could notably offset the inhibitory effect of circHIPK3 downregulation on cell proliferation and the promotive effect on cell apoptosis.

CONCLUSION

Our study corroborated that circHIPK3 regulated melanoma cell behaviors via the miR-215-5p/YY1 axis, which might provide a novel insight for the treatment of melanoma patients.

The Complex Landscape of PTEN mRNA Regulation

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a key tumor suppressor in the development and progression of different tumor types. Emerging data indicate that small reductions in PTEN protein levels can promote cancer. PTEN protein levels are tightly controlled by a plethora of mechanisms beginning with epigenetic and transcriptional regulation and ending with control of protein synthesis and stability. PTEN messenger RNA (mRNA) is also subject to exquisite regulation by microRNAs, coding and long noncoding RNAs, and RNA-binding proteins. Additionally, PTEN mRNA is markedly influenced by alternative splicing and variable polyadenylation. Herein we provide a synoptic description of the current understanding of the complex regulatory landscape of PTEN mRNA regulation including several specific processes that modulate its stability and expression, in the context of PTEN loss-associated cancers.

lncRNA LA16c‑313D11.11 modulates the development of endometrial cancer by binding to and inhibiting microRNA‑205‑5p function and indirectly increasing PTEN activity

The aim of the present study was to determine the competitive endogenous RNA (ceRNA) network associated with long‑coding RNA (lncRNA) LA16c‑313D11.11 in endometrial cancer (EC). Initially, the expression levels of LA16c‑313D11.11 in 60 EC tissues, 20 atypical hyperplasia endometrium (EAH) tissues and 20 normal endometrium tissues was determined. MicroRNA (miRNA/miR)‑205‑5p mimics and LA16c‑313D11.11 mimics were transfected into HEC‑1A and Ishikawa cells. The expression levels of miR‑205‑5p, LA16c‑313D11.11 and their target proteins were assessed using reverse transcription‑quantitative PCR or western blot analysis. Flow cytometry, Cell Counting kit‑8 assays, Transwell migration assays and wound healing assays were performed to assess the effects of LA16c‑313D11.11 and miR‑205‑5p on the migration and proliferation of tumor cells in vitro. The expression levels of LA16c‑313D11.11 and phosphatase and tensin homolog deleted on chromosome ten (PTEN) in human EAH and EC tissues were significantly decreased, whereas the expression levels of miR‑205‑5p in EAH and EC tissues were significantly increased, compared with the normal endometrium tissues. The expression of LA16c‑313D11.11 in human EC tissues negatively correlated with the expression of miR‑205‑5p. Additionally, the overexpression of LA16c‑313D11.11 significantly reduced the invasion, migration and viability of HEC‑1A and Ishikawa cells in vitro. LA16c‑313D11.11 was shown to regulate the expression of PTEN, and the invasion, migration and viability of HEC‑1A and Ishikawa cells, through its microRNA response element to compete for microRNA‑205‑5p. LA16c‑313D11.11 was also shown to modulate the PI3K/AKT signaling pathway. Therefore, LA16c‑313D11.11 acts as an effective ceRNA associated with a microRNA‑205‑5p‑PTEN axis. LA16c‑313D11.11 may inhibit the development and progression of EC by acting as a sponge of miR‑205‑5p, thus indirectly increasing the expression of PTEN.

Long Noncoding RNA (lncRNA)-Mediated Competing Endogenous RNA Networks Provide Novel Potential Biomarkers and Therapeutic Targets for Colorectal Cancer

Colorectal cancer (CRC) is the third most common cancer and has a high metastasis and reoccurrence rate. Long noncoding RNAs (lncRNAs) play an important role in CRC growth and metastasis. Recent studies revealed that lncRNAs participate in CRC progression by coordinating with microRNAs (miRNAs) and protein-coding mRNAs. LncRNAs function as competitive endogenous RNAs (ceRNAs) by competitively occupying the shared binding sequences of miRNAs, thus sequestering the miRNAs and changing the expression of their downstream target genes. Such ceRNA networks formed by lncRNA/miRNA/mRNA interactions have been found in a broad spectrum of biological processes in CRC, including liver metastasis, epithelial to mesenchymal transition (EMT), inflammation formation, and chemo-/radioresistance. In this review, we summarize typical paradigms of lncRNA-associated ceRNA networks, which are involved in the underlying molecular mechanisms of CRC initiation and progression. We comprehensively discuss the competitive crosstalk among RNA transcripts and the novel targets for CRC prognosis and therapy.

