YTHDF1 links hypoxia adaptation and non-small cell lung cancer progression

Loss of Epitranscriptomic Modification N6-Methyladenosine (m6A) Reader YTHDF1 Exacerbates Ischemic Brain Injury in a Sexually Dimorphic Manner

N6-Methyladenosine (m6A) is a neuronal-enriched, reversible post-transcriptional modification that regulates RNA metabolism. The m6A-modified RNAs recruit various m6A-binding proteins that act as readers. Differential m6A methylation patterns are implicated in ischemic brain damage, yet the precise role of m6A readers in propagating post-stroke m6A signaling remains unclear. We presently evaluated the functional significance of the brain-enriched m6A reader YTHDF1, in post-stroke pathophysiology. Focal cerebral ischemia significantly increased YTHDF1 mRNA and protein expression in adult mice of both sexes. YTHDF1-/- male, but not female, mice subjected to transient middle cerebral artery occlusion (MCAO) showed worsened motor function recovery and increased infarction compared to sex-matched YTHDF1+/+ mice. YTHDF1-/- male, but not female, mice subjected to transient MCAO also showed significantly perturbed expression of genes related to inflammation, and increased infiltration of peripheral immune cells into the peri-infarct cortex, compared with sex-matched YTHDF1+/+ mice. Thus, this study demonstrates a sexual dimorphism of YTHDF1 in regulating post-ischemic inflammation and pathophysiology. Hence, post-stroke epitranscriptomic regulation might be sex-dependent.

YTHDF1-targeting nanoassembly reverses tumoral immune evasion through epigenetics and cell cycle modulation

YTHDF1, as a key m6A reader protein, is believed to be one of the key mechanisms leading to tumor cell immune evasion and resistance via promoting MHC-I degradation. We explore therapeutic strategies that combine iron metabolism regulation with epigenetic regulation. Here, a nanoassembly that integrates Deferasirox (DFX, an FDA-approved iron chelator) and YTHDF1 siRNA (known as PPD/siYTHDF1) has been developed, which jointly promotes cell cycle arrest in tumor cells by interfering with iron metabolism and knocking down YTHDF1 protein. At the same time, YTHDF1 deficiency inhibits the mRNA translation of lysosome-related proteins, upregulates MHC-I molecule expression (2.5-fold), reduces the degradation of internalized antigens, enhances T cell-mediated immune response, and ultimately restores tumor immune surveillance and triggers powerful anti-tumor immune efficacy. After treatment, CD8+ T cells in the tumor site increased by 2.2-fold, and effector memory T cells in the spleen increased by 2.1-fold. It demonstrates a highly effective anti-tumor effect in breast cancer treatment, as well as in postoperative anti-recurrence and anti-metastasis models.

Deciphering the role of circular RNAs in cancer progression under hypoxic conditions

Hypoxia, characterized by reduced oxygen levels, plays a pivotal role in cancer progression, profoundly influencing tumor behavior and therapeutic responses. A hallmark of solid tumors, hypoxia drives significant metabolic adaptations in cancer cells, primarily mediated by hypoxia-inducible factor-1α (HIF-1α), a key transcription factor activated in low-oxygen conditions. This hypoxic environment promotes epithelial-mesenchymal transition (EMT), enhancing cancer cell migration, metastasis, and the development of cancer stem cell-like properties, which contribute to therapy resistance. Moreover, hypoxia modulates the expression of circular RNAs (circRNAs), leading to their accumulation in the tumor microenvironment. These hypoxia-responsive circRNAs regulate gene expression and cellular processes critical for cancer progression, making them promising candidates for diagnostic and prognostic biomarkers in various cancers. This review delves into the intricate interplay between hypoxic circRNAs, microRNAs, and RNA-binding proteins, emphasizing their role as molecular sponges that modulate gene expression and signaling pathways involved in cell proliferation, apoptosis, and metastasis. It also explores the relationship between circRNAs and the tumor microenvironment, particularly how hypoxia influences their expression and functional dynamics. Additionally, the review highlights the potential of circRNAs as diagnostic and prognostic tools, as well as their therapeutic applications in innovative cancer treatments. By consolidating current knowledge, this review underscores the critical role of circRNAs in cancer biology and paves the way for future research aimed at harnessing their unique properties for clinical advancements. Specifically, this review examines the biogenesis, expression patterns, and mechanistic actions of hypoxic circRNAs, focusing on their ability to act as molecular sponges for microRNAs and their interactions with RNA-binding proteins. These interactions impact key signaling pathways related to tumor growth, metastasis, and drug resistance, offering new insights into the complex regulatory networks governed by circRNAs under hypoxic stress.

RNA-binding proteins and autophagy in lung cancer: mechanistic insights and therapeutic perspectives

BACKGROUND

Lung cancer remains a leading cause of cancer-related mortality worldwide. Its progression is intricately associated with the dynamic regulation of autophagy and RNA-binding proteins (RBPs), which play crucial roles in mRNA stability, alternative splicing, and cellular stress responses.

OBJECTIVES

This review aims to systematically analyze the mechanisms through which RBPs and autophagy contribute to lung cancer progression and explore potential therapeutic strategies targeting these pathways.

METHODS

We reviewed recent studies on the molecular mechanisms by which RBPs regulate tumor proliferation, metabolic adaptation, and their interaction with autophagy. The review also examines the dual roles of autophagy in lung cancer, highlighting its context-dependent effects on cell survival and death.

RESULTS

The interactions and regulatory networks between RBPs and autophagy involve multiple levels of regulation. RBPs can directly influence autophagy processes and act as microRNA (miRNA) sponges to regulate mRNA stability. The modulation of RBPs affects the expression of autophagy-related genes (ATGs) and autophagosome formation. Additionally, RBPs participate in complex regulatory interactions with non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and other proteins.

CONCLUSIONS

This review proposes innovative therapeutic strategies that combine RBP-targeting approaches (e.g., small molecule inhibitors, CRISPR gene editing) with autophagy modulators (e.g., mTOR inhibitors, chloroquine) to enhance treatment efficacy. Nanoparticle drug delivery systems and epigenetic regulation offer further opportunities for targeted interventions. This review lays a theoretical foundation for advancing lung cancer research and provides novel insights into synergistic therapies that target both RBPs and autophagy to improve treatment outcomes for lung cancer.

YTHDF1/RNF7/p27 axis promotes prostate cancer progression

Prostate cancer (PCa) is a prevalent malignant tumor of the urinary system and remains the most common cancer among males. In this study, we showed that YTHDF1, one of the reader proteins involved in the N6-methyladenosine (m6A) modification signaling pathway, is highly expressed in PCa cancerous tissues and cells, which correlates with poor clinical outcomes. Our study revealed that YTHDF1 knockdown inhibits tumor cell proliferation, migration, and xenograft tumor formation by decreasing p27 protein stability through proteasome degradation signaling. Consistently, YTHDF1 depletion markedly reduced the clonogenic growth of Pten or/and TP53-deficient organoids. Candidate p27-targeting E3 ubiquitin ligases screening identified RNF7 as the direct downstream target for YTHDF1 in an m6A-dependent manner. The subsequent high translation of RNF7 results in the efficient degradation of the cell cycle inhibitor p27 and malignant tumor cell growth. In addition, we provided evidence showing that YTHDF1 or RNF7 depletion sensitizes tumor cells to chemotherapy drug cisplatin by increasing cellular apoptosis. Our findings revealed that the neddylation inhibitor MLN4924 effectively inhibited prostate cancer progression in vitro and in vivo. Our study highlights the YTHDF1/RNF7/p27 axis as a crucial component in PCa, suggesting its potential as a novel therapeutic target.

Effects of Benzo[a]Pyrene Exposure on Lung Cancer: A Mechanistic Study of Epigenetic m6A Levels and YTHDF1

Benzo[a]pyrene, as the primary component of air pollutants, has been implicated in the pathogenesis of non-small-cell lung cancer (NSCLC). As an m6A reader that facilitates mRNA translation, YTHDF1 serves as a crucial regulator in tumor progression. Therefore, we established Benzo[a]pyrene(B[a]P)-induced bronchial epithelial malignant transformed cells (HBE-P35) to simulate the precancerous lesions of NSCLC and investigated the regulatory axis of YTHDF1 in both HBE-P35 and A549 lung cancer cells. A high level of m6A expression was detected in both HBE-P35 and A549 cells. Over-expression of YTHDF1 was observed in NSCLC tissues and correlated with poor overall survival in NSCLC patients. TMT labeling-based proteomic analysis and clinical lung tissue microarray assays demonstrated that CDK6 and MAP3K6 were positively correlated with YTHDF1 expression. MeRIP and RIP analyses revealed that YTHDF1 mediates the m6A-dependent regulation of CDK6 and MAP3K6 protein expression. The acquisition and deletion of miR-139/145-5p, along with luciferase reporter gene assays, demonstrated that miR-139-5p can target YTHDF1. Therefore, we conclude that YTHDF1 regulates CDK6 and MAP3K6 through m6A in B[a]P-induced HBE-P35 and A549 cells, providing a potential target for lung cancer treatment.

