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Conjoint analysis of MeRIP-seq and RNA sequencing data. (A) Scatter plot presenting the differentially expressed genes in EOC. (B) Four-quadrant plots presenting the distribution of genes with significant alterations in both the m6A modification and mRNA levels. (C) Heatmap plots exhibiting the differentially expressed genes of EOC and OE groups.
Source publication
Emerging studies have revealed that N6-methyladenosine modification is involved in the development of various cancers. However, the m6A modification pattern of endometrioid ovarian cancer (EOC) has not been demonstrated. In the present study, high-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing...
Citations
... RPS6KA2 and JUNB were strongly linked with unfavorable prognosis of OC, and there was a positive correlation observed between RPS6KA2 and METTL3 in OC suggesting that RPS6KA is regulated through METTL3-dependent m6A modification (73). Silencing METTL3 in the endometrioid OC cell line COV362 significantly reduced proliferation, and induces G0/G1 cell cycle arrest to enhance cell death (102). OC cell growth increased in METTL3-cKO mice. ...
Ovarian Cancer (OC) ranks as a prominent contributor to mortality among female reproductive system associated cancers, particularly the prevalent subtype epithelial Ovarian Cancer (EOC). Despite advancements in treatment modalities, the prognosis for OC patients remains grim due to limitation of current therapeutic methodology such as high cytotoxicity of chemotherapeutic agents and tumor relapse making existing chemotherapy ineffective. Recognizing the limitations of a broad-spectrum approach to treating OC, a shift toward targeted therapies aligning with unique molecular features is imperative. This shift stems from an incomplete understanding of OC’s origin, distinguishing it from extensively researched malignancies such as cervical or colon cancer. At the molecular level, postsynthetic modifications—DNA, RNA, and protein—shape transcriptional, posttranscriptional, and posttranslational processes. Posttranscriptional regulatory mechanisms, including RNA modifications are termed epitranscriptomic and play critical roles in this process. For more than five decades, 100+ RNA post-synthetic modifications, notably N6-methyladenosine (m6A), most prevalent RNA modification in mammals, dynamically regulate messenger RNA (mRNA), and non-coding RNA (ncRNA) life orchestrated via writers, erasers, and readers. The disruption of m6A modifications are found in several cancers, including OC, underscores pivotal role of m6A. This review focused on m6A modifications in coding and non-coding RNAs, emphasizing their role as prognostic markers in OC and their impact on development, migration, invasion, and drug resistance. Additionally, RNA-modified regulators have been explored as potential molecular and therapeutic targets, offering an innovative approach to combatting this challenging malignancy.
... The m6A methyltransferases participant in the tumor growth, metastasis, and chemotherapy resistance of ovarian cancer [8]. METTL3 can promote the tumor growth of EOC [9]. Studies have shown that in EOC, m6A methylation regulators modify the tumor progression, such as high expression of WTAP relating to the poor prognosis of EOC [8]. ...
Background: The potential relation of methyltransferase-like gene polymorphisms and epithelial ovarian cancer (EOC) remains unclear.
Methods: Five SNPs (METTL5 rs3769767 A>G, METTL16 rs1056321 T>C, METTL5 rs10190853 G>A, METTL5 rs3769768 G>A and METTL16 rs11869256 A>G) of methyltransferase-like genes was selected trough NCBI dbSNP database. Two hundred and eighty-eight cases and 361 controls were enrolled from three hospitals in South China to conduct the case-control study. Genomic DNA was abstracted from peripheral blood and genotyped through a TapMan assay. Stratified analysis was conducted to explore the association of rs10190853, rs3769768, rs11869256 genotype and EOC susceptibility. The combination analysis was adopted to evaluate the relation between inferred haplotypes of the METTL5, METTL16 genes and EOC risk. Multifactor dimensionality reduction (MDR) analysis was performed to verify the interaction of SNPs.
Results: Among the five analyzed SNPs, METTL5 rs3769768 AA exhibited a significant association with increased EOC risk, while METTL5 rs10190853 GA, METTL16 rs11869256 GA was certified to decrease the susceptibility of EOC. The stratified analysis further revealed the harmful effect of METTL5 rs3769768 AA in EOC patients. On the contrary, METTL16 rs11869256 AG/GG and METTL5 rs10190853 AA showed the reduced risk of EOC in patients of specific subgroups. Combination analysis identified that haplotypes AAA highly connected with reduced risk of EOC. MDR analysis revealed that these SNPs existed no specific interactions.
