Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation

RNA methylation: A new promising biomaker in cancer liquid biopsy

RNA methylation is a vital epigenetic modification that regulates gene expression by influencing RNA processes such as transcription, degradation, translation, and transport. Aberrant methylation, including modifications like m6A, m5C, m1A, m7G, and m3C, is closely linked to tumorigenesis and progression. Liquid biopsy, a non-invasive technique analyzing tumor markers in body fluids, offers significant potential for early diagnosis and dynamic monitoring. In this context, RNA methylation, due to its tumor-specific properties, is emerging as a valuable marker. However, significant challenges remain in its clinical application. This review explores the roles of RNA methylation in cancer, recent advances in detection technologies, and its potential as a liquid biopsy marker in tumor management. It highlights its promising applications in cancer diagnosis, prognosis, and personalized treatment in the era of precision oncology.

METTL13 is essential for the survival of acute myeloid leukemia cells by regulating MYC

Recently, some methyltransferase-like (METTL) proteins have been found to play crucial roles in the development of acute myeloid leukemia (AML) through mediating RNA modifications, such as METTL3/14/16 mediated N6-methyladenosine (m6A) and METTL1 mediated N7-methylguanosine (m7G). However, the roles of other METTL proteins in AML progression remain unknown. Here, we examined the expression levels of all METTL members in AML samples and showed that METTL13 was increased in AML and positively correlated with poor prognosis. Moreover, METTL13 deficiency impaired AML cell proliferation capability in vitro, improved the survival of AML cell line xenograft immune-deficient mice, and reduced tumor infiltration in vivo. Mechanistically, MYC was downregulated after METTL13 knockdown and forced expression of MYC rescued the cell proliferation defect in METTL13-deficient AML cells. Our findings uncover the critical role of METTL13 in the survival of AML cells and identify MYC as a potential downstream target of METTL13. This work highlights METTL13 as a promising candidate target for AML therapy.

Role of m7G modification regulators as biomarkers in gastric cancer subtyping and precision immunotherapy

This study investigated the role of N7-methylguanosine (m7G) modification regulators as biomarkers in subtyping and precision immunotherapy of gastric cancer (GC). Through multi-omics analyses, including RNA sequencing, proteomics, and single-cell measurement, the study revealed heterogeneity in the m7G regulatory landscape among GC patients. Three m7G subtypes were identified, each with distinct pathways and phenotypes. Patients with low m7Gscores, based on an established scoring system, showed better survival outcomes and increased antitumor immune cell infiltration, as well as higher tumor mutation loads and lower PD-L1 expression. The predictive value of m7Gscore was confirmed in two immunotherapy cohorts. These findings highlight the potential of m7G modification in shaping the tumor microenvironment and provide new insights for immunotherapeutic strategies in GC patients.

Mechanistic insights into stem cell fate regulation via RNA methylation

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

The m7G methylation modification: An emerging player of cardiovascular diseases

Cardiovascular diseases severely endanger human health and are closely associated with epigenetic dysregulation. N7-methylguanosine (m7G), one of the common epigenetic modifications, is present in many different types of RNA molecules and has attracted significant attention due to its impact on various physiological and pathological processes. Recent studies have demonstrated that m7G methylation plays an important role in the occurrence and development of multiple cardiovascular diseases. Application of small molecule inhibitors to target m7G modification mediated by methyltransferase-like protein 1 (METTL1) has shown potentiality in the treatment of cardiovascular diseases. In this review, we summarize the basic knowledge about m7G modification and discuss its role and therapeutic potential in diverse cardiovascular diseases, aiming to provide a theoretical foundation for future research and therapeutic intervention.

The importance of physiological and disease contexts in capturing mRNA modifications

The variety of modifications decorating various RNA species has prompted researchers to study messenger RNA (mRNA) modifications that are likely to have, like N6-methyladenosine (m6A), important biological functions. Yet tackling these modifications has proved more complicated than anticipated. In this Perspective, we discuss two major obstacles to progress in epitranscriptomic research: the low abundance of most mRNA modification and the nonspecificity of many mRNA modifiers. We then shift our focus to the removal of mRNA modifications and their upstream regulation, emphasizing the context-dependent nature of epitranscriptomic regulation. We illustrate how specific modifications, such as N1-methyladenosine (m1A) and pseudouridine, are enriched in distinct environments, most notably within mitochondria and in certain physiopathological conditions. By focusing on biological settings in which non-m6A modifications are more abundant, we could deepen our understanding of their precise roles in gene regulation.

Identification and validation of hub m7G-related genes and infiltrating immune cells in osteoarthritis based on integrated computational and bioinformatics analysis

BACKGROUND

Osteoarthritis (OA) is a joint disease closely associated with synovial tissue inflammation, with the severity of synovitis impacting disease progression. m7G RNA methylation is critical in RNA processing, metabolism, and function, but its role in OA synovial tissue is not well understood. This study explores the relationship between m7G methylation and immune infiltration in OA.

METHODS

Data were obtained from the GEO database. Hub genes related to m7G were identified using differential expression and LASSO-Cox regression analysis, and a diagnostic model was developed. Functional enrichment, drug target prediction, and target gene-related miRNA prediction were performed for these genes. Immune cell infiltration was analyzed using the CIBERSORT algorithm, and unsupervised clustering analysis was conducted to examine immune infiltration patterns. RT-qPCR was used to validate hub gene expression.

RESULTS

Seven m7G hub genes (SNUPN, RNMT, NUDT1, LSM1, LARP1, CYFIP2, and CYFIP1) were identified and used to develop a nomogram for OA risk prediction. Functional enrichment indicated involvement in mRNA metabolism and RNA transport. Differences in macrophage and T-cell infiltration were observed between OA and normal groups. Two distinct m7G immune infiltration patterns were identified, with significant microenvironment differences between clusters. RT-qPCR confirmed differential hub gene expression.

CONCLUSION

A diagnostic model based on seven m7G hub genes was developed, highlighting these genes as potential biomarkers and significant players in OA pathogenesis.

Overexpression of tRNA m7G modification methyltransferase complex promotes the biosynthesis of triterpene in yeast

Background

The sustainable production of valuable compounds using microbial cell factories is an effective approach, yet further metabolic engineering strategies are needed to enhance their biosynthetic potential. Recent studies suggest that RNA modifications can influence cellular metabolism, but their role in metabolic engineering remains largely unexplored.

Methods

The production of squalene and lupeol in different yeast strains was detected by gas chromatography-mass spectrometry (GC-MS) equipment. Transcriptomic analysis was performed to identify metabolic changes associated with the epigenetic modification. The transcriptional and translational expression of targeted genes were determined by real-time quantitative polymerase chain reaction and western blotting, respectively. The mRNA stability of targeted genes was measured by mRNA decay assay.

Results

In this study, the overexpression of Trm8 and Trm82 complex, mediating the tRNA 7-methylguanosine (m7G) modification in yeast, significantly increased the production of squalene in CEN.PK2-1C. Transcriptome analysis indicated that Trm8/Trm82 overexpression upregulated the expression levels of genes involved in amino acid synthesis, glycolysis, and tricarboxylic acid cycle, and the enhanced glycolysis, upstream of acetyl-CoA biosynthesis, might be responsible for the promoted biosynthesis of squalene. Further investigation demonstrated that Trm8/Trm82 complex could increase the production of squalene and lupeol in engineered yeast.

Conclusion

These findings indicate that tRNA m7G modification can regulate central metabolism and enhance terpenoid biosynthesis. This study provides new insights into RNA modifications as a potential metabolic engineering strategy for improving the production of high-value compounds.

