Role of m6A writers, erasers and readers in cancer

METTL3/IGF2BP3 mediates ORC6 via N6-methyladenosine modification to promote the progression of pancreatic ductal adenocarcinoma

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is recognized globally as one of the most lethal tumours, and effective biomarkers to diagnose PDAC early are needed. ORC6, a subunit of the origin recognition complex (ORC), initiates DNA replication and ensures genomic stability. Previous studies have indicated that ORC6 is procarcinogenic in various cancers, yet its role in PDAC remains uninvestigated.

METHODS

We evaluated the relationships between ORC6 expression and the clinical features of patients with PDAC with the TCGA, GTEx, and GEO databases. The role of ORC6 in PDAC cells was explored by RNA interference in vitro and in vivo. Next, we verified the effect of the METTL3/IGF2BP3/ORC6 axis on PDAC progression by western blotting, RT-qPCR, RNA immunoprecipitation, and methylated RNA immunoprecipitation. Finally, transcriptome analysis was performed to explore the influence of ORC6 on p53 in PDAC cells.

RESULTS

Elevated ORC6 levels were observed in PDAC cells, which correlated with poorer clinical outcomes. Both in vivo and in vitro experiments demonstrated that ORC6 knockdown suppressed proliferation and promoted apoptosis. Additionally, we demonstrated that METTL3/IGF2BP3 interacted with ORC6 mRNA via N6-methyladenosine modification to improve ORC6 mRNA stability. Transcriptomic analysis and experiments indicated that ORC6 promoted PDAC progression by inhibiting serine-15 phosphorylation in p53.

CONCLUSION

Our findings validate the role of ORC6 in PDAC and support the hypothesis that the METTL3/IGF2BP3/ORC6/p53 axis may be a novel therapeutic target for PDAC, and inhibiting this axis may be an advantageous therapeutic strategy for curing PDAC.

Emerging importance of m6A modification in liver cancer and its potential therapeutic role

Liver cancer refers to malignant tumors that form in the liver and is usually divided into several types, the most common of which is hepatocellular carcinoma (HCC), which originates in liver cells. Other rare types of liver cancer include intrahepatic cholangiocarcinoma (iCCA). m6A modification is a chemical modification of RNA that usually manifests as the addition of a methyl group to adenine in the RNA molecule to form N6-methyladenosine. This modification exerts a critical role in various biological processes by regulating the metabolism of RNA, affecting gene expression. Recent studies have shown that m6A modification is closely related to the occurrence and development of liver cancer, and m6A regulators can further participate in the pathogenesis of liver cancer by regulating the expression of key genes and the function of specific cells. In this review, we provided an overview of the latest advances in m6A modification in liver cancer research and explored in detail the specific functions of different m6A regulators. Meanwhile, we deeply analyzed the mechanisms and roles of m6A modification in liver cancer, aiming to provide novel insights and references for the search for potential therapeutic targets. Finally, we discussed the prospects and challenges of targeting m6A regulators in liver cancer therapy.

Harnessing engineered exosomes as METTL3 carriers: Enhancing osteogenesis and suppressing lipogenesis in bone marrow mesenchymal stem cells for postmenopausal osteoporosis treatment

Postmenopausal osteoporosis (PMOP), a prevalent skeletal disorder among women post-menopause, has emerged as a pressing global public health concern. Exosomes derived from serum have exhibited encouraging therapeutic potential in addressing PMOP, albeit with underlying mechanisms requiring deeper exploration. To elucidate these mechanisms, we devised a mouse model by surgically inducing ovariectomy and isolated exosomes from serum samples. Subsequently, we employed qRT-PCR, Western blotting, and immunofluorescence analysis to quantify relevant gene and protein expression patterns. To assess the biological effects on treated cells and tissues, we utilized ARS staining, oil red O staining, and micro-CT analysis. Additionally, we examined the METTL3/FOXO1 m6A site interaction and the FOXO1/YTHDF1 complex using dual-luciferase reporter assays and RIP assays. The m6A modification levels of FOXO1 were quantified via MeRIP-PCR. Furthermore, we engineered bone marrow mesenchymal stem cell exosomes by loading abundant METTL3 mRNA and decorating their surfaces with bone-targeting peptides. The successful synthesis and bone-targeting capabilities of these modified exosomes were validated through electron microscopy, in vivo imaging, and immunofluorescence staining. Our findings reveal that METTL3, in collaboration with YTHDF1 within serum-derived exosomes, enhances FOXO1 gene transcription by fostering m6A modification of FOXO1. This, in turn, promotes osteogenic differentiation of bone marrow mesenchymal stem cells while inhibiting lipogenic differentiation. Notably, our engineered exosomes, BT-oe-METTL3-EXO, not only harbor high levels of METTL3 but also demonstrate exceptional bone-targeting efficiency. In vitro studies demonstrated that BT-oe-METTL3-EXO significantly mitigated bone mass loss induced by ovariectomy in mice, bolstered osteogenic differentiation of mouse bone marrow mesenchymal stem cells, and inhibited lipogenic differentiation. Collectively, our research underscores the pivotal regulatory function of serum-derived exosomes in human bone marrow stem cells (hBMSCs) and underscores the promising therapeutic potential of BT-oe-METTL3-EXO for combating postmenopausal osteoporosis.

Knockdown of YTHDF2 mitigates OGD-induced microglial inflammation by preventing m6A-dependent PARP14 degradation

Neuroinflammation is a key pathological factor in ischemic brain diseases, contributing to the initiation and progression of these conditions. The function of the m6A reader protein YTHDF2 in regulating neuroinflammation across various neurological contexts. To elucidate the role and regulatory mechanism of YTHDF2 in inflammation under ischemic-like conditions, this study employed an in vitro model, exposing microglia to oxygen-glucose deprivation (OGD) to mimic the stress environment. And through YTHDF2 knockdown, we investigated its effect on OGD-induced inflammation. The results demonstrated that YTHDF2 knockdown significantly suppressed the expression of pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6), in OGD-treated microglia. Mechanistic analysis revealed that YTHDF2 interacts with Parp14 mRNA under OGD conditions, reducing its RNA stability via m6A-dependent mechanisms, which in turn decreases Poly (ADP-ribose) polymerase family, member 14 (PARP14) protein expression. Additionally, YTHDF2 knockdown after OGD promoted a PARP14-driven phenotypic switch in microglia from the pro-inflammatory M1 state to the anti-inflammatory M2 state, resulting in diminished inflammation. These findings offer new insights into the regulatory function of YTHDF2 in OGD-induced microglial inflammation and propose m6A modification as a potential therapeutic target for alleviating neuroinflammation.

Placental RTN3L-dependent ER-Phagy Contributes to Fetal Testicular Dysplasia Upon Environmental Stress

Prenatal environmental stress damages fetal testicular development, leading to male infertility. However, the precise mechanisms underlying the impact of gestational environmental stress on fetal testicular development require further investigation. This study demonstrates that gestational environmental stressor cadmium exposure caused placental estradiol synthesis inhibition and fetal testicular dysplasia. Gestational estradiol supplementation restores fetal testicular dysplasia caused by environmental stress-induced placental estradiol synthesis inhibition. Analysis of human placentae and cadmium-stimulated human primary placental trophoblasts confirmed that ER-phagy is associated with the inhibition of estradiol synthesis in placentae. Subsequently, the data reveals that environmental stress significantly activates RTN3L-mediated ER-phagy. RTN3L-deficient cells and placental Rtn3l-specific knockout mice confirm that environmental stress-activated RTN3L-mediated ER-phagy inhibited placental estradiol synthesis. Total N6-methyladenosine level increasing in gestational environmental stress-exposed placentae. METTL3-mediated N6-methyladenosine modification suppression obviously restrains environmental stress-activated RTN3L-dependent ER-phagy. In conclusion, gestational environmental stress activates ER-phagy by increasing placental Rtn3l mRNA N6-methyladenosine modification, inhibiting placental estradiol synthesis, and contributing to fetal testicular dysplasia. The study demonstrates the early prevention and treatment of adult male infertility from the perspective of fetal-derived diseases.

