Altered expression profile of circular RNAs in conjunctival melanoma

Genetic polymorphisms in MIR1208 and MIR5708 are associated with susceptibility to COPD in the Chinese population

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by limited airflow and is influenced by genetic and environmental factors. The purpose of this study was to investigate the effects of gene polymorphisms in MIR5708 and MIR1208 on COPD risk.

METHODS

Four single nucleotide polymorphisms (SNPs) in MIR5708 (rs6473227 and rs16907751) and MIR1208 (rs2608029 and rs13280095) were selected and genotyped among 315 COPD patients and 314 healthy controls using the Agena MassARRAY platform. SPSS 18.0 was used for statistical analysis and data processing. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the association between genetic variants of MIR1208 and MIR5708 and COPD risk.

RESULTS

The results suggested that rs16907751 variants in MIR5708 contributed to an increased susceptibility to COPD in the allelic (P = 0.001), co-dominant (homozygous) (P = 0.001), dominant (P = 0.017), recessive (P = 0.002), and additive (P = 0.002) models. The effects of MIR5708 and MIR1208 gene polymorphisms on the risk of COPD were age-, sex-, smoking status-, and BMI-related. Furthermore, the C-A and G-A haplotypes of rs2608029 and rs13280095 in MIR1208 were identified as risk factors for COPD in the population over 70 years (P = 0.029) and in women (P = 0.049), respectively. Finally, significant associations between rs16907751genotypes with pulse rate and forced expiratory volume in 1 s were found among COPD patients.

CONCLUSION

Genetic polymorphisms in MIR5708 and MIR1208 are associated with increased risk of COPD in China.

Non-coding RNAs in skin cancers:Biological roles and molecular mechanisms

Cutaneous malignancies, including basal cell carcinoma, cutaneous squamous cell carcinoma, and cutaneous melanoma, are common human tumors. The incidence of cutaneous malignancies is increasing worldwide, and the leading cause of death is malignant invasion and metastasis. The molecular biology of oncogenes has drawn researchers’ attention because of the potential for targeted therapies. Noncoding RNAs, including microRNAs, long noncoding RNAs, and circular RNAs, have been studied extensively in recent years. This review summarizes the aspects of noncoding RNAs related to the metastasis mechanism of skin malignancies. Continuous research may facilitate the identification of new therapeutic targets and help elucidate the mechanism of tumor metastasis, thus providing new opportunities to improve the survival rate of patients with skin malignancies.

Construction of miRNA-lncRNA-mRNA co-expression network affecting EMT-mediated cisplatin resistance in ovarian cancer

Platinum resistance is one of the major concerns in ovarian cancer treatment. Recent evidence shows the critical role of epithelial-mesenchymal transition (EMT) in this resistance. Epithelial-like ovarian cancer cells show decreased sensitivity to cisplatin after cisplatin treatment. Our study prospected the association between epithelial phenotype and response to cisplatin in ovarian cancer. Microarray dataset GSE47856 was acquired from the GEO database. After identifying differentially expressed genes (DEGs) between epithelial-like and mesenchymal-like cells, the module identification analysis was performed using weighted gene co-expression network analysis (WGCNA). The gene ontology (GO) and pathway analyses of the most considerable modules were performed. The protein-protein interaction network was also constructed. The hub genes were specified using Cytoscape plugins MCODE and cytoHubba, followed by the survival analysis and data validation. Finally, the co-expression of miRNA-lncRNA-TF with the hub genes was reconstructed. The co-expression network analysis suggests 20 modules relating to the Epithelial phenotype. The antiquewhite4, brown and darkmagenta modules are the most significant non-preserved modules in the Epithelial phenotype and contain the most differentially expressed genes. GO, and KEGG pathway enrichment analyses on these modules divulge that these genes were primarily enriched in the focal adhesion, DNA replication pathways and stress response processes. ROC curve and overall survival rate analysis show that the co-expression pattern of the brown module's hub genes could be a potential prognostic biomarker for ovarian cancer cisplatin resistance.

