Regulatory Role of N6 -methyladenosine (m6 A) Methylation in RNA Processing and Human Diseases

METTL3 deficiency leads to ovarian insufficiency due to IL-1β overexpression in theca cells

Premature ovarian insufficiency (POI) is a clinical syndrome characterised by a decline in ovarian function in women before 40 years of age and is associated with oestradiol deficiency and a complex pathogenesis. However, the aetiology of POI is still unclear and effective preventative and treatment strategies are still lacking. Methyltransferase like 3 (METTL3) is an RNA methyltransferase that is involved in spermatogenesis, oocyte development and maturation, early embryonic development, and embryonic stem cell differentiation and formation, but its role in POI is unknown. In the present study, METTL3 deficiency in follicular theca cells was found to lead to reduced fertility in female mice, with a POI-like phenotype, and METTL3 knockout promoted ovarian inflammation. Further, a reduction in METTL3 in follicular theca cells led to a decrease in the m6A modification of pri-miR-21, which further reduced pri-miR-21 recognition and binding by DGCR8 proteins, leading to a decrease in the synthesis of mature miR-21-5p. Decrease of miR-21-5p promoted the secretion of interleukin-1β (IL-1β) from follicular theca cells. Acting in a paracrine manner, IL-1β inhibited the cAMP-PKA pathway and activated the NF-κB pathway in follicular granulosa cells. This activation increased the levels of reactive oxygen species in granulosa cells, causing disturbances in the intracellular Ca2+ balance and mitochondrial damage. These cellular events ultimately led to granulosa cell apoptosis and a decrease in oestradiol synthesis, resulting in POI development. Collectively, these findings reveal how METTL3 deficiency promotes the expression and secretion of IL-1β in theca cells, which regulates ovarian functions, and proposes a new theory for the development of POI disease.

Transcriptome-wide m6A methylation profile reveals its potential role underlying drought response in wheat (Triticum aestivum L.)

MAIN CONCLUSION

This study revealed the transcriptome-wide m6A methylation profile under drought stress and found that TaETC9 might regulate drought tolerance through mediating RNA methylation in wheat. Drought is one of the most destructive environmental constraints limiting crop growth and development. N6-methyladenosine (m6A) is a prevalent and important post-transcriptional modification in various eukaryotic RNA molecules, playing the crucial role in regulating drought response in plants. However, the significance of m6A in wheat (Triticum aestivum L.), particularly its involvment in drought response, remains underexplored. In this study, we investigated the transcriptome-wide m6A profile under drought stress using parallel m6A immunoprecipitation sequencing (MeRIP-seq). Totally, 4221 m6A peaks in 3733 m6A-modified genes were obtained, of which 373 methylated peaks exhibited differential expression between the control (CK) and drought-stressed treatments. These m6A loci were significantly enriched in proximity to stop codons and within the 3'-untranslated region. Integration of MeRIP-seq and RNA-seq revealed a positive correlation between m6A methylation and mRNA abundance and the genes displaying both differential methylation and expression were obtained. Finally, qRT-PCR analyses were further performed and the results found that the m6A-binding protein (TaETC9) showed significant up-regulation, while the m6A demethylase (TaALKBH10B) was significantly down-regulated under drought stress, contributing to increased m6A levels. Furthermore, the loss-of-function mutant of TaECT9 displayed significantly higher drought sensitivity compared to the wild type, highlighting its role in regulating drought tolerance. This study reported the first wheat m6A profile associated with drought stress, laying the groundwork for unraveling the potential role of RNA methylation in drought responses and enhancing stress tolerance in wheat through epigenetic approaches.

Variable calling of m6A and associated features in databases: a guide for end-users

N6-methyladenosine (m$^{6}$A) is a widely-studied methylation to messenger RNAs, which has been linked to diverse cellular processes and human diseases. Numerous databases that collate m$^{6}$A profiles of distinct cell types have been created to facilitate quick and easy mining of m$^{6}$A signatures associated with cell-specific phenotypes. However, these databases contain inherent complexities that have not been explicitly reported, which may lead to inaccurate identification and interpretation of m$^{6}$A-associated biology by end-users who are unaware of them. Here, we review various m$^{6}$A-related databases, and highlight several critical matters. In particular, differences in peak-calling pipelines across databases drive substantial variability in both peak number and coordinates with only moderate reproducibility, and the inclusion of peak calls from early m$^{6}$A sequencing protocols may lead to the reporting of false positives or negatives. The awareness of these matters will help end-users avoid the inclusion of potentially unreliable data in their studies and better utilize m$^{6}$A databases to derive biologically meaningful results.

Mechanisms and clinical landscape of N6-methyladenosine (m6A) RNA modification in gastrointestinal tract cancers

Epigenetics encompasses reversible and heritable chemical modifications of non-nuclear DNA sequences, including DNA and RNA methylation, histone modifications, non-coding RNA modifications, and chromatin rearrangements. In addition to well-studied DNA and histone methylation, RNA methylation has emerged as a hot topic in biological sciences over the past decade. N6-methyladenosine (m6A) is the most common and abundant modification in eukaryotic mRNA, affecting all RNA stages, including transcription, translation, and degradation. Advances in high-throughput sequencing technologies made it feasible to identify the chemical basis and biological functions of m6A RNA. Dysregulation of m6A levels and associated modifying proteins can both inhibit and promote cancer, highlighting the importance of the tumor microenvironment in diverse biological processes. Gastrointestinal tract cancers, including gastric, colorectal, and pancreatic cancers, are among the most common and deadly malignancies in humans. Growing evidence suggests a close association between m6A levels and the progression of gastrointestinal tumors. Global m6A modification levels are substantially modified in gastrointestinal tumor tissues and cell lines compared to healthy tissues and cells, possibly influencing various biological behaviors such as tumor cell proliferation, invasion, metastasis, and drug resistance. Exploring the diagnostic and therapeutic potential of m6A-related proteins is critical from a clinical standpoint. Developing more specific and effective m6A modulators offers new options for treating these tumors and deeper insights into gastrointestinal tract cancers.

The emerging role and mechanism of HMGA2 in breast cancer

High mobility group AT-hook 2 (HMGA2) is a member of the non-histone chromosomal high mobility group (HMG) protein family, which participate in embryonic development and other biological processes. HMGA2 overexpression is associated with breast cancer (BC) cell growth, proliferation, metastasis, and drug resistance. Furthermore, HMGA2 expression is positively associated with poor prognosis of patients with BC, and inhibiting HMGA2 signaling can stimulate BC cell progression and metastasis. In this review, we focus on HMGA2 expression changes in BC tissues and multiple BC cell lines. Wnt/β-catenin, STAT3, CNN6, and TRAIL-R2 proteins are upstream mediators of HMGA2 that can induce BC invasion and metastasis. Moreover, microRNAs (miRNAs) can suppress BC cell growth, invasion, and metastasis by inhibiting HMGA2 expression. Furthermore, long noncoding RNAs (LncRNAs) and circular RNAs (CircRNAs) mainly regulate HMGA2 mRNA and protein expression levels by sponging miRNAs, thereby promoting BC development. Additionally, certain small molecule inhibitors can suppress BC drug resistance by reducing HMGA2 expression. Finally, we summarize findings demonstrating that HMGA2 siRNA and HMGA2 siRNA-loaded nanoliposomes can suppress BC progression and metastasis.

Identification of prognostic m6A modification patterns and score system in melanoma patients

N6-methyladenosine (m6A) is the most common modification on RNAs and LncRNAs. It plays an important role in cancer stem cell differentiation, T cell differentiation, and immune homeostasis. In this study, we explored the potential roles of m6A modification of RNA in melanoma and investigated the immune cell infiltration in tumor microenvironment in diverse m6Aclusters and different m6Ascore groups. A consensus clustering algorithm determined m6A modification patterns based on 14 m6A regulators, and further explored the biological functions and the connection with TME. An m6A-related gene signature (m6Ascore) was constructed based on m6A-related genes using principal component analysis. Three m6A modification patterns were identified based on 14 m6A regulators, named as m6Aclusters A-C. The prognosis of m6Acluster A was more favorable than m6Aclusters B and C, and it was more closely associated with immune regulation. To quantify the m6A modification patterns of individual tumor, an m6Ascore was constructed, and patients were classified into high and low m6Ascore groups. The low m6Ascore group, which had a favorable prognosis, was more relevant to immunology. The expression of PD-L1 was higher and the immunophenoscore (IPS) revealed stronger response to immunotherapy in the low m6Ascore group. This study identified 3 m6A modification patterns with different immune characteristics and constructed an m6Ascore system to predict prognosis and immunogenicity of patients, which is conducive to clinical prognosis judgment and individual treatment.

