Identification of differentially expressed circular RNAs in human nasopharyngeal carcinoma

m6A-modified circCREBBP enhances radiosensitivity of esophageal squamous cell carcinoma by reducing the stability of MYC through interaction with IGF2BP3

Substantial evidence has showed a close relationship between circRNAs and m6A modification in tumorigenesis and development. However, limited research has explored the regulatory role and underlying mechanism of m6A-modified circRNAs in regulating the radiosensitivity of esophageal squamous cell carcinoma (ESCC). The aim of this study was to clarify the molecular pathway by which m6A-modified circCREBBP enhances the radiosensitivity of ESCC. Differentially expressed circRNAs were identified from radiosensitive and radioresistant ESCC tissues and cells, followed by methylated RNA immunoprecipitation analysis. The effects of these circRNAs on radiosensitivity were subsequently assessed. We identified that CircCREBBP is closely associated with m6A and radiosensitivity in ESCC. CircCREBBP expression was significantly reduced in ESCC patients resistant to concurrent radiochemotherapy. In vitro and in vivo experiments demonstrated that circCREBBP knockdown enhanced the ESCC radioresistance. Mechanistic investigations revealed that circCREBBP, modified by m6A, interacted with IGF2BP3 and competitively bound to it, thereby reducing MYC mRNA stability. This study identified circCREBBP as a new m6A-modified circRNA and confirmed the METTL3/IGF2BP3/circCREBBP/MYC axis as a potential therapeutic target in enhancing radiosensitivity in ESCC.

CircMAN1A2 contributes to nasopharyngeal carcinoma progression via enhancing the ubiquitination of ATMIN through miR-135a-3p/UBR5 axis

Recently, the dysregulation of circRNAs has been increasingly implicated in the pathogenesis of nasopharyngeal carcinoma (NPC). Among these circRNAs, circMAN1A2 has been highlighted for the up-regulated expression in NPC, whereas the underlying mechanisms have not been clearly established. Thus, the aim of this study was to delineate the tumor-supporting role of circMAN1A2 in the oncogenesis and metastases of NPC. We validated through qRT-PCR that circMAN1A2 was highly expressed in NPC tissues and NPC cells. Survival analysis through Kaplan-Meier method showed that the overall survival, disease-free survival, and distant metastasis-free survival of patients was negatively correlated with the expression of circMAN1A2. Then, gain- and loss-of function assays demonstrated that circMAN1A2 knockdown could impede the proliferation, migration, invasion, and EMT in NPC cells. Further, we conducted dual luciferase reporter gene, RIP, and RNA pull down assays, unveiling that circMAN1A2 functioned as a sponge of miR-135a-3p, and miR-135a-3p targeted UBR5. Additionally, UBR5 interacted with ATMIN to foster the ubiquitination of ATMIN, thereby expediting the malignant behaviors of NPC cells as well as the lung and inguinal lymph node metastases of NPC tumors in vivo. Together, our study uncovered the tumor-initiating and pro-metastatic role of circMAN1A2-miR-135a-3p-UBR5-ATMIN axis in NPC regulation that may be a potential therapeutic target for human NPC.

Identification of gene profiles related to the development of oral cancer using a deep learning technique

BACKGROUND

Oral cancer (OC) is a debilitating disease that can affect the quality of life of these patients adversely. Oral premalignant lesion patients have a high risk of developing OC. Therefore, identifying robust survival subgroups among them may significantly improve patient therapy and care. This study aimed to identify prognostic biomarkers that predict the time-to-development of OC and survival stratification for patients using state-of-the-art machine learning and deep learning.

METHODS

Gene expression profiles (29,096 probes) related to 86 patients from the GSE26549 dataset from the GEO repository were used. An autoencoder deep learning neural network model was used to extract features. We also used a univariate Cox regression model to select significant features obtained from the deep learning method (P < 0.05). High-risk and low-risk groups were then identified using a hierarchical clustering technique based on 100 encoded features (the number of units of the encoding layer, i.e., bottleneck of the network) from autoencoder and selected by Cox proportional hazards model and a supervised random forest (RF) classifier was used to identify gene profiles related to subtypes of OC from the original 29,096 probes.

