Molecular Mechanisms Driving mRNA Degradation by m6A Modification

MeRIP-seq data analysis and validation reveal the regulatory role of m6A modified circRNAs in the apoptosis of secondary hair follicle cells in Inner Mongolia cashmere goats

As a widely epigenetic modification, m6A (N6-methyladenosine, m6A) can regulate the degradation, translation, and other biological functions of circRNAs through dynamic reversible processes. It plays an important role in regulating the life activities of biological organisms, particularly in cell differentiation, apoptosis, embryonic development, stress response, and innate immunity. In this study, bioinformatics analysis, qRT-PCR identification, FISH subcellular localization, and ceRNA network construction were performed on m6A modified circRNAs regulating the apoptosis of secondary hair follicle cells of Inner Mongolia Albas white cashmere goats based on the skin m6A sequencing data of secondary hair follicles in anagen and catagen. The results showed that 8 m6A modified circRNAs regulating the cell apoptosis of secondary hair follicles, namely circRNA_2130, circRNA_0013, circRNA_1203, circRNA_1462, circRNA_1242, circRNA_2308, circRNA_2654 and circRNA_1442 were identified, and they are respectively derived from ANGEL2, APP, GKAP1, HNRNPC, PTBP3, NUCB1, SNRK and ZNF609 genes. Among them, circRNA_0013, circRNA_1442 and circRNA_1462 were located in the cytoplasm of the secondary hair follicle papilla, while circRNA_1203, circRNA_1242, circRNA_2130, circRNA_2308 and circRNA_2654 were located in the nucleus. There are complex and diverse regulatory relationships among 8 circRNAs, with each circRNA targeting one or more miRNAs, revealing that each m6A circRNA can exert regulatory effects through multiple potential miRNA-mRNA axes, to regulate the apoptosis of secondary hair follicle cells of cashmere goats during the growth cycles. This result provides a direction for further elucidating the regulatory mechanism of m6A modified circRNAs in cashmere growth and exploring biomarkers.

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

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

Preamplification-Free Detection of RNA N6-Methyladenosine Modification at Single-Base Resolution Using the CRISPR Tandem Assay

N6-Methyladenosine (m6A) ranks among the most prevalent modifications in RNA, which serves as a biomarker for diseases, such as lung cancer. Herein, we developed a CRISPR/Cas13a-Csm6 tandem assay (termed CRISPRm6A assay) allowing for preamplification-free, sensitive, and rapid detection of RNA m6A modifications. The coupling of Cas13a-Csm6 tandem with MazF endoribonuclease enables the assay to identify m6A RNA with single-base resolution. Compared to the CRISPRm6A assay using Cas13a alone, the tandem CRISPRm6A assay yielded an improved sensitivity for RNA detection by ∼22 times, thus enabling preamplification-free detection of RNA m6A. Particularly, the proposed assay enabled quantification of m6A abundance down to 0.5% at the picomole level in lncRNA MALAT1 and demonstrated a 100% correlation in diagnosing nonsmall cell lung cancer. In summary, the CRISPRm6A assay supports two key applications in biological samples: (1) precise determination of m6A sites and (2) quantitative measurement of m6A fractions. Therefore, the CRISPR tandem method presents a promising tool for RNA epigenetics-based diagnostics.

METTL3-Mediated m6A mRNA Modification Facilitates Neointimal Hyperplasia in Arteriovenous Fistula

BACKGROUND

Arteriovenous fistula (AVF) is the preferred vascular access for hemodialysis in patients with end-stage renal disease, yet its long-term patency is threatened by neointimal hyperplasia (NIH). N6-methyladenosine, a prevalent RNA modification catalyzed by METTL3 (methyltransferase-like 3), plays a regulatory role in cardiovascular remodeling. Our previous studies found that N6-methyladenosine methyltransferase METTL3 mediated cardiomyocyte proliferation and heart repair after myocardial ischemia. However, its impact on AVF-related NIH remains unclear.

METHODS

We examined m6A levels and METTL3 expression in human and murine AVF tissues. Using smooth muscle cell-specific METTL3 conditional knockout and METTL3-overexpressing (adeno-associated virus-METTL3) mouse models, we evaluated NIH formation. In vitro, we analyzed vascular smooth muscle cell proliferation, migration, phenotypic switching, and ferroptosis. m6A epitranscriptomic microarray and RNA stability assays were used to explore downstream targets and mechanisms.

RESULTS

METTL3 was significantly upregulated in AVF tissues and vascular smooth muscle cells undergoing dedifferentiation. METTL3 deletion attenuated, while overexpression exacerbated, NIH in vivo. METTL3 enhanced vascular smooth muscle cell proliferation, migration, and phenotypic switching, while suppressing ferroptosis. Mechanistically, METTL3 increased m6A modification of SLC7A11 (solute carrier family 7 member 11) mRNA, stabilized its transcript, and promoted translation via recruitment of the m6A reader YTHDF1 (YTH N6-methyladenosine RNA-binding protein 1). Silencing SLC7A11 or YTHDF1 abrogated METTL3-induced phenotypic changes and ferroptosis resistance.

CONCLUSIONS

The METTL3-YTHDF1-SLC7A11 axis facilitates AVF NIH by regulating vascular smooth muscle cell dedifferentiation and ferroptosis. These findings uncover a novel epitranscriptional mechanism and suggest a potential therapeutic target for AVF stenosis.

WTAP-induced m6A Methylation of Atoh8 Promotes Cell Proliferation and Fibrosis in Diabetic Nephropathy

Diabetic nephropathy (DN) is a common diabetic complication, which increases morbidity of end-stage renal failure. N6-methyladenosine (m6A) modification has been reported in association with multiple physiological processes, however, its role in diabetic nephropathy is still poorly understood. Here, we found that the levels of m6A modification were up-regulated in both high-glucose-cultured mouse mesangial cells and the renal tissues from db/db mice. The key methyltransferase WT1 associated protein (WTAP) was primarily responsible for the elevated m6A modification. Moreover, WTAP knockdown significantly inhibited the proliferation and fibrosis of mouse mesangial cells (MMCs). Mechanistically, using the combination analysis of MeRIP-Seq and RNA-Seq, we revealed that Atoh8 was a downstream target of WTAP-induced m6A modification. We first revealed that Atoh8 was lowly expressed in renal tissues of DN model mice and HG-induced mesangial cells. WTAP reduced Atoh8 expression by inhibiting Atoh8 mRNA stability. Overexpression of Atoh8 restrained the proliferation and fibrosis of mesangial cells. This study provides novel insights into the role of m6A modification in DN and suggests that WTAP and Atoh8 could serve as potential therapeutic targets for this condition.

m6A modification is incorporated into bacterial mRNA without specific functional benefit

N 6-Methyladenosine (m6A), the most abundant modification in eukaryotic messenger RNAs (mRNAs), has also been found at a low level in bacterial mRNAs. However, enzyme(s) that introduce m6A modification on mRNAs in bacteria remain elusive. In this work, we combine deep-sequencing approaches that identify m6A sites with in vitro biochemical studies to identify putative m6A methyltransferases that would modify Escherichia coli mRNAs. We tested four uncharacterized candidates predicted to encode proteins with putative methyltransferase domains, whose deletion decreased the m6A level. However, in vitro analysis with the purified putative methyltransferases revealed that none of them installs m6A on mRNA. Exposure to heat and oxidative stress also changed the m6A level; however, we found no clear correlation between the m6A change and the specific stress. Considering two deep-sequencing approaches with different resolution, we found that m6A methylation on bacterial mRNAs is very low and appears randomly introduced. These results suggest that, in contrast to eukaryotes, the m6A modification in bacterial mRNA lacks a direct enzymatic recognition mechanism and has no clear biological function.