Targeting of stromal versican by miR-144/199 inhibits multiple myeloma by downregulating FAK/STAT3 signalling

The abnormal growth of malignant plasma cells in Multiple Myeloma (MM) requires bone marrow (BM) niche consisting of proteoglycans, cytokines, etc. Versican (VCAN), a chondroitin sulphate proteoglycan promotes progression in solid tumours but there is dearth of literature in MM. Hence, we studied the involvement of VCAN in MM and its regulation by microRNAs as a therapeutic approach. Thirty MM patients and 20 controls were recruited and BM stromal cells (BMSCs) were isolated by primary culture. Molecular levels of VCAN, miR-144, miR-199 & miR-203 were determined in study subjects and cell lines. The involvement of VCAN in myeloma pathogenesis was studied using BMSCs-conditioned medium (BMSCs-CM) and VCAN-neutralizing antibody or microRNA mimics. Elevated expression of VCAN was observed in patients especially in BM stroma while microRNA expression was significantly lower and showed negative correlation with VCAN. Moreover, BMSCs-CM showed the presence of VCAN which upon supplementing to MM cells alter parameters in favour of myeloma progression, however, this effect was neutralized by VCAN antibody or miR (miR-144 and miR-199) mimics. The downstream signalling of VCAN was found to activate FAK and STAT3 which subsides by using VCAN antibody or miR mimics. The neutralization of oncogenic effect of BMSCs-CM by VCAN blockage affirms its plausible role in progression of MM. VCAN was observed as a paracrine mediator in the cross-talk of BMSCs and myeloma cells in BM microenvironment. Therefore, these findings suggest exploring VCAN as novel therapeutic target and utilization of microRNAs as a therapy to regulate VCAN for better management of MM.

Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue

Background

Numerous studies have highlighted that long non-coding RNAs (lncRNAs) can bind to microRNA (miRNA) sites as competing endogenous RNAs (ceRNAs), thereby affecting and regulating the expression of mRNAs and target genes. These lncRNA-associated ceRNAs have been theorized to play a significant role in cancer initiation and progression. However, the roles and functions of the lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of the tongue (SCCT) are still unclear.

Methods

The miRNA, mRNA and lncRNA expression profiles from 138 patients with SCCT were downloaded from The Cancer Genome Atlas database. We identified the differential expression of miRNAs, mRNAs, and lncRNAs using the limma package of R software. We used the clusterProfiler package for GO and KEGG pathway annotations. The survival package was used to estimate survival analysis according to the Kaplan-Meier curve. Finally, the GDCRNATools package was used to construct the lncRNA-miRNA-mRNA ceRNA network.

Results

In total, 1943 SCCT-specific mRNAs, 107 lncRNAs and 100 miRNAs were explored. Ten mRNAs (CSRP2, CKS2, ADGRG6, MB21D1, GMNN, RIPOR3, RAD51, PCLAF, ORC1, NAGS), 9 lncRNAs (LINC02560, HOXC13 − AS, FOXD2 − AS1, AC105277.1, AC099850.3, STARD4 − AS1, SLC16A1 − AS1, MIR503HG, MIR100HG) and 8 miRNAs (miR − 654, miR − 503, miR − 450a, miR − 379, miR − 369, miR − 190a, miR − 101, and let−7c) were found to be significantly associated with overall survival (log-rank p < 0.05). Based on the analysis of the lncRNA-miRNA-mRNA ceRNA network, one differentially expressed (DE) lncRNA, five DEmiRNAs, and three DEmRNAs were demonstrated to be related to the pathogenesis of SCCT.

Conclusions

In this study, we described the gene regulation by the lncRNA-miRNA-mRNA ceRNA network in the progression of SCCT. We propose a new lncRNA-associated ceRNA that could help in the diagnosis and treatment of SCCT.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-5983-8) contains supplementary material, which is available to authorized users.

Non-Coding RNAs and their Integrated Networks

Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs' essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.

Circle RNA hsa_circRNA_100290 serves as a ceRNA for miR-378a to regulate oral squamous cell carcinoma cells growth via Glucose transporter-1 (GLUT1) and glycolysis

Aerobic glycolysis (the Warburg effect) is a robust metabolic hallmark of most tumors, including oral squamous cell carcinoma (OSCC). Glucose transporter 1 (GLUT1), a major glucose transporter regulating the glucose uptake, is upregulated in OSCC and participated in the cell glycolysis of OSCC. The deregulation and function of noncoding RNAs in cancers have been widely reported. Reportedly, hsa_circular RNA (circRNA)_100290 (circ_SLC30A7) is significantly upregulated (fold change = 6.91, p < 0.0000001) in OSCC. According to online tools prediction (miRWalk, miRanda, and Targetscan), miR-378a could simultaneously target circRNA_100290 and GLUT1. Herein, the expression of circRNA_100290 and GLUT1 remarkably increased in oral tumor tissue specimens and cells. In OSCC cell lines, cell proliferation and glycolysis could be remarkably downregulated by circRNA_100290 silence, which could be rescued by GLUT1 overexpression. Conversely, miR-378a expression could be remarkably inhibited in tumor tissue specimens and cells. The effect of miR-378a overexpression on OSCC cells was similar to those of circRNA_100290 silence. miR-378a directly bound to circRNA_100290 and GLUT1 3'-untranslated region, circRNA_100290 could remarkably relieve miR-378a-induced inhibition on GLUT1 via acting as a competing endogenous RNA (ceRNA). miR-378a inhibition remarkably attenuated the effect of circRNA_100290 silence on cell proliferation and glycolysis in OSCC cell lines. In summary, circRNA_100290 serves as a ceRNA to counteract miR-378a-mediated GLUT1 suppression, thus promoting glycolysis and cell proliferation in OSCC. We provide a reliable experimental basis for understanding the mechanism of cell growth and glycolysis deregulation in OSCC.

