The role of RNA m5C modification in cancer metastasis

Upregulation of TTYH3 by lncRNA LUCAT1 through interacting with ALYREF facilitates the metastasis in non-small cell lung cancer

Metastasis is the predominant culprit of cancer-associated mortality in non-small cell lung cancer (NSCLC). Tweety homolog 3 (TTYH3) reportedly functions vitally in the development of diverse cancers, including NSCLC; nevertheless, its role in NSCLC metastasis remains ambiguous. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blot were initially employed to detect TTYH3 expression in NSCLC and normal lung epithelial cells. Subsequently, A549 and NCI-H1650 cells were chosen as NSCLC models in vitro and transfected with short hairpin RNAs (sh-TTYH3, sh-LUCAT1, and sh-ALYREF) or overexpression plasmids (oe-ALYREF and oe-TTYH3). Transwell assays were used for migrative and invasive tests. Epithelial mesenchymal transformation (EMT)-related proteins (E-cadherin, N-cadherin, Vimentin, and Snail) were measured by western blot. A mouse lung metastasis model was built to define the function of TTYH3 in NSCLC metastasis, followed by hematoxylin-eosin staining. RNA pull-down, RNA immunoprecipitation, qRT-PCR, western blot, and actinomycin D assays were adopted to determine the relationships among LUCAT1, ALYREF, and TTYH3. TTYH3 was highly expressed in NSCLC cells relative to normal lung cells. Functionally, TTYH3 knockdown restrained NSCLC migration, invasion, EMT, and metastasis. Mechanistic experiments demonstrated that LUCAT1 bound to ALYREF. After LUCAT1 knockdown, TTYH3 expression and mRNA stability were reduced, which was reversed by ALYREF overexpression. Furthermore, ALYREF overexpression counteracted the inhibitory effects of LUCAT1 knockdown on NSCLC cell migration, invasion, and EMT. TTYH3 overexpression eliminated the suppressive functions of ALYREF downregulation in NSCLC progression. LUCAT1 promotes TTYH3 expression via interacting with ALYREF, thereby facilitating NSCLC migration, invasion, and EMT.

Role of m5C methylation in digestive system tumors (Review)

Currently, the incidence of digestive system tumors has been increasing annually, thus becoming a prevalent cause of cancer‑related mortalities. Although significant strides have been made in targeting the molecular mechanisms that underpin the development of these tumors, their treatment and prognosis still pose substantial challenges. This is primarily due to the ambiguity of early diagnostic indicators and the fact that most digestive system tumors are detected at an advanced stage. However, epigenetic modifications are capable of altering the expression of oncogenes and regulating biological processes in cancer. In recent years, the study of methylation in relation to tumor pathogenesis has become a focus of prominent research. Among the various types of methylation, 5‑methylcytosine (m5C) methylation plays a crucial role in the development of digestive system tumors and is anticipated to serve as a novel therapeutic target. However, to date, a comprehensive and systematic review concerning the role of m5C methylation in digestive system tumors is lacking. Consequently, the present study reviewed the role of m5C methylation in digestive system tumors such as esophageal cancer, gastric cancer and hepatocellular carcinoma, with the aim of providing a valuable reference for future research endeavors.

Lysine methyltransferase SETD7 in cancer: functions, molecular mechanisms and therapeutic implications

Since its discovery as a histone methyltransferase, SETD7 has been implicated in many signaling pathways and carcinogenesis. SETD7 catalyzes the methylation of histone H3 and non-histone proteins, regulating their translation, stability and activity. SETD7 is frequently abnormally expressed and has a significant influence on cell proliferation, invasion, autophagy and immune response. As cancer is a complex disease, an outstanding concept in cancer biology is the "hallmarks of cancer". In this review, we focus on the involvement of SETD7 in the hallmarks of cancer, describing its functions and underlying mechanisms in detail. Additionally, we discuss non-coding RNAs and chemical inhibitors targeting SETD7, highlighting the potential and importance of SETD7 in cancer therapy.

LINC02167 stabilizes KSR1 mRNA in an m5C-dependent manner to regulate the ERK/MAPK signaling pathway and promotes colorectal cancer metastasis

BACKGROUND

Metastasis is a leading cause of colorectal cancer (CRC)-related mortality, yet its molecular mechanisms remain poorly understood. Long noncoding RNAs (lncRNAs) have emerged as critical regulators of CRC metastasis, but their specific roles are not fully elucidated. This study identifies and characterizes a novel lncRNA LINC02167 as a critical regulator of CRC metastasis.

METHODS

LINC02167 expression was analyzed in CRC tissues via real-time quantitative polymerase chain reaction and fluorescence in situ hybridization. Functional assays evaluated its role in CRC cell migration, invasion, and metastasis in vitro and in vivo. Mechanistic exploration involves a combination of techniques, including RNA sequencing, mass spectrometry, RNA pull-down, RNA immunoprecipitation, chromatin immunoprecipitation, luciferase reporter assays, RNA stability assays, and bioinformatics analysis, to uncover the molecular interactions and pathways regulated by LINC02167.

RESULTS

LINC02167 is markedly upregulated in CRC tissues and strongly correlates with advanced clinical features and poor prognosis. Functional analyses reveal that LINC02167 enhances CRC cell migration and invasion in vitro and promotes metastasis in vivo. Mechanistically, LINC02167 serves as a molecular scaffold, forming a complex with YBX1 and ILF3 to facilitate YBX1 binding to NSUN2-mediated m5C modification sites on KSR1 mRNA, thereby stabilizing KSR1 mRNA and activating the ERK/MAPK signaling pathway to drive CRC metastasis. Additionally, MYC-driven transcriptional activation leads to the upregulation of LINC02167 in CRC.

CONCLUSIONS

This study uncovers a novel mechanism through which LINC02167 promotes the ERK/MAPK pathway and CRC metastasis via m5C modification, underscoring its potential as a promising therapeutic target for metastatic CRC treatment.

Epitranscriptomics in atherosclerosis: Unraveling RNA modifications, editing and splicing and their implications in vascular disease

Atherosclerosis remains a leading cause of morbidity and mortality worldwide, driven by complex molecular mechanisms involving gene regulation and post-transcriptional processes. Emerging evidence highlights the critical role of epitranscriptomics, the study of chemical modifications occurring on RNA molecules, in atherosclerosis development. Epitranscriptomics provides a new layer of regulation in vascular health, influencing cellular functions in endothelial cells, smooth muscle cells, and macrophages, thereby shedding light on the pathogenesis of atherosclerosis and presenting new opportunities for novel therapeutic targets. This review provides a comprehensive overview of the epitranscriptomic landscape, focusing on key RNA modifications such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), pseudouridine (Ψ), RNA editing mechanisms including A-to-I and C-to-U editing and RNA isoforms. The functional implications of these modifications in RNA stability, alternative splicing, and microRNA biology are discussed, with a focus on their roles in inflammatory signaling, lipid metabolism, and vascular cell adaptation within atherosclerotic plaques. We also highlight how these modifications influence the generation of RNA isoforms, potentially altering cellular phenotypes and contributing to disease progression. Despite the promise of epitranscriptomics, significant challenges remain, including the technical limitations in detecting RNA modifications in complex tissues and the need for deeper mechanistic insights into their causal roles in atherosclerotic pathogenesis. Integrating epitranscriptomics with other omics approaches, such as genomics, proteomics, and metabolomics, holds the potential to provide a more holistic understanding of the disease.

Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing

5-Methylcytosine (m5C) is one of the posttranscriptional modifications in mRNA and is involved in the pathogenesis of various diseases. However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m5C mapping still needs improvement. Here, we develop a detection method named DRAM (deaminase and reader protein assisted RNA methylation analysis), in which deaminases (APOBEC1 and TadA-8e) are fused with m5C reader proteins (ALYREF and YBX1) to identify the m5C sites through deamination events neighboring the methylation sites. This antibody-free and bisulfite-free approach provides transcriptome-wide editing regions which are highly overlapped with the publicly available bisulfite-sequencing (BS-seq) datasets and allows for a more stable and comprehensive identification of the m5C loci. In addition, DRAM system even supports ultralow input RNA (10 ng). We anticipate that the DRAM system could pave the way for uncovering further biological functions of m5C modifications.

Exploring the impact of cuproptosis on prostate cancer prognosis via RNA methylation regulation based on single cell and bulk RNA sequencing data

Background

Cuproptosis, along with RNA methylation regulators, has recently come to the fore as innovative mechanisms governing cell death, exerting profound impact on the onset and progression of multiple cancers. Nonetheless, the prognostic implications and underlying regulatory mechanisms of them associated with prostate cancer (PCa) remain to be thoroughly investigated.

Methods

Genomic and clinical data for PCa from The Cancer Genome Atlas datasets were analyzed to identify a prognostic model through univariate and Least Absolute Shrinkage and Selection Operator Cox regression analyses that were validated utilizing external datasets. We used receiver operating characteristic curves and C-index to evaluate the accuracy of our prognostic model. In conjunction with this, we conducted single-cell RNA sequencing (scRNA-seq) analyses to investigate underlying mechanisms and evaluate the degree of immune infiltration, as well as to assess patients' responses to diverse chemotherapy agents. Especially, qPCR assay was utilized to unveil the expression of signature genes in PCa.

Results

We meticulously selected six Cuproptosis-Associated RNA Methylation Regulators (CARMRs) to establish a risk prognosis model, which was further verified to obtain enhanced predictive capacity in external validation cohorts. Insights from immune infiltration and scRNA-seq analyses have elucidated the immune characteristics of PCa, and highlighted the immunosuppressive role of regulatory T cells on immune response. Additionally, drug susceptibility analysis demonstrated that patients with PCa in the low-risk category derived better benefit from bicalutamide treatment, whereas those in the high-risk group exhibited a favor response to adriamycin and docetaxel treatments. The qPCR and immunohistochemistry (IHC) staining assays also reveal the a dramatically altered expression pattern of TRDMT1 and ALYREF in PCa tissues.

Conclusion

In general, we established a model involving CARMRs that can better predict the risk of recurrence of PCa and have identified the possible mechanisms affecting PCa progression, thereby promoting further research in this field.

Comprehensive analysis of RNA methylation-related genes to identify molecular cluster for predicting prognosis and immune profiles in bladder cancer

m6A, m5C and m7G are common types of RNA methylation modifications that are widely involved in key mechanisms regulating malignancy. However, the role of RNA methylation-related genes in the immune microenvironment of bladder cancer (BLCA) remains elusive. In this study, we established RNA methylation molecular subtypes by analyzing the TCGA and GEO datasets. Risk model and nomogram were constructed by LASSO and multivariate Cox regression analysis and validated by external datasets. Genetic variations, functional enrichment analysis and immune cell infiltration were analyzed. The expression levels of hub genes were detected by real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC). The effect of FN1 on cellular function was determined using experimental assays. Finally, we identified a 7-gene signature associated with BLCA prognosis. GSE19423 validated the predictive value of the risk model. The IMvigor210 data showed the model had promising predictive efficacy for BLCA immunotherapy. Significant differences in biological function, immune cell infiltration and drug sensitivity were observed between high- and low-risk groups. Furthermore, FN1 was upregulated in BLCA, as determined by qRT-PCR and IHC. Depletion of FN1 using siRNA impaired cell motility in T24 and 5637 cells. In conclusion, RNA methylation-related risk model can predict the prognosis, immune landscape and response to immunotherapy in BLCA. Among the 7-gene signature, FN1 is a pivotal gene that promotes the migration of bladder cancer cells.

Detection, molecular function and mechanisms of m5C in cancer

Interest in RNA posttranscriptional modifications, particularly 5-methylcytosine (m5C), has surged in recent years. Studies have shown that m5C plays a key role in cellular processes and is closely linked to tumourigenesis. This growing focus emphasises the importance of understanding the diverse impacts of m5C modifications in both normal cellular functions and cancer development. Moreover, strides in methodologies for discerning m5C have facilitated intricate transcriptome cartography of RNA methylation at the solitary nucleotide echelon. This technical progress has fueled a surge in m5C-centric investigations, facilitating further exploration of this RNA modification. This review provides a comprehensive analysis of the oncogenic potential of m5C RNA modification, elucidating the precise molecular mechanisms driving its role in cancer development. It consolidates current knowledge regarding the biological consequences of m5C RNA modification in tumour cells. Understanding the role of methylation-related processes in tumourigenesis shows promise for advancing cancer diagnosis and therapeutic strategies. HIGHLIGHTS: m5C modifications are dynamically regulated by writers, readers, and erasers, influencing cancer progression, metastasis, and immune evasion. Distinct m5C regulatory networks exist across cancers, modulating oncogenic pathways and therapy responses. m5C signatures serve as biomarkers for cancer prognosis and treatment stratification, highlighting their role in precision oncology.

ALKBH1 knockdown promotes the growth, migration and invasion of HTR-8/SVneo cells through regulating the m5C modification PSMD14

Preeclampsia (PE) is a pregnancy disease characterized by insufficient invasion and growth of trophoblast cells. adeno-associated virus encoding alkB homolog 1 (ALKBH1) is a demethylase in 5-methylcytosine (m5C) methylation modification. This study was performed to explore the role of ALKBH1 in hypoxia treated human extravasated trophoblast cells. Hypoxia treated human extravasated trophoblast cells (HTR-8/SVneo) was used to simulate the occurrence of PE in vitro. The cells phenotype was detected by CCK-8 and Transwell assays. The m5c levels and m5C levels of PSMD14 were analyzed by m5C dot blot and M5C Me-RIP assays. Then, the interaction between ALKBH1 and PSMD14 were confirmed by RIP and dual-luciferase reporter assays. ALKBH1 was up-regulated in hypoxia treated HTR-8/SVneo cells. Additionally, ALKBH1 knockdown increased the m5C contents, cell viability, migration and invasion abilities of hypoxia treated HTR-8/SVneo cells. Furthermore, ALKBH1 knockdown increased the m5C and mRNA levels, and mRNA stability of PSMD14. RIP and dual-luciferase reporter assays demonstrated that ALKBH1 interacted with PSMD14. Besides, PSMD14 knockdown reversed the effects of ALKBH1 silencing on cell viability, migration and invasion abilities of hypoxia treated HTR-8/SVneo cells. ALKBH1 mediated m5C levels were decreased in the hypoxia treated HTR-8/SVneo cells, which further decreased the cell viability, migration and invasion abilities through targeting the PSMD14 levels.

MLLT3 Regulates Melanoma Stemness and Progression by Inhibiting HMGB1 Nuclear Entry and MAGEA1 M5C Modification

Melanoma stem cells are a kind of cells with self-renewal and multi-directional differentiation potential. They are one of the key factors in the occurrence, development and metastasis of melanoma. This study demonstrates that MLLT3 is a transcription factor that regulates the stemness and progression of melanoma. MLLT3 interacted with HMGB1 to inhibit its entry into the nucleus, MLLT3 interacted with YBX1 to inhibit its reading of m5C of MAGEA1, thereby inhibiting the mRNA stability of MAGEA1, and directly transcribed P53 to inhibit the stemness, proliferation and metastasis of melanoma cells. This study further explored the potential mechanism of the interaction between miR-542-3p/miR-3922-3p and MLLT3. Furthermore, the scRNA-seq of melanoma cells with MLLT3 knock-out resulted in important changes in cell subsets, activating the TP53 and MAPK pathways and transforming into stem cells. The results indicate that the transcription factor MLLT3 is a suppressor gene that regulates the stemness and progression of melanoma, and is expected to become a target for melanoma therapy.