FMRP ligand circZNF609 destabilizes RAC1 mRNA to reduce metastasis in acral melanoma and cutaneous melanoma

BACKGROUND

Melanoma is a type of malignant tumor with high aggressiveness and poor prognosis. At present, metastasis of melanoma is still an important cause of death in melanoma patients. However, the potential functions and molecular mechanisms of most circular RNAs (circRNAs) in melanoma metastasis remain unknown.

METHODS

circRNAs dysregulated in melanoma cell subgroups with different metastatic abilities according to a screening model based on repeated Transwell assays were identified with a circRNA array. The expression and prognostic significance of circZNF609 in skin cutaneous melanoma and acral melanoma cells and tissues were determined by qRT-PCR, nucleoplasmic separation assays and fluorescence in situ hybridization. In vitro wound healing, Transwell and 3D invasion assays were used to analyse melanoma cell metastasis ability. Tail vein injection and intrasplenic injection were used to study in vivo lung metastasis and liver metastasis, respectively. The mechanism of circZNF609 was further evaluated via RNA immunoprecipitation, RNA pull-down, silver staining, and immunofluorescence colocalization assays.

RESULTS

circZNF609 was stably expressed at low levels in melanoma tissues and cells and was negatively correlated with Breslow depth, clinical stage and prognosis of melanoma patients. circZNF609 inhibited metastasis of acral and cutaneous melanoma in vivo and in vitro. Mechanistically, circZNF609 promoted the binding of FMRP protein and RAC1 mRNA, thereby enhancing the inhibitory effect of FMRP protein on the stability of RAC1 mRNA and ultimately inhibiting melanoma metastasis.

CONCLUSIONS

Our findings revealed that circZNF609 plays a vital role in the metastasis of acral and cutaneous melanoma through the circRNF609-FMRP-RAC1 axis and indicated that circZNF609 regulates the stability of RAC1 mRNA by combining with FMRP, which might provide insight into melanoma pathogenesis and a new potential target for treatment of melanoma.

Systematic Construction and Validation of an Immune-Related Gene-Based Model to Predict Prognosis for Ovarian Cancer

Ovarian cancer (OC) is a malignancy with poor prognosis, stubborn resistance, and frequent recurrence. Recently, it has been widely recognized that immune-related genes (IRGs) have demonstrated their indispensable importance in the occurrence and progression of OC. Given this, this study aimed to identify IRGs with predictive value and build a prognostic model for a more accurate assessment. First, we obtained transcriptome and clinical information of ovarian samples from both TCGA and GTEx databases. After integration, we figured out 10 genes as immune-related prognostic genes (IRPGs) by performing the univariate Cox regression analysis. Subsequently, we established a TF-associated network to investigate its internal mechanism. The prognosis model consisting of 5 IRPGs was constructed later by lasso regression analysis. The comparison of the score with the clinical factors validated its independence and superiority in OC's prognosis. Moreover, the association between the signature and immune cell infiltration demonstrated its ability to image the immune situation of the tumor microenvironment. Finally, the reliability of the risk model was confirmed by the GEO cohort. Together, our study has constructed an independent prognostic model for OC, which may deepen the understanding of the immune microenvironment and help present novel biomarkers or ideas for targeted therapy.

The m6A reading protein YTHDF3 potentiates tumorigenicity of cancer stem-like cells in ocular melanoma through facilitating CTNNB1 translation

