Metformin attenuates multiple myeloma cell proliferation and encourages apoptosis by suppressing METTL3-mediated m6A methylation of THRAP3, RBM25, and USP4

RNA binding motif protein 25 is a negative prognostic biomarker and promotes cell proliferation via alternative splicing in hepatocellular carcinoma

BACKGROUND

The purpose of this study was to identify the role of RNA binding motif protein 25 (RBM25) in hepatocellular carcinoma (HCC).

METHODS

The expression of RBM25 was analyzed by public databases and IHC assay. The associations between RBM25 expression and clinicopathological characteristics of HCC patients were investigated. Cell proliferation and apoptosis were measured. RNA sequencing was utilized to analyze global transcription levels and alternative splicing (AS) events. Furthermore, GO and KEGG analyses based on differentially expressed genes were performed to predict underlying mechanisms.

RESULTS

The high and low expression rates of RBM25 were 55.6 %(133/239) and 44.4 %(106/239), respectively. Furthermore, high level of RBM25 was significantly associated with high level of AFP and poor differentiation. Moreover, liver cirrhosis, differentiation, and RBM25 expression were the independent risk factors related to overall survival (OS). Differentiation and MVI were the independent factors affecting recurrence-free survival (RFS). OS of the case with high RBM25 expression was shorter after hepatectomy than that of low RBM25 expression in liver cirrhosis(-), tumor size ≤ 5 cm, MVI(+) and TNM stage Ⅰ subgroup. Also, high expression of RBM25 was associated with a shorter RFS in tumor size ≤ 5 cm and MVI(+) subgroup. The deletion of RBM25 hindered cell proliferation. RBM25 was involved in AS of multiple genes, including HDAC1, ITGB3BP, RCC1, and TFDP1, which were associated with cell cycle and cell division.

CONCLUSION

RBM25 could be used as a candidate to evaluate the prognosis of HCC, which might be associated with the role of RBM25 in promoting cell proliferation.

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment

Nanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic or transcriptomic and epigenetic information without additional library preparation. At present, only a limited set of modifications can be directly basecalled (for example, 5-methylcytosine), while most others require exploratory methods that often begin with alignment of nanopore signal to a nucleotide reference. We present Uncalled4, a toolkit for nanopore signal alignment, analysis and visualization. Uncalled4 features an efficient banded signal alignment algorithm, BAM signal alignment file format, statistics for comparing signal alignment methods and a reproducible de novo training method for k-mer-based pore models, revealing potential errors in Oxford Nanopore Technologies' state-of-the-art DNA model. We apply Uncalled4 to RNA 6-methyladenine (m6A) detection in seven human cell lines, identifying 26% more modifications than Nanopolish using m6Anet, including in several genes where m6A has known implications in cancer. Uncalled4 is available open source at github.com/skovaka/uncalled4 .

A novel mechanism in regulating drug sensitivity, growth, and apoptosis of bortezomib-resistant multiple myeloma cells: the USP4/KLF2/HMGA2 cascade

BACKGROUND

Multiple myeloma (MM) is a malignant disorder originating from plasma cells. Bortezomib (BTZ) resistance has become a huge obstacle to MM treatment. Herein, we elucidated the action of Kruppel-like factor 2 (KLF2), a crucial transcription factor (TF), on BTZ resistance of MM.

METHODS

Two BTZ-resistant cell lines (MM1.S/BTZ and NCI-H929/BTZ) were generated and used. KLF2 mRNA was quantified by quantitative PCR, and protein expression was analyzed by immunoblotting. MTT cell cytotoxicity assay was used to test BTZ sensitivity. Cell growth was detected by MTT and EdU assays. Flow cytometry was used for apoptosis and cycle distribution analyses. The USP4/KLF2 relationship was examined by Co-IP and protein stability assays. The KLF2/HMGA2 interplay was confirmed by luciferase and ChIP assays.

