SAMTOR is an S-adenosylmethionine sensor for the mTORC1 pathway

The role of branched chain aminotransferase in the interrelated pathways of type 2 diabetes mellitus and Alzheimer's disease

Objectives

This review assessed the role of Branched-Chain Amino Acid Transaminase (BCAT) enzymes in human metabolism, and their involvement in the catabolism of branched-chain amino acids (BCAAs) and exploring the association between Type 2 Diabetes Mellitus (T2DM) and Alzheimer's disease (AD) through insulin resistance.

Methods

The analysis involves a comprehensive literature review of recent research findings related to BCAT enzymes, BCAA metabolism, T2DM, and AD. Relevant studies and articles were identified through systematic searches in databases such as PubMed, ScienceDirect, and other scholarly resources. Inclusion criteria encompassed research articles, reviews, and studies published in peer-reviewed journals, with a focus on human metabolism, BCAT enzymes, and the interplay between BCAA metabolism, T2DM, and AD.

Results

The association between T2DM and AD suggests a potential metabolic link, particularly through dysregulated BCAA metabolism leading to insulin resistance. The impact of impaired insulin signaling is implicated in brain function and the accumulation of amyloid plaques facilitated by BCAT.

Conclusion

The identified link between BCAT, BCAA metabolism, T2DM, and AD suggests that disruptions in BCAT levels could serve as valuable indicators for early detection of insulin resistance and cognitive impairment as observed in Type 3 Diabetes which may present a promising therapeutic target.

The Molecular Basis of Amino Acids Sensing

Amino acids are organic compounds that serve as the building blocks of proteins and peptides. Additionally, they function as bioactive molecules that play important roles in metabolic regulation and signal transduction. The ability of cells to sense fluctuations in intracellular and extracellular amino acid levels is vital for effectively regulating protein synthesis and catabolism, maintaining homeostasis, adapting to diverse nutritional environments and influencing cell fate decision. In this review, the recent molecular insights into amino acids sensing are discussed, along with the different sensing mechanisms in distinct organisms.

mTOR inhibitors in targeting autophagy and autophagy-associated signaling for cancer cell death and therapy

The mechanistic target of rapamycin (mTOR) is a protein kinase that plays a central regulatory switch to control multifaceted cellular processes, including autophagy. As a nutrient sensor, mTOR inhibits autophagy by phosphorylating and inactivating key regulators, including ULK1, Beclin-1, UVRAG, and TFEB, preventing autophagy initiation and lysosomal biogenesis. It also suppresses autophagy-related protein expression, prioritizing growth over cellular recycling. Under nutrient deprivation, mTORC1 activity decreases, allowing autophagy to restore cellular homeostasis. Hyperautophagic activities lead to autophagic cell death; sometime after the point of no return, the cell goes for non-apoptotic, non-necrotic cell death i.e., Autosis. In cancer, the crosstalk between autophagy and mTOR is context-dependent, driving either cell survival or autophagy-dependent cell death. Using mTOR inhibitors, autophagic cell death can be induced to regulate cell growth, and proliferation is a potential therapeutic option for cancer treatment. mTOR inhibitors are broadly categorized into two types, i.e., natural and synthetic mTOR inhibitors. Although several studies in preclinical and clinical trials of various synthetic mTOR inhibitors are now in focus for cancer therapies, limited work has been done to explore autophagic cell death-inducing mTOR inhibitors. In addition, many natural mTOR inhibitors display better efficacy over synthetic mTOR inhibitors due to their lower toxicity, biocompatibility, and potential to overcome drug resistance in inducing autophagic cell death for cancer treatment.

Vitamin B12 in Cell Plasticity and Repair

Cellular plasticity, which refers to the capacity of cells to alter their identity or potency in response to a variety of stimuli, is emerging as an essential component in tissue repair. Despite the fact that stem cells have historically been considered to be the major agents of plasticity, new research has demonstrated that even differentiated cells in organs including the stomach, pancreas, and lungs are capable of displaying plasticity under specific physiological conditions, such as during injury and repair. One element essential for many physiological processes is vitamin B12 (VB12). Beyond its well-known roles in red blood cell production and nervous system maintenance, VB12 is critical for one-carbon metabolism and DNA synthesis and repair, processes indispensable for cellular health and tissue integrity. With its wide spectrum of actions, VB12 may have the potential to significantly influence tissue plasticity and repair, paving the way for new therapeutic interventions. Investigating fundamental processes and considering consequences for illness and aging, this perspective contemplates the junction of VB12, cell plasticity, and tissue repair.

Methionine in embryonic development: metabolism, redox homeostasis, epigenetic modification and signaling pathway

Methionine, an essential sulfur-containing amino acid, plays a critical role in methyl metabolism, folate metabolism, polyamine synthesis, redox homeostasis maintenance, epigenetic modification and signaling pathway regulation, particularly during embryonic development. Animal and human studies have increasingly documented that methionine deficiency or excess can negatively impact metabolic processes, translation, epigenetics, and signaling pathways, with ultimate detrimental effects on pregnancy outcomes. However, the underlying mechanisms by which methionine precisely regulates epigenetic modifications and affects signaling pathways remain to be elucidated. In this review, we discuss methionine and the metabolism of its metabolites, the influence of folate-mediated carbon metabolism, redox reactions, DNA and RNA methylation, and histone modifications, as well as the mammalian rapamycin complex and silent information regulator 1-MYC signaling pathway. This review also summarizes our present understanding of the contribution of methionine to these processes, and current nutritional and pharmaceutical strategies for the prevention and treatment of developmental defects in embryos.

The Amelioration of Methionine Restriction on the Celiac Toxic Effects of p31-43 Gliadin Peptide Is Disrupted by S-Adenosyl-Methionine

Methionine restriction (MR) has been found to alleviate the progression of diseases such as cognitive disorders and cancer, but it is not clear whether regulating methionine availability can have a beneficial effect on wheat gluten-induced celiac disease. We aimed to excavate the effects of MR on the celiac toxic effects of p31-43 gliadin peptide. In this study, we systematically investigated the effects of MR on p31-43 gliadin peptide-induced oxidative damage, the elevation of tissue transglutaminase enzyme activity, the overexpression of inflammatory factors, the increase of permeability, and T-lymphocyte dysfunction by utilizing Caco-2 epithelial cells and lymphocytes derived from mouse mesenteric lymph nodes to elucidate the effectiveness of MR. Moreover, the potential mechanism of MR on innate and adaptive immune regulation was explored with the help of S-adenosyl-methionine (SAM), a critical metabolic intermediate in methionine cycle. We discovered that MR effectively suppressed the celiac toxic effects of p31-43 gliadin peptide. Furthermore, we illustrated the controlling role of SAM in MR to regulate the toxic effects of gliadin in terms of both gliadin-induced innate and adaptive immune responses and found that SAM could directly affect the effectiveness of MR. This study might offer novel insights for the utilization of MR in celiac disease (such as MR interventions or gluten-free diets with specific methionine content) as well as the roles of SAM in MR.

S-adenosylmethionine deficit disrupts very low-density lipoprotein metabolism promoting liver lipid accumulation in mice

Hepatic deletion of methionine adenosyltransferase-1a (Mat1a) in mice reduces S-adenosylmethionine (SAMe), a key methyl donor essential for many biological processes, which promotes the development and progression of metabolic dysfunction-associated steatotic liver disease (MASLD). Hyperglycemia and reduced MAT1A expression, along with low SAMe levels, are common in MASLD patients. This study explores how Mat1a-knockout (KO) hepatocytes respond to prolonged high glucose conditions, focusing on glucose metabolism and lipid accumulation. Hepatocytes from methionine adenosyltransferase-1a-knockout (Mat1a-KO) mice were incubated in high glucose conditions overnight, allowing for analysis of key metabolic intermediates and gene expression related to glycolysis, gluconeogenesis, glyceroneogenesis, phospholipid synthesis, and very low density lipoprotein (VLDL) secretion. SAMe deficiency in Mat1a-KO hepatocytes led to reduced protein methyltransferase-1 activity, resulting in increased expression of glycolytic enzymes (glucokinase, phosphofructokinase, and pyruvate kinase) and decreased expression of gluconeogenic enzymes (phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase, and glucose-6-phosphatase). These alterations led to a reduction in dihydroxyacetone phosphate (DHAP), which subsequently inhibited mammalian target of rapamycin complex 1 (mTORC1) activity. This inhibition resulted in decreased phosphatidylcholine synthesis via the CDP-choline pathway and impaired VLDL secretion, ultimately causing lipid accumulation. Thus, under high glucose conditions, SAMe deficiency in hepatocytes depletes DHAP, inhibits mTORC1 activity, and promotes lipid buildup.