Decoding N6-methyladenosine's dynamic role in stem cell fate and early embryo development: insights into RNA-chromatin interactions

N6-methyladenosine (m6A), a reversible and dynamic RNA modification, plays pivotal roles in regulating stem cell pluripotency and early embryogenesis. Disruptions in m6A homeostasis lead to profound developmental defects, impairing processes such as stem cell self-renewal, lineage specification, oocyte maturation, zygotic genome activation, and maternal RNA degradation after fertilization. Beyond its well-recognized roles in mRNA transport, stability, and translation, recent studies have highlighted m6A's critical role in transcriptional regulation through intricate RNA-chromatin interactions, notably involving chromatin-associated regulatory RNAs (carRNAs) and retrotransposon RNAs. This review delves into the dynamic regulatory landscape of m6A, highlighting its critical interplay with chromatin modifications, and explores its broader implications in stem cell biology and early embryonic development.

Exploration of mRNA-modifying METTL3 oncogene as momentous prognostic biomarker responsible for colorectal cancer development

Background

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, emphasizing the need for improved prognostic biomarkers. Recent studies have identified the mRNA-modifying METTL3 oncogene as a potential biomarker in CRC progression.

Objective

This study aimed to investigate the expression patterns of METTL3 in CRC, assess its association with clinical outcomes, identify interacting proteins and biological pathways, and explore its correlation with immune cell infiltration.

Methods

Comprehensive analyses were conducted using public datasets, including transcriptome profiles from The Cancer Genome Atlas and the GSE103512 dataset. Protein-protein interaction (PPI) networks, pathway enrichment, and immune infiltration analyses were performed to elucidate METTL3's role in CRC progression.

Results

METTL3 expression was significantly higher in CRC tissues compared to normal tissues (p < 0.001). Mutations in METTL3 were detected in approximately 6% of CRC cases, with fusion events involving the SRPK2 gene. PPI analysis identified ten interacting proteins, including METTL4, EIF3H, RBM15B1, CBLL1, WTAP, NCBP1, RBM15, ZC3H13, METTL14, and KIAA1429. METTL3 expression showed a positive correlation with METTL4, METTL14, NCBP1, and WTAP expression (R > 0.5, p < 0.001). Higher METTL3 expression was associated with immunosuppressive phenotypes, such as increased infiltration of tumor-associated macrophages, regulatory T cells, and cancer-associated fibroblasts (p < 0.001). Pathway enrichment analysis revealed METTL3's involvement in crucial pathways, including the cell cycle and renal cell carcinoma (p < 0.01). Gene ontology analysis highlighted its role in mRNA and RNA-related processes.

Conclusion

The study supports the potential of METTL3 as a prognostic biomarker in CRC and highlights its involvement in immune modulation and cancer progression. These findings lay the groundwork for future studies aimed at developing targeted therapies and improving patient outcomes.

Epitranscriptomic regulation of HIF-1: bidirectional regulatory pathways

BACKGROUND

Epitranscriptomics, the study of RNA modifications such as N6-methyladenosine (m6A), provides a novel layer of gene expression regulation with implications for numerous biological processes, including cellular adaptation to hypoxia. Hypoxia-inducible factor-1 (HIF-1), a master regulator of the cellular response to low oxygen, plays a critical role in adaptive and pathological processes, including cancer, ischemic heart disease, and metabolic disorders. Recent discoveries accent the dynamic interplay between m6A modifications and HIF-1 signaling, revealing a complex bidirectional regulatory network. While the roles of other RNA modifications in HIF-1 regulation remain largely unexplored, emerging evidence suggests their potential significance.

MAIN BODY

This review examines the reciprocal regulation between HIF-1 and epitranscriptomic machinery, including m6A writers, readers, and erasers. HIF-1 modulates the expression of key m6A components, while its own mRNA is regulated by m6A modifications, positioning HIF-1 as both a regulator and a target in this system. This interaction enhances our understanding of cellular hypoxic responses and opens avenues for clinical applications in treating conditions like cancer and ischemic heart disease. Promising progress has been made in developing selective inhibitors targeting the m6A-HIF-1 regulatory axis. However, challenges such as off-target effects and the complexity of RNA modification dynamics remain significant barriers to clinical translation.

CONCLUSION

The intricate interplay between m6A and HIF-1 highlights the critical role of epitranscriptomics in hypoxia-driven processes. Further research into these regulatory networks could drive therapeutic innovation in cancer, ischemic heart disease, and other hypoxia-related conditions. Overcoming challenges in specificity and off-target effects will be essential for realizing the potential of these emerging therapies.

OSGEP, A Negative Ferroptotic Regulator, Alleviates Cerebral Ischemia-Reperfusion Injury Through Modulating m6A Methylation of GPX4 mRNA

Cerebral ischemia-reperfusion injury (CIRI) is a devastating condition that triggers neuronal death and cerebral infarction. O-sialoglycoprotein endopeptidase (OSGEP), identified as a crucial element of the highly conserved KEOPS complex, regulated cellular proliferation and mitochondrial metabolism. Despite its known role in cellular homeostasis, the potential contribution of OSGEP to the development of CIRI remains elusive. This study was designed to investigate the potential role of ferroptosis in the pathogenesis of CIRI and indicate whether OSGEP could suppress ferroptosis to alleviate CIRI by modulating GPX4 m6A methylation. To this end, MCAO and OGD/R models were employed to closely simulate the CIRI. The potent ferroptosis inhibitors conferred prominent neuroprotection in both in vivo and in vitro models. Moreover, OSGEP expression level was not only downregulated in MCAO-treated mice and in cultured cerebrocortical neurons subjected to OGD/R, but also it was related to the prognosis of acute ischemic stroke (AIS) cases. Additionally, OSGEP overexpression exerted potent anti-ferroptotic effects in both MCAO and OGD/R models, while OSGEP depletion exhibited the opposite effect. Moreover, OSGEP regulated GPX4 expression by modulating m6A methylation of its mRNA. Furthermore, the inhibitory effect of OSGEP on ferroptosis was dependent on the presence of GPX4. Specifically, OSGEP knockout exacerbated ferroptosis-like cell death under MCAO condition. Besides, OSGEP regulated GPX4 mRNA stability through competition with YTHDC1 for binding to GPX4 mRNA and forming a complex with HNRNPUL1 in the neuronal primary cultures subjected to OGD/R. These findings highlighted the critical role of OSGEP, as a new contributing anti-ferroptotic factor, in the pathogenesis of CIRI.

Identification of IGF2BPs-related mRNA signature for predicting the overall survival of lung adenocarcinoma

Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) are m⁶A readers that stabilize target mRNAs by recognizing the GG(m⁶A)C sequence. While previous studies have explored the biological mechanisms of IGF2BPs in lung cancer, their prognostic value remains unclear. This study investigated the expression, molecular mechanisms, and prognostic significance of IGF2BPs in lung adenocarcinoma (LUAD) using TCGA and GEO datasets. IGF2BP1/2/3 were found to be highly expressed in LUAD, with high mRNA stability scores (RS) associated with shorter overall survival (OS) and linked to hypoxia, EMT, IL2-STAT5 signaling, immune suppression, and decreased gefitinib sensitivity. In cell-based experiments, siRNA knockdown of IGF2BPs in LUAD cell lines reduced TGF-β signaling pathway-related genes and inhibited cell proliferation. Our findings suggest that the IGF2BPs gene signature is a prognostic biomarker in LUAD, contributing to tumor progression, immune escape, and poor prognosis by activating specific pathways.