METTL3 orchestrates cancer progression by m6A-dependent modulation of oncogenic lncRNAs

RNA modifications, particularly N6-methyladenosine (m6A), play crucial roles in gene expression regulation. While extensively studied in the context of mRNA, the impact of m6A on long non-coding RNAs (lncRNAs) remains elusive. This research aimed to reveal the regulatory landscape of m6A in lncRNA expression. In a comprehensive analysis across 6219 samples spanning 12 cancer types, we unveiled METTL3 as the most potent regulator of lncRNA expression among the examined 19 m6A regulators. A total of 397 METTL3-mediated m6A-modified lncRNAs (mmlncRs) were unveiled across 12 cancer types, indicating a consistent mechanism of METTL3-mediated lncRNA regulation. Functional assays demonstrated that METTL3 knockout significantly impeded lung cancer cell proliferation and progression. Leveraging RNA-seq and MeRIP-seq, we identified C1RL-AS1 as a bona fide m6A target of METTL3 in lung cancer, revealing its oncogenic role. Mechanistically, METTL3 depletion disrupts m6A modification on C1RL-AS1, leading to its downregulated expression. YTHDF2 binds to C1RL-AS1, maintaining its stability in a m6A-dependent manner. This study provides a valuable resource for the exploration of mmlncRs as promising therapeutic targets in cancers, shedding light on the intricate regulatory networks orchestrated by METTL3.

YTHDF3 drives tumor growth and metastasis by recruiting eIF4B to promote Notch2 translation in breast cancer

YTH domain family protein 3 (YTHDF3), an m6A RNA reader, is implicated in various cancers, but its role in breast cancer progression and metastasis remains unclear. In this study, we explore the oncogenic potential of YTHDF3 in breast cancer, focusing on its impact on epithelial-mesenchymal transition (EMT) and metastasis. We found that YTHDF3 is significantly upregulated in breast cancer tissues and associated with poor relapse-free survival (RFS). Functional studies demonstrated that YTHDF3 promotes EMT in breast cancer cell lines by enhancing cell migration, invasion, and metastasis in vivo. Mechanistically, we show that YTHDF3 regulates Notch2, a key driver of EMT, through an m6A-dependent mechanism. YTHDF3 binds to m6A-modified Notch2 mRNA and recruits eIF4B to facilitate its translation, leading to increased Notch2 translation and subsequent inducing EMT. Our findings highlight the importance of the YTHDF3-Notch2 axis in driving EMT and metastasis in breast cancer. Furthermore, targeting YTHDF3 with lipid nanoparticles (LNPs) encapsulating siRNA and indocyanine green (ICG) significantly suppressed tumor growth and lung metastasis while enabling real-time therapeutic monitoring via ICG fluorescence imaging. These findings establish YTHDF3 as a critical driver of EMT and metastasis through m6A-dependent Notch2 translation, highlighting its potential as a therapeutic target in breast cancer.

Circular RNA circCD44 targets methyltransferase-like 3/homeobox containing 1 to facilitate esophageal squamous cell carcinoma progression

Esophageal squamous cell carcinoma (ESCC) is a prevalent gastrointestinal malignancy with unclear functional mechanisms of circular RNAs. This study focused on investigating the role of circCD44 in ESCC progression. The expression of circCD44 and homeobox containing 1 (HMBOX1) was found to be elevated in ESCC cell lines. The overexpression of circCD44 or HMBOX1 enhanced proliferation and invasion, while inhibiting apoptosis in ESCC cells, whereas knockdown of these genes had inverse effects. METTL3 was observed to bind to circCD44 and HMBOX1 mRNA, promoting m6A modification in HMBOX1 mRNA and subsequent HMBOX1 protein expression. Knockdown of METTL3 or HMBOX1 attenuated the oncogenic effects of circCD44 overexpression both in vitro and in vivo. These findings suggest that circCD44 promotes ESCC progression by facilitating HMBOX1 mRNA m6A modification and protein expression through METTL3 binding, providing insights into the molecular mechanisms underlying ESCC pathogenesis.

Methyltransferase-like 3-mediated RNA N6-methyladenosine contributes to immune dysregulation: diagnostic biomarker and therapeutic target

Methyltransferase-like 3 (METTL3) plays a crucial role in post-transcriptional gene regulation. Substantial evidence links METTL3 to various immune dysfunctions, such as the suppression of antiviral immunity during viral infections and the disruption of immune tolerance in conditions like autoimmune diseases, myeloid leukemia, skin cancers, and anticancer immunotherapy. However, a thorough review and analysis of this evidence is currently missing, which limits the understanding of METTL3's mechanisms and significance in immune dysfunctions. This review aims to elucidate the roles and mechanisms of METTL3 in these immune issues, highlighting its connections and proposing new insights into its modulation of immune responses. Analysis results in this review suggest that METTL3 hampers antiviral immunity, worsens viral replication and infection, and disrupts immune tolerance; conversely, regulating METTL3 enhances antiviral immunity and facilitates viral clearance. Moreover, clinical data corroborates these findings, showing that METTL3 overexpression is associated with increased susceptibility to viral infections and autoimmune conditions. This review establishes a theoretical basis for considering METTL3 as a novel regulator, an important diagnostic biomarker, and a potential target for treating immune dysfunctions.

A pan-cancer analysis reveals the oncogenic and immunological role of insulin-like growth factor 2 mRNA-binding protein family members

PURPOSE

To investigate the expression and clinical significance of insulin-like growth factor 2 mRNA-binding protein family members (IGF2BPs) in pan-cancer and evaluate their potential as targets for tumor immunotherapy.

METHODS

Based on data from the cancer genome atlas (TCGA) database, pan-cancer analysis was conducted to examine the clinical significance of IGF2BPs expression in twenty-two tumors.

RESULTS

Differential expression analysis showed high expression of IGF2BPs in most tumor tissues. Survival and mutation analyses suggested that the overexpression of IGF2BPs was associated with poor prognosis and mutation status of certain tumors. Methylation analysis revealed the methylation levels of IGF2BP1/2/3 in certain tumors were intricately linked to their mRNA expression, patient prognosis, and immune cell infiltration. Enrichment analysis indicated that abnormal expression of IGF2BPs was associated with various common tumor-related pathways in different tumors, including AMPK, Hippo, PI3K-Akt, EMT, and p53. In addition, immune correlation analysis revealed that IGF2BPs were closely related to immunotherapy-related indicators (immune cell infiltration, major histocompatibility complex (MHC), immune checkpoints, tumor mutation burden (TMB), and microsatellite instability (MSI)) in some tumors. Drug sensitivity analysis indicated that IGF2BPs were sensitive to some common chemotherapeutic drugs (alvocidib, dasatinib, trametinib, and selumetinib).

CONCLUSION

IGF2BPs exhibit significantly high expression in most tumors and are associated with prognosis, pathological stage, mutational status, methylation levels, and the relevant indicators of immunotherapy sensitivity in multiple tumors. Moreover, IGF2BPs may play an oncogenic role by activating common signaling pathways. Therefore, IGF2BPs may be potential prognostic markers for tumor therapy and targets for immunotherapy and drug therapy.

m6A-modified LINC02418 induces transcriptional and post-transcriptional modification of CTNNB1 via interacting with YBX1 and IGF2BP1 in colorectal cancer

Colorectal cancer (CRC) represents a significant menace to human health, but its molecular pathogenesis remains unclear. Herein, we explored the functional role of LINC02418 in CRC progression. The function of LINC02418 in CRC was determined through vitro and in vivo experiments. The molecular mechanism of LINC02418 in CRC was explored by quantitative real-time PCR (qPCR) analyses, western blot, luciferase reporter assay, methylated RNA immunoprecipitation (MeRIP) assay, RNA pull-down, RNA immunoprecipitation (RIP) assay and chromatin immunoprecipitation (ChIP) assay. The results revealed that LINC02418 expression was upregulated in CRC tissues and the high expression of LINC02418 was related to unfavorable survival of CRC patients. Besides, knockdown of LINC02418 expression resulted in the inhibition of proliferation and metastasis of CRC cells in vitro and in vivo. Mechanistically, we found METTL3-mediated m6A modification induced the aberrant expression of LINC02418 in CRC. LINC02418 could interact with YBX1 and enhance YBX1 DNA-binding ability to the CTNNB1 promoter, resulting in transcriptional activation of CTNNB1. In the post-transcriptional stage, LINC02418 could also enhance CTNNB1 stability by promoting the interaction between IGF2BP1 protein and CTNNB1 mRNA. What is more, LINC02418 expression could be transcriptionally enhanced by YBX1 protein. Collectively, this study unveils a novel oncogenic mechanism for LINC02418 in CRC and the LINC02418 might be a novel therapeutic target in CRC treatment.