RESULTS

Upregulation of KLF2 was observed in MM serum and BTZ-resistant MM cells. Depletion of KLF2 suppressed cell growth and enhanced apoptosis and BTZ sensitivity in MM1.S/BTZ and NCI-H929/BTZ cells. Moreover, USP4 increased the stability of KLF2 protein by deubiquitination and affected cell growth, apoptosis and BTZ sensitivity via KLF2. KLF2 functioned as a regulator of HMGA2 transcription and modulated cell growth, apoptosis and BTZ sensitivity through HMGA2. Additionally, USP4 modulated HMGA2 expression via KLF2 in the two BTZ-resistant cell lines.

CONCLUSION

Our study demonstrates the crucial role of the USP4/KLF2/HMGA2 cascade in regulating cell growth, apoptosis and BTZ sensitivity in BTZ-resistant MM cells, providing novel targets for improving anti-MM efficacy of BTZ.

The METTL3/TRAP1 axis as a key regulator of 5-fluorouracil chemosensitivity in colorectal cancer

Colorectal cancer (CRC) remains a significant clinical challenge, with 5-Fluorouracil (5-FU) being the frontline chemotherapy. However, chemoresistance remains a major obstacle to effective treatment. METTL3, a key methyltransferase involved in RNA methylation processes, has been implicated in CRC carcinogenesis. However, its role in modulating CRC sensitivity to 5-FU remains elusive. In this study, we aimed to investigate the role and mechanisms of METTL3 in regulating 5-FU chemosensitivity in CRC cells. Initially, we observed that 5-FU treatment inhibited cell viability and induced apoptosis, accompanied by a reduction in METTL3 expression in HCT-116 and HCT-8 cells. Subsequent assays including drug sensitivity, EdU, colony formation, TUNEL staining, and flow cytometry revealed that METTL3 depletion enhanced 5-FU sensitivity and increased apoptosis induction both in vitro and in vivo. Conversely, METTL3 overexpression conferred resistance to 5-FU in both cell lines. Moreover, knockdown of METTL3 in 5-FU-resistant CRC cell lines HCT-116/FU and HCT-15/FU significantly decreased 5-FU tolerance and induced apoptosis upon 5-FU treatment. Mechanistically, we found that METTL3 regulated 5-FU sensitivity and apoptosis induction by modulating TRAP1 expression. Further investigations using m6A colorimetric ELISA, dot blot, MeRIP-qPCR and RNA stability assays demonstrated that METTL3 regulated TRAP1 mRNA stability in an m6A-dependent manner. Additionally, overexpression of TRAP1 mitigated the cytotoxic effects of 5-FU on CRC cells. In summary, our study uncovers the pivotal role of the METTL3/TRAP1 axis in modulating 5-FU chemosensitivity in CRC. These findings provide new insights into the mechanisms underlying CRC resistance to 5-FU and may offer potential targets for future therapeutic interventions.

The YTHDC1 reader protein recognizes and regulates the lncRNA MEG3 following its METTL3-mediated m6A methylation: a novel mechanism early during radiation-induced liver injury

While apoptotic cell death is known to be central to the pathogenesis of radiation-induced liver injury (RILI), the mechanistic basis for this apoptotic activity remains poorly understood. N6-methyladenosine (m6A) modifications are the most common form of reversible methylation observed on lncRNAs in eukaryotic cells, with their presence leading to pronounced changes in the activity of a range of biological processes. The degree to which m6A modification plays a role in the induction of apoptotic cell death in response to ionizing radiation (IR) in the context of RILI remains to be established. Here, IR-induced apoptosis was found to significantly decrease the levels of m6A present, with a pronounced decrease in the expression of methyltransferase-like 3 (METTL3) at 2 d post radiation in vitro. From a mechanistic perspective, a methylated RNA immunoprecipitation assay found that lncRNA MEG3 was a major METTL3 target. The expression of MEG3 was upregulated via METTL3-mediated m6A in a process that was dependent on YTHDC1, ultimately reversing the miR-20b-mediated inhibition of BNIP2 expression. Together, these findings demonstrate that the responsivity of METTL3 activity to IR plays a role in IR-induced apoptotic cell death, leading to the reverse of miR-20b-mediated BNIP2 inhibition through the YTHDC1-dependent m6A modification of MEG3, suggesting that this process may play a central role in RILI incidence.

