METTL1 mediated tRNA m7G modification promotes leukaemogenesis of AML via tRNA regulated translational control

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

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

The m7G methylation modification: An emerging player of cardiovascular diseases

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

A 6-tsRNA signature for early detection, treatment response monitoring, and prognosis prediction in diffuse large B cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) presents considerable clinical challenges due to its aggressive nature and diverse clinical progression. New molecular biomarkers are urgently needed for outcome prediction. We analyzed blood samples from DLBCL patients and healthy individuals using short, non-coding RNA sequencing. A classifier based on six tsRNAs was developed through random forest and primary component analysis. This classifier, established using Cox proportional hazards modeling with repeated 10-fold cross-validation on an internal cohort of 100 samples analyzed using RT-qPCR, effectively identified high-risk patients with significantly lower overall survival compared to low-risk patients (Hazard ratio: 6.657, 95%CI 2.827-15.68, P = 0.0006). Validation in an external cohort of 160 samples using RT-qPCR confirmed the classifier's robust performance. High-risk status was strongly associated with disease histological subtype, stage, and International Prognostic Index scores. Integration of the classifier into the IPI model enhanced the precision and consistency of prognostic predictions. A dynamic study revealed that patients experiencing a 1.06-fold decrease after one therapy cycle (early molecular response) exhibited better treatment outcomes and prognosis. Furthermore, the 6-tsRNA signature accurately differentiated healthy individuals from DLBCL (AUC 0.882, 95%CI 0.826-0.939). These findings underscore the potential of the identified 6-tsRNA profile as a biomarker for monitoring treatment effectiveness and predicting DLBCL outcomes.

RNA Methyltransferase NSUN5 Promotes Esophageal Cancer via 5-Methylcytosine Modification of METTL1

Aberrant RNA modifications can drive carcinogenic transformation and tumor progression, with 5-methylcytosine (m5C) emerging as one of the predominant RNA modifications in eukaryotic cells. However, the function and molecular mechanisms of m5C in esophageal cancer (ESCA) remain insufficiently defined. Here we report that the m5C methyltransferase NOP2/Sun domain family member 5 (NSUN5) is significantly upregulated in ESCA tumors and shows promising diagnostic potential. Functionally, knockdown of NSUN5 impairs the proliferation capacity of ESCA cells and arrests cell cycle at the G0/G1 phase, while enforced expression of NSUN5 accelerates ESCA progression. In vivo, deficiency of NSUN5 significantly reduces tumor growth in a cell-based xenograft mouse model. Mechanistically, NSUN5 correlates with the oncogenic methyltransferase like 1 (METTL1), positively regulating its expression; NSUN5 binds directly to the METTL1 transcript, facilitating its m5C modification in ESCA cells. Additionally, overexpression of METTL1 effectively counteracts the tumor-suppressive effects resulting from NSUN5 ablation in both in vitro and in vivo settings. A comprehensive pan-cancer analysis further underscores NSUN5's essential role in digestive system tumors, with downregulation of NSUN5 notably inhibiting gastric and colon cancer cell growth. These findings provide new insights into epigenetic regulation in ESCA and propose the NSUN5/METTL1 axis as a promising therapeutic target for this malignancy.

The diverse landscape of RNA modifications in cancer development and progression

BACKGROUND

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

OBJECTIVE

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Hydroxy-wybutosine tRNA modifications as indicators of disease progression and therapeutic targets in leukaemia