Construction and validation of a prognostic model of lncRNAs associated with RNA methylation in lung adenocarcinoma

Background

Lung adenocarcinoma (LUAD) is a common type of lung cancer and one of the leading causes of cancer death worldwide. Long non-coding RNAs (lncRNAs) play a crucial role in tumors. The purpose of this study was to explore the expression of lncRNAs associated with RNA methylation modification and their prognostic value in LUAD.

Methods

The RNA sequencing and clinical data were downloaded from The Cancer Genome Atlas dataset, and the messenger RNA and lncRNAs were annotated by Ensemble. The lncRNAs related to RNA methylation regulators (RMlncRNAs) were filtered by Pearson correlation analysis between differentially expressed lncRNAs and RNA methylation regulators. Univariate Cox regression analysis, multivariate Cox regression analysis, and least absolute shrinkage and selection operator regression analysis were used to construct a prognostic model. The receiver operating characteristic curve (ROC) was plotted to validate the predictive value of the prognostic model. Then, tumor mutational burden (TMB) and microsatellite instability were used to compare the immunotherapy response. Finally, to perform a drug sensitivity analysis, the half-maximal inhibitory concentration (IC50) of targeted drugs was calculated using pRRophetic package.

Results

In total, 18 RMlncRNAs associated with the prognosis of LUAD patients were identified. Then, six feature lncRNAs (NFYC-AS1, OGFRP1, MIR4435-2HG, TDRKH-AS1, DANCR, and TMPO-AS1) were used to construct a prognostic model. The ROC curves for training, testing, and validation sets showed that the prognosis model was effective. The subindex based on the prognostic model had a high correlation with TMB. The high-risk group might be subject to greater immune resistance according to the comparison of Tumor Immune Dysfunction and Exclusion scores. Finally, the IC50 of 11 drugs had differences between high- and low-risk group, and only three of the drug's target genes (ERBB4, CASP8, and CD86) were differentially expressed.

Conclusions

In conclusion, a prognostic model based on six feature lncRNAs (NFYC-AS1, OGFRP1, MIR4435-2HG, TDRKH-AS1, DANCR, and TMPO-AS1) was constructed by bioinformatics analysis, which might provide a new insight into the evaluation and treatment of LUAD.

WTAP, a conserved m6A writer, can promote the antiviral immunity of Miichthysmiiuy

N6-methyladenosine (m6A) is one of the most prevalent modifications found in eukaryotic mRNA and has been implicated in the regulation of cell proliferation, development, invasion, apoptosis, and immunity. In this study, we first conducted a structural and evolutionary analysis of Wilms' tumour 1-associating protein (WTAP) in vertebrates, and the results showed that WTAP in vertebrates is conserved particularly in mammals and fish. We subsequently investigated the involvement of WTAP in the antiviral immune response of fish and discovered that the expression of Miichthys miiuy (mmiWTAP) decreased in response to stimulation with Siniperca chuatsi rhabdovirus (SCRV) and poly(I:C). Immunofluorescence assays revealed that mmiWTAP was distributed in both the nucleus and the cytoplasm. Furthermore, overexpression of mmiWTAP enhanced the mRNA expression of MAVS and antiviral genes, thereby inhibiting SCRV replication. The beneficial effects of WTAP on MAVS and antiviral factors were disrupted upon introduction of cycloleucine, a methylation inhibitor, suggesting that the positive regulatory role of mmiWTAP in the antiviral immune response is reliant on its methyltransferase activity. These findings provide new insights into the involvement of m6A regulatory networks in fish antiviral immunity.

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.

Unveiling the role of RNA methylation in glioma: Mechanisms, prognostic biomarkers, and therapeutic targets

Gliomas, the most prevalent malignant brain tumors in the central nervous system, are marked by rapid growth, high recurrence rates, and poor prognosis. Glioblastoma (GBM) stands out as the most aggressive subtype, characterized by significant heterogeneity. The etiology of gliomas remains elusive. RNA modifications, particularly reversible methylation, play a crucial role in regulating transcription and translation throughout the RNA lifecycle. Increasing evidence highlights the prevalence of RNA methylation in primary central nervous system malignancies, underscoring its pivotal role in glioma pathogenesis. This review focuses on recent findings regarding changes in RNA methylation expression and their effects on glioma development and progression, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G). Given the extensive roles of RNA methylation in gliomas, the potential of RNA methylation-related regulators as prognostic markers and therapeutic targets was also explored, aiming to enhance clinical management and improve patient outcomes.

HCP5 Derived Novel Microprotein Triggers Progression of Gastric Cancer through Regulating Ferroptosis

The context of long noncoding RNAs (lncRNAs) contains many unannotated open reading frames (ORFs). These ORFs potentially encode novel proteins or peptides with crucial roles in various human cancers, yet the translational potential of these lncRNAs and the functions of the protein products remain largely unexplored, especially in gastric cancer (GC). In this study, a comprehensive analysis is performed and identified a GC associated lncRNA known as HCP5, which contains a non-canonical ORF. Further analysis showed that HCP5-132aa, a microprotein encoded by HCP5 harboring this ORF, is highly expressed in GC cells and tissues, and can promote the proliferation of GC cells by inhibiting ferroptosis. Mechanistically, HCP5-132aa enhances the interaction between YBX1 and ELAVL1, facilitates recognition of YBX1 at the m5C site in the 3'UTR of SLC7A11 and G6PD mRNA, and preserves their stability via ELAVL1. By employing a Cas9/sgRNA delivery system with AAV in vivo, effectively knocked out the HCP5-132aa and inhibition of tumor growth in a patient-derived xenograft model are achieved. These findings demonstrate that the novel protein HCP5-132aa, derived from lncRNA HCP5, mediates the repression of ferroptosis, thereby driving the progression of GC and identifying a new potential therapeutic target for its treatment.

The Quiet Giant: Identification, Effectors, Molecular Mechanism, Physiological and Pathological Function in mRNA 5-methylcytosine Modification

5-Methylcytosine (m5C) is a prevalent nucleotide alteration observed in transfer RNA (tRNA) and ribosomal RNA (rRNA), and it is also widely distributed in the transcriptome, serving as one of the internal modifications of messenger RNA (mRNA) in higher eukaryotes. Increasing evidence has substantiated the presence of m5C in mRNA. As research on m5C progresses, there is an initial comprehension of its molecular mechanisms and biological significance in mRNA. This work aims to provide a comprehensive summary of the most recent advancements in the identification and screening, distribution, molecular functions, and biological effects of m5C in mRNA. We outline the current status of research and provide prospects for potential future applications.

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.

Development of a novel disulfidptosis-correlated m6A/m1A/m5C/m7G gene signature to predict prognosis and therapeutic response for lung adenocarcinoma patients by integrated machine-learning

BACKGROUND

Lung adenocarcinoma (LUAD) represents a significant global health burden, necessitating advanced prognostic tools for improved patient management. RNA modifications (m6A, m1A, m5C, m7G), and disulfidptosis, a novel cell death mechanism, have emerged as promising biomarkers and therapeutic targets in cancer.

METHODS

We systematically compiled disulfidptosis-correlated genes and RNA modification-related genes from existing literature. A novel disulfidptosis-correlated m6A/m1A/m5C/m7G riskscore was computed using integrated machine-learning algorithms. Transcriptomic data from TCGA and GEO databases were downloaded analyzed. Single-cell RNA-sequencing data from the TISCH database was processed using the Seurat package. Genes' protein-protein interaction network was constructed using the String database. Functional phenotype analysis was performed using GSVA, ClusterProfiler, and IOBR packages. Consensus clustering divided patients into two distinct groups. Drug sensitivity predictions were obtained from the GDSC1 database and predicted using the Oncopredict package.

