Circular RNA hsa_circ_0005114‑miR‑142‑3p/miR‑590‑5p-adenomatous polyposis coli protein axis as a potential target for treatment of glioma
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- Published online on: November 19, 2020 https://doi.org/10.3892/ol.2020.12320
- Article Number: 58
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Copyright: © Wei et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
Abstract
Introduction
Glioma is the most common malignant primary brain tumor, with an incidence of 4.7–7.3/100,000 individuals (1–4) and a mortality rate of 1.2–4.0/100,000 individuals (5). Despite advances in treatment options (such as radical surgery and chemo-radiotherapy), the prognosis of most patients remains poor due to high recurrence rates and invasiveness, with the 5-year survival rate of only 3–6% for grade IV (1,4). Therefore, it is important to further resolve the mechanisms underlying glioma progression to identify novel targets and develop new therapeutic approaches.
Circular (circ)RNAs are a newly identified class of non-coding (nc)RNAs with a covalent loop structure lacking the 5′-end cap and 3′-end ploy A tail, which prevents degradation by RNA exonucleases and confers strong stability in specific cells, such as tumor cells (6–8). Therefore, abnormal expression of circRNAs may be a potential mechanism for the development and progression of cancer, including glioma. This hypothesis has been demonstrated in several studies. For example, Zhou et al (9) demonstrated that hsa_circ_0008344 was significantly upregulated in glioblastoma tissues compared with the adjacent normal brain tissue. Zhou et al also reported that knockdown of hsa_circ_0008344 suppressed glioblastoma cell proliferation, colony formation, migration and invasion, but facilitated apoptosis. Wang et al (10) found that hsa_circ_0001649 expression was decreased in glioma specimens and cell lines. In addition, downregulated hsa_circ_0001649 is significantly associated with advanced grade and poor prognosis for patients with glioma. The functions and mechanism of circRNAs remain unclear; however, accumulating evidence indicates circRNAs have micro (mi)RNA (miR) response elements (MREs) (6–8), while MREs are widely known to be located in the 3′-untranslated region (3′-UTR) of the target mRNAs and miRNAs inhibit mRNA translation by binding to MREs. Thus, circRNAs may directly bind to miRNAs, impacting the interaction between miRNAs and mRNAs and contributing to the progression of glioma. This is known as the competitive endogenous RNA (ceRNA) hypothesis (6–8). This mechanism of circRNA function has been reported in several studies. For example, circ-pituitary homeobox (PITX)1 is upregulated in cancerous tissues and four cell lines of glioma. Dual-luciferase reporter and rescue assays indicated that circ-PITX1 may exert its oncogenic functions by sponging miR-518a-5p, leading to the release of the miR-518a-5p-mediated repression of interleukin 17 receptor D (IL17RD) (11). Similarly, hsa_circ_0034642 levels are also increased in glioma tissues and cells. Mechanistically, hsa_circ_0034642 sponges miR-1205 to regulate basic leucine zipper ATF-like transcription factor (BATF)3 levels to facilitate cell proliferation, migration and invasion (12). Circ-epididymis-specific α-mannosidase (MAN2B2) regulates S100 calcium-binding protein A8 (S100A8) expression by inhibiting miR-1205 and increasing S100A8 expression rescues the tumor suppressor effects of knockout of circ-MAN2B2 (13). Upregulated hsa_circ_0074362 plays a role in glioma progression by regulating the miR-1236-3p/homeobox B7 pathway (14), and downregulated hsa_circ_0001946 may act as a ceRNA, inhibiting glioblastoma progression by modulating miR-671-5p and cerebellar degeneration-related protein 1 (15). Overall, these findings imply that circRNA/ceRNA axes may be potential targets for the treatment of glioma; however, few studies have investigated this.
The present study aimed to further screen crucial circRNA/ceRNA axes for glioma by using the circRNA sequencing data of Yuan et al (16) and Zhu et al (17). Only the common differentially expressed circRNAs (DECs) in these two datasets were used to construct the ceRNA network based on the interactions between circRNAs-miRNAs and miRNAs-mRNAs. The expression and prognostic ability of these hub miRNAs and mRNAs were also validated using The Cancer Genome Atlas (TCGA) database and microarray data, which indirectly illustrated the possible proto- or antioncogenic roles of circRNAs. The current study may provide some novel therapeutic targets for glioma.