Comprehensive analysis of m6A modification patterns and m6A-related lncRNAs as potential biomarkers in lung adenocarcinoma

BACKGROUND

N6-methyladenosine (m6A) methylation is considered to induce tumor cell proliferation, migration, and apoptosis. Understanding the mechanism of m6A-related lncRNAs in the development of lung adenocarcinoma (LUAD) may help predict prognosis.

METHODS

m6A-related lncRNAs related to lung cancer were identified and combined with the MeRIP-Seq dataset. The consensus clustering method was utilized to divide LUAD patients, and prognostic model was constructed using the Lasso Cox algorithm. The cluster profiler package was used for gene ontology and KEGG enrichment. The proportion of immune infiltration was estimated using the CIBERSORT algorithm. The decision tree was constructed by the rpart package, and nomograms were built by the rms package. The Connectivity Map database was analyzed for the therapeutic effects of small molecule drugs for LUAD. In addition, qPCR, colony formation and transwell assays were performed to validate functions of m6A-associated lncRNAs.

RESULTS

Nineteen m6A-modified lncRNAs in LUAD were identified. LUAD patients were divided into two categories based on the expression of 19 m6A-related lncRNAs. Cluster 2 patients had better antigen production and expression, while naive B cells, plasma cells, and activated NK cells were lower in cluster 1. Nine m6A-related lncRNAs were selected to establish a risk model for evaluating the prognosis of LUAD patients. The high-risk group had higher tumor mutational burden and lower TIDE scores with more gamma delta T cells and neutrophils. Nomograms showed that the prognostic model had predominant predictive ability for LUAD patients based on the risk score analyzed by the decision tree model. Benzo(a)pyrene and neurodazine might improve the prognosis of LUAD patients. The qRT-PCR results confirmed the reliability of the analytical results.

CONCLUSION

The establishment of a prognostic model of m6A-related lncRNAs can independently predict overall survival in LUAD and may help to develop personalized immunotherapy strategies.

Enlightening epigenetics: optochemical tools illuminate the path

Optochemical tools have become potent instruments for understanding biological processes at the molecular level, and the past decade has witnessed their use in epigenetics and epitranscriptomics (also known as RNA epigenetics) for deciphering gene expression regulation. By using photoresponsive molecules such as photoswitches and photocages, researchers can achieve precise control over when and where specific events occur. Therefore, these are invaluable for studying both histone and nucleotide modifications and exploring disease-related mechanisms. We systematically report and assess current examples in the field, and identify open challenges and future directions. These outstanding proof-of-concept investigations will inspire other chemical biologists to participate in these emerging fields given the potential of photochromic molecules in research and biomedicine.

m6A Methylated Long Noncoding RNA LOC339803 Regulates Intestinal Inflammatory Response

Cytokine mediated sustained inflammation increases the risk to develop different complex chronic inflammatory diseases, but the implicated mechanisms remain unclear. Increasing evidence shows that long noncoding RNAs (lncRNAs) play key roles in the pathogenesis of inflammatory disorders, while inflammation associated variants are described to affect their function or essential RNA modifications as N6-methyladenosine (m6A) methylation, increasing predisposition to inflammatory diseases. Here, the functional implication of the intestinal inflammation associated lncRNA LOC339803 in the production of cytokines by intestinal epithelial cells is described. Allele-specific m6A methylation is found to affect YTHDC1 mediated protein binding affinity. LOC339803-YTHDC1 interaction dictates chromatin localization of LOC339803 ultimately inducing the expression of NFκB mediated proinflammatory cytokines and contributing to the development of intestinal inflammation. These findings are confirmed using human intestinal biopsy samples from different intestinal inflammatory conditions and controls. Additionally, it is demonstrated that LOC339803 targeting can be a useful strategy for the amelioration of intestinal inflammation in vitro and ex vivo. Overall, the results support the importance of the methylated LOC339803 lncRNA as a mediator of intestinal inflammation, explaining genetic susceptibility and presenting this lncRNA as a potential novel therapeutic target for the treatment of inflammatory intestinal disorders.

RNA m6a Methylation Regulator Expression in Castration-Resistant Prostate Cancer Progression and Its Genetic Associations

N6-methyladenosine (m6A) methylation, a prevalent epitranscriptomic modification, plays a crucial role in regulating mRNA expression, stability, and translation in mammals. M6A regulators have gained attention for their potential implications in tumorigenesis and clinical applications, such as cancer diagnosis and therapeutics. The existing literature predominantly addresses m6A regulators in the context of primary prostate cancer (PCa). However, a notable gap in the knowledge emerges regarding the dynamic expression patterns of these regulators as PCa progresses towards the castration-resistant stage (CRPC). Employing sequential window acquisition of all theoretical mass spectra (SWATH-MS) and RNAseq analysis, we comprehensively profiled the expression of 27 m6A regulators in hormone/androgen-dependent and -independent PCa cell lines, revealing distinct clustering between tumor and adjacent normal prostate tissues. High-grade PCa tumors demonstrated the upregulation of METTL3, RBM15B, and HNRNAPA2B1 and the downregulation of ZC3H13, NUDT21, and FTO. Notably, we identified six m6A regulators associated with PCa survival. Additionally, association analysis of the PCa-associated risk loci in the cancer genome atlas program (TCGA) data unveiled genetic variations near the WTAP, HNRNPA2B1, and FTO genes as significant expression quantitative trait loci. In summary, our study unraveled abnormalities in m6A regulator expression in PCa progression, elucidating their association with PCa risk loci. Considering the heterogeneity within the PCa phenotypes and treatment responses, our findings suggest that prognostic stratification based on m6A regulator expression could enhance PCa diagnosis and prognosis.

m6A methylation modification and immune infiltration analysis in osteonecrosis of the femoral head

Osteonecrosis of the femoral head (ONFH) is a elaborate hip disease characterized by collapse of femoral head and osteoarthritis. RNA N6-methyladenosine (m6A) plays a crucial role in a lot of biological processes within eukaryotic cells. However, the role of m6A in the regulation of ONFH remains unclear. In this study, we identified the m6A regulators in ONFH and performed subtype classification. We identified 7 significantly differentially expressed m6A regulators through the analysis of differences between ONFH and normal samples in the Gene Expression Omnibus (GEO) database. A random forest algorithm was employed to monitor these regulators to assess the risk of developing ONFH. We constructed a nomogram based on these 7 regulators. The decision curve analysis suggested that patients can benefit from the nomogram model. We classified the ONFH samples into two m6A models according to these 7 regulators through consensus clustering algorithm. After that, we evaluated those two m6A patterns using principal component analysis. We assessed the scores of those two m6A patterns and their relationship with immune infiltration. We observed a higher m6A score of type A than that of type B. Finally, we performed a cross-validation of crucial m6A regulatory factors in ONFH using external datasets and femoral head bone samples. In conclusion, we believed that the m6A pattern could provide a novel diagnostic strategy and offer new insights for molecularly targeted therapy of ONFH.

Long non-coding RNA GATA6-AS1 is mediated by N6-methyladenosine methylation and inhibits the proliferation and metastasis of gastric cancer

BACKGROUND

Through experimental research on the biological function of GATA6-AS1, it was confirmed that GATA6-AS1 can inhibit the proliferation, invasion, and migration of gastric cancer cells, suggesting that GATA6-AS1 plays a role as an anti-oncogene in the occurrence and development of gastric cancer. Further experiments confirmed that the overexpression of fat mass and obesity-associated protein (FTO) inhibited the expression of GATA6-AS1, thereby promoting the occurrence and development of gastric cancer.

AIM

To investigate the effects of GATA6-AS1 on the proliferation, invasion and migration of gastric cancer cells and its mechanism of action.

METHODS

We used bioinformatics methods to analyze the Cancer Genome Atlas (https://portal.gdc.cancer.gov/. The Cancer Genome Atlas) and download expression data for GATA6-AS1 in gastric cancer tissue and normal tissue. We also constructed a GATA6-AS1 lentivirus overexpression vector which was transfected into gastric cancer cells to investigate its effects on proliferation, migration and invasion, and thereby clarify the expression of GATA6-AS1 in gastric cancer and its biological role in the genesis and development of gastric cancer. Next, we used a database (http://starbase.sysu.edu.cn/starbase2/) to analysis GATA6-AS1 whether by m6A methylation modify regulation and predict the methyltransferases that may methylate GATA6-AS1. Furthermore, RNA immunoprecipitation experiments confirmed that GATA6-AS1 was able to bind to the m6A methylation modification enzyme. These data allowed us to clarify the ability of m6A methylase to influence the action of GATA6-AS1 and its role in the occurrence and development of gastric cancer.