Citrulline regulates macrophage metabolism and inflammation to counter aging in mice

Metabolic dysregulation and altered metabolite concentrations are widely recognized as key characteristics of aging. Comprehensive exploration of endogenous metabolites that drive aging remains insufficient. Here, we conducted an untargeted metabolomics analysis of aging mice, revealing citrulline as a consistently down-regulated metabolite associated with aging. Systematic investigations demonstrated that citrulline exhibited antiaging effects by reducing cellular senescence, protecting against DNA damage, preventing cell cycle arrest, modulating macrophage metabolism, and mitigating inflammaging. Long-term citrulline supplementation in aged mice yielded beneficial effects and ameliorated age-associated phenotypes. We further elucidated that citrulline acts as an endogenous metabolite antagonist to inflammation, suppressing proinflammatory responses in macrophages. Mechanistically, citrulline served as a potential inhibitor of mammalian target of rapamycin (mTOR) activation in macrophage and regulated the mTOR-hypoxia-inducible factor 1α-glycolysis signaling pathway to counter inflammation and aging. These findings underscore the significance of citrulline deficiency as a driver of aging, highlighting citrulline supplementation as a promising therapeutic intervention to counteract aging-related changes.

A cellular and molecular basis of leptin resistance

Similar to most humans with obesity, diet-induced obese (DIO) mice have high leptin levels and fail to respond to the exogenous hormone, suggesting that their obesity is caused by leptin resistance, the pathogenesis of which is unknown. We found that leptin treatment reduced plasma levels of leucine and methionine, mTOR-activating ligands, leading us to hypothesize that chronic mTOR activation might reduce leptin signaling. Rapamycin, an mTOR inhibitor, reduced fat mass and increased leptin sensitivity in DIO mice but not in mice with defects in leptin signaling. Rapamycin restored leptin's actions on POMC neurons and failed to reduce the weight of mice with defects in melanocortin signaling. mTOR activation in POMC neurons caused leptin resistance, whereas POMC-specific mutations in mTOR activators decreased weight gain of DIO mice. Thus, increased mTOR activity in POMC neurons is necessary and sufficient for the development of leptin resistance in DIO mice, establishing a key pathogenic mechanism leading to obesity.

Mutation of an insulin-sensitive Drosophila insulin-like receptor mutant requires methionine metabolism reprogramming to extend lifespan

Insulin/insulin growth factor signaling is a conserved pathway that regulates lifespan across many species. Multiple mechanisms are proposed for how this altered signaling slows aging. To elaborate these causes, we recently developed a series of Drosophila insulin-like receptor (dInr) mutants with single amino acid substitutions that extend lifespan but differentially affect insulin sensitivity, growth and reproduction. Transheterozygotes of canonical dInr mutants (Type I) extend longevity and are insulin-resistant, small and weakly fecund. In contrast, a dominant mutation (dInr 353, Type II) within the Kinase Insert Domain (KID) robustly extends longevity but is insulin-sensitive, full-sized, and highly fecund. We applied transcriptome and metabolome analyses to explore how dInr 353 slows aging without insulin resistance. Type I and II mutants overlap in many pathways but also produce distinct transcriptomic profiles that include differences in innate immune and reproductive functions. In metabolomic analyses, the KID mutant dInr 353 reprograms methionine metabolism in a way that phenocopies dietary methionine restriction, in contrast to canonical mutants which are characterized by upregulation of the transsulfuration pathway. Because abrogation of S-adenosylhomocysteine hydrolase blocks the longevity benefit conferred by dInr 353, we conclude the methionine cycle reprogramming of Type II is sufficient to slow aging. Metabolomic analysis further revealed the Type II mutant is metabolically flexible: unlike aged wildtype, aged dInr 353 adults can reroute methionine toward the transsulfuration pathway, while Type I mutant flies upregulate the trassulfuration pathway continuously from young age. Altered insulin/insulin growth factor signaling has the potential to slow aging without the complications of insulin resistance by modulating methionine cycle dynamics.

Evidence for interaction of 5,10-methylenetetrahydrofolate reductase (MTHFR) with methylenetetrahydrofolate dehydrogenase (MTHFD1) and general control nonderepressible 1 (GCN1)

5,10-Methylenetetrahydrofolate reductase (MTHFR) is a folate cycle enzyme required for the intracellular synthesis of methionine. MTHFR was previously shown to be partially phosphorylated at 16 residues, which was abrogated by conversion of threonine 34 to alanine (T34A) or truncation of the first 37 amino acids (i.e. expression of amino acids 38-656), and promoted by methionine supplementation. Here, we over-expressed wild-type MTHFR (MTFHRWT), as well as the variants MTHFRT34A and MTHFR38-656 in 293T cells to provide further insights into these mechanisms. We demonstrate that following incubation in high methionine conditions (100-1000 μM) MTHFRWT is almost completely phosphorylated, but in methionine restricted conditions (0-10 μM) phosphorylation is reduced, while MTHFRT34A always remains unphosphorylated. Following affinity purification coupled mass spectrometry of an empty vector, MTHFRWT, MTHFRT34A and MTHFR38-656 in three separate experiments, we identified 134 proteins consistently pulled-down by all three MTHFR protein variants, of which 5 were indicated to be likely true interactors (SAINT prediction threshold of 0.95 and 2 fold-change). Amongst these were the folate cycle enzyme methylenetetrahydrofolate dehydrogenase (MTHFD1) and the amino acid starvation sensor general control nonderepressible 1 (GCN1). Immunoprecipitation-immunoblotting of MTHFRWT replicated interaction with both proteins. An AlphaFold 3 generated model of the MTHFR-MTHFD1 interaction places the MTHFD1 dehydrogenase/cyclohydrolase domain in direct contact with the MTHFR catalytic domain, suggesting their interaction may facilitate direct delivery of methylenetetrahydrofolate. Overall, we confirm methionine availability increases MTHFR phosphorylation, and identified potential interaction of MTHFR with MTHFD1 and GCN1.

Serum metabolomics analysis reveals a novel association between maternal metabolism and fetal survival in sows fed diets containing differing methionine levels and sources

Methionine (Met) metabolism is vital for one carbon metabolism, redox status and fetal development. Hence, this study investigated the effects of different levels and sources of Met on maternal metabolism, anti-oxidative capacity and fetal survival in pregnant sows. Forty primiparous sows were assigned to the following four groups: control group (basal diet, CON), 1.5S-OHMet group (supplemented methionine hydroxy analogue [OHMet] at 1.5 g/kg diet), 3.0S-OHMet group (supplemented OHMet at 3.0 g/kg diet), and 3.0S-Met group (supplemented L-Met at 3.0 g/kg diet) (n = 10). The trial lasted from day 60 of gestation to the farrowing day. Maternal 1.5S-OHMet consumption had the lowest stillborn ratio and the highest serum glucose levels during farrowing. Further analysis revealed that dietary 1.5S-OHMet consumption elevated the serum contents of glucose-6-phosphate, citric acid, butyric acid, malic acid, 3-methyladenine, 1-methyladenosine, ferulic acid and salicylic acid, but reduced the serum contents of succinic acid, oxoglutaric acid, 9(S)-hydroperoxylinoleic acid, 13(S)-hydroperoxy-octadecatrienoic acid, uric acid and urea nitrogen when compared to contents observed in the 3.0S-OHMet and 3.0S-Met groups (P < 0.05). Serum metabolomics analysis was conducted to determine the enriched differential metabolites and an enrichment analysis was performed using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The results showed that the enriched metabolites were mainly associated with central carbon metabolism, amino acid metabolism, lipid metabolism, and nucleotide metabolism. Moreover, maternal 3.0S-OHMet or 3.0S-Met consumption upregulated the trans-methylation pathway by elevating the S-adenosyl-methionine (SAM) level and the ratio of SAM to S-adenosyl-homocysteine (P < 0.05) at day 114 of gestation, while increasing homocysteine concentration (P < 0.001). However, compared to the 3.0S-Met group, maternal 3.0S-OHMet consumption elevated fetal survival and glutathione peroxidase (P < 0.05). Thus, this study provided new insights into the mechanisms through which sows fed with a 1.5S-OHMet diet during mid-to late-gestation period had high fetal survival, such as improvements in maternal amino acid, nucleotide and glycolipid metabolism.