RNA m7G methylation regulators and targets significantly contribute to chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is one of the most common lung injury diseases, closely associated with aging, air pollution and smoking exposure. The novel epigenetic modification 7-methylguanosine (m7G) RNA methylation affects the pathogenesis and progression of COPD. In this study, the combined roles of m7G methylation regulators were explored in COPD for the first time by integrated bioinformatic methods. The machine algorithms screened 7 disease signature genes relevant to clinical indicators, including CYFIP2, EIF3D, EIF4G3, GEMIN5, METTL1, SNUPN and NCBP2, and METTL1 was related to the progression in COPD. COPD patients could be well divided into two m7G subtypes by consensus clustering, and the two groups had differential immune profiles, visualized by single-cell sequencing and immune infiltration landscapes. More importantly, CAT was found to be a meaningful key target gene in METTL1-CAT axis for m7G methylation in COPD. We also used the cell premature senescence model for the preliminary validation of the above biosignature analysis results. The qRT-PCR and GSEA results revealed the important regulatory roles of the seven disease signature genes in COPD and aging-related diseases. Taken together, METTL1 and its target CAT have played an important role in COPD, as excellent candidates for its prevention and intervention.

Construction of a diagnostic model utilizing m7G regulatory factors for the characterization of diabetic nephropathy and the immune microenvironment

Diabetic nephropathy (DN), a prevalent and severe complication of diabetes, is associated with poor prognosis and limited treatment options. N7-Methylguanosine (m7G) modification plays a crucial role in regulating RNA structure and function, linking it closely to metabolic disorders. However, despite its biological significance, the interplay between m7G methylation and immune status in DN remains largely unexplored. Leveraging data from the GEO database, we conducted consensus clustering of m7G regulators in DN patients to identify distinct molecular subtypes. To construct and validate m7G-related prognostic features and risk scores, we integrated multiple machine learning approaches, including Support Vector Machine-Recursive Feature Elimination, Random Forest, LASSO, Cox regression, and ROC curves analysis. In addition, we employed GSVA, ssGSEA, CIBERSORT, and Gene Set Enrichment Analysis to investigate the associated biological pathways and the immune landscape, providing deeper insights into the role of m7G methylation in DN. Based on the expression levels of 18 m7G-related regulatory factors, we identified nine key regulators. Through machine learning techniques, we identified four significant regulators (METTL1, CYFIP2, EIF3D, and NUDT4). Consensus clustering classified these genes into two distinct m7G-related clusters. To characterize these subtypes, we conducted immune infiltration analysis, differential expression analysis, and enrichment analysis, uncovering significant biological differences between the clusters. Additionally, we developed an m7G-related risk scoring model using the PCA algorithm. The differential expression of the four key regulators was further validated through in vivo experiments, reinforcing their potential role in disease progression. The m7G-related genes METTL1, CYFIP2, EIF3D, and NUDT4 may serve as potential diagnostic biomarkers for DN, providing new insights into its molecular mechanisms and immune landscape.

m7G-modified mt-tRF3b-LeuTAA regulates mitophagy and metabolic reprogramming via SUMOylation of SIRT3 in chondrocytes

N7-methylguanosine (m7G) modification is one of the most prevalent RNA modifications, and methyltransferase-like protein-1 (METTL1) is a key component of the m7G methyltransferase complex. METTL1-catalyzed m7G as a new RNA modification pathway that regulates RNA structure, biogenesis, and cell migration. Increasing evidence indicates that m7G modification has been implicated in the pathophysiological process of osteoarthritis (OA). However, the underlying molecular mechanisms of m7G modification remains incompletely elucidated during the progression of OA. Here we found that METTL1 and m7G levels were markedly increased in OA chondrocytes. In addition, METTL1-mediated m7G modification upregulated mt-tRF3b-LeuTAA expression to exacerbate chondrocyte degeneration. Mechanistically, mt-tRF3b-LeuTAA decreased the SUMO-specific protease 1 (SENP1) protein expression and upregulated the level of sirtuin 3 (SIRT3) SUMOylation to inhibit PTEN induced kinase 1 (PINK1)/Parkin-mediated mitochondrial mitophagy. Intra-articular injection of PMC-tRF3b-LeuTAA inhibitor (Polyamidoamine-polyethylene glycol surface-modified with Minimal self-peptides and Chondrocyte-affinity peptides, PMC) attenuated destabilization of the medial meniscus (DMM) mouse cartilage degeneration in vivo. Our study demonstrates that METTL1/m7G/mt-tRF3b-LeuTAA axis accelerate cartilage degradation by inhibiting mitophagy and promoting mitochondrial dysfunction through SIRT3 SUMOylation, and suggest that targeting METTL1 and its downstream signaling axis could be a promising therapeutic target for OA treatment.

RNA methylation homeostasis in ocular diseases: All eyes on Me

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

Identification of a novel signature based on RNA methylation-associated anoikis-related genes for predicting prognosis and characterizing immune landscape in colorectal cancer

BACKGROUND

RNA methylation is a potential target for cancer therapy, while anoikis, a form of programmed cell death, is linked to cancer metastasis. However, the prognostic and immune significance of RNA methylation- and anoikis-related genes in colorectal cancer (CRC) remains unknown.

METHODS

Transcriptomic and clinicopathological data for CRC were obtained from TCGA and the GEO databases. A novel signature was constructed based on RNA methylation- and anoikis-related genes using univariate and multivariate Cox regression as well as LASSO Cox regression methods. CRC patients were stratified into low- and high-risk groups based on this signature. Differences in prognosis, immune infiltration, and drug sensitivity between two groups were analyzed. Finally, immunohistochemistry, western blot, and RT-qPCR were employed to validate the expression of the key gene SERPINE1 in CRC tissues and cells, as well as the effect of FTO on its expression.

RESULTS

We identified 79 differentially expressed RNA methylation-associated anoikis-related genes (RMRARGs) in both cancerous and normal tissues. A signature composed of 9 key genes (BID, FASN, PLK1, CDKN3, MYC, EPHA2, SERPINE1, CD36, PDK4) was established. Kaplan-Meier analysis revealed a poorer prognosis in the high-risk group. Compared to the other three published models, this signature demonstrated superior predictive performance based on the ROC curve analysis. Functional analyses highlighted differences in drug sensitivities and signaling pathways between risk groups. Furthermore, immune analysis results showed that risk score was associated with some immune cells and immune checkpoints. Immunohistochemistry showed high SERPINE1 expression in CRC tissues, with FTO expression positively correlated with SERPINE1. Furthermore, RT-qPCR and western blot indicated FTO knockdown markedly downregulated SERPINE1 levels.

CONCLUSION

Our findings underscore the prognostic value of this signature in CRC patients and its utility in assessing immune status. Additionally, the m6A demethylase FTO regulates the expression of the anoikis-related gene SERPINE1.

Structural Features of 5' Untranslated Region in Translational Control of Eukaryotes

Gene expression is a complex process regulated at multiple levels in eukaryotic cells. Translation frequently represents a pivotal step in the control of gene expression. Among the stages of translation, initiation is particularly important, as it governs ribosome recruitment and the efficiency of protein synthesis. The 5' untranslated region (5' UTR) of mRNA plays a key role in this process, often exhibiting a complicated and structured landscape. Numerous eukaryotic mRNAs possess long 5' UTRs that contain diverse regulatory elements, including RNA secondary structures, specific nucleotide motifs, and chemical modifications. These structural features can independently modulate translation through their intrinsic properties or by serving as platforms for trans-acting factors such as RNA-binding proteins. The dynamic nature of 5' UTR elements allows cells to fine-tune translation in response to environmental and cellular signals. Understanding these mechanisms is not only fundamental to molecular biology but also holds significant biomedical potential. Insights into 5' UTR-mediated regulation could drive advancements in synthetic biology and mRNA-based targeted therapies. This review outlines the current knowledge of the structural elements of the 5' UTR, the interplay between them, and their combined functional impact on translation.