RESULTS

Low expression levels of GATA6-AS1 were detected in gastric cancer. We also determined the effects of GATA6-AS1 overexpression on the biological function of gastric cancer cells. GATA6-AS1 had strong binding ability with the m6A demethylase FTO, which was expressed at high levels in gastric cancer and negatively correlated with the expression of GATA6-AS1. Following transfection with siRNA to knock down the expression of FTO, the expression levels of GATA6-AS1 were up-regulated. Finally, the proliferation, migration and invasion of gastric cancer cells were all inhibited following the knockdown of FTO expression.

CONCLUSION

During the occurrence and development of gastric cancer, the overexpression of FTO may inhibit the expression of GATA6-AS1, thus promoting the proliferation and metastasis of gastric cancer.

The m6A demethylases FTO and ALKBH5 aggravate the malignant progression of nasopharyngeal carcinoma by coregulating ARHGAP35

N6-methyladenosine (m6A) is an RNA modification that can be removed by demethylases [fat mass and obesity-associated protein (FTO) and AlkB homolog 5 (ALKBH5)], which regulate gene expression and cell function. We show that m6A levels and m6A demethylase levels are altered in nasopharyngeal carcinoma (NPC) tissues vs. normal tissues. High FTO and ALKBH5 predict a poor prognosis in NPC patients. Silencing FTO and ALKBH5 inhibited the malignant behavior of patient-derived NPC cells in a short time. However, as time progressed, the inhibitory effect of FTO or ALKBH5 was weakened, and the cosilencing of FTO and ALKBH5 maintained a better inhibitory effect. Combined transcriptome and m6A-seq analysis revealed a downstream target gene that was jointly regulated by FTO and ALKBH5 in NPC, and ARHGAP35 was chosen to do further study. The synergistic silencing of FTO and ALKBH5 increased the methylation level on the mRNA CDS of a new transcription factor (ARHGAP35) and positively regulate the protein coding capacity and mRNA stability of ARHGAP35, thus leading to increased expression of ARHGAP35 and inhibition of the malignant phenotype of tumor cells. Our study revealed that the growth and metastasis of NPC can be stably inhibited through synergistic silencing of the demethylases FTO and ALKBH5, which play a positive role in the treatment of NPC by regulating the downstream transcript ARHGAP35 and increasing its m6A level.

Discovery of a PROTAC degrader for METTL3-METTL14 complex

N6-methyladenosine (m6A) methylation is the most abundant type of RNA modification that is mainly catalyzed by the METTL3-METTL14 methyltransferase complex. This complex has been linked to multiple cancers and is considered a promising therapeutic target for acute myeloid leukemia (AML). However, only a few METTL3 inhibitors targeting the catalytic activity were developed recently. Here, we present the discovery of WD6305 as the potent and selective proteolysis-targeting chimera (PROTAC) degrader of METTL3-METTL14 complex. WD6305 suppresses m6A modification and the proliferation of AML cells, and promotes apoptosis much more effectively than its parent inhibitor. WD6305 also affects a variety of signaling pathways related to the development and proliferation of AML. Collectively, our study reveals PROTAC degradation of METTL3-METTL14 complex as a potential anti-leukemic strategy and provides desirable chemical tool for further understanding METTL3-METTL14 protein functions.

The essential roles of m6A modification in osteogenesis and common bone diseases

N6-methyladenosine (m6A) is the most prevalent modification in the eukaryotic transcriptome and has a wide range of functions in coding and noncoding RNAs. It affects the fate of the modified RNA, including its stability, splicing, and translation, and plays an important role in post-transcriptional regulation. Bones play a key role in supporting and protecting muscles and other organs, facilitating the movement of the organism, ensuring blood production, etc. Bone diseases such as osteoarthritis, osteoporosis, and bone tumors are serious public health problems. The processes of bone development and osteogenic differentiation require the precise regulation of gene expression through epigenetic mechanisms including histone, DNA, and RNA modifications. As a reversible dynamic epigenetic mark, m6A modifications affect nearly every important biological process, cellular component, and molecular function, including skeletal development and homeostasis. In recent years, studies have shown that m6A modification is involved in osteogenesis and bone-related diseases. In this review, we summarized the proteins involved in RNA m6A modification and the latest progress in elucidating the regulatory role of m6A modification in bone formation and stem cell directional differentiation. We also discussed the pathological roles and potential molecular mechanisms of m6A modification in bone-related diseases like osteoporosis and osteosarcoma and suggested potential areas for new strategies that could be used to prevent or treat bone defects and bone diseases.

YTHDC2 Retards Cell Proliferation and Triggers Apoptosis in Papillary Thyroid Cancer by Regulating CYLD-Mediated Inactivation of Akt Signaling

N6-Methyladenosine (m6A) mRNA methylation modification is regarded as an important mechanism involved in diverse physiological processes. YT521-B homology (YTH) domain family members are associated with the tumorigenesis of several cancers. However, the role of YTHDC2 in papillary thyroid cancer (PTC) progression remains unknown. Results showed that YTHDC1, YTHDF1, YTHDF2, and YTHDF3 showed no observable difference in thyroid cancer samples. YTHDC2 was significantly downregulated in thyroid cancer samples and cells. YTHDC2 inhibited cell proliferation in PTC cells. YTHDC2 elicited apoptosis in PTC cells, as demonstrated by the elevated expression of pro-apoptotic factors cl-caspase-3/caspase-3 and Bcl-2-associated (Bax), and the reduced anti-apoptotic B cell lymphoma-2 (Bcl-2) expression. There was a positive correlation between YTHDC2 and cylindromatosis (CYLD) expression based on GEPIA database. YTHDC2 increased CYLD expression in PTC cells. CYLD knockdown abolished the effects of YTHDC2 on PTC cell proliferation and apoptosis. Additionally, YTHDC2 inactivated the protein kinase B (Akt) pathway by increasing CYLD in PTC cells. Overall, YTHDC2 inhibited cell proliferation and induced apoptosis in PTC cells by regulating CYLD-mediated inactivation of Akt pathway.

FTO in Lung Cancer: Its Progression and Therapeutic Potential

One of the most fatal and frequent malignancies on the planet is lung cancer. Its occurrence and development are the results of multifactorial and multigenic interactions. In recent years, RNA N6-methyladenosine transferase (FTO) has gained significant attention in the field of oncology. FTO is the first RNA demethylase to be found to control target mRNA demethylation. The growth, proliferation, and metastasis of tumor cells are greatly influenced by FTO. Recent studies have found that imbalanced m6A methylation regulatory proteins can induce disruption of downstream RNA metabolism, strongly affecting tumor development. This paper provides an overview of the relationship between FTO and lung cancer, discussing the mechanisms by which FTO is involved in lung cancer and its potential clinical applications.

Identification of Key Genes Mediated by N6-Methyladenosine Methyltransferase METTL3 in Ischemic Stroke via Bioinformatics Analysis and Experiments

The N6-methyladenosine (m6A) methyltransferase METTL3 has been demonstrated to function in mediating m6A modification, but its role in ischemic stroke (IS) has not been fully elucidated. This study aimed to explore the downstream mechanism of METTL3-mediated m6A modification in IS. GSE16561 and GSE22255 were downloaded from the Gene Expression Omnibus database for analysis of differentially expressed genes (DEGs), and it was found that METTL3 mRNA was downregulated in IS. Then quantitative real-time polymerase chain reaction was used to verify the downregulation of METTL3 mRNA in the peripheral blood of IS patients and the cortexes of transient middle cerebral artery occlusion mice. By combining DEGs with the m6A-downregulated genes in GSE142386 which performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) on METTL3-deficient and control endothelial cells, a total of 131 genes were identified as the METTL3-mediated m6A-modified genes in IS. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the genes were mainly involved in cytokine-cytokine receptor interaction, MAPK signaling pathway and NF-kappa B signaling pathway. CTSS and SBK1 were further screened as the key METTL3-mediated m6A-modified genes by random forest model and PCR validation. The ROC curve analysis showed that the combination with CTSS and SBK1 was of good diagnostic value for IS, with the AUC of 0.810, sensitivity of 0.780, and specificity of 0.773. Overall, we found that METTL3-mediated m6A modification may influence the occurrence and development of IS by participating in inflammation-related biological processes, and two key m6A-modified genes mediated by METTL3 (CTSS and SBK1) can be used as diagnostic biomarkers for IS.