Mechanisms and rationales of SAM homeostasis

S-Adenosylmethionine (SAM) is the primary methyl donor for numerous cellular methylation reactions. Its central role in methylation and involvement with many pathways link its availability to the regulation of cellular processes, the dysregulation of which can contribute to disease states, such as cancer or neurodegeneration. Emerging evidence indicates that intracellular SAM levels are maintained within an optimal range by a variety of homeostatic mechanisms. This suggests that the need to maintain SAM homeostasis represents a significant evolutionary pressure across all kingdoms of life. Here, we review how SAM controls cellular functions at the molecular level and discuss strategies to maintain SAM homeostasis. We propose that SAM exerts a broad and underappreciated influence in cellular regulation that remains to be fully elucidated.

Pectin-Zein-IPA nanoparticles promote functional recovery and alleviate neuroinflammation after spinal cord injury

INTRODUCTION

Spinal cord injury (SCI) impairs the balance of gut microbiomes, which further aggravates inflammation in the injured areas and inhibits axonal regeneration. The intestinal microbiome plays an important role in SCI and regulating intestinal microbiome promotes SCI repair. However, current studies have shown that indole-3 propionate (IPA), a metabolite of gut bacteria, can promote axonal regeneration. However, the short half-life of IPA limits its effectiveness. Gut microbiota plays a role in the progression of SCI, but the studies about diet regulates intestinal flora metabolites to improve SCI are still limited and lack guiding significance.

RESULTS

The results showed that Pectin-Zein-IPA NPs treatment improves motor function recovery, inhibits the activation of oxidative stress, enhances axonal regeneration and activates AKT/Nrf-2 signaling pathway following SCI. Further analysis showed that Pec-Zein-IPA NPs treatment reduced the intestinal flora metabolite accumulation of L-methionine, and alleviated neuroinflammation by improving autophagy and inhibiting pyroptosis. Pec-Zein-IPA may reduced neuroinflammation after SCI by decreasing the abundance of Clostridia-UCG-014, Clostridia-vadinBB60-group, Shewanella (positively correlated with L-Methionine) and increasing the abundance of Parasutterella (negatively correlated with L-Methionine).

CONCLUSIONS

Our findings provide a strategy for oral drug research in SCI. The results suggest that Pectin-Zein-IPA NPs have potential advantages for treatment and management of SCI. Reducing L-methionine intake may help reduce neuroinflammation after SCI.

Non-dikarya fungi share the TORC1 pathway with animals, not with Saccharomyces cerevisiae

Target of rapamycin (TOR), discovered in Saccharomyces cerevisiae, is a highly conserved serine/threonine kinase acting as a regulatory hub between the cell and its environment. Like mammals, in fungi, the TOR complex 1 (TORC1) pathway is essential for coordinating cell growth in response to nutrient availability. The activation of TORC1 is similar in yeast and mammals, while its inhibition is more complex in mammals. This divergence of TORC1 regulation opens the question of how common are the yeast and mammalian variants in the fungal kingdom. In this work, we trace the evolutionary history of TORC1 components throughout the fungal kingdom. Our findings show that these fungi contain the mammalian-specific KICSTOR complex for TORC1 inhibition. They also possess orthologs of serine, arginine and methionine sensors of TORC1 pathway that orchestrate the response to nutrient starvation in mammals. The Rheb-TSC mediated activation of mammalian TORC1 that was lost in Saccharomycotina was also conserved in non-Dikarya. These findings indicate that the TORC1 pathway in non-Dikarya fungi resembles mammalian TORC1. Saccharomycotina lost many of the inhibitory components and evolved alternate regulatory mechanisms. Furthermore, our work highlights the limitations of using S. cerevisiae as a fungal model while putting forward other fungi as possible research models.

Harnessing amino acid pathways to influence myeloid cell function in tumor immunity

Amino acids are pivotal regulators of immune cell metabolism, signaling pathways, and gene expression. In myeloid cells, these processes underlie their functional plasticity, enabling shifts between pro-inflammatory, anti-inflammatory, pro-tumor, and anti-tumor activities. Within the tumor microenvironment, amino acid metabolism plays a crucial role in mediating the immunosuppressive functions of myeloid cells, contributing to tumor progression. This review delves into the mechanisms by which specific amino acids-glutamine, serine, arginine, and tryptophan-regulate myeloid cell function and polarization. Furthermore, we explore the therapeutic potential of targeting amino acid metabolism to enhance anti-tumor immunity, offering insights into novel strategies for cancer treatment.

Animal amino acid sensor - A review

Cell growth and metabolism necessitate the involvement of amino acids, which are sensed and integrated by the mammalian target of rapamycin complex 1 (mTORC1). However, the molecular mechanisms underlying amino acid sensing remain poorly understood. Research indicates that amino acids are detected by specific sensors, with the signals being relayed to mTORC1 indirectly. This paper reviews the structures and biological functions of the amino acid sensors identified thus far. Additionally, it evaluates the potential role these sensors play in the developmental changes of the livestock production.

Activation of the De Novo Serine Synthesis Pathway and Disruption of Insulin Signaling Induced by Supplemental SeMet in Vitro

Selenium (Se) intake or selenoprotein overexpression can cause abnormal glucose metabolism and increase the risk of type 2 diabetes (T2D). The purpose of this study is to observe whether glycolysis bypass in the de novo serine synthesis pathway (SSP) is activated under high-Se stress in vitro. Initially, HCT-116, L02, HepG2, and differentiated C2C12 cells were exposed to five selenomethionine (SeMet) concentrations (0.001 to 10 µmol/L) for 48 h. The expressions of glutathione peroxidase 1 (GPX1), selenoprotein P (SELENOP), 3-phosphoglycerate dehydrogenase (PHGDH), and serine hydroxy-methyltransferases 1 (SHMT1) were assessed by western blotting (WB). Then, corresponding to the peak expressions of GPX1, SELENOP, and PHGDH, 0.1 µmol/L SeMet was identified as the highest intervention concentration. With more detailed levels of SeMet (0.001 to 0.1 µmol/L) given, the differentiated C2C12 cells were treated for 48 h to analyze the expressions of selenoproteins, enzymes related with serine metabolism and insulin signaling pathway. Among the four cell lines, the expressions of selenoproteins and metabolic enzymes of serine in C2C12 cells were more sensitive to changes in Se concentrations, which was similar to that in L02 cells. In C2C12 cells, the expressions of GPX1, SELENOP, selenoprotein N (SELENON), PHGDH, and SHMT1 exhibited a parabolic inflection point at SeMet concentrations of 0.05 µmol/L or 0.075 µmol/L, while 5,10-methylenetetrahydrofolate reductase (MTHFR) and methionine synthase (MS) showed no such trend. After 15 min of insulin stimulation, glucose retained more in the culture medium due to the decreased uptake by C2C12 cells. The expressions of key enzymes (AKT, AKT (Ser-473), AKT (Thr-308), mTOR, and PI3K) in the PI3K-AKT-mTOR signaling pathway decreased with the increased level of SeMet. This study demonstrated that excessive Se intake could induce abnormal glucose metabolism via SSP and impair the normal signaling of insulin in the differentiated C2C12 cells.

mTORC1, the maestro of cell metabolism and growth

The mechanistic target of rapamycin (mTOR) pathway senses and integrates various environmental and intracellular cues to regulate cell growth and proliferation. As a key conductor of the balance between anabolic and catabolic processes, mTOR complex 1 (mTORC1) orchestrates the symphonic regulation of glycolysis, nucleic acid and lipid metabolism, protein translation and degradation, and gene expression. Dysregulation of the mTOR pathway is linked to numerous human diseases, including cancer, neurodegenerative disorders, obesity, diabetes, and aging. This review provides an in-depth understanding of how nutrients and growth signals are coordinated to influence mTOR signaling and the extensive metabolic rewiring under its command. Additionally, we discuss the use of mTORC1 inhibitors in various aging-associated metabolic diseases and the current and future potential for targeting mTOR in clinical settings. By deciphering the complex landscape of mTORC1 signaling, this review aims to inform novel therapeutic strategies and provide a road map for future research endeavors in this dynamic and rapidly evolving field.