RNA modifications in plant biotic interactions

The chemical modifications of DNA and proteins are powerful mechanisms for regulating molecular and biological functions, influencing a wide array of signaling pathways in eukaryotes. Recent advancements in epitranscriptomics have shown that RNA modifications play crucial roles in diverse biological processes. Since their discovery in the 1970s, scientists have sought to decipher, identify, and elucidate the functions of these modifications across biological systems. Over the past decade, mounting evidence has demonstrated the importance of RNA modification pathways in plants, prompting significant efforts to decipher their physiological relevance. With the advent of high-resolution mapping techniques for RNA modifications and the gradual uncovering of their biological roles, our understanding of this additional layer of regulation is beginning to take shape. In this review, we summarize recent findings on the major RNA modifications identified in plants, with an emphasis on N6-methyladenosine (m6A), the most extensively studied modification. We discuss the functional significance of the effector components involved in m6A modification and its diverse roles in plant biotic interactions, including plant-virus, plant-bacterium, plant-fungus, and plant-insect relationships. Furthermore, we highlight new technological developments driving research progress in this field and outline key challenges that remain to be addressed.

Advanced reactivity-based sequencing methods for mRNA epitranscriptome profiling

Currently, over 170 chemical modifications identified in RNA introduce an additional regulatory attribute to gene expression, known as the epitranscriptome. The development of detection methods to pinpoint the location and quantify these dynamic and reversible modifications has significantly expanded our understanding of their roles. This review goes deep into the latest progress in enzyme- and chemical-assisted sequencing methods, highlighting the opportunities presented by these reactivity-based techniques for detailed characterization of RNA modifications. Our survey provides a deeper understanding of the function and biological roles of RNA modification.

The diverse landscape of RNA modifications in cancer development and progression

BACKGROUND

RNA modifications, a central aspect of epitranscriptomics, add a regulatory layer to gene expression by modifying RNA function without altering nucleotide sequences. These modifications play vital roles across RNA species, influencing RNA stability, translation, and interaction dynamics, and are regulated by specific enzymes that add, remove, and interpret these chemical marks.

OBJECTIVE

This review examines the role of aberrant RNA modifications in cancer progression, exploring their potential as diagnostic and prognostic biomarkers and as therapeutic targets. We focus on how altered RNA modification patterns impact oncogenes, tumor suppressor genes, and overall tumor behavior.

METHODS

We performed an in-depth analysis of recent studies and advances in RNA modification research, highlighting key types and functions of RNA modifications and their roles in cancer biology. Studies involving preclinical models targeting RNA-modifying enzymes were reviewed to assess therapeutic efficacy and potential clinical applications.

RESULTS

Aberrant RNA modifications were found to significantly influence cancer initiation, growth, and metastasis. Dysregulation of RNA-modifying enzymes led to altered gene expression profiles in oncogenes and tumor suppressors, correlating with tumor aggressiveness, patient outcomes, and response to immunotherapy. Notably, inhibitors of these enzymes demonstrated potential in preclinical models by reducing tumor growth and enhancing the efficacy of existing cancer treatments.

CONCLUSIONS

RNA modifications present promising avenues for cancer diagnosis, prognosis, and therapy. Understanding the mechanisms of RNA modification dysregulation is essential for developing targeted treatments that improve patient outcomes. Further research will deepen insights into these pathways and support the clinical translation of RNA modification-targeted therapies.

Deciphering the secret codes in N7-methylguanosine modification: Context-dependent function of methyltransferase-like 1 in human diseases

N7-methylguanosine (m7G) is one of the most prevalent post-transcriptional modifications of RNA and plays a critical role in RNA translation and stability. As a pivotal m7G regulator, methyltransferase-like 1 (METTL1) is responsible for methyl group transfer during the progression of m7G modification and contributes to the structure and functional regulation of RNA. Accumulating evidence in recent years has revealed that METTL1 plays key roles in various diseases depending on its m7G RNA methyltransferase activity. Elevated levels of METTL1 are typically associated with disease development and adverse consequences. In contrast, METTL1 may act as a disease suppressor in several disorders. While the roles of m7G modifications in disease have been extensively reviewed, the critical functions of METTL1 in various types of disease and the potential targeting of METTL1 for disease treatment have not yet been highlighted. This review describes the various biological functions of METTL1, summarises recent advances in understanding its pathogenic and disease-suppressive functions and discusses the underlying molecular mechanisms. Given that METTL1 can promote or inhibit disease processes, the possibility of applying METTL1 inhibitors and agonists is further discussed, with the goal of providing novel insights for future disease diagnosis and potential intervention targets. KEY POINTS: METTL1-mediated m7G modification is crucial for various biological processes, including RNA stability, maturation and translation. METTL1 has emerged as a critical epigenetic modulator in human illnesses, with its dysregulated expression correlating with multiple diseases progression and presenting opportunities for both diagnostic biomarker development and molecular-targeted therapy. Enormous knowledge gaps persist regarding context-dependent regulatory networks of METTL1 and dynamic m7G modification patterns, necessitating mechanistic interrogation to bridge basic research with clinical translation in precision medicine.

Advancing bioinformatics with large language models: components, applications and perspectives

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of artificial neural networks with numerous parameters, trained on large amounts of unlabeled input using self-supervised or semi-supervised learning. However, their potential for solving bioinformatics problems may even exceed their proficiency in modeling human language. In this review, we will provide a comprehensive overview of the essential components of large language models (LLMs) in bioinformatics, spanning genomics, transcriptomics, proteomics, drug discovery, and single-cell analysis. Key aspects covered include tokenization methods for diverse data types, the architecture of transformer models, the core attention mechanism, and the pre-training processes underlying these models. Additionally, we will introduce currently available foundation models and highlight their downstream applications across various bioinformatics domains. Finally, drawing from our experience, we will offer practical guidance for both LLM users and developers, emphasizing strategies to optimize their use and foster further innovation in the field.

N7-methylguanosine modification in cancers: from mechanisms to therapeutic potential

N7-methylguanosine (m7G) is an important RNA modification involved in epigenetic regulation that is commonly observed in both prokaryotic and eukaryotic organisms. Their influence on the synthesis and processing of messenger RNA, ribosomal RNA, and transfer RNA allows m7G modifications to affect diverse cellular, physiological, and pathological processes. m7G modifications are pivotal in human diseases, particularly cancer progression. On one hand, m7G modification-associated modulate tumour progression and affect malignant biological characteristics, including sustained proliferation signalling, resistance to cell death, activation of invasion and metastasis, reprogramming of energy metabolism, genome instability, and immune evasion. This suggests that they may be novel therapeutic targets for cancer treatment. On the other hand, the aberrant expression of m7G modification-associated molecules is linked to clinicopathological characteristics, including tumour staging, lymph node metastasis, and unfavourable prognoses in patients with cancer, indicating their potential as tumour biomarkers. This review consolidates the discovery, identification, detection methodologies, and functional roles of m7G modification, analysing the mechanisms by which m7G modification-associated molecules contribute to tumour development, and exploring their potential clinical applications in cancer diagnostics and therapy, thereby providing innovative strategies for tumour identification and targeted treatment.

RNA modifications in cancer

RNA modifications are emerging as critical cancer regulators that influence tumorigenesis and progression. Key modifications, such as N6-methyladenosine (m6A) and 5-methylcytosine (m5C), are implicated in various cellular processes. These modifications are regulated by proteins that write, erase, and read RNA and modulate RNA stability, splicing, translation, and degradation. Recent studies have highlighted their roles in metabolic reprogramming, signaling pathways, and cell cycle control, which are essential for tumor proliferation and survival. Despite these scientific advances, the precise mechanisms by which RNA modifications affect cancer remain inadequately understood. This review comprehensively examines the role RNA modifications play in cancer proliferation, metastasis, and programmed cell death, including apoptosis, autophagy, and ferroptosis. It explores their effects on epithelial-mesenchymal transition (EMT) and the immune microenvironment, particularly in cancer metastasis. Furthermore, RNA modifications' potential in cancer therapies, including conventional treatments, immunotherapy, and targeted therapies, is discussed. By addressing these aspects, this review aims to bridge current research gaps and underscore the therapeutic potential of targeting RNA modifications to improve cancer treatment strategies and patient outcomes.