Recent Advance in Sensitive Detection of Demethylase FTO

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

METTL7B-induced histone lactylation prevents heart failure by ameliorating cardiac remodelling

INTRODUCTION

Lactylation is important for a variety of biological activities. It is reported that Class I histone deacetylases (HDAC1-3) are histone lysine delactylases. However, the role of lactylation in cardiac remodelling remains uncertain.

OBJECTIVES

To explore a novel regulator of lactylation and elucidate their functional mechanisms in cardiac remodelling and heart failure.

METHODS

GSE36961, GSE141910 and GSE174691 related to HCM (hypertrophic cardiomyopathy) were separately acquired from Gene expression Omnibus. Candidate genes related to both HCM and histone lactylation were determined by the intersection of DEGs (differentially expressed genes) and module genes sifted by WGCNA (Weighted Gene Co-Expression Network Analysis). METTL7B was screened out and its expression in hypertrophic myocardium was measured by qRT-PCR and western blotting. Furthermore, immunofluorescence, immunoprecipitation, and RNA pull-down assays were utilized to identify the biological functions of METTL7B. The myocardial biopsy of HCM and transverse aortic constriction (TAC) mouse model were performed to analyze the effects of METTL7B on cardiac remodelling in vivo.

RESULTS

We observed that the expression of METTL7B was down-regulated in hypertrophic myocardium, and the lactylation level was increased during the early stage and falling rapidly in the process of cardiac remodelling. Furthermore, we demonstrated that sodium lactate (NALA) administration fulfil a protective role on cardiac remodelling, and METTL7B alleviates cardiac remodelling and improves heart function by maintaining the activation of histone lactylation possibly at the later stage. Impressively, METTL7B suppressed the expression of USP38 via m6A dependent mRNA degradation, resulting in increasing ubiquitylation of HDAC3, which is a proven histone lysine delactylases.

CONCLUSION

We identifed METTL7B as a potential therapeutic target for myocardial remodelling and showed that it played a critical role in the promotion of myocardial lactylation, which is beneficial for improvement of cardiac function and attenuation of cardiac remodelling.

ZNF384 and m6A methylation promote the progression of hepatocellular carcinoma by regulating the interaction between LINC00342 and DAPK1

Hepatocellular carcinoma (HCC) is a malignant tumor with high morbidity and mortality. Many lncRNAs play important regulatory roles in the pathogenesis of HCC, but the mechanism of action of LINC00342 in the progression of HCC remains unclear. In this study, we assessed 24 pairs of HCC tissues and adjacent normal tissues as well as HCC cells and a nude mouse model of HCC. Gene and protein expression was evaluated by flow cytometry, CCK-8, RIP, colony formation assay, and TUNEL staining. This study revealed that LINC00342 was highly expressed in HCC tissues and cells. LINC00342 knockdown significantly inhibited the proliferation and migration of HCC cells, promoted apoptosis, inhibited tumor growth in vivo, and increased the sensitivity of HCC cells to cisplatin. The opposite effect was observed in LINC00342-overexpressing cells. Mechanistically, ZNF384 and m6A methylation can promote the transcription and stability of LINC00342, and LINC00342 can bind to DAPK1, which inhibits Cyt C release and the activation of caspase family proteins to accelerate HCC progression. Our study indicated that the inhibition of LINC00342 expression may represent a new breakthrough for HCC treatment.

Emerging roles of exosomal circRNAs in non-small cell lung cancer

Despite the prevalence of non-small cell lung cancer (NSCLC) is high, the limited early detection and management of these tumors are restricted since there is an absence of reliable and precise diagnostic biomarkers and therapeutic targets. Exosomes transport functional molecules for facilitating intercellular communication, especially in the tumor microenvironment, indicating their potential as cancer biomarkers and therapeutic targets. Circular RNA (circRNA), a type of non-coding RNA possessing a covalently closed loop structure, substantial abundance, and tissue-specific expression patterns, is stably enriched in exosomes. In recent years, significant breakthroughs have been made in research on exosomal circRNA in NSCLC. This review briefly introduces the biogenesis, characterizations, and functions of circRNAs and exosomes, and systematically describes the biological functions and mechanisms of exosomal circRNAs in NSCLC. In addition, this study summarizes their role in the progression of NSCLC and discusses their clinical significance as biomarkers and therapeutic targets for NSCLC.

YTHDC2 manipulates anti-tumoral macrophage polarization and predicts favorable outcomes in triple negative breast cancer

Triple-negative breast cancer (TNBC) possesses high malignant and metastatic rates among all subtypes. Chemotherapy is a standard of care for TNBC but only a small moiety of patients achieved complete relief (CR) after chemotherapy. The recent concept of tumor ecosystem has provided new insights into solutions from an approach of enhancing anti-tumoral immunity of macrophages. We hereby observed a positive correlation of YTHDC2 abundance with anti-tumoral gene markers of macrophages. YTHDC2-high macrophages also exerted interactions with other immune cells such as T helper cells, cytotoxic T cells, and NK cells. Further investigation on the transcriptional regulatory network identified six transcriptional factors upregulated by YTHDC2, and they together influenced the expressions of TWISTNB and the oncogene MYC. Additionally, our survival analysis prompted that YTHDC2 is prognostic of higher chemo-therapeutic efficacy and better survival outcomes. We demonstrated that ample macrophage YTHDC2 indicates anti-tumoral phenotype polarization and propitious survival outcome in post-treatment TNBC patients (Clinical trial registry name: Chinese Clinical Trial Registry, Registration No.: ChiCTR2400084513, Registration Date: 2024-05-20).

N6-methyladenosine-modified circ_0000517 promotes non-small cell lung cancer metastasis via miR-1233-3p/CDH6 axis

Circular RNAs (circRNAs) exhibit dysregulation in non-small cell lung cancer (NSCLC) and regulate the malignant biological behavior of NSCLC. The N6-methyladenosine (m6A) modification of circRNAs plays a critical role in multiple malignant tumors, and their biological relevance in NSCLC is unclear. Herein, this study was conducted to investigate the novel functional mechanism of highly expressed circ_0000517 in NSCLC by developing in vitro experiments. We found that circ_0000517 was upregulated in NSCLC tissues and cells, and that increased circ_0000517 expression was associated with m6A modification. Biologically, silenced circ_0000517 hindered the proliferation, colony formation, migration and invasion of NSCLC cells in vitro, and also suppressed the EMT-related process. Mechanistically, highly expressed circ_0000517 activated CDH6 expression and EMT evolution through sponging miR-1233-3p. Notably, miR-1233-3p had the opposite effect and reversed the promotion effect of circ_0000517 on the malignant biological behavior of NSCLC cells. Our study revealed a promising novel endogenous regulatory network that m6A-modified circ_0000517 accelerated malignant evolution of NSCLC by targeting the miR-1233-3p/CDH6 axis.

Long-read RNA sequencing reveals allele-specific N 6-methyladenosine modifications

Long-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA enables the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N 6-methyladenosine (m6A) modifications in native mRNA. We used human and mouse cells with known genetic variants to assign the allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses reveal the importance of sequences adjacent to the DRACH motif in determining m6A deposition, in addition to allelic differences that directly alter the motif. Moreover, we discover allele-specific m6A modification events with no genetic variants in close proximity to the differentially modified nucleotide, demonstrating the unique advantage of using long-reads and surpassing the capabilities of antibody-based short-read approaches. This technological advance will further our understanding of the role of genetics in determining mRNA modifications.