FTO: a critical role in obesity and obesity-related diseases

In recent years, obesity is a growing pandemic in the world and has likely contributed to increasing the incidence of obesity-related diseases. Fat mass and obesity-associated gene (FTO) is the first gene discovered which has a close connection with fat. Recent studies suggested that FTO gene has played an important role in the molecular mechanisms of many diseases. Obesity is considered to be a hereditary disease and can evoke many kinds of diseases, including polycystic ovary syndrome (PCOS), type 2 diabetes mellitus (T2DM), cancer, etc., whose exact possible molecular mechanisms responsible for the effect of FTO on obesity and obesity-related diseases remain largely unknown. In this review, we comprehensively discuss the correlation between FTO gene and obesity, cancer, PCOS, T2DM, as well as the molecular mechanism involved in these diseases.

m6A methyltransferase METTL3 contributes to sympathetic hyperactivity post-MI via promoting TRAF6-dependent mitochondrial ROS production

OBJECTIVES

N6-methyladenosine (m6A) is the most prevalent post-translational modification in eukaryotic mRNA. Recently, m6A editing modified by methyltransferase-like enzyme 3 (METTL3), the core m6A methyltransferase, has been demonstrated to be involved in cardiac sympathetic hyperactivity. This study aimed to clarify the effects and underlying mechanisms of METTL3 in the paraventricular nucleus (PVN) in mediating sympathetic activity following myocardial infarction (MI).

METHODS

We established rat MI models by left anterior descending coronary artery ligation. m6A quantification was performed.The expression of METTL3 and its downstream gene, tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6), were determined. The functional role of METTL3 in sympathetic hyperactivity and electrical conduction stability were verified by assessing renal sympathetic nerve activity (RSNA), norepinephrine (NE) levels, and programmed electrical stimulation. Rescue experiments were also conducted. The mechanism by which m6A is involved in mitochondrial reactive oxygen species (mROS) production, mediated by TRAF6/ECSIT pathway, was explored in lipopolysaccharide (LPS) treated primary microglial cells.

RESULTS

METTL3 was predominantly localized in the microglia and significantly increased within the PVN at 3 days post-MI. Inhibition of METTL3 decreased m6A levels, TRAF6 expression, and mROS production; downregulated sympathoexcitation, indicated by attenuated NE concentration and RSNA; decreased the incidence of ventricular tachycardia or fibrillation; and improved cardiac function. Mechanistically, downregulation of METTL3 prevented TRAF6 translocation to the mitochondria in the microglia and subsequent TRAF6/ECSIT pathway activation, resulting in decreased mROS production.

CONCLUSIONS

This study demonstrates that METTL3-mediated m6A modification promotes sympathetic hyperactivity through TRAF6/ECSIT pathway and mitochondrial oxidative stress in the PVN, thereby leading to ventricular arrhythmias post-MI.

Insights into RNA N6-methyladenosine in Glucose and Lipid Metabolic Diseases and Their Therapeutic Strategies

The incidence of glucose and lipid metabolism diseases, including type 2 diabetes, obesity, metabolic syndrome, and nonalcoholic fatty liver disease, is rising, which places an enormous burden on people around the world. However, the mechanism behind these disorders remains incompletely understood. N6-methyladenosine (m6A) is 1 type of posttranscriptional RNA modification, and research has shown that it plays a crucial role in several metabolic diseases. m6A methylation is reversibly and dynamically regulated by methyltransferases (writers), demethylases (erasers), and m6A binding proteins (readers). Dysregulation of RNA m6A modification is related to different metabolic processes. Targeting RNA m6A methylation is a potential treatment strategy for these chronic metabolic diseases. This review discusses studies on RNA m6A modification in metabolic diseases and existing therapeutic drugs, with the aim of providing a concise perspective on its potential applications in managing metabolic disorders.

Global m6A methylation and gene expression patterns in human microglial HMC3 cells infected with HIV-1

N6-methyladenosine (m6A) methylation of human immunodeficiency virus type 1 (HIV-1) RNA regulates viral replication, and the m6A of host RNA is affected by HIV-1 infection, but its global pattern and function are still unclear. In this study, we report that the number and position of m6A peaks in huge genes of human microglial HMC3 cells were modulated by a single cycle HIV-1 pseudotyped with VSV-G envelope glycoprotein infection using methylated RNA immunoprecipitation sequencing (MeRIP-seq). A conjoint analysis of MeRIP-seq and high-throughput sequencing for mRNA (RNA-seq) explored four groups of clearly classified genes, including 45 hyper-up (m6A-mRNA), 45 hyper-down, 120 hypo-up, and 54 hypo-down genes, in HIV-1 infected cells compared to uninfected ones. KEGG pathway analysis showed that these genes were mainly enriched in the Wnt and TNF signaling pathway, and cytokine-cytokine receptor interaction, which might be related to the immune response in HMC3 cells. And some of these genes might be associated with the pathway of axon guidance and neuroactive ligan-receptor interaction, which affect the neuronal state. However, the cognitive disorders caused by HIV-1 is associated with inflammatory changes that have not yet been well clarified. Furthermore, we confirmed the expression and m6A levels of four genes using RT-PCR and MeRIP-qPCR. Similar to the sequencing results, the expressions of these genes were significantly upregulated by HIV-1 infection. And the m6A level of IL-6 was downregulated, and those of HLA-B, CFB, and OLR1 were upregulated. These results suggest that HIV-1-induced changes in gene expression may be achieved through the regulation of methylation. Our study revealed the global m6A methylation and gene expression patterns under HIV-1 infection in human microglia, which might provide clues for understanding the interaction between HIV-1 and host cells and the cognitive disorders caused by HIV-1.

Construction of an m6A- and neutrophil extracellular traps-related lncRNA model to predict hepatocellular carcinoma prognosis and immune landscape

Purpose

To investigate the impact of N6-methyladenosine- (m6A) and neutrophil extracellular traps- (NETs) related lncRNAs (MNlncRNAs) on the prognosis of hepatocellular carcinoma (HCC).

Methods

We collected m6A and NETs-related genes from published studies. We identified the MNlncRNAs by correlation analysis. Cox regression and the least absolute selection operator (LASSO) method were used to select predictive MNlncRNAs. The expressions of predictive MNlncRNAs were detected by cell and tissue experiments. Survival, medication sensitivity, and immunological microenvironment evaluations were used to assess the model's prognostic utility. Finally, we performed cellular experiments to further validate the model's prognostic reliability.

Results

We obtained a total of 209 MNlncRNAs. 7 MNlncRNAs comprised the prognostic model, which successfully stratifies HCC patients, with the area under the curve (AUC) ranging from 0.7 to 0.8. In vitro tests confirmed that higher risk patients had worse prognosis. Risk score, immunological microenvironment, and immune checkpoint gene expression were all significantly correlated with each other in HCC. In the group at high risk, immunotherapy could be more successful. Cellular assays confirmed that HCC cells with high risk scores have a higher proliferation and invasive capacity.

Conclusion

The MNlncRNAs-related prognostic model aided in determining HCC prognosis, revealing novel therapeutic options, notably immunotherapy.

The synergistic effect of EMT regulators and m6A modification on prognosis-related immunological signatures for ovarian cancer

Recently, there has been growing interest among researchers in exploring the effects of epithelial-mesenchymal transformation (EMT) or N6-Methyladenosine (m6A) modification regulators on tumor development. However, the synergistic efficiency of these regulators in relation to ovarian cancer development remains unclear. This study aims to explore the transcription patterns of main regulators, including 19 EMT and 22 m6A, in ovarian cancer samples from TCGA datasets and normal samples from GTEx datasets. After conducting a LASSO regression analysis, ten prognostic signatures were identified, namely KIAA1429, WTAP, SNAI1, AXL, IGF2BP1, ELAVL1, CBLL1, CDH2, NANOG and ALKBH5. These signatures were found to have a comprehensive effect on immune infiltrating signatures and the final prognostic outcome. Next, utilizing the ssGSEA algorithm and conducting overall survival analyses, we have identified the key prognosis-related immunological signatures in ovarian cancer to be ALKBH5, WTAP, ELAVL1, and CDH2 as the regulators. The characteristic immune response and related genetic expression have revealed a significant correlation between the alteration of m6A regulators and EMT regulators, indicating a synergistic effect between these two factors in the development of ovarian cancer. In summary, our research offers a novel perspective and strategy to enhance the occurrence, progression, and prognosis of ovarian cancer.