Mapping epigenetic modifications by sequencing technologies

The "epigenetics" concept was first described in 1942. Thus far, chemical modifications on histones, DNA, and RNA have emerged as three important building blocks of epigenetic modifications. Many epigenetic modifications have been intensively studied and found to be involved in most essential biological processes as well as human diseases, including cancer. Precisely and quantitatively mapping over 100 [1], 17 [2], and 160 [3] different known types of epigenetic modifications in histone, DNA, and RNA is the key to understanding the role of epigenetic modifications in gene regulation in diverse biological processes. With the rapid development of sequencing technologies, scientists are able to detect specific epigenetic modifications with various quantitative, high-resolution, whole-genome/transcriptome approaches. Here, we summarize recent advances in epigenetic modification sequencing technologies, focusing on major histone, DNA, and RNA modifications in mammalian cells.

Dynamic Profiles of Internal m7G Methylation on mRNAs in the Progression from HBV Infection to Hepatocellular Carcinoma

BACKGROUND

Emerging evidence indicates a robust association between internal RNA N7-methylguanosine (m7G) modification and hepatocarcinogenesis. However, the precise implications of altered internal m7G modifications within mRNA on the progression of Hepatitis B Virus (HBV)-induced Hepatocellular Carcinoma (HCC) remain inadequately elucidated.

METHODS

This study utilized a previously published dataset from the Gene Expression Omnibus (GEO) that includes samples of normal liver tissue, HBV positive (HP) liver tissue, and HP HCC tissue to investigate the profiling of mRNA internal m7G methylation. The STRING database and in vitro experiments were employed for the screening and validation of key m7G-related genes. The Cancer Genome Atlas cohorts were utilized to analyze the association of these key genes with the prognosis of HCC patients.

RESULTS

Comparative analyses revealed internal m7G modification alterations in 1546 mRNAs between HP liver and normal liver tissues, and in 3424 mRNAs between HP HCC and HP liver tissues. Following Protein-Protein Interaction (PPI) network analyses, validation experiments confirmed sustained high levels of internal m7G methylation modifications in EZH2, SMARCA4, and YY1. Furthermore, these genes were found to exhibit m7G modification-dependent expression changes during the transition from HBV infection to HCC, and were closely associated with the prognosis of HCC patients.

CONCLUSIONS

This study provides validation of substantial dynamic alternations in mRNA internal methylation profiles during the HBV infection to HCC. EZH2, SMARCA4, and YY1 emerge as promising molecular targets within this intricate regulatory landscape, offering avenues for further research and potential therapeutic exploration.

High-throughput detection of RNA modifications at single base resolution

RNA is modified by > 170 chemical modifications that affect its structure and function. Accordingly, RNA modifications have been implicated in regulation of gene expression and cellular outcomes in a variety of species spanning the phylogenetic tree. The study of RNA modifications is accelerated by generation of high-throughput methods for detecting RNA modifications at single base resolution. Here, we review recent advancement in next generation sequencing based approaches for detection of 14 distinct RNA modifications present in rRNA, tRNA and mRNA. We further outline the molecular and computational principles underlying currently available methods.

Neuroblastoma susceptibility and association of N7-methylguanosine modification gene polymorphisms: multi-center case-control study

BACKGROUND

Neuroblastoma (NB) is a common extracranial solid malignancy in children. The N7-methylguanosine (m7G) modification gene METTL1/WDR4 polymorphisms may serve as promising molecular markers for identifying populations susceptible to NB.

METHODS

TaqMan probes was usded to genotype METTL1/WDR4 single nucleotide polymorphisms (SNPs) in 898 NB patients and 1734 healthy controls. A logistic regression model was utilized to calculate the odds ratio (OR) and 95% confidence interval (CI), evaluating the association between genotype polymorphisms and NB susceptibility. The analysis was also stratified by age, sex, tumor origin site, and clinical stage.

RESULTS

Individual polymorphism of the METTL1/WDR4 gene investigated in this study did not show significant associations with NB susceptibility. However, combined genotype analysis revealed that carrying all 5 WDR4 protective genotypes was associated with a significantly lower NB risk compared to having 0-4 protective genotypes (AOR = 0.82, 95% CI = 0.69-0.96, P = 0.014). Further stratified analyses revealed that carrying 1-3 METTL1 risk genotypes, the WDR4 rs2156316 CG/GG genotype, the WDR4 rs2248490 CG/GG genotype, and having all five WDR4 protective genotypes were all significantly correlated with NB susceptibility in distinct subpopulations.

CONCLUSIONS

In conclusion, our findings suggest significant associations between m7G modification gene METTL1/WDR4 SNPs and NB susceptibility in specific populations.

IMPACT

Genetic variation in m7G modification gene is associated with susceptibility to NB. Single nucleotide polymorphisms in METTL1/WDR4 are associated with susceptibility to NB. Single nucleotide polymorphisms of METTL1/WDR4 can be used as a biomarker for screening NB susceptible populations.

Genome-wide identification of cell type-specific susceptibility genes for Juvenile dermatomyositis through the analysis of N6-methyladenosine-associated SNPs

Genome-wide association studies (GWASs) have pinpointed genetic loci associated with juvenile dermatomyositis (JDM). Functional genes within the GWAS loci may be cell type-specific, but their identity remains largely unknown. N6-methyladenosine (m6A) plays a pivotal role in regulating various cellular processes and is linked to autoimmune diseases. This study aimed to underscore the potential functional genes within the GWAS loci through the analysis of m6A-associated SNPs (m6A-SNPs), specifically within relevant cell types. JDM-associated m6A-SNPs were identified from the GWAS summary dataset. The correlation between m6A-SNPs and gene expression was assessed through bulk tissue and single-cell eQTL analyses. To further investigate the relationship between gene expression and JDM, Mendelian randomization analysis was employed. Additionally, differential expression analyses were conducted on bulk tissues, as well as single-cell transcriptomic data comprising 6 JDM patients and 11 juvenile controls (99,396 cells). Seven m6A-SNPs associated with JDM were identified. Bulk tissue analysis revealed differential expression of HLA-DPA1, HLA-DPB1, MICB, HLA-A, HLA-F, HLA-DQB2, HLA-DRB5, TAP2, PSMB9, MICA, AIF1, and DDX39B influenced by m6A-SNPs, all showing associations with JDM in both differential expression and Mendelian randomization analyses. In single-cell analysis, the six m6A-SNPs within the HLA locus acted as cell-type-specific eQTLs, correlating with the expression of HLA-A, HLA-B, HLA-C, HLA-DPB1, HLA-DQA1, HLA-DQB1 and HLA-DRB1 in myeloid, T or B cells. Notably, these genes displayed abnormal expression in T, B, and myeloid cells of JDM patients. The present study identified m6A-SNPs within JDM susceptibility genes, shedding light on the intricate interplay between m6A-SNPs, gene expression, and JDM.