CircRNAs in Colorectal Cancer: Unveiling Their Roles and Exploring Therapeutic Potential

Colorectal cancer (CRC) is the most common malignancy of the digestive system. Although research into the causes of CRC's origin and progression has advanced over the past few decades, many details are still not fully understood. Circular RNAs (circRNAs), as a novel regulatory molecule, have been found to be closely involved in various key biological processes in CRC. CircRNAs also have been shown to encode proteins, which could offer new possibilities for therapeutic applications. This ability to produce tumor-specific proteins makes circRNA-based vaccines a potentially valuable approach for targeted cancer treatment. In this review, we summarize recent findings on the various roles of circRNAs in CRC and explore their potential in the development of protein-encoding circRNA vaccines for CRC therapy.

Gene-specific transcript buffering revealed by perturbation of coactivator complexes

Transcript buffering entails reciprocal modulation of mRNA synthesis and degradation to maintain stable RNA levels under varying cellular conditions. Current models depict a global connection between mRNA synthesis and degradation, but underlying mechanisms remain unclear. Here, we show that changes in RNA metabolism following depletion of TIP60/KAT5, the acetyltransferase subunit of the NuA4 transcriptional coactivator complex, reveal that transcript buffering occurs at a gene-specific level. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesized transcript fractions with biophysical modeling in mouse embryonic stem cells, we demonstrate that transcriptional changes caused by TIP60 depletion are offset by corresponding changes in RNA nuclear export and cytoplasmic stability, indicating gene-specific buffering. Disruption of the unrelated ATAC coactivator complex also causes gene-specific transcript buffering. We propose that cells dynamically adjust RNA splicing, export, and degradation in response to individual RNA synthesis alterations, thereby sustaining cellular homeostasis.

The Role of M6A Modification in Autoimmunity: Emerging Mechanisms and Therapeutic Implications

N6-methyladenosine (m6A), a prevalent and essential RNA modification, serves a key function in driving autoimmune disease pathogenesis. By modulating immune cell development, activation, migration, and polarization, as well as inflammatory pathways, m6A is crucial in forming innate defenses and adaptive immunity. This article provides a comprehensive overview of m6A modification features and reveals how its dysregulation affects the intensity and persistence of immune responses, disrupts immune tolerance, exacerbates tissue damage, and promotes the development of autoimmunity. Specific examples include its contributions to systemic autoimmune disorders like lupus and rheumatoid arthritis, as well as conditions that targeting specific organs like multiple sclerosis and type 1 diabetes. Furthermore, this review explores the therapeutic promise of target m6A-related enzymes ("writers," "erasers," and "readers") and summarizes recent advances in intervention strategies. By focusing on the mechanistic and therapeutic implications of m6A modification, this review sheds light on its role as a promising tool for both diagnosis and treatment in autoimmune disorders, laying the foundation for advancements in customized medicine.

Cellular dsRNA interactome captured by K1 antibody reveals the regulatory map of exogenous RNA sensing

RNA-binding proteins (RBPs) provide a critical post-transcriptional regulatory layer in determining RNA fate. Currently, UV crosslinking followed by oligo-dT pull-down is the gold standard in identifying the RBP repertoire of poly-adenylated RNAs, but such method is ineffective in capturing RBPs that recognize double-stranded RNAs (dsRNAs). Here, we utilize anti-dsRNA K1 antibody immunoprecipitation followed by quantitative mass spectrometry to comprehensively identify RBPs bound to cellular dsRNAs without external stimulus. Notably, our dsRNA interactome contains proteins involved in sensing N6-methyladenosine RNAs and stress granule components. We further perform targeted CRISPR-Cas9 knockout functional screening and discover proteins that can regulate the interferon (IFN) response during exogenous RNA sensing. Interestingly, most dsRBPs promote IFN-β secretion in response to dsRNA stimulation and act as antiviral factors during HCoV-OC43 infection. Our dsRNA interactome capture provides an unbiased and comprehensive characterization of putative dsRBPs and will facilitate our understanding of dsRNA sensing in physiological and pathological contexts.

METTL14-mediated depression of NEIL1 aggravates oxidative damage and mitochondrial dysfunction of lens epithelial cells through regulating KEAP1/NRF2 pathways

Abnormal base excision repair (BER) pathway and N6-methyladenosine (m6A) of RNA have been proved to be significantly related to age-related cataract (ARC) pathogenesis. However, the relationship between the Nei Endonuclease VIII-Like1 (NEIL1) gene (a representative DNA glycosylase of BER pathway) and its m6A modification remains unclear. Here, we showed that the expression of NEIL1 was decreased in the ARC anterior lens capsules and H2O2-stimulated SRA01/04 cells. Our findings demonstrated that ectopic expression of NEIL1 alleviated DNA oxidative damage, apoptosis and mitochondrial dysfunction through disturbing KEAP1/NRF2 interaction. Furthermore, silencing NEIL1 aggravated H2O2-induced lens opacity, whereas ML334 could mitigate lens cloudy ex vitro in rat lenses. Besides, intravitreal injection of AAV2-NEIL1 alleviated lens opacity in Emory mice in vivo. Mechanistically, the N(6)-Methyladenosine (m6A) methyltransferase-like 14 (METTL14) was identified as a factor in promoting m6A modification of NEIL1, which resulted in the recruitment of YTHDF2 to recognize and impair NEIL1 RNA stability. Collectively, these findings highlight the critical role of the m6A modification in NEIL1 on regulating oxidative stress and mitochondrial homeostasis through KEAP1/NRF2 pathways, providing a new way to explore the pathogenesis of ARC.

Cuproptosis gene characterizes the immune microenvironment of diabetic nephropathy

BACKGROUND

The cuproptosis is an intracellular copper (Cu) accumulation triggering the aggregation of mitochondrial lipoylated proteins and destabilization of iron‑sulfur (FeS) cluster proteins, leading to cell death. This copper-triggered modality of mitochondrial cell death has been associated with cuproptosis-related signature key genes (CRGs). Our study focused on the relationship between the cuproptosis CRGs and diabetic nephropathy (DN) to understand how such immune microenvironment may influence DN.

METHODS

We downloaded and compared RNA sequencing data sets of DN glomerular tissue samples vs. normal renal tissue samples (GSE142025, GSE30528, and GSE96804) from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between DN and control samples were screened. Immune cell subtypes infiltration and immune score were figured out via different algorithms. Consensus clustering was performed by the Ward's method to determine different phenotypes of DN. CRG key genes between two phenotypes were identified via machine learning algorithm. Logistic regression analysis was applied to establish a nomogram for assessing the risk of DN.

RESULTS

In DN samples, two genes NLRP3 and CDKN2A were positively correlated to the immune score. In contrast, six genes NFE2L2, LIAS, LIPT1, DLD, DBT and DLST were negatively correlated to the immune score. Via Consensus clustering based on cuproptosis CRG key genes, the DN samples were divided into cluster C1 and cluster C2. The cluster C1 was characterized by low cuproptosis CRG genes expression, high immune cell subtypes infiltration, and high enrichment of immune-related pathways. Cluster C2 was on the contrary, the Dicarbonyl/l-xylulose reductase (DCXR) and heat-responsive protein 12 (HRSP12) genes were related to clinical traits and the immune microenvironment, negatively correlated with most immune cell subtypes. The nomogram was constructed based on DCXR and HRSP12 showing good efficiency for the DN diagnosis.