RESULTS

The disulfidptosis-correlated m6A/m1A/m5C/m7G risk score effectively stratified LUAD patients into prognostically distinct groups, demonstrating superior predictive accuracy compared to conventional clinical parameters. Patients in different risk groups exhibited significant molecular and clinical differences. Subsequent analyses identified two molecular subtypes associated with RNA modification and disulfidptosis, revealing differences in immune infiltration and prognosis. Functional enrichment analyses highlighted pathways involving RNA modification and disulfidptosis, underscoring their roles in LUAD pathogenesis. Single-cell analysis revealed distinct features between high- and low-risk status cells.

CONCLUSION

This study introduces a novel disulfidptosis-correlated m6A/m1A/m5C/m7G risk score as a robust prognostic tool for LUAD, integrating insights from RNA modifications and cell death mechanisms. The risk score enhances prognostic stratification and identifies potential targets for personalized therapeutic strategies in LUAD. This comprehensive approach emphasizes the critical roles of RNA modifications and disulfidptosis in LUAD biology, paving the way for future research and clinical applications aimed at improving patient outcomes.

The noncanonical RNA-binding protein RAN stabilizes the mRNA of intranuclear stress granule assembly factor G3BP1 in nasopharyngeal carcinoma

RNA-binding proteins (RBPs) play critical roles in tumor progression by participating in the posttranscriptional regulation of RNA. However, the levels and function of RBPs in nasopharyngeal carcinoma (NPC) remain elusive. Here we identified a noncanonical RBP RAN that has the most significant role in NPC progression by a small siRNA pool screening. Functionally, RAN facilitates NPC proliferation and metastasis in vitro and in vivo. High levels of RAN are associated with poor prognosis of NPC patients and can be performed as a prognostic biomarker. Mechanistically, RAN increases the nucleus import of TDP43 and enhances TDP43 nuclear distribution. On the other hand, RAN is directly bound to the coding sequence of G3BP1 mRNA and serves as an adapter to facilitate TDP43 interacting with G3BP1 mRNA 3' UTR. These contribute to increasing G3BP1 mRNA stability in the nucleus and lead to upregulation of G3BP1, which further enhances AKT and ERK signaling and ultimately promotes NPC proliferation and metastasis. These findings reveal that RAN stabilizes intranuclear G3BP1 mRNA by dual mechanisms: recruiting TDP43 into the nucleus and enhancing its interaction with G3BP1 mRNA, suggesting a critical role of RAN in NPC progression and providing a new regulation framework of RBP-RNA.

The role of m5C RNA methylation regulators in the diagnosis and immune microenvironment of osteoarthritis

The 5-methylcytosine (m5C) is a common post-transcriptional RNA methylation modification and is involved in the pathological process of many diseases. However, little is known about the role of m5C in osteoarthritis (OA). OA gene data and the corresponding information were downloaded from the Gene Expression Omnibus database. Based on 36 m5C regulators, we constructed the landscape and diagnostic model for OA. Later, two m5C modification patterns were identified, and functional analyses were performed to evaluate whether these patterns were related to endoplasmic reticulum (ER) stress and mitochondrial autophagy. We further comprehensively analyzed the immune cell infiltration characteristics in different modification patterns in OA. We also established the post-transcriptional regulatory networks and drug-gene networks. Our findings suggested that m5C regulators were differentially expressed between OA and normal samples and could serve as novel biomarkers for the diagnosis of OA. Besides, m5C regulators may be involved in regulating ER stress, mitochondrial autophagy, and immune infiltration in OA. The m5C modification can influence the sensitivity to drugs and the potential post-transcriptional regulatory mechanisms might provide promising targets.

RNA modifications in long non-coding RNAs and their implications in cancer biology

Long non-coding RNAs (lncRNAs) represent the most diverse class of RNAs in cells and play crucial roles in maintaining cellular functions. RNA modifications, being a significant factor in regulating RNA biology, have been found to be extensively present in lncRNAs and exert regulatory effects on their behavior and biological functions. Most common types of RNA modifications in lncRNAs include N6-methyladenosine (m6A), 5-methylcytosine (m5C), and N1-methyladenosine (m1A). In this review, we summarize the major RNA modification types associated with lncRNAs, the regulatory roles of each modification, and the implications of modified lncRNAs in tumorigenesis and development. By examining these aspects, we aim to provide insights into the role of RNA modifications in lncRNAs and their potential impact on cancer biology.

NSUN2-mediated RNA methylation: Molecular mechanisms and clinical relevance in cancer

Cancer remains a leading cause of morbidity and mortality worldwide, necessitating the ongoing investigation of molecular targets for improved diagnosis, prognosis, and therapy. Among these targets, RNA modifications, particularly N5-methylcytosine (m5C) in RNA, have emerged as critical regulators of gene expression and cellular functions. NOP2/Sun RNA methyltransferase family member 2 (NSUN2) is a key enzyme in m5C modification, significantly influencing various biological processes and tumorigenesis. NSUN2 methylates multiple RNA species, including transfer RNAs (tRNAs), messenger RNAs (mRNAs), and non-coding RNAs, impacting RNA stability, translation efficiency, and cellular stress responses. These modifications, in turn, affect cell proliferation, differentiation, and survival. In cancer, NSUN2 is frequently upregulated, associated with aggressive tumor phenotypes, poor prognosis, and therapy resistance. Its role in oncogenic signaling pathways further underscores its importance in cancer biology. This review offers a comprehensive overview of NSUN2's role in cancer, focusing on its involvement in RNA methylation and its implications for tumor initiation and progression. Additionally, we explore the potential of NSUN2 as a biomarker for cancer diagnosis and prognosis, and its promise as a therapeutic target.

The role of epigenetic methylations in thyroid Cancer

Thyroid cancer (TC) represents one of the most prevalent endocrine malignancies, with a rising incidence worldwide. Epigenetic alterations, which modify gene expression without altering the underlying DNA sequence, have garnered significant attention in recent years. Increasing evidence underscores the pivotal role of epigenetic modifications, including DNA methylation, RNA methylation, and histone methylation, in the pathogenesis of TC. This review provides a comprehensive overview of these reversible and environmentally influenced epigenetic modifications, highlighting their molecular mechanisms and functional roles in TC. Additionally, the clinical implications, challenges associated with studying these epigenetic modifications, and potential future research directions are explored.

Decoding the epitranscriptome: a new frontier for cancer therapy and drug resistance

As the role of RNA modification in gene expression regulation and human diseases, the "epitranscriptome" has been shown to be an important player in regulating many physiological and pathological processes. Meanwhile, the phenomenon of cancer drug resistance is becoming more and more frequent, especially in the case of cancer chemotherapy resistance. In recent years, research on relationship between post-transcriptional modification and cancer including drug resistance has become a hot topic, especially the methylation of the sixth nitrogen site of RNA adenosine-m6A (N6-methyladenosine). m6A modification is the most common post-transcriptional modification of eukaryotic mRNA, accounting for 80% of RNA methylation modifications. At the same time, several other modifications of RNA, such as N1-methyladenosine (m1A), 5-methylcytosine (m5C), 3-methylcytosine (m3C), pseudouridine (Ψ) and N7-methylguanosine (m7G) have also been demonstrated to be involved in cancer and drug resistance. This review mainly discusses the research progress of RNA modifications in the field of cancer and drug resistance and targeting of m6A regulators by small molecule modulators, providing reference for future study and development of combination therapy to reverse cancer drug resistance.

