High-throughput sequencing profile of laryngeal cancers: analysis of co-expression and competing endogenous RNA networks of circular RNAs, long non-coding RNAs, and messenger RNAs

Abstract

Background: Circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) have been recently identified as new classes of non-coding RNAs which participate in carcinogenesis and tumor progression.However, the functions of these non-coding RNAs and gene expression patterns are largely unknown. Methods:We carried out high-throughput sequencing to analyze the differential expression of RNAs in 5 coupled laryngeal cancer (LC) and corresponding adjacent noncancerous tissues. Bioinformatics analyses were performed to predict the functions of these non-coding RNAs via co-expression, competing endogenous RNA networks and pathway enrichment analysis. The differential expression of the selected RNAs were confirmed using RT-qPCR. The CCK8, EDU, Transwell, and wound healing assays were conducted to validate the biological functions of SNHG29 in LC. Western blot assay was performed to identify the effects of SNHG29 having on the epithelial to mesenchymal transition process. Kaplan-Meier analysis was used to investigate whether the expression level of SNHG29 correlated with survival in LC patients. One-way ANOVA was used to analyze the correlation between the expression of SNHG29 and clinicopathological parameters of the included patients.Results: Compared to normal laryngeal tissues, 31,763 non-coding RNAs were upregulated and 11,557 non-coding RNAs were downregulated in cancer tissues. SNHG29 expression was low in the LC cell lines and tissues predicting a better clinical prognosis. SNHG29 was also found to inhibit the proliferation, migration, and invasion ability of LC, exerting a suppressive role in the epithelial to mesenchymal transition process as well. SNHG29 downregulation was significantly correlated with differentiation (P=0.026), T-stage (P=0.041), lymphatic metastasis (P=0.044), and clinical stage (P=0.037). We found that the biological functions of differentially expressed transcripts included cell adhesion, biological adhesion, and migration and invasion related to adherens junction pathways.Conclusions: Our study was the first to describe the non-coding RNA profile of LC, and suggested that dysregulated non-coding RNAs could be involved in LC tumorigenesis. SNHG29 was demonstrated to play crucial roles in inhibiting the pathogenesis and progression of LC. Our findings provide a new approach for further analyses of pathogenetic mechanisms, the detection of novel transcripts, and the identification of valuable biomarkers for this tumor.

Emerging functions of circular RNA in the regulation of adipocyte metabolism and obesity

“…With the development of science, technology, and biotechnology, methods to identify circRNAs have also increased rapidly [ 108 , 109 ]. However, there are still some challenges to studying the expression circRNAs and their related networks in the disease processes [ 110 , 111 ]. Although there are several independent pieces of evidence that support the miRNAs sponge function of circRNAs, but how to coordinate between the genes, miRNAs and circRNAs requires more comprehensive studies.…”

Ferroptosis-Related lncRNA Signature Correlates with the Prognosis, Tumor Microenvironment, and Therapeutic Sensitivity of Esophageal Squamous Cell Carcinoma

“…The current study selected ten prognosis-related FRLs and a signature that combined these lncRNAs displayed a favorable survival prediction value in ESCC. A recent study demonstrated that SNHG29 (small nucleolar RNA host gene 29) plays an important role in the invasion, migration, and epithelial-to-mesenchymal transition of laryngeal cancer, suggesting that SNHG29 is a potential therapeutic target [ 44 ]. In addition, another study reported that the inhibition of SNHG29 could improve antitumor immunity through the activation of the YAP pathway in colorectal cancer [ 45 ].…”

Long non-coding RNAs in brain tumors: roles and potential as therapeutic targets

“…Previously, cell-free nucleic acids, such as DNA, mRNA, and miRNA were considered as biomarkers in cancer patients [ 183 ]. Recent advances in lncRNA research, which were based on GWAS and biochemical systems, have improved the knowledge of cell-free nucleic acids including circulating lncRNAs [ 184 , 185 ]. This impressively wide range of findings can facilitate the establishment of preclinical models for identification of potent lncRNAs for application in clinical treatment in cancer [ 186 ].…”