FTO in cancer: functions, molecular mechanisms, and therapeutic implications

The role of m6A methylation in abdominal aortic aneurysms: Mechanisms, progress and future perspectives (Review)

Abdominal aortic aneurysm (AAA) is a type of cardiovascular disease. Sudden aortic rupture and subsequent bleeding are the main causes of mortality due to AAA. N6‑methyladenosine (m6A) methylation, the most common epitranscriptomic modification in eukaryotic mRNAs, has a key role in the regulation of gene expression. m6A methylation markedly influences the development and progression of AAA. The present review highlights the mechanism of m6A methylation in AAA, including current research progress and future prospects. From a mechanistic perspective, m6A methylation exerts its influence on AAA‑related genes by modulating the post‑transcriptional levels of RNA, thereby impacting the pathological process of AAA. In terms of clinical applications, the mechanisms by which m6A methylation regulators influence their development and progression in AAA involve multiple target genes and signaling pathways. These regulatory factors affect inflammatory immunomodulation, cell proliferation, apoptosis and endogenous processes by modulating the m6A modification status of target genes and the activity of immune‑related signaling pathways. Therefore, for the prevention and treatment of AAA, current therapeutic strategies should comprehensively consider the interactions and synergistic regulation among m6A methylation regulators to reveal the integrated effects of the entire regulatory network in AAA development. Consequently, a more comprehensive understanding of the precise mechanisms of m6A methylation in AAA should be attained, which will support the development of innovative therapeutic strategies aimed at m6A methylation and establish a basis for the early diagnosis and treatment of AAA.

The m6A demethylase FTO controls Th1 differentiation and immunity against infections

Antigen-specific effector CD4+ T cells are critical for defense against exogenous pathogens. However, the epigenetic mechanisms underlying CD4+ T cell immune responses, particularly RNA modifications, remain incompletely understood. In this study, we employed a T cell-specific deletion of the fat mass and obesity-associated protein (FTO), a key N6-methyladenosine (m6A) demethylase, to elucidate its role in CD4+ T cell mediated immunity. Our findings demonstrate that FTO is essential for maintaining CD4+ T cell immune responses and protective functions. Specifically, FTO deficiency restricts the expansion of CD4+ T helper (Th)1 effector cells following antigen challenge and results in decreased expression of T-bet and IFN-γ in Th1 cells. Additionally, FTO deficient CD4+ T cells exhibit impaired pathogen elimination. Collectively, our study reveals a novel epigenetic regulatory mechanism in supporting CD4+ T cell differentiation, providing new insights into the post-transcriptional regulation of CD4+ T cell immunity and highlighting the potential for therapeutic strategies.

FTO regulates ELK3-mediated metabolic rewiring and represents a unique therapeutic target in T cell leukemia

Understanding the regulation of N6-methyladenosine (m6A), the prominent internal modification in mRNA, fosters the development of potential therapeutic strategies for human cancers. While the m6A demethylases FTO and ALKBH5 are recognized for their crucial roles in various cancers, their impact on lymphoid leukemia remains uncertain. Using T cell acute lymphoblastic leukemia (T-ALL) as a model system, we identify FTO as a unique vulnerability in T cell leukemia. Knockout of FTO, but not ALKBH5, significantly suppresses leukemia initiation and progression. Mechanistic analysis reveals that FTO heightens ELK3 mRNA stability in an m6A-dependent manner. Elevated ELK3 in turn transcriptionally activates the expression of glycolytic genes. Pharmacological inhibition of FTO suppresses ELK3 expression, hampers glycolysis and manifests remarkable antileukemia efficacy. Our findings unravel the crucial role of FTO in T-ALL and highlight the FTO-ELK3 axis as a key nodule during leukemogenesis, thereby providing a fundamental basis to harness selective FTO antagonist for T-ALL therapeutics.

FTO Promotes Hepatocellular Carcinoma Progression by Mediating m6A Modification of BUB1 and Targeting TGF-βR1 to Activate the TGF-β Signaling Pathway

Background and Aims

Fat mass and obesity-associated protein (FTO) has been linked to various cancers, though its role in hepatocellular carcinoma (HCC) remains unclear. This study aimed to investigate FTO expression, its clinical relevance, functional role in HCC progression, and the underlying molecular mechanisms.

Methods

Quantitative reverse-transcription polymerase chain reaction and immunohistochemical analysis were used to assess FTO expression in HCC. Functional assays, including proliferation, invasion, and epithelial-mesenchymal transition studies, were conducted using HCC cell lines with FTO knockdown. N6-methyladenosine (m6A) RNA immunoprecipitation and RNA stability assays further elucidated the role of FTO in BUB1 mRNA methylation and stability. Co-immunoprecipitation studies were employed to confirm the interaction between BUB1 and TGF-βR1. In vivo studies in nude mice were conducted to evaluate tumor growth following FTO knockdown.

Results

FTO was significantly upregulated in HCC tissues compared to normal liver tissues, with higher expression observed in advanced tumor-node-metastasis stages and metastatic HCC. Elevated FTO correlated with poor overall survival in patients. Silencing FTO decreased HCC cell proliferation, colony formation, invasion, epithelial-mesenchymal transition, and tumor growth in nude mice. Mechanistically, FTO downregulation led to increased m6A modification of BUB1 mRNA, thereby promoting its degradation via the YTH domain family 2-dependent pathway and reducing BUB1 protein levels. Additionally, BUB1 physically interacted with TGF-βR1, activating downstream TGF-β signaling.

Conclusions

FTO is overexpressed in HCC and is associated with poor clinical outcomes. Mechanistically, FTO promotes HCC progression by stabilizing BUB1 mRNA through an m6A-YTH domain family 2-dependent pathway, which activates TGF-β signaling. Targeting the FTO-BUB1-TGF-βR1 regulatory network may offer a promising therapeutic strategy for HCC.

Topical application of insulin encapsulated by chitosan-modified PLGA nanoparticles to alleviate alkali burn-induced corneal neovascularization

Corneal neovascularization (CRNV) severely impairs corneal transparency and is one of the leading causes of vision loss worldwide. Drug therapy is the main approach to inhibit CRNV. Insulin (INS) has been reported to facilitate the healing of corneal injuries and suppress inflammation. However, but due to the unique physiological barriers of the eye, its bioavailability is low, limiting its therapeutic effect. In this study, we developed a chitosan-poly(lactic-co-glycolic acid)-INS nanoparticles (CPI NPs) system for INS delivery. The characterization of CPI NPs was satisfactory. Experimental results demonstrated that CPI NPs effectively inhibited the migration of vascular endothelial cells and the formation of tubular structures. Furthermore, CPI NPs markedly suppressed the neovascularization in a CRNV model without any observable side effects. Quantitative proteomics analysis indicated that INS treatment led to a reduction in FTO levels within the neovascularized cornea. Both in vitro and in vivo experiments substantiated the impact of CPI NPs on FTO protein expression and the N6-methyladenosine modification. In conclusion, this study successfully developed an effective ocular drug delivery system for the treatment of CRNV induced by alkali burns, thereby offering a novel therapeutic option for this condition.

Development of 3-arylaminothiophenic-2-carboxylic acid derivatives as new FTO inhibitors showing potent antileukemia activities

Fat mass and obesity-associated protein (FTO) is the first discovered RNA N6-methyladenosine (m6A) demethylase. The highly expressed FTO protein is required to trigger oncogenic pathways in acute myeloid leukemia (AML), which makes FTO a promising antileukemia drug target. In this study, we identify 3-arylaminothiophenic-2-carboxylic acid derivatives as new FTO inhibitors with good antileukemia activity. We replaced the phenyl A-ring in FB23, the first-generation of FTO inhibitor, with five-membered heterocycles and synthesized a new class of FTO inhibitors. Compound 12o/F97 shows strong enzymatic inhibitory activity and potent antiproliferative activity. 12o/F97 selectively inhibits m6A demethylation by FTO rather than ALKBH5, and has minimal effect on m1A demethylation by ALKBH3. Additionally, 12o/F97 increases the protein levels of RARA and ASB2, while decreasing that of MYC in AML cell lines. Lastly, 12o/F97 exhibits antileukemia activity in a xenograft mice model without significant side-effects. The identification of 3-arylaminothiophenic-2-carboxylic acid derivatives as new FTO inhibitors not only expands the chemical space but also holds potential for antileukemia drug development.