The role of m5C RNA modification in cancer development and therapy

RNA modifications have been demonstrated to affect the function, stability, processing, and interactions of RNA, including pseudouridylation, acetylation and methylation. RNA methylation products, such as N6-methyladenosine (m6A), 5-methylcytidine (m5C), N7-methylguanosine (m7G), 2'-O-dimethyladenosine (m6Am), and N1-methyladenosine (m1A), have been reported to participate in tumorigenesis and tumor progression. The role of m6A in carcinogenesis has been well studied and summarized. In this review, we described the biological functions of m5C RNA modifications in tumorigenesis and tumor progression. Moreover, we highlighted the molecular mechanisms of m5C RNA modification in oncogenesis. Furthermore, we discussed whether targeting m5C regulator-associated genes could be a novel strategy for improving therapeutic outcomes in patients with cancer.

Epitranscriptomics and cervical cancer: the emerging role of m6A, m5C and m1A RNA modifications

Cervical cancer (CC), one of the most prevalent and detrimental gynaecologic cancers, evolves through genetic and epigenetic alterations resulting in the promotion of oncogenic activity and dysfunction of tumour-suppressing mechanisms. Despite medical advancement, the prognosis for advanced-stage patients remains extremely low due to high recurrence rates and resistance to existing treatments. Thereby, the search for potential prognostic biomarkers is heightened to unravel new modalities of CC pathogenesis and to develop novel anti-cancer therapies. Epitranscriptomic modifications, reversible epigenetic RNA modifications, regulate various biological processes by deciding RNA fate to mediating RNA interactions. This narrative review provides insight into the cellular and molecular roles of endogenous RNA-editing proteins and their associated epitranscriptomic modifications, especially N6-methyladenosine (m6A), 5-methylcytosine (m5C) and N1-methyladenosine (m1A), in governing the development, progression and metastasis of CC. We discussed the in-depth epitranscriptomic mechanisms underlying the regulation of over 50 RNAs responsible for tumorigenesis, proliferation, migration, invasion, survival, autophagy, stemness, epithelial-mesenchymal transition, metabolism (glucose, lipid, glutamate and glutamine), resistance (drug and radiation), angiogenesis and recurrence of CC. Additionally, we provided a concise overview of the therapeutic potential of targeting the altered expression of endogenous RNA-editing proteins and aberrant deposition of RNA modifications on both coding and non-coding RNAs in CC.

RNA methyltransferase NSUN2-mediated m5C methylation promotes Cr(VI)-induced malignant transformation and lung cancer by accelerating metabolism reprogramming

Hexavalent chromium [Cr(VI)], one common environmental contaminant, has long been recognized as a carcinogen associated with lung cancer, but roles and mechanisms of Cr(VI)-induced epigenetic dysregulations in carcinogenesis remain to be investigated. In this study, we identified that RNA m5C methyltransferase NSUN2 was significantly upregulated in Cr(VI)-transformed cells and lung tissues of Cr(VI)-exposed mice. Inhibition of NSUN2 reduced cell proliferation, migration, colony formation and tube formation abilities. We found NSUN2-mediated m5C modification induced metabolic reprogramming and cell cycle by promoting the mRNA stabilities of ME1, GLUT3 and CDK2. In addition, knockdown of NSUN2 attenuated tumorigenesis and angiogenesis in vivo. RNA m5C reader ALYREF was identified to be involved in NSUN2-mediated m5C modification in Cr (VI)-induced carcinogenesis. Further study showed that EP300 induced NSUN2 upregulation through transcriptional activation by inducing histone modification at H3K27ac site for regulating Cr(VI) carcinogenesis. Our findings demonstrated novel role and mechanism of NSUN2 and epigenetic changes by increasing the RNA m5C modification that are important for Cr (VI)-induced carcinogenesis through NSUN2/ALYREF pathway. NSUN2, ALYREF, ME1, GLUT3 or/and CDK2 may be used as potential new biomarkers or/and therapeutic target(s) in the future.

Prognostic signature and immune landscape of 5-methylcytosine-related long non-coding RNAs in gastric cancer

Background

Long non-coding RNAs (lncRNAs) have been demonstrated to be useful in assessing the prognosis of cancer patients. However, few studies have focused on 5-methylcytosine-related lncRNAs (m5C-lncRNAs) in gastric cancer (GC). In this study, we aimed to establish a m5C-lncRNAs prognostic signature (m5C-LPS) and explore its potential impact on guiding clinical practice for GC.

Methods

RNA-sequence and clinicopathological data were retrieved from The Cancer Genome Atlas (TCGA) database, while the coexpression of long non-coding RNAs (lncRNAs) was determined using Pearson's correlation analysis. A m5C-LPS model was constructed using univariate and Lasso Cox regression, and its prognostic value and accuracy were subsequently validated. Subsequently, the expression of 11 m5C-lncRNAs was verified via quantitative real-time PCR (qRT-PCR) in gastric cancer (GC) cell lines. The potential biological mechanism of this signature was elucidated using Gene Set Enrichment Analysis (GSEA). Based on the GSEA findings, CIBERSORT and ESTIMATE algorithms were utilized to conduct a comprehensive investigation of the tumor immune microenvironment (TIME) in GC. Additionally, pRRophetic and TIDE algorithms were employed to predict drug sensitivity and the efficacy of immunotherapy for GC patients.

Results

280 lncRNAs were identified as m5C-lncRNAs, including RHPN1-AS1, AC093752.3, TSC22D1-AS1, AL391152.1, MAGI2-AS3, AC048382.2, AL033527.3, AC007405.2, AC036103.1, CCDC183-AS1, and ADORA2A-AS1. Their prognostic value was validated, and the expression of these 11 lncRNAs was confirmed in four gastric cancer cell lines using quantitative reverse transcription PCR (qRT-PCR). A nomogram incorporating a risk score was developed to provide more precise clinical decision-making. Gene Set Enrichment Analysis (GSEA) showed that many classical signaling pathways related to tumor progression were enriched in this signature. Analyses related to immunity and drug sensitivity demonstrated distinct differences in features between high-risk and low-risk subgroups.

Conclusion

The m5C-LPS can predict the survival of gastric cancer (GC) patients, provide novel therapeutic targets, and thus offer more thoughtful perspectives for future clinical decisions regarding GC.

Comprehensive analysis of RNA-5-methylcytosine modification in breast cancer brain metastasis

Aim: To delineate the RNA-5-methylcytosine (m5C) modification of breast cancer brain metastasis (BCBM).Methods: Methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) was performed to obtain RNA-m5C patterns of BCBM.Results: 1048 hypermethylation and 1866 hypomethylation m5C peaks were identified in BCBM compared with those in breast cancer. The most significant m5C hypermethylated genes included ENG, SHANK1, IGFN1, EVL and MMP9, whereas the most significant m5C hypomethylated genes included AREG, SAA2, TP53I11, KRT7 and LCN2. MeRIP-qPCR data were concordant with the corresponding MeRIP-seq results in terms of the observed m5C levels. Conjoint analysis identified 190 hyper-up genes characterized by concurrent m5C hypermethylation and up-regulation, alongside 284 hypo-down genes exhibiting both m5C hypomethylation and down-regulation.Conclusion: This study presents the first comprehensive analysis of RNA-m5C modification in BCBM.

A prognostic signature based on genes associated with m6A/m5C/m1A/m7G modifications and its immunological characteristics in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is characterized by a high incidence and mortality rate. Despite advancements in therapeutic interventions, the prognosis for renal cancer patients remains suboptimal. Of late, methylation modifications have emerged as promising molecular targets for tumor assessment and treatment, yet their potential has not been fully investigated in the context of ccRCC. Transcriptomic and clinical data were extracted from The Cancer Genome Atlas, Gene Expression Omnibus, and ArrayExpress databases, leading to the identification of 57 methylation-related genes (MRGs). Utilizing DESeq2 analysis, Cox regression analysis, and the LASSO regression algorithm, a Methylation-Related Risk Score (MARS) was constructed. Cluster analysis, Gene Ontology (GO) analysis, clinical feature analysis, immune infiltration analysis, and mutation analysis were further employed to evaluate the model. Our investigation identified six pivotal prognostic MRGs and established a risk score predicated on m6A/m5C/m1A/m7G regulatory factors. This score was validated across two external cohorts and can be utilized to assess individual immune infiltration statuses and predict responses to immunotherapy. Moreover, cluster analysis delineated two distinct m6A/m5C/m1A/m7G gene clusters. We have developed and validated a robust prognostic signature based on genes associated with m6A, m5C, m1A, and m7G modifications. This gene signature demonstrates significant prognostic value in assessing survival outcomes, clinical characteristics, immune infiltration, and responses to immunotherapy in ccRCC patients. This finding provides valuable insights for refining precision treatment strategies.

