Circular RNA hsa_circ_0005114-miR-142-3p/miR-590-5p-adenomatous polyposis coli protein axis as a potential target for treatment of glioma

Glioma is the most common type of brain tumor and is associated with a high mortality rate. Despite recent advances in treatment options, the overall prognosis in patients with glioma remains poor. Studies have suggested that circular (circ)RNAs serve important roles in the development and progression of glioma and may have potential as therapeutic targets. However, the expression profiles of circRNAs and their functions in glioma have rarely been studied. The present study aimed to screen differentially expressed circRNAs (DECs) between glioma and normal brain tissues using sequencing data collected from the Gene Expression Omnibus database ({"type":"entrez-geo","attrs":{"text":"GSE86202","term_id":"86202"}}GSE86202 and {"type":"entrez-geo","attrs":{"text":"GSE92322","term_id":"92322"}}GSE92322 datasets) and explain their mechanisms based on the competing endogenous (ce)RNA regulatory hypothesis. In total, 424 commonly downregulated DECs (with the Gene_symbol annotated in the circBase database) in these two datasets were identified. Using the CircInteractome and Starbase databases, 18 micro (mi)RNAs (miRs) were predicted to interact with DECs, while 22 glioma-related genes obtained from the Comparative Toxicogenomics Database were predicted to be regulated by 15 miRNAs via the miRwalk 2.0 database. A ceRNA network was established based on 115 DECs, 15 miRNAs and 22 mRNAs. LinkedOmics online analysis using The Cancer Genome Atlas (TCGA) data showed that hsa-miR-142-3p/hsa-miR-590-5p and their target gene adenomatous polyposis coli protein (APC) were all significantly associated with overall survival rate and their prognosis trend was opposite, revealing that high expression levels of hsa-miR-142-3p/hsa-miR-590-5 were associated with a poor overall survival rate, while high APC expression with a good overall survival rate. UALCAN analysis using TCGA data of glioblastoma multiforme and the {"type":"entrez-geo","attrs":{"text":"GSE25632","term_id":"25632"}}GSE25632 and {"type":"entrez-geo","attrs":{"text":"GSE103229","term_id":"103229"}}GSE103229 microarray datasets showed that hsa-miR-142-3p/hsa-miR-590-5p was upregulated and APC was downregulated. Thus, hsa-miR-142-3p/hsa-miR-590-5p-APC-related circ/ceRNA axes may be important in glioma, and hsa_circ_0005114 interacted with both of these miRNAs. Functional analysis showed that hsa_circ_0005114 was involved in insulin secretion, while APC was associated with the Wnt signaling pathway. In conclusion, hsa_circ_0005114-miR-142-3p/miR-590-5p-APC ceRNA axes may be potential targets for the treatment of glioma.     

The Down-Regulation of Circ_0059707 in Acute Myeloid Leukemia Promotes Cell Growth and Inhibits Apoptosis by Regulating miR-1287-5p

Acute myeloid leukemia (AML) is the most common type of hematological malignancy. Recently, an increasing number of reports have shown that many circular RNAs can act as effective targets for AML. However, the roles of circ_0059707 in AML remain largely unclear. In this study, we found that the expression levels of circ_0059707 were significantly decreased in AML patients with respect to normal controls (p < 0.001). Low expression levels of circ_0059707 were also associated with a poor prognosis. Furthermore, circ_0059707 overexpression inhibited cell growth and promoted apoptosis in leukemia cells, compared with control cells. Circ_0059707- and empty plasmid-transfected cells were injected subcutaneously into BALB/c nude mice. We found that the tumor volume was significantly lower in mice in the circ_0059707 group than in control mice (p < 0.01). Nuclear pyknosis, nuclear fragmentation, nuclear dissolution, and cell necrosis were observed in the circ_0059707 group by HE staining. CircInteractome analysis showed that 25 microRNAs (miRNAs), including miR-1287-5p, ©-miR-1825, a©hsa-miR-326, may be potential targets for circ_0059707. The expression of these miRNAs was analyzed in both the GEO {"type":"entrez-geo","attrs":{"text":"GSE51908","term_id":"51908"}}GSE51908 and the {"type":"entrez-geo","attrs":{"text":"GSE142700","term_id":"142700"}}GSE142700 databases. miR-1287-5p expression was lower in AML patients compared with controls in both the {"type":"entrez-geo","attrs":{"text":"GSE51908","term_id":"51908"}}GSE51908 and the {"type":"entrez-geo","attrs":{"text":"GSE142700","term_id":"142700"}}GSE142700 datasets. Moreover, we demonstrated that miR-1287-5p expression was down-regulated in AML patients and up-regulated in circ_0059707-overexpressing cells. Collectively, our research demonstrated that the down-regulation of circ_0059707 was highly evident in de novo AML patients. Our analysis also demonstrated that circ_0059707 inhibited cell growth and promoted apoptosis by up-regulating miR-1287-5p.     