RNA methylation and breast cancer: insights into m6A, m7G and m5C

Breast cancer remains the most commonly diagnosed cancer in female worldwide, marked by its molecular diversity and complex subtypes. Despite progress in targeted therapies, tumor heterogeneity and treatment resistance continue to present major challenges. Recent studies emphasize the crucial role of RNA modifications in cancer biology, with nearly 200 distinct modifications identified. Among these, methylation is particularly significant, with methylation-related factors emerging as key regulators of RNA metabolism, influencing cancer progression, metastasis, and treatment resistance. This review focuses on the roles of key RNA methylation in breast cancer, particularly N6-methyladenosine (m6A), N7-methylguanosine (m7G), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N3-methylcytidine (m3C). We examine the functions of m6A "writers" like METTL3 and METTL14, and "readers" such as the YTH domain family in modulating tumor behavior. Dysregulation of m6A "erasers" like FTO and ALKBH5 are noticed too, highlighting their impact on cancer stem cell phenotypes, chemoresistance, and immune evasion. Additionally, the role of m7G modifications in mRNA stability and translation, facilitated by METTL1/WDR4 and RNMT, is discussed as a potential therapeutic target. The involvement of m5C, m1A, and m3C modifications, particularly those mediated by NSUN2 and NSUN6, in breast cancer tumorigenesis and prognosis is also reviewed. Despite coding RNAs, the interplay between these RNA methylations and non-coding RNAs, such as lncRNAs and miRNAs, is explored, shedding light on their roles in cancer cell proliferation, invasion, and immune response modulation. This review highlights the potential of RNA methylations as novel therapeutic targets in breast cancer, offering insights for precision medicine and improved patient outcomes.

Role of RNA-binding Proteins in Regulating Cell Adhesion and Progression of the Atherosclerotic Plaque and Plaque Erosion

PURPOSE OF REVIEW

RNA-binding proteins (RBPs) have emerged as crucial regulators of post-transcriptional processes, influencing the fate of RNA. This review delves into the biological functions of RBPs and their role in alternative splicing concerning atherosclerosis (AS), highlighting their participation in essential cellular processes. Our goal is to offer new insights for cardiovascular disease research and treatment.

RECENT FINDING

Dysregulation of RBPs is associated with various human diseases, including autoimmune and neurological disorders. The role of RBPs in the pathogenesis of AS is progressively being elucidated, as they influence plaque formation and disease progression by regulating cell function and gene expression. RBPs play intricate biological roles in regulating pre-mRNA, including editing, splicing, stability and translation. Alternative splicing has been demonstrated to enhance biological complexity and diversity. Our findings indicate that alternative splicing is extensively involved in the pathogenesis of AS. The dysregulated expression of specific RBPs in AS is linked to the production of adhesion molecules and vascular endothelium damage. Further research on RBPs could pave the way for the development of novel therapeutic targets.

RNA modifications: emerging players in the regulation of reproduction and development

The intricate world of RNA modifications, collectively termed the epitranscriptome, covers over 170 identified modifications and impacts RNA metabolism and, consequently, almost all biological processes. In this review, we focus on the regulatory roles and biological functions of a panel of dominant RNA modifications (including m 6A, m 5C, Ψ, ac 4C, m 1A, and m 7G) on three RNA types-mRNA, tRNA, and rRNA-in mammalian development, particularly in the context of reproduction as well as embryonic development. We discuss in detail how those modifications, along with their regulatory proteins, affect RNA processing, structure, localization, stability, and translation efficiency. We also highlight the associations among dysfunctions in RNA modification-related proteins, abnormal modification deposition and various diseases, emphasizing the roles of RNA modifications in critical developmental processes such as stem cell self-renewal and cell fate transition. Elucidating the molecular mechanisms by which RNA modifications influence diverse developmental processes holds promise for developing innovative strategies to manage developmental disorders. Finally, we outline several unexplored areas in the field of RNA modification that warrant further investigation.

GenoM7GNet: An Efficient N7-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model

N-methylguanosine (m7G), one of the mainstream post-transcriptional RNA modifications, occupies an exceedingly significant place in medical treatments. However, classic approaches for identifying m7G sites are costly both in time and equipment. Meanwhile, the existing machine learning methods extract limited hidden information from RNA sequences, thus making it difficult to improve the accuracy. Therefore, we put forward to a deep learning network, called "GenoM7GNet," for m7G site identification. This model utilizes a Bidirectional Encoder Representation from Transformers (BERT) and is pretrained on nucleotide sequences data to capture hidden patterns from RNA sequences for m7G site prediction. Moreover, through detailed comparative experiments with various deep learning models, we discovered that the one-dimensional convolutional neural network (CNN) exhibits outstanding performance in sequence feature learning and classification. The proposed GenoM7GNet model achieved 0.953in accuracy, 0.932in sensitivity, 0.976in specificity, 0.907in Matthews Correlation Coefficient and 0.984in Area Under the receiver operating characteristic Curve on performance evaluation. Extensive experimental results further prove that our GenoM7GNet model markedly surpasses other state-of-the-art models in predicting m7G sites, exhibiting high computing performance.

Breaking the barrier: Epigenetic strategies to combat platinum resistance in colorectal cancer

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. Platinum-based drugs, such as cisplatin and oxaliplatin, are frontline chemotherapy for CRC, effective in both monotherapy and combination regimens. However, the clinical efficacy of these treatments is often undermined by the development of drug resistance, a significant obstacle in cancer therapy. In recent years, epigenetic alterations have been recognized as key players in the acquisition of resistance to platinum drugs. Targeting these dysregulated epigenetic mechanisms with small molecules represents a promising therapeutic strategy. This review explores the complex relationship between epigenetic changes and platinum resistance in CRC, highlighting current epigenetic therapies and their effectiveness in countering resistance mechanisms. By elucidating the epigenetic underpinnings of platinum resistance, this review aims to contribute to ongoing efforts to improve treatment outcomes for CRC patients.

Genome-Wide Identification of Cell Type-Specific Susceptibility Genes for SLE Through the Analysis of RNA Modification-Associated SNPs

INTRODUCTION

This study aimed to elucidate the functional genes associated with systemic lupus erythematosus (SLE) in various cell types through the utilization of RNAm-SNPs.

METHODS

Utilizing large-scale genetic data, we identified associations between RNAm-SNPs and SLE. The association between RNAm-SNPs and bulk and single-cell mRNA expression (eQTL) and protein levels (pQTL) were examined. Mendelian randomization and differential expression analyses were conducted to explore the links between gene expression, protein levels, and SLE.

RESULTS

We identified 41 RNAm-SNPs that were significantly associated with SLE. The GWAS signals exhibited notable enrichment in m6A-SNPs and m7G-SNPs. These RNAm-SNPs showed both eQTL and pQTL effects. In our single-cell analysis, 16 RNAm-SNPs exhibited associations with gene expression levels across 13 distinct cell types, including HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, HLA-DRB1 and IRF7. We identified 58 noteworthy associations between the expression levels of 20 genes and SLE across 12 distinct immune cell types. Notably, HLA-DQB1, HLA-DRB1 and IRF7 exhibited abnormalities in CD8+ T cells, IRF7 displayed abnormal expression in CD4+ T cells, while HLA-DRB1 and IRF7 were also distinctly perturbed in natural killer cells.

DISCUSSION

This study advances our understanding of the genetic basis of SLE by highlighting the significance of RNAm-SNPs and immune cell gene expression in SLE.

RNA modification in normal hematopoiesis and hematologic malignancies

N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotic cells. Previous studies have shown that m6A plays a critical role under both normal physiological and pathological conditions. Hematopoiesis and differentiation are highly regulated processes, and recent studies on m6A mRNA methylation have revealed how this modification controls cell fate in both normal and malignant hematopoietic states. However, despite these insights, a comprehensive understanding of its complex roles between normal hematopoietic development and malignant hematopoietic diseases remains elusive. This review first provides an overview of the components and biological functions of m6A modification regulators. Additionally, it highlights the origin, differentiation process, biological characteristics, and regulatory mechanisms of hematopoietic stem cells, as well as the features, immune properties, and self-renewal pathways of leukemia stem cells. Last, the article systematically reviews the latest research advancements on the roles and mechanisms of m6A regulatory factors in normal hematopoiesis and related malignant diseases. More importantly, this review explores how targeting m6A regulators and various signaling pathways could effectively intervene in the development of leukemia, providing new insights and potential therapeutic targets. Targeting m6A modification may hold promise for achieving more precise and effective leukemia treatments.