Conclusion: METTL5 rs3769768 was related to increased risk of EOC. METTL5 rs10190853 and METTL16 rs11869256 decreased the susceptibility in EOC. METTL5 and METTL16 could be potential target of molecular therapy and prognosis markers.
... Previous studies have shown that METTL3 promotes ovarian cancer proliferation, migration, and invasion [24,25]. In addition, METTL3 is an inducer of cancer stem cell self-renewal and chemoresistance in human cancers [26,27]. ...
Background:
Ovarian cancer is the second leading cause of gynecologic cancer-associated deaths. Cancer stemness and chemoresistance are responsible for ovarian cancer metastasis and the poor prognosis of patients. In this study, we determined the function of N6-methyladenine (m6A) RNA methylation and prostaglandin E receptor 2 (PTGER2) in ovarian cancer progression.
Methods:
The m6A RNA methylation-associated PTGER2 in ovarian cancer was identified using bioinformatics analysis. The role of PTGER2 in ovarian cancer was elucidated in cell lines and clinical samples with cellular and molecular experiments.
Results:
In this investigation, bioinformatics analysis based on a public cancer database was used to elucidate the impact of m6A modification on the prognosis of patients with ovarian cancer. Moreover, PTGER2 was identified as a potential oncogene associated with the distant metastasis of ovarian cancer and poor patient prognosis. Interestingly, PTGER2 expression was experimentally shown to be enhanced by N6-adenosine-methyltransferase 70 kDa subunit (METTL3)-mediated m6A modification. In addition, PTGER2 enhanced cancer stem cell self-renewal properties, the epithelial-mesenchymal transition, and DNA damage repair, thus potentiating cell stemness, therapy resistance to carboplatin, proliferation, and metastasis of ovarian cancer. Importantly, PTGER2 expression in clinical samples was associated with distant metastasis, predicted poor patient prognosis, and independently served as a prognostic predictor in ovarian cancer.
Conclusions:
Our work defines PTGER2 as an oncogene and reveals that PTGER2 is a prognostic predictor and novel therapeutic target for the management of ovarian cancer.
... While Tripartite motif-containing protein (TRIM29) is supposed as an oncogene in OC related with the malignant characteristics, YTHDF1 binds to m6A sites on TRIM29 mRNA and facilitates its translation to enhance DDP resistance [48]. Additionally, comprehensive analysis of the transcriptome-wide m6A methylome of endometrioid OC showed that m6A enriched genes were significantly associated with resistance to platinum drug [80]. ...
Marvelous advancements have been made in cancer therapies to improve clinical outcomes over the years. However, therapeutic resistance has always been a major difficulty in cancer therapy, with extremely complicated mechanisms remain elusive. N6-methyladenosine (m6A) RNA modification, a hotspot in epigenetics, has gained growing attention as a potential determinant of therapeutic resistance. As the most prevalent RNA modification, m6A is involved in every links of RNA metabolism, including RNA splicing, nuclear export, translation and stability. Three kinds of regulators, “writer” (methyltransferase), “eraser” (demethylase) and “reader” (m6A binding proteins), together orchestrate the dynamic and reversible process of m6A modification. Herein, we primarily reviewed the regulatory mechanisms of m6A in therapeutic resistance, including chemotherapy, targeted therapy, radiotherapy and immunotherapy. Then we discussed the clinical potential of m6A modification to overcome resistance and optimize cancer therapy. Additionally, we proposed existing problems in current research and prospects for future research.
... Another study reported that ubiquitin-conjugating enzyme E2 N regulated paclitaxel sensibility of OC cells via DNMT1-CHFR-Aurora A pathway (55). A transcriptome m6A methylation analysis towards endometrioid ovarian cancer showed the influence of METTL3 on endometrioid ovarian cancer, and revealed the knockout of METTL3 resulted in distinct decrease of proliferation, increasing apoptosis, and G0/ G1 blocking of cell cycle (56). Other studies proved that METTL3 increased OC progression and promoted invasion via epithelial-mesenchymal transition and AXL translation (57), and accelerated tumorigenesis and metastasis through suppressing CCNG2 expression targeting miR-1246 in OC (58). ...
Background
Ovarian cancer (OC) is a female reproductive system tumor. RNA modifications play key roles in gene expression regulation. The growing evidence demonstrates that RNA methylation is critical for various biological functions, and that its dysregulation is related to the progression of cancer in human.