RESULTS

Among 100 encoded features extracted by autoencoder, seventy features were significantly related to time-to-OC-development, based on the univariate Cox model, which was used as the inputs for the clustering of patients. Two survival risk groups were identified (P value of log-rank test = 0.003) and were used as the labels for supervised classification. The overall accuracy of the RF classifier was 0.916 over the test set, yielded 21 top genes (FUT8-DDR2-ATM-CD247-ETS1-ZEB2-COL5A2-GMAP7-CDH1-COL11A2-COL3A1-AHR-COL2A1-CHORDC1-PTP4A3-COL1A2-CCR2-PDGFRB-COL1A1-FERMT2-PIK3CB) associated with time to developing OC, selected among the original 29,096 probes.

CONCLUSIONS

Using deep learning, our study identified prominent transcriptional biomarkers in determining high-risk patients for developing oral cancer, which may be prognostic as significant targets for OC therapy. The identified genes may serve as potential targets for oral cancer chemoprevention. Additional validation of these biomarkers in experimental prospective and retrospective studies will launch them in OC clinics.

Identifying diagnostic markers and constructing a prognostic model for small-cell lung cancer based on blood exosome-related genes and machine-learning methods

Background

Small-cell lung cancer (SCLC) usually presents as an extensive disease with a poor prognosis at the time of diagnosis. Exosomes are rich in biological information and have a powerful impact on tumor progression and metastasis. Therefore, this study aimed to screen for diagnostic markers of blood exosomes in SCLC patients and to build a prognostic model.

Methods

We identified blood exosome differentially expressed (DE) RNAs in the exoRBase cohort and identified feature RNAs by the LASSO, Random Forest, and SVM-REF three algorithms. Then, we identified DE genes (DEGs) between SCLC tissues and normal lung tissues in the GEO cohort and obtained exosome-associated DEGs (EDEGs) by intersection with exosomal DEmRNAs. Finally, we performed univariate Cox, LASSO, and multivariate Cox regression analyses on EDEGs to construct the model. We then compared the patients' overall survival (OS) between the two risk groups and assessed the independent prognostic value of the model using receiver operating characteristic (ROC) curve analysis.

Results

We identified 952 DEmRNAs, 210 DElncRNAs, and 190 DEcircRNAs in exosomes and identified 13 feature RNAs with good diagnostic value. Then, we obtained 274 EDEGs and constructed a risk model containing 7 genes (TBX21, ZFHX2, HIST2H2BE, LTBP1, SIAE, HIST1H2AL, and TSPAN9). Low-risk patients had a longer OS time than high-risk patients. The risk model can independently predict the prognosis of SCLC patients with the areas under the ROC curve (AUCs) of 0.820 at 1 year, 0.952 at 3 years, and 0.989 at 5 years.

Conclusions

We identified 13 valuable diagnostic markers in the exosomes of SCLC patients and constructed a new promising prognostic model for SCLC.

circRNA Expression Pattern and circRNA-miRNA-mRNA Network in HCs, HSCs, and KCs of Murine Liver After Echinococcus multilocularis Infection

Caused by Echinococcus multilocularis (E. multilocularis), alveolar echinococcosis is reported every year around the world and severely threatens the safety of human beings and animals. However, the molecular interaction relationships between host and E. multilocularis still remains unclear. With multiple functions, circRNA plays a crucial role in regulating the development of a parasitic disease. With that in mind, the main purpose of this study was to reveal the circRNA expression profiles and circRNA-miRNA-mRNA network relationships in hepatocytes (HCs), hepatic stellate cells (HSCs), and Kupffer cells (KCs) of murine liver after E. multilocularis infection. After sequencing, 6,290 circRNAs were identified from 12 hepatic cell samples. Based on the subsequent analysis, 426 and 372 circRNAs were significantly different in HC expression at 2 and 3 months after E. multilocularis infection, and similar results were also demonstrated in HSCs (426 and 372 circRNAs) and KCs (429 and 331 circRNAs), respectively. Eight candidate circRNAs were randomly selected to identify the accuracy of the sequencing results by using qRT-PCR. Additionally, three circRNAs-miRNA-mRNA networks in HCs, HSCs, and KCs were constructed. Taken together, our study provided a systematic presentation of circRNAs in murine liver cells after E. multilocularis infection, and these networks are essential for research in circRNAs associated with E. multilocularis infection.

Hsa_circ_0007637 Facilitates Nasopharyngeal Carcinoma Progression by Sponging miR-636/TPD52 Axis

Purpose

Hsa_circ_0007637 was discovered to be differentially expressed in nasopharyngeal carcinoma (NPC). However, the exact function and mechanism of Hsa_circ_0007637 on NPC have not been studied. This study firstly researched the function and mechanism of Hsa_circ_0007637 on NPC progression.