The role of methyltransferase-like 3 (METTL3) in immune response modulation in bivalve (Mytilus coruscus) during bacterial infection

N6-methyladenosine (m6A) modification is a prevalent mRNA modification that regulates diverse biological processes in eukaryotes, including immune responses. While the role of m6A in mammalian immunity has been explored, its involvement in the immune defense of invertebrates, particularly marine bivalves which face constant pathogen challenges, remains largely unknown. Here, we investigated the function of methyltransferase-like 3 (METTL3), a key m6A "writer" enzyme, in the immune response of the marine bivalve Mytilus coruscus against Vibrio alginolyticus infection. M. coruscus METTL3 (McMETTL3) expression in the digestive gland increased (3-fold) after V. alginolyticus infection, coinciding with elevated m6A levels. Silencing McMETTL3 reduced both m6A levels and V. alginolyticus-induced apoptosis in digestive gland cells. In silico analysis identified a C1q-like protein family member (McC1QL) as a potential downstream target of McMETTL3, exhibiting an increase (7.2-fold) in m6A modification and an increase (1.5-fold) in expression during infection. Functional experiments confirmed that McC1QL knockdown inhibited McMETTL3-driven apoptosis (10.83 %). These findings demonstrate that METTL3 regulates apoptosis and immune responses in invertebrates via m6A modification of target genes like McC1QL. This study provides novel insights into the m6A-mediated immune regulation mechanisms in marine bivalves and may offer potential avenues for developing innovative disease control strategies in aquaculture.

ZC3H13 may participate in the ferroptosis process of sepsis-induced cardiomyopathy by regulating the expression of Pnn and Rbm25

BACKGROUND

N6 methyladenosine (m6A) regulates the ferroptosis in different diseases. However, there is no report about the role of the m6A regulator in the ferroptosis process of septic cardiomyopathy (SCM). This study aims to find the potential m6A regulator that participates in the ferroptosis process of SCM.

METHODS

Genes related to m6A were identified through bioinformatics analysis in GSE142615. Then, the expression of Rrp8, Trmt6, Trmt61a, Ythdf1, and ZC3H13 was detected in lipopolysaccharide (LPS)-treated HL-1 cells using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). After overexpression or interference with ZC3H13, Cell Counting Kit-8 measured cell proliferation, flow cytometry detected apoptosis and reactive oxygen species (ROS) accumulation was observed. Then, we identified the potential downstream genes of ZC3H13 through further bioinformatics analysis followed by qRT-PCR and western blotting validation.

RESULTS

There were five differentially expressed genes related to m6A, including Rrp8, Trmt6, Trmt61a, Ythdf1, and ZC3H13. The expression of Rrp8, Trmt6, Trmt61a, Ythdf1, and ZC3H13 mRNA was significantly up-regulated in the LPS-treated HL-1 cells, with ZC3H13 having the highest expression. Furthermore, overexpression of ZC3H13 inhibited the proliferation of HL-1 cells and promoted apoptosis and ROS accumulation. While, interfering with ZC3H13 promoted the proliferation of LPS-treated HL-1 cells, and reduced apoptosis and ROS accumulation. Additionally, si-ZC3H13 promoted the expression of Pnn, GPX4, and SLC7A11; while inhibiting the expression of Rbm25 and Caspase 3.

CONCLUSIONS

In a word, the silence of ZC3H13 increased the proliferation and ferroptosis-related protein expression, decreased apoptosis and ROS accumulation, as well as maybe by regulating Pnn and Rbm25 expression.