Sprouting sympathetic fibres release CXCL16 and norepinephrine to synergistically mediate sensory neuronal hyperexcitability in a rodent model of neuropathic pain

BACKGROUND

Chronic neuropathic pain generally has a poor response to treatment with conventional drugs. Sympathectomy can alleviate neuropathic pain in some patients, suggesting that abnormal sympathetic-somatosensory signaling interactions might underlie some forms of neuropathic pain. The molecular mechanisms underlying sympathetic-somatosensory interactions in neuropathic pain remain obscure.

METHODS

Lumbar sympathectomy was performed in spared nerve injury (SNI) mice or rats, and the up-down method was used to measure the mechanical paw withdrawal threshold. Dorsal root ganglia (DRG) injection and perfusion were used to deliver virus or drugs. Methylated RNA immunoprecipitation sequencing, RNA-sequencing, and immunoelectron microscopy were used to identify neurotransmitters.

RESULTS

We found that sprouting tyrosine hydroxylase-positive sympathetic fibres in DRG mediated the maintenance of mechanical allodynia after SNI (day 28, P<0.001). We further found that SNI significantly increased the N6-methyladenosine level of CXCL16 messenger RNA (day 28, P<0.001), which was attributable to the reduced N6-methyladenosine demethylase fat mass and obesity-associated protein (P=0.002) and increased interaction with YTHDF1 (P=0.013) in the sympathetic ganglion. Enhanced expression of CXCL16 in the sympathetic ganglia can lead to increases release into the DRG and act synergistically with norepinephrine from sympathetic terminals to enhance DRG neuronal excitability.

CONCLUSIONS

Norepinephrine and CXCL16 co-released from sympathetic nerve terminals in the DRG synergistically contribute to maintenance of neuropathic pain in a rodent model.

Molecular mechanisms of m6A modifications regulating tumor radioresistance

Radiotherapy is one of the most effective treatments for malignant tumors. Radioresistance is a major factor that contributes to radiotherapy failure and poor prognosis. Recent studies have elucidated the pivotal role of aberrant N6-methyladenosine (m6A) modification, the predominant internal mRNA modification in eukaryotic cells, influences cancer progression by disrupting gene expression and other critical cellular processes. Furthermore, aberrant m6A methylation provides a substrate for tumor therapy; however, whether it regulates tumor radioresistance remains unclear. Methylated transferase (writer), demethylated transferase (eraser), and methylated recognition protein (reader) are the three essential proteins that regulate m6A modification via different mechanisms in different tumors. This review summarizes the latest research advances in m6A methylation and aims to provide novel perspectives on the advancement of regimens to overcome radioresistance and tumor invasion.

IGF2BP3 promotes the proliferation and cisplatin resistance of bladder cancer by enhancing the mRNA stability of CDK6 in an m6A dependent manner

Cisplatin-based chemotherapy is a primary treatment for bladder cancer, yet the development of chemoresistance poses a significant therapeutic challenge. Insulin-like growth factor II mRNA binding protein 3 (IGF2BP3) is an RNA-binding protein and a key m6A reader that regulates various cancers through m6A-dependent mechanisms. However, its role in chemotherapy resistance in bladder cancer remains unclear. Our in vivo and in vitro experiments identified IGF2BP3 as a key regulator of cisplatin resistance in bladder cancer. We demonstrated that IGF2BP3 enhances the stability of CDK6 mRNA in an m6A-dependent manner, leading to increased CDK6 expression. This, in turn, promoted tumor cell proliferation and resistance to cisplatin chemotherapy. Moreover, we showed that the CDK6 inhibitor palbociclib effectively suppresses the pro-growth and chemoresistant effects induced by IGF2BP3 overexpression. These results suggested that the IGF2BP3/m6A/CDK6 axis plays a pivotal role in bladder cancer progression and chemoresistance, and that targeting this pathway with CDK6 inhibitors such as palbociclib may offer a promising therapeutic strategy for overcoming cisplatin resistance in bladder cancer.

The role of m6A modification during macrophage metabolic reprogramming in human diseases and animal models

Macrophage metabolic reprogramming refers to the process by which macrophages adjust their physiological pathways to meet survival and functional demands in different immune microenvironments. This involves a range of metabolic pathways, including glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, fatty acid oxidation, and cholesterol transport. By modulating the expression and activity of key enzymes and molecules within these pathways, macrophages can make the transition between pro- and anti-inflammatory phenotypes, thereby linking metabolic reprogramming to inflammatory responses and the progression of several diseases, such as atherosclerosis, inflammatory bowel disease (IBD), and acute lung injury (ALI). N6-methyladenosine (m6A) modification has emerged as a critical regulatory mechanism during macrophage metabolic reprogramming, broadly affecting RNA stability, translation, and degradation. Therapeutic strategies targeting m6A modification can regulate the onset of metabolic diseases by influencing macrophage metabolic changes, for instance, small molecule inhibitors of methyltransferase-like 3 (METTL3) can affect glucose metabolism and inhibit IBD. This review systematically explores recent findings on the role and molecular mechanisms of m6A modification during macrophage metabolic reprogramming in human diseases and animal models, underscoring its potential as a therapeutic target for metabolic diseases.

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.

METTL3-mediated m6A modification of SLC7A11 enhances nasopharyngeal carcinoma radioresistance by inhibiting ferroptosis

Radiotherapy is the primary treatment for nasopharyngeal carcinoma (NPC); nonetheless, radioresistance remains the leading cause of localized recurrence. Our study demonstrates a significant increase in the N6-methyladenosine (m6A) methylase METTL3 in NPC and other tumors. Mechanistically, METTL3 acts as an m6A methylase, enhancing the m6A modification of the solute carrier family 7 member 11 (SLC7A11) transcript, which increases its stability and expression, thereby inhibiting radiation-induced ferroptosis and ultimately inducing radioresistance in NPC. Furthermore, silencing SLC7A11 or employing the ferroptosis inducer Erastin negated the promoting effect of METTL3 on NPC cell radioresistance. These findings suggest that METTL3 could be a novel therapeutic target for overcoming radiotherapy resistance in NPC.

Identification of m6A methyltransferase-related WTAP and ZC3H13 predicts immune infiltrates in glioblastoma

Glioblastoma (GBM) is a prevalent and highly fatal primary malignant brain tumor. N6-methyladenosine (m6A) modification plays a critical role in the development of brain tumor. WTAP and ZC3H13 have been identified across various species. Immune contexture, which includes the tumor microenvironment (TME), plays a significant role in cancer progression and treatment. This study aimed to explore the potential impact between WTAP and ZC3H13 on the immunological characteristics of GBM. We utilized data from TCGA-GBM, GEO and CGGA datasets to obtain platform and probe data. Patients with GBM were stratified into two clusters based on the expression of WTAP and ZC3H13 using consensus clustering approach. Immune infiltration within the tumor microenvironment was assessed using ESTIMATE, CIBERSORT and ssGSEA methodologies. Functional disparities were determined through gene set enrichment analysis (GSEA). Tumor mutation burden (TMB) and immune checkpoint inhibitors (ICIs) were also analyzed. Co-expression network analysis (WGCNA) was used to identify genes associated with WTAP/ZC3H13 and immunity. Validation was performed using GEO and CGGA datasets. Our analysis revealed that cluster1 exhibited higher WTAP expression but lower ZC3H13 expression compared to cluster2. Cluster1 showed higher levels of immune infiltration and TMB compared to cluster2. WGCNA identified 15 genes closely associated with WTAP/ZC3H13 expression and immune scores, notably CTLA4, CD27, ICOS, and LAG3. Our results suggested that WTAP and ZC3H13 influence on immune contexture of GBM, providing new insights into tumor immunity in GBM.