Recent Advance in Sensitive Detection of Demethylase FTO

Methylation modification is a critical regulatory mechanism in epigenetics and plays a significant role in various biological processes. N6-methyladenosine (m6A) is the most common modification found in RNA. The fat mass and obesity-associated protein (FTO) facilitate the demethylation of m6A in RNA, and its abnormal expression is closely linked to the development of several diseases. As a result, FTO has the potential to serve as an important biomarker for clinical disease diagnosis. Despite its significance, there has been a lack of comprehensive reviews addressing advancements in detection methods for the demethylase FTO. This review provides an overview of the progress in FTO detection methods, ranging from traditional approaches to innovative techniques, with a particular emphasis on recently reported advancements. These novel detection methods can be categorized into strategies based on enzymes, functional nucleic acids (FNA), and conformational changes. We summarize the principles and applications of these detection methods and discuss the current challenges and prospects in this field.

Epigenetic targets and their inhibitors in the treatment of idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a deadly lung disease characterized by fibroblast proliferation, excessive extracellular matrix buildup, inflammation, and tissue damage, resulting in respiratory failure and death. Recent studies suggest that impaired interactions among epithelial, mesenchymal, immune, and endothelial cells play a key role in IPF development. Advances in bioinformatics have also linked epigenetics, which bridges gene expression and environmental factors, to IPF. Despite the incomplete understanding of the pathogenic mechanisms underlying IPF, recent preclinical studies have identified several novel epigenetic therapeutic targets, including DNMT, EZH2, G9a/GLP, PRMT1/7, KDM6B, HDAC, CBP/p300, BRD4, METTL3, FTO, and ALKBH5, along with potential small-molecule inhibitors relevant for its treatment. This review explores the pathogenesis of IPF, emphasizing epigenetic therapeutic targets and potential small molecule drugs. It also analyzes the structure-activity relationships of these epigenetic drugs and summarizes their biological activities. The objective is to advance the development of innovative epigenetic therapies for IPF.

Mechanistic insights into stem cell fate regulation via RNA methylation

Stem cells possess an extraordinary ability for self-renewal and differentiation, making them essential for tissue repair, regeneration, and anti-aging. RNA methylation is crucial in regulating stem cell fate by modulating gene expression. This review synthesizes current research on RNA methylation modifications, such as m6A, m7G, m5C, and m1A, and their impact on adult stem cell fate. It provides a comprehensive overview of the molecular machinery involved in RNA methylation, emphasizes the critical roles of these modifications in stem cell biology, reviews the latest advancements in sequencing technologies, and discusses potential crosstalk between RNA methylation and epigenetic mechanisms.

The m6A demethylase FTO promotes C/EBPβ-LIP translation to perform oncogenic functions in breast cancer cells

N6-methyladenosine (m6A) is a prevalent posttranscriptional mRNA modification involved in the regulation of transcript turnover, translation, and other aspects of RNA fate. The modification is mediated by multicomponent methyltransferase complexes (so-called writers) and is reversed through the action of the m6A-demethylases fat mass and obesity-associated (FTO) and alkB homolog 5 (ALKBH5) (so-called erasers). FTO promotes cell proliferation, colony formation and metastasis in models of triple-negative breast cancer (TNBC). However, little is known about genome-wide or specific downstream regulation by FTO. Here, we examined changes in the genome-wide transcriptome and translatome following FTO knockdown in TNBC cells. Unexpectedly, FTO knockdown had a limited effect on the translatome, while transcriptome analysis revealed that genes related to extracellular matrix (ECM) and epithelial-mesenchymal transition (EMT) are regulated through yet unidentified mechanisms. Differential translation of CEBPB mRNA into the C/EBPβ transcription factor isoform C/EBPβ-LIP is known to act in a pro-oncogenic manner in TNBC cells through regulation of EMT genes. Here we show that FTO is required for efficient C/EBPβ-LIP expression, suggesting that FTO has oncogenic functions through regulation of C/EBPβ-LIP.

Predictive models and WTAP targeting for idiopathic pulmonary fibrosis (IPF)

Emerging evidence suggests that N6-methyladenosine (m6A) modification significantly influences lung injury, lung cancer, and immune responses. The current study explores the potential involvement of m6A modification in the development of IPF. This research analyzed the GSE93606 dataset of 20 non-IPF and 154 IPF patients, identifying 26 m6A regulators and developing predictive models with RF and SVM, assessed via ROC curves. A nomogram was created with selected m6A factors, including molecular subtyping, PCA for m6A features, immune cell analysis, DEG identification, and functional enrichment. In vitro experiments on MRC-5 cells used RT-qPCR and Western blotting, and virtual drug screening targeted the WTAP protein through molecular docking. Analysis revealed 26 differential m6A regulators in IPF patients, with 16 significant; IGFBP2 and YTHDF2 were overexpressed, while others decreased. RF and SVM models identified predictive m6A regulators, and a nomogram was developed using five factors to predict IPF incidence. Distinct m6A patterns showed changes in RNA levels of specific genes in the BLM-induced group, and five compounds targeting WTAP were identified. This research explored m6A factors' impact on IPF diagnosis and prognosis, identifying WTAP as a potential biomarker.

Regulatory mechanisms of m6A RNA methylation in esophageal cancer: a comprehensive review

Esophageal cancer is an aggressively malignant neoplasm characterized by a high mortality rate. Frequently diagnosed at an advanced stage, it presents challenges for optimal therapeutic intervention due to its non-specific symptoms, resulting in lost opportunities for effective treatment, such as surgery, radiotherapy, chemotherapy and target therapy. The N6-methyladenosine (m6A) modification represents the most critical post-transcriptional modification of eukaryotic messenger RNA (mRNA). The reversible m6A modification is mediated by three regulatory factors: m6A methyltransferases, demethylating enzymes, and m6A recognition proteins. These components identify and bind to specific RNA methylation sites, thereby modulating essential biological functions such as RNA processing, nuclear export, stability, translation and degradation, which significantly influence tumorigenesis, invasion, and metastasis. Given the importance of m6A modification, this paper offers a comprehensive examination of the regulatory mechanisms, biological functions, and future therapeutic implications of m6A RNA methylation in the context of esophageal cancer.

FTO controls CD8+ T cell survival and effector response by modulating m6A methylation of Fas

Functional CD8+ T cell immunity is essential for immune surveillance and host defense against infection and tumors. Epigenetic mechanisms, particularly RNA modification, in controlling CD8+ T cell immune response is not fully elucidated. Here, by T cell-specific deletion of fat mass and obesity-associated protein (FTO), a critical N6-methyladenosine (m6A) demethylase, we revealed that FTO was indispensable for adequate CD8+ T cell immune response and protective function. FTO ablation led to considerable cell death in activated CD8+ T cells, which was attributed to cell apoptosis. MeRIP-seq analysis revealed an increase in m6A methylation on Fas mRNA in FTO-deficient CD8+ T cells. The loss of FTO promoted Fas expression via enhancing the Fas mRNA stability, which depended on the m6A reader insulin-like growth factor-2 mRNA-biding proteins 3 (IGF2BP3). Mutation of the Fas m6A sites or knockdown IGF2BP3 could normalize the upregulated Fas expression and apoptosis levels caused by FTO ablation in CD8+ T cells. Our findings delineate a novel epigenetic regulatory mechanism of FTO-mediated m6A modification in supporting CD8+ T cell survival and effector responses, providing new insights into understanding the post-transcriptional regulation in CD8+ T cell immunological functions and the potential therapeutic intervention.