Epigenetic regulation in female reproduction: the impact of m6A on maternal-fetal health

With the development of public health, female diseases have become the focus of current concern. The unique reproductive anatomy of women leads to the development of gynecological diseases gradually become an important part of the socio-economic burden. Epigenetics plays an irreplaceable role in gynecologic diseases. As an important mRNA modification, m6A is involved in the maturation of ovum cells and maternal-fetal microenvironment. At present, researchers have found that m6A is involved in the regulation of gestational diabetes and other reproductive system diseases, but the specific mechanism is not clear. In this manuscript, we summarize the components of m6A, the biological function of m6A, the progression of m6A in the maternal-fetal microenvironment and a variety of gynecological diseases as well as the progression of targeted m6A treatment-related diseases, providing a new perspective for clinical treatment-related diseases.

YTH N6-methyladenosine RNA Binding Protein 1 Inhibits Smooth Muscle Cell Phenotypic Modulation and Neointimal Hyperplasia

Smooth muscle cell (SMC) phenotypic transition contributes to several major vascular diseases such as intimal hyperplasia and restenosis, atherosclerosis, and aneurysm. However, the molecular mechanisms underlying this process are not fully understood. The objectives of this study are to determine the role of mRNA N6-methyladenosine (m6A) modification in SMC phenotypic modulation and injury-induced neointima formation. By using an m6A quantification kit, we found that m6A levels are altered during the early stage of SMC phenotypic modulation. RNA sequencing revealed that m6A modifications in the mRNAs of 708 genes are elevated while modifications in the mRNAs of 300 genes are decreased. These modifications occur in genes widely distributed in most chromosomes and involved in many cellular processes and signaling/gene regulations. Meanwhile, the regulators for m6A modifications are altered by PDGF-BB, a known factor inducing SMC phenotypic modulation. Although m6A writers and erasers are not altered during SMC phenotypic modulation, m6A reader YTHDF1 is dramatically reduced as early as 12 h following PDGF-BB treatment, a time much earlier than the downregulation of SMC contractile proteins. Importantly, the overexpression of YTHDF1 reverses the expression of SMC contractile proteins, suggesting a restoration of contractile SMC phenotype. By using a rat carotid artery balloon-injury model, we found that injury significantly decreases YTHDF1 levels in the medial SMCs while inducing neointima formation. Of significance, restoring YTHDF1 expression through lentiviral transduction blocks injury-induced neointima formation. Moreover, YTHDF1 delivery restores the expression of SMC contractile proteins that is diminished in arterial media layers due to the injury. These data demonstrate that YTHDF1 plays a protective role in maintaining the contractile SMC phenotype and vascular homeostasis during injury-induced pathological vascular remodeling.

ALKBH5 acts a tumor-suppressive biomarker and is associated with immunotherapy response in hepatocellular carcinoma

As immune-checkpoint inhibitors (ICIs) therapy has made great strides in hepatocellular carcinoma (HCC) treatment, improving patient response to this strategy has become the main focus of research. Accumulating evidence has shown that m6A methylation plays a crucial role in the tumorigenesis and progression of HCC, while the precise impact of the m6A demethylase ALKBH5 on the tumor immune microenvironment (TIME) of HCC remains poorly defined. The clinical significance of ALKBH5 and TIM3 were evaluated in human HCC tissues. The biological function of ALKBH5 was analyzed in vitro and in vivo. The HCC molecular subtypes were identified based on key ALKBH5-regulated methylation-related genes (MRGs). The differences in survival, clinical features, TIME and immunotherapy response between these two subtypes were then evaluated. The regulation of ALKBH5 on TIM3 was detected by qPCR, western blotting and MeRIP. ALKBH5 was downregulated in HCC and associated with worse prognosis. ALKBH5 inhibited the proliferation and migration activities of HCC cells in vitro and in vivo. The HCC subtype with high expression of key MRGs was characterized by immunosuppression phenotypes and a worse response to ICIs. Moreover, TIM3 was identified as a target of ALKBH5. Upregulated TIM3 level was negatively correlated with survival in HCC. The results of this study suggest that ALKBH5 is an important regulator in HCC progression. ALKBH5 exerts its influence on the TIME and immunotherapy response by targeting TIM3 in HCC. This work provides new insight into the correlation between m6A modification and ICI response, which may help provide therapeutic benefits to HCC patients.

Development of an AI model for predicting hypoxia status and prognosis in non-small cell lung cancer using multi-modal data

Background

Prognosis prediction is crucial for non-small cell lung cancer (NSCLC) treatment planning. While tumor hypoxia significantly impacts patient outcomes, identifying hypoxic genomic markers remains challenging. This study sought to identify hypoxic computed tomography (CT) radiomic features and create an artificial intelligence (AI) model for NSCLC through the integration of multi-modal data.

Methods

In total, 452 NSCLC patients were enrolled in this study, including patients from The Second Affiliated Hospital of Soochow University (SC, n=112), The Cancer Genome Atlas (TCGA)-NSCLC dataset (n=74), the radiogenomics dataset (n=130), and the Gene Expression Omnibus (GEO) datasets (GSE19188: n=82, and GSE87340: n=54). Hypoxia status was classified using optimized cut-off values of hypoxia enrichment scores, which were calculated through single-sample gene set enrichment analysis (ssGSEA) of hypoxic genes. Radiomic features were extracted using three-dimensional (3D)-Slicer software. The least absolute shrinkage and selection operator (LASSO) algorithm was used to identify hypoxic CT radiomic features. A model named ssuBERT (semantic structured unit embedded in Bidirectional Encoder Representations from Transformers) was developed to analyze electronic health records (EHRs). An AI model for overall survival prediction was constructed by integrating CT radiomic features, ssuBERT features, and clinical data, and evaluated using five-fold cross-validation.

Results

Higher hypoxia levels were correlated with worse survival outcomes. Twenty-eight radiomic features showed significant discriminatory power in detecting hypoxia status with an area under the curve (AUC) of 0.8295. The ssuBERT model achieved a weighted accuracy of 0.945 in recognizing semantic structured units in EHRs. The EHR model exhibited superior predictive performance among the single-modal models with an AUC of 0.7662. However, the multi-modal AI model had the highest average AUC of 0.8449 and an F1 score of 0.7557.

Conclusions

The AI model demonstrated potential in predicting NSCLC patient prognosis through multi-modal data integration, warranting further validation.

The therapeutic potential of RNA m(6)A in lung cancer

Lung cancer (LC) is a highly malignant and metastatic form of cancer. The global incidence of and mortality from LC is steadily increasing; the mean 5-year overall survival (OS) rate for LC is less than 20%. This frustrating situation may be attributed to the fact that the pathogenesis of LC remains poorly understood and there is still no cure for mid to advanced LC. Methylation at the N6-position of adenosine (N6mA) of RNA (m(6)A) is widely present in human tissues and organs, and has been found to be necessary for cell development and maintenance of homeostasis. However, numerous basic and clinical studies have demonstrated that RNA m(6)A is deregulated in many human malignancies including LC. This can drive LC malignant characteristics such as proliferation, stemness, invasion, epithelial-mesenchymal transition (EMT), metastasis, and therapeutic resistance. Intriguingly, an increasing number of studies have also shown that eliminating RNA m(6)A dysfunction can exert significant anti-cancer effects on LC such as suppression of cell proliferation and viability, induction of cell death, and reversal of treatment insensitivity. The current review comprehensively discusses the therapeutic potential of RNA m(6)A and its underlying molecular mechanisms in LC, providing useful information for the development of novel LC treatment strategies.

The ubiquitin ligase STUB1 suppresses tumorigenesis of renal cell carcinomas through regulating YTHDF1 stability

STIP1 homology and U-box protein 1 (STUB1), a crucial member of the RING family E3 ubiquitin ligase, serve dual roles as an oncogene and a tumor suppressor in various human cancers. However, the role and mechanism of STUB1 in clear cell renal cell carcinoma (ccRCC) remain poorly defined. Here, we identified YTHDF1 as a novel STUB1 interaction partner using affinity purification mass spectrometry. Furthermore, we revealed that STUB1 promotes the ubiquitination and degradation of YTHDF1. Consequently, STUB1 depletion leads to YTHDF1 upregulation in renal cancer cells. Functionally, STUB1 depletion promoted migration and invasion of ccRCC cells in a YTHDF1-dependent manner. Additionally, the depletion of STUB1 also increased the tumorigenic potential of ccRCC in a xenograft model. Importantly, STUB1 expression is downregulated in ccRCC tissues, and its low expression level correlates with advanced tumor stage and poor overall survival in ccRCC patients. Taken together, these findings reveal that STUB1 inhibits the tumorigenicity of ccRCC by regulating YTHDF1 stability.

