N-acetyltransferase NAT10 controls cell fates via connecting mRNA cytidine acetylation to chromatin signaling

N-acetyltransferase 10 promotes glioblastoma malignancy via mRNA stabilization of Jumonji and AT-rich interaction domain containing 2

Glioblastoma (GBM) is the most common and aggressive form of malignant brain cancer, with a poor prognosis and a five-year survival rate of approximately 15%. The malignancy of GBM, including its treatment resistance and high recurrence rate, is largely attributed to the presence of cancer stem cells. Recent studies have identified the N-acetyltransferase 10 (NAT10), an enzyme responsible for catalyzing N4-acetylcytidine (ac4C) modification in RNA, as a key factor in cancer biology, with diverse roles across multiple cancer types. However, the specific contribution of this RNA modification to the malignancy of GBM remains unexplored. Here, we demonstrate that NAT10 expression is associated with poor prognosis in GBM patients and that NAT10 promotes GBM malignancy by enhancing stemness properties in human GBM cell line U251 and A172. A search for the underlying mechanism of NAT10-mediated enhancement of GBM stemness led to identification of polycomb repressive complex 2 (PRC2)-related genes as an epigenetic regulator. NAT10 mediates the acetylation of the coding region of Jumonji and AT-rich Interaction Domain containing 2 (JARID2) mRNA, which results in increased mRNA stability and elevated protein levels. Notably, knockdown of JARID2 significantly reduced GBM stemness, suppressed tumor growth, and extended the survival of xenograft mice. Our findings suggest that NAT10-mediated acetylation of JARID2 mRNA up-regulates its protein levels, thereby promoting stemness and contributing to the malignancy of GBM. Targeting this NAT10-JARID2 axis may represent a novel therapeutic approach for treatment of GBM.

Nat10-mediated N4-acetylcytidine modification enhances Nfatc1 translation to exacerbate osteoclastogenesis in postmenopausal osteoporosis

Increased differentiation or activity of osteoclasts is the key pathogenic factor of postmenopausal osteoporosis (PMOP). N4-acetylcytidine (ac4C) modification, catalyzed by Nat10, is a novel posttranscriptional mRNA modification related to many diseases. However, its impact on regulating osteoclast activation in PMOP remains uncertain. Here, we initially observed that Nat10-mediated ac4C positively correlates with osteoclast differentiation of monocytes and low bone mass in PMOP. The specific knockout of Nat10 in monocytes and remodelin, a Nat10 inhibitor, alleviates ovariectomized (OVX)-induced bone loss by downregulating osteoclast differentiation. Mechanistically, epitranscriptomic analyses reveal that the nuclear factor of activated T cells cytoplasmic 1 (Nfatc1) is the key downstream target of ac4C modification during osteoclast differentiation. Subsequently, translatomic results demonstrate that Nat10-mediated ac4C enhances the translation efficiency (TE) of Nfatc1, thereby inducing Nfatc1 expression and consequent osteoclast maturation. Cumulatively, these findings reveal the promotive role of Nat10 in osteoclast differentiation and PMOP from a novel field of RNA modifications and suggest that Nat10 can be a target of epigenetic therapy for preventing bone loss in PMOP.

Endoplasmic Reticulum Stress in Acute Myeloid Leukemia: Pathogenesis, Prognostic Implications, and Therapeutic Strategies

Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy that poses a significant therapeutic challenge due to its high recurrence rate and demanding treatment regimens. Increasing evidence suggests that endoplasmic reticulum (ER) stress and downstream activation of the unfolded protein response (UPR) pathway play a key role in the pathogenesis of AML. ER stress is triggered by the accumulation of misfolded or unfolded proteins within the ER. This causes activation of the UPR to restore cellular homeostasis. However, the UPR can shift from promoting survival to inducing apoptosis under prolonged or excessive stress conditions. AML cells can manipulate the UPR pathway to evade apoptosis, promoting tumor progression and resistance against various therapeutic strategies. This review provides the current knowledge on ER stress in AML and its prognostic and therapeutic implications.

