Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer

Prognostic signature analysis and survival prediction of esophageal cancer based on N6-methyladenosine associated lncRNAs

Esophageal cancer (ESCA) has a bad prognosis. Long non-coding RNA (lncRNA) impacts on cell proliferation. However, the prognosis function of N6-methyladenosine (m6A)-associated lncRNAs (m6A-lncRNAs) in ESCA remains unknown. Univariate Cox analysis was applied to investigate prognosis related m6A-lncRNAs, based on which the samples were clustered. Wilcoxon rank and Chi-square tests were adopted to compare the clinical traits, survival, pathway activity and immune infiltration in different clusters where overall survival, clinical traits (N stage), tumor-invasive immune cells and pathway activity were found significantly different. Through least absolute shrinkage and selection operator and proportional hazard (Lasso-Cox) model, five m6A-lncRNAs were selected to construct the prognostic signature (m6A-lncSig) and risk score. To investigate the link between risk score and clinical traits or immunological microenvironments, Chi-square test and Spearman correlation analysis were utilized. Risk score was found connected with N stage, tumor stage, different clusters, macrophages M2, B cells naive and T cells CD4 memory resting. Risk score and tumor stage were found as independent prognostic variables. And the constructed nomogram model had high accuracy in predicting prognosis. The obtained m6A-lncSig could be taken as potential prognostic biomarker for ESCA patients. This study offers a theoretical foundation for clinical diagnosis and prognosis of ESCA.

The emerging role of m6A modification of non-coding RNA in gastrointestinal cancers: a comprehensive review

Gastrointestinal (GI) cancer is a series of malignant tumors with a high incidence globally. Although approaches for tumor diagnosis and therapy have advanced substantially, the mechanisms underlying the occurrence and progression of GI cancer are still unclear. Increasing evidence supports an important role for N6-methyladenosine (m6A) modification in many biological processes, including cancer-related processes via splicing, export, degradation, and translation of mRNAs. Under distinct cancer contexts, m6A regulators have different expression patterns and can regulate or be regulated by mRNAs and non-coding RNAs, especially long non-coding RNAs. The roles of m6A in cancer development have attracted increasing attention in epigenetics research. In this review, we synthesize progress in our understanding of m6A and its roles in GI cancer, especially esophageal, gastric, and colorectal cancers. Furthermore, we clarify the mechanism by which m6A contributes to GI cancer, providing a basis for the development of diagnostic, prognostic, and therapeutic targets.

The implications of N6-methyladenosine (m6A) modification in esophageal carcinoma

Esophageal carcinoma (EC) is always diagnosed at advanced stage and its the mortality rate remains high. The patients usually miss the best opportunity for treatment because of non-specific symptoms and the survival rates are low. N6-methyladenosine (m6A) the predominant modification in eukaryotic messenger RNA(mRNA), serves vital roles in numerous bioprocess. This chemical modification is dynamic, reversible and consists of three regulators: m6A methyltransferases (writers), demethylases (erasers) and m6A-binding proteins (readers). Recently, a growing number of evidences have indicated relationships between m6A and EC. Whereas, lacking of cognition about the molecular mechanism of m6A modification in esophageal carcinoma. We will focus on the biological function roles of m6A modification in the tumorigenesis and development of EC. Recent studies showed that immunotherapy had a positive impact on EC. The relationship between m6A and immunotherapy in EC deserves further research and discussion. We will also discuss the potential clinical applications regarding diagnosis, treatment and prognosis of m6A modification for EC and provide perspectives for further studies.

m6A reading protein RBMX as a biomarker for prognosis and tumor progression in esophageal cancer

Background

As a member of m6A methylated binding protein, RNA binding motif protein X-linked (RBMX) has been reported to be associated with tumor invasion, metastasis and prognosis. However, the prognostic significance of RBMX expression in esophageal cancer (ESCA) remains unclear.