CONCLUSION

We conclude that the immune microenvironment imbalance and metabolic disorders lead to the occurrence of DN. The signature cuproptosis genes, regulating the immune microenvironment and metabolism, represented the DN disease clustering to describe the heterogeneity and characterize immune microenvironment. Both HRSP12 and DCXR key genes are related to DN disease phenotypes and immune microenvironment characteristic and may help in DN diagnosis.

Targeting the ALKBH5-NLRP3 positive feedback loop alleviates cardiomyocyte pyroptosis after myocardial infarction

Several studies have associated the epitranscriptomic RNA modification of N6-methyladenosine (m6A) with cardiovascular diseases; however, how m6A modification affects cardiomyocyte pyroptosis after myocardial infarction (MI) remains unknown. Here, we showed that AlkB homolog 5 (ALKBH5), an m6A demethylase, is crucial in cardiomyocyte pyroptosis after MI. We used MI rat and mouse models, a cell hypoxia model of rat primary cardiomyocytes (RCMs), and rat embryonic ventricle cell line (H9c2) to explore the functional role of m6A modification and ALKBH5 in the heart and cardiomyocytes. Using plasmids and small interfering RNAs, the expressions of ALKBH5 and NOD-like receptor family pyrin domain-containing 3 (NLRP3) were determined to study their functions in regulating cardiomyocyte m6A and pyroptosis, respectively. We characterized the role of ALKBH5, which exhibited elevated expression in the ischemic heart tissue of rats and mice and hypoxic cardiomyocytes (RCMs and H9c2 cells). ALKBH5 knockdown alleviated hypoxia-induced H9c2 cell pyroptosis by inhibiting NLRP3 inflammasome activation, whereas ALKBH5 overexpression had the opposite effect. NLRP3 knockdown alleviated hypoxia-induced H9c2 cardiomyocyte pyroptosis by inhibiting ALKBH5 expression, whereas NLRP3 overexpression had the opposite effect. Mechanistically, ALKBH5 mediated m6A modification of NLRP3 mRNA in an IGF2BP2-dependent manner, and NLRP3, as a nuclear transcription factor, regulated the ALKBH5 transcription process. Targeting the ALKBH5-NLRP3 loop with the small-molecule inhibitors alleviated cardiomyocyte pyroptosis. Our results highlight that ALKBH5-NLRP3 forms a positive feedback loop that promotes cardiomyocyte pyroptosis after MI. Therefore, inhibiting the ALKBH5-NLRP3 loop is a potential strategy for treating cardiovascular diseases.

METTL14-mediated m6A modification of LINC00340 exerts oncogenic role in retinoblastoma by regulating Notch signaling pathway

PURPOSE

Retinoblastoma (RB) is a common primary intraocular cancer developed in early childhood. The N6-methyladenosine (m6A) modification of long non-coding RNAs (lncRNAs) have been reported to participate in tumorigenesis. However, the study on the m6A modification of lncRNA in RB is still limited. This study proposed to reveal the role of lncRNA LINC00340 in RB depending on m6A modification.

METHODS

The levels of LINC00340 and methyltransferase-like 14 (METTL14) were detected using qRT-PCR. The effects of LINC00340 interacting with METTL14 on RB cells were assessed by CCK8, colony formation, and flow cytometry assays. The changes of proteins associated with Notch signaling pathway were detected using western blotting. The regulatory mechanism of LINC00340 interacting with METTL14 in RB cells was confirmed by MeRIP, qRT-PCR, and actinomycin D treatment assays.

RESULTS

The expression of LINC00340 and METTL14 in RB samples were elevated, as well as their levels in RB samples showed the positive correlation. Silencing LINC00340 in RB cells could impair RB cell growth and enhance apoptosis via activating Notch signaling pathway, but overexpressing LINC00340 in RB cells showed the opposite effects. In addition, upregulating METTL14 effectively relieved the repressive effects of silencing LINC00340 on RB cells due to METTL14-mediated m6A modification of LINC00340.

CONCLUSIONS

The findings of study reveal that METTL14-mediated m6A modification of LINC00340 exerts oncogenic function in RB via Notch signaling pathway, which may uncover a novel molecular mechanism driving RB progression and identify a potential therapeutic target for RB.

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.

The mRNA Stability of PIEZO1, Regulated by Methyltransferase-Like 3 via N6-Methylation of Adenosine Modification in a YT521-B Homology Domain Family 2-Dependent Manner, Facilitates the Progression of Diabetic Retinopathy

Diabetic retinopathy (DR) is the major ocular complication of diabetes caused by chronic hyperglycemia, which leads to incurable blindness. Currently, the effectiveness of therapeutic interventions is limited. This study aimed to investigate the function of piezo-type mechanosensitive ion channel component 1 (PIEZO1) and its potential regulatory mechanism in DR progression. PIEZO1 expression was up-regulated in the retinal tissues of streptozotocin-induced diabetic mice and high-glucose (HG)-triggered Müller cells. Functionally, the knockdown of PIEZO1 improved the abnormal retinal function of diabetic mice and impeded inflammatory cytokine secretion and gliosis of Müller cells under HG conditions. Mechanistic investigations using RNA immunoprecipitation-real-time quantitative PCR, methylation RNA immunoprecipitation-real-time quantitative PCR, and luciferase reporter assays demonstrated that PIEZO1 was a downstream target of methyltransferase-like 3 (METTL3). METTL3-mediated N6-methyladenosine (m6A) modification within the coding sequence of PIEZO1 mRNA significantly shortened its half-life. In HG-stimulated cells, there was a negative regulatory relationship between PIEZO1 and YTH (YT521-B homology) domain family 2 (YTHDF2), a recognized m6A reader. The loss of YTHDF2 resulted in an extended half-life of PIEZO1 in cells with overexpression of METTL3, indicating that the effect of METTL3 on the mRNA stability of PIEZO1 was dependent on YTHDF2. Taken together, this study demonstrated the protective role of the PIEZO1 silencing in DR development, and that the degradation of PIEZO1 mRNA is accelerated by METTL3/YTHDF2-mediated m6A modification.

mRNA stability fine-tunes gene expression in the developing cortex to control neurogenesis

RNA abundance is controlled by rates of synthesis and degradation. Although mis-regulation of RNA turnover is linked to neurodevelopmental disorders, how it contributes to cortical development is largely unknown. Here, we discover the landscape of RNA stability regulation in the cerebral cortex and demonstrate that intact RNA decay machinery is essential for corticogenesis in vivo. We use SLAM-seq to measure RNA half-lives transcriptome-wide across multiple stages of cortical development. Leveraging these data, we discover cis-acting features associated with RNA stability and probe the relationship between RNA half-life and developmental expression changes. Notably, RNAs that are up-regulated across development tend to be more stable, while down-regulated RNAs are less stable. Using compound mouse genetics, we discover CNOT3, a core component of the CCR4-NOT deadenylase complex linked to neurodevelopmental disease, is essential for cortical development. Conditional knockout of Cnot3 in neural progenitors and their progeny in the developing mouse cortex leads to severe microcephaly due to altered cell fate and p53-dependent apoptosis. Finally, we define the molecular targets of CNOT3, revealing it controls expression of poorly expressed, non-optimal mRNAs in the cortex, including cell cycle-related transcripts. Collectively, our findings demonstrate that fine-tuned control of RNA turnover is crucial for brain development.