N6-methyladenosine (m6A) is the most universal internal RNA modification on messenger RNAs and regulates the fate and functions of m6A-modified transcripts through m6A-specific binding proteins. Nevertheless, the functional role and potential mechanism of the m6A reading proteins in ocular melanoma tumorigenicity, especially cancer stem-like cell (CSC) properties, remain to be elucidated. Herein, we demonstrated that the m6A reading protein YTHDF3 promotes the translation of the target transcript CTNNB1, contributing to ocular melanoma propagation and migration through m6A methylation. YTHDF3 is highly expressed in ocular melanoma stem-like cells and abundantly enriched in ocular melanoma tissues, which is related to poor clinical prognosis. Moreover, YTHDF3 is required for the maintenance of CSC properties and tumor initiation capacity in ocular melanoma both in vitro and in vivo. Ocular melanoma cells with targeted YTHDF3 knockdown exhibited inhibitory tumor proliferation and migration abilities. Transcriptome-wide mapping of m6A peaks and YTHDF3 binding peaks on mRNAs revealed a key target gene candidate, CTNNB1. Mechanistically, YTHDF3 enhances CTNNB1 translation through recognizing and binding the m6A peaks on CTNNB1 mRNA.

Non-coding RNAs in melanoma: Biological functions and potential clinical applications

Malignant melanoma (MM) is a malignant tumor that originates from melanocytes and has a high mortality rate. Therefore, early diagnosis and treatment are very important for survival. So far, the exact molecular mechanism leading to the occurrence of melanoma, especially the molecular metastatic mechanism, remains largely unknown. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNA (circRNAs), have been investigated and found to play vital roles in regulating tumor occurrence and development, including melanoma. In this review, we summarize the progress of recent research on the effects of ncRNAs on melanoma and attempt to elucidate the role of ncRNAs as molecular markers or potential targets that will provide promising application perspectives on melanoma.

Current Management of Conjunctival Melanoma Part 2: Treatment and Future Directions

Conjunctival melanoma is a rare disease which requires tailored management in most cases. The mainstays of treatment can be classified as surgery, topical chemotherapy, radiotherapy, cryotherapy, and other emerging treatment modalities. Herein we review conventional approaches as well as more recently introduced treatment options, together with advances in molecular biology in this particular disease.

Characteristics of circRNA and its approach as diagnostic tool in melanoma

One of the most common types of cancer in the world is skin cancer, which has been divided into two groups: non-melanoma and melanoma skin cancer. Different external and internal agents are considered as risk factors for melanoma skin cancer pathogenesis but the exact mechanisms are not yet confirmed. Genetic and epigenetic changes, UV exposure, arsenic compounds, and chemical substances are contributory factors to the development of melanoma. A correlation has emerged between new therapies and the discovery of a basic molecular pattern for skin cancer patients. Circular RNAs (circRNAs) are described as a unique group of extensively expressed endogenous regulatory RNAs with closed-loop structure bonds connecting the 5' and 3' ends, which are commonly expressed in mammalian cells. In this review, we describe the biogenesis of circular RNAs and its function in cancerous conditions focusing on the crosstalk between different circRNAs and melanoma. Increasing evidence suggests that circRNAs appears to be relative to the origin and development of skin-related diseases like malignant melanoma. Different circular RNAs like hsa_circ_0025039, hsa_circRNA006612, circRNA005537, and circANRIL, by targeting different cellular and molecular targets (e.g., CDK4, DAB2IP, ZEB1, miR-889, and let-7 c-3p), can participate in melanoma cancer progression.

Circular RNA circRNA_0082835 promotes progression and lymphatic metastasis of primary melanoma by sponging microRNA miRNA-429

To identify how circular RNA circRNA_0082835 impacts melanoma cells and lymphatic metastasis to observe whether it exerts effects through its action mechanism of sponging microRNA miR-429. Clinical baseline information was collected, and clinical samples were used for detection on circRNA_0082835 and EZH2. The expression of circRNA_0082835, EZH2, and miR-429 was detected by quantitative real-time PCR (RT-qPCR). Cell proliferation was tested with cell counting kit-8 (CCK-8). Flow cytometry was applied to examination of cell cycle levels. Cell invasion and migration were observed by transwell and wound healing. The expression of Wnt/β-catenin pathway, cell cycle and epithelial–mesenchymal transition (EMT) marker proteins was analyzed by western blot. Dual-luciferase determined the binding of miR-429 and circ_0082835. As a result, the expression of circRNA_0082835 was increased and that of miR-429 was decreased with the increase in lymphatic metastasis level. CircRNA_0082835 expression was downregulated by circ_0082835 interference, upregulated by EZH2 interference and also downregulated after transfection of both shRNA-circ_0082835 and shRNA-EZH2. Inhibiting circ_0082835 and EZH2 suppressed the proliferation, invasion and migration, regulated the cell cycle levels, inhibited Wnt/β-catenin and attenuated EMT in melanoma cells. Inhibition of circ_0082835 and/or EZH2 elevated miR-429 expression. The binding among miR-429 and circ_0082835 was verified. MiR-429 inhibitor reversed the effect of circ_0082835 interference while having no significant impact on EZH2. In conclusion, circRNA_0082835 sponges miR-429 to affect the anti-tumor effect of miR-429 in primary melanoma and lymphatic metastasis.