Hyodeoxycholic acid ameliorates cholestatic liver fibrosis by facilitating m6A-regulated expression of a novel anti-fibrotic target ETV4

BACKGROUND & AIMS

Cholestatic liver fibrosis is a common pathological feature of various biliary tract diseases. The underlying pathological mechanisms are not fully understood, posing significant obstacles to the discovery of new drug targets. The aims of the current study were to evaluate protective effects of hyodeoxycholic acid (HDCA) against cholestatic liver fibrosis and to ascertain whether ETV4 is a novel anti-fibrotic target involved in the therapeutic effects of HDCA.

METHODS

The therapeutic effect of HDCA was verified using bile duct ligation and Abcb4-/- mouse models. Etv4-/- mice were subjected to bile duct ligation to investigate the role of ETV4 in liver fibrogenesis and the therapeutic effects of HDCA. The N6-methyladenosine (m6A) modification was investigated using methylated m6A RNA immunoprecipitation-qPCR and immunofluorescence/fluorescence in situ hybridization techniques.

RESULTS

HDCA levels were decreased in both cholestatic patients and mice, while HDCA supplementation significantly ameliorated cholestatic liver fibrosis. By inducing ETV4 expression in cholangiocytes, HDCA induced MMP9 secretion, facilitating extracellular matrix degradation. Findings in patients with cholestatic fibrosis and Etv4-/- mice further revealed a promising role of ETV4 in improving liver fibrosis and in mediating the therapeutic effects of HDCA. Mechanistically, HDCA promoted m6A modification of ETV4 mRNA, which thereby promotes IGF2BP1 recognition and PABPC1 recruitment to inhibit ETV4 mRNA deadenylation, leading to increased mRNA stability, storage in P-bodies, and prolonged translation. Mutation of the m6A site on ETV4 mRNA or knockdown of critical genes involved in m6A modification significantly abolished the therapeutic effects of HDCA.

CONCLUSIONS

The present study underscores ETV4 as a novel anti-fibrotic target and demonstrates that HDCA remodels extracellular matrix by facilitating m6A-regulated ETV4 expression, offering potential therapeutic approaches for cholestatic liver fibrosis.

IMPACT AND IMPLICATIONS

This study delves into the underlying mechanisms of cholestatic liver fibrosis and reveals potential therapeutic targets. The research highlights ETV4 as a novel anti-fibrotic target that is essential for the therapeutic effects of hyodeoxycholic acid against cholestatic liver fibrosis. These findings are important for both the scientific community and patients with cholestatic liver diseases, offering valuable insights for future therapeutic strategies that focus on regulating m6A-dependent epigenetic modifications of anti-fibrotic targets like ETV4 and developing new interventions utilizing hyodeoxycholic acid.

CSTF2 Supports Hypoxia Tolerance in Hepatocellular Carcinoma by Enabling m6A Modification Evasion of PGK1 to Enhance Glycolysis

Cleavage stimulation factor subunit 2 (CSTF2) is a fundamental factor in the regulation of 3'-end cleavage and alternative polyadenylation of pre-mRNAs. Previous work has identified a tumor-promoting role of CSTF2, suggesting that it may represent a potential therapeutic target. In this study, we aimed to elucidate the mechanistic function of CSTF2 in hepatocellular carcinoma (HCC). CSTF2 upregulation was frequent in HCC, and elevated levels of CSTF2 correlated with poor patient prognosis. Although CSTF2 inhibition did not suppress HCC growth under nonstress conditions, it supported tolerance and survival of HCC cells under hypoxic conditions. Mechanistically, CSTF2 increased phosphoglycerate kinase 1 (PGK1) protein production to enhance glycolysis, thereby sustaining the energy supply under hypoxic conditions. CSTF2 shortened the 3' untranslated region of PGK1 pre-mRNA by binding near the proximal polyadenylation site. This shortening led to a loss of N6-methyladenosine (m6A) modification sites that are bound by YTH m6A RNA-binding protein F2 and increase degradation of PGK1 mRNA. Concurrently, hypoxia increased m6A modification of PGK1 mRNA near the proximal polyadenylation site that was recognized by the YTH m6A RNA-binding protein C1, which recruited CSTF2 to enhance the shortening of the PGK1 3' untranslated region. A small-molecule screen identified masitinib as an inhibitor of CSTF2. Masitinib counteracted PGK1 upregulation by CSTF2 and suppressed the growth of HCC xenograft and patient-derived organoid models. In conclusion, this study revealed a function of CSTF2 in supporting HCC survival under hypoxia conditions through m6A modification evasion and metabolic reprogramming, indicating that inhibiting CSTF2 may overcome hypoxia tolerance in HCC. Significance: Targeting CSTF2 inhibits hepatocellular carcinoma survival in hypoxic microenvironments, which may be a promising therapeutic strategy for treating liver cancer.

Improved biosynthesis of tyrosol by epigenetic modification-based regulation and metabolic engineering in Saccharomyces cerevisiae

Aromatic amino acids and their derivatives are high value chemicals widely used in food, pharmaceutical and feed industries. Current preparation methods for aromatic amino acid products are fraught with limitations. In this study, the efficient biosynthesis of aromatic amino acid compound tyrosol was investigated by epigenetic modification-based regulation and optimization of the biosynthetic pathway of aromatic amino acids. The production of tyrosol was significantly improved by the overexpression of m6A modification writer Ime4 and reader Pho92, and the positive regulator Gcr2. Introduction of Bbxfpk and deletion of Gpp1 further improved tyrosol production. Then the feedback inhibition of the shikimate pathway was relieved by the mutants Aro4K229L and Aro7G141S. The final tyrosol producing engineered strain was constructed by the deletion of PHA2, replacement of the native promoter of ARO10 with the strong promoter PGK1p, and introduction of tyrosine decarboxylase PcAAS. In the background of m6A modification regulation, this strain ultimately produced 954.69 ± 43.72 mg/L of tyrosol, promoted by 61.7-fold in shake-flask fermentation.

FTO effects the proliferation, invasion, and glycolytic metabolism of colon cancer by regulating PKM2

PURPOSE

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. The Fat mass and obesity-associated protein (FTO), a genetic variant associated with obesity, significantly impact the energetic metabolism of mechanical tumors. However, research on the function of FTO in CRC is scarce.

METHODS

Bioinformatics analysis of TCGA and UALCAN databases was conducted to examine FTO expression in CRC. Immunohistochemistry was used to assess FTO and PKM2 protein expression in clinical specimens. In vitro experiments utilized five human colon cancer cell lines and a normal colon epithelial cell line, with Western blotting and RT-PCR for protein and mRNA quantification, respectively, and lentiviral transfection to modulate FTO expression. Cellular behaviors such as proliferation, migration, invasion, and apoptosis were evaluated using various assays. Immunofluorescence and Seahorse Xfe96 metabolic analysis were employed to study PKM2 expression changes and glycolytic stress. The effects of PKM2 inhibition by shikonin on cell viability and glycolytic activity were assessed using CCK-8 assay and Seahorse analysis.