Human HDAC6 senses valine abundancy to regulate DNA damage

As an essential branched amino acid, valine is pivotal for protein synthesis, neurological behaviour, haematopoiesis and leukaemia progression1-3. However, the mechanism by which cellular valine abundancy is sensed for subsequent cellular functions remains undefined. Here we identify that human histone deacetylase 6 (HDAC6) serves as a valine sensor by directly binding valine through a primate-specific SE14 repeat domain. The nucleus and cytoplasm shuttling of human, but not mouse, HDAC6 is tightly controlled by the intracellular levels of valine. Valine deprivation leads to HDAC6 retention in the nucleus and induces DNA damage. Mechanistically, nuclear-localized HDAC6 binds and deacetylates ten-eleven translocation 2 (TET2) to initiate active DNA demethylation, which promotes DNA damage through thymine DNA glycosylase-driven excision. Dietary valine restriction inhibits tumour growth in xenograft and patient-derived xenograft models, and enhances the therapeutic efficacy of PARP inhibitors. Collectively, our study identifies human HDAC6 as a valine sensor that mediates active DNA demethylation and DNA damage in response to valine deprivation, and highlights the potential of dietary valine restriction for cancer treatment.

Determination of Nutrient Ligand-Sensor Binding Affinity

Cells contain dedicated mechanisms to sense nutrient levels in the environment to regulate their growth by balancing anabolism and catabolism [1, 2]. The mechanistic Target of Rapamycin Complex 1 (mTORC1), a multi-protein kinase complex, serves as an essential growth regulator that integrates various upstream inputs including growth factors and nutrients like amino acids [1, 2] Nutrient sensors upstream of mTORC1 directly bind cognate nutrient ligands to convey their availability and thereby regulate mTORC1 signaling [1, 2]. A reliable method is needed to quantitatively determine the binding affinity (Kd) of the nutrient sensor to its ligand. In parallel, quantitative metabolomic analysis can reveal metabolite levels in fed and starved cells; which represent the physiological range of the nutrient of interest. Whether or not the binding affinity is within the physiological range serves as an indicator to determine the physiological relevance of the sensing mechanism. This chapter describes a generalizable protocol that allows reproducible determination of nutrient ligand-nutrient sensor binding affinity. Here, the S-adenosylmethionine (nutrient ligand)-SAMTOR (nutrient sensor) pair is used as an example [3]. Nutrient sensor purification, radioactive nutrient ligand incubation, and eventual scintillation counting are included, along with a description of the mathematical equation that is used to calculate the binding affinity.

Leveraging single-cell and multi-omics approaches to identify MTOR-centered deubiquitination signatures in esophageal cancer therapy

Background

Esophageal squamous cell carcinoma (ESCC) remains a significant challenge in oncology due to its aggressive nature and heterogeneity. As one of the deadliest malignancies, ESCC research lags behind other cancer types. The balance between ubiquitination and deubiquitination processes plays a crucial role in cellular functions, with its disruption linked to various diseases, including cancer.

Methods

Our study utilized diverse analytical approaches, encompassing Cox regression models, single-cell RNA sequencing, intercellular communication analysis, and Gene Ontology enrichment. We also conducted mutation profiling and explored potential immunotherapeutic agents. Furthermore, in vitro cellular experiments and in vivo mouse models were performed to validate findings. These methodologies aimed to establish deubiquitination-related gene signatures (DRGS) for predicting ESCC patient outcomes and response to immunotherapy.

Results

By integrating datasets from TCGA-ESCC and GSE53624, we developed a DRGS model based on 14 deubiquitination-related genes (DUBGs). This signature effectively forecasts ESCC prognosis, drug responsiveness, and immune cell infiltration patterns. It also influences the mutational landscape of patients. Those classified as high-risk exhibited reduced survival rates, increased genetic alterations, and more complex cellular interactions, potentially explaining their poor outcomes. Notably, in vitro and in vivo experiments identified MTOR, a key component of the signature, as a promising therapeutic target for ESCC treatment.

Conclusion

Our research highlights the significance of 14 DUBGs in ESCC progression. The risk score derived from this gene set enables clinical stratification of patients into distinct prognostic groups. Moreover, MTOR emerges as a potential target for personalized ESCC therapy, offering new avenues for treatment strategies.

The convergence of mTOR signaling and ethanol teratogenesis

Ethanol is one of the most common teratogens and causes of human developmental disabilities. Fetal alcohol spectrum disorders (FASD), which describes the wide range of deficits due to prenatal ethanol exposure, are estimated to affect between 1.1 % and 5.0 % of births in the United States. Ethanol dysregulates numerous cellular mechanisms such as programmed cell death (apoptosis), protein synthesis, autophagy, and various aspects of cell signaling, all of which contribute to FASD. The mechanistic target of rapamycin (mTOR) regulates these cellular mechanisms via sensing of nutrients like amino acids and glucose, DNA damage, and growth factor signaling. Despite an extensive literature on ethanol teratogenesis and mTOR signaling, there has been less attention paid to their interaction. Here, we discuss the impact of ethanol teratogenesis on mTORC1's ability to coordinate growth factor and amino acid sensing with protein synthesis, autophagy, and apoptosis. Notably, the effect of ethanol exposure on mTOR signaling depends on the timing and dose of ethanol as well as the system studied. Overall, the overlap between the functions of mTORC1 and the phenotypes observed in FASD suggest a mechanistic interaction. However, more work is required to fully understand the impact of ethanol teratogenesis on mTOR signaling.

Effects of dietary methionine on the growth and protein synthesis of juvenile Chinese mitten crabs (Eriocheir sinensis) fed fish meal-free diets

This study investigated the effects of dietary methionine (Met) on growth performance and protein synthesis in juvenile Chinese mitten crabs (Eriocheir sinensis) fed fish meal (FM)-free diets. Three diets free of FM containing 0.48% (LM), 1.05% (MM), and 1.72% (HM) Met were assessed, and the cysteine content in all the diets was adjusted to 0.46%. The control diet contained 35% FM without Met supplementation. Extra lysine was added to all of the FM-free diets to match the lysine level in the control diet. Juvenile E. sinensis (800 crabs weighing 0.74 ± 0.01 g each) were fed these four diets for eight weeks, with five replicates for each treatment. Both the LM and HM groups presented lower weight gain than all the other groups did (P = 0.002). The survival of the crabs was lower in the LM and HM groups than in the MM group (P = 0.005). Compared with those in the other groups, the growth performance of the crabs in the MM group improved, and lipid deposition and protein accumulation increased. These positive outcomes are associated with high protein expression linked to the mammalian target of the rapamycin (mTOR) pathway and low expression of genes and proteins linked to the PRKR-like endoplasmic reticulum kinase (PERK) pathway. The study of Met supplementation has explored the response of the PERK pathway through reducing glutathione (GSH) levels to promote protein synthesis. The injection of Met and L-buthionine-sulfoximine (BSO), an inhibitor of GSH synthesis, suppressed GSH production and altered the expression of genes and proteins related to protein synthesis pathways. This study suggests that Met supplementation in FM-free diets can increase the growth and protein synthesis of E. sinensis by modulating specific cellular pathways, particularly the mTOR and PERK pathways.