Therapeutic approaches for acute myeloid leukaemia (AML) and myelodysplastic syndromes (MDS) differ due to distinct diagnostic criteria and treatment strengths. However, reliable biomarkers to differentiate AML from MDS are needed. This study investigated transfer RNA (tRNA) modifications, particularly hydroxy-wybutosine (OHyW), in the transition from MDS to AML. We found a significant decrease in OHyW and its biosynthetic enzyme leucine carboxyl methyltransferase 2 (LCMT2, alias symbol is TYW4) levels in AML compared to MDS. Mass spectrometric analysis revealed distinct tRNA modification patterns, with AML showing decreased OHyW and increased precursor levels, indicating a disrupted biosynthetic pathway. Lower LCMT2 expression correlated with reduced drug sensitivity and limited differentiation potential in AML cell lines. The results highlight the pivotal role of tRNA modifications in the progression from MDS to AML and suggest that targeting LCMT2 may enhance therapeutic outcomes in AML. By understanding these molecular mechanisms, we can develop new diagnostic markers and therapeutic strategies, potentially transforming the clinical management of AML and improving patient outcomes.

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

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

tRNA-derived small RNAs: their role in the mechanisms, biomarkers, and therapeutic strategies of colorectal cancer

Colorectal cancer (CRC) is the third most prevalent malignancy and the second leading cause of cancer-related mortality worldwide, with an increasing shift towards younger age of onset. In recent years, there has been increasing recognition of the significance of tRNA-derived small RNAs (tsRNAs), encompassing tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs). Their involvement in regulating translation, gene expression, reverse transcription, and epigenetics has gradually come to light. Emerging research has revealed dysregulation of tsRNAs in CRC, implicating their role in CRC initiation and progression, and highlighting their potential in early diagnosis, prognosis, and therapeutic strategies. Although the clinical application of tsRNAs is still in its early stages, recent findings highlight a close relationship between the biogenesis and function of tsRNAs, tRNA chemical modifications, and the tumor immune microenvironment (TIME). Additionally, similar to other small RNAs, tsRNAs can be effectively delivered via nanoparticles (NPs). Consequently, future research should focus on elucidating the clinical significance of tsRNAs concerning base modifications, TIME regulation, cancer immunotherapy, and NPs delivery systems to facilitate their clinical translation.

RNA modification in normal hematopoiesis and hematologic malignancies

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

tRNA and tsRNA: From Heterogeneity to Multifaceted Regulators

As the most ancient RNA, transfer RNAs (tRNAs) play a more complex role than their constitutive function as amino acid transporters in the protein synthesis process. The transcription and maturation of tRNA in cells are subject to stringent regulation, resulting in the formation of tissue- and cell-specific tRNA pools with variations in tRNA overall abundance, composition, modification, and charging levels. The heterogeneity of tRNA pools contributes to facilitating the formation of histocyte-specific protein expression patterns and is involved in diverse biological processes. Moreover, tRNAs can be recognized by various RNase under physiological and pathological conditions to generate tRNA-derived small RNAs (tsRNAs) and serve as small regulatory RNAs in various biological processes. Here, we summarize these recent insights into the heterogeneity of tRNA and highlight the advances in the regulation of tRNA function and tsRNA biogenesis by tRNA modifications. We synthesize diverse mechanisms of tRNA and tsRNA in embryonic development, cell fate determination, and epigenetic inheritance regulation. We also discuss the potential clinical applications based on the new knowledge of tRNA and tsRNA as diagnostic and prognostic biomarkers and new therapeutic strategies for multiple diseases.

Mitochondrial transcriptome of Candida albicans in flagranti - direct RNA sequencing reveals a new layer of information

BACKGROUND

Organellar transcriptomes are relatively under-studied systems, with data related to full-length transcripts and posttranscriptional modifications remaining sparse. Direct RNA sequencing presents the possibility of accessing a previously unavailable layer of information pertaining to transcriptomic data, as well as circumventing the biases introduced by second-generation RNA-seq platforms. Direct long-read ONT sequencing allows for the isoform analysis of full-length transcripts and the detection of posttranscriptional modifications. However, there are still relatively few projects employing this method specifically for studying organellar transcriptomes.