Materials and methods
Data collection
In total, two circRNA datasets of glioblastoma with the accession numbers GSE86202 (16) and GSE92322 (17) were downloaded from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). Three glioma and paired normal brain tissues were used for RNA sequencing on Illumina HiSeq 2500 (Homo sapiens, GPL16791) in GSE86202 dataset (16), while 10 samples (five glioma and paired normal brain tissues) were included for circRNA sequencing on Illumina HiSeq 2000 (Homo sapiens, GPL11154) in GSE92322 dataset (17).
Screening of DECs
The normalized data of each dataset was downloaded from the GEO database. The gene symbol and circID of circRNAs were annotated using the circBase database (http://www.circbase.org) (18) according to the chromosome location and information of the positive-negative chain. The DECs were identified using edgeR package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) (19). |log2FC (fold-change) |>1 and P<0.05 were defined as the significance threshold values. The heatmap of DECs was created using pheatmap package (version 1.0.8; http://cran.r-project.org/web/packages/pheatmap) of R language (version 3.4.1; http://www.r-project.org/) (20).
Construction of circRNA-miRNA-mRNA ceRNA network
The miRNAs that interacted with common DECs in two datasets were predicted using the CircInteractome (https://circinteractome.nia.nih.gov) (21) and StarBase (http://starbase.sysu.edu.cn/starbase2/) (22) databases. Only the shared miRNAs predicted in these two databases were used for further analysis. The target genes of these miRNAs were subsequently predicted using the miRwalk 2.0 database (23), which included 12 prediction programs (miRWalk, MicroT4, miRanda, miRBridge, miRDB, miRMap, miRNAMap, PICTAR2, PITA, RNA22, RNAhybrid and Targetscan). Only the target genes predicted by at least six algorithms were retained, which were then compared with established glioma-related genes collected from the Comparative Toxicogenomics database (CTD) (24) to obtain glioma-associated miRNA-mRNA interaction pairs. The circRNA-miRNA-mRNA-ceRNA network was then established based on these interaction relationships between DECs-miRNAs and miRNAs-mRNAs using Cytoscape software (version 3.6.1; www.cytoscape.org/) (25).
Functional enrichment analysis for DECs and target genes in the ceRNA network
Enrichment analyses for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) [including biological process (BP), cellular component (CC) and molecular function (MF)] terms were conducted using the ClusterProfiler tool (26) to predict the possible function of DECs and target genes in the ceRNA network. P<0.05 adjusted for multiple testing according to Benjamini and Hochberg (27) was regarded as the cut-off value.
Prognosis and expression validation for miRNAs and target genes in the ceRNA network
The LinkedOmics online database (http://www.linkedomics.org/) (28) was searched to explore the associations between miRNAs/mRNAs and overall survival (OS) rate for glioma based on a Cox regression, after which Kaplan-Meier survival curves were automatically provided. TCGA-glioblastoma multiforme-low grade glioma (GBMLGG) miRNASeq/RNA-seq and clinical data were selected for miRNAs/mRNAs analysis. The UALCAN web-portal (http://ualcan.path.uab.edu/index.html) (29) was used for validation of the expression of target genes of miRNAs between unmatched glioblastoma multiforme and normal control tissues using TCGA data, in which the statistical significance was estimated using unpaired Student's t-tests. GSE103229 (including five glioblastoma and five normal control tissues) and GSE25632 (including 82 glioblastoma and five normal controls) (30) microarray datasets in the GEO database were used to determine the expression of crucial miRNAs with GEO2R, an interactive web-based statistical tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/). P<0.05 was considered to indicate a statistically significant difference.
Results
Identification of DECs
In the GSE86202 dataset, 23,463/37,085 circRNAs were annotated to the circID in the circBase database and 6,131 had corresponding Gene_symbols. In the GSE92322 dataset, 12,863/59,386 circRNAs were annotated to the circID in the circBase database and 4,676 of them had corresponding Gene_symbol.
Using the edgeR package, a total of 22 upregulated (20 had circID and Gene_symbol) and 2,068 (1,874 had circID and 1,332 had Gene_symbol) DECs were identified between glioma and paired normal brain tissues in the GSE86202 dataset. Meanwhile, 29 upregulated (zero had circID and Gene_symbol) and 1,205 (1,196 had circID and 884 had Gene_symbol) DECs were identified in the GSE92322 dataset (Table I). The heat maps of these DECs are displayed in Fig. 1. These findings suggested that these DECs may be effective to classify the samples into two groups.