Insights into the role of N6-methyladenosine (m6A) in plant-virus interactions

N6-methyladenosine (m6A) is a common and dynamic epitranscriptomic modification in eukaryotic RNAs, affecting stability, splicing, translation, and degradation. Recent technological advancements have revealed the complex nature of m6A modifications, highlighting their importance in plant and animal species. The m6A modification is a reversible process, with "writers" depositing methylation, "erasers" demethylating it, and "reader" proteins recognizing m6A and executing various biological functions. Studying the relationship between m6A methylation and viral infection is crucial. Animal viruses, including retroviruses, RNA viruses, and DNA viruses, often employ the host's m6A machinery to replicate or avoid immune responses. In plant viruses, host methyltransferases or demethylases can stabilize or degrade viral RNA, depending on the virus-host interaction. Additionally, viral infections can modify the host's m6A machinery, impacting the viral life cycle. This review examines the role of m6A modifications in plant viral pathogenesis, focussing on RNA viruses infecting crops like alfalfa, turnip, wheat, rice, and potato. Understanding the role of m6A in virus-host interactions can aid in studying plant viral disease development and discovering novel antiviral targets for crop protection. In this review, we summarize current information on m6A in RNA biology, focussing on its function in viral infections and plant-virus interactions.

YTHDF2 promotes ATP synthesis and immune evasion in B cell malignancies

Long-term durable remission in patients with B cell malignancies following chimeric antigen receptor (CAR)-T cell immunotherapy remains unsatisfactory, often due to antigen escape. Malignant B cell transformation and oncogenic growth relies on efficient ATP synthesis, although the underlying mechanisms remain unclear. Here, we report that YTHDF2 facilitates energy supply and antigen escape in B cell malignancies, and its overexpression alone is sufficient to cause B cell transformation and tumorigenesis. Mechanistically, YTHDF2 functions as a dual reader where it stabilizes mRNAs as a 5-methylcytosine (m5C) reader via recruiting PABPC1, thereby enhancing their expression and ATP synthesis. Concomitantly, YTHDF2 also promotes immune evasion by destabilizing other mRNAs as an N6-methyladenosine (m6A) reader. Small-molecule-mediated targeting of YTHDF2 suppresses aggressive B cell malignancies and sensitizes them to CAR-T cell therapy.

YTHDF2 contributes to psoriasis by promoting proliferation and inflammatory response through regulation of the Wnt signaling pathway

YT521-B homology domain family 2 (YTHDF2), a pivotal m6A-binding protein, is now understood to significantly influence a diverse array of biological functions, including cell migration, proliferation, differentiation, and inflammatory responses. Additionally, YTHDF2 participates in mRNA decay and pre-rRNA processing. This study explored the specific role of YTHDF2 in the pathogenesis of psoriasis and its underlying mechanisms. Our preliminary findings revealed upregulation of YTHDF2 expression in psoriasis. Subsequent silencing of YTHDF2 in a psoriatic cell model resulted in a marked decrease in mRNA expression of IL-17A, S100A8, and S100A9, accompanied by a reduction in cell proliferation. Conversely, overexpression of YTHDF2 led to the opposite effects. Treatment with DC-Y27-13, a YTHDF2 inhibitor, demonstrated a therapeutic effect in psoriasis mice. Next, mRNA sequencing analysis identified significant enrichment of differentially expressed genes within the Wnt signaling pathway. Further investigation revealed that deletion of YTHDF2 increased the half-life and expression of Dickkopf homolog 3 (DKK3), a potent inhibitor of the Wnt signaling pathway. Consequently, the inhibition of Wnt signaling attenuated the inflammatory response and inhibited cell proliferation.

Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogen Plasmodium falciparum

Plasmodium falciparum is an obligate human parasite of the phylum Apicomplexa and is the causative agent of the most lethal form of human malaria. Although N6-methyladenosine modification is thought to be one of the major post-transcriptional regulatory mechanisms for stage-specific gene expression in apicomplexan parasites, the precise base position of m6A in mRNAs or noncoding RNAs in these parasites remains unknown. Here, we report global nucleotide-resolution mapping of m6A residues in P. falciparum using DART-seq technology, which quantitatively displayed a stage-specific, dynamic distribution pattern with enrichment near mRNA 3' ends. In this process we identified 894, 788, and 1,762 m6A-modified genes in Ring, Trophozoite and Schizont stages respectively, with an average of 5-7 m6A sites per-transcript at the individual gene level. Notably, several genes involved in malaria pathophysiology, such as KAHRP, ETRAMPs, SERA and stress response genes, such as members of Heat Shock Protein (HSP) family are highly enriched in m6A and therefore could be regulated by this RNA modification. Since we observed preferential methylation at the 3' ends of P. falciparum transcripts and because malaria polyadenylation specificity factor PfCPSF30 harbors an m6A reader 'YTH' domain, we reasoned that m6A might play an important role in 3'-end processing of malaria mRNAs. To investigate this, we used two complementary high-throughput RNA 3'-end mapping approaches, which provided an initial framework to explore potential roles of m6A in the regulation of alternative polyadenylation (APA) during malaria development in human hosts.

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

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

Supplementary Information

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

Influence of RNA Methylation on Cancerous Cells: A Prospective Approach for Alteration of In Vivo Cellular Composition

RNA methylation is a dynamic and ubiquitous post-transcriptional modification that plays a pivotal role in regulating gene expression in various conditions like cancer, neurological disorders, cardiovascular diseases, viral infections, metabolic disorders, and autoimmune diseases. RNA methylation manifests across diverse RNA species including messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA), exerting pivotal roles in gene expression regulation and various biological phenomena. Aberrant activity of writer, eraser, and reader proteins enables dysregulated methylation landscape across diverse malignancy transcriptomes, frequently promoting cancer pathogenesis. Numerous oncogenic drivers, tumour suppressors, invasion/metastasis factors, and signalling cascade components undergo methylation changes that modulate respective mRNA stability, translation, splicing, transport, and protein-RNA interactions accordingly. Functional studies confirm methylation-dependent alterations drive proliferation, survival, motility, angiogenesis, stemness, metabolism, and therapeutic evasion programs systemically. Methyltransferase overexpression typifies certain breast, liver, gastric, and other carcinomas correlating with adverse clinical outcomes like diminished overall survival. Mapping efforts uncover nodal transcripts for targeted drug development against hyperactivated regulators including METTL3. Some erasers and readers also suitable lead candidates based on apparent synthetic lethality. Proteomic screens additionally highlight relevant methylation-sensitive effector pathways amenable to combinatorial blockade, reversing compensatory signalling mechanisms that facilitate solid tumour progression. Quantifying global methylation burdens and responsible enzymes clinically predicts patient prognosis, risk stratification for adjuvant therapy, and overall therapeutic responsiveness.

Rapid and direct detection of m6A methylation by DNAzyme-based and smartphone-assisted electrochemical biosensor

m6A methylation detection is crucial for understanding RNA functions, revealing disease mechanisms, guiding drug development and advancing epigenetics research. Nevertheless, high-throughput sequencing and liquid chromatography-based traditional methods still face challenges to rapid and direct detection of m6A methylation. Here we report a DNAzyme-based and smartphone-assisted electrochemical biosensor for rapid detection of m6A. We initially identified m6A methylation-sensitive DNAzyme mutants through site mutation screening. These mutants were then combined with tetrahedral DNA to modify the electrodes, creating a 3D sensing interface. The detection of m6A was accomplished by using DNAzyme to capture and cleave the m6A sequence. The electrochemical biosensor detected the m6A sequence at nanomolar concentrations with a low detection limit of 0.69 nM and a wide detection range from 10 to 104 nM within 60 min. As a proof of concept, the 3'-UTR sequence of rice was selected as the m6A analyte. Combined with a smartphone, our biosensor shows good specificity, sensitivity, and easy-to-perform features, which indicates great prospects in the field of RNA modification detection and epigenetic analysis.