Self-Produced O2 CNs-Based Nanocarriers of DNA Hydrophobization Strategy Triggers Photodynamic and Mitochondrial-Derived Ferroptosis for Hepatocellular Carcinoma Combined Treatment

Hypoxia can aggravate tumor occurrence, development, invasion, and metastasis, and greatly inhibit the photodynamic therapy (PDT) effect. Herein, carbon nitride (CNs)-based DNA and photosensitizer co-delivery systems (BPSCNs) with oxygen-producing functions are developed to address this problem. Selenide glucose (Seglu) is used as the dopant to prepare red/NIR-active CNs (SegluCNs). The tumor-targeting unit Bio-PEG2000 is utilized to construct BPSCNs nanoparticles through esterification reactions. Furthermore, DNA hydrophobization is realized via mixing P53 gene with a positively charged mitochondrial-targeted near-infrared (NIR) emitting photosensitizer (MTTPY), which is encapsulated in non-cationic BPSCNs for synergistic delivery. Ester bonds in BPSCNs@MTTPY-P53 complexes can be disrupted by lipase in the liver to facilitate P53 release, upregulated P53 expression, and promoted HIF-1α degradation in mitochondria. In addition, the oxygen produced by the complexes improved the hypoxic microenvironment of hepatocellular carcinoma (HCC), synergistically downregulated HIF-1α expression in mitochondria, promoted mitochondrial-derived ferroptosis and enhanced the PDT effect of the MTTPY unit. Both in vivo and in vitro experiments indicated that the transfected P53-DNA, produced O2 and ROS by these complexes synergistically led to mitochondrial-derived ferroptosis in hepatoma cells through the HIF-1α/SLC7A11 pathway, and completely avoiding PDT resistance caused by hypoxia, exerting a significant therapeutic role in HCC treatment.

WTAP-Mediated m6A Modification of circSMOC1 Accelerates the Tumorigenesis of Non-Small Cell Lung Cancer by Regulating miR-612/CCL28 Axis

Accumulating evidence reveals that deregulated N6-methyladenosine (m6A) RNA methylation and circular RNAs (circRNAs) are required for the tumorigenesis of non-small cell lung cancer (NSCLC). We aimed to uncover the underlying mechanisms by which WTAP-mediated m6A modification of circRNA contributes to NSCLC. The differentially-expressed circRNAs were identified by a circRNA profiling microarray. The association of circSMOC1 with clinicopathological features and prognosis in patients with NSCLC was estimated by fluorescence in situ hybridization. WTAP-mediated m6A modification of circRNA was validated by RNA immunoprecipitation (RIP) and methylated RIP (MeRIP) assays. The role of circSMOC1 in NSCLC cells was validated by in vitro functional experiments and in vivo tumorigenesis models. CircSMOC1-specific binding with miR-612 was verified by RIP, luciferase gene report and RT-qPCR assays. The effect of circSMOC1 and/or miR-612 on CCL28 expression was detected by RT-qPCR and Western blotting analysis. We found that the expression levels of circSMOC1 were elevated in NSCLC tissues and associated with TNM stage and poor survival in patients with NSCLC. Knockdown of circSMOC1 impaired the tumorigenesis of NSCLC in vitro and in vivo, whereas restored expression of circSMOC1 displayed the opposite effect. Furthermore, WTAP was upregulated in NSCLC and mediated m6A modification of circSMOC1 and circSMOC1 abolished WTAP knockdown-caused tumour-suppressive effects. Then, circSMOC1 acted as a sponge of miR-612 to upregulate CCL28 and miR-612 inhibitors abrogated circSMOC1 knockdown-caused anti-proliferation effects and CCL28 downregulation in NSCLC cells. Knockdown of CCL28 inhibited cell proliferation and invasion and counteracted miR-612 inhibitor-caused tumour-promoting effects. Our findings unveil that WTAP-mediated m6A modification of circSMOC1 facilitates the tumorigenesis of NSCLC by regulating the miR-612/CCL28 axis.

[Research Advances in the Roles of High-Altitude Hypoxic Stress in Hepatocellular Carcinoma]

Hepatocellular carcinoma (HCC), one of the most prevalent malignant tumors causing the highest mortality globally, imposes an especially heavy burden of disease in China. Individuals living in high-altitude areas have a lower incidence of and mortality resulting from HCC compared with those in low-altitude regions do, potentially due to adaptive evolution in responses to hypoxic stress. Notably, high-altitude hypoxic stress is associated with the development and progression of HCC. Hypoxic stress may be involved in the development and progression of HCC by modulating the senescence, apoptosis, metabolism, tumor microenvironment, and tumor immunity of HCC cells. Additionally, the latest clinical findings indicate that high-altitude hypoxic environment has a significant impact on liver regeneration after HCC resection surgery. However, there is still a debate going on regarding whether high-altitude hypoxic stress promotes or inhibits the progression of HCC. This review covers three main aspects, the impact of adaptive evolution to high-altitude hypoxic stress on the development and progression of HCC in long-term residents of high-altitude areas, the effects of high-altitude hypoxic stress on the senescence, apoptosis, metabolism, tumor microenvironment, tumor metabolism, and tumor immunity of HCC cells, and the effect of high-altitude hypoxic stress on liver regeneration after HCC resection. We discussed the effect of changes in oxygen concentrations, cellular context, and tissue microenvironment on HCC development and progression. Moreover, we highlighted the potential for using research findings on mechanisms underlying high-altitude hypoxic stress to optimize HCC treatment strategies.

Whole-genome sequencing identifies functional genes for environmental adaptation in Chinese sheep

Sheep (Ovis aries), among the first domesticated species, are now globally widespread and exhibit remarkable adaptability to diverse environments. In this study, we perform whole-genome sequencing of 266 animals from 18 distinct Chinese sheep populations, each displaying unique phenotypes indicative of adaptation to varying environmental conditions. Integrating 131 environmental factors with single nucleotide polymorphism variations, we conduct a comprehensive genetic-environmental association analysis. This analysis identifies 35 key genes likely integral to the environmental adaptation of sheep. The functions of these genes include fat tail formation (HOXA10, HOXA11, JAZF1), wool characteristics (FER, FGF5, MITF, PDE4B), horn phenotypes (RXFP2), reproduction (HIBADH, TRIM71, C6H4orf22), and growth traits (ADGRL3, TRHDE). Notably, we observe a significant correlation between the frequency of missense mutations in the PAPSS2 and RXFP2 genes and variations in altitude. Our study reveals candidate genes for adaptive variation in sheep and demonstrates the diversity in how sheep adapt to their environment.

N6-Methyladenosine methylation modification in breast cancer: current insights

Breast cancer is the most common cancer type among women. Despite advanced treatment strategies, some patients still face challenges in disease control, prompting the exploration of new therapeutic approaches. N6-Methyladenosine (m6A) methylation modification regulates RNA and plays a crucial role in various tumor biological processes, closely linked to breast cancer occurrence, development, prognosis, and treatment. M6A regulators impact breast cancer progression, development, and drug resistance by modulating RNA metabolism and tumor-related pathways. Researchers have begun to understand the regulatory mechanisms of m6A methylation in breast cancer. This paper discusses the roles of m6A regulators in breast cancer progression, prognosis, and treatment, offering new perspectives for breast cancer diagnosis and treatment.

YTHDF1-regulated ALOX5 in retinal pigment epithelial cells under hypoxia enhances VEGF expression and promotes viability, migration, and angiogenesis of vascular endothelial cells

Upregulation of vascular endothelial growth factor (VEGF) and enhanced angiogenesis have been implicated in the severe progression of age-related macular degeneration (AMD). Abnormal arachidonate 5-lipoxygenase (ALOX5) is associated with AMD pathogenesis. However, no reports have shown the causal role of ALOX5 in angiogenesis during AMD. In the present study, ARPE-19 cells were exposed to hypoxia, an inducer of VEGF expression. Potential proteins implicated in AMD progression were predicted using bioinformatics. RNA affinity antisense purification-mass spectrometry (RAP-MS) was applied to identify the binding proteins of ALOX5 3'UTR. Expression of ALOX5 and YTH N6-methyladenosine RNA-binding protein 1 (YTHDF1) was detected by qRT-PCR and western blotting. VEGF expression and secretion were assessed by immunofluorescence and ELISA, respectively. The chicken embryo chorioallantoic membrane (CAM) was used to analyze the effect of ALOX5 on angiogenesis. RNA stability was assayed using the Actinomycin D assay. The results show that hypoxia promoted cell growth and increased VEGF expression in ARPE-19 cells. ALOX5 was associated with AMD progression, and hypoxia upregulated ALOX5 expression in ARPE-19 cells. ALOX5 silencing reduced VEGF expression induced by hypoxia in ARPE-19 cells. Moreover, the conditioned medium of ALOX5-silenced ARPE-19 cells could suppress the viability and migration of HUVECs and diminish angiogenesis in the CAM. Furthermore, YTHDF1 was validated to bind to ALOX5 3'UTR, and YTHDF1 promoted ALOX5 expression by elevating the stability of ALOX5 mRNA. In conclusion, our findings demonstrate that YTHDF1-regulated ALOX5 increases VEGF expression in hypoxia-exposed ARPE-19 cells and enhances the viability, migration, and angiogenesis of vascular endothelial cells.