MiR-374b-5p inhibits KDM5B-induced epithelial-mesenchymal transition in pancreatic cancer

Micro(mi)RNAs play a critical regulatory role in the progression and metastasis of pancreatic cancer (PC). In this study, we aimed to reveal the mechanisms of miR-374b-5p in regulating epithelial-mesenchymal transition (EMT) in PC. Gene Expression Omnibus datasets ({"type":"entrez-geo","attrs":{"text":"GSE24279","term_id":"24279"}}GSE24279 and {"type":"entrez-geo","attrs":{"text":"GSE71533","term_id":"71533"}}GSE71533) and the pancreatic ductal adenocarcinoma (PDAC) cohort of The Cancer Genome Atlas were employed to screen for potential prognostic miRNAs. The expression of miR-374b-5p was measured by quantitative real-time polymerase chain reaction (qRT-PCR) in 78 paired PDAC tissue samples. The biological effects of miR-374b-5p were investigated using in vitro and in vivo assays. Luciferase reporter assays and immunohistochemical tests were conducted to verify the interaction between miR-374b-5p and its predicted direct target, KDM5B. MiR-374b-5p was downregulated in PC tissues, and a low level of miR-374b-5p was associated with poor overall survival, greater tumor size, and more lymph node metastasis in PC. In vitro assays indicated that overexpression of miR-374b-5p suppressed the proliferation, migration, and invasion of PC cells. Mechanistically, miR-374b-5p suppressed the expression of KDM5B, which inhibited E-cadherin expression but promoted N-cadherin and vimentin expression. Finally, in vivo assays demonstrated that miR-374b-5p overexpression suppressed tumor growth and lung metastasis in PANC-1 cells. Thus, our findings indicate that miR-374b-5p could be a potential prognostic biomarker and therapeutic target for KDM5B-induced EMT in PC.     

The hsa_circ_0007396-miR-767-3p-CHD4 axis is involved in the progression and carcinogenesis of gastric cancer