Methods

Based on the TIMER database, GEPIA database, cBioPortal database, CIBERSORT deconvolution algorithm, String-DB database, LinkedOmics database, etc., the RBMX expression level, mRNA expression level, prognostic relationship, genetic mutation, immune cell infiltration level, protein interaction network, differential co-expression genes and functional enrichment in esophageal carcinoma were analyzed. Immunohistochemistry was used to detect the expression of RBMX in 53 cases of esophageal carcinoma and adjacent esophageal tissues.

Results

The RBMX expression in ESCA tissue was significantly higher than that in the normal tissues. The overall survival (OS) of patients with high RBMX expression was significantly lower than that of patients with low expression (P=0.04). The protein encoded by the RBMX gene appeared to copy number amplification, mutation and deep deletion. The expression level of RBMX was positively correlated with the levels of follicular helper T cells, eosinophils and initial B cells (P<0.05). Genes significantly and positively correlated with RBMX expression included HNRNPA1L2, SFRS13A, HNRNPA1, etc., which were mainly enriched in biological processes (BPs) such as cell division, mRNA splicing, RNA binding and mRNA 3'-UTR binding.

Conclusions

RBMX may be as a biomarker of poor prognosis of ESCA. RBMX is closely related to the survival and prognosis, genetic mutation and immune cell infiltration of patients with ESCA.

The diverse role of RNA methylation in esophageal cancer

Esophageal cancer is one of the major life-threatening diseases in the world. RNA methylation is the most common post-transcriptional modification and a wide-ranging regulatory system controlling gene expression. Numerous studies have revealed that dysregulation of RNA methylation is critical for cancer development and progression. However, the diverse role of RNA methylation and its regulators in esophageal cancer remains to be elucidated and summarized. In this review, we focus on the regulation of major RNA methylation, including m ⁶A, m ⁵C, and m ⁷G, as well as the expression patterns and clinical implications of its regulators in esophageal cancer. We systematically summarize how these RNA modifications affect the "life cycle" of target RNAs, including mRNA, microRNA, long non-coding RNA, and tRNA. The downstream signaling pathways associated with RNA methylation during the development and treatment of esophageal cancer are also discussed in detail. Further studies on how these modifications function together in the microenvironment of esophageal cancer will draw a clearer picture of the clinical application of novel and specific therapeutic strategies.

Effects of writers, erasers and readers within miRNA-related m6A modification in cancers

BACKGROUND

As one of the most abundant post-transcriptional mRNA modifications, N6-methyladenosine (m6A) has attracted extensive attention from scientists. Emerging evidence indicates that m6A modification plays a significant role in cancer-related signalling pathways. Existing research demonstrates that m6A modifications were also identified in miRNAs and contribute to cancer-related signalling pathways.

METHODS

A literature retrieval has been performed to collect m6A-miRNA-related original articles published in recent years. Later, a systematic analysis has been conducted to abstract and classify the relationships between m6A modification and miRNAs, and their contributions to tumorigenesis and cancer development.

RESULTS

Accumulating literature provides important insights into multiple relationships between m6A modifications and miRNAs. Mechanically, m6A writer and eraser alter pri-miRNAs m6A levels, and m6A readers could dually modulate pri-miRNAs processing and pri-miRNAs degradation. It is also been demonstrated that miRNAs impair m6A regulators' translation to influence m6A medication function in return. Aberrant expressions of m6A regulators and miRNAs could dysregulate proliferative, apoptosis, cell adhesion-related, and malignant transformation signalling pathways, and contribute to tumour occurrence and development.

CONCLUSION

This review summarizes the interrelationship between m6A modification and miRNAs; highlights the combined effects of each type of m6A regulator and miRNAs in cancers. These findings enhance our understanding of m6A-miRNAs' multiple interactions and significant modulatory role in tumorigenesis and progression.