Discovery of the 2,3-Dihydrobenzopyrane-4-one as a Potent FTO Inhibitor against Obesity-Related Metabolic Diseases

The involvement of the fat mass and obesity-associated gene (FTO) in the development and advancement of metabolic disorders is widely recognized. However, the existing FTO inhibitor entacapone has been limited in clinical application due to its low potency and short plasma elimination half-life. Here, through drug library screening and in depth structure-activity relationship analysis, title compound 40, eriodictyol was identified as a potent FTO inhibitor, and showed good binding to FTO by surface plasmon resonance (SPR) and Microscale thermophoresis (MST) detection. The residues Arg96, Tyr108, Ser229, Asp233, and Glu234 of FTO are essential for binding. Meanwhile, eriodictyol attenuated obesity-related metabolic diseases by enhancing glucose metabolism pathways via the FTO-FOXO1-G6PC/PCK1 axis and increasing adipose tissue heat production for weight loss via the FTO-FOXO1-Ucp1 axis in vivo. Surprisingly, eriodictyol showed good pharmacokinetic properties and no obvious toxicity. These results could provide the reference for design of new FTO inhibitors against obesity-related metabolic diseases.

IGF2BP2: an m6A reader that affects cellular function and disease progression

Insulin-like growth factor 2 messenger RNA (mRNA)-binding protein 2 (IGF2BP2) is a widely studied N6-methyladenosine (m6A) modification reader, primarily functioning to recognize and bind to m6A modification sites on the mRNA of downstream target genes, thereby enhancing their stability. Previous studies have suggested that the IGF2BP2-m6A modification plays an essential role in cellular functions and the progression of various diseases. In this review, we focus on summarizing the molecular mechanisms by which IGF2BP2 enhances the mRNA stability of downstream target genes through m6A modification, thereby regulating cell ferroptosis, epithelial-mesenchymal transition (EMT), stemness, angiogenesis, inflammatory responses, and lipid metabolism, ultimately affecting disease progression. Additionally, we update the related research progress on IGF2BP2. This article aims to elucidate the effects of IGF2BP2 on cell ferroptosis, EMT, stemness, angiogenesis, inflammatory responses, and lipid metabolism, providing a new perspective for a comprehensive understanding of the relationship between IGF2BP2 and cell functions such as ferroptosis and EMT, as well as the potential for targeted IGF2BP2 therapy for tumors and other diseases.

Summary of the mechanism of ferroptosis regulated by m6A modification in cancer progression

The most common form of internal RNA modification in eukaryotes is called n6-methyladenosine (m6A) methylation. It has become more and more well-known as a research issue in recent years since it alters RNA metabolism and is involved in numerous biological processes. Currently, m6A alteration offers new opportunities in clinical applications and is intimately linked to carcinogenesis. Ferroptosis-a form of iron-dependent, lipid peroxidation-induced regulated cell death-was discovered. In the development of cancer, it has become an important factor. According to newly available data, ferroptosis regulates tumor growth, and cancer exhibits aberrant m6A levels in crucial ferroptosis regulatory components. On the other hand, m6A has multiple roles in the development of tumors, and the relationship between m6A-modified ferroptosis and malignancies is quite intricate. In this review, we first give a thorough review of the regulatory and functional roles of m6A methylation, focusing on the molecular processes of m6A through the regulation of ferroptosis in human cancer progression and metastasis, which are strongly associated to cancer initiation, progression, and drug resistance. Therefore, it is crucial to clarify the relationship between m6A-mediated regulation of ferroptosis in cancer progression, providing a new strategy for cancer treatment with substantial clinical implications.

FTO-mediated m6A Methylation of KCNAB2 Inhibits Tumor Property of Non-Small Cell Lung Cancer Cells and M2 Macrophage Polarization by Inactivating the PI3K/AKT Pathway

Potassium voltage-gated channel subfamily A regulatory beta subunit 2 (KCNAB2) is a potassium voltage-gated channel subfamily A member that plays a role in non-small cell lung cancer (NSCLC). However, its functional impact and mechanism in NSCLC are not fully understood. Here, we analyzed its effects on NSCLC cell behaviors and the underlying mechanism.mRNA expression levels were detected by quantitative real-time polymerase chain reaction (qRT-PCR),(qRT-PCR), while protein expression was quantified by western blotting blot analysis or immunohistochemistry assay. NSCLC cell proliferation, migration, invasion, macrophage polarization, and apoptosis were evaluated through cell-based assays including cell counting kit-8 (CCK-8)(CCK-8) assay, flow cytometry, Tunel assay, wound-healing assay, and transwell invasion assay. The role of FTO alpha-ketoglutarate dependent dioxygenase (FTO)-mediated(FTO)-mediated m6A methylation in the regulation of KCNAB2 expression and their impacts on NSCLC cell behavior and M2 macrophage polarization were assessed through m6A RNA immunoprecipitation assay and rescue experiments. Xenograft mouse model assay was used to determine the effect of KCNAB2 on tumor formation in vivo.in vivo.KCNAB2 expression was downregulated and FTO expression was upregulated in NSCLC tissues and cells when compared with controls. Moreover, the expression of KCNAB2 was found to be lower in stage III NSCLC patients compared to those at stages I and II, and it was also lower in patients with positive lymph node metastasis compared to those with negative lymph node metastasis. Overexpression of KCNAB2 inhibited NSCLC cell proliferation, migration, invasion, and M2 macrophage polarization, while inducing cell apoptosis. These effects were mediated, at least partially, by inactivating the phosphoinositide 3-kinase (PI3K)/AKT(PI3K)/AKT pathway. Moreover, ectopic expression of KCNAB2 delayed tumor formation in vivo. FTOin vivo. FTO was found to mediate m6A methylation of KCNAB2, and knockdown of FTO resulted in the upregulation of KCNAB2 expression, leading to inhibition of NSCLC cell behavior and M2 macrophage polarization.KCNAB2 overexpression inhibited NSCLC cell behavior and M2 macrophage polarization by inactivating the PI3KPI3K/AKT/AKT pathway. Furthermore, FTOFTO-mediated-mediated m6A methylation was involved in the regulation of KCNAB2 expression in NSCLC. These results enhance our understanding of the role of KCNAB2 in NSCLC and suggest its potential as a therapeutic target.

The role of chloride intracellular channel 4 in tumors

Tumors are among the most predominant health problems in the world, and the annual incidence of cancer is increasing globally; therefore, there is an urgent need to identify effective therapeutic targets. Chloride intracellular channel 4 (CLIC4) belongs to the family of chloride intracellular channels (CLICs), which are widely expressed in various tissues and organs, such as the brain, lung, pancreas, colorectum, and ovary, and play important roles in promoting apoptosis, promoting angiogenesis, maintaining normal proliferation of endothelial cells, and regulating the assembly and reconstruction of the cytoskeleton. The expression and function of CLIC4 in tumors varies. It has been reported that CLIC4 is low expressed in gastric cancer, skin cancer and prostate cancer, suggesting a tumor suppressor role. Interestingly, CLIC4 is overexpressed in pancreatic, ovarian and breast cancers, indicating a cancer-promoting role. CLIC4 expression is dysregulated in some solid tumors, which may be because CLIC4 is involved in the growth, migration or invasion of some cancer cells through various mechanisms. Regulation of CLIC4 expression may be a potential therapeutic strategy for some tumors. CLIC4 may be a promising therapeutic target and a biomarker for some cancers. In this study, we review the role of CLIC4 in several cancers and its value in the diagnosis and treatment of tumors.

FTO suppresses DNA repair by inhibiting PARP1

Maintaining genomic integrity and faithful transmission of genetic information is essential for the survival and proliferation of cells and organisms. DNA damage, which threatens the integrity of the genome, is rapidly sensed and repaired by mechanisms collectively known as the DNA damage response. The RNA demethylase FTO has been implicated in this process; however, the underlying mechanism by which FTO regulates DNA repair remains unclear. Here, we use an unbiased quantitative proteomic approach to identify the proximal interactome of endogenous FTO protein. Our results demonstrate a direct interaction with the DNA damage sensor protein PARP1, which dissociates upon ultraviolet stimulation. FTO inhibits PARP1 catalytic activity and controls its clustering in the nucleolus. Loss of FTO enhances PARP1 enzymatic activity and the rate of PARP1 recruitment to DNA damage sites, accelerating DNA repair and promoting cell survival. Interestingly, FTO regulates PARP1 function and DNA damage response independent of its catalytic activity. We conclude that FTO is an endogenous negative regulator of PARP1 and the DNA damage response in cells beyond its role as an RNA demethylase.