METTL3-Dependent YTHDF2 Mediates TSC1 Expression to Regulate Alveolar Epithelial Mesenchymal Transition and Promote Idiopathic Pulmonary Fibrosis

Diffuse, progressive interstitial lung disease with few treatment options and low survival rates is known as idiopathic pulmonary fibrosis (IPF). Alveolar epithelial cell damage and dysfunction are the main features of IPF. TSC1 has been documented to exert a pivotal function in governing cellular growth, proliferation, and ontogenesis. This work investigated TSC1's function and mechanism in IPF. Mice were given BLM to cause pulmonary fibrosis, and A549 cells underwent epithelial mesenchymal transition (EMT) in response to TGF-β1. According to the data, TSC1 expression was reduced in IPF. Overexpression of TSC1 was established by adenopathy-associated virus in vivo and adenovirus in vitro to significantly block the EMT process. Besides, the findings from the RNA-sequencing analysis indicate that overexpression of TSC1 mitigated the EMT process by suppressing the activation of the AKT/mTOR pathway via downregulation of ACTN4 expression. To examine the upstream regulatory mechanism, we employed the SRAMP database to predict m6A modification of TSC1 mRNA, followed by verification of m6A modification levels and expression using MERIP-qPCR, Dot blot, RT-qPCR, and WB. The results indicated a high degree of m6A modification in TSC1 mRNA in pulmonary fibrosis. The expression of METTL3 was further found to be significantly elevated. METTL3 knockdown impeded EMT progression. METTL3 inhibits TSC1 expression by increasing TSC1 m6A modification through the reading protein YTHDF2. In conclusion, our study elucidated that the METTL3/YTHDF2/TSC1 signaling axis activates the AKT/mTOR pathway to promote the development of IPF. This study provides potential molecular-level therapeutic targets for IPF disease.

The role of N6-methyladenosine modification in tumor angiogenesis

Tumor angiogenesis is a characteristics of malignant cancer progression that facilitates cancer cell growth, diffusion and metastasis, and has an indispensable role in cancer development. N6-methyladenosine (m6A) is among the most prevalent internal modifications in eukaryotic RNAs, and has considerable influence on RNA metabolism, including its transcription, splicing, localization, translation, recognition, and degradation. The m6A modification is generated by m6A methyltransferases ("writers"), removed by m6A demethylases ("erasers"), and recognized by m6A-binding proteins ("readers"). There is accumulating evidence that abnormal m6A modification is involved in the pathogenesis of multiple diseases, including cancers, and promotes cancer occurrence, development, and progression through its considerable impact on oncoprotein expression. Furthermore, increasing studies have demonstrated that m6A modification can influence angiogenesis in cancers through multiple pathways to regulate malignant processes. In this review, we elaborate the role of m6A modification in tumor angiogenesis-related molecules and pathways in detail, providing insights into the interactions between m6A and tumor angiogenesis. Moreover, we describe how targeting m6A modification in combination with anti-angiogenesis drugs is expected to be a promising anti-tumor treatment strategy, with potential value for addressing the challenge of drug resistance.

AKT kinases as therapeutic targets

AKT, or protein kinase B, is a central node of the PI3K signaling pathway that is pivotal for a range of normal cellular physiologies that also underlie several pathological conditions, including inflammatory and autoimmune diseases, overgrowth syndromes, and neoplastic transformation. These pathologies, notably cancer, arise if either the activity of AKT or its positive or negative upstream or downstream regulators or effectors goes unchecked, superimposed on by its intersection with a slew of other pathways. Targeting the PI3K/AKT pathway is, therefore, a prudent countermeasure. AKT inhibitors have been tested in many clinical trials, primarily in combination with other drugs. While some have recently garnered attention for their favorable profile, concern over resistance and off-target effects have continued to hinder their widespread adoption in the clinic, mandating a discussion on alternative modes of targeting. In this review, we discuss isoform-centric targeting that may be more effective and less toxic than traditional pan-AKT inhibitors and its significance for disease prevention and treatment, including immunotherapy. We also touch on the emerging mutant- or allele-selective covalent allosteric AKT inhibitors (CAAIs), as well as indirect, novel AKT-targeting approaches, and end with a briefing on the ongoing quest for more reliable biomarkers predicting sensitivity and response to AKT inhibitors, and their current state of affairs.

Emerging prospects of mRNA cancer vaccines: mechanisms, formulations, and challenges in cancer immunotherapy

Cancer continues to pose an alarming threat to global health, necessitating the need for the development of efficient therapeutic solutions despite massive advances in the treatment. mRNA cancer vaccines have emerged as a hopeful avenue, propelled by the victory of mRNA technology in COVID-19 vaccines. The article delves into the intricate mechanisms and formulations of cancer vaccines, highlighting the ongoing efforts to strengthen mRNA stability and ensure successful translation inside target cells. Moreover, it discusses the design and mechanism of action of mRNA, showcasing its potential as a useful benchmark for developing efficacious cancer vaccines. The significance of mRNA therapy and selecting appropriate tumor antigens for the personalized development of mRNA vaccines are emphasized, providing insights into the immune mechanism. Additionally, the review explores the integration of mRNA vaccines with other immunotherapies and the utilization of progressive delivery platforms, such as lipid nanoparticles, to improve immune responses and address challenges related to immune evasion and tumor heterogeneity. While underscoring the advantages of mRNA vaccines, the review also addresses the challenges associated with the susceptibility of RNA to degradation and the difficulty in identifying optimum tumor-specific antigens, along with the potential solutions. Furthermore, it provides a comprehensive overview of the ongoing research efforts aimed at addressing these hurdles and enhancing the effectiveness of mRNA-based cancer vaccines. Overall, this review is a focused and inclusive impression of the present state of mRNA cancer vaccines, outlining their possibilities, challenges, and future predictions in the fight against cancer, ultimately aiding in the development of more targeted therapies against cancer.

Peptide Degrader-Based Targeting of METTL3/14 Improves Immunotherapy Response in Cutaneous Melanoma

METTL3 has emerged as a promising therapeutic target in cancer treatment, although its oncogenic functions in melanoma development and potential for therapeutic targeting drug have not been fully explored. In this study, we define the oncogenic role of METTL3 in melanoma development and progression. Building on this insight, we examine our recently designed peptide inhibitor RM3, which targets the binding interface of METTL3/14 complex for disruption and subsequent ubiquitin-mediated proteasomal degradation via the E3 ligase STUB1. RM3 treatment reduces proliferation, migration, and invasion, and induces apoptosis in melanoma cells in vitro and in vivo. Subsequent transcriptomic analysis identified changes in immuno-related genes following RM3-mediated suppression of METTL3/14 N6-methyladenosine (m6A) methyltransferase activity, suggesting a potential for interaction with immunotherapy. A combination treatment of RM3 with anti-PD-1 antibody results in significantly higher beneficial tumor response in vivo, with a good safety profile. Collectively, these findings not only delineate the oncogenic role of METTL3 in melanoma but also showcase RM3, acting as a peptide degrader, as a novel and promising strategy for melanoma treatment.