Emerging Mutual Regulatory Roles between m6A Modification and microRNAs

N⁶-metyladenosine (m⁶A), one of the most common RNA methylation modifications in mammals, has attracted extensive attentions owing to its regulatory roles in a variety of physiological and pathological processes. As a reversible epigenetic modification on RNAs, m⁶A is dynamically mediated by the functional interplay among the regulatory proteins of methyltransferases, demethylases and methyl-binding proteins. In recent years, it has become increasingly clear that m⁶A modification is associated with the production and function of microRNAs (miRNAs). In this review, we summarize the specific kinds of m⁶A modification methyltransferases, demethylases and methyl-binding proteins. In particular, we focus on describing the roles of m⁶A modification and its regulatory proteins in the production and function of miRNAs in a variety of pathological and physiological processes. More importantly, we further discuss the mediating mechanisms of miRNAs in m⁶A modification and its regulatory proteins during the occurrence and development of various diseases.

CircDOCK1 Regulates miR-186/DNMT3A to Promote Osteosarcoma Progression

BACKGROUND

Circular RNAs (circRNAs), as a class of endogenous RNAs, are implicated in osteosarcoma (OS) progression. However, the functional properties of circDOCK1 in OS have been largely unexplored. The present study demonstrated the regulatory mechanism of circDOCK1 in OS.

METHODS

QRT-PCR and Western blots were used to determine the abundances of circDOCK1, miR-186, and DNMT3A. Cell counting kit-8 (CCK-8), 5-Ethynyl-2'-deoxyuridine (EdU), colony formation, Transwell, and wound healing assays were used to examine cellular multiplication, motility, and invasion. Luciferase reporter analysis, RNA immunoprecipitation (RIP), and pull-down assays were used to verify target relationships. Xenograft models were used to analyze in vivo function.

RESULTS

OS tissues and cells showed high levels of circDOCK1. By knocking down circDOCK1, cellular multiplication, motility, and invasion were suppressed. Furthermore, silencing circDOCK1 suppressed the growth of tumor xenografts. According to mechanistic studies, miR-186 targets DNA methyltransferases 3A (DNMT3A) directly and acts as a circDOCK1 target. Furthermore, circDOCK1 upregulated DNMT3A expression through sponging miR-186 to regulate the progression of OS.

CONCLUSIONS

CircDOCK1 promotes OS progression by interacting with miR-186/DNMT3ADNMT3A, representing a novel therapeutic approach.

A Novel m7G-Related Gene Signature Predicts the Prognosis of Colon Cancer

Colon cancer (CC), one of the most common malignancies worldwide, lacks an effective prognostic prediction biomarker. N7-methylguanosine (m7G) methylation is a common RNA modification type and has been proven to influence tumorigenesis. However, the correlation between m7G-related genes and CC remains unclear. The gene expression levels and clinical information of CC patients were downloaded from public databases. Twenty-nine m7G-related genes were obtained from the published literature. Via unsupervised clustering based on the expression levels of m7G-related genes, CC patients were divided into three m7G clusters. Based on differentially expressed genes (DEGs) from the above three groups, CC patients were further divided into three gene clusters. The m7G score, a prognostic model, was established using principal component analysis (PCA) based on 15 prognosis-associated m7G genes. KM curve analysis demonstrated that the overall survival rate was remarkably higher in the high-m7G score group, which was much more significant in advanced CC patients as confirmed by subgroup analysis. Correlation analysis indicated that the m7G score was associated with tumor mutational burden (TMB), PD-L1 expression, immune infiltration, and drug sensitivity. The expression level of prognosis-related m7G genes was further confirmed in human CC cell lines and samples. This study established an m7G gene-based prognostic model (m7G score), which demonstrated the important roles of m7G-related genes during CC initiation and progression. The m7G score could be a practical biomarker to predict immunotherapy response and prognosis in CC patients.

