Identification and analysis of circRNA-miRNA-mRNA regulatory network in hepatocellular carcinoma

A novel upregulated hsa_circ_0032746 regulates the oncogenesis of esophageal squamous cell carcinoma by regulating miR-4270/MCM3 axis

INTRODUCTION

Circular RNAs (CircRNA) have emerged as an interest of research in recent years due to its regulatory role in various kinds of cancers of human body. Esophageal squamous cell carcinoma (ESCC) is one of the major disease subtype in Asian countries, including China. CircRNAs are formed by back-splicing covalently joined 3'- and 5'- ends rather than canonical splicing and are found to have binding affinity with miRNAs that conjointly contribute to oncogenesis.

MATERIALS AND METHODS

4 pairs of normal, cancer adjacent tissues and cancer tissues were analyzed by high-throughput RNA sequencing and 84 differentially upregulated circRNAs were detected in cancer tissues. hsa_circ_0032746 was silenced by siRNA and lentivirus and then further proliferation, migration and invasion were performed by CCK-8 and transwell assays. Bioinformatic analysis  predicted binding affinity of circRNA/miRNA/mRNA axis.

RESULTS

After qPCR validation, we selected a novel upregulated hsa_circ_0032746 to explore its biogenetic functions which showed high expression in cancer tissues but not in cancer adjacent tissues. The clinicopathological relation of hsa_circ_0032746 showed positive correlation with the tumor location (P = 0.026) and gender (P = 0.05). We also predicted that hsa_circ_0032746 could sponge with microRNA. Bioinformatic analysis predicted 11 microRNA response element (MRE) sequences of hsa_circ_0032746 and dual luciferase reporter assay confirmed binding affinity with miR4270 evidencing further study of circRNA/miRNA role. The knockdown of hsa_circ_0032746 by siRNA and lentivirus demonstrated that proliferation, invasion and migration of ESCC were inhibited in vitro and vivo experiments. Bioinformatic analysis further predicted MCM3 as a target of miR-4270 and was found upregulated in ESCC upon validation. miR4270 mimic decreased the level of hsa_circ_0032746 and MCM3 while further rescue experiments demonstrated that hsa_circ_0032746 was dependent on miR4270/MCM3 axis on the development process of ESCC.

CONCLUSION

We revealed for the first time that circ_0032746/mir4270/MCM3 contributes in proliferation, migration and invasion of ESCC and could have potential prognostic and therapeutic significance.

CircUSP10 promotes liver cancer progression by regulating miR-211-5p/TCF12/EMT signaling pathway

There is no precise diagnosis or prognosis for liver cancer (LC) using a single biomarker. Circular RNAs (circRNAs) contribute to the pathogenesis of different cancers, but their role in LC is not entirely understood. In this study, circUSP10, an aberrantly expressed circRNA in LC, was screened using the Gene Expression Omnibus database, and its tissue-specific expression was verified using qRT-PCR. In vitro, functional assays and nude mouse tumorigenesis models were used to investigate circUSP10 role in LC. RNA immunoprecipitation and dual-luciferase reporter assays were performed to study the mechanistic relationship between circUSP10, miR-211-5p, and transcription factor 12 (TCF12). We found that circUSP10 expression was upregulated in LC tissues and cells. CircUSP10 expression was linked to tumor size and tumor node metastasis stage and negatively correlated with LC prognosis. In vitro assays confirmed circUSP10-mediated proliferation, migration, and invasion of LC cells and their association with the epithelial-mesenchymal transition (EMT) pathway. Mechanistically, circUSP10 adsorbed miR-211-5p, which regulated TCF12 and promoted tumorigenesis via the EMT signaling pathway. Therefore, our results suggest that circUSP10 may promote LC progression by modulating the miR-211-5p/TCF12/EMT signaling cascade and may serve as a potential biomarker for LC diagnosis and prognosis.