NSUN4 mediated RNA 5-methylcytosine promotes the malignant progression of glioma through improving the CDC42 mRNA stabilization

5-Methylcytosine (m5C) methylation is a significant post-transcriptional modification that play a crucial role in the development and progression of numerous cancers. Whereas the functions and molecular mechanisms underlying m5C methylation in gliomas remain unclear. This study dedicated to explore changes of m5C levels and the clinical significance of the m5C writer NSUN4 in gliomas. We found that high m5C levels were negatively related to prognosis of patients with glioma. Moreover, gain- and loss-of-function experiments revealed the role of NSUN4 in enhancing m5C modification of mRNA to promote the malignant progression of glioma. Mechanistically speaking, NSUN4-mediated m5C alterations regulated ALYREF binding to CDC42 mRNA, thereby impacting the mRNA stability of CDC42. We also demonstrated that CDC42 promoted glioma proliferation, migration, and invasion by activating the PI3K-AKT pathway. Additionally, rescue experiments proved that CDC42 overexpression weaken the inhibitory effect of NSUN4 knockdown on the malignant progression of gliomas in vitro and in vivo. Our findings elucidated that NSUN4-mediated high m5C levels promote ALYREF binding to CDC42 mRNA and regulate its stability, thereby driving the malignant progression of glioma. This provides theoretical support for targeted the treatment of gliomas.

YBX1 promotes homologous recombination and resistance to platinum-induced stress in ovarian cancer by recognizing m5C modification

Platinum-based chemotherapy causes genetic damage and induces apoptosis in ovarian cancer cells. Enhancing the ability to resist platinum drug-induced DNA damage and apoptotic stress is critical for tumor cells to acquire drug resistance. Here, we found that Y-box binding protein 1 (YBX1) was highly expressed in cisplatin-resistant patient-derived organoids (PDOs) and was a crucial gene for alleviating platinum-induced stress and maintaining drug resistance characteristics in ovarian cancer cells. Mechanistically, YBX1 recognized m5C modifications in CHD3 mRNA and maintained mRNA stability by recruiting PABPC1 protein. This regulatory process enhanced chromatin accessibility and improved the efficiency of homologous recombination (HR) repair, facilitating tumor cells to withstand platinum-induced apoptotic stress. In addition, SU056, an inhibitor of YBX1, exhibited the potential to reverse platinum resistance in subcutaneous and PDO orthotopic xenograft models. In conclusion, YBX1 is critical for ovarian cancer cells to alleviate the platinum-induced stress and may be a potential target for reversing drug-resistant therapies.

Mechanism insights and therapeutic intervention of tumor metastasis: latest developments and perspectives

Metastasis remains a pivotal characteristic of cancer and is the primary contributor to cancer-associated mortality. Despite its significance, the mechanisms governing metastasis are not fully elucidated. Contemporary findings in the domain of cancer biology have shed light on the molecular aspects of this intricate process. Tumor cells undergoing invasion engage with other cellular entities and proteins en route to their destination. Insights into these engagements have enhanced our comprehension of the principles directing the movement and adaptability of metastatic cells. The tumor microenvironment plays a pivotal role in facilitating the invasion and proliferation of cancer cells by enabling tumor cells to navigate through stromal barriers. Such attributes are influenced by genetic and epigenetic changes occurring in the tumor cells and their surrounding milieu. A profound understanding of the metastatic process's biological mechanisms is indispensable for devising efficacious therapeutic strategies. This review delves into recent developments concerning metastasis-associated genes, important signaling pathways, tumor microenvironment, metabolic processes, peripheral immunity, and mechanical forces and cancer metastasis. In addition, we combine recent advances with a particular emphasis on the prospect of developing effective interventions including the most popular cancer immunotherapies and nanotechnology to combat metastasis. We have also identified the limitations of current research on tumor metastasis, encompassing drug resistance, restricted animal models, inadequate biomarkers and early detection methods, as well as heterogeneity among others. It is anticipated that this comprehensive review will significantly contribute to the advancement of cancer metastasis research.

ALYREF/THOC4 expression and cell growth modulation in retinoblastoma

In this study, we tested the hypothesis that ALYREF/THOC4, a poor prognostic factor in different cancer types, has potential as a drug target and prognostic biomarker for retinoblastoma (RB). Immunostaining (IHC), Western blot, and RT-qPCR analyses detected overexpression of ALYREF in the RB cell lines Y79, RB143, WERI-RB1, and RB116. IHC analysis on RB tumor array showed that 11/14 of RB tumors were ALYREF+ to varying degrees, with eight tumors at maximum 3+ intensity. The IHC analysis also detected ALYREF+ cells in normal retina, mainly in the inner nuclear and ganglion cell layer, while some tumor-bearing human eyes were ALYREF+ in the optic nerve suggesting a role in optic invasion/tumor invasion. The expression of ALYREF within the tumor itself, in the optic nerve, as well as in adjacent "normal" retina, suggest that this pattern of expression may lead to ALYREF being a potentially useful prognostic indicator for RB, as it is for other tumors. siRNA knockdown of ALYREF resulted in a 40 % decrease in cell growth in both WERI-RB1 and Y79 cells (p<0.05) and this was associated with decreased expression of mRNAs for the cell proliferation markers Ki67 and PCNA (p<0.005). These results suggest a role for ALYREF in RB cell growth regulation and its potential as both a target and a biomarker for tumor growth inhibition by anti-cancer therapies.

A novel m6A/m5C/m1A/m7G-related classification and risk signature predicts prognosis and reveals immunotherapy inclination in gastric cancer

BACKGROUND

Gastric cancer (GC) is characterized by high morbidity and mortality rates, and the prognosis is not optimistic. Therefore, the search for new biomarkers is crucial. Methylation modifications in RNA modifications play a crucial role in tumors. However, the role of methylation modification of integrated m6A/m5C/m1A/m7G, in GC and its related analysis have not been reported. It still needs to be studied in depth. Our study aims to deepen our understanding of m6A/m5C/m1A/m7G methylation and potentially provide new strategies for GC treatment.

METHODS

We used TCGA-STAD (The Cancer Genome Atlas-Stomach Adenocarcinoma) as a training set and GSE84433 as a validation set to analyze and determine potential associations between m6A/m5C/m1A/m7G-related genes and clinical risk of GC. In addition, we explored the prognostic value and potential biological mechanisms of m6A/m5C/m1A/m7G-related genes in GC through consistent clustering, differential expression gene identification, enrichment analysis, and immune infiltration analysis. Finally, we constructed m6A/m5C/m1A/m7G-related risk signature (MRRS) to evaluate the correlation between risk grade and survival prognosis, drug sensitivity, and immune infiltration, and validated the validity by immunohistochemical staining.

RESULTS

We identified subgroups of C1, C2, and C3 patients by consensus clustering using data from 45 m6A/m5C/m1A/m7G-related genes. The three groups showed significant differences in survival, immune scores, and immune cell infiltration. We then constructed MRRS using least absolute shrinkage and selection operator (LASSO) regression analysis, including SLC5A6, FKBP10, GPC3, and GGH, which could accurately differentiate between high-/low-risk populations. Its accuracy was further validated in the validation set and immunohistochemical staining. These results suggest that m6A/m5C/m1A/m7G are closely related to the GC tumor immune microenvironment, and MRRS has good performance in predicting the survival of GC patients.