CD44 3'-Untranslated Region Functions as a Competing Endogenous RNA to Enhance NK Sensitivity of Liver Cancer Stem Cell by Regulating ULBP2 Expression

Liver CSCs are a rare subpopulation of heterogenous liver cancer cells with self-renewal and differentiation properties, which has emerged as a promising therapeutic target. Compelling data shows that NK cells selectively eliminate human cancer derived CSCs like colorectal carcinoma, melanoma, and glioblastoma. But the effect of NK cells on liver CSCs still remains unknown. To study the cytotoxic effect of NK cells on liver CSCs and the mechanism, we performed cytotoxicity assay, ELISA assays, CRISPRi, qRT-PCR, immunoblotting, RNA immunoprecipitation, and luciferase reporter using two types of CSCs reprogrammed from HCC. CSCs derived from liver cancer were susceptible to NK cell mediated cytotoxicity. The susceptibility of liver CSCs to NK cell-mediated cytotoxicity declined significantly after silencing CD44 by CRISPRi-mediated gene knockdown. CD44 3ʹ UTR functioned as a ceRNA to regulate the expression of ULBP2 mainly by competing miR-34a. CD44 3ʹ UTR functioned as a ceRNA to enhance NK sensitivity of liver cancer stem cell by regulating ULBP2 expression.

Clinical significance of circulatory microRNA-203 in serum as novel potential diagnostic marker for multiple myeloma

PURPOSE

Multiple myeloma (MM) is a hematological malignancy marked by uncontrolled proliferation and accumulation of plasma cells in bone marrow. Despite presence of numerous diagnostic markers for MM, their invasive and non-specific nature demands identification of some effective biomarker. Small non-coding RNAs, i.e., microRNAs being secreted out in circulation could depict the change in homeostasis. Earlier, we reported diagnostic potential of a proteoglycan, Versican (VCAN) in MM, hence, VCAN linked cell-free microRNAs have been explored to study their diagnostic involvement in MM.

METHODS

Biopsy proven MM patients and controls were recruited. The relative microRNA expression of VCAN linked microRNAs (miR-143, miR-144, miR-199, and miR-203) along with levels of VCAN have been investigated in bone marrow supernatant fluid (BMSF) and blood serum and their correlation were done with clinico-pathological parameters. The diagnostic potential was assessed using ROC curve.

RESULTS

Relative microRNA expression of all microRNAs was found significantly lower in MM patients in both BMSF and serum while VCAN levels were substantially higher in patients. VCAN levels showed positive trend while microRNAs expression showed negative trend with severity of disease. miR-203 showed significant correlation with myeloma-associated parameters and also showed optimum sensitivity and specificity for diagnosis of MM in serum.

CONCLUSIONS

Downregulation of cell-free microRNAs illustrates their importance in MM. The negative trend of microRNAs with disease progression suggests their diagnostic significance. Correlation of miR-203 with myeloma clinical parameters along with optimum sensitivity and specificity affirms its non-invasive diagnostic potential in MM which could further be validated in larger patient cohort.

mRNA 5' ends targeted by cytoplasmic recapping cluster at CAGE tags and select transcripts are alternatively spliced

Until cytoplasmic recapping was discovered, decapping was thought to irreversibly destine an mRNA to degradation. Contradicting this idea, we readily observe mRNAs targeted by cytoplasmic capping in uncapped, yet stable forms. 5' rapid amplification of cDNA ends (RACE) shows that nearly all uncapped ends correspond to capped analysis of gene expression tags and that the recapping of ZNF207 mRNA may be restricted to a single splice isoform. Here, a modified RACE approach detected uncapped 5' RNA ends mapping to 46 mRNAs in cells expressing a dominant negative cytoplasmic capping enzyme and in normal cells. Eleven of 46 cloned mRNAs also contained splice isoform-limiting sequences. Collectively, these data reinforce earlier work and suggest that alternative splicing may play a role in targeting transcripts for - and/or determining the position of - cytoplasmic capping.

circRNA‑CER mediates malignant progression of breast cancer through targeting the miR‑136/MMP13 axis