Functional enrichment analysis for DECs
A comparison between the two aforementioned datasets reported that 424 downregulated DECs with Gene_symbol were shared. The functions of DECs were enriched according to their corresponding Gene_symbols. The results showed that 23 KEGG pathways were enriched (Table II and Fig. 2A), mainly including ‘retrograde endocannabinoid signaling’, ‘ErbB signaling pathway’ and ‘insulin secretion’ for hsa_circ_0005114. Meanwhile, KEGG pathways enriched for hsa_circ_0100496 were ‘calcium signaling pathway’, ‘cholinergic synapse’ and ‘choline metabolism in cancer’, and ‘N-Glycan biosynthesis’ was enriched for hsa_circ_0000120. Furthermore, 143 GO terms (including 87 BPs, 38 CCs and 18 MFs; Table III and Fig. 2B) were also enriched, including ‘regulation of cell morphogenesis’ (hsa_circ_0005114 and hsa_circ_0001936), ‘regulation of neuron projection development’ (hsa_circ_0005114), ‘central nervous system neuron differentiation’ (hsa_circ_0117841), ‘positive regulation of neuron differentiation’ (hsa_circ_0005114, hsa_circ_0104727) and ‘cell-cell junction’ (hsa_circ_0001368). These findings suggested that hsa_circ_0005114 may be crucial for the development of glioma since it was enriched in KEGG pathways and GO terms.
 | Table II.Kyoto Encyclopedia of Genes and Genomes pathways enriched for differentially expressed circRNAs. |
Construction of the ceRNA network and functional enrichment
After uploading the circID (197 common in the two datasets) to the CircInteractome database, 313 miRNAs were predicted to interact with DECs. Using Gene_symbol, 276 miRNAs were predicted to interact with DECs using Starbase. Among them, 18 miRNAs were shared, including hsa-miR-139-5p, −142-3p, −184, −217, −324-5p, −326, −330-5p, −338-3p, −346, −375, −384, −421, −496, −543, −590-5p, −599, −615-3p and −875-5p). Subsequently, the target genes were predicted for these 18 miRNAs using the miRwalk 2.0 database, which were then compared with 65 pre-established glioma-related genes collected from the CTD database. In total, 22 genes were shared, including BRD4, SUZ12, VEGFA, NOTCH3, NOTCH2, RUNX3, CTNND2, EGFR, CDK6, PML, BHLHE40, EGF, NOTCH1, TNFSF10, LZTR1, RUNX1, MDM4, MET, IL1B, JAG1, APC and RECK. Then, the ceRNA network was established based on 115 DECs, 15 miRNAs and the aforementioned 22 mRNAs (Fig. 3).
Function analysis for the target genes of miRNAs in this ceRNA network showed that 44 KEGG pathways (Table IV and Fig. 4A) and 736 GO terms (including 713 BPs, three CCs and 20 MFs) (Table V and Fig. 4B) were enriched, such as ‘regulation of actin cytoskeleton’ (Table IV), various cancer pathways (including ‘miRNAs in cancer’, ‘breast cancer’, ‘endometrial cancer’, ‘gastric cancer’, ‘hepatocellular carcinoma’ and ‘colorectal cancer’; Fig. 4A), ‘Wnt signaling pathway’, ‘cell cycle arrest’, ‘cell fate commitment’ (Fig. 4B) and cell junction assembly (Table V), in all of which the APC gene was included. These findings suggested that the circRNAs-miRNAs that regulated APC may be crucial for the development of glioma.
| Table IV.Kyoto Encyclopedia of Genes and Genomes pathways enriched for genes in the competing endogenous RNA network. |
Prognosis and expression analysis for miRNAs and target genes
LinkedOmics online analysis using TCGA data showed that 19 mRNAs and nine miRNAs were significantly associated with OS (Table VI and Fig. 5). These prognosis-related miRNAs and mRNAs constituted 20 interaction relationships in the ceRNA network. However, the prognosis trend between hsa-miR-217/hsa-miR-324-5p/hsa-miR-590-5p/hsa-miR-599/hsa-miR-875-5p and their target genes were consistent, with high expression levels of both miRNAs and their target genes indicating a poor prognosis, which is not in accordance with the negative regulatory mechanisms of miRNAs on mRNAs. Thus, only hsa-miR-139-5p-NOTCH1/RUNX1/CDK6/TNFSF10/VEGFA and hsa-miR-142-3p-APC-related ceRNA axes may be important. Furthermore, as all the circRNAs in the ceRNA network were downregulated, its interactive miRNAs should be upregulated according to the ceRNA theory (6–8); however, similarly to circRNAs, high expression levels of hsa-miR-139-5p were also associated with an excellent overall survival rate, indicating that hsa-miR-139-5p was also downregulated in glioma. Thus, hsa-miR-139-5p-related interaction relationships were excluded from further analyses and only hsa-miR-142-3p-APC-related ceRNA axes (in which high hsa-miR-142-3p expression was associated with poor OS, while high APC expression was associated with a good prognosis, as shown in Fig. 5) were crucial.