Methods

Hsa_circ_0007637, miR-636 and TPD52 expressions in 80 NPC patients were detected by quantitative real-time polymerase chain reaction. Hsa_circ_0007637 effect on NPC cell proliferation, apopticosis, invasion and migration was investigated by cell counting kit-8 assay, flow cytometry, transwell experiment and wound healing assay accordingly. Dual-luciferase reporter gene assay, RNA immunoprecipitation experiment and RNA fluorescence in situ hybridization experiment were performed to identify the binding between Hsa_circ_0007637 and miR-636. Dual-luciferase reporter gene assay and RNA pull down assay were conducted to verify the binding between miR-636 and TPD52. TPD52 protein expression in NPC cells was determined by Western blot. In vivo study was performed using nude mice. Immunohistochemistry was performed to assess TPD52 and Ki67 expression in tissues.

Results

Hsa_circ_0007637 was overexpressed in NPC tissues and cells. High Hsa_circ_0007637 expression predicted a poor outcome for NPC patients. Hsa_circ_0007637 knockdown decreased proliferation, invasion, migration and increased apoptosis of NPC cells (P < 0.01). Hsa_circ_0007637 could enhance TPD52 expression via sponging miR-636. miR-636 overexpression or TPD52 knockdown weakened the promoting effect of Hsa_circ_0007637 on NPC cells malignant phenotype (P < 0.01). Hsa_circ_0007637 knockdown suppressed NPC cells growth in vivo (P < 0.01).

Conclusion

Hsa_circ_0007637 facilitates NPC progression by sponging miR-636/TPD52 axis.

Circular RNA circ_0008450 regulates the proliferation, migration, invasion, apoptosis and chemosensitivity of CDDP-resistant nasopharyngeal carcinoma cells by the miR-338-3p/SMAD5 axis

Circular RNAs have recently been implicated in the tumorigenesis and chemoresistance of nasopharyngeal carcinoma (NPC). In this report, we identified the precise action of circ_0008450 in NPC progression and cisplatin (CDDP) resistance. The levels of circ_0008450, microRNA (miR)-338-3p and SMAD family member 5 (SMAD5) were gauged by quantitative real-time PCR or western blot. Cell proliferation and IC50 value for CDDP were detected by the Cell Counting Kit-8 assay. Cell colony formation, cell cycle progression, apoptosis, migration and invasion were assessed by colony formation, flow cytometry and transwell assays, respectively. Targeted relationships among circ_0008450, miR-338-3p and SMAD5 were determined by dual-luciferase reporter and RNA immunoprecipitation assays. Tumor models were assayed to evaluate the role of circ_0008450 in tumor growth. Our data indicated that up-regulated circ_0008450 was correlated with NPC CDDP resistance. Moreover, the knockdown of circ_0008450 suppressed cell proliferation, migration, invasion, and promoted apoptosis and CDDP sensitivity in vitro, as well as weakened tumor growth in vivo. Mechanistically, circ_0008450 directly bound to miR-338-3p, and the regulatory effects of circ_0008450 on cell malignant behaviors and CDDP sensitivity were mediated by miR-338-3p in vitro. SMAD5 was a direct target of miR-338-3p and circ_0008450 mediated SMAD5 expression through miR-338-3p. Furthermore, the enforced level of miR-338-3p regulated cell malignant behaviors and CDDP sensitivity in vitro via down-regulating SMAD5. Additionally, the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway was modulated by the circ_0008450/miR-338-3p axis in the two CDDP-resistant NPC cell lines. Our current study suggested that circ_0008450 modulated the malignant behaviors and drug sensitivity of CDDP-resistant NPC cells at least in part by targeting the miR-338-3p/SMAD5 axis, providing potential targets for improving the treatment of chemoresistant NPC.

Circular RNAs: Functions and mechanisms in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a malignant epithelial tumor of the nasopharyngeal mucosa with a high incidence rate in southern China and Southeast Asia and an evident ethnic and geographical distribution. Circular RNAs (circRNAs) are single-stranded noncoding RNAs with covalent, closed-loop structures. They are characterized by high stability and abundance, are evolutionarily conserved, and exhibit tissue/developmental stage specificity. Previous studies have shown that circRNAs are associated with the occurrence and development of various malignant tumors. However, the expression patterns and clinical significance of circRNAs in NPC remain ambiguous. Hence, the present review focuses on the biogenesis and regulation of circRNAs, and the functional roles of abnormally expressed circRNAs in NPC. In addition, the current review discusses the possibility of utilizing circRNAs as potential clinical biomarkers for the diagnosis and prognosis of NPC.