Effect of miR-4270 Suppression on Migration in Hepatocellular Carcinoma Cell Line (HepG2)

Background

Liver transplantation and surgical resection are two major strategies for treatment of hepatocellular carcinoma (HCC) patients. One approach to treating HCC is the suppression of metastasis to other tissues. Herein, we aimed to study the effect of miR-4270 inhibitor on migration of HepG2 cells as well as activity of matrix metalloproteinase (MMP) these cells in order to find a strategy to suppress metastasis in future.

Methods

HepG2 cells were treated with 0, 10, 20, 30, 40, 50, 60, 70, 80, and 90 nM of miR-4270 inhibitor, and then the cell viability was measured by trypan blue staining. Afterwards, cell migration and MMP activity of HepG2 cells were assessed by wound healing assay and zymography, respectively. The MMP gene expression was determined by real-time reverse transcription polymerase chain reaction.

Results

Results showed that miR-4270 inhibitor decreased the cell viability of HepG2 cells in a concentration-dependent manner. Also, inhibition of the miR-4270 reduced invasion, MMP activity, and expression of MMP genes in HepG2 cells, respectively.

Conclusion

Our findings suggest that miR-4270 inhibitor decreases in vitro migration, which could help find a new approach for HCC therapy patients.

Effect of miR-4270 Suppression on Migration in Hepatocellular Carcinoma Cell Line (HepG2)

Background

Liver transplantation and surgical resection are two major strategies for treatment of hepatocellular carcinoma (HCC) patients. One approach to treating HCC is the suppression of metastasis to other tissues. Herein, we aimed to study the effect of miR-4270 inhibitor on migration of HepG2 cells as well as activity of matrix metalloproteinase (MMP) these cells in order to find a strategy to suppress metastasis in future.

Methods

HepG2 cells were treated with 0, 10, 20, 30, 40, 50, 60, 70, 80, and 90 nM of miR-4270 inhibitor, and then the cell viability was measured by trypan blue staining. Afterwards, cell migration and MMP activity of HepG2 cells were assessed by wound healing assay and zymography, respectively. The MMP gene expression was determined by real-time reverse transcription polymerase chain reaction.

Results

Results showed that miR-4270 inhibitor decreased the cell viability of HepG2 cells in a concentration-dependent manner. Also, inhibition of the miR-4270 reduced invasion, MMP activity, and expression of MMP genes in HepG2 cells, respectively.

Conclusion

Our findings suggest that miR-4270 inhibitor decreases in vitro migration, which could help find a new approach for HCC therapy patients.

Melatonin promotes the development of the secondary hair follicles by regulating circMPP5

BACKGROUND

The quality and yield of cashmere fibre are closely related to the differentiation and development of secondary hair follicles in the skin of cashmere goats. The higher the density of secondary hair follicles, the higher the quality and yield of cashmere from the fleece. Development of secondary hair follicles commences in the embryonic stage of life and is completed 6 months after birth. Preliminary experimental results from our laboratory showed that melatonin (MT) treatment of goat kids after their birth could increase the density of secondary hair follicles and, thus, improve the subsequent yield and quality of cashmere. These changes in the secondary hair follicles resulted from increases in levels of antioxidant and expression of anti-apoptotic protein, and from a reduction in apoptosis. The present study was conducted to explore the molecular mechanism of MT-induced secondary hair follicle differentiation and development by using whole-genome analysis.

RESULTS

MT had no adverse effect on the growth performance of cashmere kids but significantly improved the character of the secondary hair follicles and the quality of cashmere, and this dominant effect continued to the second year. Melatonin promotes the proliferation of secondary hair follicle cells at an early age. The formation of secondary hair follicles in the MT group was earlier than that in the control group in the second year. The genome-wide data results involved KEGG analysis of 1044 DEmRNAs, 91 DElncRNAs, 1054 DEcircRNAs, and 61 DEmiRNAs which revealed that the mitogen-activated protein kinase (MAPK) signaling pathway is involved in the development of secondary hair follicles, with key genes (FGF2, FGF21, FGFR3, MAPK3 (ERK1)) being up-regulated and expressed. We also found that the circMPP5 could sponged miR-211 and regulate the expression of MAPK3.