Metabolism and mRNA translation: a nexus of cancer plasticity

Tumors often face energy deprivation due to mutations, hypoxia, and nutritional deficiencies within the harsh tumor microenvironment (TME), and as an effect of anticancer treatments. This metabolic stress triggers adaptive reprogramming of mRNA translation, which in turn adjusts metabolic plasticity and associated signaling pathways to ensure tumor cell survival. Emerging evidence is beginning to reveal the complex interplay between metabolism and mRNA translation, shedding light on the mechanisms that synchronize ribosome assembly and reconfigure translation programs under metabolic stress. This review explores recent advances in our understanding of the coordination between metabolism and mRNA translation, offering insights that could inform therapeutic strategies targeting both cancer metabolism and translation, with the aim of disrupting cancer cell plasticity and survival.

Engineered transcription-associated Cas9 targeting in eukaryotic cells

DNA targeting Class 2 CRISPR-Cas effector nucleases, including the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interactions that sequentially license their binding and cleavage activities at protospacer target sites. Both interactions are nucleic acid sequence specific but function constitutively; thus, they provide intrinsic spatial control over DNA targeting activities but naturally lack temporal control. Here we show that engineered Cas9 fusion proteins which bind to nascent RNAs near a protospacer can facilitate spatiotemporal coupling between transcription and DNA targeting at that protospacer: Transcription-associated Cas9 Targeting (TraCT). Engineered TraCT is enabled in eukaryotic yeast or human cells when suboptimal PAM interactions limit basal activity and when one or more nascent RNA substrates are still tethered to the actively transcribed target DNA in cis. Using yeast, we further show that this phenomenon can be applied for selective editing at one of two identical targets in distinct gene loci, or, in diploid allelic loci that are differentially transcribed. Our work demonstrates that temporal control over Cas9's targeting activity at specific DNA sites may be engineered without modifying Cas9's core domains and guide RNA components or their expression levels. More broadly, it establishes co-transcriptional RNA binding as a cis-acting mechanism that can conditionally stimulate CRISPR-Cas DNA targeting in eukaryotic cells.

JPH203 alleviates peritoneal fibrosis via inhibition of amino acid-mediated mTORC1 signaling

BACKGROUND AND AIMS

The mesothelial-mesenchymal transition (MMT) of mesothelial cells has been recognized as a critical process during progression of peritoneal fibrosis (PF). Despite its crucial role in amino acid transport and metabolism, the involvement of L-type amino acid transporter 1 (LAT1) and the potential therapeutic role of its inhibitor, JPH203, in fibrotic diseases remain unexplored. Considering the paucity of research on amino acid-mediated mTORC1 activation in PF, our study endeavors to elucidate the protective effects of JPH203 against PF and explore the involvement of amino acid-mediated mTORC1 signaling in this context.

METHODS

We established the transforming growth factor beta 1 (TGF-β1) induced MMT model in primary human mesothelial cells and the peritoneal dialysis fluid (PDF) induced PF model in mice. The therapeutic effects of JPH203 on PF were then examined on these two models by real-time quantitative polymerase chain reaction, western blotting, immunofluorescence staining, Masson's trichrome staining, H&E staining, picro-sirius red staining, and immunohistochemistry. The involvement of amino acid-mediated mTORC1 signaling was screened by RNA sequencing and further verified by western blotting in vitro.

RESULTS

LAT1 was significantly upregulated and JPH203 markedly attenuated fibrotic phenotype both in vitro and in vivo. RNA-seq unveiled a significant enrichment of mTOR signaling pathway in response to JPH203 treatment. Western blotting results indicated that JPH203 alleviates PF by inhibiting amino acid-mediated mTORC1 signaling, which differs from the direct inhibition observed with rapamycin.

CONCLUSION

JPH203 alleviates PF by inhibiting amino acid-mediated mTORC1 signaling.

Nutrient sensing of mTORC1 signaling in cancer and aging

The mechanistic target of rapamycin complex 1 (mTORC1) is indispensable for preserving cellular and organismal homeostasis by balancing the anabolic and catabolic processes in response to various environmental cues, such as nutrients, growth factors, energy status, oxygen levels, and stress. Dysregulation of mTORC1 signaling is associated with the progression of many types of human disorders including cancer, age-related diseases, neurodegenerative disorders, and metabolic diseases. The way mTORC1 senses various upstream signals and converts them into specific downstream responses remains a crucial question with significant impacts for our perception of the related physiological and pathological process. In this review, we discuss the recent molecular and functional insights into the nutrient sensing of the mTORC1 signaling pathway, along with the emerging role of deregulating nutrient-mTORC1 signaling in cancer and age-related disorders.

Developing patient-derived organoids to demonstrate JX24120 inhibits SAMe synthesis in endometrial cancer by targeting MAT2B

Endometrial cancer (EC) is one of the most common gynecologic malignancies, which lacking effective drugs for intractable conditions or patients unsuitable for surgeries. Recently, the patient-derived organoids (PDOs) are found feasible for cancer research and drug discoveries. Here, we have successfully established a panel of PDOs from EC and conducted drug repurposing screening and mechanism analysis for cancer treatment. We confirmed that the regulatory β subunit of methionine adenosyltransferase (MAT2B) is highly correlated with malignant progression in endometrial cancer. Through drug screening on PDOs, we identify JX24120, chlorpromazine derivative, as a specific inhibitor for MAT2B, which directly binds to MAT2B (Kd = 4.724 μM) and inhibits the viability of EC PDOs and canonical cell lines. Correspondingly, gene editing assessment demonstrates that JX24120 suppresses tumor growth depending on the presence of MAT2B in vivo and in vitro. Mechanistically, JX24120 induces inhibition of S-adenosylmethionine (SAMe) synthesis, leading to suppressed mTORC1 signaling, abnormal energy metabolism and protein synthesis, and eventually apoptosis. Taken together, our study offers a novel approach for drug discovery and efficacy assessment by using the PDOs models. These findings suggest that JX24120 may be a potent MAT2B inhibitor and will hopefully serve as a prospective compound for endometrial cancer therapy.

Regulatory Mechanisms of Aging Through the Nutritional and Metabolic Control of Amino Acid Signaling in Model Organisms

Life activities are supported by the intricate metabolic network that is fueled by nutrients. Nutritional and genetic studies in model organisms have determined that dietary restriction and certain mutations in the insulin signaling pathway lead to lifespan extension. Subsequently, the detailed mechanisms of aging as well as various nutrient signaling pathways and their relationships have been investigated in a wide range of organisms, from yeast to mammals. This review summarizes the roles of nutritional and metabolic signaling in aging and lifespan with a focus on amino acids, the building blocks of organisms. We discuss how lifespan is affected by the sensing, transduction, and metabolism of specific amino acids and consider the influences of life stage, sex, and genetic background on the nutritional control of aging. Our goal is to enhance our understanding of how nutrients affect aging and thus contribute to the biology of aging and lifespan.

The Pivotal Role of One-Carbon Metabolism in Neoplastic Progression During the Aging Process

One-carbon (1C) metabolism is a complex network of metabolic reactions closely related to producing 1C units (as methyl groups) and utilizing them for different anabolic processes, including nucleotide synthesis, methylation, protein synthesis, and reductive metabolism. These pathways support the high proliferative rate of cancer cells. While drugs that target 1C metabolism (like methotrexate) have been used for cancer treatment, they often have significant side effects. Therefore, developing new drugs with minimal side effects is necessary for effective cancer treatment. Methionine, glycine, and serine are the main three precursors of 1C metabolism. One-carbon metabolism is vital not only for proliferative cells but also for non-proliferative cells in regulating energy homeostasis and the aging process. Understanding the potential role of 1C metabolism in aging is crucial for advancing our knowledge of neoplastic progression. This review provides a comprehensive understanding of the molecular complexities of 1C metabolism in the context of cancer and aging, paving the way for researchers to explore new avenues for developing advanced therapeutic interventions for cancer.