The Role of m6A Modification and m6A Regulators in Esophageal Cancer

N6-methyladenosine (m6A) modification, the most prevalent RNA modification, is involved in all aspects of RNA metabolism, including RNA processing, nuclear export, stability, translation and degradation. Therefore, m6A modification can participate in various physiological functions, such as tissue development, heat shock response, DNA damage response, circadian clock control and even in carcinogenesis through regulating the expression or structure of the gene. The deposition, removal and recognition of m6A are carried out by methyltransferases, demethylases and m6A RNA binding proteins, respectively. Aberrant m6A modification and the dysregulation of m6A regulators play critical roles in the occurrence and development of various cancers. The pathogenesis of esophageal cancer (ESCA) remains unclear and the five-year survival rate of advanced ESCA patients is still dismal. Here, we systematically reviewed the recent studies of m6A modification and m6A regulators in ESCA and comprehensively analyzed the role and possible mechanism of m6A modification and m6A regulators in the occurrence, progression, remedy and prognosis of ESCA. Defining the effect of m6A modification and m6A regulators in ESCA might be helpful for determining the pathogenesis of ESCA and providing some ideas for an early diagnosis, individualized treatment and improved prognosis of ESCA patients.

The development of a novel signature based on the m6A RNA methylation regulator-related ceRNA network to predict prognosis and therapy response in sarcomas

Background: N⁶ methyladenosine (m⁶A)-related noncoding RNAs (including lncRNAs and miRNAs) are closely related to the development of cancer. However, the gene signature and prognostic value of m⁶A regulators and m⁶A-associated RNAs in regulating sarcoma (SARC) development and progression remain largely unexplored. Therefore, further research is required.

Methods: We obtained expression data for RNA sequencing (RNA-seq) and miRNAs of SARC from The Cancer Genome Atlas (TCGA) datasets. Correlation analysis and two target gene prediction databases (miRTarBase and LncBase v.2) were used to deduce m⁶A-related miRNAs and lncRNAs, and Cytoscape software was used to construct ceRNA-regulating networks. Based on univariate Cox regression and least absolute shrinkage and selection operator (LASSO) Cox regression analyses, an m⁶A-associated RNA risk signature (m6Ascore) model was established. Prognostic differences between subgroups were explored using Kaplan–Meier (KM) analysis. Risk score-related biological phenotypes were analyzed in terms of functional enrichment, tumor immune signature, and tumor mutation signature. Finally, potential immunotherapy features and drug sensitivity predictions for this model were also discussed.

Results: A total of 16 miRNAs, 104 lncRNAs, and 11 mRNAs were incorporated into the ceRNA network. The risk score was obtained based on RP11-283I3.6, hsa-miR-455-3p, and CBLL1. Patients were divided into two risk groups using the risk score, with patients in the low-risk group having longer overall survival (OS) than those in the high-risk group. The receiver operating characteristic (ROC) curves indicated that risk characteristic performed well in predicting the prognosis of patients with SARC. In addition, lower m6Ascore was also positively correlated with the abundance of immune cells such as monocytes and mast cells activated, and several immune checkpoint genes were highly expressed in the low-m6Ascore group. According to our analysis, lower m6Ascore may lead to better immunotherapy response and OS outcomes. The risk signature was significantly associated with the chemosensitivity of SARC. Finally, a nomogram was constructed to predict the OS in patients with SARC. The concordance index (C-index) for the nomogram was 0.744 (95% CI: 0.707–0.784). The decision curve analysis (DCA), calibration plot, and ROC curve all showed that this nomogram had good predictive performance.

Conclusion: This m6Ascore risk model based on m⁶A RNA methylation regulator-related RNAs may be promising for clinical prediction of prognosis and might contain potential biomarkers for treatment response prediction for SARC patients.

A Novel M7G-Related MicroRNAs Risk Signature Predicts the Prognosis and Tumor Microenvironment of Kidney Renal Clear Cell Carcinoma

Background: M7G modification is extremely vital for the development of many cancers, especially tumor immunity. M7G modification is a novel functional regulator of miRNA, and the researches on m7G-related miRNAs in kidney renal clear cell carcinoma (KIRC) are still insufficient. This research aims to establish a risk signature on the foundation of m7G-associated miRNAs, which can precisely forecast the prognosis of KIRC patients.