FTO Promotes Osteogenic Differentiation of Human BMSCs via Demethylation of TGFB2 m6A Modifications

OBJECTIVE

To elucidate the role of m6A modification in the osteogenic differentiation of human BMSCs (hBMSCs) and the underlying mechanisms.

MATERIALS & METHODS

In this research, we analyzed the m6A modification and its impact on mRNA expression and osteogenic differentiation of hBMSCs. FTO was knocked down in hBMSCs using shRNAs, and the effect on osteogenic differentiation was evaluated. m6A-seq was performed to identify key m6A-methylation mRNAs during osteogenic differentiation. TGFB2 was knocked down to validate its role in FTO-regulated m6A-methylation-mediated osteogenesis.

RESULTS

We found downregulated global m6A modification in osteogenically differentiating hBMSCs. m6A eraser FTO expression was upregulated during the osteogenic differentiation of hBMSCs. FTO knockdown inhibited the osteogenic differentiation of hBMSCs. Downregulation of mRNA m6A modification was prominent in osteogenically differentiating hBMSCs. mRNA m6A modifications in osteogenically differentiating hBMSCs were mainly attributed to MAPK, focal adhesion, and TGFβ signaling. Finally, we revealed that FTO demethylates m6A abundance of TGFB2, promoting the TGFB2 expression in hBMSCs. Knockdown of TGFB2 inhibited the osteogenic differentiation of hBMSCs.

CONCLUSION

These results indicate that upregulated m6A eraser FTO downregulates m6A modifications promoting TGFB2 expression in hBMSCs that trigger osteogenic differentiation, suggesting activation of FTO or TGFB2 as a strategy to promote hBMSC-based bone defect repair.

The Role of M6A LncRNA Modification in Papillary Thyroid Cancer

Thyroid Cancer (TC) is the most common endocrine cancer, of which papillary thyroid cancer (PTC), a well-differentiated type of TC, accounts for 80-90%. Long non-coding RNAs (lncRNAs), which comprise non-protein-coding segments of the genome, have been found to play a crucial role in various biological processes, including cancer development. The activity of lncRNAs is modified through epigenetic modifications, with N6-Methyladenosine (m6A) modifications implicated in the progression of several malignancies. The activity of m6A is further regulated by modifying enzymes classified as "readers", writers", and "erasers", of which specific enzymes have been found to play a role in various aspects of PTC. Recent research has highlighted the significance of m6A modification in regulating the expression and function of lncRNAs associated with PTC pathogenesis. Dysregulation of this process implicates tumor proliferation, invasion, and metastasis, with subsequent impact on prognosis. Therefore, understanding the interplay between m6A modification and lncRNAs provides valuable insights into the molecular mechanisms underlying PTC progression. This narrative review aims to explore the established role of several prominent m6A modifying enzymes and lncRNAs on cancer pathogenesis and seeks to clarify the function of these enzymes in PTC pathogenesis.

A patenting perspective of fat mass and obesity associated protein (FTO) inhibitors: 2017-present

INTRODUCTION

The fat mass and obesity-associated protein (FTO) catalytically demethylates RNA N6-methyl adenosine (m6A) modification, dynamically regulates gene expression in eukaryotes. Interestingly, FTO is highly expressed and functions as an oncogenic factor in a wide range of cancers. Therefore, using small-molecule inhibitors to target FTO has been established as a promising therapeutic strategy for combating cancers.

AREAS COVERED

Patent literature claiming novel chemical entities as FTO inhibitors disclosed from 2017 to present is available in Espacenet, including dozens of patent documents.

EXPERT OPINION

The pivotal influence of FTO demethylase in a particular epigenetic layer of regulation of gene expression renders it promising for FTO to be a therapeutical target for many diseases, including malignant cancers. Several institutions were prompted and have patented chemical frameworks as FTO inhibitors. Remarkedly, the FTO inhibitor CS1 (Bisantrene) has advanced to clinical trials for treating acute myeloid leukemia (AML). The successful advancement of CS1 into clinical trials would continuingly stimulate researches on RNA epigenetic enzymes targeted first-in-class anticancer drug discovery.

RNA methylation homeostasis in ocular diseases: All eyes on Me

RNA methylation is a pivotal epigenetic modification that adjusts various aspects of RNA biology, including nuclear transport, stability, and the efficiency of translation for specific RNA candidates. The methylation of RNA involves the addition of methyl groups to specific bases and can occur at different sites, resulting in distinct forms, such as N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), and 7-methylguanosine (m7G). Maintaining an optimal equilibrium of RNA methylation is crucial for fundamental cellular activities such as cell survival, proliferation, and migration. The balance of RNA methylation is linked to various pathophysiological conditions, including senescence, cancer development, stress responses, and blood vessel formation, all of which are pivotal for comprehending a spectrum of eye diseases. Recent findings have highlighted the significant role of diverse RNA methylation patterns in ophthalmological conditions such as age-related macular degeneration, diabetic retinopathy, cataracts, glaucoma, uveitis, retinoblastoma, uveal melanoma, thyroid eye disease, and myopia, which are critical for vision health. This thorough review endeavors to dissect the influence of RNA methylation on common and vision-impairing ocular disorders. It explores the nuanced roles that RNA methylation plays in key pathophysiological mechanisms, such as oxidative stress and angiogenesis, which are integral to the onset and progression of these diseases. By synthesizing the latest research, this review offers valuable insights into how RNA methylation could be harnessed for therapeutic interventions in the field of ophthalmology.

m6A RNA methylation: a pivotal regulator of tumor immunity and a promising target for cancer immunotherapy

M6A modification is one of the most common regulatory mechanisms of gene expression in eukaryotic cells, influencing processes such as RNA splicing, degradation, stability, and protein translation. Studies have shown that m6A methylation is closely associated with tumorigenesis and progression, and it plays a key regulatory role in tumor immune responses. m6A modification participates in regulating the differentiation and maturation of immune cells, as well as related anti-tumor immune responses. In the tumor microenvironment, m6A modification can also affect immune cell recruitment, activation, and polarization, thereby promoting or inhibiting tumor cell proliferation and metastasis, and reshaping the tumor immune microenvironment. In recent years, immunotherapies for tumors, such as immune checkpoint inhibitors and adoptive cell immunotherapy, have been increasingly applied in clinical settings, achieving favorable outcomes. Targeting m6A modifications to modulate the immune system, such as using small-molecule inhibitors to target dysregulated m6A regulatory factors or inducing immune cell reprogramming, can enhance anti-tumor immune responses and strengthen immune cell recognition and cytotoxicity against tumor cells. m6A modification represents a new direction in tumor immunotherapy with promising clinical potential. This review discusses the regulatory role of m6A methylation on immune cells and tumor immune responses and explores new strategies for immunotherapy.

Energy Stress-Induced circEPB41(2) Promotes Lipogenesis in Hepatocellular Carcinoma

The tumor microenvironment plays a pivotal role in the metabolic reprogramming of cancer cells. A better understanding of the underlying mechanisms regulating cancer metabolism could help identify potential therapeutic targets. Here, we identified circEPB41(2) as a metabolically regulated circular RNA that mediates lipid metabolism in hepatocellular carcinoma (HCC). circEPB41(2) was induced in response to glucose deprivation via HNRNPA1-dependent alternative splicing. Upregulation of circEPB41(2) led to enhanced lipogenic gene expression that promoted lipogenesis. Mechanistically, circEPB41(2) cooperated with the N6-methyladenosine demethylase FTO to decrease the mRNA stability of the histone deacetylase sirtuin 6, thereby increasing histone H3 lysine 9 acetylation and histone H3 lysine 27 acetylation levels to activate lipogenic gene expression. Silencing of circEPB41(2) inhibited both in vitro proliferation of HCC cells and in vivo growth of tumor xenografts. Clinically, circEPB41(2) was elevated in HCC, and high circEPB41(2) expression was associated with poor patient prognosis. Overall, this study reveals that circEPB41(2) is an important regulator of lipid metabolic reprogramming and indicates that targeting the circEPB41(2)-FTO-sirtuin 6 axis could represent a promising anticancer strategy for treating HCC. Significance: circEPB41(2) is induced by glucose deprivation and mediates epigenetic alterations to drive lipogenesis and tumor growth in hepatocellular carcinoma, suggesting circEPB41(2) could be a potential therapeutic target in liver cancer.