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.

Functions of N6-methyladenosine (m6A) RNA modifications in acute myeloid leukemia

N6-methyladenosine is the most common modification of eukaryotic RNA. N6-methyladenosine participates in RNA splicing, nuclear export, translation, and degradation through regulation by methyltransferases, methylation readers, and demethylases, affecting messenger RNA stability and translation efficiency. Through the dynamic and reversible regulatory network composed of "writers, erasers, and readers," N6-methyladenosine modification plays a unique role in the process of hematopoiesis. Acute myeloid leukemia is a heterogeneous disease characterized by malignant proliferation of hematopoietic stem cells/progenitor cells. Many studies have shown that N6-methyladenosine-related proteins are abnormally expressed in acute myeloid leukemia and play an important role in the occurrence and development of acute myeloid leukemia, acting as carcinogenic or anticancer factors. Here, we describe the mechanisms of action of reversing N6-methyladenosine modification in hematopoiesis and acute myeloid leukemia occurrence and progression to provide a basis for further research on the role of N6-methyladenosine methylation and its regulatory factors in normal hematopoiesis and acute myeloid leukemia, to ultimately estimate its potential clinical value.

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.

hucMSC-Ex alleviates inflammatory bowel disease in mice by enhancing M2-type macrophage polarization via the METTL3-Slc37a2-YTHDF1 axis

Human umbilical cord mesenchymal stem cell-derived exosomes (hucMSC-Ex) have emerged as a new treatment strategy for inflammatory bowel disease (IBD) due to their immunoregulatory function. N6-methyladenosine (m6A) plays a crucial role in regulating intestinal immunity, especially in IBD where macrophages play an important role, although its mechanism is not yet fully understood. From this perspective, this research aimed to evaluate the effect of hucMSC-Ex on m6A modification of macrophages in IBD. In the process of alleviating inflammation, hucMSC-Ex promotes macrophage polarization toward the M2 type and regulates intracellular m6A levels by upregulating the expression of m6A "Writer" METTL3 and "Reader" YTHDF1. Solute Carrier Family 37 Member 2 (Slc37a2) was identified by Methylation RNA immunoprecipitation sequencing as the target molecule of the hucMSC-Ex. Mechanically, hucMSC-Ex promoted the binding of METTL3 to the Slc37a2 mRNA complex, and enhanced the binding of Slc37a2 to YTHDF1 to upregulate the intracellular expression of Slc37a2, thereby attenuating the pro-inflammatory function of macrophage. This study confirms the modulatory role of hucMSC-Ex on the m6A modification of macrophages in IBD, providing a new scientific basis for the treatment of IBD with hucMSC-Ex.

Immunogenomic features of radiologically distinctive nodules in multiple primary lung cancer

OBJECTIVES

To provide molecular and immunological attributes mechanistic insights for the management of radiologically distinctive multiple primary lung cancer (MPLC).

METHODS

The Bulk RNA-seq data of MPLC were obtained from our center. The Bulk RNA-seq data and CT images of patients with single primary lung cancer (SPLC) were obtained from GSE103584. Immune infiltration algorithms were performed to investigate the disparities in the immunological microenvironment between the two groups. Single-cell gene analysis was used to explore immune cells composition and communication relationships between cells in MPLC.

RESULTS

In MPLC, 11 pure ground-glass opacity nodules (pGGN) and 10 mixed GGN (mGGN) were identified, while in SPLC, the numbers were 18 pGGN and 22 mGGN, respectively. In MPLC, compared to pGGN, mGGN demonstrated a significantly elevated infiltration of CD8+ T cells. Single-cell gene analysis demonstrated that CD8+ T cells play a central role in the signaling among immune cells in MPLC. The transcription factors including MAFG, RUNX3, and TBX21 may play pivotal roles in regulation of CD8+ T cells. Notably, compared to SPLC nodules for both mGGN and pGGN, MPLC nodules demonstrated a significantly elevated degree of tumor-infiltrating immune cells, with this difference being particularly pronounced in mGGN. There was a positive correlation between the proportion of immune cells and consolidation/tumor ratio (CTR).

CONCLUSIONS

Our findings provided a comprehensive description about the difference in the immune microenvironment between pGGN and mGGN in early-stage MPLC, as well as between MPLC and SPLC for both mGGN and pGGN. The findings may provide evidence for the design of immunotherapeutic strategies for MPLC.

Benzo(a)pyrene promotes the malignant progression of malignant-transformed BEAS-2B cells by regulating YTH N6-methyladenosine RNA binding protein 1 to inhibit ferroptosis

Benzo[a]pyrene (BaP) is associated with the development of lung cancer, but the underlying mechanism has not been completely clarified. Here, we used 10 μM BaP to induce malignant transformation of human bronchial epithelial BEAS-2B cells, named BEAS-2B-T. Results indicated that BaP (6.25, 12.5 and 25 μM) treatment significantly promoted the migration and invasion of BEAS-2B-T cells. Meanwhile, BaP exposure inhibited ferroptosis in BEAS-2B-T, ferroptosis-related indexes Fe2+, malondialdehyde (MDA), lipid peroxidation (LPO) and reactive oxygen species (ROS) decreased significantly. The protein level of ferroptosis-related molecule transferrin receptor (TFRC) decreased significantly, while solute carrier family 7 membrane 11 (SLC7A11), ferritin heavy chain 1 (FTH1) and glutathione peroxidase 4 (GPX4) increased significantly. The intervention of ferroptosis dramatically effected the migration and invasion of BEAS-2B-T induced by BaP. Furthermore, the expression of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) was markedly increased after BaP exposure. YTHDF1 knockdown inhibited BEAS-2B-T migration and invasion by promoting ferroptosis. In the meantime, the contents of Fe2+, MDA, LPO and ROS increased significantly, TFRC was markedly increased, and SLC7A11, FTH1, and GPX4 were markedly decreased. Moreover, overexpression of YTHDF1 promoted BEAS-2B-T migration and invasion by inhibiting ferroptosis. Importantly, knockdown of YTHDF1 promoted ferroptosis and reduced BEAS-2B-T migration and invasion during BaP exposure, and overexpression of YTHDF1 increased migration and invasion of BEAS-2B-T by inhibiting ferroptosis during BaP exposure. RNA immunoprecipitation assays indicated that the binding of YTHDF1 to SLC7A11 and FTH1 markedly increased after YTHDF1 overexpression. Therefore, we concluded that BaP promotes the malignant progression of BEAS-2B-T cells through YTHDF1 upregulating SLC7A11 and FTH1 to inhibit ferroptosis. This study reveals new epigenetic and ferroptosis markers for preventing and treating lung cancer induced by environmental carcinogens.

FTO blocks RNA translational activity via the loss of N6-methyladenosine methylation at 5' UTR regulated by RBM5 in cisplatin-resistant NSCLC

N6-methyladenosine (m6A) methylation has been widely regarded in numerous biological functions including CR. Nonetheless, the molecular process of m6A methylation behind CR in non-small cell lung cancer (NSCLC) has no apparent significance. We identified in this study that the expression of FTO alpha-ketoglutarate dependent dioxygenase (FTO) was downregulated in CR NSCLC tissues and cells in vivo and in vitro. Additionally, RIP-seq indicated that loss of FTO contributed to the elevated m6A methylation at 5'-untranslated region of RNAs which were closely connected with tumor resistance and malignancy, and FTO exerted to exclude the recruitment of eIF3A to these target genes in CR NSCLC. Moreover, FTO-enriched transcripts displayed a reduced translational capability in CR NSCLC compared to the regular NSCLC cells. Finally, we also identified RNA binding motif protein 5 (RBM5) that could specially interact with FTO in regular NSCLC compared to CR NSCLC. Deficiency of RBM5 resulted in the abnormal recognition of transcripts by FTO, and led to the translation silencing of genes associated with CR such as ATP7A, ERCC1, CD99, CDKN3, XRCC5, and NOL3. Taken together, our data characterized FTO as a novel translation regulator and revealed the molecular mechanism on gene translation through the synergistic effects with RBM5 and m6A methylation in CR NSCLC cells.