Epigenetics-targeted drugs: current paradigms and future challenges

Epigenetics governs a chromatin state regulatory system through five key mechanisms: DNA modification, histone modification, RNA modification, chromatin remodeling, and non-coding RNA regulation. These mechanisms and their associated enzymes convey genetic information independently of DNA base sequences, playing essential roles in organismal development and homeostasis. Conversely, disruptions in epigenetic landscapes critically influence the pathogenesis of various human diseases. This understanding has laid a robust theoretical groundwork for developing drugs that target epigenetics-modifying enzymes in pathological conditions. Over the past two decades, a growing array of small molecule drugs targeting epigenetic enzymes such as DNA methyltransferase, histone deacetylase, isocitrate dehydrogenase, and enhancer of zeste homolog 2, have been thoroughly investigated and implemented as therapeutic options, particularly in oncology. Additionally, numerous epigenetics-targeted drugs are undergoing clinical trials, offering promising prospects for clinical benefits. This review delineates the roles of epigenetics in physiological and pathological contexts and underscores pioneering studies on the discovery and clinical implementation of epigenetics-targeted drugs. These include inhibitors, agonists, degraders, and multitarget agents, aiming to identify practical challenges and promising avenues for future research. Ultimately, this review aims to deepen the understanding of epigenetics-oriented therapeutic strategies and their further application in clinical settings.

Biological roles of THRAP3, STMN1 and GNA13 in human blood cancer cells

Blood cancers, such as diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma (BL) and acute myeloid leukemia (AML), are aggressive neoplasms that are characterized by undesired clinical courses with dismal survival rates. The objective of the current work is to study the expression THRAP3, STMN1 and GNA13 in DLBCL, BL and AML, and to investigate if these proteins are implicated in the prognosis and progression of the blood cancers. Isolation of normal blood cells was performed using lymphoprep coupled with gradient centrifugation and magnetic beads. Flow-cytometric analysis showed high quality of the isolated cells. Western blotting identified THRAP3, STMN1 and GNA13 to be overexpressed in the blood cancer cells but hardly detected in normal blood cells from healthy donors. Consistently, investigations performed using genotype-tissue expression (GTEx) and gene expression profiling interactive analysis (GEPIA) showed that the three proteins had higher mRNA expression in various cancers compared with matched normal tissues (p ≤ 0.01). Furthermore, the up-regulated transcript expression of these proteins was a feature of short overall survival (OS; p ≤ 0.02) in patients with the blood cancers. Interestingly, functional profiling using gProfiler and protein-protein interaction network analysis using STRING with cytoscape reported THRAP3 to be associated with cancer-dependent proliferation and survival pathways (corrected p ≤ 0.05) and to interact with proteins (p = 1 × 10-16) implicated in tumourigenesis and chemotherapy resistance. Taken together, these findings indicated a possible implication of THRAP3, STMN1 and GNA13 in the progression and prognosis of the blood cancers. Additional work using clinical samples of the blood cancers is required to further investigate and validate the results reported here.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04093-5.

Examining the evidence for mutual modulation between m6A modification and circular RNAs: current knowledge and future prospects

The resistance of cancer cells to treatment significantly impedes the success of therapy, leading to the recurrence of various types of cancers. Understanding the specific mechanisms of therapy resistance may offer novel approaches for alleviating drug resistance in cancer. Recent research has shown a reciprocal relationship between circular RNAs (circRNAs) and N6-methyladenosine (m6A) modification, and their interaction can affect the resistance and sensitivity of cancer therapy. This review aims to summarize the latest developments in the m6A modification of circRNAs and their importance in regulating therapy resistance in cancer. Furthermore, we explore their mutual interaction and exact mechanisms and provide insights into potential future approaches for reversing cancer resistance.