The deficiency of N6-methyladenosine demethylase ALKBH5 enhances the neurodegenerative damage induced by cobalt

Cobalt exposure, even at low concentrations, induces neurodegenerative damage, such as Alzheimer's disease (AD). The specific underlying mechanisms remain unclear. Our previous study demonstrated that m⁶A methylation alteration is involved in cobalt-induced neurodegenerative damage, such as in AD. However, the role of m⁶A RNA methylation and its underlying mechanisms are poorly understood. In this study, both epidemiological and laboratory studies showed that cobalt exposure could downregulate the expression of the m⁶A demethylase ALKBH5, suggesting a key role for ALKBH5. Moreover, Methylated RNA immunoprecipitation and sequencing (MeRIP-seq) analysis revealed that ALKBH5 deficiency is associated with neurodegenerative diseases. KEGG pathway and Gene ontology analyses further revealed that the differentially m⁶A-modified genes resulting from ALKBH5 downregulation and cobalt exposure were aggregated in the pathways of proliferation, apoptosis, and autophagy. Subsequently, ALKBH5 deficiency was shown to exacerbate cell viability decline, motivate cell apoptosis and attenuate cell autophagy induced by cobalt with experimental techniques of gene overexpression/inhibition. In addition, morphological changes in neurons and the expression of AD-related proteins, such as APP, P-Tau, and Tau, in the cerebral hippocampus of wild-type and ALKBH5 knockout mice after chronic cobalt exposure were also investigated. Both in vitro and in vivo results showed that lower expression of ALKBH5 aggravated cobalt-induced neurodegenerative damage. These results suggest that ALKBH5, as an epigenetic regulator, could be a potential target for alleviating cobalt-induced neurodegenerative damage. In addition, we propose a novel strategy for the prevention and treatment of environmental toxicant-related neurodegeneration from an epigenetic perspective.

N6-methyladenosine RNA modification regulates cotton drought response in a Ca2+ and ABA-dependent manner

N⁶ -methyladenosine (m⁶ A) is the most prevalent internal modification present in mRNAs, and is considered to participate in a range of developmental and biological processes. Drought response is highly regulated at the genomic, transcriptional and post-transcriptional levels. However, the biological function and regulatory mechanism of m⁶ A modification in the drought stress response is still poorly understood. We generated a transcriptome-wide m⁶ A map using drought-resistant and drought-sensitive varieties of cotton under different water deficient conditions to uncover patterns of m⁶ A methylation in cotton response to drought stress. The results reveal that m⁶ A represents a common modification and exhibit dramatic changes in distribution during drought stress. More 5'UTR m⁶ A was deposited in the drought-resistant variety and was associated with a positive effect on drought resistance by regulating mRNA abundance. Interestingly, we observed that increased m⁶ A abundance was associated with increased mRNA abundance under drought, contributing to drought resistance, and vice versa. The demethylase GhALKBH10B was found to decrease m⁶ A levels, facilitating the mRNA decay of ABA signal-related genes (GhZEP, GhNCED4 and GhPP2CA) and Ca²⁺ signal-related genes (GhECA1, GhCNGC4, GhANN1 and GhCML13), and mutation of GhALKBH10B enhanced drought resistance at seedling stage in cotton. Virus-induced gene silencing (VIGS) of two Ca²⁺ -related genes, GhECA1 and GhCNGC4, reduced drought resistance with the decreased m⁶ A enrichment on silenced genes in cotton. Collectively, we reveal a novel mechanism of post-transcriptional modification involved in affecting drought response in cotton, by mediating m⁶ A methylation on targeted transcripts in the ABA and Ca²⁺ signalling transduction pathways.

m6A methyltransferase METTL3 facilitates multiple myeloma cell growth through the m6A modification of BZW2

N6-methyladenosine (m6A) methyltransferase-like 3 (METTL3) has been confirmed to be involved in multiple myeloma (MM) progression, and basic leucine zipper and W2 domains 2 (BZW2) is considered to be a regulator for MM development. However, whether METTL3 mediates MM progression by regulating BZW2 remains unclear. The messenger RNA (mRNA) and protein levels of METTL3 and BZW2 in MM specimens and cells were determined using quantitative real-time PCR and western blot analysis. Cell proliferation and apoptosis were assessed by cell counting kit 8 assay, 5-ethynyl-2'-deoxyuridine assay, colony formation assay, and flow cytometry. Methylated RNA immunoprecipitation-qPCR was used to detect the m6A modification level of BZW2. Xenograft tumor models were constructed to confirm the effect of METTL3 knockdown on MM tumor growth in vivo. Our results showed that BZW2 was upregulated in MM bone marrow specimens and cells. BZW2 downregulation reduced MM cell proliferation and promoted apoptosis, while its overexpression enhanced MM cell proliferation and inhibited apoptosis. METTL3 was highly expressed in MM bone marrow specimens, and its expression was positively correlated with BZW2 expression. BZW2 expression was positively regulated by METTL3. Mechanistically, METTL3 could upregulate BZW2 expression by modulating its m6A modification. Additionally, METTL3 accelerated MM cell proliferation and restrained apoptosis via increasing BZW2 expression. In vivo experiments showed that METTL3 knockdown reduced MM tumor growth by decreasing BZW2 expression. In conclusion, these data indicated that METTL3-mediated the m6A methylation of BZW2 to promote MM progression, suggesting a novel therapeutic target for MM.

Methyltransferase-like 3 promotes cervical cancer metastasis by enhancing cathepsin L mRNA stability in an N6-methyladenosine-dependent manner

N6-methyladenosine (m6A) is a highly abundant RNA modification in eukaryotic cells. Methyltransferase-like 3 (METTL3), a major protein in the m6A methyltransferase complex, plays important roles in many malignancies, but its role in cervical cancer metastasis remains uncertain. Here, we found that METTL3 was significantly upregulated in cervical cancer tissue, and its upregulation was associated with a poor prognosis in cervical cancer patients. Knockdown of METTL3 significantly reduced cervical cancer cell migration and invasion. Conversely, METTL3 overexpression markedly promoted cervical cancer cell metastasis in vitro and in vivo. Furthermore, METTL3 mediated the m6A modification of cathepsin L (CTSL) mRNA at the 5'-UTR, and the m6A reader protein insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) bound to the m6A sites and enhanced CTSL mRNA stability. Our results indicated that METTL3 enhanced CTSL mRNA stability through an m6A-IGF2BP2-dependent mechanism, thereby promoting cervical cancer cell metastasis. These findings provide insights into a novel m6A modification pattern involved in cervical cancer development.

N6-methylation of RNA-bound adenosine regulator HNRNPC promotes vascular endothelial dysfunction in type 2 diabetes mellitus by activating the PSEN1-mediated Notch pathway

AIM

The regulatory mechanism of m6A regulators in vascular endothelial function of type 2 diabetes mellitus (T2DM) remains largely unknown. We addressed this issue based on the data retrieved Gene Expression Omnibus (GEO) database and experimental validations.

METHODS

Expression of m6A methylation regulators was evaluated in T2DM samples of GSE76894 dataset and GSE156341 dataset. Further analysis of candidate m6A methylation regulators was conducted in the thoracic aorta of db/db mice and high glucose (HG)-induced human umbilical vein endothelial cells (HUVECs). Ectopic expression and depletion experiments were conducted to detect effects of m6A methylation regulators on vascular endothelial function in T2DM.

RESULTS

It emerged that three m6A methylation regulators (HNRNPC, RBM15B, and ZC3H13) were highly expressed in T2DM, which were related to vascular EC function, showing diagnostic values for T2DM. HNRNPC expression in the thoracic aorta of db/db mice was higher than that in heterozygous db mice, and HNRNPC expression in HG-induced HUVECs was upregulated when compared with normal glucose-exposed HUVECs. Furthermore, HNRNPC activated PSEN1-dependent Notch pathway to induce eNOS inactivation and NO production decrease, thereby causing vascular endothelial dysfunction in T2DM.

CONCLUSIONS

HNRNPC impaired vascular endothelial function to enhance the development of vascular complications in T2DM through PSEN1-mediated Notch signaling pathway.