CONCLUSIONS

We conclude that MT achieves its effects by regulating the MAPK pathway through the circMPP5 sponged the miR-211, regulating the expression of MAPK3, to induce the differentiation and proliferation of secondary hair follicle cells. In addition there is up-regulation of expression of the anti-apoptotic protein causing reduced apoptosis of hair follicle cells. Collectively, these events increase the numbers of secondary hair follicles, thus improving the production of cashmere from these goats.

Circ_0000284 upregulates RHPN2 to facilitate pancreatic cancer proliferation, metastasis, and angiogenesis through sponging miR-1179

BACKGROUND

Circular RNA (circRNA) has been confirmed to be a key regulator for pancreatic cancer (PC) progression, but the role of circ_0000284 in PC development remains unclear.

METHODS

Quantitative real-time PCR was used to measure the expression of circ_0000284, microRNA (miR)-1179, and rhophilin 2 (RHPN2). PC cell proliferation, metastasis, angiogenesis, and apoptosis were assessed by EdU assay, transwell assay, tube formation assay, and flow cytometry. Relative protein expression was determined by western blot analysis. The interaction between miR-1179 and circ_0000284 or RHPN2 was confirmed by dual-luciferase reporter assay and RNA pull-down assay.

RESULTS

Circ_0000284 was significantly upregulated in PC tissues and cells, and its knockdown inhibited PC cell proliferation, migration, invasion, and angiogenesis while promoting apoptosis. MiR-1179 was downregulated in PC tissues and cells, and it could be sponged by circ_0000284. Moreover, the miR-1179 inhibitor reversed the regulation of circ_0000284 knockdown on PC cell progression. The highly expressed RHPN2 was found in PC tissues and cells, and it could be targeted by miR-1179. Also, circ_0000284 sponged miR-1179 to regulate RHPN2 expression. Overexpressed RHPN2 could reverse the regulation of circ_0000284 knockdown on PC cell progression. In addition, interference of circ_0000284 was discovered to repress PC tumor growth by regulating miR-1179/RHPN2.RHPN2.

CONCLUSION

To sum up, our data confirmed that circ_0000284 facilitated PC malignant progression depending on the regulation of miR-1179/RHPN2 axis, suggesting that circ_0000284 might be a potential target for PC treatment.

Construction and analysis of expression profile of exosomal lncRNAs in pleural effusion in lung adenocarcinoma

BACKGROUND

Lung adenocarcinoma (LUAD) is a highly malignant tumor with a very low five-year survival rate. In this study, we aimed to identify differentially expressed long-chain non-coding RNA (lncRNAs) and mRNAs from benign and malignant pleural effusion exosomes.

METHODS

We used gene microassay and quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) to detect and verify differentially expressed mRNAs and lncRNAs in benign and malignant pleural effusion exosomes. Gene Ontology (GO) functional significance and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway significance enrichment analyses were performed to identify the difference in biological processes and functions between different mRNAs. We selected the lncRNA ZBED5-AS1 with an upregulated differential fold of 3.003 and conducted a preliminary study on its cellular function.

RESULTS

Gene microassay results revealed that 177 differentially expressed lncRNAs were upregulated, and 215 were downregulated. The top 10 upregulated were FMN1, AL118505.1, LINC00452, AL109811.2, CATG00000040683.1, AC137932.1, AC008619.1, AL450344.1, AC092718.6, and ZBED5-AS1. The top 10 downregulated were TEX41, G067726, JAZF1-AS1, AC027328.1, AL445645.1, AL022345.4, AC008572.1, AC123777.1, AC093714.1, and PHKG1. For the mRNAs, 79 were upregulated, and 123 were notably downregulated. GO analysis revealed that the upregulated differential mRNAs were mainly involved in "cellular response to acidic pH" (biological processes), "endoplasmic reticulum part" (cellular components), and "at DNA binding, cyclase activity" (molecular functions). KEGG pathways were found to be related to V. cholerae infection, Parkinson's disease, and cell adhesion molecules. RT-qPCR showed that ZBED5-AS1 was highly expressed in LUAD tissues, cells, and benign and malignant pleural fluid exosomes. Overexpression of ZBED5-AS1 could significantly promote the proliferation, migration, invasion, and colony formation of LUAD cells, and knockdown had the opposite consequence.