CONCLUSIONS

In this study, we highlighted the association of m6A/m5C/m1A/m7G subtypes with changes in the GC immunotumor microenvironment. We constructed and validated MRRS, which is valuable in predicting survival, immune infiltration and drug sensitivity in GC patients. This helps to deepen our understanding of m6A/m5C/m1A/m7G methylation and potentially provides new strategies for GC treatment.

Readers of RNA Modification in Cancer and Their Anticancer Inhibitors

Cancer treatment has always been a challenge for humanity. The inadequacies of current technologies underscore the limitations of our efforts against this disease. Nevertheless, the advent of targeted therapy has introduced a promising avenue, furnishing us with more efficacious tools. Consequently, researchers have turned their attention toward epigenetics, offering a novel perspective in this realm. The investigation of epigenetics has brought RNA readers to the forefront, as they play pivotal roles in recognizing and regulating RNA functions. Recently, the development of inhibitors targeting these RNA readers has emerged as a focal point in research and holds promise for further strides in targeted therapy. In this review, we comprehensively summarize various types of inhibitors targeting RNA readers, including non-coding RNA (ncRNA) inhibitors, small-molecule inhibitors, and other potential inhibitors. We systematically elucidate their mechanisms in suppressing cancer progression by inhibiting readers, aiming to present inhibitors of readers at the current stage and provide more insights into the development of anticancer drugs.

MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models

RNA modification serves as a pivotal component in numerous biological processes. Among the prevalent modifications, 5-methylcytosine (m5C) significantly influences mRNA export, translation efficiency and cell differentiation and are also associated with human diseases, including Alzheimer's disease, autoimmune disease, cancer, and cardiovascular diseases. Identification of m5C is critically responsible for understanding the RNA modification mechanisms and the epigenetic regulation of associated diseases. However, the large-scale experimental identification of m5C present significant challenges due to labor intensity and time requirements. Several computational tools, using machine learning, have been developed to supplement experimental methods, but identifying these sites lack accuracy and efficiency. In this study, we introduce a new predictor, MLm5C, for precise prediction of m5C sites using sequence data. Briefly, we evaluated eleven RNA sequence-derived features with four basic machine learning algorithms to generate baseline models. From these 44 models, we ranked them based on their performance and subsequently stacked the Top 20 baseline models as the best model, named MLm5C. The MLm5C outperformed the-state-of-the-art predictors. Notably, the optimization of the sequence length surrounding the modification sites significantly improved the prediction performance. MLm5C is an invaluable tool in accelerating the detection of m5C sites within the human genome, thereby facilitating in the characterization of their roles in post-transcriptional regulation.

Biological function molecular pathways and druggability of DNMT2/TRDMT1

5-methylcytosine (m5C) is among the most common epigenetic modification in DNA and RNA molecules, and plays an important role in the animal development and disease pathogenesis. Interestingly, unlike other m5C DNA methyltransferases (DNMTs), DNMT2/TRDMT1 has the double-substrate specificity and adopts a DNMT-similar catalytic mechanism to methylate RNA. Moreover, it is widely involved in a variety of physiological regulatory processes, such as the gene expression, precise protein synthesis, immune response, and disease occurrence. Thus, comprehending the epigenetic mechanism and function of DNMT2/TRDMT1 will probably provide new strategies to treat some refractory diseases. Here, we discuss recent studies on the spatiotemporal expression pattern and post-translational modifications of DNMT2/TRDMT1, and summarize the research advances in substrate characteristics, catalytic recognition mechanism, DNMT2/TRDMT1-related genes or proteins, pharmacological application, and inhibitor development. This review will shed light on the pharmacological design by targeting DNMT2/TRDMT1 to treat parasitic, viral and oncologic diseases.

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

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

Prognostic signature and immune efficacy of m1A-, m5C-, m6A-, m7G-, and DNA methylation-related regulators in hepatocellular carcinoma

Background: Hepatocellular carcinoma (HCC) is the main type of primary liver cancer, and its related death ranks third worldwide. The curative methods and progress prediction markers of HCC are not sufficient enough. Nevertheless, little progress has been made in the signature of m1A-, m5C-, m6A-, m7G-, and DNA methylation of HCC. Results: We calibrated a risk gene signature model that can be used to categorize HCC patients based on univariate, multivariate, and LASSO Cox regression analysis. This gene signature classified the patients into high- and low-risk subgroups. Patients in the high-risk group showed significantly reduced overall survival (OS) compared with patients in the low-risk group. The gene set variation analysis (GSVA), immune infiltration, and immunotherapy response were analyzed. The results demonstrated that an immunosuppressive environment was exited and the high-risk group had higher sensitivity to 5-fluorouracil, cisplatin, sorafenib, tamoxifen, and epirubicin. These results indicated personalized therapy should be taken into consideration. Conclusions: Our findings enriched our understanding of the molecular heterogeneity, tumor microenvironment (TME), and drug susceptibility of HCC. m1A-, m5C-, m6A-, m7G-, and DNA methylation-related regulators may be promising biomarkers for future research.

Non‐m6A RNA modifications in haematological malignancies

Dysregulated RNA modifications, stemming from the aberrant expression and/or malfunction of RNA modification regulators operating through various pathways, play pivotal roles in driving the progression of haematological malignancies. Among RNA modifications, N6-methyladenosine (m6A) RNA modification, the most abundant internal mRNA modification, stands out as the most extensively studied modification. This prominence underscores the crucial role of the layer of epitranscriptomic regulation in controlling haematopoietic cell fate and therefore the development of haematological malignancies. Additionally, other RNA modifications (non-m6A RNA modifications) have gained increasing attention for their essential roles in haematological malignancies. Although the roles of the m6A modification machinery in haematopoietic malignancies have been well reviewed thus far, such reviews are lacking for non-m6A RNA modifications. In this review, we mainly focus on the roles and implications of non-m6A RNA modifications, including N4-acetylcytidine, pseudouridylation, 5-methylcytosine, adenosine to inosine editing, 2'-O-methylation, N1-methyladenosine and N7-methylguanosine in haematopoietic malignancies. We summarise the regulatory enzymes and cellular functions of non-m6A RNA modifications, followed by the discussions of the recent studies on the biological roles and underlying mechanisms of non-m6A RNA modifications in haematological malignancies. We also highlight the potential of therapeutically targeting dysregulated non-m6A modifiers in blood cancer.

Emerging role of RNA modification and long noncoding RNA interaction in cancer

RNA modification, especially N6-methyladenosine, 5-methylcytosine, and N7-methylguanosine methylation, participates in the occurrence and progression of cancer through multiple pathways. The function and expression of these epigenetic regulators have gradually become a hot topic in cancer research. Mutation and regulation of noncoding RNA, especially lncRNA, play a major role in cancer. Generally, lncRNAs exert tumor-suppressive or oncogenic functions and its dysregulation can promote tumor occurrence and metastasis. In this review, we summarize N6-methyladenosine, 5-methylcytosine, and N7-methylguanosine modifications in lncRNAs. Furthermore, we discuss the relationship between epigenetic RNA modification and lncRNA interaction and cancer progression in various cancers. Therefore, this review gives a comprehensive understanding of the mechanisms by which RNA modification affects the progression of various cancers by regulating lncRNAs, which may shed new light on cancer research and provide new insights into cancer therapy.