The YTH domain-containing protein family: Emerging players in immunomodulation and tumour immunotherapy targets

BACKGROUND

The modification of N6-methyladenosine (m6A) plays a pivotal role in tumor by altering both innate and adaptive immune systems through various pathways, including the regulation of messenger RNA. The YTH domain protein family, acting as "readers" of m6A modifications, affects RNA splicing, stability, and immunogenicity, thereby playing essential roles in immune regulation and antitumor immunity. Despite their significance, the impact of the YTH domain protein family on tumor initiation and progression, as well as their involvement in tumor immune regulation and therapy, remains underexplored and lacks comprehensive review.

CONCLUSION

This review introduces the molecular characteristics of the YTH domain protein family and their physiological and pathological roles in biological behavior, emphasizing their mechanisms in regulating immune responses and antitumor immunity. Additionally, the review discusses the roles of the YTH domain protein family in immune-related diseases and tumor resistance, highlighting that abnormal expression or dysfunction of YTH proteins is closely linked to tumor resistance.

KEY POINTS

This review provides an in-depth understanding of the YTH domain protein family in immune regulation and antitumor immunity, suggesting new strategies and directions for immunotherapy of related diseases. These insights not only deepen our comprehension of m6A modifications and YTH protein functions but also pave the way for future research and clinical applications.

Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance

The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.

Progression of m6A in the tumor microenvironment: hypoxia, immune and metabolic reprogramming

Recently, N6-methyladenosine (m6A) has aroused widespread discussion in the scientific community as a mode of RNA modification. m6A comprises writers, erasers, and readers, which regulates RNA production, nuclear export, and translation and is very important for human health. A large number of studies have found that the regulation of m6A is closely related to the occurrence and invasion of tumors, while the homeostasis and function of the tumor microenvironment (TME) determine the occurrence and development of tumors to some extent. TME is composed of a variety of immune cells (T cells, B cells, etc.) and nonimmune cells (tumor-associated mesenchymal stem cells (TA-MSCs), cancer-associated fibroblasts (CAFs), etc.). Current studies suggest that m6A is involved in regulating the function of various cells in the TME, thereby affecting tumor progression. In this manuscript, we present the composition of m6A and TME, the relationship between m6A methylation and characteristic changes in TME, the role of m6A methylation in TME, and potential therapeutic strategies to provide new perspectives for better treatment of tumors in clinical work.

The role of m6A in angiogenesis and vascular diseases

Angiogenesis, whether physiological or pathological, plays a pivotal role in various physiological and disease conditions. This intricate process relies on a complex and meticulously orchestrated signal transduction network that connects endothelial cells, their associated parietal cells (VSMCs and pericytes), and various other cell types, including immune cells. Given the significance of m6A and its connection to angiogenesis and vascular disease, researchers must adopt a comprehensive and ongoing approach to their investigations. This study aims to ascertain whether a common key mechanism of m6A exists in angiogenesis and vascular diseases and to elucidate the potential application of m6A in treating vascular diseases.

YTHDF1 mediates N-methyl-N-nitrosourea-induced gastric carcinogenesis by controlling HSPH1 translation

YT521-B homology (YTH) domain family (YTHDF) proteins serve as readers that directly recognise m6A modifications. In this study, we aim to probe the role of YTHDF1 in environmental carcinogen-induced malignant transformation of gastric cells and gastric cancer (GC) carcinogenesis. We established a long-term low-dose MNU-induced malignant transformation model in gastric epithelial cells. In vivo and in vitro experiments were conducted to validate the malignant phenotype and characterise the roles of YTHDF1 and its downstream genes in malignant transformation cells. Additionally, we explored downstream m6A modification targets of YTHDF1 using RNA-sequencing, RNA immunoprecipitation, and proteomics analyses, and conducted validation experiments in cell experiments and clinical samples. Long-term low-dose exposure of MNU converted normal Gges-1 cells into malignant cells. YTHDF1 mRNA and protein expression are increased in MNU-induced malignant cells (p<0.001). Meanwhile, YTHDF1 knockdown inhibits the malignant potential of MNU-treated cells (p<0.01). YTHDF1 knockdown specifically suppresses HSPH1 protein, but not RNA levels. RIP-qPCR validates HSPH1 is the target of YTHDF1 (p<0.01). HSPH1 knockdown impairs the malignant potential of MNU-induced transformed cells. The increased expression of the key regulatory factor YTHDF1 in MNU-induced gastric carcinogenesis affects malignant transformation and tumorigenesis by regulating the translation of downstream HSPH1. These findings provide new potential targets for preventing and treating environmental chemical-induced gastric carcinogenesis.

METTL14 promotes lipid metabolism reprogramming and sustains nasopharyngeal carcinoma progression via enhancing m6A modification of ANKRD22 mRNA

BACKGROUND

N6-methyladenosine (m6A) modification is essential for modulating RNA processing as well as expression, particularly in the context of malignant tumour progression. However, the exploration of m6A modification in nasopharyngeal carcinoma (NPC) remains very limited.

METHODS

RNA m6A levels were analysed in NPC using m6A dot blot assay. The expression level of methyltransferase-like 14 (METTL14) within NPC tissues was analysed from public databases as well as RT-qPCR and immunohistochemistry. The influences on METTL14 expression on NPC proliferation and metastasis were explored via in vitro as well as in vivo functional assays. Targeted genes of METTL14 were screened using the m6A and gene expression profiling microarray data. Actinomycin D treatment and polysome analysis were used to detect the half-life and translational efficiency of ANKRD22. Flow cytometry, immunofluorescence and immunoprecipitation were used to validate the role of ANKRD22 on lipid metabolism in NPC cells. ChIP-qPCR analysis of H3K27AC signalling near the promoters of METTL14, GINS3, POLE2, PLEK2 and FERMT1 genes.

RESULTS

We revealed METTL14, in NPC, correlating with poor patient prognosis. In vitro and in vivo assays indicated METTL14 actively promoted NPC cells proliferation and metastasis. METTL14 catalysed m6A modification on ANKRD22 messenger ribonucleic acid (mRNA), recognized by the reader IGF2BP2, leading to increased mRNA stability and higher translational efficiency. Moreover, ANKRD22, a metabolism-related protein on mitochondria, interacted with SLC25A1 to enhance citrate transport, elevating intracellular acetyl-CoA content. This dual impact of ANKRD22 promoted lipid metabolism reprogramming and cellular lipid synthesis while upregulating the expression of genes associated with the cell cycle (GINS3 and POLE2) and the cytoskeleton (PLEK2 and FERMT1) through heightened epigenetic histone acetylation levels in the nucleus. Intriguingly, our findings highlighted elevated ANKRD22-mediated histone H3 lysine 27 acetylation (H3K27AC) signals near the METTL14 promoter, which contributes to a positive feedback loop perpetuating malignant progression in NPC.

CONCLUSIONS

The identified METTL14-ANKRD22-SLC25A1 axis emerges as a promising therapeutic target for NPC, and also these molecules may serve as novel diagnostic biomarkers.

The role of RNA methylation in tumor immunity and its potential in immunotherapy

RNA methylation, a prevalent post-transcriptional modification, has garnered considerable attention in research circles. It exerts regulatory control over diverse biological functions by modulating RNA splicing, translation, transport, and stability. Notably, studies have illuminated the substantial impact of RNA methylation on tumor immunity. The primary types of RNA methylation encompass N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G), and 3-methylcytidine (m3C). Compelling evidence underscores the involvement of RNA methylation in regulating the tumor microenvironment (TME). By affecting RNA translation and stability through the "writers", "erasers" and "readers", RNA methylation exerts influence over the dysregulation of immune cells and immune factors. Consequently, RNA methylation plays a pivotal role in modulating tumor immunity and mediating various biological behaviors, encompassing proliferation, invasion, metastasis, etc. In this review, we discussed the mechanisms and functions of several RNA methylations, providing a comprehensive overview of their biological roles and underlying mechanisms within the tumor microenvironment and among immunocytes. By exploring how these RNA modifications mediate tumor immune evasion, we also examine their potential applications in immunotherapy. This review aims to provide novel insights and strategies for identifying novel targets in RNA methylation and advancing cancer immunotherapy efficacy.