N-acetyltransferase 10 catalyzes RNA N4-acetylcytidine to regulate photosynthesis in rice

N4-acetylcytidine (ac4C) is a novel mRNA modification that enhances RNA stability and translation in mammals and plants. We previously identified ac4C in Arabidopsis, introduced by two homologs of human N-acetyltransferase 10 (NAT10). While ac4C influences leaf development in Arabidopsis, its role in rice is unclear. In this study, we identify OsNAT10 as the ac4C writer in rice. osnat10 mutants show developmental defects, including shorter roots, fewer tillers, and lower yield. Compared with wild type, ac4C-modified genes are less abundant in osnat10, particularly those related to photosynthesis. Additionally, osnat10 exhibits decreased photosynthetic capacity and reduced RNA stability and translation efficiency of ac4C target genes, like LIGHT-INDUCED RICE 1 (LIR1). Overexpressing OsLIR1 partially rescues osnat10 defects, underscoring OsNAT10's role in photosynthesis regulation. Our findings highlight ac4C's crucial function in photosynthesis and plant development, offering insights into epitranscriptomic modifications for crop improvement.

NAT10-mediated N4-acetylcytidine modification in KLF9 mRNA promotes adipogenesis

Dysfunctional adipogenesis is a major contributor of obesity. N-acetyltransferase 10 (NAT10) plays a crucial role in regulating N4-acetylcysteine (ac4C) modification in tRNA, 18SrRNA, and mRNA. As the sole "writer" in the ac4C modification process, NAT10 enhances mRNA stability and translation efficiency. There are few reports on the relationship between NAT10 and adipogenesis, as well as obesity. Our study revealed a significant upregulation of NAT10 in adipose tissues of obese individuals and high-fat diet-fed mice. Furthermore, our findings revealed that the overexpression of NAT10 promotes adipogenesis, while its silencing inhibits adipogenesis in both human adipose tissue-derived stem cells (hADSCs) and 3T3-L1 cells. These results indicate the intimate relationship between NAT10 and obesity. After silencing mouse NAT10 (mNAT10), we identified 30 genes that exhibited both hypo-ac4C modification and downregulation in their expression, utilizing a combined approach of acRIP-sequencing (acRIP-seq) and RNA-sequencing (RNA-seq). Among these genes, we validated KLF9 as a target of NAT10 through acRIP-PCR. KLF9, a pivotal transcription factor that positively regulates adipogenesis. Our findings showed that NAT10 enhances the stability of KLF9 mRNA and further activates the CEBPA/B-PPARG pathway. Furthermore, a dual-luciferase reporter assay demonstrated that NAT10 can bind to three motifs of mouse KLF9 and one motif of human KLF9. In vivo studies revealed that adipose tissue-targeted mouse AAV-NAT10 (AAV-shRNA-mNAT10) inhibits adipose tissue expansion in mice. Additionally, Remodelin, a specific NAT10 inhibitor, significantly reduced body weight, adipocyte size, and adipose tissue expansion in high-fat diet-fed mice by inhibiting KLF9 mRNA ac4C modification. These findings provide novel insights and experimental evidence of the prevention and treatment of obesity, highlighting NAT10 and its downstream targets as potential therapeutic targets.

Unveiling ac4C modification pattern: a prospective target for improving the response to immunotherapeutic strategies in melanoma

Emerging evidence has confirmed the inextricable connection between N4-acetylcytidine (ac4C) mRNA modification and the clinical characteristics of malignancies. Nonetheless, it is uncertain whether and how ac4C mRNA modification patterns affect clinical outcomes in melanoma patients. This research integrated single-cell sequencing data and transcriptomics to pinpoint ac4C-related genes (acRG) linked to melanoma progression and evaluate their clinical implications. Cells with elevated acRG score were predominantly located within the melanocytes cluster. Intercellular communications between melanocytes and other cell subtypes were markedly strengthened in the acRG-high group. We developed and confirmed an excellent acRG-related signature (acRGS) utilizing a comprehensive set of 101 algorithm combinations derived from 10 machine learning algorithms. Hereby, the acRGS, including MYO10, ZNF667, MRAS, SCO2, MAPK10, PNMA6A, KPNA2, NT5DC2, BAIAP2L2 and NDST3, delineated ac4C-associated mRNA modification patterns in melanoma. The acRGS possesses distinctly superior performance to 120 previously reported signatures in melanoma and could predict the overall survival of melanoma patients across four external datasets. The substantial associations among immune checkpoint genes, immune cell infiltration, and tumor mutation burden with acRGS indicate that acRGS is helpful in identifying melanoma patients who are sensitive to immunotherapy. Besides, we confirmed that MYO10 was mainly overexpressed in melanoma tissues, and elevated MYO10 was positively correlated with malignant phenotypes and unfavorable prognosis in melanoma patients. Silencing MYO10 expression inhibited melanoma cell proliferation, migration and invasion in vitro as well as tumor growth in vivo. Taken together, the acRGS could function as a reliable and prospective tool to improve the clinical prognosis for melanoma individuals.