Circular RNA as a Potential Biomarker for Melanoma: A Systematic Review

Circular RNAs (circRNAs) are newly discovered RNAs with covalently looped structures. Due to their resistance to RNAase degradation and tissue-specific expression, circRNAs are expected to be potential biomarkers in early diagnosis and target treatment of many diseases. However, the role of circRNAs in melanoma still needs to be systematically reviewed for better understanding and further research. Based on published articles in PubMed, Embase, Cochrane Library, and Web of Science database, we systematically reviewed the implications and recent advances of circRNAs in melanoma, focusing on function, mechanism, and correlation with melanoma progression. According to inclusion and exclusion criteria, a total of 19 articles were finally included in this systematic review. Of the 19 studies, 17 used human samples, including melanoma tissues (n = 16) and blood serum of patients with melanoma (n = 1). The sample size of the study group ranged from 20 to 105 based on the reported data. Several studies explored the association between circRNAs and clinicopathological characteristics. circRNA dysregulation was commonly observed in melanoma patients. circRNAs function in melanoma by miRNA sponging and interaction with RNA binding proteins (RBP), ultimately controlling several important signaling pathways and cancer-related cellular processes, including proliferation, migration, invasion, metastasis, apoptosis, and glucose metabolism. circRNA expression could be associated with prognostic factors and drug responses, consolidating the potential clinical value in melanoma. Herein, we clarified the functional, prognostic, and predictive roles of circRNAs in melanoma in this systematic review, providing future directions for studies on melanoma-associated circRNAs.

CircRNA Is a Rising Star in Researches of Ocular Diseases

A newly rediscovered subclass of noncoding RNAs, circular RNAs (circRNAs), is produced by a back-splicing mechanism with a covalently closed loop structure. They not only serve as the sponge for microRNAs (miRNAs) and proteins but also regulate gene expression and epigenetic modification, translate into peptides, and generate pseudogenes. Dysregulation of circRNA expression has opened a new chapter in the etiology of various human disorders, including cancer and cardiovascular, neurodegenerative, and ocular diseases. Recent studies recognized the vital roles that circRNAs played in the pathogenesis of various eye diseases, highlighting circRNAs as promising biomarkers for diagnosis and assessment of progression and prognosis. Interventions targeting circRNAs provide insights for developing novel treatments for these ocular diseases. This review summarizes our current perception of the properties, biogenesis, and functions of circRNAs and the development of circRNA researches related to ophthalmologic diseases, including diabetic retinopathy, age-related macular degeneration, retinopathy of prematurity, glaucoma, corneal neovascularization, cataract, pterygium, proliferative vitreoretinopathy, retinoblastoma, and ocular melanoma.

Circular RNAs: new genetic tools in melanoma

Melanoma is the most lethal form of skin cancer. New technologies have resulted in major advances in the diagnosis and treatment of melanoma and other cancer types. Recently, some studies have investigated the role of circular RNAs (circRNAs) in different cancers. CircRNAs are a member of long noncoding RNA family mainly formed through back-splicing and have a closed-loop structure. These molecules affect several biological and oncogenic cascades in diverse ways via acting as microRNA sponge, interacting with RNA-binding proteins and acting as a transcription regulator. In this review, we made an insight into the impact of circRNA dysregulation in the melanoma tumorigenesis based on the presented evidences.