RESULTS

An upregulation of FTO was observed in colon cancer through data mining and analysis of pathological specimens. Besides, we discovered that the impact of FTO on colon cancer glycolysis has significant implications for colon proliferation, invasion, and metastasis. The protein expression of PKM2 and the intensity of fluorescence staining in the nucleus of PKM2 were detected to be increased in colon carcinoma cells with over-expression of FTO.

CONCLUSION

FTO plays a significant role in CRC progression by regulating PKM2 and promoting glycolysis.

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.

m6A methylation modification: Potential pathways to suppress osteosarcoma metastasis

Osteosarcoma is a highly aggressive malignant bone tumor prone to metastasis, and its metastatic process is one of the main reasons for treatment failure and poor prognosis. Recent studies have demonstrated that modification of m6A methylation plays an important role in osteosarcoma metastasis, influencing both invasion and metastasis through various signaling pathways. Therefore, clarification of the specific effects of m6A methylation modification in osteosarcoma may reveal ways to improve the prognosis of osteosarcoma patients. The roles of various components involved in the m6A methylation modification process in osteosarcoma have been investigated, with studies focusing more on their effects than on their mechanisms. In this review, we focus on the interactions between the "writers," "erasers," and "readers" of m6A methylation and tumor metastasis-related factors to enhance the understanding of osteosarcoma and m6A methylation modification, with the aim of identifying clinical diagnostic biomarkers and potential therapeutic targets for osteosarcoma metastasis.

POU4F1 enhances lung cancer gemcitabine resistance by regulating METTL3-dependent TWF1 mRNA N6 adenosine methylation

This study aimed to investigate the role of POU Class 4 Homeobox 1 (POU4F1) in regulating gemcitabine (GEM) resistance in lung cancer cells. The mRNA and protein expressions were assessed using RT-qPCR, western blot, immunofluorescence, and immunohistochemistry. Cell viability and proliferation were assessed by CCK-8 assay and EdU assay. TUNEL staining and flow cytometry were employed to detect cell apoptosis. The m6A modification of TWF1 was detected using MeRIP assay. The interactions between molecules were validated using dual luciferase reporter gene, ChIP, and RIP assays. POU4F1 knockdown inhibited GEM resistance and autophagy in lung cancer cells. Mechanistically, POU4F1 transcriptionally activated methyltransferase-like protein 3 (METTL3) in GEM-resistant cells by binding to the METTL3 promoter. METTL3 promoted the N6-methyladenosine (m6A) modification and expression level of twinfilin-1 (TWF1). Overexpression of METTL3 and TWF1 weakened the effects of POU4F1 knockdown on GEM resistance and autophagy. Moreover, knockdown POU4F1 also enhanced GEM anti-tumor sensitivity in vivo. In conclusion, POU4F1 upregulation promoted GEM resistance in lung cancer cells by promoting autophagy through increasing METTL3-mediated TWF1 m6A modification.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04161-w.

METTL3 promotes immature dental pulp stem cells-induced angiogenesis by regulating ETS1 mRNA stability in an m6A-HuR-dependent manner

Angiogenesis serves as the determinate element of pulp regeneration. Dental pulp stem cell (DPSC) implantation can promote the regeneration of dental pulp tissue. Herein, the role of m6A methyltransferase methyltransferase-like 3 (METTL3) in regulating DPSCs-induced angiogenesis during pulp regeneration therapy was investigated. Cell DPSC viability, HUVEC migration, and angiogenesis ability were analyzed by CCK-8 assay, wound healing, Transwell assay, and tube formation assay. The global and EST1 mRNA m6A levels were detected by m6A dot blot and Me-RIP. The interactions between E26 transformation-specific proto-oncogene 1(ETS1), human antigen R(HuR), and METTL3 were analyzed by RIP assay. The relationship between METTL3 and the m6A site of ETS1 was performed by dual-luciferase reporter assay. ETS1 mRNA stability was examined with actinomycin D. Herein, our results revealed that human immature DPSCs (hIDPSCs) showed stronger ability to induce angiogenesis than human mature DPSCs (hMDPSCs), which might be related to ETS1 upregulation. ETS1 knockdown inhibited DPSCs-induced angiogenesis. Our mechanistic experiments demonstrated that METTL3 increased ETS1 mRNA stability and expression level on DPSCs in an m6A-HuR-dependent manner. ETS1 upregulation abolished sh-METTL3's inhibition on DPSCs-induced angiogenesis. METTL3 upregulation promoted DPSCs-induced angiogenesis by enhancing ETS1 mRNA stability in an m6A-HuR-dependent manner. This study reveals a new mechanism by which m6A methylation regulates angiogenesis in DPSCs, providing new insights for stem cell-based tissue engineering.

METTL3‑mediated N6‑methyladenosine modification of MMP9 mRNA promotes colorectal cancer proliferation and migration

N6‑methyladenosine (m6A) is the predominant chemical modification of eukaryotic mRNA, dynamically mediated by the RNA methyltransferase, methyltransferase-like 3 (METTL3). m6A modification plays a critical role in cancer progression through post‑transcriptional regulation in various types of cancer. However, the role of METTL3 and its associated m6A modification in colorectal tumorigenesis remains to be fully elucidated. In the present study, it was demonstrated that METTL3 expression and the m6A levels were both upregulated in colorectal cancer (CRC) and positively associated with clinical progression, based on the bioinformatics analysis of cancer databases. Furthermore, knockdown and overexpression of METTL3 notably affected CRC cell viability, apoptosis and migration in vitro. Similarly, xenograft animal models confirmed that METTL3 promoted CRC tumorigenicity in vivo. Mechanistically, it was revealed that the m6A modification of matrix metallopeptidase 9 (MMP9) mRNA mediated by METTL3 promoted its expression in CRC by decreasing its degradation. Collectively, the findings of the present study suggested that the METTL3/MMP9 axis could serve as a novel promising therapeutic candidate for CRC.

CircABCC1 reduces endometrial receptivity via METTL3/FAM155B axis

OBJECTIVE

Impaired endometrial receptivity is the main cause of embryo implantation failure. Little information is available on the role of circRNAs in endometrial receptivity. Here, the effect of circABCC1 on endometrial receptivity and its mechanism were investigated.

METHODS

GEO database was screened for key biomarkers for recurrent implantation failure (RIF). Endometrial epithelial cells (EECs) were cultured and transfected with circABCC1- and/or FAM155B-related vectors, followed by CCK-8 detection of cell proliferation, western blotting detection of receptivity-related factors LIF and DKK1, and ELISA detection of LIF secretion. An in vitro adhesion model was established to detect trophoblast adhesion to EECs. RIP was used to detect the binding of METTL3 to circABCC1 and FAM155B mRNA, and MeRIP-qPCR was used to detect m6A modification of FAM155B mRNA.

RESULTS

CircABCC1 and FAM155B were highly expressed in patients with RIF. CircABCC1 or FAM155B overexpression reduced EEC proliferation, LIF and DKK1 expression, LIF secretion, and trophoblast adhesion; circABCC1 or FAM155B knockdown led to the opposite results. CircABCC1 and METTL3 positively regulated FAM155B expression. METTL3 bound circABCC1 and FAM155B mRNA. METTL3 overexpression increased m6A modification of FAM155B mRNA. FAM155B overexpression partially eliminated circABCC1 knockdown-induced promotion of EEC proliferation, LIF and DKK1 expression, LIF secretion, and trophoblast adhesion.

CONCLUSION

CircABCC1 binds to METTL3 to regulate FAM155B mRNA modification and promote FAM155B expression, thereby inhibiting EEC proliferation and reducing endometrial receptivity.