Association between methyltransferase-like 3 and non-small cell lung cancer: pathogenesis, therapeutic resistance, and clinical applications

Non-small cell lung cancer (NSCLC) is a malignant cancer that with high incidence, recurrence, and mortality rates in human beings, posing significant threats to human health. Moreover, effective early diagnosis of NSCLC remains limited primarily by the lack of accurate biomarkers. Therefore, there is an urgent need to understand the mechanisms underlying NSCLC pathogenesis and treatment failure. Methyltransferase-like 3 (METTL3) is a prototypical member of a family of which its members transfer methyl groups. It has been implicated in modulating the pathogenesis of NSCLC, as well as conferring resistance to NSCLC therapeutics. The targeting of METTL3 for NSCLC treatment has been reported. However, the relationship between METTL3 and NSCLC remains to be demonstrated. In this review, we discuss relevant interrelationships by summarising the studies on METTL3 in NSCLC pathogenesis, therapeutic resistance, and clinical applications. Current research suggests that the upregulation of METTL3 expression propels the tumorigenesis, progression, and treatment resistance of NSCLC. Therefore, we propose that METTL3 is an excellent candidate biomarker for NSCLC diagnosis and prognosis. Therapeutic targeting of METTL3 has significant potential for NSCLC treatment. This review provides a summary of the association between METTL3 and NSCLC, which would be a valuable reference for both basic and clinical research.

Novel Insights into the Links between N6-Methyladenosine and Regulated Cell Death in Musculoskeletal Diseases

Musculoskeletal diseases (MSDs), including osteoarthritis (OA), osteosarcoma (OS), multiple myeloma (MM), intervertebral disc degeneration (IDD), osteoporosis (OP), and rheumatoid arthritis (RA), present noteworthy obstacles associated with pain, disability, and impaired quality of life on a global scale. In recent years, it has become increasingly apparent that N6-methyladenosine (m6A) is a key regulator in the expression of genes in a multitude of biological processes. m6A is composed of 0.1-0.4% adenylate residues, especially at the beginning of 3'-UTR near the translation stop codon. The m6A regulator can be classified into three types, namely the "writer", "reader", and "eraser". Studies have shown that the epigenetic modulation of m6A influences mRNA processing, nuclear export, translation, and splicing. Regulated cell death (RCD) is the autonomous and orderly death of cells under genetic control to maintain the stability of the internal environment. Moreover, distorted RCDs are widely used to influence the course of various diseases and receiving increasing attention from researchers. In the past few years, increasing evidence has indicated that m6A can regulate gene expression and thus influence different RCD processes, which has a central role in the etiology and evolution of MSDs. The RCDs currently confirmed to be associated with m6A are autophagy-dependent cell death, apoptosis, necroptosis, pyroptosis, ferroptosis, immunogenic cell death, NETotic cell death and oxeiptosis. The m6A-RCD axis can regulate the inflammatory response in chondrocytes and the invasive and migratory of MM cells to bone remodeling capacity, thereby influencing the development of MSDs. This review gives a complete overview of the regulatory functions on the m6A-RCD axis across muscle, bone, and cartilage. In addition, we also discuss recent advances in the control of RCD by m6A-targeted factors and explore the clinical application prospects of therapies targeting the m6A-RCD in MSD prevention and treatment. These may provide new ideas and directions for understanding the pathophysiological mechanism of MSDs and the clinical prevention and treatment of these diseases.

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment

Nanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic/transcriptomic and epigenetic information without additional library preparation. Presently, only a limited set of modifications can be directly basecalled (e.g. 5-methylcytosine), while most others require exploratory methods that often begin with alignment of nanopore signal to a nucleotide reference. We present Uncalled4, a toolkit for nanopore signal alignment, analysis, and visualization. Uncalled4 features an efficient banded signal alignment algorithm, BAM signal alignment file format, statistics for comparing signal alignment methods, and a reproducible de novo training method for k-mer-based pore models, revealing potential errors in ONT's state-of-the-art DNA model. We apply Uncalled4 to RNA 6-methyladenine (m6A) detection in seven human cell lines, identifying 26% more modifications than Nanopolish using m6Anet, including in several genes where m6A has known implications in cancer. Uncalled4 is available open-source at github.com/skovaka/uncalled4.