Chondrocyte extracellular matrix‑related circular RNAs (circRNA‑CER) have been demonstrated to be involved in various diseases. However, its role in the development of human breast cancer is not clearly understood. The aims of the present study were to assess circRNA‑CER expression in paired cancer tissue and adjacent non‑tumor tissue from 24 patients with breast cancer, and to explore the roles and mechanisms by which circRNA‑CER mediates the malignant progression of breast cancer cells. The results revealed that circRNA‑CER and matrix metalloproteinase 13 (MMP13) were upregulated, whereas miR‑136 was downregulated in breast cancer tissues compared with adjacent non‑tumor tissues. In vitro silencing of circRNA‑CER using small interfering RNA (siRNA) had inhibitory effects on MCF‑7 breast cancer cell proliferation and migration, and similar results were obtained following overexpression of microRNA (miR)‑136 in MCF‑7 cells by transfection with miR‑136 mimics. The subsequent mechanistic study revealed that the expression levels of MMP13 were significantly lower in MCF‑7 cells following transfection with miR‑136 mimics, and silencing of circRNA‑CER enhanced miR‑136 and decreased MMP13 expression levels. Furthermore, silencing of miR‑136 by transfection with miR‑136 inhibitors resulted in an increase in MCF‑7 cell proliferation and migration. miR‑136 inhibitor‑derived biological effects were reversed by co‑transfection of cells with miR‑136 inhibitors and circRNA‑CER siRNA. Taken together, the present results suggested that circRNA‑CER may serve an important role in the progression of breast cancer by regulating the activity of the miR‑136/MMP13 axis, and may be a potential biomarker for the prediction and treatment of breast cancer.

Proteoglycans Are Attractive Biomarkers and Therapeutic Targets in Hepatocellular Carcinoma

Proteoglycans, which consist of a protein core and glycosaminoglycan chains, are major components of the extracellular matrix and play physiological roles in maintaining tissue homeostasis. In the carcinogenic tissue microenvironment, proteoglycan expression changes dramatically. Altered proteoglycan expression on tumor and stromal cells affects cancer cell signaling pathways, which alters growth, migration, and angiogenesis and could facilitate tumorigenesis. This dysregulation of proteoglycans has been implicated in the pathogenesis of diseases such as hepatocellular carcinoma (HCC) and the underlying mechanism has been studied extensively. This review summarizes the current knowledge of the roles of proteoglycans in the genesis and progression of HCC. It focuses on well-investigated proteoglycans such as serglycin, syndecan-1, glypican 3, agrin, collagen XVIII/endostatin, versican, and decorin, with particular emphasis on the potential of these factors as biomarkers and therapeutic targets in HCC regarding the future perspective of precision medicine toward the "cure of HCC".

Is miR-144 an effective inhibitor of PTEN mRNA: a controversy in breast cancer

Breast cancer is the first common cancer among women worldwide. One of the major signaling pathways playing a role in the onset and progression of this disease is PI3K/Akt/mTOR, which can be inhibited by PTEN. miRNAs are small non-coding molecules that regulate the expression of their targets by inhibition or suppression, and thus, their dysregulated expression results in the development of cancer. Using various software applications predicting miRNAs and evaluating GEO microarray data, miR-144 was selected as an inhibitor of PTEN. The expression of miR-144 and PTEN was evaluated in 18 triple negative breast cancer (TNBC) clinical samples and cell lines including 4T1, MDA-MB-231, MDA-MB-468, SK-BR-3, and MCF-7 in comparison with normal cells. PTEN and miR-144 expression analysis revealed their elevated expression in MCF-7 cells. MDA-MB-468, SK-BR-3, and MDA-MB-231 cells showed decreased levels of PTEN and increased levels of miR-144. In contrast, 4T1 cells had an increased expression of PTEN and decreased expression of miR-144. In clinical samples, miR-144 was up-regulated in 22% of the cases and PTEN was down-regulated in 78% of the cases. The results showed that the expression of PTEN and miR-144 was inversely correlated in metastatic breast cancer cell lines. However, in TNBC clinical samples, there was no correlation between the expression of miR-144 and PTEN. Literature shows that there are other influencing factors affecting the expression of miRNAs. Therefore, care should be taken in interpreting the results of gene expression studies and its relation with cancer diagnosis/prognosis.

miR-205 inhibits cell growth by targeting AKT-mTOR signaling in progesterone-resistant endometrial cancer Ishikawa cells

PURPOSE

miR-205 is significantly up-regulated in endometrioid adenocarcinoma. In this study, the significant anticancer effect of a miR-205 inhibitor was investigated in both endometrial carcinoma and progesterone-resistant endometrial carcinoma cells.

RESULTS

Compared with Ishikawa endometrial cancer cells, miR-205 was expressed at higher levels in a progesterone-resistant (PR) sub-cell line. Inhibition of miR-205 suppressed the growth of cancer cells in a dose- and time-dependent manner. Moreover, the miR-205 inhibitor induced a marked increase in the percentage of Ishikawa-PR cells in G2/M phases and a decrease in the percentage of cells in G0/G1 and S phases. In addition, miR-205 inhibitor-treated tumor cells exhibited increased apoptosis. Moreover, miR-205 was found to negatively regulate PTEN expression and lead to autophagy and activation of the AKT/mTOR pathway in PR cells, and PTEN protein levels significantly decreased with development of progesterone resistance in endometrial cancer cells. Western blot assay showed up-regulated autophagy, as indicated by expression of LC3-II/LC3-I and beclin1, in Ishikawa cells; in particular, autophagy was markedly induced in PR cells treated with the miR-205 inhibitor.