Identification and experimental validation of key m6A modification regulators as potential biomarkers of osteoporosis

Osteoporosis (OP) is a severe systemic bone metabolic disease that occurs worldwide. During the coronavirus pandemic, prioritization of urgent services and delay of elective care attenuated routine screening and monitoring of OP patients. There is an urgent need for novel and effective screening diagnostic biomarkers that require minimal technical and time investments. Several studies have indicated that N6-methyladenosine (m6A) regulators play essential roles in metabolic diseases, including OP. The aim of this study was to identify key m6A regulators as biomarkers of OP through gene expression data analysis and experimental verification. GSE56815 dataset was served as the training dataset for 40 women with high bone mineral density (BMD) and 40 women with low BMD. The expression levels of 14 major m6A regulators were analyzed to screen for differentially expressed m6A regulators in the two groups. The impact of m6A modification on bone metabolism microenvironment characteristics was explored, including osteoblast-related and osteoclast-related gene sets. Most m6A regulators and bone metabolism-related gene sets were dysregulated in the low-BMD samples, and their relationship was also tightly linked. In addition, consensus cluster analysis was performed, and two distinct m6A modification patterns were identified in the low-BMD samples. Subsequently, by univariate and multivariate logistic regression analyses, we identified four key m6A regulators, namely, METTL16, CBLL1, FTO, and YTHDF2. We built a diagnostic model based on the four m6A regulators. CBLL1 and YTHDF2 were protective factors, whereas METTL16 and FTO were risk factors, and the ROC curve and test dataset validated that this model had moderate accuracy in distinguishing high- and low-BMD samples. Furthermore, a regulatory network was constructed of the four hub m6A regulators and 26 m6A target bone metabolism-related genes, which enhanced our understanding of the regulatory mechanisms of m6A modification in OP. Finally, the expression of the four key m6A regulators was validated in vivo and in vitro, which is consistent with the bioinformatic analysis results. Our findings identified four key m6A regulators that are essential for bone metabolism and have specific diagnostic value in OP. These modules could be used as biomarkers of OP in the future.

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.

m6A methylation: Critical roles in aging and neurological diseases

N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic cells, which participates in the functional regulation of various biological processes. It regulates the expression of targeted genes by affecting RNA translocation, alternative splicing, maturation, stability, and degradation. As recent evidence shows, of all organs, brain has the highest abundance of m6A methylation of RNAs, which indicates its regulating role in central nervous system (CNS) development and the remodeling of the cerebrovascular system. Recent studies have shown that altered m6A levels are crucial in the aging process and the onset and progression of age-related diseases. Considering that the incidence of cerebrovascular and degenerative neurologic diseases increase with aging, the importance of m6A in neurological manifestations cannot be ignored. In this manuscript, we focus on the role of m6A methylation in aging and neurological manifestations, hoping to provide a new direction for the molecular mechanism and novel therapeutic targets.

N6-methyladenosine modulation classes and immune microenvironment regulation in ischemic stroke

N6-methyladenosine (m6A) modifications play an important role in the differentiation and regulation of immune cells. However, research on m6A in ischemic stroke (IS) is still in its infancy, and their role of the immune microenvironment remains unknown. In this study, we systematically assessed the modification classes of m6A regulators in IS based on the GEO database (GSE16561 and GSE22255). We found that in IS patients, IGF2BP2, IGF2BP1, and YTHDF2 expression was significantly upregulated, and ELAVL1, LRPPRC, METTL3, ALKBH5, CBLL1, and METTL14 expression was significantly downregulated. Seven IS-related genes (ELAVL1, IGF2BP2, LRPPRC, YTHDF2, ALKBH5, METTL14, and YTHDC1) were finally screened by logistic and least absolute shrinkage and selection operator (LASSO) regressions, and the AUC of the riskScore was 0.942, which was a good classification. For immune infiltration, there were highly significant differences in memory B cells, CD8 T cells, monocytes, activated dendritic cells, and mast cells between IS and normal samples. The IS samples were grouped into three classes by consistent clustering, and 15 m6A genes were differentially expressed in the different classes. Multiple infiltrating immune cells, immune-associated genes, and HLA-associated genes differed significantly across m6A modification classes, indicating the diversity and complexity of m6A modifications in the immune microenvironment of IS. Finally, 487 genes associated with the m6A modification class were identified, and 227 potential drugs were found. Our findings demonstrated that m6A modification plays a crucial role in the immune regulation of IS.

Breast cancer combined prognostic model based on lactate metabolism genes

To investigate the impact of lactate metabolism genes, lactate metabolism-related genes (LMRG), and immune infiltrating cells on the prognosis of breast cancer. LMRG was identified via single-cell sequencing. Immune cell infiltration was obtained by the CIBERSORT method. The prognostic genes were chosen by cox regression and the least absolute selection operator approach. lactate metabolism-associated immune-infiltrating cells was determined by difference analysis. The GSE20685 dataset was used as an external validation cohort. The model's prognostic usefulness was evaluated utilizing survival, immunological microenvironment, and drug sensitivity assessments. NDUFAF6 was most associated with breast cancer prognosis. We obtained a total of 450 LMRG. SUSD3, IL18, MAL2, and CDKN1C comprised the Model2. NK cell activation was most relevant to lactate metabolism. The combined prognostic model outperformed the individual model, with the area under the curve ranging from 0.7 to 0.8 in all three cohorts. The lactate metabolism-related combination model assisted in evaluating breast cancer prognosis, providing new insights for treatment, particularly immunotherapy.

The Intricate Interplay between the ZNF217 Oncogene and Epigenetic Processes Shapes Tumor Progression

The oncogenic transcription factor ZNF217 orchestrates several molecular signaling networks to reprogram integrated circuits governing hallmark capabilities within cancer cells. High levels of ZNF217 expression provide advantages to a specific subset of cancer cells to reprogram tumor progression, drug resistance and cancer cell plasticity. ZNF217 expression level, thus, provides a powerful biomarker of poor prognosis and a predictive biomarker for anticancer therapies. Cancer epigenetic mechanisms are well known to support the acquisition of hallmark characteristics during oncogenesis. However, the complex interactions between ZNF217 and epigenetic processes have been poorly appreciated. Deregulated DNA methylation status at ZNF217 locus or an intricate cross-talk between ZNF217 and noncoding RNA networks could explain aberrant ZNF217 expression levels in a cancer cell context. On the other hand, the ZNF217 protein controls gene expression signatures and molecular signaling for tumor progression by tuning DNA methylation status at key promoters by interfering with noncoding RNAs or by refining the epitranscriptome. Altogether, this review focuses on the recent advances in the understanding of ZNF217 collaboration with epigenetics processes to orchestrate oncogenesis. We also discuss the exciting burgeoning translational medicine and candidate therapeutic strategies emerging from those recent findings connecting ZNF217 to epigenetic deregulation in cancer.

RNA Modifications Meet Tumors

RNA modifications occur through the whole process of gene expression regulation, including transcription, translation, and post-translational processes. They are closely associated with gene expression, RNA stability, and cell cycle. RNA modifications in tumor cells play a vital role in tumor development and metastasis, changes in the tumor microenvironment, drug resistance in tumors, construction of tumor cell-cell "internet", etc. Several types of RNA modifications have been identified to date and have various effects on the biological characteristics of different tumors. In this review, we discussed the function of RNA modifications, including N 6-methyladenine (m6A), 5-methylcytosine (m5C), N 7-methyladenosine (m7G), N 1-methyladenosine (m1A), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I), in the microenvironment and therapy of solid and liquid tumors.

Alteration of the N6-methyladenosine epitranscriptomic profile in synthetic phthalate-treated human induced pluripotent stem cell-derived endothelial cells

Background: This study aimed to characterize the N6-methyladenosine epitranscriptomic profile induced by mono(2-ethylhexyl) phthalate (MEHP) exposure using a human-induced pluripotent stem cell-derived endothelial cell model. Methods: A multiomic approach was employed by performing RNA sequencing in parallel with an N6-methyladenosine-specific microarray to identify mRNAs, lncRNAs, and miRNAs affected by MEHP exposure. Results: An integrative multiomic analysis identified relevant biological features affected by MEHP, while functional assays provided a phenotypic characterization of these effects. Transcripts regulated by the epitranscriptome were validated with quantitative PCR and methylated RNA immunoprecipitation. Conclusion: The authors' profiling of the epitranscriptome expands the scope of toxicological insights into known environmental toxins to under surveyed cellular contexts and emerging domains of regulation and is, therefore, a valuable resource to human health.

H H, Bharathavikru RS. Resetting the epigenome: Methylation dynamics in cancer stem cells

The molecular mechanisms that regulate stem cell pluripotency and differentiation has shown the crucial role that methylation plays in this process. DNA methylation has been shown to be important in the context of developmental pathways, and the role of histone methylation in establishment of the bivalent state of genes is equally important. Recent studies have shed light on the role of RNA methylation changes in stem cell biology. The dynamicity of these methylation changes not only regulates the effective maintenance of pluripotency or differentiation, but also provides an amenable platform for perturbation by cellular stress pathways that are inherent in immune responses such as inflammation or oncogenic programs involving cancer stem cells. We summarize the recent research on the role of methylation dynamics and how it is reset during differentiation and de-differentiation.