CONCLUSION

The pleural effusion exosomes from patients with LUAD include several improperly expressed genes, and lncRNA-ZBED5-AS1 is a new biomarker that aids in our understanding of the occurrence and progression of LUAD.

Circ_0000291 contributes to hepatocellular carcinoma tumorigenesis by binding to miR-1322 to up-regulate UBE2T

INTRODUCTION AND OBJECTIVES

Circular RNAs (circRNAs) are identified to show important regulatory functions in cancer biology. We attempted to analyze the role of circ_0000291 in hepatocellular carcinoma (HCC) progression and its related mechanism.

METHODS

The circular characteristic of circ_0000291 was tested using exonuclease RNase R. Cell proliferation was analyzed by 5-Ethynyl-2'-deoxyuridine (EdU) incorporation and colony formation assays. Cell apoptosis was measured by flow cytometry and a caspase 3 activity assay kit. Transwell assays were performed to analyze cell migration and invasion abilities. Sphere formation assay was conducted to analyze cell stemness. Dual-luciferase reporter and RNA-pull down assays were conducted to verify the interaction between microRNA-1322 (miR-1322) and circ_0000291 or ubiquitin conjugating enzyme E2 T (UBE2T).

RESULTS

Circ_0000291 was markedly up-regulated in HCC tissues and cell lines. HCC patients with high expression of circ_0000291 displayed a low survival rate. Circ_0000291 knockdown restrained the proliferation, migration, invasion, and stemness and induced the apoptosis of HCC cells. Circ_0000291 directly interacted with miR-1322 and negatively regulated miR-1322 expression. Circ_0000291 knockdown-mediated anti-tumor impacts in HCC cells were largely overturned by the interference of miR-1322. miR-1322 directly paired with the 3' untranslated region (3'UTR) of UBE2T, and UBE2T was negatively regulated by miR-1322. UBE2T overexpression largely reversed circ_0000291 silencing-induced effects in HCC cells. Circ_0000291 positively regulated UBE2T expression by absorbing miR-1322 in HCC cells. Circ_0000291 silencing notably reduced the tumorigenic potential in vivo.

CONCLUSION

Circ_0000291 facilitated HCC progression by targeting miR-1322/UBE2T axis, which provided novel potential biomarkers and targets for HCC patients.

To investigate the internal association between SARS-CoV-2 infections and cancer through bioinformatics

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), also known as COVID-19, is currently prevalent worldwide and poses a significant threat to human health. Individuals with cancer may have an elevated risk for SARS-CoV-2 infections and adverse outcomes. Therefore, it is necessary to explore the internal relationship between these two diseases. In this study, transcriptome analyses were performed to detect mutual pathways and molecular biomarkers in three types of common cancers of the breast, liver, colon, and COVID-19. Such analyses could offer a valuable understanding of the association between COVID-19 and cancer patients. In an analysis of RNA sequencing datasets for three types of cancers and COVID-19, we identified a sum of 38 common differentially expressed genes (DEGs). A variety of combinational statistical approaches and bioinformatics techniques were utilized to generate the protein-protein interaction (PPI) network. Subsequently, hub genes and critical modules were found using this network. In addition, a functional analysis was conducted using ontologies keywords, and pathway analysis was also performed. Some common associations between cancer and the risk and prognosis of COVID-19 were discovered. The datasets also revealed transcriptional factors-gene interplay, protein-drug interaction, and a DEGs-miRNAs coregulatory network with common DEGs. The potential medications discovered in this investigation could be useful in treating cancer and COVID-19.