MATERIALS AND METHODS

We measured and analyzed cell growth curves with and without miR-205 inhibition with the MTT assay, miR-205 expression by qRT-PCR, cell cycle and apoptosis using annexin V/propidium iodide staining and flow cytometry, and autophagy, apoptosis, and AKT-mTOR signaling by western blotting.

CONCLUSIONS

Inhibition of miR-205, which targets the AKT-mTOR pathway, in endometrial cancer cells provides a potential, new treatment for PR endometrial carcinoma.

MiR-186-5p upregulation inhibits proliferation, metastasis and epithelial-to-mesenchymal transition of colorectal cancer cell by targeting ZEB1

MicroRNA-186-5p (miR-186-5p) is upregulated and exhibits as a crucial oncogene in various human tumors. However, the functions and underlying mechanisms of this microRNA on colorectal cancer remain largely unknown. Here, we report that miR-186-5p share a lower expression in colorectal cancer cell lines (HT116, H29, SW620 and LoVo) than in normal colonic epithelial cell line NCM460. MiR-186-5p overexpression inhibits proliferation, metastasis and epithelial-to-mesenchymal transition (EMT) of colorectal cancer cell line LoVo. Zinc Finger E-Box Binding Homeobox 1 (ZEB1), an EMT related marker, is predicted as a target of miR-186-5p. Luciferase reporter assay, qRT-PCR and western blot analysis showed that miR-186-5p directly targeted the 3'-untranslated regions (3'UTR) of ZEB1 messenger RNA. Further functional experiments indicated that overexpression of miR-186-5p suppress the proliferation and metastasis ability of LoVo, which was consistent with the inhibitory effects by knockdown of ZEB1. Additionally, overexpression of ZEB1 could significantly reverse the miR-186-5p mimics initiated suppression impact of proliferation, metastasis and EMT on LoVo. In summary, miRNA-186-5p affects the proliferation, metastasis and EMT process of colorectal cancer cell by inhibition of ZEB1. Hence, it may serve as a promising therapeutic target for colorectal cancer.

Competing endogenous RNA networks in human cancer: hypothesis, validation, and perspectives

Non-coding RNAs represent a majority of the human transcriptome. However, less is known about the functions and regulatory mechanisms of most non-coding species. Moreover, little is known about the potential non-coding functions of coding RNAs. The competing endogenous RNAs (ceRNAs) hypothesis is proposed recently. This hypothesis describes potential communication networks among all transcript RNA species mediated by miRNAs and miRNA-recognizing elements (MREs) within RNA transcripts. Here we review the evolution of the ceRNA hypothesis, summarize the validation experiments and discusses the significance and perspectives of this hypothesis in human cancer.

Effects of microRNA-136 on melanoma cell proliferation, apoptosis, and epithelial-mesenchymal transition by targetting PMEL through the Wnt signaling pathway

The study aims to evaluate the effects of miR-136 on the proliferation, apoptosis, and epithelial–mesenchymal transition (EMT) of melanoma cells by targetting premelanosome protein (PMEL) through the Wnt signaling pathway. After establishment of melanoma mouse models, melanoma (model group) and normal tissues (normal group) were collected. Immunohistochemistry was performed to determine PMEL protein concentration. Mouse melanoma cells were assigned into control, blank, negative control (NC), miR-136 mimics, miR-136 inhibitors, siRNA-PMEL, and miR-136 inhibitors + siRNA-PMEL, LiC1 (Wnt signaling pathway activator), and siRNA-PMEL+ LiCl groups. MTT, Scratch test, Transwell assay, and flow cytometry were performed to measure cell proliferation, migration, invasion, and apoptosis. Quantitative real-time PCR (qRT-PCR) and Western blotting were performed to evaluate miR-136, PMEL, β-catenin, Wnt3a, Bcl-2, Bax, Caspase, E-cadherin, and N-cadherin expressions. PMEL is highly expressed in melanoma tissues. MiR-136, Bax, Caspase, and E-cadherin expressions decreased in the model group, whereas PMEL, β-catenin, Bcl-2, Wnt3a, and N-cadherin expressions increased. Bax, Caspase, and E-cadherin expressions increased in the miR-136 mimics and siRNA-PMEL groups, whereas the expressions decreased in the miR-136 inhibitors group and LiC1 group. PMEL, β-catenin, Bcl-2, Wnt3a, and N-cadherin expressions, cell proliferation, migration, and invasion decreased, and the apoptosis rate inceased in the miR-136 mimics and siRNA-PMEL groups; whereas the tendencies were opposite to those in the miR-136 inhibitors group and LiC1 group. In the siRNA-PMEL+ LiCl group, PMEL expression decreased. These findings indicated that overexpression of miR-136 inhibits melanoma cell EMT, proliferation, migration, invasion, and promotes apoptosis by targetting PMEL through down-regulation of the Wnt signaling pathway.