Critical role of m6A modification in T-helper cell disorders

Diseases with T-helper cell subset imbalance involve multiple systems and organs. In addition to this, the pathogenesis of these diseases is always complex, and involves Th1, Th2, Th9, Th17, Th22, and Tfh cells. T-helper cell subset imbalance mediates immune responses to various pathogenic factors, by secreting specific cytokines. Although several studies have revealed the specific mechanisms of the occurrence and development of these diseases from different aspects, there is still a need for more comprehensive and in-depth studies that can compensate for the corresponding gaps in the diagnosis, targeted therapy, and prognosis of these diseases. N6-methyladenosine(m⁶A) modification is the most prevalent and abundant post-transcriptional modification in eukaryotic RNAs. In recent years, the critical role of m⁶A modification has been confirmed in multiple diseases with T-helper cell subset imbalance. m⁶A modification affects the immune cell development, inflammatory processes, biological behaviour of tumours, and immune response in these diseases. In this review, we focussed on how the enzymes involved in m⁶A modification, directly or indirectly, influence the pathogenesis and phenotype of various diseases with T-helper cell subset imbalance, and could therefore, serve as potential diagnostic markers and therapeutic targets for these diseases. In addition, this review also discusses the focus of future research in this area. Finally, we summarise the prospects of m⁶A modification in immunotherapy and chemotherapy.

m6A regulator-mediated RNA methylation modification patterns are involved in immune microenvironment regulation of coronary heart disease

Background

Although the roles of m6A modification in the immune responses to human diseases have been increasingly revealed, their roles in immune microenvironment regulation in coronary heart disease (CHD) are poorly understood.

Methods

The GSE20680 and GSE20681 datasets related to CHD were acquired from the Gene Expression Omnibus (GEO) database. A total of 30 m6A regulators were used to perform LASSO regression to identify the significant genes involved in CHD. Unsupervised clustering analysis was conducted using the m6A regulators to distinguish the m6A RNA methylation patterns in patients with CHD. The differentially expressed genes (DEGs) and biological characteristics, including GO and KEGG enrichment results, were assessed for the different m6A patterns to analyse the impacts of m6A regulators on CHD. Hub genes were identified, and subsequent microRNAs-mRNAs (miRNAs–mRNAs) and mRNAs-transcriptional factors (mRNA-TFs) interaction networks were constructed by the protein and protein interaction (PPI) network method using Cytoscape software. The infiltrating proportion of immune cells was assessed by ssGSEA and the CIBERSORT algorithm. Quantitative real-time PCR (qRT-PCR) was performed to detect the expression of the significant m6A regulators and hub genes.

Results

Four of 30 m6A regulators (HNRNPC, YTHDC2, YTHDF3, and ZC3H13) were identified to be significant in the development of CHD. Two m6A RNA methylation clusters were distinguished by unsupervised clustering analysis based on the expression of the 30 m6A regulators. A total of 491 genes were identified as DEGs between the two clusters. A PPI network including 308 mRNAs corresponding to proteins was constructed, and 30 genes were identified as hub genes that were enriched in the bioprocesses of peptide cross-linking, keratinocyte differentiation. Twenty-seven hub genes were found to be related to miRNAs, and seven hub genes were found to be related to TFs. Moreover, among the 30 hub genes, eight genes were found to be upregulated in CHD, and three were found to be downregulated in CHD compared to the normal people. The high m6A modification pattern was associated with a higher infiltrated abundance of immune cells.

Conclusion

Our findings demonstrated that m6A modification plays crucial roles in the diversity and complexity of the immune microenvironment in CHD.

Alteration of N6-methyladenosine epitranscriptome profiles in bilateral ureteral obstruction-induced obstructive nephropathy in juvenile rats

BACKGROUND

Urinary tract obstruction is a common cause of renal failure in children and infants, and the pathophysiological mechanisms of obstructive nephropathy are largely unclear. It has been reported that m6A modulation is involved in renal injury. However, whether m6A RNA modulation is associated with obstructive nephropathy has not yet been reported. The aim of this study was to investigate the m6A epitranscriptome profiles in the kidneys of bilateral ureteral obstruction (BUO) in young rats.

METHODS

The total level of m6A in the kidneys was measured by liquid chromatography-tandem mass spectrometry. The mRNAs of related genes were detected by real-time PCR. Methylated RNA immunoprecipitation sequencing was performed to map the epitranscriptome-wide m6A profile.

RESULTS

Global m6A levels were increased after BUO, and the mRNA expression levels of m6A methyltransferases and demethylases were significantly decreased in BUO group rat kidneys; the expression levels of EGFR and Brcal were significantly upregulated, while the mRNA expression levels of Notch1 were downregulated (P < 0.05). A total of 154 genes associated with 163 m6A peaks were identified.

CONCLUSION

The m6A epitranscriptome was significantly altered in BUO rat kidneys, which is potentially implicated in the pathophysiological processes of obstructive nephropathy.

IMPACT

The m6A RNA modification was associated with the process of renal injury in ureteral obstructive nephropathy by participating in multiple dimensions. The dysregulation of m6A methyltransferases and demethylases may be related to the pathophysiological changes of BUO-induced obstructive nephropathy. The m6A RNA modulation of the genes EGFR, Brca1, and Notch1 that were related to the regulation of aquaporin2 might be the potential mechanism for the polyuresis after ureteral obstruction.

m6A-Regulator Expression Signatures Identify a Subset of Follicular Lymphoma Harboring an Exhausted Tumor Microenvironment

The role of N6-methyladenosine (m6A) modification in tumor microenvironment has rarely been explored in follicular lymphoma (FL). To examine the role of m6A modification in biological behavior, especially the immune landscape of FL, we utilized the Gene Expression Omnibus database to determine the expression signatures of m6A-regulators by unsupervised clustering, and then condense into a risk score, which was validated in an external cohort from the Tianjin Medical University Cancer Institute and Hospital. Finally, 16 m6A-regulators in 351 FL patients were evaluated and two m6A clusters were identified, characterized by differences in prognosis and biological behaviors. The m6A score was further developed based on 20-genes to quantify the m6A-regulator expression signature in each patient with FL. The low m6A score was associated with inferior prognosis of patients, with a median survival time of 8.84 (95% confidence interval [CI]: 7.251-10.429) years, which was remarkably shorter than that of patients with high m6A scores (15.73 years, 95% CI: 11.729-19.731; p&lt;0.0001). Genes like TNFRSF14, CREBBP, and CARD11 were shown to be more often mutated in the low m6A group. This group was enriched with immune/inflammatory response but along with the abundant infiltration of exhausted T cells and the upregulated PD-1 and PD-L1 expression. Finally, we verified the m6A score could predict the response to anti-PD-L1 antibodies in an immunotherapy cohort. To conclude, the m6A score recognizes a section of FL patients harboring an exhausted tumor microenvironment and may help guide more effective immunotherapy strategies for patients with FL.

Ibuprofen promotes p75 neurotrophin receptor expression through modifying promoter methylation and N6-methyladenosine-RNA-methylation in human gastric cancer cells

It is acknowledged that nonsteroidal anti-inflammatory drugs (NSAIDs) can participate in various signaling pathways, while information about their epigenetic effects are limited. p75NTR (p75 neurotrophin receptor) can inhibit tumor growth by inducing cell cycle arrest and regulating cell cycle arrest and apoptotic cell death. The expression of p75NTR is influenced by epigenetic roles. We explored the effects of ibuprofen on p75NTR expression and investigated whether promoter methylation and N6-methyladenosine (m6A) RNA methylation regulates this process in human gastric cancer cells (SGC7901 and MKN45). Cell lines were treated with ibuprofen 0, 2.5, 5, 10, 20 µM, and then DNA, RNA, and protein were isolated 24 h later. Expression and promoter methylation of p75NTR were detected by RT-qPCR and Western blot. The levels of m6A-p75NTR were measured by RNA immunoprecipitation. We also used RT-qPCR to determine the levels of m6A-related regulators, METTL3, METTL14, ALKBH5, FTO, YTHDC2, and YTHDF1-3. Ibuprofen attenuated p75NTR promoter methylation (p < 0.01) and increased p75NTR level (p < 0.001). Ibuprofen increased m6A-p53 expression (p < 0.01) by promoting the expression of METTL3 (p < 0.01) and METTL14 (p < 0.05); and increased levels of YTHDF1 (p < 0.001), YTHDF3 (p < 0.001), and YTHDC2 (p < 0.01) that finally reinforced p53 translation (p < 0.01). Therefore, our results present that ibuprofen epigenetically increased p75NTR expression by downregulating promoter methylation and upregulating m6A-RNA-methylation in SGC7901 and MKN45 cells. Our study unveils a novel mechanism for p75NTR regulation by NSAIDs and helps the design of treatment targets.