RNA cytidine acetyltransferase NAT10 maintains T cell pathogenicity in inflammatory bowel disease

The emerging field of epitranscriptomics is reshaping our understanding of post-transcriptional gene regulation in inflammatory diseases. N4-acetylcytidine (ac4C), the only known acetylation modification in RNA catalyzed by N-acetyltransferase 10 (NAT10), is known to enhance mRNA stability and translation, yet its role in inflammatory bowel disease (IBD) remains unclear. In this study, we discovered that Nat10 expression correlates with inflammatory and apoptotic pathways in human ulcerative colitis CD4+ T cells. Our further analysis revealed that the deficiency of NAT10 led to a disruption of T cell development at steady state, and identified a pivotal role for NAT10 in preserving the pathogenicity of naïve CD4+ T cells to induce adoptive transfer colitis. Mechanistically, the lack of NAT10 triggers the diminished stability of the anti-apoptotic gene BCL2-associated athanogene 3 (Bag3), initiating a cascade of events that includes the upregulation of apoptosis-related genes and an accelerated rate of apoptosis in T cells. Our findings reveal a previously unrecognized role of the NAT10-ac4C-Bag3 axis in preserving T cell balance and suggests that targeting RNA ac4C modification could be a promising therapeutic approach for IBD.

Metabolism Meets Translation: Dietary and Metabolic Influences on tRNA Modifications and Codon Biased Translation

Transfer RNA (tRNA) is not merely a passive carrier of amino acids, but an active regulator of mRNA translation controlling codon bias and optimality. The synthesis of various tRNA modifications is regulated by many "writer" enzymes, which utilize substrates from metabolic pathways or dietary sources. Metabolic and bioenergetic pathways, such as one-carbon (1C) metabolism and the tricarboxylic acid (TCA) cycle produce essential substrates for tRNA modifications synthesis, such as S-Adenosyl methionine (SAM), sulfur species, and α-ketoglutarate (α-KG). The activity of these metabolic pathways can directly impact codon decoding and translation via regulating tRNA modifications levels. In this review, we discuss the complex interactions between diet, metabolism, tRNA modifications, and mRNA translation. We discuss how nutrient availability, bioenergetics, and intermediates of metabolic pathways, modulate the tRNA modification landscape to fine-tune protein synthesis. Moreover, we highlight how dysregulation of these metabolic-tRNA interactions contributes to disease pathogenesis, including cancer, metabolic disorders, and neurodegenerative diseases. We also discuss the new emerging field of GlycoRNA biology drawing parallels from glycobiology and metabolic diseases to guide future directions in this area. Throughout our discussion, we highlight the links between specific modifications, their metabolic/dietary precursors, and various diseases, emphasizing the importance of a metabolism-centric tRNA view in understanding many pathologies. Future research should focus on uncovering the interplay between metabolism and tRNA in specific cellular and disease contexts. Addressing these gaps will guide new research into novel disease interventions.

NAT10-mediated mRNA N4-acetylation is essential for the translational regulation during oocyte meiotic maturation in mice

The precise translational regulation of maternal messenger RNAs (mRNAs) drives mammalian oocyte maturation. However, the function and mechanism of posttranscriptional chemical modifications, especially the newly identified N4-acetylcytidine (ac4C) modification catalyzed by N-acetyltransferase 10 (NAT10), are unknown. In this study, we developed a low-input ac4C sequencing technology, ac4C LACE-seq, and mapped 8241 ac4C peaks at the whole-transcriptome level using 50 mouse oocytes at the germinal vesicle stage. Oocyte-specific Nat10 knockout wiped out ac4C signals in oocytes and caused severe defects in meiotic maturation and female infertility. Mechanically, Nat10 deletion led to a failure of ac4C deposition on mRNAs encoding key maternal factors, which regulate transcriptome stability and maternal-to-zygotic transition. Nat10-deleted oocytes showed decreased mRNA translation efficiency due to the direct inhibition of ac4C sites on specific transcripts during meiotic maturation. In summary, we developed a low-input, high-sensitivity mRNA ac4C profiling approach and highlighted the important physiological function of ac4C in the precise regulation of oocyte meiotic maturation by enhancing translation efficiency.