METTL3/YTDHF1 Stabilizes MTCH2 mRNA to Regulate Ferroptosis in Glioma Cells

BACKGROUND

Gliomas are aggressive brain tumors known for their poor prognosis and resistance to standard treatment options. Ferroptosis is an iron-dependent form of regulated cell death that has emerged as a promising target for cancer treatment. This study examined how the methyltransferase-like 3/YTH domain family protein 1 (METTL3/YTHDF1) axis influences ferroptosis and glioma progression by stabilizing mitochondrial carrier homolog 2 (MTCH2) messenger RNA (mRNA).

METHODS

MTCH2 expression in glioma tissues and cell lines was evaluated through quantitative real-time polymerase chain reaction (PCR) and western blot analyses. To assess the effects of MTCH2 knockdown and overexpression on glioma cell functions, we performed a series of functional assays, including cell viability, colony formation, and measurements of lipid reactive oxygen species (lipid ROS) and malondialdehyde (MDA) levels. Additionally, we conducted RNA immunoprecipitation (RIP) and RNA stability assays to explore the underlying mechanisms governing the interaction between METTL3, YTHDF1, and the stability of MTCH2 mRNA.

RESULTS

MTCH2 was significantly upregulated in glioma tissues and cell lines. Silencing of MTCH2 resulted in decreased glioma cell proliferation and induced ferroptosis, as evidenced by increased lipid peroxidation and ROS accumulation. Conversely, overexpression of MTCH2 enhanced glioma cell survival and reduced ferroptosis. METTL3-mediated N6-methyladenosine (m6A) modification enhanced MTCH2 mRNA stability by enabling YTHDF1 to bind and protect the modified mRNA from degradation.

CONCLUSION

The METTL3/YTHDF1/MTCH2 axis plays a critical role in glioma progression by inhibiting ferroptosis and promoting tumor cell survival. Targeting this pathway may provide a new and effective treatment strategy for glioma patients.

Discovery of Novel RNA Demethylase FTO Inhibitors Featuring an Acylhydrazone Scaffold with Potent Antileukemia Activity

Fat mass obesity-associated protein (FTO) has been emerging as a potential therapeutic target for drug discovery in RNA epigenetics. In this work, a series of novel FTO inhibitors featuring an acylhydrazone scaffold were identified, and the optimized compounds 8t-v showed potent FTO inhibitory activities with IC50 values ranging from 7.1 to 9.4 μM. FTO inhibitor 8t, as the lead compound, exhibited potent antiproliferative capacities against MOLM13, NB4, and THP-1 with IC50 values of 0.35, 0.59, and 0.70 μM, respectively, and remarkably induced NB4 cell apoptosis. Compound 8t also inhibited the FTO demethylation, enhanced the abundance of m6A, stabilized FTO protein folding, and regulated the oncogenic FTO signaling pathway. Importantly, compound 8t significantly caused a tumor volume reduction and tumor weight loss with a tumor growth inhibition (TGI) value of 51% in NB4 xenograft mice. Overall, our work provided valuable lead compounds for FTO inhibitors featuring an acylhydrazone scaffold with potent antileukemia activity both in vitro and in vivo.

Exploring m6A modifications in gastric cancer: from molecular mechanisms to clinical applications

The significance of m6A modifications in several biological processes has been increasingly recognized, particularly in the context of cancer. For instance, m6A modifications in gastric cancer (GC) have been significantly implicated in tumor progression, metastasis, and treatment resistance. GC is characterized by the differential expression of m6A regulators. High expression writers such as METTL3 and WTAP are associated with poor prognosis and aggressive clinical features. Conversely, low expression of METTL14 is linked to worse clinical outcomes, whereas elevated levels of demethylases, such as FTO and ALKBH5, correlate with better survival rates. These m6A regulators influence several cellular biological functions, including proliferation, invasion, migration, glycolysis, and chemotherapy resistance, thereby affecting tumor growth and therapeutic outcomes. The assessment of m6A modification patterns and the expression profiles of m6A-related genes hold substantial potential for improving the clinical diagnosis and treatment of GC. In this review, we provide an updated and comprehensive summary of the role of m6A modifications in GC, emphasizing their molecular mechanisms, clinical significance, and translational applications in developing novel diagnostic and therapeutic strategies.

Bioinformatic Analysis of m6A Regulator-Mediated RNA Methylation Modification Patterns and Immune Microenvironment Characterization in Endometriosis

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.

Upregulation of circGDI2 inhibits tumorigenesis by stabilizing the expression of RNA m6A demethylase FTO in oral squamous cell carcinoma

Background

Oral squamous cell carcinoma (OSCC) is a malignant tumour that is difficult to identify and prone to metastasis and invasion. Circular RNAs (circRNAs) are important cancer regulators and can be used as potential biomarkers. However, OSCC-related circRNAs need to be further explored. We investigated the role of circGDI2 in OSCC and explored its downstream regulatory mechanisms.

Methods

Quantitative real-time PCR was used to detect the expression levels of circGDI2 and fat mass and obesity-associated protein (FTO) in cells. Lentiviral transfection was used to construct stable circGDI2 overexpressing cells for subsequent cell function tests. RNA pull-down, RNA Immunoprecipitation (RIP), western blotting, and protein stability assays were conducted to detect circGDI2 binding proteins and their functions. CCK8, Transwell, and wound healing assays were used to verify cell functions after overexpressing circGDI2 or suppressing FTO expression. Animal experiments were performed to verify the results in vivo.

Results

The expression of circGDI2 was markedly decreased in both OSCC cell lines and patient tissues. Overexpression of circGDI2 in OSCC cell lines led to decreased proliferation, migration, and invasion abilities. Knockdown of circGDI2 showed the opposite trend. CircGDI2 has been validated to interact with the FTO protein within cells, as evidenced by mass spectrometry and RIP assays. This interaction was found to prevent the degradation of the FTO protein. Dot blot analysis showed a reduction in N6-methyladenosine (m6A) modification after circGDI2 overexpression. Reduced FTO levels reversed the inhibitory effects of circGDI2 overexpression on cell proliferation, migration, and invasion in vitro and on tumorigenesis in vivo.

Conclusions

CircGDI2 functions as a tumour suppressor by binding to the FTO protein to reduce RNA m6A modification levels and ultimately inhibit proliferation and migration in OSCC cells. This study indicates the potential use of circGDI2 as a new target for the prevention and treatment of OSCC.

hnRNPU-mediated pathogenic alternative splicing drives gastric cancer progression

BACKGROUND

Alternative splicing (AS) is a process that facilitates the differential inclusion of exonic sequences from precursor messenger RNAs, significantly enhancing the diversity of the transcriptome and proteome. In cancer, pathogenic AS events are closely related to cancer progression. This study aims to investigate the role and regulatory mechanisms of AS in gastric cancer (GC).

METHODS

We analyzed AS events in various tumor samples and identified hnRNPU as a key splicing factor in GC. The effects of hnRNPU on cancer progression were assessed through in vitro and in vivo experiments. Gene knockout models and the FTO inhibitor (meclofenamic acid) were used to validate the interaction between hnRNPU and FTO and their impact on AS.

RESULTS

We found that hnRNPU serves as a key splicing factor in GC, and its high expression is associated with poor clinical prognosis. Genetic depletion of hnRNPU significantly reduced GC progression. Mechanistically, the m6A demethylase FTO interacts with hnRNPU transcripts, decreasing the m6A modification levels of hnRNPU, which leads to exon 14 skipping of the MET gene, thereby promoting GC progression. The FTO inhibitor meclofenamic acid effectively inhibited GC cell growth both in vitro and in vivo.

CONCLUSION

The FTO/hnRNPU axis induces aberrant exon skipping of MET, thereby promoting GC cell growth. Targeting the FTO/hnRNPU axis may interfere with abnormal AS events and provide a potential diagnostic and therapeutic strategy for GC.