YTHDF1's grip on CRC vasculature: insights into LINC01106 and miR-449b-5p-VEGFA axis

BACKGROUND

Investigating the unexplored territory of lncRNA m6A modification in colorectal cancer (CRC) vasculature, this study focuses on LINC01106 and YTHDF1.

METHODS

Clinical assessments reveal upregulated LINC01106 promoting vascular generation via the miR-449b-5p-VEGFA pathway.

RESULTS

YTHDF1, elevated in CRC tissues, emerges as an adverse prognostic factor. Functional experiments showcase YTHDF1's inhibitory effects on CRC cell dynamics. Mechanistically, Me-CLIP identifies m6A-modified LINC01106, validated as a YTHDF1 target through Me-RIP.

CONCLUSIONS

This study sheds light on the YTHDF1-mediated m6A modification of LINC01106, presenting it as a key player in suppressing CRC vascular generation.

Ramifications of m6A Modification on ncRNAs in Cancer

N6-methyladenosine (m6A) is an RNA modification wherein the N6-position of adenosine is methylated. It is one of the most prevalent internal modifications of RNA and regulates various aspects of RNA metabolism. M6A is deposited by m6A methyltransferases, removed by m6A demethylases, and recognized by reader proteins, which modulate splicing, export, translation, and stability of the modified mRNA. Recent evidence suggests that various classes of non- coding RNAs (ncRNAs), including microRNAs (miRNAs), circular RNAs (circRNAs), and long con-coding RNAs (lncRNAs), are also targeted by this modification. Depending on the ncRNA species, m6A may affect the processing, stability, or localization of these molecules. The m6A- modified ncRNAs are implicated in a number of diseases, including cancer. In this review, the author summarizes the role of m6A modification in the regulation and functions of ncRNAs in tumor development. Moreover, the potential applications in cancer prognosis and therapeutics are discussed.

Internal m 6 A and m 7 G RNA modifications in hematopoietic system and acute myeloid leukemia

ABSTRACT

Epitranscriptomics focuses on the RNA-modification-mediated post-transcriptional regulation of gene expression. The past decade has witnessed tremendous progress in our understanding of the landscapes and biological functions of RNA modifications, as prompted by the emergence of potent analytical approaches. The hematopoietic system provides a lifelong supply of blood cells, and gene expression is tightly controlled during the differentiation of hematopoietic stem cells (HSCs). The dysregulation of gene expression during hematopoiesis may lead to severe disorders, including acute myeloid leukemia (AML). Emerging evidence supports the involvement of the mRNA modification system in normal hematopoiesis and AML pathogenesis, which has led to the development of small-molecule inhibitors that target N6-methyladenosine (m 6 A) modification machinery as treatments. Here, we summarize the latest findings and our most up-to-date information on the roles of m 6 A and N7-methylguanine in both physiological and pathological conditions in the hematopoietic system. Furthermore, we will discuss the therapeutic potential and limitations of cancer treatments targeting m 6 A.

RNA m6A methylation and regulatory proteins in pulmonary arterial hypertension

m6A (N6‑methyladenosine) is the most common and abundant apparent modification in mRNA of eukaryotes. The modification of m6A is regulated dynamically and reversibly by methyltransferase (writer), demethylase (eraser), and binding protein (reader). It plays a significant role in various processes of mRNA metabolism, including regulation of transcription, maturation, translation, degradation, and stability. Pulmonary arterial hypertension (PAH) is a malignant cardiopulmonary vascular disease characterized by abnormal proliferation of pulmonary artery smooth muscle cells. Despite the existence of several effective and targeted therapies, there is currently no cure for PAH and the prognosis remains poor. Recent studies have highlighted the crucial role of m6A modification in cardiovascular diseases. Investigating the role of RNA m6A methylation in PAH could provide valuable insights for drug development. This review aims to explore the mechanism and function of m6A in the pathogenesis of PAH and discuss the potential targeting of RNA m6A methylation modification as a treatment for PAH.

Demethylases in tumors and the tumor microenvironment: Key modifiers of N6-methyladenosine methylation

RNA methylation modifications are widespread in eukaryotes and prokaryotes, with N6-methyladenosine (m6A) the most common among them. Demethylases, including Fat mass and obesity associated gene (FTO) and AlkB homolog 5 (ALKBH5), are important in maintaining the balance between RNA methylation and demethylation. Recent studies have clearly shown that demethylases affect the biological functions of tumors by regulating their m6A levels. However, their effects are complicated, and even opposite results have appeared in different articles. Here, we summarize the complex regulatory networks of demethylases, including the most important and common pathways, to clarify the role of demethylases in tumors. In addition, we describe the relationships between demethylases and the tumor microenvironment, and introduce their regulatory mechanisms. Finally, we discuss evaluation of demethylases for tumor diagnosis and prognosis, as well as the clinical application of demethylase inhibitors, providing a strong basis for their large-scale clinical application in the future.

RNA modifications in pulmonary diseases

Threatening public health, pulmonary disease (PD) encompasses diverse lung injuries like chronic obstructive PD, pulmonary fibrosis, asthma, pulmonary infections due to pathogen invasion, and fatal lung cancer. The crucial involvement of RNA epigenetic modifications in PD pathogenesis is underscored by robust evidence. These modifications not only shape cell fates but also finely modulate the expression of genes linked to disease progression, suggesting their utility as biomarkers and targets for therapeutic strategies. The critical RNA modifications implicated in PDs are summarized in this review, including N6-methylation of adenosine, N1-methylation of adenosine, 5-methylcytosine, pseudouridine (5-ribosyl uracil), 7-methylguanosine, and adenosine to inosine editing, along with relevant regulatory mechanisms. By shedding light on the pathology of PDs, these summaries could spur the identification of new biomarkers and therapeutic strategies, ultimately paving the way for early PD diagnosis and treatment innovation.

Potential therapeutic strategy for cancer: Multi-dimensional cross-talk between circRNAs and parental genes

In many ways, circular RNAs (circRNAs) have been demonstrated to be crucial in the onset and advancement of cancer throughout the last ten years and have become a new focus of intense research in the field of RNAs. Accumulating studies have demonstrated that circRNAs can regulate parental gene expression via a variety of biological pathways. Furthermore, research into the complex interactions between circRNAs and their parental genes will shed light on their biological roles and open up new avenues for circRNAs' potential clinical translational uses. However, to date, multi-dimensional cross-talk between circRNAs and parental genes have not been systematically elucidated. Particularly intriguing is circRNA's exploration of tumor targeting, and potential therapeutic uses based on the parental gene regulation perspective. Here, we discuss their biogenesis, take a fresh look at the molecular mechanisms through which circRNAs control the expression of their parental genes in cancer. We further highlight We further highlight the latest circRNA clinical translational applications, including prognostic diagnostic markers, cancer vaccines, gDNA, and so on. Demonstrating the potential benefits and future applications of circRNA therapy.

RNA methylation-related inhibitors: Biological basis and therapeutic potential for cancer therapy

RNA methylation is widespread in nature. Abnormal expression of proteins associated with RNA methylation is strongly associated with a number of human diseases including cancer. Increasing evidence suggests that targeting RNA methylation holds promise for cancer treatment. This review specifically describes several common RNA modifications, such as the relatively well-studied N6-methyladenosine, as well as 5-methylcytosine and pseudouridine (Ψ). The regulatory factors involved in these modifications and their roles in RNA are also comprehensively discussed. We summarise the diverse regulatory functions of these modifications across different types of RNAs. Furthermore, we elucidate the structural characteristics of these modifications along with the development of specific inhibitors targeting them. Additionally, recent advancements in small molecule inhibitors targeting RNA modifications are presented to underscore their immense potential and clinical significance in enhancing therapeutic efficacy against cancer. KEY POINTS: In this paper, several important types of RNA modifications and their related regulatory factors are systematically summarised. Several regulatory factors related to RNA modification types were associated with cancer progression, and their relationships with cancer cell migration, invasion, drug resistance and immune environment were summarised. In this paper, the inhibitors targeting different regulators that have been proposed in recent studies are summarised in detail, which is of great significance for the development of RNA modification regulators and cancer treatment in the future.