RNA m5C methylation: a potential modulator of innate immune pathways in hepatocellular carcinoma

RNA 5-methylcytosine (m5C) methylation plays a crucial role in hepatocellular carcinoma (HCC). As reported, aberrant m5C methylation is closely associated with the progression, therapeutic efficacy, and prognosis of HCC. The innate immune system functions as the primary defense mechanism in the body against pathogenic infections and tumors since it can activate innate immune pathways through pattern recognition receptors to exert anti-infection and anti-tumor effects. Recently, m5C methylation has been demonstrated to affect the activation of innate immune pathways including TLR, cGAS-STING, and RIG-I pathways by modulating RNA function, unveiling new mechanisms underlying the regulation of innate immune responses by tumor cells. However, research on m5C methylation and its interplay with innate immune pathways is still in its infancy. Therefore, this review details the biological significance of RNA m5C methylation in HCC and discusses its potential regulatory relationship with TLR, cGAS-STING, and RIG-I pathways, thereby providing fresh insights into the role of RNA methylation in the innate immune mechanisms and treatment of HCC.

Integrated single-cell and spatial transcriptomic analysis reveals YBX1 drives immune regulation in GBM progression

The RNA modification 5-methylcytosine (m5C) is widespread across various RNA types, significantly impacting RNA stability and translational efficiency. Accumulating evidence highlights its significant role within the tumorigenesis and progression of multiple malignancies. Nevertheless, the specific process through m5C is implicated in Glioblastoma (GBM) remains unclear. We conducted acomprehensive analysis of m5C expression distribution in single-cell GBM data. Our findings revealed elevated m5C scores in GBM single-cell data compared to the normal group. Additionally, multiple tumors exhibited significantly higher m5C scores than the normal group. Moreover, there was a positive correlation observed between the m5C score and inflammation score. m5C regulatory factor YBX1 exhibited a heightened expression in GBM, correlating closely with metastatic tendencies and an unfavorable prognosis across various cancer types. YBX1 has different biological functions in myeloid cells 1 and myeloid cells 2. YBX1 may act as immunosuppressive regulator by inhibiting the NF-κB pathway and inflammatory response in myeloid cells 1. YBX1 is essential for immune infiltrates, which creates a highly immunosuppressive tumor microenvironment by TNF signaling pathway in myeloid cells 2. YBX1+ neoplastic cells promote cell proliferation by NF-κB pathway. APOE mediates the interaction of YBX1+ myeloid cells and neoplastic cells by NF-κB.

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

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

Identification of molecular subtypes and a prognostic signature based on m6A/m5C/m1A-related genes in lung adenocarcinoma

Lung cancer, specifically the histological subtype lung adenocarcinoma (LUAD), has the highest global occurrence and fatality rate. Extensive research has indicated that RNA alterations encompassing m6A, m5C, and m1A contribute actively to tumorigenesis, drug resistance, and immunotherapy responses in LUAD. Nevertheless, the absence of a dependable predictive model based on m6A/m5C/m1A-associated genes hinders accurately predicting the prognosis of patients diagnosed with LUAD. In this study, we collected patient data from The Cancer Genome Atlas (TCGA) and identified genes related to m6A/m5C/m1A modifications using the GeneCards database. The "ConsensusClusterPlus" R package was used to produce molecular subtypes by utilizing genes relevant to m6A/m5C/m1A identified through differential expression and univariate Cox analyses. An independent prognostic factor was identified by constructing a prognostic signature comprising six genes (SNHG12, PABPC1, IGF2BP1, FOXM1, CBFA2T3, and CASC8). Poor overall survival and elevated expression of human leukocyte antigens and immune checkpoints were correlated with higher risk scores. We examined the associations between the sets of genes regulated by m6A/m5C/m1A and the risk model, as well as the immune cell infiltration, using algorithms such as ESTIMATE, CIBERSORT, TIMER, ssGSEA, and exclusion (TIDE). Moreover, we compared tumor stemness indices (TSIs) by considering the molecular subtypes related to m6A/m5C/m1A and risk signatures. Analyses were performed based on the risk signature, including stratification, somatic mutation analysis, nomogram construction, chemotherapeutic response prediction, and small-molecule drug prediction. In summary, we developed a prognostic signature consisting of six genes that have the potential for prognostication in patients with LUAD and the design of personalized treatments that could provide new versions of personalized management for these patients.

The role of RNA-modifying proteins in renal cell carcinoma

Gene expression is one of the most critical cellular processes. It is controlled by complex mechanisms at the genomic, epigenomic, transcriptomic, and proteomic levels. Any aberration in these mechanisms can lead to dysregulated gene expression. One recently discovered process that controls gene expression includes chemical modifications of RNA molecules by RNA-modifying proteins, a field known as epitranscriptomics. Epitranscriptomics can regulate mRNA splicing, nuclear export, stabilization, translation, or induce degradation of target RNA molecules. Dysregulation in RNA-modifying proteins has been found to contribute to many pathological conditions, such as cancer, diabetes, obesity, cardiovascular diseases, and neurological diseases, among others. This article reviews the role of epitranscriptomics in the pathogenesis and progression of renal cell carcinoma. It summarizes the molecular function of RNA-modifying proteins in the pathogenesis of renal cell carcinoma.

Identification of ALYREF in pan cancer as a novel cancer prognostic biomarker and potential regulatory mechanism in gastric cancer

ALYREF is considered as a specific mRNA m5C-binding protein which recognizes m5C sites in RNA and facilitates the export of RNA from the nucleus to the cytoplasm. Expressed in various tissues and highly involved in the transcriptional regulation, ALYREF has the potential to become a novel diagnostic marker and therapeutic target for cancer patients. However, few studies focused on its function during carcinogenesis and progress. In order to explore the role of ALYREF on tumorigenesis, TCGA and GTEx databases were used to investigate the relationship of ALYREF to pan-cancer. We found that ALYREF was highly expressed in majority of cancer types and that elevated expression level was positively associated with poor prognosis in many cancers. GO and KEGG analysis showed that ALYREF to be essential in regulating the cell cycle and gene mismatch repair in tumor progression. The correlation analysis of tumor heterogeneity indicated that ALYREF could be specially correlated to the tumor stemness in stomach adenocarcinoma (STAD). Furthermore, we investigate the potential function of ALYREF on gastric carcinogenesis. Prognostic analysis of different molecular subtypes of gastric cancer (GC) unfolded that high ALYREF expression leads to poor prognosis in certain subtypes of GC. Finally, enrichment analysis revealed that ALYREF-related genes possess the function of regulating cell cycle and apoptosis that cause further influences in GC tumor progression. For further verification, we knocked down the expression of ALYREF by siRNA in GC cell line AGS. Knockdown of ALYREF distinctly contributed to inhibition of GC cell proliferation. Moreover, it is observed that knocked-down of ALYREF induced AGS cells arrested in G1 phase and increased cell apoptosis. Our findings highlighted the essential function of ALYREF in tumorigenesis and revealed the specific contribution of ALYREF to gastric carcinogenesis through pan-cancer analysis and biological experiments.

Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF)

The increasing interest in RNA modifications has significantly advanced epigenomic and epitranscriptomic technologies. This study focuses on the immuno-oncological impact of ALYREF in human cancer through a pan-cancer analysis, enhancing understanding of this gene's role in cancer. We observed differential ALYREF expression between tumor and normal samples, correlating strongly with prognosis in various cancers, particularly kidney renal papillary cell carcinoma (KIRP) and liver hepatocellular carcinoma (LIHC). ALYREF showed a negative correlation with most tumor-infiltrating cells in lung squamous cell carcinoma (LUSC) and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), while positive correlations were noted in LIHC, kidney chromophobe (KICH), mesothelioma (MESO), KIRP, pheochromocytoma and paraganglioma (PARD), and glioma (GBMLGG). Additionally, ALYREF expression was closely associated with tumor heterogeneity, stemness indices, and a high mutation rate in TP53 across these cancers. In conclusion, ALYREF may serve as an oncogenic biomarker in numerous cancers, meriting further research attention.