Accordingly, hsa_circ_0000120/ 0001367/ 0001368/ 0001369/ 0001936/ 0004516/ 0005114/ 0060425/0064615/0130887-hsa-miR-142-3p-APC ceRNA axes may be potential targets for the development of glioma. Additionally, UALCAN analysis using TCGA data of glioblastoma multiforme demonstrated that APC was significantly downregulated in glioma compared with in normal tissues (P=0.0000822); while GSE25632 microarray analysis showed the expression of hsa-miR-142-3p was significantly higher in glioma compared with that in normal tissues (log2FC=1.21, P=0.00284), further confirming the creditability of these crucial ceRNA axes for glioma (data not shown).
In addition, both of GSE25632 (log2FC=5.75, P=0.0226) and GSE103229 (log2FC=1.65, P=0.0208) microarray analyses revealed that hsa-miR-590-5p was upregulated in glioma compared with that in normal tissues (data not shown). In fact, the interaction between hsa-miR-590-5p and APC was also predicted by RNA22 and RNAhybrid using miRwalk2.0 analysis (data not shown). Therefore, circRNAs interacting with hsa-miR-590-5p were also important, including hsa_circ_0005114, 0069718, 0098551, 0100496, 0104726, 0104727 and 0117841 (Fig. 3), among which hsa_circ_0005114 interacted with hsa-miR-142-3p. Therefore, the hsa_circ_0005114-miR-142-3p/miR-590-5p-APC ceRNA axis may represent a potential mechanism for the development of glioma.
Discussion
In the present study, 16 crucial downregulated circRNAs were identified that may sponge miR-142-3p/miR-590-5p to suppress glioma progression via regulating the APC gene. Most of them, to the best of our knowledge, were newly reported circRNAs associated with cancer, except for hsa_circ_0001368 that has a tumor-suppression role in gastric cancer by regulating the miR-6506-5p/forkhead box (FOX) protein O3 axis (31). However, hsa_circ_0005114 may be particularly important as it was a circRNA interacting with both miR-142-3p and miR-590-5p.
The present analysis did not identify the roles of hsa_circ_0005114 in cancer; however, hsa_circ_0005114 is derived from the regulating synaptic membrane exocytosis (RIMS)2 gene. Thus, the function of hsa_circ_0005114 may be similar to that of RIMS2. Notably, Mukasa et al (32) observed that RIMS2 expression is significantly higher in normal brain tissues compared with glioblastoma. In addition, it was reported that RIMS2 mediates the cAMP-guanidine nucleotide exchange factor II pathway to promote incretin-potentiated insulin secretion (33,34). The downregulation of RIMS2 may lead to the lower levels of insulin and the development of diabetes and obesity, as while 11.1% of patients with glioma (35) and 30% of those with brain tumor are diagnosed with obesity and insulin resistance/impaired glucose tolerance (36). Therefore, hsa_circ_0005114 may be involved in glioma by influencing the insulin secretion pathway, which was also predicted in the present function enrichment analysis. However, how hsa_circ_0005114 influences insulin secretion needs further investigation. A recent study proposed that high insulin index is positively associated with a high risk of glioma development (37). However, another study reported that decreased insulin receptor expression impairs cellular functions and represses orthotopic glioblastoma (38). These conflicting reports may be attributed to the dual roles of insulin (39).