Glucose homeostasis controls N-acetyltransferase 10-mediated ac4C modification of HK2 to drive gastric tumorigenesis

Rationale: Abnormal metabolic states contribute to a variety of diseases, including cancer. RNA modifications have diverse biological functions and are implicated in cancer development, including gastric cancer (GC). However, the direct relationship between glucose homeostasis and 4-acetylcytosine (ac4C) modification in GC remains unclear. Methods: The prognostic value of RNA acetyltransferase NAT10 expression was evaluated in a human GC cohort. Additionally, preoperative PET/CT data from GC patients and Micro-PET/CT imaging of mice were employed to assess the relationship between NAT10 and glucose metabolism. The biological role of NAT10 in GC was investigated through various experiments, including GC xenografts, organoids, and a conditional knockout (cKO) mouse model. The underlying mechanisms were examined using dot blotting, immunofluorescence staining, co-immunoprecipitation, and high-throughput sequencing, among other techniques. Results: Glucose deprivation activates the autophagy-lysosome pathway, leading to the degradation of NAT10 by enhancing its interaction with the sequestosome 1 (SQSTM1)/microtubule-associated protein 1 light chain 3 alpha (LC3) complex, ultimately resulting in a reduction of ac4C modification. Furthermore, the levels of ac4C and NAT10 are elevated in GC tissues and correlate with poor prognosis. A strong correlation exists between NAT10 levels and 18F-FDG uptake in GC patients. Furthermore, NAT10 drives glycolytic metabolism and gastric carcinogenesis in vitro and in vivo. Mechanistically, NAT10 stimulates ac4C modification at the intersection of the coding sequence (CDS) and 3' untranslated region (3'UTR) of hexokinase 2 (HK2) mRNA, enhancing its stability and activating the glycolytic pathway, thereby driving gastric tumorigenesis. Conclusion: Our findings highlight the critical crosstalk between glucose homeostasis and the ac4C epitranscriptome in gastric carcinogenesis. This finding offers a potential strategy of targeting NAT10/HK2 axis for the treatment of GC patients, especially those with highly active glucose metabolism.

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

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

Dynamics and necessity of SIRT1 for maternal-zygotic transition

Dynamic changes in maternal‒zygotic transition (MZT) require complex regulation of zygote formation, maternal transcript decay, embryonic genome activation (EGA), and cell cycle progression. Although these changes are well described, some key regulatory factors are still elusive. Sirtuin-1 (SIRT1), an NAD+-dependent histone deacetylase, is a versatile driver of MZT via its epigenetic and nonepigenetic substrates. This study focused on the dynamics of SIRT1 in early embryos and its contribution to MZT. A conditional SIRT1-deficient knockout mouse model was used, accompanied by porcine and human embryos. Embryos across mammalian species showed the prominent localization of SIRT1 in the nucleus throughout early embryonic development. Accordingly, SIRT1 interacts with histone H4 on lysine K16 (H4K16) in both mouse and human blastocysts. While maternal SIRT1 is dispensable for MZT, at least one allele of embryonic Sirt1 is required for early embryonic development around the time of EGA. This role of SIRT1 is surprisingly mediated via a transcription-independent mode of action.

NAT10 and cytidine acetylation in mRNA: intersecting paths in development and disease

N4-acetylcytidine (ac4C) is an RNA modification that is catalyzed by the enzyme NAT10. Constitutively found in tRNA and rRNA, ac4C displays a dynamic presence in mRNA that is shaped by developmental and induced shifts in NAT10 levels. However, deciphering ac4C functions in mRNA has been hampered by its context-dependent influences in translation and the complexity of isolating effects on specific mRNAs from other NAT10 activities. Recent advances have begun to overcome these obstacles by leveraging natural variations in mRNA acetylation in cancer, developmental transitions, and immune responses. Here, we synthesize the current literature with a focus on nuances that may fuel the perception of cellular discrepancies toward the development of a cohesive model of ac4C function in mRNA.