Investigation of circRNA Expression Profiles and Analysis of circRNA-miRNA-mRNA Networks in an Animal (Mouse) Model of Age-Related Macular Degeneration

PURPOSES

To (i) identify dysregulated circular RNAs (circRNAs) and (ii) elucidate their potential functions in an animal (mouse) model of choroidal neovascularization (CNV), a prominent feature of neovascular age-related macular degeneration (AMD).

METHODS

Expression profiles for circRNA were identified by microarray analysis. Selected circRNAs were confirmed by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Bioinformatic analyses of identified circRNAs were performed to predict (i) circRNA/microRNA interactions and (ii) occurrence of competing endogenous RNA (ceRNA) networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were applied to predict both the biological functions and potential pathways of the altered parental genes involved in CNV.

RESULTS

Microarray analysis indicated that 100 circRNAs in RPE-choroid-sclera complexes from CNV mice were significantly altered compared with those from control mice (fold change≥1.5, p < .05). Of these, six were validated by qRT-PCR, and included up-regulated mmu_circRNA_20332 and mmu_circRNA_19388, and down-regulated mmu_circRNA_36481, mmu_circRNA_006555, mmu_circRNA_012588, and mmu_circRNA_005578. GO analysis revealed that the altered parental genes involved in ceRNA networks were mostly enriched in immune system processes and portions of neurons. KEGG analysis revealed that these altered parental genes were also amplified in extracellular matrix (ECM)-receptor interactions, chemokine signaling pathways, and advanced glycation end-product (AGE)-receptors for advanced glycation end-product (RAGE) signaling pathways in diabetic complications.

CONCLUSION

The study identified statistically significant differences between CNV-mouse circRNAs and control mouse circRNAs, suggesting that circRNAs play vital roles in the pathogenesis of CNV. It is, therefore, reasonable to consider circRNAs as potential therapeutic targets for regulating CNV in AMD patients.

Identification and characterization of novel type of RNAs, circRNAs in crucian carp Carassius auratus gibelio

Circular RNAs (circRNAs) with regulatory potency activity was identified from varieties of species. Crucian carp (Carassius auratus gibelio) is one of the most freshwater aquaculture species in China. Every year, huge economic damage to the farming was caused by the virus and bacterial infection. Until now, there is any information about circRNA reported from the Crucian carp. In this study, the expression pattern of circRNA in Crucian carp was investigated with transcriptomic analysis. The results showed that only 37 circRNAs were identified from the Crucian carp, and these circRNAs biogenesis was formed with canonical GU-AG splicing mechanism with unevenly distributed on the chromosomes. Wherein, most of the circRNAs were derived from the sense overlapping strategy. Reverse transcript PCR and Sanger sequencing data indicated that these circRNAs were existed authenticity in Crucian carp. The bioinformatics analysis indicated that circRNAs identified from the Crucian carp with potential miRNA sponge regulate the expression level of mRNAs. GO annotation and KEGG pathway analysis of these circRNAs showed that more than 20% circRNAs were related with catalytic activity and binding in the category of molecular function, and these circRNAs were enriched in 9 signaling pathways, such as, Wnt signaling pathway, MAPK signaling pathway, Ubiquitin mediated proteolysis et al. 220 mRNAs would be regulated by the circRNAs via miRNAs mediation. These target mRNAs were further analyzed with functional annotation and KEGG analysis. GO annotation analysis showed that several genes were related with function of nucleotide binding, transcription regulatory activity. KEGG pathway analysis showed that 5 genes were enriched in the pathway of Endocytosis. The circRNA-miRNA-mRNA regulation network indicated that one miRNA can link one or more circRNA and one or more mRNA. Overall, these results will not only help us to further understand the novel RNA transcripts in Crucian carp, but also provide the novel clue to investigate the interaction between host and pathogens from this novel circRNA molecule.