In addition to insulin secretion mechanisms, the present study predicted that hsa_circ_0005114 may exert tumor suppressor functions by upregulating miR-142-3p and miR-590-5p, which subsequently inhibited the expression of APC. Studies have demonstrated that miR-590-5p is upregulated in liver (40), colorectal (41), gastric (42) and cervical cancer (43). miR-590-5p promotes cancer cell proliferation, invasion and therapy resistance by targeting FOXO1 (34), TGF-β R2 (44), matrix metalloproteinases (41), reversion-inducing cysteine-rich protein with Kazal motifs (36) and cell adhesion molecule L1-like (43). Furthermore, a previous study also showed that miR-590-3p is upregulated in human glioma tissues (especially high grade) and radioresistant human glioblastoma cells (45). The use of anti-miR-590-3p suppresses cell viability, decreases colony formation capacity, increases the apoptotic rate and enhances the radiosensitivity. A luciferase reporter assay demonstrated that leucine-rich repeats and immunoglobulin-like domains protein 1 is the direct target of miR-590-3p. Similarly, other studies using quantitative PCR also detected that miR-142-3p expression is significantly upregulated in renal cell carcinoma (46) and nasopharyngeal carcinoma (47) compared with adjacent tissues. Downregulation of miR-142-3p significantly suppresses cell proliferation, migration and cell cycle progression, promotes apoptosis in vitro (46) and blocks tumor growth in a mouse model via upregulating its targeted genes, including suppressor of cytokine signaling 6 (47) and Ras-related C3 botulinum toxin substrate 1 in colorectal cancer (48). High expression of miR-142-3p is correlated with histological differentiation and a poor prognosis for patients with esophageal squamous cell carcinoma (49). In line with the aforementioned findings, the present study reported that miR-590-5p and miR-142-3p were upregulated in glioblastoma tissues compared with normal controls and were associated with a worse prognosis. However, the targeted genes of these two miRNAs were not completely validated in cancer. It was predicted that APC, a regulator of the WNT signaling pathway (50), may be a direct target for both miR-590-5p and miR-142-3p. Their negative regulatory relationship was indirectly investigated by Naseri et al (51) who showed that delivery of anti-miR-142-3p by exosomes to breast cancer cells leads to a significant increase in APC mRNA levels. In addition, Wu et al (52) used dual-luciferase and western blot analysis in mesenchymal stem cells to demonstrate that miR-590-3p binds to the 3′UTR of APC mRNA. Notably, APC encodes a protein that acts as an antagonist of the Wnt signaling pathway (53), which is often activated in cancer (54). Thus, APC may be downregulated during carcinogenesis, which has been confirmed in various cancer types, including glioma (55–57). For example, Cole et al (55) reported that APC expression is decreased in pancreatic ductal adenocarcinoma tissues, and that APC siRNA treatment promotes cell proliferation and migration. Wang et al (56) reported that the expression of APC mRNA is significantly decreased in ovarian tumor cells and tissues compared with in normal ovarian cells and tissues. In addition, overexpression of APC induces increased apoptosis of ovarian tumor cells by decreasing the ATP binding cassette subfamily B member 1 (also known as multidrug resistance gene 1)/chemokine (C-X-C motif) ligand 1 signaling pathway. Zhang et al (57) demonstrated that APC expression is downregulated in colorectal cancer tissues, which is associated with the expression of miR-494. Overexpression of miR-494 promotes colorectal cancer cell proliferation by inhibiting APC and consequently inducing Wnt/β-catenin signaling. Western blot assays of Li et al (58) also suggested that miR-106a-5p reduces APC protein levels and upregulates target proteins of the Wnt/β-catenin pathway, resulting in the invasion of glioblastoma cells (58). In accordance with these studies, the present study reported that APC expression was decreased in glioblastoma tissues compared with normal controls and high expression of APC was associated with a good prognosis. Functional enrichment analysis showed APC was involved in Wnt signaling pathway, cell fate commitment, and cell junction.
Overall, the present study suggested that hsa_circ_0005114-miR-142-3p/miR-590-5p-APC ceRNA axes may be mechanisms for the development and progression of glioma. These axes may also have potential as novel targets for the treatment of glioma. However, additional in vitro and in vivo experiments, such as gene interaction experiments involving knockout/overexpression of hsa_circ_0005114-miR-142-3p/miR-590-5p-APC and their influence on tumor cells (using cell proliferation, apoptosis, invasion and migration assays) and tumor growth, are required to validate these conclusions in the future, and the lack of these experiments is a limitation of the present study.
Acknowledgements
Not applicable.
Funding
The present study was funded by grants from The Natural Science Foundation of China (grant no. 81400404) and The Science and Technology of Jilin Province (grant no. 20200201470JC).
Availability of data and materials
The GSE86202, GSE92322, GSE103229 and GSE25632 datasets were downloaded from the Gene Expression Omnibus repository (http://www.ncbi.nlm.nih.gov/geo/). LinkedOmics and UALCAN database used the miRNA and mRNA sequencing data of The Cancer Genome Atlas (https://gdc-portal.nci.nih.gov/) for analysis.
Authors' contributions
BW, LW and JWZ conceived and designed the study. BW collected and analyzed the data. LW and JWZ contributed to the interpretation of data. BW and LW drafted the manuscript. JWZ revised the manuscript. All authors read and approved the final manuscript.
Ethics approval and consent to participate
Not applicable.
Patient consent for publication
Not applicable.
Competing interests
The authors declare that they have no competing interests.
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