XIAP 3'-untranslated region as a ceRNA promotes FSCN1 function in inducing the progression of breast cancer by binding endogenous miR-29a-5p

The non-coding 3′-untranslated region (UTR) of genes play an important role in the regulation of microRNA (miRNA) functions, since it can bind and inactivate multiple miRNAs. Herein, we report that ectopic expression of XIAP 3′UTR increased human breast cancer cells proliferation, colony formation, migration, invasion and xenograft tumor growth and suppressed tumor cell death. To investigate this process, we further correlated the genome-wide transcriptional profiling with the gene expression alterations after transfecting XIAP 3′UTR in MCF-7 cells. We identified a robust, genome-wide mechanism of cell migration, motility and epithelial to mesenchymal transition by which mediated by a previously described cellular component movement factor FSCN1. Expression of XIAP and FSCN1 were up-regulated synergistically after transfecting XIAP 3′UTR in vitro and in vivo. Interactions between XIAP and FSCN1 appear to be a key determinant of these processes. Co-transfection with Dicer siRNA reversed the XIAP 3′UTR-mediated oncogenicity, suggesting the miRNAs might be involved in that process. Furthermore, we demonstrated that one miRNA, miR-29a-5p, can bind to both the XIAP and FSCN1 3′UTRs and play an important role in that interactions. We showed that the 3′UTR of XIAP was able to antagonize miR-29a-5p, and resulted in the increased translation of XIAP and FSCN1. Thus, our findings reveal important new insights into how XIAP 3′UTR works, suggesting that the non-coding XIAP 3′UTR serves as a competitor for miRNA binding and subsequently inactivates miRNA functions, by which XIAP 3′UTR frees the target mRNAs from being repressed.

Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain

MicroRNAs orchestrate brain functioning via interaction with microRNA recognition elements (MRE) on target transcripts. However, the global impact of potential competition on the microRNA pool between coding and non-coding brain transcripts that share MREs with them remains unexplored. Here we report that non-coding pseudogene transcripts carrying MREs (PSG^+MRE) often show duplicated origin, evolutionary conservation and higher expression in human temporal lobe neurons than comparable duplicated MRE-deficient pseudogenes (PSG^-MRE). PSG^+MRE participate in neuronal RNA-induced silencing complexes (RISC), indicating functional involvement. Furthermore, downregulation cell culture experiments validated bidirectional co-regulation of PSG^+MRE with MRE-sharing coding transcripts, frequently not their mother genes, and with targeted microRNAs; also, PSG^+MRE single-nucleotide polymorphisms associated with schizophrenia, bipolar disorder and autism, suggesting interaction with mental diseases. Our findings indicate functional roles of duplicated PSG^+MRE in brain development and cognition, supporting physiological impact of the reciprocal co-regulation of PSG^+MRE with MRE-sharing coding transcripts in human brain neurons.

microRNA inhibitors: Natural and artificial sequestration of microRNA

MicroRNA (miRNAs) is post-transcriptional regulator of mRNA. However, the prevalence and activity of miRNA are regulated by other regulators. miRNA inhibitors are natural or artificial RNA transcripts that sequestrate miRNAs and decrease or even eliminate miRNA activity. Competing endogenous RNAs (ceRNAs) are natural and intracellular miRNA inhibitors that compete to bind to shared miRNA recognition elements (MREs) to decrease microRNA availability and relieve the repression of target RNAs. In recent years, studies have revealed that ceRNA crosstalk is involved in many pathophysiological processes and adds a new dimension to miRNA regulation. Artificial miRNA inhibitors are RNA transcripts that are synthesized via chemical and genetic methods. Artificial miRNA inhibitors can be used in miRNA loss-of-function research and gene therapies for certain diseases. In this review, we summarize the recent advances in the two different types of miRNA inhibitors.

Potential diagnostic implications of miR-144 overexpression in human oesophageal cancer

Background & objectives:

Insidious symptomatology, late clinical presentation and poor prognosis of oesophageal cancer (EC) highlight the pressing need for novel non-invasive biomarkers for early tumour diagnosis and better prognosis. The present study was carried out to evaluate the clinical significance of circulating and tissue miR-144 expression in oesophageal cancer.

Methods:

Clinical significance of miR-144 expression was evaluated in preneoplastic (12) and neoplastic (35) oesophageal cancer tissues as well as matched distant non-malignant tissues using real-time PCR (qPCR). Circulating levels of miR-144 were also analyzed in serum samples of EC patients as well as normal individuals to determine the diagnostic potential of miR-144. Further, targets of miR-144 were predicted using bioinformatic tools and their gene ontology (GO) terms were assigned.