Exploring m6A methylation in skin Cancer: Insights into molecular mechanisms and treatment

N6-methyladenosine (m6A) is the most common and prevalent internal mRNA modification in eukaryotes. m6A modification is a dynamic and reversible process regulated by methyltransferases, demethylases, and m6A binding proteins. Skin cancers, including melanoma and nonmelanoma skin cancers (NMSCs), are among the most commonly diagnosed cancers worldwide. m6A methylation is involved in the regulation of RNA splicing, translation, degradation, stability, translocation, export, and folding. Aberrant m6A modification participates in the pathophysiological processes of skin cancers and is associated with tumor cell proliferation, invasion, migration, and metastasis during cancer progression. In this review, we provide a comprehensive summary of the biological functions of m6A and the most up-to-date evidence related to m6A RNA modification in skin cancer. We also emphasize the potential clinical applications in the diagnosis and treatment of skin cancers.

METTL14 plays an oncogenic role in NSCLC by modulating ferroptosis and the m6A modification of GPX4

CONTEXT

N6-methyladenosine (m6A) of RNA is involved in the progression of non-small cell lung cancer (NSCLC).

OBJECTIVE

This study investigated the role of METTL14 in NSCLC and the mechanism.

MATERIALS AND METHODS

Expression levels were assessed by quantitative real-time PCR and ELISA assays. Cells viability was assessed by cell counting kit-8. M6A methylation was analysed by methylated RNA immunoprecipitation (MeRIP), RIP, luciferase assay, and mRNA stability assay.

RESULTS

The results showed that METTL14 was highly expressed in NSCLC tissues and cell lines. Knockdown of METTL14 inhibited the cell viability while induced ferroptosis of NSCLC cells. Mechanistically, METTL14 interacts with GPX4, mediates m6A modification of GPX4, enhances its mRNA stability, and upregulates its expression. In addition, IGF2BP1 recognises the m6A-methylated GPX4 and mediates the elevated mRNA stability. Moreover, GPX4 reversed the effects of METTL14 depletion.

DISCUSSION AND CONCLUSION

The METTL14/GPX4 axis promotes NSCLC progression by inhibiting cell ferroptosis through the recognition of m6A modification mediated by IGF2BP1.

Detecting the Tumor Prognostic Factors From the YTH Domain Family Through Integrative Pan-Cancer Analysis

Objectives

Emerging evidence suggests that N6-methyladenosine (m6A) methylation plays a critical role in cancers through various mechanisms. This work aims to reveal the essential role of m6A methylation "readers" in regulation of cancer prognosis at the pan-cancer level.

Methods

Herein, we focused on one special protein family of the "readers" of m6A methylation, YT521-B homology (YTH) domain family genes, which were observed to be frequently dysregulated in tumor tissues and closely associated with cancer prognosis. Then, a comprehensive analysis of modulation in cancer prognosis was conducted by integrating RNA sequencing (RNAseq) datasets of YTH family genes and clinical information at the pan-cancer level.

Results

YTH family genes were significantly differentially expressed in most of the cancers, particularly increased in Gastrointestinal cancers, and decreased in Endocrine and Urologic cancers. In addition, they were observed to be associated with overall survival (OS) and disease-specific survival (DSS) with various extent, especially in lower grade glioma (LGG), thyroid cancer (THCA), liver hepatocellular carcinoma (LIHC) and kidney clear cell carcinoma (KIRC), so were some "writers" (METLL3, METLL14, WTAP) and "erasers" (FTO, ALKBH5). Further survival analysis illustrated that YTH family genes specifically YTHScore constructed by combining 5 YTH family genes, as well as RWEScore calculated by combining genes from "readers"-"writers"-"erasers" could dramatically distinguish tumor prognosis in 4 representative cancers. As expected, YTHScore presented an equally comparable prognostic classification with RWEScore. Finally, analysis of immune signatures and clinical characteristics implied that, the activity of the innate immune, diagnostic age, clinical stage, Tumor-Node-Metastasis (TNM) stage and immune types, might play specific roles in modulating tumor prognosis.

Conclusions

The study demonstrated that YTH family genes had the potential to predict tumor prognosis, in which the YTHScore illustrated equal ability to predict tumor prognosis compared to RWEScore, thus providing insights into prognostic biomarkers and therapeutic targets at the pan-cancer level.

Propofol attenuates prostate cancer progression by upregulating TRHDE-AS1 expression, and METTL14 could mediate its m6A modification

Propofol has become a microtubule-stabilizing drug for prostate cancer (PC) therapy, but propofol resistance impairs the therapeutic effect. This study aimed to explore the regulatory mechanism of propofol in the pathogenesis of PC through mechanisms involving N6-methyladenosine (m6A) modification. The changes in PC cell malignancy were evaluated by means of transwell, cell counting kit 8 (CCK-8), western blotting and tumour xenograft model assays. Long noncoding RNA TRHDE-AS1 and m6A methyltransferase METTL14 expression levels were determined via reverse transcription quantitative polymerase chain reaction (RT-qPCR). The m6A modification of TRHDE-AS1 which was mediated by METTL14 was confirmed by conducting methylated RNA immunoprecipitation (MeRIP) assay. We observed that propofol (200 μM) inhibited PC cell malignancy in vivo and in vitro, elucidating that it impaired cell proliferation, migration and tumour growth but induced apoptosis. TRHDE-AS1 expression was observed to be lower in PC cells and tissues, and propofol induced TRHDE-AS1 upregulation in PC cells. Propofol was capable of reversing the tumour-promoting effect of TRHDE-AS1 knockdown in PC cells. Additionally, METTL14 was upstream of TRHDE-AS1 to induce m6A modification of TRHDE-AS1 in PC cells. Collectively, our results show that propofol prevents PC progression by upregulating TRHDE-AS1 expression and METTL14 is involved in the m6A modification of TRHDE-AS1. These findings suggest that TRHDE-AS1 may be a potential therapeutic target for the improvement of propofol's therapeutic effect.

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.

WTAP-mediated m6A modification regulates NLRP3/Caspase-1/GSDMD to inhibit pyroptosis and exacerbate colorectal cancer

Aim: Wilms' tumor 1-associating protein (WTAP), plays a part in colorectal cancer (CRC) progression. However, it is not yet known how WTAP affects cancer progression by influencing leukocyte rich repeat containing proteins (NLR) - family members 3 (NLRP3) - related inflammasomes.Materials & methods: We first validated the expression of WTAP in CRC at the tissue and cellular levels. Subsequently, by transfecting si-NC and si-WTAP into cells, we verified functions of WTAP in proliferation, invasion, migration and apoptosis of CRC cells. Finally, we analyzed the N6-methyladenosine (m6A) modification of NLRP3 by WTAP using methylated RNA immunoprecipitation (MeRIP)-qPCR technology, confirming that WTAP mediated the repression of NLRP3 inflammasome and the malignant progression of tumor cells.Results: WTAP was substantially upregulated in CRC tissues and cells. WTAP reinforced the migration, proliferation and invasion ability of CRC cells, and repressed apoptosis. Mechanistically, WTAP mediated the m6A modification of NLRP3, which suppressed the expression of NLRP3 and dampened the NLRP3/Caspase-1/GSDMD axis activation as well as pyroptosis, thereby facilitating the malignant progression of CRC.Conclusion: WTAP mediates m6A modification to modulate the repression of the NLRP3/Caspase-1/GSDMD axis in pyroptosis, reinforcing the malignant progression of CRC.

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.

Autophagy: a critical mechanism of N6-methyladenosine modification involved in tumor progression and therapy resistance

N6-Methyladenosine (m6A) is an evolutionarily highly conserved epigenetic modification that affects eukaryotic RNAs, especially mRNAs, and m6A modification is commonly linked to tumor proliferation, progression, and therapeutic resistance by participating in RNA metabolism. Autophagy is an intracellular degradation and recycling biological process by which cells remove damaged organelles, protein aggregates, and other intracellular wastes, and release nutrients to maintain cell survival when energy is scarce. Recent studies have shown that m6A modification plays a critical role in the regulation of autophagy, affecting the initiation of autophagy, the formation and assembly of autophagosomes, and lysosomal function by regulating critical regulatory molecules involved in the process of autophagy. Moreover, autophagy can also affect the expression of the three types of regulators related to m6A, which in turn affects the levels of their target genes via m6A modification. Thus, m6A modification and autophagy form a sophisticated regulatory network through mutual regulation, which plays an important role in tumor progression and therapeutic resistance. In this manuscript, we reviewed the effects of m6A modification on autophagy as well as the effects of autophagy on m6A modification and the roles of the m6A-autophagy axis in tumor progression and therapy resistance. Additionally, we summarized the value and application prospects of key molecules in the m6A-autophagy axis in tumor diagnosis and therapy.