Method
OC samples were classified into different subtypes (Clusters 1 and 2) based on various RNA-modification regulatory genes (RRGs) in the process of RNA modifications (m1A, m6A, m6Am, m5C, m7G, ac4C, m3C, and Ψ) by nonnegative matrix factorization method (NMF). Based on differently expressed RRGs (DERRGs) between clusters, a pathologically specific RNA-modification regulatory gene signature was constructed with Lasso regression. Kaplan-Meier analysis and receiver operating characteristic (ROC) curves were used to evaluate the prognostic ability of the identified model. The correlations of clinicopathological features, immune subtypes, immune scores, immune cells, and tumor mutation burden (TMB) were also estimated between different NMF clusters and riskscore groups.
Results
In this study, 59 RRGs in the process of RNA modifications (m1A, m6A, m6Am, m5C, m7G, ac4C, m3C, and Ψ) were obtained from TCGA database. These RRGs were interactional, and sample clusters based on these regulators were significantly correlated with survival rate, clinical characteristics (involving survival status and pathologic stage), drug sensibility, and immune microenvironment. Furthermore, Lasso regression based on these 21 DERRGs between clusters 1 and 2 constructed a four-DERRG signature (ALYREF, ZC3H13, WTAP, and METTL1). Based on this signature, 307 OC patients were classified into high- and low-risk groups based on median value of riskscores from lasso regression. This identified signature was significantly associated with overall survival, radiation therapy, age, clinical stage, cancer status, and immune cells (involving CD4+ memory resting T cells, plasma cells, and Macrophages M1) of ovarian cancer patients. Further, GSEA revealed that multiple biological behaviors were significantly enriched in different groups.
Conclusions
OC patients were classified into two subtypes per these RRGs. This study identified four-DERRG signature (ALYREF, ZC3H13, WTAP, and METTL1) in OC, which was an independent prognostic model for patient stratification, prognostic evaluation, and prediction of response to immunotherapy in ovarian cancer by classifying OC patients into high- and low-risk groups.
... Yang et al. identified m 6 A modifications in the EOC transcriptome of end ovarian cancer by MeRIP-seq for the first time and described methylated m 6 A to differentially expressed genes. This provides a new direction for the underlying ular mechanisms and signaling pathways of EOC development [53]. During a hensive analysis of mRNA m 6 A modifications in human colorectal cancer, Li et ducted a combined analysis by MeRIP-seq and RNA-seq to predict RNA-bind teins and identify methylation-related genes FMR1, IGF2BP2, and IGF2BP3 that involved in the development of CRC [54]. ...
... Yang et al. identified m 6 A modifications in the EOC transcriptome of endometrial ovarian cancer by MeRIP-seq for the first time and described methylated m 6 A to modify differentially expressed genes. This provides a new direction for the underlying molecular mechanisms and signaling pathways of EOC development [53]. During a comprehensive analysis of mRNA m 6 A modifications in human colorectal cancer, Li et al. conducted a combined analysis by MeRIP-seq and RNA-seq to predict RNA-binding proteins and identify methylation-related genes FMR1, IGF2BP2, and IGF2BP3 that may be involved in the development of CRC [54]. ...
N6-methyladenosine (m6A) methylation is a type of methylation modification discovered on RNA molecules, mainly on mRNAs, as well as on other RNAs. Similar to DNA methylation, m6A methylation regulates the post-transcriptional expression level of genes without altering their base sequences. It modulates gene expression mainly by affecting the binding of mRNAs to reader proteins, thereby regulating variable splicing, translation efficiency, and stability of mRNAs. Early in the research, the study of m6A-related biological functions was greatly hindered due to the lack of effective detection methods. As second-generation sequencing and bioinformatics develop, several methods have been available to detect and predict m6A methylation sites in recent years. Moreover, m6A methylation is also closely related to the development of lipid metabolism, as shown in current studies. Combined with recent research, this paper reviews the concept, detection, and prediction means of m6A methylation, especially the relationship between m6A and lipid metabolism, providing a new clue to enrich the molecular mechanism of lipid metabolism.