A review of current developments in RNA modifications in lung cancer

Lung cancer has the highest incidence and mortality rates worldwide and is the primary cause of cancer-related death. Despite the rapid development of diagnostic methods and targeted drugs in recent years, many lung cancer patients do not benefit from effective therapies. The emergence of drug resistance has led to a reduction in the therapeutic effectiveness of targeted drugs, highlighting a crucial need to explore novel therapeutic targets. Many studies have found that epigenetic plays an important role in the occurrence of lung cancer. This review describes the biological function of epigenetic RNA modifications, such as m6A, m5C, m7G, and m1A, and recent advancements in their role in the development, progression, and prognosis of lung cancer. This review aims to provide new guidance for the treatment of lung cancer.

Expression Profile and Prognostic Significance of Pivotal Regulators for N7-Methylguanosine Methylation in Diffuse Large B-Cell Lymphoma

N7-methylguanosine (m7G) occurs by adding a methyl group to the N7 atom of the RNA guanine. Emerging evidence suggests that m7G modification has emerged as a crucial regulator of tumorigenesis, progression, invasion, and metastasis in multiple cancers. Nevertheless, the utility of m7G modification in diffuse large B-cell lymphoma (DLBCL) remains undefined, notably the interaction with the tumor microenvironment (TME). Here, we aimed to identify the expression profile of m7G regulators in DLBCL, construct a novel risk model, and explore their connection with TME. We initially investigated the difference and correlation in m7G regulators' expression in normal and tumor groups, classified patients by consistent clustering analysis, investigated the functional and prognostic significance of the resulting subtypes, and identified prognosis-associated genes by one-way Cox and least absolute shrinkage and selection operator (LASSO) regression calculations, and constructed a risk model. Further analysis showed that correlation among immune cell infiltration with m7G risk score and determined that it impacts the prognosis of DLBCL patients. Our research demonstrated the relevance of m7G regulators to DLBCL prognosis, providing theoretical support for precise prognostic stratification and immunotherapeutic assessment in DLBCL.

A novel m7G-related miRNA prognostic signature for predicting clinical outcome and immune microenvironment in colon cancer

Background: Colon cancer (CC) is a highly prevalent malignancy worldwide, characterized by elevated mortality rates and poor prognosis. N7-methylguanosine (m7G) methylation is an emerging RNA modification type and involved in the development of many tumors. Despite this, the correlation between m7G-related miRNAs and CC remains to be elucidated. This research aimed to investigate the clinical significance of m7G-related miRNAs in predicting both the prognosis and tumor microenvironment (TME) of CC. Method: We retrieved transcriptome data and associated clinical information from a publicly accessible database. Using univariate Cox and LASSO regression analyses, we established a signature of m7G-related miRNAs. Additionally, we used CIBERSORT and ssGSEA algorithms to explore the association between the prognostic risk score and the TME in CC patients. By considering the risk signature and immune infiltration, we identified differentially expressed genes that contribute to the prognosis of CC. Finally, the expression patterns of prognostic miRNAs were verified using quantitative reverse transcriptase PCR (qRT-PCR) in cell lines. Results: We constructed a prognostic risk signature based on seven m7G-related miRNAs (miR-136-5p, miR-6887-3p, miR-195-5p, miR-149-3p, miR-4433a-5p, miR-31-5p, and miR-129-2-3p). Subsequently, we observed remarkable differences in patient outcomes between the high- and low-risk groups. The area under the curve (AUC) for 1-, 3-, and 5-year survivals in the ROC curve were 0.735, 0.707, and 0.632, respectively. Furthermore, our results showed that the risk score can serve as an independent prognostic biomarker for overall survival prediction. In terms of immune analysis, the results revealed a significant association between the risk signature and immune infiltration, as well as immune checkpoint expression. Finally, our study showed that CCDC160 and RLN3 is the gene most relevant to immune cells and function in CC. Conclusion: Our study conducted a comprehensive and systematic analysis of m7G-associated miRNAs to construct prognostic profiles of CC. We developed a prognostic risk model based on m7G-miRNAs, with the resulting risk scores demonstrating considerable potential as prognostic biomarkers. These findings provide substantial evidence for the critical role of m7G-related miRNAs in colon cancer and may offer new immunotherapeutic targets for patients with this disease.

Dynamic RNA methylation modifications and their regulatory role in mammalian development and diseases

Among over 170 different types of chemical modifications on RNA nucleobases identified so far, RNA methylation is the major type of epitranscriptomic modifications existing on almost all types of RNAs, and has been demonstrated to participate in the entire process of RNA metabolism, including transcription, pre-mRNA alternative splicing and maturation, mRNA nucleus export, mRNA degradation and stabilization, mRNA translation. Attributing to the development of high-throughput detection technologies and the identification of both dynamic regulators and recognition proteins, mechanisms of RNA methylation modification in regulating the normal development of the organism as well as various disease occurrence and developmental abnormalities upon RNA methylation dysregulation have become increasingly clear. Here, we particularly focus on three types of RNA methylations: N6-methylcytosine (m6A), 5-methylcytosine (m5C), and N7-methyladenosine (m7G). We summarize the elements related to their dynamic installment and removal, specific binding proteins, and the development of high-throughput detection technologies. Then, for a comprehensive understanding of their biological significance, we also overview the latest knowledge on the underlying mechanisms and key roles of these three mRNA methylation modifications in gametogenesis, embryonic development, immune system development, as well as disease and tumor progression.

Development and validation of a 6-gene signature derived from RNA modification-associated genes for the diagnosis of Acute Stanford Type A Aortic Dissection

Background

Acute Stanford Type A Aortic Dissection (ATAAD) is a critical medical emergency characterized by significant morbidity and mortality. This study aims to identify specific gene expression patterns and RNA modification associated with ATAAD.

Methods

The GSE153434 dataset was obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis was conducted to identify differential expression genes (DEGs) associated with ATAAD. To validate the involvement of RNA modification in ATAAD, RNA modification-related genes (M6A, M1A, M5C, APA, A-to-I) were acquired from GeneCards, following by Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis. A gene prediction signature consisting of key genes was established, and Real-time PCR was used to validate the gene expression in clinical samples. The patients were then divided into high and low-risk groups, and subsequent enrichment analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), Gene Set Variation Analysis (GSVA), and assessments of immune infiltration. A co-expression network analysis (WGCNA) was performed to explore gene-phenotype relationships and identify key genes.

Results

A total of 45 RNA modification genes were acquired. Six gene signatures (YTHDC1, WTAP, CFI, ADARB1, ADARB2, TET3) were developed for ATAAD diagnosis and risk stratification. Enrichment analysis suggested the potential involvement of inflammation and extracellular matrix pathways in the progression of ATAAD. The incorporation of pertinent genes from the GSE147026 dataset into the six-gene signature further validated the model's effectiveness. A significant upregulation in WTAP, ADARB2, and TET3 expression, whereas YTHDC1 exhibited a noteworthy downregulation in the ATAAD group.

Conclusion

Six-gene signature could serve as an efficient model for predicting the diagnosis of ATAAD.