The antagonistic effect of FTO on METTL14 promotes AKT3 m6A demethylation and the progression of esophageal cancer

BACKGROUND

As the most abundant modification in eukaryotic messenger RNAs (mRNAs), N6-methyladenosine (m6A) plays vital roles in many biological processes.

METHODS

Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and transcriptomic RNA sequencing (RNA-seq) were used to screen for m6A targets in esophageal cancer cells and patients. The role of m6A RNA methylase in esophageal cancer was also analyzed using bioinformatics. In vitro and in vivo experiments were used to analyze gene expression and function. CCK-8, colony formation, cell apoptosis and immunofluorescence staining assays were performed to evaluate the proliferation, migration and invasion of esophageal cancer cells, respectively. Western blot analysis, RNA stability, RIP and luciferase reporter assays were performed to elucidate the underlying mechanism involved.

RESULTS

We found that the m6A demethylase FTO was significantly upregulated in esophageal cancer cell lines and patient tissues. In vivo and in vitro assays demonstrated that FTO was involved in the proliferation and apoptosis of esophageal cancer cells. Moreover, we found that the m6A methyltransferase METTL14 negatively regulates FTO function in esophageal cancer progression. FTO alone is not related to the prognosis of esophageal cancer, and its function is antagonized by METTL14. By using transcriptome-wide m6A-seq and RNA-seq assays, we revealed that AKT3 is a downstream target of FTO and acts in concert to regulate the tumorigenesis and metastasis of esophageal cancer. Taken together, these findings provide insight into m6A-mediated tumorigenesis in esophageal cancer and could lead to the design of new therapeutic strategies.

NEAT1_1 confers gefitinib resistance in lung adenocarcinoma through promoting AKR1C1-mediated ferroptosis defence

Gefitinib is one of the most extensively utilized epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) for treating advanced lung adenocarcinoma (LUAD) patients harboring EGFR mutation. However, the emergence of drug resistance significantly compromised the clinical efficacy of EGFR-TKIs. Gaining further insights into the molecular mechanisms underlying gefitinib resistance holds promise for developing novel strategies to overcome the resistance and improve the prognosis in LUAD patients. Here, we identified that the inhibitory efficacy of gefitinib on EGFR-mutated LUAD cells was partially dependent on the induction of ferroptosis, and ferroptosis protection resulted in gefitinib resistance. Among the ferroptosis suppressors, aldo-keto reductase family 1 member C1 (AKR1C1) exhibited significant upregulation in gefitinib-resistant strains of LUAD cells and predicted poor progression-free survival (PFS) and overall survival (OS) of LUAD patients who received first-generation EGFR-TKI treatment. Knockdown of AKR1C1 partially reversed drug resistance by re-sensitizing the LUAD cells to gefitinib-mediated ferroptosis. The decreased expression of miR-338-3p contributed to the aberrant upregulation of AKR1C1 in gefitinib-resistant LUAD cells. Furthermore, upregulated long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1_1 (NEAT1_1) sponged miR-338-3p to neutralize its suppression on AKR1C1. Dual-luciferase reporter assay and miRNA rescue experiment confirmed the NEAT1_1/miR-338-3p/AKR1C1 axis in EGFR-mutated LUAD cells. Gain- and loss-of-function assays demonstrated that the NEAT1_1/miR-338-3p/AKR1C1 axis promoted gefitinib resistance, proliferation, migration, and invasion in LUAD cells. This study reveals the effects of NEAT1_1/miR-338-3p/AKR1C1 axis-mediated ferroptosis defence in gefitinib resistance in LUAD. Thus, targeting NEAT1_1/miR-338-3p/AKR1C1 axis might be a novel strategy for overcoming gefitinib resistance in LUAD harboring EGFR mutation.

N6-methyladenosine promotes aberrant redox homeostasis required for arsenic carcinogenesis by controlling the adaptation of key antioxidant enzymes

N6-methyladenosine (m6A), a high-profile RNA epigenetic modification, responds to oxidative stress and temporal-specifically mediates arsenic carcinogenesis. However, how m6A affects aberrant redox homeostasis required for arsenic carcinogenesis is poorly understood. Here, we established arsenic-carcinogenic models of different stages, including As-treated, As-transformed, and As-tumorigenic cell models. We found that arsenic-induced reactive oxygen species (ROS) elevated m6A levels, thus triggering m6A-dependent antioxidant defenses. During arsenic-induced cell transformation, METTL3-upregulated m6A on the mRNAs of SOD1, SOD2, CAT, TXN, and GPX1 promoted the mRNA translation and protein expressions of these antioxidant enzymes by increasing YTHDF1-mediated mRNA stability. Meanwhile, FTO-downregulated m6A on PRDX5 mRNA increased PRDX5 translation and expression by reducing YTHDF2-mediated mRNA decay. After upregulated antioxidant defenses balanced with high levels of ROS induced by arsenic, the m6A balance formed in mRNAs of six key antioxidant enzymes (SOD1, SOD2, CAT, TXN, GPX1, and PRDX5) and promoted high expressions of these antioxidant enzymes to maintain aberrant redox homeostasis. METTL3 inhibitor STM2457, FTO inhibitor FB23-2, or YTHDF1 knockdown disturbed the aberrant redox homeostasis by breaking the m6A balance, causing cell death in arsenic-induced tumors. Our results demonstrated that m6A promotes the formation and maintenance of aberrant redox homeostasis required for arsenic carcinogenesis by time-dependently orchestrating the adaptive expressions of six key m6A-targeted antioxidant enzymes. This study advances our understanding of arsenic carcinogenicity from the novel aspect of m6A-dependent adaptation to arsenic-induced oxidative stress.

YTHDF1's Regulatory Involvement in Breast Cancer Prognosis, Immunity, and the ceRNA Network

YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), an m6A reader, has a role in the development and progression of breast cancer as well as the immunological microenvironment. The networks of competing endogenous RNA in cancer have received much attention in research. In tumor gene therapy, the regulatory networks of m6A and competing endogenous RNA are increasingly emerging as a new route. We evaluated the relationship between the YTHDF1 expression, overall survival, and clinicopathology of breast cancer using TCGA, PrognoScan, and other datasets. We used Western blot to demonstrate that YTHDF1 is substantially expressed in breast cancer tissues. Furthermore, we explored YTHDF1's functions in the tumor mutational burden, microsatellite instability, and tumor microenvironment. Our findings indicate that YTHDF1 is a critical component of the m6A regulatory proteins in breast cancer and may have a particular function in the immunological microenvironment. Crucially, we investigated the relationship between YTHDF1 and the associated competitive endogenous RNA regulatory networks, innovatively creating three such networks (Dehydrogenase/Reductase 4-Antisense RNA 1-miR-378g-YTHDF1, HLA Complex Group 9-miR-378g-YTHDF1, Taurine Up-regulated 1-miR-378g-YTHDF1). Furthermore, we showed that miR-378g could inhibit the expression of YTHDF1, and that miR-378g/YTHDF1 could impact MDA-MB-231 proliferation. We speculate that YTHDF1 may serve as a biomarker for poor prognosis and differential diagnosis, impact the growth of breast cancer cells via the ceRNA network axis, and be a target for immunotherapy against breast cancer.

METTL3 suppresses invasion of lung cancer via SH3BP5 m6A modification

The metastasis of lung cancer poses a major clinical challenge, and m6A modification has been implicated in regulating the invasive capabilities of tumor cells. However, the mechanisms underlying m6A modification in lung cancer metastasis are not well understood. This study aims to explore the biological functions and molecular mechanisms of methyltransferase-like 3 (METTL3) in lung cancer. In this study, METTL3 were found to be downregulated in lung cancer tissues. Functionally, METTL3 inhibited the migration and invasion abilities of lung cancer cells in vitro. Furthermore, SH3 domain binding protein 5 (SH3BP5) was identified as a downstream target of METTL3. Overexpression of SH3BP5 suppressed the invasive capacity of lung cancer cells, and this regulation was m6A-dependent. Finally, we discovered that YTH N6-methyladenosine RNA binding protein F1 (YTHDF1) mediated stability is responsible for maintaining the m6A modification of SH3BP5 mRNA. Overall, our study provides insights into the critical role of METTL3-mediated m6A modification and m6A-dependent regulatory mechanisms in the progression of human lung cancer. We demonstrated that METTL3 regulates the mRNA stability of SH3BP5 in a YTHDF1-dependent manner, thereby impacting the invasive capacity of lung cancer cells.