Recent advances in methylation modifications of microRNA

microRNAs (miRNAs) are short single-stranded non-coding RNAs between 21 and 25 nt in length in eukaryotic organisms, which control post-transcriptional gene expression. Through complementary base pairing, miRNAs generally bind to their target messenger RNAs and repress protein production by destabilizing the messenger RNA and translational silencing. They regulate almost all life activities, such as cell proliferation, differentiation, apoptosis, tumorigenesis, and host-pathogen interactions. Methylation modification is the most common RNA modification in eukaryotes. miRNA methylation exists in different types, mainly N6-methyladenosine, 5-methylcytosine, and 7-methylguanine, which can change the expression level and biological mode of action of miRNAs and improve the activity of regulating gene expression in a very fine-tuned way with flexibility. In this review, we will summarize the recent findings concerning methylation modifications of miRNA, focusing on their biogenesis and the potential role of miRNA fate and functions.

Fenamates: Forgotten treasure for cancer treatment and prevention: Mechanisms of action, structural modification, and bright future

Fenamates as classical nonsteroidal anti-inflammatory agents are widely used for relieving pain. Preclinical studies and epidemiological data highlight their chemo-preventive and chemotherapeutic potential for cancer. However, comprehensive reviews of fenamates in cancer are limited. To accelerate the repurposing of fenamates, this review summarizes the results of fenamates alone or in combination with existing chemotherapeutic agents. This paper also explores targets of fenamates in cancer therapy, including COX, AKR family, AR, gap junction, FTO, TEAD, DHODH, TAS2R14, ion channels, and DNA. Besides, this paper discusses other mechanisms, such as regulating Wnt/β-catenin, TGF-β, p38 MAPK, and NF-κB pathway, and the regulation of the expressions of Sp, EGR-1, NAG-1, ATF-3, ErbB2, AR, as well as the modulation of the tumor immune microenvironment. Furthermore, this paper outlined the structural modifications of fenamates, highlighting their potential as promising leads for anticancer drugs.

Selected Genetic Characteristics of the Vietnamese Minority Living in the Czech Republic

The aim of this study was to analyse the allelic distribution of selected genes in the Czech and Vietnamese populations. We analysed samples from 94 Vietnamese volunteers and 2,859 Czech population-based subjects (2,559 from the Czechs post-MONICA and 300 volunteers from the South region of the Czech Republic). There were significant differences between the two populations for most, but not all, of the SNPs analysed. In particular, the prevalence of risk alleles in the analysed polymorphisms tended to be lower in the Vietnamese community compared to the Czech population, especially within the FTO (rs17817449; associated with obesity risk, P < 0.0001), TCF7L2 (rs7903146; linked to type 2 dia-betes, P < 0.0001) and ADH1B (rs1229984; related to alcohol consumption, P < 0.0001) genes. The genotype within the MCM6/LCT cluster (rs4988235) associated with lactase persistence was not present in the Vietnamese population. Slight genotype differences were detected for one HFE polymorphism (rs1799945 with P = 0.005; but not for rs1800562). Only the genotype frequencies within the MC4R and APOE genes were almost identical in both populations. We conclude that the Vietnamese population may have a lower genetic predisposition to the non-communicable diseases such as obesity or diabetes mellitus.

Novel insights into the interaction between IGF2BPs and ncRNAs in cancers

Insulin-like growth factor II mRNA-binding proteins (IGF2BPs), a family of RNA-binding proteins, are pivotal in regulating RNA dynamics, encompassing processes such as localization, metabolism, stability, and translation through the formation of ribonucleoprotein complexes. First identified in 1999 for their affinity to insulin-like growth factor II mRNA, IGF2BPs have been implicated in promoting tumor malignancy behaviors, including proliferation, metastasis, and the maintenance of stemness, which are associated with unfavorable outcomes in various cancers. Additionally, non-coding RNAs (ncRNAs), particularly long non-coding RNAs, circular RNAs, and microRNAs, play critical roles in cancer progression through intricate protein-RNA interactions. Recent studies, predominantly from 2018 onward, indicate that IGF2BPs can recognize and modulate ncRNAs via N6-methyladenosine (m6A) modifications, enriching the regulatory landscape of RNA-protein interactions in the context of cancer. This review explores the latest insights into the interplay between IGF2BPs and ncRNAs, emphasizing their potential influence on cancer biology.

FOXF2 suppressed esophageal squamous cell carcinoma by reducing M2 TAMs via modulating RNF144A-FTO axis

Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers because of its high invasiveness and low survival. Tumor-associated macrophages (TAMs) are closely associated with the tumor cell proliferation, metastasis and immunosuppression. As a member of the FOX family, forkhead box F2 (FOXF2) was down-regulated in ESCC. However, its role in ESCC and TAMs, as well as the underlying mechanism, remains unclear. We found that differentially expressed genes (DEGs) in ESCC were enriched in proliferation, migration, macrophage and cancer pathways. Among these DEGs, FOXF2 caught our eyes. FOXF2 was down-regulated in ESCC. Overexpression FOXF2 inhibited the proliferation of ESCC cells and the M2 polarization of TAMs, but silenced FOXF2 reversed these results. Notably, FOXF2 promoted the transcription of ring finger protein 144A (RNF144A), which is an E3 ubiquitin ligase, causing the ubiquitination and degradation of FTO Alpha-Ketoglutarate Dependent Dioxygenase (FTO), an N6-methyladenosine (m6A) demethylase. Furthermore, overexpression of FTO abolished the effects of FOXF2 on TAM polarization. In conclusion, FOXF2 alleviates ESCC via promoting the transcription of RNF144A which results in the ubiquitylation and degradation of FTO. Targeting FOXF2/RNF144A/FOT axis might be a possible strategy for the treatment of ESCC.

m6A demethylation of NNMT in CAFs promotes gastric cancer progression by enhancing macrophage M2 polarization

Cancer associated fibroblasts (CAFs) are the predominant stromal cells in the tumor microenvironment of gastric cancer (GC), interacting with both immune and tumor cells to drive cancer progression. However, the precise link between these interactions and their potential as therapeutic targets remains poorly understood. In this study, we identified for the first time that nicotinamide N-methyltransferase (NNMT) derived from CAFs promoted M2 macrophage polarization, which, in turn, facilitated the proliferation and migration of GC cells. Additionally, we discovered that NNMT expression in CAFs was regulated by the Fat mass and obesity related protein (FTO) via m6A demethylation. Both NNMT and FTO were highly expressed in tumor tissues and CAFs, with a positive correlation between FTO and NNMT levels in clinical samples. Mechanistically, FTO bound to NNMT mRNA, reducing m6A modification and enhancing NNMT expression. Knockdown of either NNMT or FTO in CAFs effectively inhibited M2 macrophage polarization and suppressed GC progression. These findings were validated in patient-derived organoid models and nude mouse models of GC. Collectively, our data revealed that FTO promoted M2 macrophage polarization by regulating the m6A demethylation of NNMT in CAFs, thereby driving GC progression. This identified a potential novel target for GC diagnosis and therapy.

FTO in health and disease

Fat mass and obesity-associated (FTO) protein, a key enzyme integral to the dynamic regulation of epitranscriptomic modifications in RNAs, significantly influences crucial RNA lifecycle processes, including splicing, export, decay, and translation. The role of FTO in altering the epitranscriptome manifests across a spectrum of physiological and pathological conditions. This review aims to consolidate current understanding regarding the implications of FTO in health and disease, with a special emphasis on its involvement in obesity and non-communicable diseases associated with obesity, such as diabetes, cardiovascular disease, and cancer. It also summarizes the established molecules with FTO-inhibiting activity. Given the extensive impact of FTO on both physiology and pathophysiology, this overview provides illustrative insights into its roles, rather than an exhaustive account. A proper understanding of FTO function in human diseases could lead to new treatment approaches, potentially unlocking novel avenues for addressing both metabolic disorders and malignancies. The evolving insights into FTO's regulatory mechanisms hold great promise for future advancements in disease treatment and prevention.