BackgroundCircular RNAs (circRNAs) have been linked to numerous human cancers, including gastric cancer (GC), in numerous recent investigations. The expression of circRNA and the mechanisms involved in GC are still unknown.MethodsIn this work, Gene Expression Omnibus 2R (GEO2R) online tool was first used to screen 6 candidates of differentially expressed circRNAs in 2 datasets, {"type":"entrez-geo","attrs":{"text":"GSE83521","term_id":"83521"}}GSE83521 and {"type":"entrez-geo","attrs":{"text":"GSE89143","term_id":"89143"}}GSE89143. Then, using Cancer-Specific CircRNA Database (CSCD), the structural loop diagrams of these circRNAs were generated. After combining the Circular RNA Interactome (CRI) and CSCD databases for miRNA co-prediction, a candidate circRNA-miRNA sub-network was successfully created. The expression of these miRNAs was further examined using Cytoscape software, and 2 miRNAs, miR-767-5p and miR-767-3p.ResultsWe used GEO2R to analyze the differential expression of {"type":"entrez-geo","attrs":{"text":"GSE83521","term_id":"83521"}}GSE83521 and {"type":"entrez-geo","attrs":{"text":"GSE89143","term_id":"89143"}}GSE89143 datasets in GEO database. Through the construction of the structural ring diagram of CSCD database, we found that hsa_circRNA_100571, hsa_circRNA_103102, hsa_circRNA_100754, hsa_circRNA_100737, hsa_circRNA_100269, hsa_circRNA_102476, hsa_circRNA_101287 is the final candidate circRNA in GC. MiR-767-5p and miR-767-3p were found to be important miRNAs in GC. The miRNet database indicated their downstream target genes. In various studies, namely central gene screening, correlation analysis, and protein-protein interaction (PPI), we detected chromodomain helicase DNA binding protein 4 (CHD4) as a key potential candidate of hsa-mir-767-3p. Next, we conducted validation of clinical data. We included the clinical data of 100 patients with GC, and found that patients with low CHD4 expression had significantly higher OS and PFS than those with high CHD4 expression (P<0.001, P=0.005). Cox regression analysis showed that low CHD4 expression was an independent risk factor for tumor progression (P=0.001). At the same time, tumor differentiation and chemotherapy also had a certain impact on the progression of GC (all P<0.05). Therefore, CHD4 may provide a promising therapeutic target for the future treatment of GC.ConclusionsWe identified an important hsa_circ_0007396-miR-767-3p-CHD4 axis, which is associated with GC proliferation and carcinogenesis, and may represent a promising therapeutic target for the future cure of GC.     

Four potential microRNAs affect the progression of pancreatic ductal adenocarcinoma by targeting MET via the PI3K/AKT signaling pathway

Pancreatic ductal adenocarcinoma (PDAC) is the most common tumor subtype of pancreatic cancer, which exhibits poor patient prognosis due to the lack of effective biomarkers in the diagnosis and treatment. The present study aimed to identify the potential biomarkers of PDAC carcinogenesis and progression using three microarray datasets, {"type":"entrez-geo","attrs":{"text":"GSE15471","term_id":"15471"}}GSE15471, {"type":"entrez-geo","attrs":{"text":"GSE16515","term_id":"16515"}}GSE16515 and {"type":"entrez-geo","attrs":{"text":"GSE28735","term_id":"28735"}}GSE28735, which were downloaded from the Gene Expression Omnibus database. The datasets were analyzed to screen out differentially expressed genes (DEGs) in PDAC tissues and adjacent normal tissues. A total of 143 DEGs were identified, including 132 upregulated genes and 11 downregulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional and signaling pathway enrichment analyses were performed on the DEGs, and the Search Tool for the Retrieval of Interacting Genes/Proteins database was used to construct a protein-protein interaction network. The main functions of DEGs include extracellular matrix degradation, and regulation of matrix metalloproteinase activity and the PI3K-Akt signaling pathway. The five hub genes were subsequently screened using Cytoscape software, and survival analysis demonstrated that abnormal expression levels of the hub genes was associated with poor disease-free survival and overall survival. Biological experiments were performed to confirm whether mesenchymal-to-epithelial transition (MET) factors promote the proliferation, migration and invasion of PDAC cells via the PI3K/AKT signaling pathway. In addition, six MET-targeted microRNAs (miRNAs) were identified, four of which had conserved binding sites with MET. Based on the signaling pathway enrichment analysis of these miRNAs, it is suggested that they can affect the progression of PDAC by targeting MET via the PI3K/AKT signaling pathway. In conclusion, the hub genes and miRNAs that were identified in the present study contribute to the molecular mechanisms of PDAC carcinogenesis and progression. They also provide candidate biomarkers for early diagnosis and treatment of patients with PDAC.     