WTAP-dependent N6-methyladenosine methylation of lncRNA TEX41 promotes renal cell carcinoma progression

The methyltransferase Wilms' tumor 1-associated protein (WTAP) has been reported to be dysregulated in various tumors. However, its role in renal cell carcinoma (RCC) remains elusive. Here, we explored whether WTAP was upregulated in RCC specimens compared to normal tissues. Functionally, WTAP promoted RCC cell proliferation and metastasis in vivo and in vitro. Mechanistically, WTAP act as an N6-methyladenosine transferase to regulate the m6A modification of long noncoding RNA TEX41. Then, the upregulated m6A modification destabilized TEX41 in a YTHDF2-dependent manner. Furthermore, TEX41 interacted with the SUZ12 protein and increased the histone methyltransferase activity of SUZ12, resulting in HDAC1 silencing. Totally, our study demonstrated the oncogenic the role of WTAP/TEX41/SUZ12/HDAC1 axis in RCC progression.

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.

Transcriptome-wide N6-methyladenosine modification profiling of long non-coding RNAs in patients with recurrent implantation failure

N6-methyladenosine (m6A) is involved in most biological processes and actively participates in the regulation of reproduction. According to recent research, long non-coding RNAs (lncRNAs) and their m6A modifications are involved in reproductive diseases. In the present study, using m6A-modified RNA immunoprecipitation sequencing (m6A-seq), we established the m6A methylation transcription profiles in patients with recurrent implantation failure (RIF) for the first time. There were 1443 significantly upregulated m6A peaks and 425 significantly downregulated m6A peaks in RIF. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that genes associated with differentially methylated lncRNAs are involved in the p53 signalling pathway and amino acid metabolism. The competing endogenous RNA network revealed a regulatory relationship between lncRNAs, microRNAs and messenger RNAs. We verified the m6A methylation abundances of lncRNAs by using m6A-RNA immunoprecipitation (MeRIP)-real-time polymerase chain reaction. This study lays a foundation for further exploration of the potential role of m6A modification in the pathogenesis of RIF.

HNRNPC modulates PKM alternative splicing via m6A methylation, upregulating PKM2 expression to promote aerobic glycolysis in papillary thyroid carcinoma and drive malignant progression

The heterogeneous nuclear ribonucleoprotein C (HNRNPC) plays a crucial role in tumorigenesis, yet its role in papillary thyroid carcinoma (PTC) remains elusive. Herein, we elucidated the function and molecular mechanism of HNRNPC in PTC tumorigenesis and progression. Our study unveiled a significant upregulation of HNRNPC in PTC, and knockdown of HNRNPC markedly inhibited the proliferation, invasion, and metastasis of BCPAP cells. Furthermore, HNRNPC modulated PKM alternative splicing in BCPAP cells primarily through m6A modification. Additionally, by upregulating PKM2 expression, HNRNPC promoted aerobic glycolysis in BCPAP cells, thereby facilitating malignant progression in PTC. In summary, our findings demonstrate that HNRNPC regulates PKM alternative splicing through m6A methylation modification and promotes the proliferation, invasion and metastasis of PTC through glucose metabolism pathways mediated by PKM2. These discoveries provide new biomarkers for screening and diagnosing PTC patients and offer novel therapeutic targets for personalized treatment strategies.

The indispensability of methyltransferase-like 3 in the immune system: from maintaining homeostasis to driving function

Methyltransferase-like 3(METTL3), recognized as the primary N6-methyladenosine methyltransferase, influences cellular functions such as proliferation, migration, invasion, differentiation, and fate determination by regulating gene expression post-transcriptionally. Recent studies have highlighted the indispensability of METTL3 in various immune cells such as hematopoietic stem/progenitor cells, innate immune cells (monocytes, macrophages, dendritic cells), and adaptive immune cells (thymic epithelial cell, T cells, natural killer cells). However, a comprehensive summary and analysis of these findings to elucidate the relationship between METTL3 and the immune system is yet to be undertaken. Therefore, in this review, we systematically collate reports detailing the mechanism underlying the role of METTL3 in regulating various immune processes and examine the modification of METTL3 and its potential implications. This review suggests that METTL3 plays an essential role in the immune system, ranging from maintaining homeostasis to regulating functions. Collectively, this review provides a comprehensive analysis of the relationship between METTL3 and the immune system, serving convenient researchers to understand the frontiers of immunological research and facilitate future clinical applications.

The m6A eraser FTO suppresses ferroptosis via mediating ACSL4 in LPS-induced macrophage inflammation

Acute lung injury (ALI) is a serious disorder characterized by the release of pro-inflammatory cytokines and cascade activation of macrophages. Ferroptosis, a form of iron-dependent cell death triggered by intracellular phospholipid peroxidation, has been implicated as an internal mechanism underlying ALI. In this study, we investigated the effects of m6A demethylase fat mass and obesity-associated protein (FTO) on the inhibition of macrophage ferroptosis in ALI. Using a mouse model of lipopolysaccharide (LPS)-induced ALI, we observed the induction of ferroptosis and its co-localization with the macrophage marker F4/80, suggesting that ferroptosis might be induced in macrophages. Ferroptosis was promoted during LPS-induced inflammation in macrophages in vitro, and the inflammation was counteracted by the ferroptosis inhibitor ferrostatin-1 (fer-1). Given that FTO showed lower expression levels in the lung tissue of mice with ALI and inflammatory macrophages, we further dissected the regulatory capacity of FTO in ferroptosis. The results demonstrated that FTO alleviated macrophage inflammation by inhibiting ferroptosis. Mechanistically, FTO decreased the stability of ACSL4 mRNA via YTHDF1, subsequently inhibiting ferroptosis and inflammation by interrupting polyunsaturated fatty acid consumption. Moreover, FTO downregulated the synthesis and secretion of prostaglandin E2, thereby reducing ferroptosis and inflammation. In vivo, the FTO inhibitor FB23-2 aggravated lung injury, the inflammatory response, and ferroptosis in mice with ALI; however, fer-1 therapy mitigated these effects. Overall, our findings revealed that FTO may function as an inhibitor of the inflammatory response driven by ferroptosis, emphasizing its potential as a target for ALI treatment.

ALKBH5 Regulates Osteogenic Differentiation via the lncRNA/mRNA Complex

Human adipose-derived stem cells (hASCs) are commonly used in bone tissue regeneration. The N6-methyladenosine (m6A) modification has emerged as a novel regulatory mechanism for gene expression, playing a critical role in osteogenic differentiation of stem cells. However, the precise role and mechanism of alkylation repair homolog 5 (ALKBH5) in hASC osteogenesis remain incompletely elucidated and warrant further investigation. Herein, we employed methylated RNA immunoprecipitation sequencing, RNA sequencing, and weighted gene coexpression network analysis to identify a key long noncoding RNA (lncRNA) in hASCs: lncRNA AK311120. Functional experiments demonstrated that lnc-AK311120 promoted the osteogenic differentiation of hASCs, while a mutation at the m6A central site A of lnc-AK311120 was found to decrease the level of m6A modification. The osteogenic effect of ALKBH5 was confirmed both in vitro and in vivo using a mandibular defect model in nude mice. Subsequent investigations revealed that knockdown of ALKBH5 resulted in a significant increase in the m6A modification level of lnc-AK311120, accompanied by a downregulation in the expression level of lnc-AK311120. Additional rescue experiments demonstrated that overexpression of lnc-AK311120 could restore the phenotype after ALKBH5 knockdown. We observed that AK311120 interacted with the RNA-binding proteins DExH-Box helicase 9 (DHX9) and YTH domain containing 2 (YTHDC2) to form a ternary complex, while mitogen-activated protein kinase kinase 7 (MAP2K7) served as the shared downstream target gene of DHX9 and YTHDC2. Knockdown of AK311120 led to a reduction in the binding affinity between DHX9/YTHDC2 and the target gene MAP2K7. Furthermore, ALKBH5 facilitated the translation of MAP2K7 and activated the downstream JNK signaling pathway through the AK311120-DHX9-YTHDC2 complex, without affecting its messenger RNA level. Collectively, we have investigated the regulatory effect and mechanism of ALKBH5-mediated demethylation of lncRNA in hASC osteogenesis for the first time, offering a promising approach for bone tissue engineering.