A Demethylation-Switchable Aptamer Design Enables Lag-Free Monitoring of m6A Demethylase FTO with Energy Self-Sufficient and Structurally Integrated Features

Cellular context profiling of modification effector proteins is critical for an in-depth understanding of their biological roles in RNA N6-methyladenosine (m6A) modification regulation and function. However, challenges still remain due to the high context complexities, which call for a versatile toolbox for accurate live-cell monitoring of effectors. Here, we propose a demethylation-switchable aptamer sensor engineered with a site-specific m6A (DSA-m6A) for lag-free monitoring of the m6A demethylase FTO activity in living cells. As a proof of concept, a DNA aptamer against adenosine triphosphate (ATP) is selected to construct the DSA-m6A model, as the "universal energy currency" role of ATP could guarantee the equally fast and spontaneous conformation change of DSA-m6A sensor upon demethylation and ATP binding in living organisms, thus enabling sensitive monitoring of FTO activity with neither time delay nor recourse to extra supply of substances. This ATP-driven DSA-m6A design facilitates biomedical research, including live-cell imaging, inhibitor screening, single-cell tracking of dynamic FTO nuclear translocation upon starvation stimuli, FTO characterization in a biomimetic heterotypic three-dimensional (3D) multicellular spheroid model, as well as the first report on the in vivo imaging of FTO activity. This strategy provides a simple yet versatile toolbox for clinical diagnosis, drug discovery, therapeutic evaluation, and biological study of RNA demethylation.

Targeting DTX2/UFD1-mediated FTO degradation to regulate antitumor immunity

Here, we show that vitamin E succinate (VES) acts as a degrader for the m6A RNA demethylase fat mass and obesity-associated protein (FTO), thus suppressing tumor growth and resistance to immunotherapy. FTO is ubiquitinated by its E3 ligase DTX2, followed by UFD1 recruitment and subsequent degradation in the proteasome. VES binds to FTO and DTX2, leading to enhanced FTO-DTX2 interaction, FTO ubiquitination, and degradation in FTO-dependent tumor cells. VES suppressed tumor growth and enhanced antitumor immunity and response to immunotherapy in vivo in mouse models. Genetic FTO knockdown or VES treatment increased m6A methylation in the LIF (Leukemia Inhibitory Factor) gene and decreased LIF mRNA decay, and thus sensitized melanoma cells to T cell-mediated cytotoxicity. Taken together, our findings reveal the underlying molecular mechanism for FTO protein degradation and identify a dietary degrader for FTO that inhibits tumor growth and overcomes immunotherapy resistance.

Off-Target Inhibition of Human Dihydroorotate Dehydrogenase (hDHODH) Highlights Challenges in the Development of Fat Mass and Obesity-Associated Protein (FTO) Inhibitors

FTO, an N 6-methyladenosine (m6A) and N 6,2'-O-dimethyladenosine (m6Am) RNA demethylase, is a promising target for treating acute myeloid leukemia (AML) due to the significant anticancer activity of its inhibitors in preclinical models. Here, we demonstrate that the FTO inhibitor FB23-2 suppresses proliferation across both AML and CML cell lines, irrespective of FTO dependency, indicating an alternative mechanism of action. Metabolomic analysis revealed that FB23-2 induces the accumulation of dihydroorotate (DHO), a key intermediate in pyrimidine nucleotide synthesis catalyzed by human dihydroorotate dehydrogenase (hDHODH). Notably, structural similarities between the catalytic pockets of FTO and hDHODH enabled FB23-2 to inhibit both enzymes. In contrast, the hDHODH-inactive FB23-2 analog, ZLD115, required FTO for its antiproliferative activity. Similarly, the FTO inhibitor CS2 (brequinar), known as one of the most potent hDHODH inhibitors, exhibited FTO-independent antileukemic effects. Uridine supplementation fully rescued leukemia cells from FB23-2 and CS2-induced growth inhibition, but not ZLD115, confirming the inhibition of pyrimidine synthesis as the primary mechanism of action underlying their antileukemic activity. These findings underscore the importance of considering off-target effects on hDHODH in the development of FTO inhibitors to optimize their therapeutic potential and minimize unintended consequences.

Assembly of Dandelion-Like Nanoprobe for Sensitive Detection of N6-Methyladenosine Demethylase by Single-Molecule Counting

N6-methyladenosine (m6A) demethylase is essential for enzymatically removing methyl groups from m6A modifications and is significantly implicated in the pathogenesis and advancement of various cancers, which makes it a promising biomarker for cancer detection and research. As a proof of concept, we select the fat mass and obesity-associated protein (FTO) as the target m6A demethylase and develop a dandelion-like nanoprobe-based sensing platform by employing biobar-code amplification (BCA) for signal amplification. We construct two meticulously designed three-dimensional structures: reporter-loaded gold nanoparticles (Reporter@Au NPs) and substrate-loaded magnetic microparticles (Substrate@MMPs), which can self-assemble to form dandelion-like nanoprobes via complementary base pairing. In the presence of FTO, the m6A-containing substrates are demethylated, triggering the MazF-assisted cleavage reaction and thereby releasing the Reporter@Au NPs. Furthermore, upon digestion by exonucleases, the Reporter@Au NPs may liberate a significant quantity of Cy3 signals. Remarkably, the combined effects of Au NPs' superior enrichment capacity, MMPs' exceptional magnetic separation efficiency, and the precision of the single-molecule detection platform endow the FTO sensor with exceptional sensitivity and specificity with a detection limit of 7.46 × 10-16 M. Additionally, this method offers a versatile platform for the detection of m6A demethylase and the screening of corresponding inhibitors, thereby advancing clinical diagnosis and drug development.

FTO-mediated demethylation of MTUS1/ATIP1 promotes tumor progression in head and neck squamous cell carcinoma

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) has been recognized as the seventh most prevalent malignant tumor globally. It is a malignant neoplasm that arises from the mucosal epithelium of head and neck region. In our previous research, we have demonstrated that MTUS1/ATIP1 exhibits anti-cancer properties in HNSCC. Nevertheless, the underlying mechanism responsible for the reduction of MTUS1/ATIP1 expression has not been investigated.

METHODS

HNSCC and adjacent normal tissues were collected and examined using m6A MeRIP-seq, qRT-PCR, and IHC to investigate the relationship between MTUS1/ATIP1 and FTO. MeRIP-qPCR, m6A dot blot, RNA and protein stability assays, and RNC-qRT-PCR were employed to elucidate the mechanism by which FTO mediates demethylation of MTUS1/ATIP1 in HNSCC. Functional assays, subcutaneous tumorigenesis, and in situ tongue cancer models were conducted to assess the impact of the FTO-MTUS1/ATIP1 pathway on proliferative capacity of HNSCC tumors.

RESULTS

FTO was observed to be markedly upregulated and showed a negative correlation with MTUS1/ATIP1 expression in HNSCC. FTO was responsible for mediating m6A demethylation in the 3'UTR of MTUS1/ATIP1, leading to its degradation. Additionally, silencing MTUS1/ATIP1 successfully reversed the tumor-promoting effects on HNSCC triggered by FTO in in vitro and in vivo.

CONCLUSIONS

Our research elucidated the functional importance of FTO-mediated m6A demethylation of MTUS1/ATIP1, suggesting that targeting the FTO-MTUS1/ATIP1 axis could be a prospective novel approach for treating HNSCC.

Epigenetics-targeted drugs: current paradigms and future challenges

Epigenetics governs a chromatin state regulatory system through five key mechanisms: DNA modification, histone modification, RNA modification, chromatin remodeling, and non-coding RNA regulation. These mechanisms and their associated enzymes convey genetic information independently of DNA base sequences, playing essential roles in organismal development and homeostasis. Conversely, disruptions in epigenetic landscapes critically influence the pathogenesis of various human diseases. This understanding has laid a robust theoretical groundwork for developing drugs that target epigenetics-modifying enzymes in pathological conditions. Over the past two decades, a growing array of small molecule drugs targeting epigenetic enzymes such as DNA methyltransferase, histone deacetylase, isocitrate dehydrogenase, and enhancer of zeste homolog 2, have been thoroughly investigated and implemented as therapeutic options, particularly in oncology. Additionally, numerous epigenetics-targeted drugs are undergoing clinical trials, offering promising prospects for clinical benefits. This review delineates the roles of epigenetics in physiological and pathological contexts and underscores pioneering studies on the discovery and clinical implementation of epigenetics-targeted drugs. These include inhibitors, agonists, degraders, and multitarget agents, aiming to identify practical challenges and promising avenues for future research. Ultimately, this review aims to deepen the understanding of epigenetics-oriented therapeutic strategies and their further application in clinical settings.