RESULTS

Candida albicans is a promising model for investigating nucleo-mitochondrial interactions. This work comprises ONT sequencing of the Candida albicans mitochondrial transcriptome along with the development of a dedicated data analysis pipeline. This approach allowed for the detection of complete transcript isoforms and posttranslational RNA modifications, as well as an analysis of C. albicans deletion mutants in genes coding for the 5' and 3' mitochondrial RNA exonucleases CaPET127 and CaDSS1. It also enabled for corrections to previous studies in terms of 3' and 5' transcript ends. A number of intermediate splicing isoforms was also discovered, along with mature and unspliced transcripts and changes in their abundances resulting from disruption of both 5' and 3' exonucleolytic processing. Multiple putative posttranscriptional modification sites have also been detected.

CONCLUSIONS

This preliminary work demonstrates the suitability of direct RNA sequencing for studying yeast mitochondrial transcriptomes in general and provides new insights into the workings of the C. albicans mitochondrial transcriptome in particular. It also provides a general roadmap for analyzing mitochondrial transcriptomic data from other organisms.

tRNA modifications and tRNA-derived small RNAs: new insights of tRNA in human disease

tRNAs are codon decoders that convert the transcriptome into the proteome. The field of tRNA research is excited by the increasing discovery of specific tRNA modifications that are installed at specific, evolutionarily conserved positions by a set of specialized tRNA-modifying enzymes and the biogenesis of tRNA-derived regulatory fragments (tsRNAs) which exhibit copious activities through multiple mechanisms. Dysregulation of tRNA modification usually has pathological consequences, a phenomenon referred to as "tRNA modopathy". Current evidence suggests that certain tRNA-modifying enzymes and tsRNAs may serve as promising diagnostic biomarkers and therapeutic targets, particularly for chemoresistant cancers. In this review, we discuss the latest discoveries that elucidate the molecular mechanisms underlying the functions of clinically relevant tRNA modifications and tsRNAs, with a focus on malignancies. We also discuss the therapeutic potential of tRNA/tsRNA-based therapies, aiming to provide insights for the development of innovative therapeutic strategies. Further efforts to unravel the complexities inherent in tRNA biology hold the promise of yielding better biomarkers for the diagnosis and prognosis of diseases, thereby advancing the development of precision medicine for health improvement.

Exploring the role of m7G modification in Cancer: Mechanisms, regulatory proteins, and biomarker potential

The dysregulation of N(7)-methylguanosine (m7G) modification is increasingly recognized as a key factor in the pathogenesis of cancers. Aberrant expression of these regulatory proteins in various cancers, including lung, liver, and bladder cancers, suggests a universal role in tumorigenesis. Studies have established a strong correlation between the expression levels of m7G regulatory proteins, such as Methyltransferase like 1 (METTL1) and WD repeat domain 4 (WDR4), and clinical parameters including tumor stage, grade, and patient prognosis. For example, in hepatocellular carcinoma, high METTL1 expression is associated with advanced tumor stage and poor prognosis. Similarly, WDR4 overexpression in colorectal cancer correlates with increased tumor invasiveness and reduced patient survival. This correlation underscores the potential of these proteins as valuable biomarkers for cancer diagnosis and prognosis. Additionally, m7G modification regulatory proteins influence cancer progression by modulating the expression of target genes involved in critical biological processes, including cell proliferation, apoptosis, migration, and invasion. Their ability to regulate these processes highlights their significance in the intricate network of molecular interactions driving tumor development and metastasis. Given their pivotal role in cancer biology, m7G modification regulatory proteins are emerging as promising therapeutic targets. Targeting these proteins could offer a novel approach to disrupt the malignant behavior of cancer cells and enhance treatment outcomes. Furthermore, their diagnostic and prognostic value could aid in the early detection of cancer and the selection of appropriate therapeutic strategies, ultimately enhancing patient management and survival rates. This review aims to explore the mechanisms of action of RNA m7G modification regulatory proteins in tumors and their potential applications in cancer progression and treatment. By delving into the roles of these regulatory proteins, we intend to provide a theoretical foundation for the development of novel cancer treatment strategies.