YTHDF1 facilitates esophageal cancer progression via augmenting m6A-dependent TINAGL1 translation

N6-methyladenosine (m6A) is the most abundant internal RNA modification and plays a critical role in carcinogenesis and tumor progression. As a powerful m6A reader, YTHDF1 is implicated in multiple malignancies. However, the functions and underlying mechanisms of YTHDF1 in esophageal cancer (ESCA) are elusive. Here, we revealed that YTHDF1 expression was remarkably up-regulated in ESCA and linked with poor prognosis. Functionally, YTHDF1 promoted ESCA cell proliferation, migration, and metastasis in vitro and in vivo. Mechanistically, we demonstrated that TINAGL1 might be a potential target of YTHDF1. We revealed that YTHDF1 recognized and bound to m6A-modified sites of TINAGL1 mRNA, resulting in enhanced translation of TINAGL1. Furthermore, TINAGL1 knockdown partially rescued tumor-promoting effects of YTHDF1 overexpression. Therefore, we unveil that YTHDF1 facilitates ESCA progression by promoting TINAGL1 translation in an m6A-dependent manner, which offers an attractive therapeutic target for ESCA.

Reading the m6A-encoded epitranscriptomic information in development and diseases

N6-methyladenosine (m6A) represents the most prevalent internal and reversible modification on RNAs. Different cell types display their unique m6A profiles, which are determined by the functions of m6A writers and erasers. M6A modifications lead to different outcomes such as decay, stabilization, or transport of the RNAs. The m6A-encoded epigenetic information is interpreted by m6A readers and their interacting proteins. M6A readers are essential for different biological processes, and the defects in m6A readers have been discovered in diverse diseases. Here, we review the latest advances in the roles of m6A readers in development and diseases. These recent studies not only highlight the importance of m6A readers in regulating cell fate transitions, but also point to the potential application of drugs targeting m6A readers in diseases.

m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data

N6-methyladenosine (m6A) is one of the most abundant and well-known modifications in messenger RNAs since its discovery in the 1970s. Recent studies have demonstrated that m6A is involved in various biological processes, such as alternative splicing and RNA degradation, playing an important role in a variety of diseases. To better understand the role of m6A, transcriptome-wide m6A profiling data are indispensable. In recent years, the Oxford Nanopore Technology Direct RNA Sequencing (DRS) platform has shown promise for RNA modification detection based on current disruptions measured in transcripts. However, decoding current intensity data into modification profiles remains a challenging task. Here, we introduce the m6A Transcriptome-wide Mapper (m6ATM), a novel Python-based computational pipeline that applies deep neural networks to predict m6A sites at a single-base resolution using DRS data. The m6ATM model architecture incorporates a WaveNet encoder and a dual-stream multiple-instance learning model to extract features from specific target sites and characterize the m6A epitranscriptome. For validation, m6ATM achieved an accuracy of 80% to 98% across in vitro transcription datasets containing varying m6A modification ratios and outperformed other tools in benchmarking with human cell line data. Moreover, we demonstrated the versatility of m6ATM in providing reliable stoichiometric information and used it to pinpoint PEG10 as a potential m6A target transcript in liver cancer cells. In conclusion, m6ATM is a high-performance m6A detection tool, and our results pave the way for future advancements in epitranscriptomic research.

The role of KRT7 in metastasis and prognosis of pancreatic cancer

PURPOSE

The aim of this study is to delve into the value of N6-Methyladenosine (m6A)-associated genes (MAGs) in pancreatic cancer (PC) prognosis.

METHODS

PC sequencing data and corresponding clinicopathological information were retrieved from GEO and TCGA databases. We filtered 19 MAGs in PC specimens and implemented functional annotation in biology. Later, the m6A modification pattern was stratified into m6Acluster A-B according to MAG expression levels, and further categorized into genecluster A-C based on differentially expressed genes between m6Acluster A and B. Next, a MAG-based prognostic prediction model was established by the least absolute shrinkage and selection operator (LASSO) regression analysis and multivariate Cox regression analysis. At last, the role of KRT7 in PC were explored.

RESULTS

We found m6Acluster A pattern presented enrichment pathways associated with cell apoptosis, proliferation, migration, and cancer pathways. Additionally, high-risk group displayed more dismal prognosis and a higher programmed death-ligand 1 expression. The survival prediction ability of the model was verified in three independent PC GEO datasets. KRT7 is the most momentous risk gene in the established prognostic model. Among 18 clinical samples, the KRT7 protein in the surviving patient samples is lower than that in the deceased patient samples. We also identified elevated expression of KRT7 in PC tumor tissues compared to normal tissues using GEPIA 2. Then, the metastasis of PC cells was promoted by overexpressed KRT7 in vitro and in vivo. And IGF2BP3 upregulated KRT7 by increasing the mRNA stability of KRT7.

CONCLUSIONS

The PPM built based on CXCL5, LY6K and KRT7 is an encouraging biomarker to define the prognosis. Additionally, IGF2BP3 promoted KRT7 by stabilizing mRNA of KRT7. And KRT7 promoted the metastasis of PC cells by promoting EMT.

POP1 Facilitates Proliferation in Triple-Negative Breast Cancer via m6A-Dependent Degradation of CDKN1A mRNA

Triple-negative breast cancer (TNBC) is currently the worst prognostic subtype of breast cancer, and there is no effective treatment other than chemotherapy. Processing of precursors 1 (POP1) is the most substantially up-regulated RNA-binding protein (RBP) in TNBC. However, the role of POP1 in TNBC remains clarified. A series of molecular biological experiments in vitro and in vivo and clinical correlation analyses were conducted to clarify the biological function and regulatory mechanism of POP1 in TNBC. Here, we identified that POP1 is significantly up-regulated in TNBC and associated with poor prognosis. We further demonstrate that POP1 promotes the cell cycle and proliferation of TNBC in vitro and vivo. Mechanistically, POP1 directly binds to the coding sequence (CDS) region of CDKN1A mRNA and degrades it. The degradation process depends on the N6-methyladenosine (m6A) modification at the 497th site of CDKN1A and the recognition of this modification by YTH N6-methyladenosine RNA binding protein 2 (YTHDF2). Moreover, the m6A inhibitor STM2457 potently impaired the proliferation of POP1-overexpressed TNBC cells and improved the sensitivity to paclitaxel. In summary, our findings reveal the pivotal role of POP1 in promoting TNBC proliferation by degrading the mRNA of CDKN1A and that inhibition of m6A with STM2457 is a promising therapeutic strategy for TNBC.

DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates

Messenger RNA splicing and degradation are critical for gene expression regulation, the abnormality of which leads to diseases. Previous methods for estimating kinetic rates have limitations, assuming uniform rates across cells. DeepKINET is a deep generative model that estimates splicing and degradation rates at single-cell resolution from scRNA-seq data. DeepKINET outperforms existing methods on simulated and metabolic labeling datasets. Applied to forebrain and breast cancer data, it identifies RNA-binding proteins responsible for kinetic rate diversity. DeepKINET also analyzes the effects of splicing factor mutations on target genes in erythroid lineage cells. DeepKINET effectively reveals cellular heterogeneity in post-transcriptional regulation.