Comprehensive bioinformatics analysis of functional molecules in colorectal cancer

BackgroundColorectal cancer (CRC) is the 3rd most common cancer and the 2nd leading cause of cancer-related death. Numerous studies have found that aberrations in cellular molecules play an important role in the development of tumors. Studying and determining the interactions between these molecules can contribute to the diagnosis, treatment, and prognosis of tumors.MethodsThe {"type":"entrez-geo","attrs":{"text":"GSE151021","term_id":"151021"}}GSE151021, {"type":"entrez-geo","attrs":{"text":"GSE156720","term_id":"156720"}}GSE156720, and {"type":"entrez-geo","attrs":{"text":"GSE156719","term_id":"156719"}}GSE156719 data sets were analyzed to screen the differentially expressed messenger RNAs (DEmRNAs), long non-coding RNAs (DElncRNAs), and microRNAs (DEmiRNAs) in CRC. Database for Annotation, Visualization and Integrated Discovery (DAVID) and the Search Tool for the Retrieval of Interacting Genes/Proteins software were used to examine gene enrichment and the hub genes. Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and UALCAN was used to verify the expression of the hub genes. To analyze the overall survival (OS) of the hub genes, Kaplan-Meier plotter (KM plotter) was performed. Finally, the miRCancer database, TargetScan, and {"type":"entrez-geo","attrs":{"text":"GSE156719","term_id":"156719"}}GSE156719 were used to identify the targets of the identified miRNAs. To predict the lncRNA-miRNA interactions, we used DIANA-LncBase v2 and {"type":"entrez-geo","attrs":{"text":"GSE156720","term_id":"156720"}}GSE156720. Finally, the visualization protein‑protein interaction (PPI), competitive endogenous RNA (ceRNA) network was constructed using Cytoscape v3.1.ResultsBy analyzing {"type":"entrez-geo","attrs":{"text":"GSE151021","term_id":"151021"}}GSE151021 and {"type":"entrez-geo","attrs":{"text":"GSE156720","term_id":"156720"}}GSE156720, 23 upregulated mRNAs and 10 downregulated mRNAs were identified as sharing the differentially expressed genes (DEGs) between CRC and adjacent tissues. Furthermore, nucleolar protein 14 (NOP14), the sonic hedgehog (SHH) signaling molecule, phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1), the BCL2 apoptosis regulator (BCL2), and zinc finger E-box binding homeobox 2 (ZEB2) were considered hub genes. The constructed lncRNA-miRNA-mRNA network revealed 7 intersecting miRNAs (4 upregulated and 3 downregulated), 79 lncRNAs (40 upregulated and 39 downregulated), and 5 mRNAs (3 upregulated and 2 downregulated). Finally, we determined that the dysregulation of lncRNAs, such as HCG16, CASC9, SNHG16, HAND2-AS1, and NR2F1-AS1, secluded altered the expression of several miRNAs, such as hsa-miR-193a-5p, hsa-miR-485-5p, hsa-miR-17-5p, and hsa-miR-92a-3p, and affected the occurrence and development of CRC.ConclusionsWe identified a series of DElncRNAs, DEmRNAs, and DEmiRNAs in CRC that might be considered potential biomarkers in understanding the complex molecular pathways leading to CRC development.     

A novel ferroptosis-related gene signature for clinically predicting recurrence after hepatectomy of hepatocellular carcinoma patients