Unveiling GATOR2 Function: Novel Insights from Drosophila Research

The multiprotein Target of Rapamycin (TOR) Complex 1 (TORC1) is a serine/threonine kinase that stimulates anabolic metabolism and suppresses catabolism. Deregulation of TORC1 is implicated in various human pathologies, including cancer, epilepsy, and neurodegenerative disorders. The Gap Activity Towards Rags (GATOR) complex contains two subcomplexes: GATOR1, which inhibits TORC1 activity; and GATOR2, which counteracts GATOR1s function. Structural and biochemical studies have elucidated how GATOR1 regulates TORC1 activity by acting as a GTPase activating protein for Rag GTPase. However, while cryogenic electron microscopy has determined that the structure of the multi-protein GATOR2 complex is conserved from yeast to humans, how GATOR2 inhibits GATOR1 remains unclear. Here, we describe recent whole-animal studies in Drosophila that have yielded novel insights into GATOR2 function, including identifying a novel role for the GATOR2 subunit WDR59, redefining the core proteins sufficient for GATOR2 activity, and defining a TORC1-independent role for GATOR2 in the regulation of the lysosomal autophagic endomembrane system. Additionally, the recent characterization of a novel methionine receptor in Drosophila that acts through the GATOR2 complex suggests an attractive model for the evolution of species-specific nutrient sensors. Research on GATOR2 function in Drosophila highlights how whole-animal genetic models can be used to dissect intracellular signaling pathways to identify tissue-specific functions and functional redundancies that may be missed in studies confined to rapidly proliferating cell lines.

Closing in on human methylation-the versatile family of seven-β-strand (METTL) methyltransferases

Methylation is a common biochemical reaction, and a number of methyltransferase (MTase) enzymes mediate the various methylation events occurring in living cells. Almost all MTases use the methyl donor S-adenosylmethionine (AdoMet), and, in humans, the largest group of AdoMet-dependent MTases are the so-called seven-β-strand (7BS) MTases. Collectively, the 7BS MTases target a wide range of biomolecules, i.e. nucleic acids and proteins, as well as several small metabolites and signaling molecules. They play essential roles in key processes such as gene regulation, protein synthesis and metabolism, as well as neurotransmitter synthesis and clearance. A decade ago, roughly half of the human 7BS MTases had been characterized experimentally, whereas the remaining ones merely represented hypothetical enzymes predicted from bioinformatics analysis, many of which were denoted METTLs (METhylTransferase-Like). Since then, considerable progress has been made, and the function of > 80% of the human 7BS MTases has been uncovered. In this review, I provide an overview of the (estimated) 120 human 7BS MTases, grouping them according to substrate specificities and sequence similarity. I also elaborate on the challenges faced when studying these enzymes and describe recent major advances in the field.

mTORC1 signaling and diabetic kidney disease

Diabetic kidney disease (DKD) represents the most lethal complication in both type 1 and type 2 diabetes. The disease progresses without obvious symptoms and is often refractory when apparent symptoms have emerged. Although the molecular mechanisms underlying the onset/progression of DKD have been extensively studied, only a few effective therapies are currently available. Pathogenesis of DKD involves multifaced events caused by diabetes, which include alterations of metabolisms, signals, and hemodynamics. While the considerable efficacy of sodium/glucose cotransporter-2 (SGLT2) inhibitors or angiotensin II receptor blockers (ARBs) for DKD has been recognized, the ever-increasing number of patients with diabetes and DKD warrants additional practical therapeutic approaches that prevent DKD from diabetes. One plausible but promising target is the mechanistic target of the rapamycin complex 1 (mTORC1) signaling pathway, which senses cellular nutrients to control various anabolic and catabolic processes. This review introduces the current understanding of the mTOR signaling pathway and its roles in the development of DKD and other chronic kidney diseases (CKDs), and discusses potential therapeutic approaches targeting this pathway for the future treatment of DKD.

A low concentration of choline chloride alters the developmental program of the bovine preimplantation embryo

Choline is a known developmental programming agent of the bovine preimplantation embryo. Culture of the embryo with 1.8 mmol/L choline, a concentration much higher than in blood, alters development to cause increased weaning weight and other changes during the postnatal period. It was hypothesized here that choline exerts similar effects on the developmental program of the embryo when added at concentrations similar to those in peripheral blood (i.e., 4 mol/L). Oocytes were collected via ovum pick up and embryos were produced in vitro. Embryos were cultured until day 7 after fertilization in medium with 4 mol/L choline chloride, or, as a vehicle control, with an additional 4 mol/L sodium chloride. Blastocysts were transferred into recipients and pregnancy was diagnosed at approximately 28 d of gestation. Subsequent calves (n=37 for vehicle and n=35 for choline) were weighed at birth and at weaning. Addition of choline to culture medium did not affect the proportion of embryos that became blastocysts or the proportion of transferred blastocysts that produced a pregnancy. Birth weight was unaffected by treatment but calves derived from choline-treated embryos were heavier at time of weaning and gained more per day from birth until weaning than calves derived from embryos treated with vehicle. Results demonstrate that choline can act on the preimplantation embryo at a physiologically-relevant concentration to alter postnatal phenotype. Observations are further evidence for the importance of the first days of embryonic development for the phenotype of the resulting calf.

Alterations in one‑carbon metabolism and protein synthesis signals due to methionine supplementation and lipopolysaccharide challenge in Holstein fetal liver explants

One‑carbon metabolism (OCM) fueled by methionine (Met), choline, and folic acid is key for embryo development and fetal growth. We investigated effects of lipopolysaccharide (LPS) to induce inflammation in fetal liver tissue with or without Met on components of OCM and protein synthesis activity. Fetal liver harvested at slaughter from six multiparous pregnant Holstein dairy cows (37 ± 6 kg milk/d, 100 ± 3 d gestation) were incubated (0.2 ± 0.02 g) for 4 h at 37 °C with each of the following: ideal profile of amino acids (control; Lysine:Met 2.9:1), control plus LPS (1 μg/mL), increased Met supply (Met, Lys:Met 2.5:1), and Met+LPS. Data were analyzed as a 2 × 2 factorial (PROC MIXED, SAS 9.4). Ratios of mechanistic target of rapamycin (p-mTOR:mTOR) and eukaryotic elongation factor 2 (p-eEF2:eEF2) protein were lowest (P < 0.0 5) with LPS and highest with Met. Tissue amino acid concentrations were lowest (P < 0.0 5) with Met regardless of LPS suggesting enhanced use via mTOR. The marked increase (P = 0.02) in phosphorylation of S6 ribosomal protein (p-RPS6) with LPS suggested a pro-inflammatory response that was partly alleviated with Met+LPS. No effect (P = 0.4 5) on methionine adenosyl transferase 1 A (MAT1A) protein abundance was detected. Activity of betaine-homocysteine S-methyltransferase (BHMT) was greatest with Met, but Met+LPS dampened this effect (P = 0.0 5). Overall, fetal liver responds to inflammatory challenges and Met supply. The latter can stimulate protein synthesis via mTOR and alter some OCM reactions while having a modest anti-inflammatory effect.

Eukaryotic cell size regulation and its implications for cellular function and dysfunction

Depending on cell type, environmental inputs, and disease, the cells in the human body can have widely different sizes. In recent years, it has become clear that cell size is a major regulator of cell function. However, we are only beginning to understand how the optimization of cell function determines a given cell's optimal size. Here, we review currently known size control strategies of eukaryotic cells and the intricate link of cell size to intracellular biomolecular scaling, organelle homeostasis, and cell cycle progression. We detail the cell size-dependent regulation of early development and the impact of cell size on cell differentiation. Given the importance of cell size for normal cellular physiology, cell size control must account for changing environmental conditions. We describe how cells sense environmental stimuli, such as nutrient availability, and accordingly adapt their size by regulating cell growth and cell cycle progression. Moreover, we discuss the correlation of pathological states with misregulation of cell size and how for a long time this was considered a downstream consequence of cellular dysfunction. We review newer studies that reveal a reversed causality, with misregulated cell size leading to pathophysiological phenotypes such as senescence and aging. In summary, we highlight the important roles of cell size in cellular function and dysfunction, which could have major implications for both diagnostics and treatment in the clinic.