Mettl1-dependent m7G tRNA modification is essential for maintaining spermatogenesis and fertility in Drosophila melanogaster

Modification of guanosine to N7-methylguanosine (m7G) in the variable loop region of tRNA is catalyzed by the METTL1/WDR4 heterodimer and stabilizes target tRNA. Here, we reveal essential functions of Mettl1 in Drosophila fertility. Knockout of Mettl1 (Mettl1-KO) causes no major effect on the development of non-gonadal tissues, but abolishes the production of elongated spermatids and mature sperm, which is fully rescued by expression of a Mettl1-transgene, but not a catalytic-dead Mettl1 transgene. This demonstrates that Mettl1-dependent m7G is required for spermatogenesis. Mettl1-KO results in a loss of m7G modification on a subset of tRNAs and decreased tRNA abundance. Ribosome profiling shows that Mettl1-KO led to ribosomes stalling at codons decoded by tRNAs that were reduced in abundance. Mettl1-KO also significantly reduces the translation efficiency of genes involved in elongated spermatid formation and sperm stability. Germ cell-specific expression of Mettl1 rescues disrupted m7G tRNA modification and tRNA abundance in Mettl1-KO testes but not in non-gonadal tissues. Ribosome stalling is much less detectable in non-gonadal tissues than in Mettl1-KO testes. These findings reveal a developmental role for m7G tRNA modification and indicate that m7G modification-dependent tRNA abundance differs among tissues.

Metabolic rewiring during bone development underlies tRNA m7G-associated primordial dwarfism

Translation of mRNA to protein is tightly regulated by transfer RNAs (tRNAs), which are subject to various chemical modifications that maintain structure, stability, and function. Deficiency of tRNA N7-methylguanosine (m7G) modification in patients causes a type of primordial dwarfism, but the underlying mechanism remains unknown. Here we report that the loss of m7G rewires cellular metabolism, leading to the pathogenesis of primordial dwarfism. Conditional deletion of the catalytic enzyme Mettl1 or missense mutation of the scaffold protein Wdr4 severely impaired endochondral bone formation and bone mass accrual. Mechanistically, Mettl1 knockout decreased abundance of m7G-modified tRNAs and inhibited translation of mRNAs relating to cytoskeleton and Rho GTPase signaling. Meanwhile, Mettl1 knockout enhanced cellular energy metabolism despite incompetent proliferation and osteogenic commitment. Further exploration revealed that impairment of Rho GTPase signaling upregulated the level of branched-chain amino acid transaminase 1 (BCAT1) that rewired cell metabolism and restricted intracellular α-ketoglutarate (αKG). Supplementation of αKG ameliorated the skeletal defect of Mettl1-deficient mice. In addition to the selective translation of metabolism-related mRNAs, we further revealed that Mettl1 knockout globally regulated translation via integrated stress response (ISR) and mammalian target of rapamycin complex 1 (mTORC1) signaling. Restoring translation by targeting either ISR or mTORC1 aggravated bone defects of Mettl1-deficient mice. Overall, our study unveils a critical role of m7G tRNA modification in bone development by regulation of cellular metabolism and indicates suspension of translation initiation as a quality control mechanism in response to tRNA dysregulation.

Identification of RNMT as an immunotherapeutic and prognostic biomarker: From pan-cancer analysis to lung squamous cell carcinoma validation

BACKGROUND

Dysregulation of RNA guanine-7 methyltransferase (RNMT) plays a crucial role in the tumor progression and immune responses. However, the detailed role of RNMT in pan-cancer is still unknown.

METHODS

Bulk transcriptomic data of pan-cancer were obtained from the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Cancer Cell Line Encyclopedia (CCLE) databases. Single-cell transcriptomic and proteomics data of lung squamous cell carcinoma (LUSC) were analyzed in the Tumor Immune Single-cell Hub 2 (TISCH2) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) databases, respectively. The correlation between RNMT expression and cancer prognosis was analyzed by Cox proportional hazards regression and Kaplan-Meier analyses. The correlation of RNMT expression with common immunoregulators, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), and DNA methyltransferase (DNMT) was analyzed. Additionally, the correlation between RNMT expression and immune infiltration level was evaluated. A total of 1287 machine learning combinations were used to construct prognostic models for LUSC. qRT-PCR and Western blot were used to validate the bioinformatics findings of RNMT upregulation in LUSC.

RESULTS

RNMT was widely expressed across different cancers, with significant correlation to prognosis in cancers such as kidney chromophobe (KICH) (p = 0.0033, HR = 7.12), liver hepatocellular carcinoma (LIHC) (p = 0.01, HR = 1.41), and others. Notably, RNMT participates in the regulation of the tumor microenvironment. RNMT expression positively correlated with immune cell expression (Spearman's rank correlation, p < 0.05). Moreover, RNMT expression was strongly associated with immunoregulators, TMB, MSI, MMR, and DNMT in most cancer types. Notably, RNMT expression displayed excellent prognostic and immunological performance in LUSC. The expression of RNMT was mainly enriched in B cells of LUSC tissues. qRT-PCR and Western blot verified the high expression of RNMT in LUSC.

CONCLUSION

RNMT expression widely correlated with prognosis and immune infiltration in various tumors, especially LUSC. The RNMT detection may provide a new idea for future tumor immune studies and treatment strategies.

Unravelling the impact of RNA methylation genetic and epigenetic machinery in the treatment of cardiomyopathy

Cardiomyopathy (CM) represents a heterogeneous group of diseases primarily affecting cardiac structure and function, with genetic and epigenetic dysregulation playing a pivotal role in its pathogenesis. Emerging evidence from the burgeoning field of epitranscriptomics has brought to light the significant impact of various RNA modifications, notably N6-methyladenosine (m6A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N1-methyladenosine (m1A), 2'-O-methylation (Nm), and 6,2'-O-dimethyladenosine (m6Am), on cardiomyocyte function and the broader processes of cardiac and vascular remodelling. These modifications have been shown to influence key pathological mechanisms including mitochondrial dysfunction, oxidative stress, cardiomyocyte apoptosis, inflammation, immune response, and myocardial fibrosis. Importantly, aberrations in the RNA methylation machinery have been observed in human CM cases and animal models, highlighting the critical role of RNA methylating enzymes and their potential as therapeutic targets or biomarkers for CM. This review underscores the necessity for a deeper understanding of RNA methylation processes in the context of CM, to illuminate novel therapeutic avenues and diagnostic tools, thereby addressing a significant gap in the current management strategies for this complex disease.

Targeting m7G-enriched circKDM1A prevents colorectal cancer progression

Plenty of circRNAs have been reported to play an important role in colorectal cancer (CRC), while the reason of abnormal circRNA expression in cancer still keep elusive. Here, we found that m7G RNA modifications were enriched in some circRNAs, these m7G modifications in circRNAs were catalyzed by METTL1, and the GG motif was the main site preference for m7G modifications in circRNAs. We further confirmed that METTL1 played a cancer-promoting role in CRC. We then screened a highly expressed circRNA, called circKDM1A, and found that METTL1 prevented the degradation of circKDM1A by m7G modification. CircKDM1A was further verified to promote proliferation, invasion and migration of CRC in vivo and in vitro. Its cancer-promoting ability was weakened after the m7G site mutation. CircKDM1A was verified to activate AKT pathway by upregulating PDK1, consequently promoting CRC progression. These results suggest that m7G-modified circRNA promotes CRC progression via activating AKT pathway. Our study uncovers an essential physiological function and mechanism of METTL1-mediated m7G modification in the regulation of circRNA stability and cancer progression.