High recurrence rate in HCC is the primary cause of the poor prognosis after hepatectomy. Therefore, in this study, we aimed to construct a gene signature for predicting the recurrence rate in HCC. The mRNA expression profiles and clinical information of HCC patients from GEO and TCGA databases were used, and ferroptosis-related gene list was obtained from the FerrDb database. We identified 39 ferroptosis-related genes (FDEGs) that were differentially expressed between HCC samples and normal tissues from the {"type":"entrez-geo","attrs":{"text":"GSE14520","term_id":"14520"}}GSE14520 dataset. The univariate and multivariate Cox regression analyses were employed to construct a prognostic signature. Seven FDEGs (MAPK9, SLC1A4, PCK2, ACSL3, STMN1, CDO1, and CXCL2) were included to construct a risk model, which was validated in the TCGA dataset. Patients in high-risk groups exhibited a significantly poor prognosis compared with patients in low-risk groups in both the training set ({"type":"entrez-geo","attrs":{"text":"GSE14520","term_id":"14520"}}GSE14520 cohort) and the validation set (TCGA cohort). Multivariate cox regression analyses demonstrated that the 7-gene signature was an independent risk factor for RFS in HCC patients. KEGG analysis showed that FDEGs were mainly enriched in Ferroptosis, Hepatocellular carcinoma pathway, and MAPK signaling pathway. GSEA analysis suggested that the high-risk group was correlated with multiple oncogenic signatures and invasive-related pathways. These results indicated that this risk model can accurately predict recurrence after hepatectomy and offer novel research directions for personalized treatment in HCC patients.     

Exosomal microRNA: A Diagnostic Marker for Lung Cancer

BackgroundTo date, there is no screening test for lung cancer shown to affect overall mortality. MicroRNAs (miRNAs) are a class of small noncoding RNA genes found to be abnormally expressed in several types of cancer, suggesting a role in the pathogenesis of human cancer. Their accumulation within the peripheral circulation appears to be unique to cancer. The genome-wide expression profiling of miRNAs has been shown to be significantly different among primary lung cancers and corresponding noncancerous lung tissues. In studies demonstrating diagnostic miRNA signatures of NSCLC, specific miRNAs were overexpressed compared with normal lung tissue (miR-17-3p, miR-21, miR-106a, miR-146, miR-155, miR-191, miR-192, miR-203, miR-205, miR-210, miR-212, and miR-214). In this study, we evaluate the levels of circulating tumor exosomes, the circulating levels of exosomal small RNA, and specific exosomal miRNAs in patients with and without lung adenocarcinoma, correlating the levels with the American Joint Committee on Cancer (AJCC) stage of disease to validate it as an acceptable marker for diagnosis and prognosis in patients with adenocarcinoma of the lung.Patients and MethodsPlasma from patients with lung adenocarcinoma and a control group without known lung cancer or other active cancer were collected. Exosomes were isolated from plasma samples by a 2-step procedure using size-exclusion chromatography and magnetic activated cell sorting (MACS). Plasma samples (1 mL) were separated on Sepharose 2B, monitoring elution at 280 nm, and using a modified MACS procedure, exosomes of tumor origin were isolated using anti—epithelial cell adhesion molecule. Small RNA was isolated from circulating tumor exosomes using mirVana isolation kit (Ambion, Austin, TX) and this low molecular RNA enriched fraction was used for miRNA profiling as defined by microarray analysis. Low molecular weight RNA (5 μg) was used for hybridization on miRNA microarray chips. These miRNA were identified as hsa-miR-17-3p, hsa-miR-21, hsa-miR-106a, hsa-miR-146, hsa-miR-155, miR-191, miR-192, miR-203, miR-205, miR-210, miR212, and hsa-miR-214.ResultsTo date, 28 patients and 9 controls, AJCC stages I-IV, ages 21–80 years, were enrolled in the study. Exosome concentration ranged from 1.02–9.24 mg/mL for the lung adenocarcinoma group versus 0.62–1.7 mg/mL in the control group. The total miRNA concentration ranged from 131.1–275 ug/mL for the lung adenocarcinoma group versus 44.9–131.1 ug/mL in the control group. The mean exosome value in the lung cancer group was 2.85 mg/mL (CI, 1.94–3.76) and 0.77 mg/mL (CI, 0.68–0.86; P < .001). The mean RNA value in the lung cancer group was 158.6 ug/mL (CI, 145.7–171.5) and 68.1 ug/mL (CI, 57.2–78.9; P < .001). The only patient in the control group who had an exosome concentration > 1.0 mg/mL and RNA concentration > 100 ug/mL had a history of vulvar cancer without evidence of active disease. No correlation between the levels and the stage of disease was found. To compare the presence of specific miRNAs between tumors and their corresponding circulating exosomes, miRNA fractions were isolated and profiled from circulating tumor exosomes and the original tumor. MicroRNA profiling was performed in duplicate, using microarrays containing probes for 467 human mature miRNA. Comparisons between peripheral circulation-derived exosomes and tumors indicated that the miRNA signatures were not significantly different. This approach confirmed that the 12 specific miRNA were elevated in NSCLC and that the associations of these 12 were mirrored in the circulating exosomes. The levels of tumor-derived miRNA profiles exhibited a strong correlation with the levels of peripheral blood-derived exosomal miRNAs (for miR-17-3p, r = 0.76; miR-21, r = 0.77; miR-146, r = 0.88; miR-155, r = 0.85; miR-191, r = 0.83; miR-203, r = 0.85; miR-205, r = 0.91; and miR-214, r = 0.71).ConclusionThe significant difference in total exosome and miRNA levels between patients with lung cancer and controls suggests that exosomal miRNA is a screening test for lung adenocarcinoma. There is no obvious correlation between the total exosomal miRNA levels and stage of disease; however, it has been suggested in miRNA profiling studies of tumor tissue, that miRNA expression might be critical for the development of cancer but not for its progression. If specific miRNA levels predict response to treatment and can add prognostic information in addition to conventional staging needs further study. While validation studies will be necessary before bypassing the use with tumor mass biopsies, the use of exosomal miRNA profiling could extend this approach to screening of asymptomatic individuals as well as for monitoring disease recurrence.     