Results:

Real-time PCR analysis revealed significant upregulation of miR-144 in 29 of 35 (83%) EC tissues as compared to matched distant non-malignant tissues (P=0.010). All the dysplastic tissues showed upregulation of miR-144 as compared to their matched distant non-malignant tissues. Relative levels of circulating miR-144 in serum significantly distinguished EC patients from normal controls (P=0.015; AUC = 0.731) with high sensitivity of 94.7 per cent. Bioinformatically predicted target, PUR-aplha (PURA) was found to be significantly (P=0.018) downregulated in 81 per cent (26/32) EC patients and its expression was found to be significantly and negatively correlated with miR-144 expression at mRNA level.

Interpretation & conclusions:

Our findings showed significant upregulation of miR-144 in serum samples of EC patients indicating its potential as minimally invasive marker. Further studies need to be done to understand the role of miR-144 in the pathogenesis of EC.

High-throughput validation of ceRNA regulatory networks

Background

MicroRNAs (miRNAs) play multiple roles in tumor biology. Interestingly, reports from multiple groups suggest that miRNA targets may be coupled through competitive stoichiometric sequestration. Specifically, computational models predicted and experimental assays confirmed that miRNA activity is dependent on miRNA target abundance, and consequently, changes in the abundance of some miRNA targets lead to changes to the regulation and abundance of their other targets. The resulting indirect regulatory influence between miRNA targets resembles competition and has been dubbed competitive endogenous RNA (ceRNA). Recent studies have questioned the physiological relevance of ceRNA interactions, our ability to accurately predict these interactions, and the number of genes that are impacted by ceRNA interactions in specific cellular contexts.

Results

To address these concerns, we reverse engineered ceRNA networks (ceRNETs) in breast and prostate adenocarcinomas using context-specific TCGA profiles, and tested whether ceRNA interactions can predict the effects of RNAi-mediated gene silencing perturbations in PC3 and MCF7 cells._ENREF_22 Our results, based on tests of thousands of inferred ceRNA interactions that are predicted to alter hundreds of cancer genes in each of the two tumor contexts, confirmed statistically significant effects for half of the predicted targets.

Conclusions

Our results suggest that the expression of a significant fraction of cancer genes may be regulated by ceRNA interactions in each of the two tumor contexts.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3790-7) contains supplementary material, which is available to authorized users.

A Macro View of MicroRNAs: The Discovery of MicroRNAs and Their Role in Hematopoiesis and Hematologic Disease

MicroRNAs (MiRNAs) are a class of endogenously encoded ~22 nucleotide, noncoding, single-stranded RNAs that contribute to development, body planning, stem cell differentiation, and tissue identity through posttranscriptional regulation and degradation of transcripts. Given their importance, it is predictable that dysregulation of MiRNAs, which target a wide variety of transcripts, can result in malignant transformation. In this review, we explore the discovery of MiRNAs, their mechanism of action, and the tools that aid in their discovery and study. Strikingly, many of the studies that have expanded our understanding of the contributions of MiRNAs to normal physiology and in the development of diseases have come from studies in the hematopoietic system and hematologic malignancies, with some of the earliest identified functions for mammalian MiRNAs coming from observations made in leukemias. So, with a special focus on the hematologic system, we will discuss how MiRNAs contribute to differentiation of stem cells and how dysregulation of MiRNAs contributes to the development of malignancy, by providing examples of specific MiRNAs that function as oncogenes or tumor suppressors, as well as of defects in MiRNA processing. Finally, we will discuss the promise of MiRNA-based therapeutics and challenges for the future study of disease-causing MiRNAs.

circRNA_100290 plays a role in oral cancer by functioning as a sponge of the miR-29 family

Circular RNAs (circRNAs) represent a class of non-coding RNAs that are widely expressed in mammals. However, it is largely unknown about the function of human circRNAs and the roles of circRNAs in human oral squamous cell carcinomas (OSCC). Here we performed a comprehensive study of circRNAs in human OSCC using circRNA and mRNA microarrays, and identified many circRNAs that are differentially expressed between OSCC tissue and paired non-cancerous matched tissue. We further found a circRNA termed circRNA_100290 that served as a critical regulator in OSCC development. We discovered that circRNA_100290 was upregulated and co-expressed with CDK6 in OSCC tissue. Knockdown of circRNA_100290 decreased expression of CDK6 and inhibited proliferation of OSCC cell lines in vitro and in vivo. Via luciferase reporter assays, circRNA_100290 was observed to directly bind to miR-29 family members. Further EGFP/RFP reporter assays showed that CDK6 was the direct target of miR-29b. Taken together, we conclude that circRNA_100290 may function as a competing endogenous RNA to regulate CDK6 expression through sponging up miR-29b family members. Taken together, it indicates that circRNAs may exert regulatory functions in OSCC and may be a potential target for OSCC therapy.