METTL Family in Healthy and Disease

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

Dysregulation of tRNA methylation in cancer: Mechanisms and targeting therapeutic strategies

tRNA is the RNA type that undergoes the most modifications among known RNA, and in recent years, tRNA methylation has emerged as a crucial process in regulating gene translation. Dysregulation of tRNA abundance occurs in cancer cells, along with increased expression and activity of tRNA methyltransferases to raise the level of tRNA modification and stability. This leads to hijacking of translation and synthesis of multiple proteins associated with tumor proliferation, metastasis, invasion, autophagy, chemotherapy resistance, and metabolic reprogramming. In this review, we provide an overview of current research on tRNA methylation in cancer to clarify its involvement in human malignancies and establish a theoretical framework for future therapeutic interventions targeting tRNA methylation processes.

WDR4 promotes HCC pathogenesis through N7-methylguanosine by regulating and interacting with METTL1

BACKGROUND

The N7-methylguanosine (m7G), a modification at defined internal positions within tRNAs and rRNAs, is correlated with tumor progression. Methyltransferase like 1 (METTL1)/ WD repeat domain 4 (WDR4) mediated tRNA m7G modification, which could alter many oncogenic mRNAs translation to promote progress of multiple cancer types. However, whether and how the internal mRNA m7G modification is involved in tumorigenesis remains unclear.

METHODS

The immunohistochemistry assay was conducted to detect the expression of WDR4 and METTL1 in hepatocellular carcinoma (HCC) and the expression of both genes whether contributes to the prognosis of the survival rate of HCC patients. Then, CCK8, colony formation assays and tumor xenograft models were conducted to determine the effects of WDR4 on HCC cells in vitro and vivo. Besides, dot blot assay, m7G-MeRIP-seq and RNA-seq analysis were conducted to determine whether WDR4 contributes to m7G modification and underlying mechanism in HCC cells. Finally, rescue and CO-IP assay were conducted to explore whether WDR4 and METTL1 proteins form a complex in Huh7 cells.

RESULTS

WDR4 modulates m7G modification at the internal sites of tumor-promoting mRNAs by forming the WDR4-METTL1 complex. WDR4 knockdown downregulated the expression of mRNA and protein levels of METTL1 gene and thus further modulate the formation of WDR4-METTL1 complex indirectly. METTL1 expression was markedly correlated with WDR4 expression in HCC tissues. HCC patients with high expression of both genes had a poor prognosis.

CONCLUSIONS

WDR4 may contribute to HCC pathogenesis by interacting with and regulating the expression of METTL1 to synergistically modulate the m7G modification of target mRNAs in tumor cells.

Critical roles and clinical perspectives of RNA methylation in cancer

RNA modification, especially RNA methylation, is a critical posttranscriptional process influencing cellular functions and disease progression, accounting for over 60% of all RNA modifications. It plays a significant role in RNA metabolism, affecting RNA processing, stability, and translation, thereby modulating gene expression and cell functions essential for proliferation, survival, and metastasis. Increasing studies have revealed the disruption in RNA metabolism mediated by RNA methylation has been implicated in various aspects of cancer progression, particularly in metabolic reprogramming and immunity. This disruption of RNA methylation has profound implications for tumor growth, metastasis, and therapy response. Herein, we elucidate the fundamental characteristics of RNA methylation and their impact on RNA metabolism and gene expression. We highlight the intricate relationship between RNA methylation, cancer metabolic reprogramming, and immunity, using the well-characterized phenomenon of cancer metabolic reprogramming as a framework to discuss RNA methylation's specific roles and mechanisms in cancer progression. Furthermore, we explore the potential of targeting RNA methylation regulators as a novel approach for cancer therapy. By underscoring the complex mechanisms by which RNA methylation contributes to cancer progression, this review provides a foundation for developing new prognostic markers and therapeutic strategies aimed at modulating RNA methylation in cancer treatment.