Inhibition of METTL3 attenuates renal injury and inflammation by alleviating TAB3 m6A modifications via IGF2BP2-dependent mechanisms

The role of N⁶-methyladenosine (m6A) modifications in renal diseases is largely unknown. Here, we characterized the role of N⁶-adenosine-methyltransferase-like 3 (METTL3), whose expression is elevated in renal tubules in different acute kidney injury (AKI) models as well as in human biopsies and cultured tubular epithelial cells (TECs). METTL3 silencing alleviated renal inflammation and programmed cell death in TECs in response to stimulation by tumor necrosis factor-α (TNF-α), cisplatin, and lipopolysaccharide (LPS), whereas METTL3 overexpression had the opposite effects. Conditional knockout of METTL3 from mouse kidneys attenuated cisplatin- and ischemic/reperfusion (I/R)-induced renal dysfunction, injury, and inflammation. Moreover, TAB3 [TGF-β-activated kinase 1 (MAP3K7) binding protein 3] was identified as a target of METTL3 by m6A methylated RNA immunoprecipitation sequencing and RNA sequencing. The stability of TAB3 was increased through binding of IGF2BP2 (insulin-like growth factor 2 binding protein 2) to its m6A-modified stop codon regions. The proinflammatory effects of TAB3 were then explored both in vitro and in vivo. Adeno-associated virus 9 (AAV9)-mediated METTL3 silencing attenuated renal injury and inflammation in cisplatin- and LPS-induced AKI mouse models. We further identified Cpd-564 as a METTL3 inhibitor that had better protective effects against cisplatin- and ischemia/reperfusion-induced renal injury and inflammation than S-adenosyl-l-homocysteine, a previously identified METTL3 inhibitor. Collectively, METTL3 promoted m6A modifications of TAB3 and enhanced its stability via IGF2BP2-dependent mechanisms. Both genetic and pharmacological inhibition of METTL3 attenuated renal injury and inflammation, suggesting that the METTL3/TAB3 axis is a potential target for treatment of AKI.

Impact of Nutrition on Age-Related Epigenetic RNA Modifications in Rats

Nutrition plastically modulates the epigenetic landscape in various tissues of an organism during life via epigenetic changes. In the present study, to clarify whether this modulation involves RNA methylation, we evaluated global RNA methylation profiles and the expression of writer, reader, and eraser genes, encoding for enzymes involved in the RNA methylation. The study was carried out in the heart, liver, and kidney samples from rats of different ages in response to a low-calorie diet. We found that, although each tissue showed peculiar RNA methylation levels, a general increase in these levels was observed throughout the lifespan as well as in response to the six-month diet. Similarly, a prominent remodeling of the expression of writer, reader, and eraser genes emerged. Our data provide a comprehensive overview of the role exerted by diet on the tissue-specific epigenetic plasticity of RNA according to aging in rats, providing the first evidence that methylation of RNA, similarly to DNA methylation, can represent an effective biomarker of aging. What is more, the fact that it is regulated by nutrition provides the basis for the development of targeted approaches capable of guaranteeing the maintenance of a state of good health.

METTL3 modulates m6A modification of CDC25B and promotes head and neck squamous cell carcinoma malignant progression

BACKGROUND

N6-methyladenosine (m6A) RNA methylation and its methyltransferase METTL3 have been widely reported to be involved in different cancers by regulating RNA metabolism and function. Here, we aimed to explore the biological function and clinical significance of m6A modification and METTL3 in head and neck squamous cell carcinoma (HNSCC).

METHODS

The prognostic value of METTL3 expression was evaluated using tissue microarray and immunohistochemical staining analyses in a human HNSCC cohort. The biological role and mechanism of METTL3 in HNSCC tumour growth, metastasis and angiogenesis were determined in vitro and in vivo.

RESULTS

M6A levels and METTL3 expressions in HNSCC tissues were significantly increased compared with paired adjacent tissues. Meanwhile, METTL3 was an independent risk factor for the prognosis of HNSCC patients. Moreover, METTL3 overexpression promoted HNSCC cell proliferation, migration, invasion, and angiogenesis, while knockdown of METTL3 had an opposite effect in vivo and in vitro. Mechanistically, METTL3 enhanced the m6A modification of CDC25B mRNA, which maintained its stability and upregulated its expression, thereby activating G2/M phase of cell cycle and leading to HNSCC malignant progression.

CONCLUSIONS

METTL3 may be a potential prognostic biomarker and therapeutic target for HNSCC.

Emerging role of m6A modification in osteogenesis of stem cells

The differentiation of stem cells into osteoblasts is a key link in the treatment of bone defects and other orthopedic diseases. N6-methyladenosine (m6A) modification, an important post-transcriptional modification, is a methylation that occurs at the N6 site of RNA adenylate. The modification plays a regulatory role in the growth and development of biological individuals, the directional differentiation of stem cells and the occurrence of diseases. It is involved in various processes of the fate decision of stem cells. And it regulates the development and constant renewal of bone and keeps bone homeostasis by controlling and maintaining the balance between osteogenesis and adipogenesis. Meanwhile, it also affects the progress of orthopedic-associated diseases such as degenerative osteoporosis and bone tumor. In this review, we mainly summarize the new findings of three key molecules including Writers, Erasers and Readers which regulate m6A modification, and the emerging role of m6A modification in determining the fate and directed differentiation potential of stem cells, especially highlight the regulatory mechanism of osteogenic differentiation, the balance between osteogenesis and adipogenesis and the occurrence and development of bone-related diseases. It may provide some important ideas about finding new strategies to recover from bone defect and degenerative bone disease.

The m6A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay

The role of N6-methyladenosine (m6A) modifications has increasingly been associated with a diverse set of roles in modulating viruses and influencing the outcomes of viral infection. Here, we report that the landscape of m6A deposition is drastically shifted during Kaposi's sarcoma-associated herpesvirus (KSHV) lytic infection for both viral and host transcripts. In line with previous reports, we also saw an overall decrease in host methylation in favor of viral messenger RNA (mRNA), along with 5' hypomethylation and 3' hypermethylation. During KSHV lytic infection, a major shift in overall mRNA abundance is driven by the viral endoribonuclease SOX, which induces the decay of greater than 70% of transcripts. Here, we reveal that interlukin-6 (IL-6) mRNA, a well-characterized, SOX-resistant transcript, is m6A modified during lytic infection. Furthermore, we show that this modification falls within the IL-6 SOX resistance element, an RNA element in the IL-6 3' untranslated region (UTR) that was previously shown to be sufficient for protection from SOX cleavage. We show that the presence of this m6A modification is essential to confer SOX resistance to the IL-6 mRNA. We next show that this modification recruits the m6A reader YTHDC2 and found that YTHDC2 is necessary for the escape of the IL-6 transcript. These results shed light on how the host cell has evolved to use RNA modifications to circumvent viral manipulation of RNA fate during KSHV infection.

Emerging role of m6 A modification in cardiovascular diseases

Cardiovascular diseases (CVDs) contribute to the leading cause of death worldwide. Despite significantly improvements in CVDs diagnosis and treatment, a continued effort to explore novel therapeutic strategies is urgently need. N6-methyladenosine (m⁶ A) RNA methylation, well known as the most prevalent type of RNA modifications, involved in RNA stability, nuclear exports, translation and decoy, plays a crucial role in the pathogenesis of a variety of diseases, including CVDs, cancer and drug resistance. Here, our article summarizes cellular functions of m⁶ A modulators and recent research progress concerning the functions and mechanisms of m⁶ A methylation in CVDs, in hope of providing references for exploring novel therapeutic approaches and potential biomarkers in the treatment of CVDs. This article is protected by copyright. All rights reserved.

Discovery of substituted indole derivatives as allosteric inhibitors of m6 A-RNA methyltransferase, METTL3-14 complex

m⁶ A RNA methyltransferase (METTL3-14) catalyzes the methylation of adenosine in mRNA and plays important roles in mRNA functions, and it has been implicated in the progression of multiple cancers, including acute myeloid leukemia (AML). In this study, we describe the discovery of the first allosteric inhibitor of the METTL3-14 complex based on structure-activity relationship (SAR) and optimization studies of the hit compound, 4-[2-[5-chloro-1-(diphenylmethyl)-2-methyl-1H-indol-3-yl]-ethoxy]benzoic acid (CDIBA). Compound 43n was optimized throughout the modifications of 4 different regions of the structure, and it displayed potent enzyme inhibitory activity of the METTL3-14 complex (IC₅₀  = 2.81 μM) and an antiproliferative effect in the AML cell lines by suppressing the m⁶ A level of mRNA. The inhibition mechanism and binding mode of 43n were based on the interaction of the reversible and noncompetitive inhibitory profile at the allosteric site along with selectivity for the METTL3-14 complex relative to each subunit enzyme or truncated complex enzyme.