The circRNA circSIAE Inhibits Replication of Coxsackie Virus B3 by Targeting miR-331-3p and Thousand and One Amino-Acid Kinase 2

Coxsackie virus B3 (CVB3), an enterovirus, is the main pathogen causing viral myocarditis, pericarditis, hepatitis and other inflammation-related diseases. Non-coding RNAs with a closed loop molecular structure, called circular RNAs (circRNAs), have been shown to be involved in multiple virus-related processes, but roles and mechanisms in CVB3 infection have not been systematically studied. In this study, when HeLa cells were infected with CVB3, the expression of hsa_circ_0000367 (circSIAE) was significantly decreased as demonstrated by real-time quantitative PCR assays. We found that circSIAE downregulated the expression of miR-331-3p through direct binding and inhibited the replication of CVB3 in HeLa and 293T cells. The analysis of signals downstream of miR-331-3p suggested that miR-331-3p promotes CVB3 replication, viral plaque formation and fluorescent virus cell production through interactions with the gene coding for thousand and one amino-acid kinase 2 (TAOK2). In conclusion, this study found that circSIAE can target TAOK2 through sponge adsorption of miR-331-3p to inhibit the replication and proliferation of CVB3 virus, providing an early molecular target for the diagnosis of CVB3 infection.

Upregulation of MicroRNA-937 Predicts a Poor Prognosis and Promotes Hepatocellular Carcinoma Cell Proliferation, Migration, and Invasion

Hepatocellular carcinoma (HCC) has a high dead rate partly due to late diagnosis. This study aimed to investigate the prognostic value of miR-937 in HCC and its role in the HCC progression. HCC tissue and adjacent non-cancerous tissues (NCT) (n = 125) were detected about the expression level of miR-937 via real-time quantitative PCR. The relationship between miR-937 expression and each important clinical characteristic was evaluated. And the prognostic significance of miR-937 was assessed by Kaplan-Meier curve and Cox regression analysis. CCK-8 and Transwell assays were conducted to observe the effects of miR-937 on HCC cell proliferation, migration, and invasion. The miR-937 expression was upregulated in HCC tissues, as well as in HCC cell lines. The upregulation of miR-937 showed a significant association with lymph node metastasis and TNM stage. Upregulation of miR-937 predicted poor prognosis of HCC patients. Overexpression of miR-937 promoted HCC cell ability of proliferation, migration, and invasiveness, while knockdown of miR-937 inhibited these cellular behaviors. miR-937 expression was upregulated in HCC and may serve as a promising prognostic factor and treated target for HCC patients. miR-937 might exert a promoter role in HCC through accelerated tumor cell proliferation, migration, and invasion.

Current Molecular Biology and Therapeutic Strategy Status and Prospects for circRNAs in HBV-Associated Hepatocellular Carcinoma

Circular RNAs (circRNAs) are newly classified noncoding RNA (ncRNA) members with a covalently closed continuous loop structure that are involved in immune responses against hepatitis B virus (HBV) infections and play important biological roles in the occurrence and pathogenesis of HCC progression. The roles of circRNAs in HBV-associated HCC (HBV-HCC) have gained increasing attention. Substantial evidence has revealed that both tissue and circulating circRNAs may serve as potential biomarkers for diagnostic, prognostic and therapeutic purposes. So far, at least four circRNA/miRNA regulatory axes such as circRNA_101764/miR-181, circRNA_100338/miR-141-3p, circ-ARL3/miR-1305, circ-ATP5H/miR-138-5p, and several circulating circRNAs were reported to be associated with HBV-HCC development. Notably, TGF/SMAD, JAK/STAT, Notch and Wnt/β-catenin signaling pathways may play pivotal roles in this HBV-driven HCC via several circRNAs. Moreover, in non-HBV HCC patients or HCC patients partially infected by HBV, numerous circRNAs have been identified to be important regulators impacting the malignant biological behavior of HCC. Furthermore, the role of circRNAs in HCC drug resistance has become a focus of research with the aim of reversing chemoresistance and immune resistance. Herein, we review the molecular biology of circRNAs in HBV-HCC and their potential in therapeutic strategies.

Function of Circular RNAs in Fish and Their Potential Application as Biomarkers

Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.