The lncRNA H19 Promotes Cell Proliferation by Competitively Binding to miR-200a and Derepressing β-Catenin Expression in Colorectal Cancer

H19, a paternally imprinted noncoding RNA, has been found to be overexpressed in various cancers, including colorectal cancer (CRC), and may function as an oncogene. However, the mechanism by which H19 regulates CRC progression remains poorly understood. In this study, we aimed to assess H19 expression levels in CRC tissues, determine the effect of H19 on CRC proliferation, and explore the mechanism by which H19 regulates the proliferation of CRC. We measured H19 expression using qRT-PCR and analysed the effects of H19 on colon cancer cell proliferation via cell growth curve, cell viability assay, and colony formation assays. To elucidate the mechanism underlying these effects, we analysed the interactions between H19 and miRNAs and identified the target gene to which H19 and miRNA competitively bind using a series of molecular biological techniques. H19 expression was upregulated in CRC tissues compared with adjacent noncancerous tissues. H19 overexpression facilitated colon cancer cell proliferation, whereas H19 knockdown inhibited cell proliferation. miR-200a bound to H19 and inhibited its expression, thereby decreasing CRC cell proliferation. β-Catenin was identified as a target gene of miR-200a. H19 regulated β-catenin expression and activity by competitively binding to miR-200a. H19 promotes cell proliferation by competitively binding to miR-200a and derepressing β-catenin in CRC.

miR-144 functions as a tumor suppressor in breast cancer through inhibiting ZEB1/2-mediated epithelial mesenchymal transition process

Breast cancer is the most common cancer in women worldwide. Local invasion, metastasis, and chemotherapy resistance are the obstacles for treatment of breast cancer. In this study, we aim to investigate the role of miR-144 in breast cancer. We demonstrate that the expression of miR-144 is downregulated in breast cancer and cell lines, and lower miR-144 expression is associated with poor differentiation, higher clinical stage, and lymph node metastasis in patients with breast cancer. The rescue of miR-144 expression is able to inhibit the cell proliferation and the ability of cell migration and invasion. In addition, we show that miR-144 can directly target at 3′-untranslation region of zinc finger E-box-binding homeobox 1 and 2, that is, ZEB1 and ZEB2, and regulate their expression at transcriptional and translational levels. Moreover, we also demonstrate that ectopic expression of miR-144 can inhibit the process of epithelial mesenchymal transition in MCF-7 and MDA-MB-231 cells. Thus, we here demonstrate that miR-144 functions as a tumor suppressor in breast cancer at least partly through inhibiting ZEB1/2-mediated epithelial mesenchymal transition process. Our findings indicate that the miR-144-ZEB1/2 signaling could represent a promising therapeutic target for breast cancer treatment.

A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

Long non-coding RNAs (lncRNAs) play critical and complicated roles in the regulation of various biological processes, including chromatin modification, transcription and post-transcriptional processing. Interestingly, some lncRNAs serve as miRNA "sponges" that inhibit interaction with miRNA targets in post-transcriptional regulation. We constructed a putative competing endogenous RNA (ceRNA) network by integrating lncRNA, miRNA and mRNA expression based on high-throughput RNA sequencing and microarray data to enable a comparison of the SHEE and SHEEC cell lines. Using Targetscan and miRanda bioinformatics algorithms and miRTarbase microRNA-target interactions database, we established that 51 miRNAs sharing 13,623 MREs with 2260 genes and 82 lncRNAs were involved in this ceRNA network. Through a biological function analysis, the ceRNA network appeared to be primarily involved in cell proliferation, apoptosis, the cell cycle, invasion and metastasis. Functional pathway analyses demonstrated that the ceRNA network potentially modulated multiple signaling pathways, such as the MAPK, Ras, HIF-1, Rap1, and PI3K/Akt signaling pathways. These results might provide new clues to better understand the regulation of the ceRNA network in cancer.

miR-136 suppresses tumor invasion and metastasis by targeting RASAL2 in triple-negative breast cancer

MicroRNAs play an important role in the regulation of cancer migration, invasion and metastasis. Patients with triple-negative breast cancer (TNBC) have a high incidence of early relapse and metastasis; however, the molecular basis for metastasis and recurrence in these individuals remains largely unknown. Herein, we demonstrate that miR-136 is an anti-invasive microRNA in TNBC and suppresses mesenchymal invasion and metastasis. Our results demonstrated that miR-136 was downregulated in TNBC and negative correlated with the WHO grades. However, RASAL2 was identified as a functional target of miR-136, and was overexpressed in TNBC and correlates with pathological grades. Moreover, overexpression of RASAL2 in a breast cancer cell line rescued miR-136-mediated cell migration and invasion. In conclusion, these results indicate that the miR-136/RASAL2/MET axis act as a suppressor of TNBC metastasis.

Endogenous microRNA sponges: evidence and controversy

The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for long non-coding RNAs, pseudogene transcripts and circular RNAs, as well as an alternative function for messenger RNAs. Empirical evidence supporting the hypothesis is accumulating but not without attracting scepticism. Recent studies that model transcriptome-wide binding-site abundance suggest that physiological changes in expression of most individual transcripts will not compromise miRNA activity. In this Review, we critically evaluate the evidence for and against the ceRNA hypothesis to assess the impact of endogenous miRNA-sponge interactions.