Methods: Transcriptome data and clinical data used in this study come from The Cancer Genome Atlas database. Our team utilized univariable Cox, Lasso and multivariable Cox analyses to construct a m7G-associated miRNAs risk signature that can forecast the prognosis of KIRC patients. Kaplan-Meier method, time-dependent receiver operating characteristic (ROC) curve, and the independent analysis of risk signatures were employed to verify the predictability and accuracy of the risk signature. Subsequently, based on CIBERSORT, ESTIMATE and ssGSEA algorithms, we speculated the potential impact of the proposed risk signature on tumor immune microenvironment. Ultimately, by virtue of the risk signature and tumor immunity, the hub genes affecting the prognosis of KIRC patients were screened out.

Results: Our team established and verified a prognostic signature comprising 7 m7G-associated miRNAs (miR-342-3p, miR-221-3p, miR-222-3p, miR-1277-3p, miR-6718-5p, miR-1251-5p, and miR-486-5p). The results of the Kaplan-Meier survival analysis revealed that the prognosis of KIRC sufferers in the high-risk group was often unsatisfactory. The accuracy of the prediction ability of the risk signature was verified by calculating the area under the ROC curve. Univariate-multivariate Cox analyses further showed that this risk signature could be utilized as an independent prognosis-related biomarker for KIRC sufferers. The results of the immune analysis revealed that remarkable diversities existed in immune status and tumor microenvironment between high-risk and low-risk groups. On the foundation of the proposed risk signature and other clinical factors, a nomogram was established to quantitatively forecast the survival of KIRC sufferers at 1, 3 and 5 years.

Conclusion: Based on m7G-related miRNAs, a risk signature was successfully constructed, which could precisely forecast the prognosis of sufferers and guide personalized immunotherapy for KIRC patients.

Role of main RNA modifications in cancer: N6-methyladenosine, 5-methylcytosine, and pseudouridine

Cancer is one of the major diseases threatening human life and health worldwide. Epigenetic modification refers to heritable changes in the genetic material without any changes in the nucleic acid sequence and results in heritable phenotypic changes. Epigenetic modifications regulate many biological processes, such as growth, aging, and various diseases, including cancer. With the advancement of next-generation sequencing technology, the role of RNA modifications in cancer progression has become increasingly prominent and is a hot spot in scientific research. This review studied several common RNA modifications, such as N⁶-methyladenosine, 5-methylcytosine, and pseudouridine. The deposition and roles of these modifications in coding and noncoding RNAs are summarized in detail. Based on the RNA modification background, this review summarized the expression, function, and underlying molecular mechanism of these modifications and their regulators in cancer and further discussed the role of some existing small-molecule inhibitors. More in-depth studies on RNA modification and cancer are needed to broaden the understanding of epigenetics and cancer diagnosis, treatment, and prognosis.

m6A target microRNAs in serum for cancer detection

Recent studies have revealed the significant dysregulation of m⁶A level in peripheral blood in several cancer types and its value in diagnosis. Nonetheless, a biomarker for accurate screening of multiple cancer types has not been established based on the perspective of m⁶A modification. In this study, we aimed to develop a serum diagnostic signature based on the m⁶A target miRNAs for the mass detection of cancer. A total of 14965 serum samples with 12 cancer types were included. Based on training cohort (n=7299), we developed the m6A-miRNAs signature using a support vector machine algorithm for cancer detection. The m6A-miRNAs signature showed high accuracy, and its area under the curve (AUC) in the training, internal validation and external validation cohort reached 0.979 (95%CI 0.976 - 0.982), 0.976 (95%CI 0.973 - 0.979) and 0.936 (95%CI 0.922 - 0.951), respectively. In the performance of distinguishing cancer types, the m6A-miRNAs signature showed superior sensitivity in each cancer type and presented a satisfactory AUC in identifying lung cancer, gastric cancer and hepatocellular carcinoma. Additionally, the diagnostic performance of m6A-miRNAs was not interfered by the gender, age and benign disease. In short, this study revealed the value of serum circulating m⁶A miRNAs in cancer detection and provided a new direction and strategy for the development of novel biomarkers with high accuracy, low cost and less invasiveness for mass cancer screening, such as RNA modification.