This study aimed to synchronously determine epitranscriptome-wide RNA N6-methyladenosine (m6A) modifications and mRNA expression profile in high grade serous ovarian cancer (HGSOC). The methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to comprehensively examine the m6A modification profile and the RNA-sequencing (RNA-seq) was performed to analyze the mRNA expression profile in HGSOC and normal fallopian tube (FT) tissues. Go and KEGG analyses were carried out in the enrichment of those differentially methylated and expressed genes. MeRIP-seq data showed 53,794 m6A methylated peaks related to 19,938 genes in the HGSOC group and 51,818 m6A peaks representing 19,681 genes in the FT group. RNA-seq results revealed 2321 upregulated and 2486 downregulated genes in HGSOC. Conjoint analysis of MeRIP-seq and RNA-seq data identified differentially expressed genes in which 659 were hypermethylated (330 up- and 329 down-regulated) and 897 were hypomethylated (475 up- and 422 down-regulated). Functional enrichment analysis indicated that these differentially modulated genes are involved in pathways related to cancer development. Among methylation regulators, the m6A eraser (FTO) expression was significantly lower, but the m6A readers (IGF2BP2 and IGF2BP3) were higher in HGSOC, which was validated by the subsequent real-time PCR assay. Exploration through public databases further corroborated their possible clinical application of certain methylation regulators and differentially expressed genes. For the first time, our study screens the epitranscriptome-wide m6A modification and expression profiles of their modulated genes and signaling pathways in HGSOC. Our findings provide an alternative direction in exploring the molecular mechanisms of ovarian pathogenesis and potential biomarkers in the diagnosis and predicting the prognosis of the disease.
Epigenetic regulation plays an essential role in immunity and inflammation in endometriosis. In this study, we aimed to explore differences in m6A regulators between endometriosis patients and normal women and analyze the effect of m6A modification on immune and inflammatory microenvironment. The samples for analysis were downloaded from the Gene Expression Omnibus database, including ectopic endometrium (EC), eutopic endometrium (EU), and normal eutopic endometrium (NM) samples from non-endometriosis women. The validation process involved utilizing our previous RNA-sequencing data. Subsequently, a correlation analysis was performed to ascertain the relationship between m6A and the inflammatory microenvironment profile, encompassing infiltrating immunocytes, immune-inflammation reaction gene sets, and human leukocyte antigen genes. LASSO analyses were used to develop risk signature. The findings of this study indicate that the m6A regulators FTO were observed to be significantly up-regulated, while YTHDF2, CBLL1, and METTL3 were down-regulated in endometriosis tissues. The CIBERSORT analysis revealed that the local inflammatory microenvironment of ectopic lesions plays a crucial role in the development of endometriosis. Notably, M2 macrophages exhibited a significant difference between the EC and NM groups. Moreover, M2 macrophages demonstrated a positive correlation with FTO (0.39) and a negative correlation with CBLL1 (− 0.35). Furthermore, consistent clustering of EC and EU samples resulted in the identification of three distinct cell subtypes. Among different cell subtypes, significant differences were in immunoinfiltrating cells, plasma cells, naive CD4 T cells, memory activated CD4 T cells, gamma delta T cells, resting NK cells and activated NK cells but not in macrophages. Furthermore, the identification of various compounds capable of targeting these m6A genes was achieved. In conclusions, our integrated bioinformatics analysis results demonstrated that m6A-related genes METTL3, CBLL1 and YTHDF2 may be useful biomarkers for endometriosis in ectopic endometrium. The potential therapeutic approach of targeting m6A regulators holds promise for the treatment of endometriosis.
Aim
N6-methyladenosine (m6A) RNA methylation exerts a regulatory effect on endometrioid ovarian cancer (EOC), but the specific m6A regulator genes in EOC remain to be explored. This study investigated that sulforaphene (Sul) is implicated in EOC development by regulating methyltransferase-like 3 (METTL3).
Methods
The dysregulated m6A RNA methylation genes in EOC were determined by methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing. The roles of METTL3 and/or Sul on viability, proliferative ability, cell cycle, and apoptosis of EOC cells were determined by MTT, colony formation, flow cytometry, and TUNEL staining assay, respectively. The expression of METTL3 and apoptosis-related proteins in EOC cells was detected by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot assays.
Results
Five m6A RNA methylation regulators (METTL3, ELF3, IGF2BP2, FTO, and METTL14) were differentially expressed in EOC, among which METTL3 had the highest expression level. Silencing METTL3 reduced the clonal expansion and viability of EOC cells, and caused the cells to arrest in the G0/G1 phase. This also promoted apoptosis in the EOC cells and activated the FAS/FADD and mitochondrial apoptosis pathways. In contrast, overexpressing METTL3 had the opposite effect. Sul, in a dose-dependent manner, reduced the viability of EOC cells but promoted their apoptosis. Sul also increased the levels of IGF2BP2 and FAS, while decreasing the levels of KRT8 and METTL3. Furthermore, Sul was able to reverse the effects of METTL3 overexpression on EOC cells.
Conclusions
Sul could suppress cell proliferation and promote apoptosis of EOC cells by inhibiting the METTL3 to activate the FAS/FADD and apoptosis-associated pathways.