CENPF as an independent prognostic and metastasis biomarker corresponding to CD4+ memory T cells in cutaneous melanoma

Owing to recent advances in immunotherapies, the overall survival of patients with skin cutaneous melanoma (SKCM) has increased; however, the 5‐year survival rate of metastatic patients remains poor. Skin cutaneous melanoma—upregulated genes were screened via analysis of differentially expressed genes ({"type":"entrez-geo","attrs":{"text":"GSE3189","term_id":"3189"}}GSE3189 and {"type":"entrez-geo","attrs":{"text":"GSE46517","term_id":"46517"}}GSE46517), and metastasis‐related oncogenes were identified via weighted gene coexpression network analysis of the {"type":"entrez-geo","attrs":{"text":"GSE46517","term_id":"46517"}}GSE46517 dataset. As confirmed by the Tumor Immune Estimation Resource, we found highly expressed centromere protein F (CENPF) in SKCM and its metastases. Immunostaining of human melanoma tissues demonstrated high CENPF expression. According to the Kaplan‐Meier survival curve log‐rank test, receiver‐operating characteristic curve, and univariate and multivariate analyses, the Cancer Genome Atlas (TCGA) database suggested CENPF be a typical independent predictor of SKCM. The CIBERSORT algorithm classified the types of the immune cells from {"type":"entrez-geo","attrs":{"text":"GSE46517","term_id":"46517"}}GSE46517 and showed higher proportion of CD4+ memory‐activated T cells in metastatic melanoma. Single‐sample gene set enrichment analysis of TCGA data confirmed the correlation between CENPF and activated CD4+ T cells. Centromere protein F was positively correlated with tumor mutational burden and CD4+ memory T cell markers (interleukin [IL]‐23A, CD28, and CD62L), negatively associated with memory T cell maintenance factors (IL‐7 and IL‐15) by correlation analysis. Moreover, immunofluorescence showed high coexpression of CENPF and IL23A, CD4 in melanoma. Upregulated CENPF might lead to premature depletion of CD4+ memory T cells and immunosuppression. Nomogram indicated CENPF clinical predictive value for 1‐, 3‐, 5‐, and 7‐year melanoma overall survival. Therefore, CENPF plays a vital role in the progression and metastasis of melanoma and can be an effective therapeutic target.