STM-ac4C: a hybrid model for identification of N4-acetylcytidine (ac4C) in human mRNA based on selective kernel convolution, temporal convolutional network, and multi-head self-attention

N4-acetylcysteine (ac4C) is a chemical modification in mRNAs that alters the structure and function of mRNA by adding an acetyl group to the N4 position of cytosine. Researchers have shown that ac4C is closely associated with the occurrence and development of various cancers. Therefore, accurate prediction of ac4C modification sites on human mRNA is crucial for revealing its role in diseases and developing new diagnostic and therapeutic strategies. However, existing deep learning models still have limitations in prediction accuracy and generalization ability, which restrict their effectiveness in handling complex biological sequence data. This paper introduces a deep learning-based model, STM-ac4C, for predicting ac4C modification sites on human mRNA. The model combines the advantages of selective kernel convolution, temporal convolutional networks, and multi-head self-attention mechanisms to effectively extract and integrate multi-level features of RNA sequences, thereby achieving high-precision prediction of ac4C sites. On the independent test dataset, STM-ac4C showed improvements of 1.81%, 3.5%, and 0.37% in accuracy, Matthews correlation coefficient, and area under the curve, respectively, compared to the existing state-of-the-art technologies. Moreover, its performance on additional balanced and imbalanced datasets also confirmed the model's robustness and generalization ability. Various experimental results indicate that STM-ac4C outperforms existing methods in predictive performance. In summary, STM-ac4C excels in predicting ac4C modification sites on human mRNA, providing a powerful new tool for a deeper understanding of the biological significance of mRNA modifications and cancer treatment. Additionally, the model reveals key sequence features that influence the prediction of ac4C sites through sequence region impact analysis, offering new perspectives for future research. The source code and experimental data are available at https://github.com/ymy12341/STM-ac4C.

ac4C: a fragile modification with stabilizing functions in RNA metabolism

In recent years, concerted efforts to map and understand epitranscriptomic modifications in mRNA have unveiled new complexities in the regulation of gene expression. These studies cumulatively point to diverse functions in mRNA metabolism, spanning pre-mRNA processing, mRNA degradation, and translation. However, this emerging landscape is not without its intricacies and sources of discrepancies. Disparities in detection methodologies, divergent interpretations of functional outcomes, and the complex nature of biological systems across different cell types pose significant challenges. With a focus of N4-acetylcytidine (ac4C), this review endeavors to unravel conflicting narratives by examining the technological, biological, and methodological factors that have contributed to discrepancies and thwarted research progress. Our goal is to mitigate detection inconsistencies and establish a unified model to elucidate the contribution of ac4C to mRNA metabolism and cellular equilibrium.

Super enhancer related gene ANP32B promotes the proliferation of acute myeloid leukemia by enhancing MYC through histone acetylation

BACKGROUND

Acute myeloid leukemia (AML) is a malignancy of the hematopoietic system, and childhood AML accounts for about 20% of pediatric leukemia. ANP32B, an important nuclear protein associated with proliferation, has been found to regulate hematopoiesis and CML leukemogenesis by inhibiting p53 activity. However, recent study suggests that ANP32B exerts a suppressive effect on B-cell acute lymphoblastic leukemia (ALL) in mice by activating PU.1. Nevertheless, the precise underlying mechanism of ANP32B in AML remains elusive.

RESULTS

Super enhancer related gene ANP32B was significantly upregulated in AML patients. The expression of ANP32B exhibited a negative correlation with overall survival. Knocking down ANP32B suppressed the proliferation of AML cell lines MV4-11 and Kasumi-1, along with downregulation of C-MYC expression. Additionally, it led to a significant decrease in H3K27ac levels in AML cell lines. In vivo experiments further demonstrated that ANP32B knockdown effectively inhibited tumor growth.

CONCLUSIONS

ANP32B plays a significant role in promoting tumor proliferation in AML. The downregulation of ANP32B induces cell cycle arrest and promotes apoptosis in AML cell lines. Mechanistic analysis suggests that ANP32B may epigenetically regulate the expression of MYC through histone H3K27 acetylation. ANP32B could serve as a prognostic biomarker and potential therapeutic target for AML patients.