IGF2BP3 promotes mRNA degradation through internal m7G modification

Recent studies have suggested that mRNA internal m7G and its writer protein METTL1 are closely related to cell metabolism and cancer regulation. Here, we identify that IGF2BP family proteins IGF2BP1-3 can preferentially bind internal mRNA m7G. Such interactions, especially IGF2BP3 with m7G, could promote the degradation of m7G target transcripts in cancer cells. IGF2BP3 is more responsive to changes of m7G modification, while IGF2BP1 prefers m6A to stabilize the bound transcripts. We also demonstrate that p53 transcript, TP53, is m7G-modified at its 3'UTR in cancer cells. In glioblastoma, the methylation level and the half lifetime of the modified transcript could be modulated by tuning IGF2BP3, or by site-specific targeting of m7G through a dCas13b-guided system, resulting in modulation of cancer progression and chemosensitivity.

m7GRegpred: substrate prediction of N7-methylguanosine (m7G) writers and readers based on sequencing features

N7-Methylguanosine (m7G) is important RNA modification at internal and the cap structure of five terminal end of message RNA. It is essential for RNA stability of RNA, the efficiency of translation, and various intracellular RNA processing pathways. Given the significance of the m7G modification, numerous studies have been conducted to predict m7G sites. To further elucidate the regulatory mechanisms surrounding m7G, we introduce a novel bioinformatics framework, m7GRegpred, designed to forecast the targets of the m7G methyltransferases METTL1 and WDR4, and m7G readers QKI5, QKI6, and QKI7 for the first time. We integrated different features to build predictors, with AUROC scores of 0.856, 0.857, 0.780, 0.776, 0.818 for METTL1, WDR4, QKI5, QKI6, and QKI7, respectively. In addition, the effect of window lengths and algorism were systemically evaluated in this work. The finial model was summarized in a user-friendly webserver: http://modinfor.com/m7GRegpred/. Our research indicates that the substrates of m7G regulators can be identified and may potentially advance the study of m7G regulators under unique conditions.

The role of RNA modifications in hepatocellular carcinoma: functional mechanism and potential applications

Hepatocellular carcinoma (HCC) is a highly aggressive cancer with a poor prognosis. The molecular mechanisms underlying its development remain unclear. Recent studies have highlighted the crucial role of RNA modifications in HCC progression, which indicates their potential as therapeutic targets and biomarkers for managing HCC. In this review, we discuss the functional role and molecular mechanisms of RNA modifications in HCC through a review and summary of relevant literature, to explore the potential therapeutic agents and biomarkers for diagnostic and prognostic of HCC. This review indicates that specific RNA modification pathways, such as N6-methyladenosine, 5-methylcytosine, N7-methylguanosine, and N1-methyladenosine, are erroneously regulated and are involved in the proliferation, autophagy, innate immunity, invasion, metastasis, immune cell infiltration, and drug resistance of HCC. These findings provide a new perspective for understanding the molecular mechanisms of HCC, as well as potential targets for the diagnosis and treatment of HCC by targeting specific RNA-modifying enzymes or recognition proteins. More than ten RNA-modifying regulators showed the potential for use for the diagnosis, prognosis and treatment decision utility biomarkers of HCC. Their application value for HCC biomarkers necessitates extensive multi-center sample validation in the future. A growing number of RNA modifier inhibitors are being developed, but the lack of preclinical experiments and clinical studies targeting RNA modification in HCC poses a significant obstacle, and further research is needed to evaluate their application value in HCC treatment. In conclusion, this review provides an in-depth understanding of the complex interplay between RNA modifications and HCC while emphasizing the promising potential of RNA modifications as therapeutic targets and biomarkers for managing HCC.

METTL Family in Healthy and Disease

Transcription, RNA splicing, RNA translation, and post-translational protein modification are fundamental processes of gene expression. Epigenetic modifications, such as DNA methylation, RNA modifications, and protein modifications, play a crucial role in regulating gene expression. The methyltransferase-like protein (METTL) family, a constituent of the 7-β-strand (7BS) methyltransferase subfamily, is broadly distributed across the cell nucleus, cytoplasm, and mitochondria. Members of the METTL family, through their S-adenosyl methionine (SAM) binding domain, can transfer methyl groups to DNA, RNA, or proteins, thereby impacting processes such as DNA replication, transcription, and mRNA translation, to participate in the maintenance of normal function or promote disease development. This review primarily examines the involvement of the METTL family in normal cell differentiation, the maintenance of mitochondrial function, and its association with tumor formation, the nervous system, and cardiovascular diseases. Notably, the METTL family is intricately linked to cellular translation, particularly in its regulation of translation factors. Members represent important molecules in disease development processes and are associated with patient immunity and tolerance to radiotherapy and chemotherapy. Moreover, future research directions could include the development of drugs or antibodies targeting its structural domains, and utilizing nanomaterials to carry miRNA corresponding to METTL family mRNA. Additionally, the precise mechanisms underlying the interactions between the METTL family and cellular translation factors remain to be clarified.

The potential of RNA methylation in the treatment of cardiovascular diseases

RNA methylation has emerged as a dynamic regulatory mechanism that impacts gene expression and protein synthesis. Among the known RNA methylation modifications, N6-methyladenosine (m6A), 5-methylcytosine (m5C), 3-methylcytosine (m3C), and N7-methylguanosine (m7G) have been studied extensively. In particular, m6A is the most abundant RNA modification and has attracted significant attention due to its potential effect on multiple biological processes. Recent studies have demonstrated that RNA methylation plays an important role in the development and progression of cardiovascular disease (CVD). To identify key pathogenic genes of CVD and potential therapeutic targets, we reviewed several common RNA methylation and summarized the research progress of RNA methylation in diverse CVDs, intending to inspire effective treatment strategies.

Moss-m7G: A Motif-Based Interpretable Deep Learning Method for RNA N7-Methlguanosine Site Prediction

N-7methylguanosine (m7G) modification plays a crucial role in various biological processes and is closely associated with the development and progression of many cancers. Accurate identification of m7G modification sites is essential for understanding their regulatory mechanisms and advancing cancer therapy. Previous studies often suffered from insufficient research data, underutilization of motif information, and lack of interpretability. In this work, we designed a novel motif-based interpretable method for m7G modification site prediction, called Moss-m7G. This approach enables the analysis of RNA sequences from a motif-centric perspective. Our proposed word-detection module and motif-embedding module within Moss-m7G extract motif information from sequences, transforming the raw sequences from base-level into motif-level and generating embeddings for these motif sequences. Compared with base sequences, motif sequences contain richer contextual information, which is further analyzed and integrated through the Transformer model. We constructed a comprehensive m7G data set to implement the training and testing process to address the data insufficiency noted in prior research. Our experimental results affirm the effectiveness and superiority of Moss-m7G in predicting m7G modification sites. Moreover, the introduction of the word-detection module enhances the interpretability of the model, providing insights into the predictive mechanisms.

The m7G Methyltransferase Mettl1 Drives Cardiac Hypertrophy by Regulating SRSF9-Mediated Splicing of NFATc4

Cardiac hypertrophy is a key factor driving heart failure (HF), yet its pathogenesis remains incompletely elucidated. Mettl1-catalyzed RNA N7-methylguanosine (m7G) modification has been implicated in ischemic cardiac injury and fibrosis. This study aims to elucidate the role of Mettl1 and the mechanism underlying non-ischemic cardiac hypertrophy and HF. It is found that Mettl1 is upregulated in human failing hearts and hypertrophic murine hearts following transverse aortic constriction (TAC) and Angiotensin II (Ang II) infusion. YY1 acts as a transcriptional factor for Mettl1 during cardiac hypertrophy. Mettl1 knockout alleviates cardiac hypertrophy and dysfunction upon pressure overload from TAC or Ang II stimulation. Conversely, cardiac-specific overexpression of Mettl1 results in cardiac remodeling. Mechanically, Mettl1 increases SRSF9 expression by inducing m7G modification of SRSF9 mRNA, facilitating alternative splicing and stabilization of NFATc4, thereby promoting cardiac hypertrophy. Moreover, the knockdown of SRSF9 protects against TAC- or Mettl1-induced cardiac hypertrophic phenotypes in vivo and in vitro. The study identifies Mettl1 as a crucial regulator of cardiac hypertrophy, providing a novel therapeutic target for HF.