Modification patterns and metabolic characteristics of m6A regulators in digestive tract tumors

M6A is essential for tumor occurrence and progression. The expression patterns of m6A regulators differ in various kinds of tumors. Transcriptomic expression statistics together with clinical data from a database were analyzed to distinguish patients with digestive tract tumors. Based on the expression patterns of diverse m6A regulators, patients were divided into several clusters. Survival analysis suggested significant differences in patient prognosis among the m6A clusters. The results showed overlapping of m6A expression patterns with energy metabolism and nucleotide metabolism. Functional analyses imply that m6A modifications in tumor cells probably drive metabolic reprogramming to sustain rapid proliferation of cancer cells. Our analysis highlights the m6A risk characterizes various kinds of metabolic features and predicts chemotherapy sensitivity in digestive tract tumors, providing evidence for m6A regulators as markers to predict patient outcomes.

The role of m6A and m6Am RNA modifications in the pathogenesis of diabetes mellitus

The rapidly developing research field of epitranscriptomics has recently emerged into the spotlight of researchers due to its vast regulatory effects on gene expression and thereby cellular physiology and pathophysiology. N⁶-methyladenosine (m⁶A) and N⁶,2'-O-dimethyladenosine (m⁶Am) are among the most prevalent and well-characterized modified nucleosides in eukaryotic RNA. Both of these modifications are dynamically regulated by a complex set of epitranscriptomic regulators called writers, readers, and erasers. Altered levels of m⁶A and also several regulatory proteins were already associated with diabetic tissues. This review summarizes the current knowledge and gaps about m⁶A and m⁶Am modifications and their respective regulators in the pathophysiology of diabetes mellitus. It focuses mainly on the more prevalent type 2 diabetes mellitus (T2DM) and its treatment by metformin, the first-line antidiabetic agent. A better understanding of epitranscriptomic modifications in this highly prevalent disease deserves further investigation and might reveal clinically relevant discoveries in the future.

m6A methyltransferase METTL3 facilitates multiple myeloma cell growth through the m6A modification of BZW2

N6-methyladenosine (m6A) methyltransferase-like 3 (METTL3) has been confirmed to be involved in multiple myeloma (MM) progression, and basic leucine zipper and W2 domains 2 (BZW2) is considered to be a regulator for MM development. However, whether METTL3 mediates MM progression by regulating BZW2 remains unclear. The messenger RNA (mRNA) and protein levels of METTL3 and BZW2 in MM specimens and cells were determined using quantitative real-time PCR and western blot analysis. Cell proliferation and apoptosis were assessed by cell counting kit 8 assay, 5-ethynyl-2'-deoxyuridine assay, colony formation assay, and flow cytometry. Methylated RNA immunoprecipitation-qPCR was used to detect the m6A modification level of BZW2. Xenograft tumor models were constructed to confirm the effect of METTL3 knockdown on MM tumor growth in vivo. Our results showed that BZW2 was upregulated in MM bone marrow specimens and cells. BZW2 downregulation reduced MM cell proliferation and promoted apoptosis, while its overexpression enhanced MM cell proliferation and inhibited apoptosis. METTL3 was highly expressed in MM bone marrow specimens, and its expression was positively correlated with BZW2 expression. BZW2 expression was positively regulated by METTL3. Mechanistically, METTL3 could upregulate BZW2 expression by modulating its m6A modification. Additionally, METTL3 accelerated MM cell proliferation and restrained apoptosis via increasing BZW2 expression. In vivo experiments showed that METTL3 knockdown reduced MM tumor growth by decreasing BZW2 expression. In conclusion, these data indicated that METTL3-mediated the m6A methylation of BZW2 to promote MM progression, suggesting a novel therapeutic target for MM.