Provision of choline chloride to the bovine preimplantation embryo alters postnatal body size and DNA methylation†

Choline is a vital micronutrient. In this study, we aimed to confirm, and expand on previous findings, how choline impacts embryos from the first 7 days of development to affect postnatal phenotype. Bos indicus embryos were cultured in a choline-free medium (termed vehicle) or medium supplemented with 1.8 mM choline. Blastocyst-stage embryos were transferred into crossbred recipients. Once born, calves were evaluated at birth, 94 days, 178 days, and at weaning (average age = 239 days). Following weaning, all calves were enrolled into a feed efficiency trial before being separated by sex, with males being slaughtered at ~580 days of age. Results confirm that exposure of 1.8 mM choline chloride during the first 7 days of development alters postnatal characteristics of the resultant calves. Calves of both sexes from choline-treated embryos were consistently heavier through weaning and males had heavier testes at 3 months of age. There were sex-dependent alterations in DNA methylation in whole blood caused by choline treatment. After weaning, feed efficiency was affected by an interaction with sex, with choline calves being more efficient for females and less efficient for males. Calves from choline-treated embryos were heavier, or tended to be heavier, than calves from vehicle embryos at all observations after weaning. Carcass weight was heavier for choline calves and the cross-sectional area of the longissimus thoracis muscle was increased by choline.

The molecular genetics of PI3K/PTEN/AKT/mTOR pathway in the malformations of cortical development

Malformations of cortical development (MCD) are a group of developmental disorders characterized by abnormal cortical structures caused by genetic or harmful environmental factors. Many kinds of MCD are caused by genetic variation. MCD is the common cause of intellectual disability and intractable epilepsy. With rapid advances in imaging and sequencing technologies, the diagnostic rate of MCD has been increasing, and many potential genes causing MCD have been successively identified. However, the high genetic heterogeneity of MCD makes it challenging to understand the molecular pathogenesis of MCD and to identify effective targeted drugs. Thus, in this review, we outline important events of cortical development. Then we illustrate the progress of molecular genetic studies about MCD focusing on the PI3K/PTEN/AKT/mTOR pathway. Finally, we briefly discuss the diagnostic methods, disease models, and therapeutic strategies for MCD. The information will facilitate further research on MCD. Understanding the role of the PI3K/PTEN/AKT/mTOR pathway in MCD could lead to a novel strategy for treating MCD-related diseases.

Research progress on interferon and cellular senescence

Since the 12 major signs of aging were revealed in 2023, people's interpretation of aging will go further, which is of great significance for understanding the occurrence, development, and intervention in the aging process. As one of the 12 major signs of aging, cellular senescence refers to the process in which the proliferation and differentiation ability of cells decrease under stress stimulation or over time, often manifested as changes in cell morphology, cell cycle arrest, and decreased metabolic function. Interferon (IFN), as a secreted ligand for specific cell surface receptors, can trigger the transcription of interferon-stimulated genes (ISGs) and play an important role in cellular senescence. In addition, IFN serves as an important component of SASP, and the activation of the IFN signaling pathway has been shown to contribute to cell apoptosis and senescence. It is expected to delay cellular senescence by linking IFN with cellular senescence and studying the effects of IFN on cellular senescence and its mechanism. This article provides a review of the research on the relationship between IFN and cellular senescence by consulting relevant literature.

Rag-Ragulator is the central organizer of the physical architecture of the mTORC1 nutrient-sensing pathway

The mechanistic target of rapamycin complex 1 (mTORC1) pathway regulates cell growth and metabolism in response to many environmental cues, including nutrients. Amino acids signal to mTORC1 by modulating the guanine nucleotide loading states of the heterodimeric Rag GTPases, which bind and recruit mTORC1 to the lysosomal surface, its site of activation. The Rag GTPases are tethered to the lysosome by the Ragulator complex and regulated by the GATOR1, GATOR2, and KICSTOR multiprotein complexes that localize to the lysosomal surface through an unknown mechanism(s). Here, we show that mTORC1 is completely insensitive to amino acids in cells lacking the Rag GTPases or the Ragulator component p18. Moreover, not only are the Rag GTPases and Ragulator required for amino acids to regulate mTORC1, they are also essential for the lysosomal recruitment of the GATOR1, GATOR2, and KICSTOR complexes, which stably associate and traffic to the lysosome as the "GATOR" supercomplex. The nucleotide state of RagA/B controls the lysosomal association of GATOR, in a fashion competitively antagonized by the N terminus of the amino acid transporter SLC38A9. Targeting of Ragulator to the surface of mitochondria is sufficient to relocalize the Rags and GATOR to this organelle, but not to enable the nutrient-regulated recruitment of mTORC1 to mitochondria. Thus, our results reveal that the Rag-Ragulator complex is the central organizer of the physical architecture of the mTORC1 nutrient-sensing pathway and underscore that mTORC1 activation requires signal transduction on the lysosomal surface.

Engineered transcription-associated Cas9 targeting in eukaryotic cells

DNA targeting Class 2 CRISPR-Cas effector nucleases, including the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interactions that sequentially license their binding and cleavage activities at protospacer target sites. Both interactions are nucleic acid sequence specific but function constitutively; thus, they provide intrinsic spatial control over DNA targeting activities but naturally lack temporal control. Here we show that engineered Cas9 fusion proteins which bind to nascent RNAs near a protospacer can facilitate spatiotemporal coupling between transcription and DNA targeting at that protospacer: Transcription-associated Cas9 Targeting (TraCT). Engineered TraCT is enabled in eukaryotic yeast or human cells when suboptimal PAM interactions limit basal activity and when one or more nascent RNA substrates are still tethered to the actively transcribed target DNA in cis. Using yeast, we further show that this phenomenon can be applied for selective editing at one of two identical targets in distinct gene loci, or, in diploid allelic loci that are differentially transcribed. Our work demonstrates that temporal control over Cas9's targeting activity at specific DNA sites may be engineered without modifying Cas9's core domains and guide RNA components or their expression levels. More broadly, it establishes co-transcriptional RNA binding as a cis-acting mechanism that can conditionally stimulate CRISPR-Cas DNA targeting in eukaryotic cells.

Sulfur starvation-induced autophagy in Saccharomyces cerevisiae involves SAM-dependent signaling and transcription activator Met4

Autophagy is a key lysosomal degradative mechanism allowing a prosurvival response to stresses, especially nutrient starvation. Here we investigate the mechanism of autophagy induction in response to sulfur starvation in Saccharomyces cerevisiae. We found that sulfur deprivation leads to rapid and widespread transcriptional induction of autophagy-related (ATG) genes in ways not seen under nitrogen starvation. This distinctive response depends mainly on the transcription activator of sulfur metabolism Met4. Consistently, Met4 is essential for autophagy under sulfur starvation. Depletion of either cysteine, methionine or SAM induces autophagy flux. However, only SAM depletion can trigger strong transcriptional induction of ATG genes and a fully functional autophagic response. Furthermore, combined inactivation of Met4 and Atg1 causes a dramatic decrease in cell survival under sulfur starvation, highlighting the interplay between sulfur metabolism and autophagy to maintain cell viability. Thus, we describe a pathway of sulfur starvation-induced autophagy depending on Met4 and involving SAM as signaling sulfur metabolite.