N6-Methyladenosine Modification of PERP by RBM15 Enhances the Tumorigenesis of Lung Adenocarcinoma via p53 Signaling Pathway

The promotive effect of P53 apoptosis effector related to PMP-22 (PERP) on lung adenocarcinoma (LUAD) has been confirmed. However, the N6-methyladenosine (m6A) modification of PERP to regulate LUAD progression have not been revealed. Bioinformatic analysis predicted the mechanism of PERP interacting with RBM15 and p53 pathway using GEPIA and The Cancer Genome Atlas (TCGA) databases. The qRT-PCR, cell function experiments, and western blotting were applied to further confirm the function and mechanism of PERP and RBM15 in LUAD cells. Methylated RNA immunoprecipitation (MeRIP) and mRNA stability assays were used to reveal the interaction between PERP and RBM15 in LUAD cells. PERP with high expression in LUAD showed the poor survival. Silencing PERP prevented LUAD cells to proliferate, migrate, and invade via activating p53 pathway, whereas overexpressing PERP showed the opposite effect on LUAD cells. Mechanistically, RBM15 overexpression could promote PERP m6A modification to enhance the PERP mRNA stability. In addition, RBM15 overexpression leading to LUAD cell malignancy was reversed by PERP knockdown. This study reveals that the m6A modification of PERP regulated by RBM15 enhances the tumorigenesis of LUAD by inhibiting the p53 signaling pathway, which may provide novel insights into the LUAD mechanism.

The interplay between epitranscriptomic RNA modifications and neurodegenerative disorders: Mechanistic insights and potential therapeutic strategies

Neurodegenerative disorders encompass a group of age-related conditions characterized by the gradual decline in both the structure and functionality of the central nervous system (CNS). RNA modifications, arising from the epitranscriptome or RNA-modifying protein mutations, have recently been observed to contribute significantly to neurodegenerative disorders. Specific modifications like N6-methyladenine (m6A), N1-methyladenine (m1A), 5-methylcytosine (m5C), pseudouridine and adenosine-to-inosine (A-to-I) play key roles, with their regulators serving as crucial therapeutic targets. These epitranscriptomic changes intricately control gene expression, influencing cellular functions and contributing to disease pathology. Dysregulation of RNA metabolism, affecting mRNA processing and noncoding RNA biogenesis, is a central factor in these diseases. This review underscores the complex relationship between RNA modifications and neurodegenerative disorders, emphasizing the influence of RNA modification and the epitranscriptome, exploring the function of RNA modification enzymes in neurodegenerative processes, investigating the functional consequences of RNA modifications within neurodegenerative pathways, and evaluating the potential therapeutic advancements derived from assessing the epitranscriptome.

Multiple roles of p53 in cancer development: Regulation of tumor microenvironment, m6A modification and diverse cell death mechanisms

BACKGROUND

The protein p53, encoded by the most frequently mutated gene TP53 in human cancers, has diverse functions in tumor suppression. As a best known transcription factor, p53 can regulate various fundamental cellular responses, ranging from the cell-cycle arrest, DNA repair, senescence to the programmed cell death (PCD), which includes autophagy, apoptosis, ferroptosis, cuproptosis, pyroptosis and disulfidoptosis. Accumulating evidence has indicated that the tumor microenvironment (TME), N6-methyladenosine (m6A) modification and diverse PCD are important for the progression, proliferation and metastases of cancers.

AIM OF REVIEW

This paper aims to systematically and comprehensively summarize the multiple roles of p53 in the development of cancers from the regulation of TME, m6A Modification and diverse PCD.

KEY SCIENTIFIC CONCEPTS OF REVIEW

TME, a crucial local homeostasis environment, influences every step of tumorigenesis and metastasis. m6A, the most prevalent and abundant endogenous modification in eukaryotic RNAs, plays an essential role in various biological processes, containing the progression of cancers. Additionally, PCD is an evolutionarily conserved mechanism of cell suicide and a common process in living organisms. Some forms of PCD contribute to the occurrence and development of cancer. However, the complex roles of p53 within the TME, m6A modification and diverse PCD mechanisms are still not completely understood. Presently, the function roles of p53 including the wild-type and mutant p53 in different context are summarized. Additionally, the interaction between the cancer immunity, cancer cell death and RNA m6A methylation and the p53 regulation during the development and progress of cancers were discussed. Moreover, the key molecular mechanisms by which p53 participates in the regulation of TME, m6A and diverse PCD are also explored. All the findings will facilitate the development of novel therapeutic approaches.

METTL3-STAT5B interaction facilitates the co-transcriptional m6A modification of mRNA to promote breast tumorigenesis

Enhanced expression of methyltransferase-like 3 (METTL3) promotes the m6A modification of specific mRNAs, contributing to breast tumorigenesis. While the mRNA substrates targeted by METTL3 are well characterized, the factors dictating the selection of these specific mRNA remain elusive. This study aimed to examine the regulatory role of the transcription factor STAT5B in METTL3-induced m6A modification. METTL3 specifically interacts with STAT5B in response to mitogenic stimulation by epidermal growth factor (EGF). Chromatin immunoprecipitation and CRISPR/Cas9 mutagenesis showed that STAT5B recruits METTL3 to gene promoters like CCND1, where METTL3 interacts with RPB1, dependent on CDK9-mediated RPB1 (Ser2) phosphorylation during transcription elongation. Inhibition and depletion of either STAT5B or CDK9 prevented the EGF-induced m6A modification of CCND1. The translation efficiency of CCND1 was increased following m6A modification, thereby increasing cell proliferation. STAT5B facilitated METTL3-induced tumor formation by increasing CCND1 expression in an orthotopic mouse model. In clinical context, a positive correlation was observed between p-STAT5B and METTL3 expression in high-grade breast tumors. This study elucidates a novel mechanism that underlies the specificity of m6A modification in breast cancer cells, thereby underscoring its potential therapeutic value.

Regulation of m6A (N6-Methyladenosine) methylation modifiers in solid cancers

Solid cancers constitute a tremendous burden on global healthcare, requiring a deeper understanding of the molecular mechanisms underlying cancer development and progression. Epigenetic changes, notably N6-methyladenosine (m6A) RNA methylation, have emerged as important contributors to the biology of solid tumors in recent years. This epigenetic mark dynamically affects gene expression at the post-transcriptional level and modulates a variety of cellular processes, making it a focus of research in the context of solid tumors. m6A modification patterns are dysregulated in a variety of solid cancers, including ovarian, breast, lung, colorectal, pancreatic, and others. This dysregulated m6A landscape has been shown to induce significant changes in the expression of oncogenes, tumor suppressors, and genes involved in cancer stem cells, metastasis, and treatment resistance. In solid tumors, the interaction of m6A "writers" (e.g., METTL3, METTL14, and others), "erasers" (e.g., ALKBH5, FTO), and "readers" (e.g., members of YTHDF proteins and others) delicately changes the m6A methylome. Targeting m6A regulators as a potential therapeutic method to control gene expression and prevent tumor development seems a novel strategy. To enhance treatment results, advances in this area of research have led to the development of targeted treatments aiming at restoring or altering m6A alteration patterns in solid tumors.

Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level

It is widely accepted that N6-methyladenosine (m6A) exhibits significant intercellular specificity, which poses challenges for its detection using existing m6A quantitative methods. In this study, we introduced Single-cell m6A Analysis (Scm6A), a machine learning-based approach for single-cell m6A quantification. Scm6A leverages input features derived from the expression levels of m6A trans regulators and cis sequence features, and offers remarkable prediction efficiency and reliability. To further validate the robustness and precision of Scm6A, we first applied Scm6A to single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) and calculated the m6A levels in CD4+ and CD8+ T cells. We also applied a winscore-based m6A calculation method to conduct N6-methyladenosine sequencing (m6A-seq) analysis on CD4+ and CD8+ T cells isolated through magnetic-activated cell sorting (MACS) from the same samples. Notably, the m6A levels calculated by Scm6A exhibited a significant positive correlation with those quantified through m6A-seq in different cells isolated by MACS, providing compelling evidence for Scm6A's reliability. Additionally, we performed single-cell-level m6A analysis on lung cancer tissues as well as blood samples from patients with coronavirus disease 2019 (COVID-19), and demonstrated the landscape and regulatory mechanisms of m6A in different T cell subtypes from these diseases. In summary, Scm6A is a novel, dependable, and accurate method for single-cell m6A detection and has broad applications in the realm of m6A-related research.

Modulation of host N6-methyladenosine modification by gut microbiota in colorectal cancer

As a research hotspot in the field of molecular biology, N6-methyladenosine (m6A) modification has made progress in the treatment of colorectal cancer (CRC), leukemia and other cancers. Numerous studies have demonstrated that the tumour microenvironment (TME) regulates the level of m6A modification in the host and activates a series of complex epigenetic signalling pathways through interactions with CRC cells, thus affecting the progression and prognosis of CRC. However, with the diversity in the composition of TME factors, this action is reciprocal and complex. Encouragingly, some studies have experimentally revealed that the intestinal flora can alter CRC cell proliferation by directly acting on m6A and thereby altering CRC cell proliferation. This review summarizes the data, supporting the idea that the intestinal flora can influence host m6A levels through pathways such as methyl donor metabolism and thus affect the progression of CRC. We also review the role of m6A modification in the diagnosis, treatment, and prognostic assessment of CRC and discuss the current status, limitations, and potential clinical value of m6A modification in this field. We propose that additional in-depth research on m6A alterations in CRC patients and their TME-related targeted therapeutic issues will lead to better therapeutic outcomes for CRC patients.

Regulatory roles of N6-methyladenosine (m6A) methylation in RNA processing and non-communicable diseases

Post-transcriptional RNA modification is an emerging epigenetic control mechanism in cells that is important in many different cellular and organismal processes. N6-methyladenosine (m6A) is one of the most prevalent, prolific, and ubiquitous internal transcriptional alterations in eukaryotic mRNAs, making it an important topic in the field of Epigenetics. m6A methylation acts as a dynamical regulatory process that regulates the activity of genes and participates in multiple physiological processes, by supporting multiple aspects of essential mRNA metabolic processes, including pre-mRNA splicing, nuclear export, translation, miRNA synthesis, and stability. Extensive research has linked aberrations in m6A modification and m6A-associated proteins to a wide range of human diseases. However, the impact of m6A on mRNA metabolism and its pathological connection between m6A and other non-communicable diseases, including cardiovascular disease, neurodegenerative disorders, liver diseases, and cancer remains in fragmentation. Here, we review the existing understanding of the overall role of mechanisms by which m6A exerts its activities and address new discoveries that highlight m6A's diverse involvement in gene expression regulation. We discuss m6A deposition on mRNA and its consequences on degradation, translation, and transcription, as well as m6A methylation of non-coding chromosomal-associated RNA species. This study could give new information about the molecular process, early detection, tailored treatment, and predictive evaluation of human non-communicable diseases like cancer. We also explore more about new data that suggests targeting m6A regulators in diseases may have therapeutic advantages.

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.

Comparative Hox genes expression within the dimorphic annelid Streblospio benedicti reveals patterning variation during development

Hox genes are transcriptional regulators that elicit cell positional identity along the anterior-posterior region of the body plan across different lineages of Metazoan. Comparison of Hox gene expression across distinct species reveals their evolutionary conservation; however, their gains and losses in different lineages can correlate with body plan modifications and morphological novelty. We compare the expression of 11 Hox genes found within Streblospio benedicti, a marine annelid that produces two types of offspring with distinct developmental and morphological features. For these two distinct larval types, we compare Hox gene expression through ontogeny using hybridization chain reaction (HCR) probes for in situ hybridization and RNA-seq data. We find that Hox gene expression patterning for both types is typically similar at equivalent developmental stages. However, some Hox genes have spatial or temporal differences between the larval types that are associated with morphological and life-history differences. This is the first comparison of developmental divergence in Hox gene expression within a single species and these changes reveal how body plan differences may arise in larval evolution.

Chemical and topological design of multicapped mRNA and capped circular RNA to augment translation

Protein and vaccine therapies based on mRNA would benefit from an increase in translation capacity. Here, we report a method to augment translation named ligation-enabled mRNA-oligonucleotide assembly (LEGO). We systematically screen different chemotopological motifs and find that a branched mRNA cap effectively initiates translation on linear or circular mRNAs without internal ribosome entry sites. Two types of chemical modification, locked nucleic acid (LNA) N7-methylguanosine modifications on the cap and LNA + 5 × 2' O-methyl on the 5' untranslated region, enhance RNA-eukaryotic translation initiation factor (eIF4E-eIF4G) binding and RNA stability against decapping in vitro. Through multidimensional chemotopological engineering of dual-capped mRNA and capped circular RNA, we enhanced mRNA protein production by up to tenfold in vivo, resulting in 17-fold and 3.7-fold higher antibody production after prime and boost doses in a severe acute respiratory syndrome coronavirus 2 vaccine setting, respectively. The LEGO platform opens possibilities to design unnatural RNA structures and topologies beyond canonical linear and circular RNAs for both basic research and therapeutic applications.

Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications

Long-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA promises the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNA. We utilized human and mouse cells with known genetic variants to assign allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses revealed the importance of sequences adjacent to the DRACH-motif in determining m6A deposition, in addition to allelic differences that directly alter the motif. Moreover, we discovered allele-specific m6A modification (ASM) events with no genetic variants in close proximity to the differentially modified nucleotide, demonstrating the unique advantage of using long reads and surpassing the capabilities of antibody-based short-read approaches. This technological advancement promises to advance our understanding of the role of genetics in determining mRNA modifications.

The roles and mechanisms of coding and noncoding RNA variations in cancer

Functional variations in coding and noncoding RNAs are crucial in tumorigenesis, with cancer-specific alterations often resulting from chemical modifications and posttranscriptional processes mediated by enzymes. These RNA variations have been linked to tumor cell proliferation, growth, metastasis, and drug resistance and are valuable for identifying diagnostic or prognostic cancer biomarkers. The diversity of posttranscriptional RNA modifications, such as splicing, polyadenylation, methylation, and editing, is particularly significant due to their prevalence and impact on cancer progression. Additionally, other modifications, including RNA acetylation, circularization, miRNA isomerization, and pseudouridination, are recognized as key contributors to cancer development. Understanding the mechanisms underlying these RNA modifications in cancer can enhance our knowledge of cancer biology and facilitate the development of innovative therapeutic strategies. Targeting these RNA modifications and their regulatory enzymes may pave the way for novel RNA-based therapies, enabling tailored interventions for specific cancer subtypes. This review provides a comprehensive overview of the roles and mechanisms of various coding and noncoding RNA modifications in cancer progression and highlights recent advancements in RNA-based therapeutic applications.