Dynamic multilayered control of m6A RNA demethylase activity

Similar to DNA and histone, RNA can also be methylated. In its most common form, a N6-methyladenosine (m6A) chemical modification is introduced into nascent messenger ribonucleic acid (mRNA) by a specialized methyltransferase complex and removed by the RNA demethylases, Fat mass and obesity-associated (FTO), and ALKBH5. The fate of m6A-marked mRNA is uniquely diverse, ranging from degradation to stabilization/translation, which has been suggested to be largely dependent on its interaction with the family of YT521-B homology (YTH) domain-containing proteins. Here, we highlight a series of control levers that impinge on the RNA demethylases. We present evidence to indicate that intermediary metabolism and various posttranslation modifications modulate the activity, stability, and the subcellular localization of FTO and ALKBH5, further dispelling the notion that m6A methylation is not a dynamic process. We also discuss how examination of these underappreciated regulatory nodes adds a more nuanced view of the role of FTO and ALKBH5 and should guide their study in cancer and nonmalignant conditions alike.

Epigenetics and alternative splicing in cancer: old enemies, new perspectives

In recent years, significant strides in both conceptual understanding and technological capabilities have bolstered our comprehension of the factors underpinning cancer initiation and progression. While substantial insights have unraveled the molecular mechanisms driving carcinogenesis, there has been an overshadowing of the critical contribution made by epigenetic pathways, which works in concert with genetics. Mounting evidence demonstrates cancer as a complex interplay between genetics and epigenetics. Notably, epigenetic elements play a pivotal role in governing alternative pre-mRNA splicing, a primary contributor to protein diversity. In this review, we have provided detailed insights into the bidirectional communication between epigenetic modifiers and alternative splicing, providing examples of specific genes and isoforms affected. Notably, succinct discussion on targeting epigenetic regulators and the potential of the emerging field of epigenome editing to modulate splicing patterns is also presented. In summary, this review offers valuable insights into the intricate interplay between epigenetics and alternative splicing in cancer, paving the way for novel approaches to understanding and targeting this critical process.

Crosstalk Between m6A RNA Methylation and miRNA Biogenesis in Cancer: An Unholy Nexus

N6-methyladenosine (m6A) is one of the most prevalent internal reversible chemical modification of RNAs in eukaryotes, which has attracted widespread attention recently owing to its regulatory roles in a plethora of normal developmental processes and human diseases like cancer. Deposition of the m6A mark on RNAs is mediated by the dynamic interplay between m6A regulatory proteins such as m6A RNA methyltransferases (m6A writers), m6A RNA demethylases (m6A erasers) and m6A RNA binding proteins (m6A readers). m6A regulators are ectopically expressed in various cancer types, often leading to aberrant expression of tumor-suppressor and oncogenic mRNAs either directly or indirectly via regulating the biogenesis of non-coding RNAs like miRNAs. miRNAs are tiny regulators of gene expression, which often impact various hallmarks of cancer and thus influence tumorigenesis. It is becoming increasingly clear that m6A RNA modification impacts biogenesis and function of miRNAs, and recent studies have interestingly, uncovered many miRNAs whose biogenesis and function are regulated by m6A writers, erasers and readers. In this review, we discuss various mechanisms by which m6A RNA methylation regulates miRNA biogenesis, the functional crosstalk between m6A RNA methylation and miRNAs and how it modulates various aspects of tumorigenesis. The potential of m6A RNA methylation regulated miRNAs as biomarkers and novel therapeutic targets to treat various cancers is also addressed.

Unraveling the landscape of m6A RNA methylation in wound healing and scars

Wound healing is a complex process involving sequential stages of hemostasis, inflammation, proliferation, and remodeling. Multiple cell types and factors, including underlying conditions like diabetes and bacterial colonization, can influence healing outcomes and scar formation. N6-methyladenosine (m6A), a predominant RNA modification, plays crucial roles in gene expression regulation, impacting various biological processes and diseases. m6A regulates embryonic skin morphogenesis, wound repair, and pathophysiological processes like inflammation and angiogenesis. Recent studies have highlighted the role of m6A in wound healing, scar formation, and tissue remodeling. Additionally, m6A presents a unique expression pattern in pathological wounds and scars, potentially influencing wound healing and scar formation through modulating gene expression and cellular signaling, thereby serving as potential biomarkers or therapeutic targets. Targeting m6A modifications are potential strategies to enhance wound healing and reduce scar formation. This review aims to explore the roles and mechanisms of m6A RNA methylation in wound healing and scars, and discuss current challenges and perspectives. Continued research in this field will provide significant value for optimal wound repair and scar treatment.

The regulatory mechanisms of N6-methyladenosine modification in ferroptosis and its implications in disease pathogenesis

HEADING AIMS

Based on the current knowledge of the molecular mechanisms by which m6A influences ferroptosis, our objective is to underscore the intricate and interdependent relationships between m6A and the principal regulatory pathways of ferroptosis, as well as other molecules, emphasizing its relevance to diseases associated with this cell death mode.

MATERIALS AND METHODS

We conducted a literature search using the keywords "m6A and ferroptosis" across PubMed, Web of Science, and Medline. The search was limited to English-language publications from 2017 to 2024. Retrieved articles were managed using Endnote software. Two authors independently screened the search results and reviewed the full texts of selected articles.

KEY FINDINGS

Abnormal m6A levels are often identified as critical regulators of ferroptosis. Specifically, "writers", "readers" and "erasers" that dynamically modulate m6A function regulate various pathways in ferroptosis including iron metabolism, lipid metabolism and antioxidant system. Additionally, we provide an overview of the role of m6A-mediated ferroptosis in multiple diseases and summarize the potential applications of m6A-mediated ferroptosis, including its use as a therapeutic target for diseases and as diagnostic as well as prognostic biomarkers.

SIGNIFICANCE

N6-methyladenosine (m6A) modification, a prevalent RNA modification in eukaryotic cells, is crucial in regulating various aspects of RNA metabolism. Notably, accumulating evidence has implicated m6A modification in ferroptosis, a form of iron-dependent cell death characterized by elevated iron levels and lipid peroxide accumulation. Overall, this review sheds light on the potential diagnostic and therapeutic applications of m6A regulators in addressing conditions associated with ferroptosis.

N6-Methyladenosine (m6A) Reader IGF2BP1 Accelerates Gastric Cancer Development and Immune Escape by Targeting PD-L1

N6-methyladenosine (m6A) functions as an important regulator in various human cancers, including gastric cancer. The immunotherapy targeting PD-1/PD-L1 has brought hope for advanced gastric cancer therapeutic. Here, present research aims to investigate the roles of m6A reader IGF2BP1 on gastric cancer tumor development and immune escape. Results indicated that IGF2BP1 up-regulated in the gastric cancer tissue and correlated with poor prognosis of gastric cancer patients. IGF2BP1 overexpression augmented the proliferation of co-cultured gastric cancer cells, and mitigated the CD8+ T cells mediated anti-tumor response, including IFN-γ secretion, surface PD-L1 level, and cytotoxicity of CD8+ T cells. Meanwhile, IGF2BP1 silencing exerted the opposite effects. In silico analysis revealed that there was a remarkable m6A modified site on PD-L1 mRNA. Moreover, the IGF2BP1 overexpression enhanced the stability of PD-L1 mRNA, thereby deteriorating the immune escape of gastric cancer cells. Collectively, these results describe a novel regulatory mechanism of IGF2BP1 by regulating PD-L1 through m6A epigenetic modification, which might provide insights for gastric cancer immunotherapies.