The significant role of amino acid metabolic reprogramming in cancer

Amino acid metabolism plays a pivotal role in tumor microenvironment, influencing various aspects of cancer progression. The metabolic reprogramming of amino acids in tumor cells is intricately linked to protein synthesis, nucleotide synthesis, modulation of signaling pathways, regulation of tumor cell metabolism, maintenance of oxidative stress homeostasis, and epigenetic modifications. Furthermore, the dysregulation of amino acid metabolism also impacts tumor microenvironment and tumor immunity. Amino acids can act as signaling molecules that modulate immune cell function and immune tolerance within the tumor microenvironment, reshaping the anti-tumor immune response and promoting immune evasion by cancer cells. Moreover, amino acid metabolism can influence the behavior of stromal cells, such as cancer-associated fibroblasts, regulate ECM remodeling and promote angiogenesis, thereby facilitating tumor growth and metastasis. Understanding the intricate interplay between amino acid metabolism and the tumor microenvironment is of crucial significance. Expanding our knowledge of the multifaceted roles of amino acid metabolism in tumor microenvironment holds significant promise for the development of more effective cancer therapies aimed at disrupting the metabolic dependencies of cancer cells and modulating the tumor microenvironment to enhance anti-tumor immune responses and inhibit tumor progression.

Dysfunctional VLDL metabolism in MASLD

Lipidomics has unveiled the intricate human lipidome, emphasizing the extensive diversity within lipid classes in mammalian tissues critical for cellular functions. This diversity poses a challenge in maintaining a delicate balance between adaptability to recurring physiological changes and overall stability. Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD), linked to factors such as obesity and diabetes, stems from a compromise in the structural and functional stability of the liver within the complexities of lipid metabolism. This compromise inaccurately senses an increase in energy status, such as during fasting-feeding cycles or an upsurge in lipogenesis. Serum lipidomic studies have delineated three distinct metabolic phenotypes, or "metabotypes" in MASLD. MASLD-A is characterized by lower very low-density lipoprotein (VLDL) secretion and triglyceride (TG) levels, associated with a reduced risk of cardiovascular disease (CVD). In contrast, MASLD-C exhibits increased VLDL secretion and TG levels, correlating with elevated CVD risk. An intermediate subtype, with a blend of features, is designated as the MASLD-B metabotype. In this perspective, we examine into recent findings that show the multifaceted regulation of VLDL secretion by S-adenosylmethionine, the primary cellular methyl donor. Furthermore, we explore the differential CVD and hepatic cancer risk across MASLD metabotypes and discuss the context and potential paths forward to gear the findings from genetic studies towards a better understanding of the observed heterogeneity in MASLD.

Ragopathies and the rising influence of RagGTPases on human diseases

RagGTPases (Rags) play an essential role in the regulation of cell metabolism by controlling the activities of both mechanistic target of rapamycin complex 1 (mTORC1) and Transcription factor EB (TFEB). Several diseases, herein named ragopathies, are associated to Rags dysfunction. These diseases may be caused by mutations either in genes encoding the Rags, or in their upstream regulators. The resulting phenotypes may encompass a variety of clinical features such as cataract, kidney tubulopathy, dilated cardiomyopathy and several types of cancer. In this review, we focus on the key clinical, molecular and physio-pathological features of ragopathies, aiming to shed light on their underlying mechanisms.

Metabolic dialogues: regulators of chimeric antigen receptor T cell function in the tumor microenvironment

Tumor-infiltrating lymphocytes (TILs) and chimeric antigen receptor (CAR) T cells have demonstrated remarkable success in the treatment of relapsed/refractory melanoma and hematological malignancies, respectively. These treatments have marked a pivotal shift in cancer management. However, as "living drugs," their effectiveness is dependent on their ability to proliferate and persist in patients. Recent studies indicate that the mechanisms regulating these crucial functions, as well as the T cell's differentiation state, are conditioned by metabolic shifts and the distinct utilization of metabolic pathways. These metabolic shifts, conditioned by nutrient availability as well as cell surface expression of metabolite transporters, are coupled to signaling pathways and the epigenetic landscape of the cell, modulating transcriptional, translational, and post-translational profiles. In this review, we discuss the processes underlying the metabolic remodeling of activated T cells, the impact of a tumor metabolic environment on T cell function, and potential metabolic-based strategies to enhance T cell immunotherapy.

Synergy of Rapamycin and Methioninase on Colorectal Cancer Cells Requires Simultaneous and Not Sequential Administration: Implications for mTOR Inhibition

Background/Aim

Rapamycin inhibits the mTOR protein kinase. Methioninase (rMETase), by degrading methionine, targets the methionine addiction of cancer cells and has been shown to improve the efficacy of chemotherapy drugs, reducing their effective doses. Our previous study demonstrated that rapamycin and rMETase work synergistically against colorectal-cancer cells, but not on normal cells, when administered simultaneously in vitro. In the present study, we aimed to further our previous findings by exploring whether  synergy exists between rapamycin and rMETase when used sequentially against HCT-116 colorectal-carcinoma cells, compared to simultaneous administration, in vitro.

Materials and Methods

The half-maximal inhibitory concentrations (IC50) of rapamycin alone and rMETase alone against the HCT-116 human colorectal-cancer cell line were previously determined using the CCK-8 cell viability assay (11). We then examined the efficacy of rapamycin and rMETase, both at their IC50, administered simultaneously or sequentially on the HCT-116 cell line, with rapamycin administered before rMETase and vice versa.

Results

The IC50 for rapamycin and rMETase, determined from previous experiments (11), was 1.38 nM and 0.39 U/ml, respectively, of HCT-116 cells. When rMETase was administered four days before rapamycin, both at the IC50, there was a 30.46% inhibition of HCT-116 cells. When rapamycin was administered four days before rMETase, both at the IC50, there was an inhibition of 41.13%. When both rapamycin and rMETase were simultaneously administered, both at the IC50, there was a 71.03% inhibition.

Conclusion

Rapamycin and rMETase have synergistic efficacy against colorectal-cancer cells in vitro when administered simultaneously, but not sequentially.

Rumen-protected methionine supplementation during the transition period under artificially induced heat stress: impacts on cow-calf performance

Dairy cows experiencing heat stress (HS) during the pre-calving portion of the transition period give birth to smaller calves and produce less milk and milk protein. Supplementation of rumen-protected methionine (RPM) has been shown to modulate protein, energy, and placenta metabolism, making it a potential candidate to ameliorate HS effects. We investigated the effects of supplementing RPM to transition cows under HS induced by electric heat blanket (EHB) on cow-calf performance. Six weeks before expected calving, 53 Holstein cows were housed in a tie-stall barn and fed a control diet (CON, 2.2% Met of MP) or a CON diet supplemented with Smartamine®M (MET, 2.6% Met of MP, Adisseo Inc., France). Four weeks pre-calving, all MET and half CON cows were fitted with an EHB. The other half of the CON cows were considered thermoneutral (TN), resulting in 3 treatments: CONTN (n = 19), CONHS (n = 17), and METHS (n = 17). Respiratory rate (RR), skin temperature (ST), and rectal temperature (RT) were measured thrice weekly and core body temperatures recorded bi-weekly. Post-calving body weights (BW) and BCS were recorded weekly, and DMI was calculated and averaged weekly. Milk yield was recorded daily and milk components were analyzed every third DIM. Biweekly AA and weekly nonesterified fatty acids (NEFA), β-hydroxybutyrate (BHB), insulin, and glucose were measured from plasma. Calf birth weight and 24 h growth, thermoregulation, and hematology profile were measured and apparent efficiency of absorption (AEA) of immunoglobulins was calculated. Data were analyzed using the MIXED procedure of SAS with 2 preplanned orthogonal contrasts: CONTN vs. the average of CONHS and METHS (C1) and CONHS vs. METHS (C2). Relative to TN, EHB cows had increased RT during the post-calving weeks and increased RR and ST during the entire transition period. Body weight, BCS, DMI, and milk yield were not impacted by the EHB or RPM. However, protein % and SNF were lower in CONHS, relative to METHS cows. At calving, METHS dams had higher glucose concentrations, relative to CONHS, and during the post-calving weeks, the EHB cows had lower NEFA concentrations than TN cows. Calf birthweight and AEA were reduced by HS, while RR was increased by HS. Calf withers height tended to be shorter and RT were lower in CONHS, compared with MTHS heifers. Overall, RPM supplementation to transition cows reverts the negative impact of HS on blood glucose concentration at calving and milk protein % in the dams and increases wither height while decreasing RT in the calf.